cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.rsxxym
title: Occurrence Download

description: A dataset containing 286037 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Balaenoptera physalus"
 ]
}

 The dataset includes 286037 records from 453 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002274-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.13140/rg.2.2.30886.59205
title: C04_Performance and Knowledge Management_Measuring and Interpreting Individual Difference
DOI: 10.15468/dl.aq25vn
title: Occurrence Download

description: A dataset containing 1840 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "CoordinateUncertaintyInMeters 980.0-1000000.0",
 "Geometry POLYGON((-133.69753 18.41564,-40.5144 18.41564,-40.5144 61.13992,-133.69753 61.13992,-133.69753 18.41564))",
 "TaxonKey is Euonymus alatus"
 ]
}

 The dataset includes 1840 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002297-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17037/data.00004763
title: Y-Check Zimbabwe 2022-23 dataset

description: Data collected from 2,097 adolescents aged 10-19 years who gave informed consent, or informed assent with parental/guardian consent, to participate in a prospective intervention study to assess the feasibility and short-term impact of an adolescent health check-up programme in selected schools and community venues in Chitungwiza, Zimbabwe between October 2022 to September 2023. It contains variables collected through a questionnaire on socio-demographic information, health-related knowledge; intentions, agency, and perceived social support for behaviour change; engagement with health services; prevalence of health conditions and health-related behaviours screened; improvements in previously-diagnosed health and well-being conditions by the time of follow-up, and referral attendance.
description: The evaluation questionnaire (at baseline, and follow-up), the exit interview (at baseline), and screening at follow-up were collected digitally offline in ODK, while the Y-Check screening data (at baseline) were collected in a bespoke application on android tablets. A small amount of data was collected on paper (referral forms, laboratory results, oral health charts, and referral forms) and double-entered into ODK. The tablets were synchronized at the end of every day at BRTI research centre offices.
DOI: 10.5281/zenodo.17671293
title: Data sample for "Spatial-Spectral Deep Learning for Prostate Cancer Tissue Classification in Infrared Spectroscopy"

description: Sample data corresponding to Figure 6, Figure 8, and Supporting Figure S5 of the paper "Spatial-Spectral Deep Learning for Prostate Cancer Tissue Classification in Infrared Spectroscopy" in Analytical Chemistry.

Included are four FTIR TMA cores of prostate tissue: s10_c048, s17_c015, s33_c059, s33_c070. Each core is provided with preprocessed spectra (no suffix), or as raw spectra (_raw suffix). Each core has an associated annotation file, tissue mask file, chemical image file generated as the area under the amide I band, and an aligned H&E image from a serial section. Wavenumbers corresponding to channels in the hyperspectral images are uploaded as vectors. Hyperspectral images are in hdf5 format, and can be loaded using e.g. h5py for Python.

Please direct any questions about the data or paper to: lyra.oleary@manchester.ac.uk
DOI: 10.15468/dl.q6hy28
title: Occurrence Download

description: A dataset containing 26381 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "PublishingCountry is Colombia",
 {
 "and" : [
 "Country is Colombia",
 {
 "not" : {
 "Issue" : [
 "is Country coordinate mismatch"
 ]
 }
 }
 ]
 }
 ]
 },
 {
 "and" : [
 "StateProvince is one of (Atlántico, Atlántico - Magdalena, Atlántico Department, Atlántico Dept., Atlántico department, Atlantico, Atlantico Department, Atlantico dept., Atlantico Dept., Atlantico Province, Atlantico department)",
 "Elevation 30-500m"
 ]
 }
 ]
}

 The dataset includes 26381 records from 124 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002298-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mna8c2
title: Occurrence Download

description: A dataset containing 19 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Pennatulacea",
 "HasCoordinate is TRUE",
 "HasGeospatialIssue is FALSE",
 "OccurrenceStatus is Present",
 "Geometry POLYGON ((-6.379433678493399 36.6471836712949, -6.374718404427256 34.66363768271924, 0.9543947417097343 29.134155273245142, 17.480493163947187 27.87837271836389, 32.331968630468964 30.68640273606468, 36.149187634704276 30.967423604826195, 38.9312684534068 36.87379431548948, 30.43306827897902 40.981570519250965, 27.108722917411114 41.266034804024514, 23.371620285406095 46.13242793611795, 12.69847319495932 48.76856667532462, 2.700434806016574 44.139249865010356, -5.593757812463025 37.870383351043074, -6.379433678493399 36.6471836712949))"
 ]
}

 The dataset includes 19 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002299-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.34740/kaggle/dsv/13817990
title: Peer-to-Peer Boliviano (BOB) Exchange Data
DOI: 10.15468/dl.wj63zw
title: Occurrence Download

description: A dataset containing 2040 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Pennatulacea",
 "HasCoordinate is TRUE",
 "HasGeospatialIssue is FALSE",
 "OccurrenceStatus is Present",
 "Geometry POLYGON ((-36.39403675661231 84.73835423927648, -36.39403675661231 11.146352749935545, -13.906729959262805 11.343880561496235, -6.376497939989747 33.31400176165954, -6.346145610641429 38.06503945087297, 11.037618137472236 52.207575394984815, 29.05136669308905 52.83328517409882, 43.084770536523365 53.256883560873234, 42.773815884711894 85.0033094321106, -36.39403675661231 84.73835423927648))"
 ]
}

 The dataset includes 2040 records from 38 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002300-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.86vzac
title: Occurrence Download

description: A dataset containing 828 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "OccurrenceStatus is Present",
 "TaxonKey is Pristimantis lanthanites"
 ]
}

 The dataset includes 828 records from 31 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002301-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17660825
title: Reproducibility Archive for Machine Learning-Based Virtual Screening and Molecular Dynamics Simulations for GSK3β Inhibitors in Alzheimer's Disease

description: This Zenodo repository contains the complete reproducibility archive for the study:

“Machine Learning-Based Virtual Screening and Molecular Dynamics Simulations for GSK3β Inhibitors in Alzheimer’s Disease”

The archive includes:

Machine Learning

·       Raw and processed datasets

·       Full descriptor matrices (normalized + raw)

·       Pre-processing, feature selection, and PCA scripts

·       Hyperparameter tuning and model development notebooks

Virtual Screening

·       ASINEX screening datasets (full, AD-filtered, ML-filtered)

·       Screening workflow notebooks and scripts

Molecular Docking

·       Receptor files (cleaned PDB, PDBQT)

·       Ligand structures (SDF)

·       Grid parameter files- config file

·       Docking logs and best poses for selected ligands

·       Docking preparation and analysis notebooks

·       Binding energy results from docking

Molecular Dynamics (AMBER + GROMACS Hybrid Workflow)

·       All AMBER input files: tleap.in, min.in, heat.in, density.in, equil.in, mmpbsa.in

·       GROMACS production input (prod.mdp), GRO/TOP/TPR files

·       Ligand parameterization files (mol2, frcmod)

·       Conversion scripts (acpype, parmed)

·       Per-ligand MD directories with input files

·       RMSD, RMSF, SASA, Rg, PCA, HBond, DSSP analysis scripts and outputs

·       Per-residue MMGBSA and MMPBSA energy results

Webtool

·       Full Streamlit webtool implementation

·       Final trained RF and ET models (.pkl)

·       Applicability domain statistics (means, covariance matrices, cutoffs)

·       ML models, AD cutoffs

·       Validation datasets and codes

 

This archive is provided to ensure complete transparency and computational reproducibility for peer review.It will be made public upon acceptance of the manuscript.

First author: Ajwin Joseph MartinCorresponding author: Dr. Dileep Kumar
DOI: 10.6084/m9.figshare.29210456
title: Honeybee flight data after encountering a detour

description: Flight bearing data of honeybees after encountering a detour, included in the publication Hadjitofi et al. (2025):<br>Anna Hadjitofi, Marie Messerich, Tim Landgraf, Barbara Webb; Honeybees express foodward flight vectors after a detour. <i>J Exp Biol</i> 15 November 2025; 228 (22): jeb251072. doi: https://doi.org/10.1242/jeb.251072.SummaryThe honeybee waggle dance communicates a flight vector to a food source<sup>1</sup>, but it is challenging to isolate how precisely dancers and recruits can navigate using this vector information independently of environmental cues. Our work<sup>2</sup> introduced an enforced-detour paradigm<sup>3</sup>, using narrow tunnels, to quantify the initial flight vectors expressed by experienced foragers and new recruits en route to the food. This dataset includes post-detour flight bearings captured at successive distances from the tunnel exit, along with in-hive waggle dance data. Our exploration of the data suggests that bees exhibit immediate corrective turns consistent with using path integration to fly towards the food; and that the communicated or recalled vector provides an approximate location rather than pinpoint accuracy.Data & CodeA python script has been provided (<i>generate_plots_JEB.py</i>) that can be used to reproduce the figures in the paper. This script demonstrates how the supplied data files (given in csv) format can be used to plot the data.The code used to simulate the assimilation circuit for the dance recruits is available at the dance2vec Github repo (see also Hadjitofi and Webb (2024)<sup>4</sup>).Other small software tools include: the use of pypylon to orchestrate filming with Basler cameras (beebasler); and the use of background subtraction algorithms for tracking the bees' flight in video recordings (bee flight tracer).ReferencesFrisch, K. V. (1993). <i>The dance language and orientation of bees</i>. Harvard University Press.Hadjitofi, A., Messerich, M., Landgraf, T., & Barbara Webb (2025). Honeybees express foodward flight vectors after a detour. <i>J Exp Biol</i>, <i>228</i>(22).Collett, M., Collett, T. S., & Wehner, R. (1999). Calibration of vector navigation in desert ants. <i>Current Biology</i>, <i>9</i>(18).Hadjitofi, A., & Webb, B. (2024). Dynamic antennal positioning allows honeybee followers to decode the dance. <i>Current Biology</i>, <i>34</i>(8), 1772-1779.
DOI: 10.6084/m9.figshare.29210456.v1
title: Honeybee flight data after encountering a detour

description: Flight bearing data of honeybees after encountering a detour, included in the publication Hadjitofi et al. (2025):<br>Anna Hadjitofi, Marie Messerich, Tim Landgraf, Barbara Webb; Honeybees express foodward flight vectors after a detour. <i>J Exp Biol</i> 15 November 2025; 228 (22): jeb251072. doi: https://doi.org/10.1242/jeb.251072.SummaryThe honeybee waggle dance communicates a flight vector to a food source<sup>1</sup>, but it is challenging to isolate how precisely dancers and recruits can navigate using this vector information independently of environmental cues. Our work<sup>2</sup> introduced an enforced-detour paradigm<sup>3</sup>, using narrow tunnels, to quantify the initial flight vectors expressed by experienced foragers and new recruits en route to the food. This dataset includes post-detour flight bearings captured at successive distances from the tunnel exit, along with in-hive waggle dance data. Our exploration of the data suggests that bees exhibit immediate corrective turns consistent with using path integration to fly towards the food; and that the communicated or recalled vector provides an approximate location rather than pinpoint accuracy.Data & CodeA python script has been provided (<i>generate_plots_JEB.py</i>) that can be used to reproduce the figures in the paper. This script demonstrates how the supplied data files (given in csv) format can be used to plot the data.The code used to simulate the assimilation circuit for the dance recruits is available at the dance2vec Github repo (see also Hadjitofi and Webb (2024)<sup>4</sup>).Other small software tools include: the use of pypylon to orchestrate filming with Basler cameras (beebasler); and the use of background subtraction algorithms for tracking the bees' flight in video recordings (bee flight tracer).ReferencesFrisch, K. V. (1993). <i>The dance language and orientation of bees</i>. Harvard University Press.Hadjitofi, A., Messerich, M., Landgraf, T., & Barbara Webb (2025). Honeybees express foodward flight vectors after a detour. <i>J Exp Biol</i>, <i>228</i>(22).Collett, M., Collett, T. S., & Wehner, R. (1999). Calibration of vector navigation in desert ants. <i>Current Biology</i>, <i>9</i>(18).Hadjitofi, A., & Webb, B. (2024). Dynamic antennal positioning allows honeybee followers to decode the dance. <i>Current Biology</i>, <i>34</i>(8), 1772-1779.
DOI: 10.15468/dl.tzqxtb
title: Occurrence Download

description: A dataset containing 539 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Macroderma gigas"
 ]
}

 The dataset includes 539 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002303-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.30579944.v1
title: <b>CDKG-LM_data</b>

description: This data is the research data used in the paper "Adaptive Cross-Domain Knowledge-Guided Modeling of Urban Population Potential Peak Point Attenuation Laws".Due to confidentiality and privacy considerations, the publicly available data have been de-identified.Data collected on 10 December 2019 were used for model development, while data from 11–13 December 2019 were used for validation. The dataset contained four fields: date, origin grid ID, destination grid ID, and number of flows. The data were organized into square grids with a spatial resolution of 250 m × 250 m, totaling 13,176 grids within the study area. The OD flow dataset on 10 December 2019 contained 71,287 records.
DOI: 10.15468/dl.65tx92
title: Occurrence Download

description: A dataset containing 8527 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Global Register of Introduced and Invasive Species - United States (Contiguous) (ver.2.0, 2022)"
 ]
}

 The dataset includes 8527 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002304-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17670611
title: De novo assembled transcriptome of Red Rubin (Ocimum basilicum) cultivar

description: RNA-Seq libraries were prepared and sequenced on an Illumina NovaSeq platform (Genewiz, Leipzig, Germany), generating 150 bp paired-end reads. Raw sequencing reads are available in the National Center for Biotechnology Information (NCBI) database (PRJNA1367508). In addition, we included in the dataset RNA-Seq libraries from RR leaves available in the Sequence Read Archive (SRA) database (accession number SRA313233). Raw reads were quality-checked with FastQC (v0.12.0) and trimmed using Trimmomatic (v0.39) to remove adapters and low-quality sequences (Q < 20; read length < 36 bp). Only high-quality reads were retained for downstream analyses. De novo transcriptome assembly was performed using the Trinity software suite (v2.13.2). Isoform reduction and redundancy removal was performed with CD-HIT.
DOI: 10.5281/zenodo.17670612
title: De novo assembled transcriptome of Red Rubin (Ocimum basilicum) cultivar

description: RNA-Seq libraries were prepared and sequenced on an Illumina NovaSeq platform (Genewiz, Leipzig, Germany), generating 150 bp paired-end reads. Raw sequencing reads are available in the National Center for Biotechnology Information (NCBI) database (PRJNA1367508). In addition, we included in the dataset RNA-Seq libraries from RR leaves available in the Sequence Read Archive (SRA) database (accession number SRA313233). Raw reads were quality-checked with FastQC (v0.12.0) and trimmed using Trimmomatic (v0.39) to remove adapters and low-quality sequences (Q < 20; read length < 36 bp). Only high-quality reads were retained for downstream analyses. De novo transcriptome assembly was performed using the Trinity software suite (v2.13.2). Isoform reduction and redundancy removal was performed with CD-HIT.
DOI: 10.15468/dl.k6kkrm
title: Occurrence Download

description: A dataset containing 388 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "OccurrenceStatus is Present",
 "TaxonKey is Arremon flavirostris"
 ]
}

 The dataset includes 388 records from 41 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002306-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17672290
title: Research data for the publication "Continuous Biomass oxidation in a Taylor-Flow Microreactor"

description: Reseach Data Set for the publication "Continuous Biomass oxidation in a Taylor-Flow Microreactor"
DOI: 10.5281/zenodo.14916672
title: Research data for the publication "Continuous Biomass oxidation in a Taylor-Flow Microreactor"

description: Reseach Data Set for the publication "Continuous Biomass oxidation in a Taylor-Flow Microreactor"
DOI: 10.15468/dl.6wb87h
title: Occurrence Download

description: A dataset containing 38418 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "HasCoordinate is true",
 "Geometry POLYGON((10.0 65.0, 15.0 65.0, 15.0 70.0, 10.0 70.0, 10.0 65.0))",
 "EventDate is greater than or equal to 2025-01-01",
 "EventDate is less than or equal to 2025-02-01"
 ]
}

 The dataset includes 38418 records from 36 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002305-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25773/twbs-d963
title: A Model Archive for Estuarine exchange flow in the Albemarle-Pamlico Estuarine System
DOI: 10.6084/m9.figshare.29165626
title: Development and validation of a high-density SNP chip tailored for genomic analysis in Indian backyard chickens

description: 1. Indian backyard chicken breeds are well adapted to local climatic conditions and possess distinct genetic characteristics, necessitating a dedicated SNP chip to address their unique genetic diversity, breed identification and conservation needs. In this study, a high-density SNP chip, <i>Axiom_Kukkut</i> was developed with SNP markers derived from genomes of 16 indigenous chicken breeds, Red Jungle Fowl and White Leghorn. 2. A total of 622,376 markers and an inter-marker distance of 1.9 kb, the <i>Axiom_Kukkut</i> provided a denser marker distribution compared to existing arrays. The chip was validated by genotyping a set of samples from diverse Indian chicken breeds. All the SNPs were used for validation. An average call rate of 99.92% and 91.28%, as high resolution polymorphic markers, demonstrated the high precision of the designed array. 3. Population stratification analysis revealed high genetic diversity and distinct linkage disequilibrium patterns among various breeds. Multivariate principal component analysis confirmed the genetic distinctiveness of Red Jungle Fowl and Uttara, suggesting low genetic diversity due to geographic isolation or specific breeding practices. 4. The customised SNP chip allows a multitude of possibilities, including applications in genome-wide association analysis, identification of selection signatures, population genetics and breed improvement programmes for Indian chicken. Continued refinement will expand its utility to include exotic and commercial breeds as well, enhancing its overall applicability across a wider range of chicken populations.
DOI: 10.6084/m9.figshare.29165626.v1
title: Development and validation of a high-density SNP chip tailored for genomic analysis in Indian backyard chickens

description: 1. Indian backyard chicken breeds are well adapted to local climatic conditions and possess distinct genetic characteristics, necessitating a dedicated SNP chip to address their unique genetic diversity, breed identification and conservation needs. In this study, a high-density SNP chip, <i>Axiom_Kukkut</i> was developed with SNP markers derived from genomes of 16 indigenous chicken breeds, Red Jungle Fowl and White Leghorn. 2. A total of 622,376 markers and an inter-marker distance of 1.9 kb, the <i>Axiom_Kukkut</i> provided a denser marker distribution compared to existing arrays. The chip was validated by genotyping a set of samples from diverse Indian chicken breeds. All the SNPs were used for validation. An average call rate of 99.92% and 91.28%, as high resolution polymorphic markers, demonstrated the high precision of the designed array. 3. Population stratification analysis revealed high genetic diversity and distinct linkage disequilibrium patterns among various breeds. Multivariate principal component analysis confirmed the genetic distinctiveness of Red Jungle Fowl and Uttara, suggesting low genetic diversity due to geographic isolation or specific breeding practices. 4. The customised SNP chip allows a multitude of possibilities, including applications in genome-wide association analysis, identification of selection signatures, population genetics and breed improvement programmes for Indian chicken. Continued refinement will expand its utility to include exotic and commercial breeds as well, enhancing its overall applicability across a wider range of chicken populations.