cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.16642754
title: Data: Activity-based selection for enhanced base editor mutational scanning

description: Source count data for all experiments in "Activity-based selection for enhanced base editor mutational scanning" (Kaplan et al 2025). Please refer to the file organization spreadsheet to associate filenames with their respective experimental details. 

 

Abstract: Base editing is a CRISPR-based technology that enables high-throughput, nucleotide-level functional interrogation of the genome, which is essential for understanding the genetic basis of human disease and informing therapeutic development. Base editing screens have emerged as a powerful experimental approach, yet significant cell-to-cell variability in editing efficiency introduces noise that may obscure meaningful results. Here, we develop a co-selection method that enriches for cells with high base editing activity, substantially increasing editing efficiency at a target locus. We evaluate this activity-based selection method against a traditional screening approach by tiling guide RNAs across TP53, demonstrating its enhanced capacity to pinpoint specific mutations and protein regions of functional importance. We anticipate that this modular selection method will enhance the resolution of base editing screens across many applications.
DOI: 10.17632/rs9zy95xdv
title: Ho'oponopono Experiment

description: The data is collected from the sample aged 18-25 years. The research data will help look upon deviations, if any, on the theory of Ho'oponopono experiment, and cite any changes in human patterns, as compared to 1970s and 21st century.
DOI: 10.5281/zenodo.16642753
title: Data: Activity-based selection for enhanced base editor mutational scanning

description: Source count data for all experiments in "Activity-based selection for enhanced base editor mutational scanning" (Kaplan et al 2025). Please refer to the file organization spreadsheet to associate filenames with their respective experimental details. 

 

Abstract: Base editing is a CRISPR-based technology that enables high-throughput, nucleotide-level functional interrogation of the genome, which is essential for understanding the genetic basis of human disease and informing therapeutic development. Base editing screens have emerged as a powerful experimental approach, yet significant cell-to-cell variability in editing efficiency introduces noise that may obscure meaningful results. Here, we develop a co-selection method that enriches for cells with high base editing activity, substantially increasing editing efficiency at a target locus. We evaluate this activity-based selection method against a traditional screening approach by tiling guide RNAs across TP53, demonstrating its enhanced capacity to pinpoint specific mutations and protein regions of functional importance. We anticipate that this modular selection method will enhance the resolution of base editing screens across many applications.
DOI: 10.17632/rs9zy95xdv.1
title: Ho'oponopono Experiment

description: The data is collected from the sample aged 18-25 years. The research data will help look upon deviations, if any, on the theory of Ho'oponopono experiment, and cite any changes in human patterns, as compared to 1970s and 21st century.
DOI: 10.15468/dl.2thbu8
title: Occurrence Download

description: A dataset containing 258 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cedrela fissilis",
 "HasCoordinate is true",
 "BasisOfRecord is Human Observation"
 ]
}

 The dataset includes 258 records from 33 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0080956-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17632/8vkb89v6nv
title: ADKAR Change Management in Gen-Z

description: This research data is collected from nearly 200 Gen-Z young adults aged 18-25 years and college going.
DOI: 10.17632/8vkb89v6nv.1
title: ADKAR Change Management in Gen-Z

description: This research data is collected from nearly 200 Gen-Z young adults aged 18-25 years and college going.
DOI: 10.17632/8ywpvmm7vj
title: SSC sampling data

description: Partial salt sampling data of saline-alkali land
DOI: 10.17632/8ywpvmm7vj.1
title: SSC sampling data

description: Partial salt sampling data of saline-alkali land
DOI: 10.15468/dl.zsu4a8
title: Occurrence Download

description: A dataset containing 34 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Paraguay",
 "TaxonKey is Bothrops diporus"
 ]
}

 The dataset includes 34 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0080954-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17632/5y9td2yszy
title: LINF_240015000

description: Protein of unknown function - conserved; Leishmania infantum (strain JPCM5)
DOI: 10.17632/5y9td2yszy.1
title: LINF_240015000

description: Protein of unknown function - conserved; Leishmania infantum (strain JPCM5)
DOI: 10.15468/dl.25hqae
title: Occurrence Download

description: A dataset containing 61 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Pomoxis annularis",
 "Country is Mexico",
 "HasCoordinate is true"
 ]
}

 The dataset includes 61 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0080955-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17632/2d3jcp85hc
title: LINF_240015400

description: F-box domain-containing protein | Flp1; Leishmania infantum (strain JPCM5)
DOI: 10.15468/dl.8tkvcn
title: Occurrence Download

description: A dataset containing 144 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Ptiloprora meekiana)",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "License is one of (CC-BY 4.0, CC0 1.0)"
 ]
}

 The dataset includes 144 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0024821-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cqdjmn
title: Occurrence Download

description: A dataset containing 5 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pyracantha densiflora"
 ]
}

 The dataset includes 5 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0024822-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5522/04/28163222.v1
title: <b>Revisiting the Central Dogma: the distinct roles of genome, methylation, transcription, and translation on protein expression in</b><b> </b><b><i>Arabidopsis thaliana</i></b>

description: <b>Background</b><b> </b>We investigated the flow of information from genome sequence to protein expression implied by the Central Dogma, to determine the impact of intermediate genomic levels in plants.<b>Results</b><b> </b>We performed genomic profiling of rosettes in two <i>Arabidopsis</i> accessions, Col-0 and Can-0, and assembled their genomes using long reads and chromatin interaction data. We measured gene and protein expression in biological replicates grown in a controlled environment, also measuring CpG methylation, ribosome-associated transcript levels and tRNA abundance. Each omic level is highly reproducible between biological replicates and between accessions despite their 0.5% sequence divergence; the single best predictor of any level in one accession is the corresponding level in the other. Within each accession, gene codon frequencies accurately model both mRNA and protein expression. The effects of a codon on mRNA and protein expression are highly correlated but are unrelated to genome-wide codon frequencies or to tRNA levels which instead match genome-wide amino acid frequencies. Ribosome-associated transcripts closely track mRNA levels.<b>Conclusions</b><b> </b>In the absence of environmental perturbation, neither methylation, tRNA nor ribosome-associated transcript levels add appreciable information about constitutive protein abundance beyond that in DNA codon frequencies and mRNA expression levels. The impact of constitutive gbM is mostly explained by gene codon composition. tRNA abundance tracks overall amino acid demand. However, genetic differences between accessions associate with differential gbM by inflating differential expression variation. Our data show that the Central Dogma holds only if both sequence and abundance information in mRNA are considered.
DOI: 10.15468/dl.zdxs8p
title: Occurrence Download

description: A dataset containing 13 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Ptiloprora plumbea)",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "License is one of (CC-BY 4.0, CC0 1.0)"
 ]
}

 The dataset includes 13 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0024823-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6nf4qw
title: Occurrence Download

description: A dataset containing 15115 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Podiceps cristatus",
 "Year 1960-2025"
 ]
}

 The dataset includes 15115 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0024824-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.evr3ks
title: Occurrence Download

description: A dataset containing 6299 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Ptilopsis granti)",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "License is one of (CC-BY 4.0, CC0 1.0)"
 ]
}

 The dataset includes 6299 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0024825-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5hpwvf
title: Occurrence Download

description: A dataset containing 2264 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Ptilopsis leucotis)",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "License is one of (CC-BY 4.0, CC0 1.0)"
 ]
}

 The dataset includes 2264 records from 31 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0024826-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.16759777
title: Comparative analysis of eccDNA and circRNA tools shows increased accuracy of tool combination

description: Input files of the paper "Comparative analysis of eccDNA and circRNA tools shows increased accuracy of tool combination". This project is linked to the following GitHub repository: https://github.com/ZabalaAitor/benchmarking/
DOI: 10.15468/dl.9kw338
title: Occurrence Download

description: A dataset containing 732 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Ptilorrhoa castanonota)",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "License is one of (CC-BY 4.0, CC0 1.0)"
 ]
}

 The dataset includes 732 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0024828-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6j7ze2
title: Occurrence Download

description: A dataset containing 993 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Ptilorrhoa caerulescens)",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "License is one of (CC-BY 4.0, CC0 1.0)"
 ]
}

 The dataset includes 993 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0024827-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2be3ab
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Ptilorrhoa geislerorum)",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "License is one of (CC-BY 4.0, CC0 1.0)"
 ]
}

 The dataset includes 8 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0024829-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5v6hmm
title: Occurrence Download

description: A dataset containing 971051 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "BasisOfRecord is one of (Human Observation, Machine Observation, Occurrence evidence, Observation)",
 "TaxonKey is one of (Vanellus chilensis)",
 "Country is one of (Anguilla, Antigua and Barbuda, Argentina, Aruba, Bahamas, Barbados, Belize, Bolivia (Plurinational State of), Bonaire, Sint Eustatius and Saba, Bouvet Island, Brazil, Cayman Islands, Chile, Colombia, Costa Rica, Cuba, Curaçao, Dominica, Dominican Republic, Ecuador, El Salvador, Falkland Islands (Malvinas), French Guiana, Grenada, Guadeloupe, Guatemala, Guyana, Haiti, Honduras, Jamaica, Martinique, Mexico, Montserrat, Nicaragua, Panama, Paraguay, Peru, Puerto Rico, Saint Barthélemy, Saint Kitts and Nevis, Saint Lucia, Saint Martin (French part), Saint Vincent and the Grenadines, Sint Maarten (Dutch part), South Georgia and the South Sandwich Islands, Suriname, Trinidad and Tobago, Turks and Caicos Islands, Uruguay, Venezuela (Bolivarian Republic of), Virgin Islands (British), Virgin Islands (U.S.))"
 ]
}

 The dataset includes 971051 records from 493 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0024810-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.45erbg
title: Occurrence Download

description: A dataset containing 14 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pyracantha inermis"
 ]
}

 The dataset includes 14 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0024830-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.n8e8p8
title: Occurrence Download

description: A dataset containing 2488 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Phocoena phocoena relicta"
 ]
}

 The dataset includes 2488 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0024831-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.httd64
title: Occurrence Download

description: A dataset containing 800 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Ptilorrhoa leucosticta)",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "License is one of (CC-BY 4.0, CC0 1.0)"
 ]
}

 The dataset includes 800 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0024832-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9s5kdg
title: Occurrence Download

description: A dataset containing 20229 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Ptilostomus afer)",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "License is one of (CC-BY 4.0, CC0 1.0)"
 ]
}

 The dataset includes 20229 records from 32 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0024833-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.e52tu5
title: Occurrence Download

description: A dataset containing 16756 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Ptilotula flavescens)",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "License is one of (CC-BY 4.0, CC0 1.0)"
 ]
}

 The dataset includes 16756 records from 23 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0024834-250802193616735/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.29850395
title: Dataset. Non-Invasive Cervical Spinal Stimulation and Respiratory Recovery After Spinal Cord Injury . Randomizaed Controlled trial with a high crossover rate.

description: This dataset includes full data extracted from tests to subjects with SCI. Raw data for the two groups (control and intervention) can be found for demographic categories (age, sex, height, weight, etiology, UEMS, NLI, AIS, time since injury, tSCS intensity) and different values tests and scales: UEMS; AIS; total sensory score, FVC, MIP, MEP MIP%, MEP%, FVC(L), FEV1(L), FEV1/FVC(%), PEF(L/s), FEF50(L/s), FEF25/75%(L/s), FEV1/FEV0.5, FVC(L), FEV1(L), FEV1/FVC(%), PEF(L/s), FEF50(L/s),
DOI: 10.6084/m9.figshare.29850395.v1
title: Dataset. Non-Invasive Cervical Spinal Stimulation and Respiratory Recovery After Spinal Cord Injury . Randomizaed Controlled trial with a high crossover rate.

description: This dataset includes full data extracted from tests to subjects with SCI. Raw data for the two groups (control and intervention) can be found for demographic categories (age, sex, height, weight, etiology, UEMS, NLI, AIS, time since injury, tSCS intensity) and different values tests and scales: UEMS; AIS; total sensory score, FVC, MIP, MEP MIP%, MEP%, FVC(L), FEV1(L), FEV1/FVC(%), PEF(L/s), FEF50(L/s), FEF25/75%(L/s), FEV1/FEV0.5, FVC(L), FEV1(L), FEV1/FVC(%), PEF(L/s), FEF50(L/s),
DOI: 10.15468/dl.zdhr64
title: Occurrence Download

description: A dataset containing 236668 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Vulpes vulpes",
 "Country is France",
 "HasCoordinate is true"
 ]
}

 The dataset includes 236668 records from 3274 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0024815-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nqvzfy
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Alternanthera halimifolia",
 "Country is Cuba",
 "HasCoordinate is true"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0082061-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7s9bab
title: Occurrence Download

description: A dataset containing 182196 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cerapteryx graminis",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 182196 records from 236 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0081971-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.scnfka
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{"type":"and","predicates":[{"type":"equals","key":"GADM_LEVEL_2_GID","value":"TUR.37.11_1","matchCase":false},{"type":"equals","key":"CLASS_KEY","value":"212","matchCase":false},{"type":"greaterThanOrEquals","key":"YEAR","value":"2015","matchCase":false},{"type":"not","predicate":{"type":"in","key":"BASIS_OF_RECORD","values":["MATERIAL_CITATION","MATERIAL_SAMPLE","PRESERVED_SPECIMEN"],"matchCase":false}},{"type":"lessThanOrEquals","key":"COORDINATE_UNCERTAINTY_IN_METERS","value":"10000","matchCase":false},{"type":"equals","key":"LICENSE","value":"CC BY 4.0","matchCase":false}]}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006925-260108223611665/datasets/export for details.
DOI: 10.5281/zenodo.10831629
title: Data for An open-source deep learning algorithm for efficient detection of fishes in underwater images from diverse reef ecosystems

description: FishForYolo.zip comprises images in .jpeg format along with normalized labels in YOLO format and non-normalized labels. This dataset is utilized for both training and testing purposes.




The shooting.csv file contains the mapping between videos and their respective shooting instances, which denote all videos captured at a particular location and time. It is used for data analysis.

split.yaml delineates the partitioning of data into training, validation, and testing sets. This file is integral for the model to access annotations appropriately during its execution.

labels_log.csv contains the annotations in CSV format, supplemented with additional details such as bounding box area or label region. It is instrumental for conducting thorough data analysis.

SU_preds.zip contains the predictions of our best model on the test set (in the labels directory). The directory structure mirrors that of FishForYolo.zip. It also contains a file "all_preds.csv" which contains the predictions in CSV format.
DOI: 10.5281/zenodo.10831628
title: Data for An open-source deep learning algorithm for efficient detection of fishes in underwater images from diverse reef ecosystems

description: FishForYolo.zip comprises images in .jpeg format along with normalized labels in YOLO format and non-normalized labels. This dataset is utilized for both training and testing purposes.




The shooting.csv file contains the mapping between videos and their respective shooting instances, which denote all videos captured at a particular location and time. It is used for data analysis.

split.yaml delineates the partitioning of data into training, validation, and testing sets. This file is integral for the model to access annotations appropriately during its execution.

labels_log.csv contains the annotations in CSV format, supplemented with additional details such as bounding box area or label region. It is instrumental for conducting thorough data analysis.

SU_preds.zip contains the predictions of our best model on the test set (in the labels directory). The directory structure mirrors that of FishForYolo.zip. It also contains a file "all_preds.csv" which contains the predictions in CSV format.