cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.17455545
title: Grafting Cell-Penetrating Poly(disulfide)s to Substrates of Interest:  Dynamic Covalent Bioconjugation for Traceless Delivery: Original Data

description: Original data underlying the publication. Data are organized according to the supporting information.
DOI: 10.15468/dl.rz7rgm
title: Occurrence Download

description: A dataset containing 958 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-66.0529 41.76201,-58.73593 45.61783,-62.18226 48.03894,-66.41383 50.11487,-74.3794 45.52159,-66.0529 41.76201))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Pastinaca sativa",
 "Year 1626-2025"
 ]
}

 The dataset includes 958 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003114-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tnyrgd
title: Occurrence Download

description: A dataset containing 27929 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Taxodium distichum",
 "Year 1981-2022"
 ]
}

 The dataset includes 27929 records from 326 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003115-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14925024
title: Recurrent evolution of selfishness from an essential tRNA synthetase in Caenorhabditis tropicalis

description: This dataset contains the following files:



Funannotate-based predicted ORF databases of two wild C. tropicalis isolates - EG6180 and NIC203 (files EG6180.proteins.fa and NIC203.proteins.fa). EG6180 protein database supplemented with KSS-1::FLAG and KSS-2::FLAG sequences was used for KSS-1::FLAG and KSS-2::FLAG pull-down annotation.

ORFs annotations of two wild C. tropicalis isolates - EG6180 and NIC203 (files EG6180_EG-ORF.gff3 and NIC203_NIC-ORF.gff3). We manually fixed exon-intron borders for pzl-1 and kss-3 genes in both annotation files based on mRNA-seq reads mapping and rtPCR. The NIC203 and EG6180 soft-masked genome assemblies and RNA-seq reads were input to funannotate, a pipeline for genome annotation (https://funannotate.readthedocs.io/en/latest/). We used the following recommended modifications for annotating a nematode genome: we allowed an intron size of up to 20,000bp (based on the largest introns in C. elegans), changed Busco database to nematoda, and specified the -species “other” flag where recommended in the online documentation of the pipeline.

Mass-spectrometry identification of KSS-1::FLAG and KSS-2::FLAG pull-down interactomes (files KSS-1-pull-down.xlsm and KSS-2-pull-down.xlsm).

Mass-spectrometry characterisation of purified KLMT-1 protein sample (file KLMT-1-mass-spectrometry.xlsm)

Mass-spectrometry characterisation of purified KLMT-1-KSS-1::Strep-SKR-1 protein complex (file KLMT-1-KSS-1CS-SKR-1-mass-spectrometry.xlsm)
DOI: 10.5281/zenodo.17456948
title: Recurrent evolution of selfishness from an essential tRNA synthetase in Caenorhabditis tropicalis

description: This dataset contains the following files:



Funannotate-based predicted ORF databases of two wild C. tropicalis isolates - EG6180 and NIC203 (files EG6180.proteins.fa and NIC203.proteins.fa). EG6180 protein database supplemented with KSS-1::FLAG and KSS-2::FLAG sequences was used for KSS-1::FLAG and KSS-2::FLAG pull-down annotation.

ORFs annotations of two wild C. tropicalis isolates - EG6180 and NIC203 (files EG6180_EG-ORF.gff3 and NIC203_NIC-ORF.gff3). We manually fixed exon-intron borders for pzl-1 and kss-3 genes in both annotation files based on mRNA-seq reads mapping and rtPCR. The NIC203 and EG6180 soft-masked genome assemblies and RNA-seq reads were input to funannotate, a pipeline for genome annotation (https://funannotate.readthedocs.io/en/latest/). We used the following recommended modifications for annotating a nematode genome: we allowed an intron size of up to 20,000bp (based on the largest introns in C. elegans), changed Busco database to nematoda, and specified the -species “other” flag where recommended in the online documentation of the pipeline.

Mass-spectrometry identification of KSS-1::FLAG and KSS-2::FLAG pull-down interactomes (files KSS-1-pull-down.xlsm and KSS-2-pull-down.xlsm).

Mass-spectrometry characterisation of purified KLMT-1 protein sample (file KLMT-1-mass-spectrometry.xlsm)

Mass-spectrometry characterisation of purified KLMT-1-KSS-1::Strep-SKR-1 protein complex (file KLMT-1-KSS-1CS-SKR-1-mass-spectrometry.xlsm)
DOI: 10.15468/dl.46adzr
title: Occurrence Download

description: A dataset containing 55 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Italy",
 "TaxonKey is Drusus aprutiensis"
 ]
}

 The dataset includes 55 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003117-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kuezwq
title: Occurrence Download

description: A dataset containing 32 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Observation, Human Observation)",
 "Geometry POLYGON((-100.07892 18.2153,-97.81736 18.2153,-97.81736 20.27292,-100.07892 20.27292,-100.07892 18.2153))",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Lophodytes cucullatus",
 "Year 1960-2025"
 ]
}

 The dataset includes 32 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003118-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.u228jv
title: Occurrence Download

description: A dataset containing 127474235 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Aves",
 "Country is United States of America",
 "StateProvince is one of (Alabama, Alaska, Arizona, Arkansas, California, Colorado, Connecticut, Delaware, Florida, Georgia, Hawaii, Idaho, Illinois, Indiana, Iowa, Kansas, Kentucky, Louisiana, Maine, Maryland, Massachusetts, Michigan, Minnesota, Mississippi, Missouri, Montana, Nebraska, Nevada, New Hampshire, New Jersey, New Mexico, New York, North Carolina, North Dakota, Ohio, Oklahoma, Oregon, Pennsylvania, Rhode Island, South Carolina, South Dakota, Tennessee, Texas, Utah, Vermont, Virginia, Washington, West Virginia, Wisconsin, Wyoming)",
 "Year is greater than or equal to 2023",
 "Year is less than or equal to 2023"
 ]
}

 The dataset includes 127474235 records from 38 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003085-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.sgz9m8
title: Occurrence Download

description: A dataset containing 2736 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Colombia",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Ceiba",
 "Year 2020-2025"
 ]
}

 The dataset includes 2736 records from 107 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003116-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cc2uyq
title: Occurrence Download

description: A dataset containing 134321733 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Aves",
 "Country is United States of America",
 "StateProvince is one of (Alabama, Alaska, Arizona, Arkansas, California, Colorado, Connecticut, Delaware, Florida, Georgia, Hawaii, Idaho, Illinois, Indiana, Iowa, Kansas, Kentucky, Louisiana, Maine, Maryland, Massachusetts, Michigan, Minnesota, Mississippi, Missouri, Montana, Nebraska, Nevada, New Hampshire, New Jersey, New Mexico, New York, North Carolina, North Dakota, Ohio, Oklahoma, Oregon, Pennsylvania, Rhode Island, South Carolina, South Dakota, Tennessee, Texas, Utah, Vermont, Virginia, Washington, West Virginia, Wisconsin, Wyoming)",
 "Year is greater than or equal to 2024",
 "Year is less than or equal to 2024"
 ]
}

 The dataset includes 134321733 records from 35 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003086-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.s5cu47
title: Occurrence Download

description: A dataset containing 7 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Taxus wallichiana chinensis",
 "Year 1981-2022"
 ]
}

 The dataset includes 7 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003120-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qustm9
title: Occurrence Download

description: A dataset containing 46704 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Eriobotrya japonica",
 "Year 1981-2022"
 ]
}

 The dataset includes 46704 records from 336 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003119-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.57783/f2de-ms83
title: OpenAI Billing - DEV
DOI: 10.6084/m9.figshare.30066926
title: Boosting AI-Generated Biomedical Images with Confidence through Advanced Statistical Inference

description: Generative artificial intelligence (AI) has transformed the biomedical imaging field through image synthesis, addressing challenges of data availability, privacy, and diversity in biomedical research. This article proposes a novel nonparametric method within the functional data framework to discern significant differences between the mean and covariance functions of original and synthetic biomedical imaging data, thereby enhancing the fidelity and utility of synthetic data. Focusing on surface-based synthetic imaging data, our approach employs triangulated spherical splines to address spatial heterogeneity. A key contribution is the construction of simultaneous confidence regions (SCRs) to rigorously quantify uncertainty in original-synthetic differences. The asymptotic properties of the proposed SCRs are established, providing exact coverage probabilities and demonstrating equivalence to those derived from noise-free imaging data. Simulation studies validate the coverage properties of the SCRs and evaluate the size and power of the associated hypothesis tests. The proposed method is applied to compare the original and synthetic brain imaging data from the Human Connectome Project, where it highlights significant differences between original and synthetic images. We demonstrate that a straightforward transformation can align the mean and covariance functions of synthetic images with those of the original data, improving their reliability and utility for biomedical research applications. Supplementary materials for this article are available online, including a standardized description of the materials available for reproducing the work.
DOI: 10.6084/m9.figshare.30066926.v1
title: Boosting AI-Generated Biomedical Images with Confidence through Advanced Statistical Inference

description: Generative artificial intelligence (AI) has transformed the biomedical imaging field through image synthesis, addressing challenges of data availability, privacy, and diversity in biomedical research. This article proposes a novel nonparametric method within the functional data framework to discern significant differences between the mean and covariance functions of original and synthetic biomedical imaging data, thereby enhancing the fidelity and utility of synthetic data. Focusing on surface-based synthetic imaging data, our approach employs triangulated spherical splines to address spatial heterogeneity. A key contribution is the construction of simultaneous confidence regions (SCRs) to rigorously quantify uncertainty in original-synthetic differences. The asymptotic properties of the proposed SCRs are established, providing exact coverage probabilities and demonstrating equivalence to those derived from noise-free imaging data. Simulation studies validate the coverage properties of the SCRs and evaluate the size and power of the associated hypothesis tests. The proposed method is applied to compare the original and synthetic brain imaging data from the Human Connectome Project, where it highlights significant differences between original and synthetic images. We demonstrate that a straightforward transformation can align the mean and covariance functions of synthetic images with those of the original data, improving their reliability and utility for biomedical research applications. Supplementary materials for this article are available online, including a standardized description of the materials available for reproducing the work.
DOI: 10.6084/m9.figshare.30066930
title: Efficiency of QMLE for Dynamic Panel Data Models with Interactive Effects

description: This article studies the problem of efficient estimation of panel data models in the presence of an increasing number of incidental parameters. We formulate the dynamic panel as a simultaneous equations system, and derive the efficiency bound under the normality assumption. We then show that the Gaussian quasi-maximum likelihood estimator (QMLE) applied to the system achieves the efficiency bound without the normality assumption. Comparison of QMLE with the fixed effects approach is made. Supplementary materials for this article are available online, including a standardized description of the materials available for reproducing the work.
DOI: 10.15468/dl.5yfx2c
title: Occurrence Download

description: A dataset containing 1662 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Continent is Asia",
 "OccurrenceStatus is Present",
 "TaxonKey is Chrysolophus pictus"
 ]
}

 The dataset includes 1662 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003123-251025141854904/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.30066930.v2
title: Efficiency of QMLE for Dynamic Panel Data Models with Interactive Effects

description: This article studies the problem of efficient estimation of panel data models in the presence of an increasing number of incidental parameters. We formulate the dynamic panel as a simultaneous equations system, and derive the efficiency bound under the normality assumption. We then show that the Gaussian quasi-maximum likelihood estimator (QMLE) applied to the system achieves the efficiency bound without the normality assumption. Comparison of QMLE with the fixed effects approach is made. Supplementary materials for this article are available online, including a standardized description of the materials available for reproducing the work.
DOI: 10.6084/m9.figshare.30066930.v1
title: Efficiency of QMLE for dynamic panel data models with interactive effects

description: This paper studies the problem of efficient estimation of panel data models in the presence of an increasing number of incidental parameters. We formulate the dynamic panel as a simultaneous equations system, and derive the efficiency bound under the normality assumption. We then show that the Gaussian quasi-maximum likelihood estimator (QMLE) applied to the system achieves the efficiency bound without the normality assumption. Comparison of QMLE with the fixed effects approach is made.
DOI: 10.15468/dl.74cvkv
title: Occurrence Download

description: A dataset containing 150 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Specimen, Observation)",
 "Continent is one of (North America, South America)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Vampyrum spectrum"
 ]
}

 The dataset includes 150 records from 43 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003122-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.84rmgx
title: Occurrence Download

description: A dataset containing 19865 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Observation, Human Observation, Living Specimen, Occurrence evidence, Specimen)",
 "OccurrenceStatus is Present",
 "TaxonKey is Triticum durum"
 ]
}

 The dataset includes 19865 records from 36 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003124-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ejqswn
title: Occurrence Download

description: A dataset listing the 136 species recorded in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "PublishingCountry is Colombia",
 {
 "and" : [
 "Country is Colombia",
 {
 "not" : {
 "Issue" : [
 "is Country coordinate mismatch"
 ]
 }
 }
 ]
 }
 ]
 },
 {
 "and" : [
 "PublishingOrg is one of (eac88d99-9f6c-4031-8fc4-8088f0e0dfe7)",
 "TaxonKey is one of (Aves [GBIF Backbone Taxonomy])",
 "StateProvince is one of (Chocó)"
 ]
 }
 ]
}

 The dataset's 136 records were derived from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003109-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7scrun
title: Occurrence Download

description: A dataset containing 759 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Colombia",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Ochroma",
 "Year 2020-2025"
 ]
}

 The dataset includes 759 records from 91 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003125-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5517/ccdc.csd.cc26kxc2
title: CCDC 2043004: Experimental Crystal Structure Determination

description: Related Article: le zhang|2020|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc296c74
title: CCDC 2121275: Experimental Crystal Structure Determination

description: Related Article: Yuichi Okii, Takashi Yamamoto, Toshio Naito, Kensuke Konishi, Hiroki Akutsu and Yasuhiro Nakazawa|2022|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc29cdqt
title: CCDC 2126126: Experimental Crystal Structure Determination

description: Related Article: Nico Graw|2021|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2bywqx
title: CCDC 2173680: Experimental Crystal Structure Determination

description: Related Article: S.Dudkin, A. Chuprin, S. Belova, G. Zelinskii, A. Vologzhanina, Ya. Voloshin|2023|CSD Communication|||
description: Related Article: Semyon V. Dudkin, Alexander S. Chuprin, Svetlana A. Belova, Genrikh E. Zelinskii, Anna V. Vologzhanina, Yan Z. Voloshin|2023|J.Porphyrins Phthalocyanines|27|293|doi:10.1142/S1088424622500924
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5281/zenodo.15223953
title: Unlocking River Biofilm Microbial Diversity: Comparative Analysis of Sequencing Technologies

description: Raw data for the paper entitled Unlocking River Biofilm Microbial Diversity: Comparative Analysis of Sequencing Technologies. Taxa tables were generated using the SILVA v138.1 reference database and DADA2.Raw fastq files can be found here: https://www.ncbi.nlm.nih.gov/bioproject/1353123

Accession: PRJNA1353123
DOI: 10.5281/zenodo.17432155
title: Unlocking River Biofilm Microbial Diversity: Comparative Analysis of Sequencing Technologies

description: Raw data for the paper entitled Unlocking River Biofilm Microbial Diversity: Comparative Analysis of Sequencing Technologies. Taxa tables were generated using the SILVA v138.1 reference database and DADA2.Raw fastq files can be found here: https://www.ncbi.nlm.nih.gov/bioproject/1353123

Accession: PRJNA1353123
DOI: 10.5281/zenodo.15404231
title: Supporting Data for Efficiency of Digital Photolithographic Synthesis of Large, High-Quality DNA Libraries and Microarrays using a Guanine O6 Dephosphitylation Strategy

description: This dataset supports the manuscript "Efficiency of Digital Photolithographic Synthesis of Large, High-Quality DNA Libraries and Microarrays using a Guanine O6 Dephosphitylation Strategy."

This is an updated version of "10.5281/zenodo.15404232". The current version has updated details on "sequencing calculation" and have corrected the sequence direction in "Sequencing_Data_Analysis.xlsx"

It includes the following experiments to analyze the effect of position-dependent G-rich centres on the photolithographic synthesis of DNA microarray:



Hybridization Assay

qPCR

Sequencing


All the data is organized in subfolders, with individual ReadMe files explaining the experiment protocol and data. For sequencing analysis scripts, see: 10.5281/zenodo.15411466

Please cite this dataset using the Zenodo DOI below when referencing these results: 10.5281/zenodo.17048135.