cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.26311089
title: Exposure to light at night (LAN) and risk of overweight/obesity, hypertension, and diabetes: a systematic review and meta-analysis

description: Current studies have presented conflicting findings regarding the associations between light at night (LAN) exposure and the risk of overweight/obesity, hypertension, and diabetes. Our study systematically summarized the evidence of the association between LAN exposure and the risk of overweight/obesity, hypertension, and diabetes. We searched five databases (PubMed, Web of Science, Embase, Scopus, and Cochrane) for observational studies published up to 1 August 2023. The pooled odds ratio (ORs) and 95% confidence intervals (CIs) were estimated by random-effects models for the association. Eighteen studies were included in the meta-analysis. Compared with the group with the lowest level of LAN, the group with the highest level of LAN is associated with an increased risk of overweight/obesity (pooled OR = 1.19, 95%CI: 1.13–1.26), hypertension (pooled OR: 1.86, 95% CI:1.28–2.72), and diabetes (pooled OR = 1.21, 95%CI: 1.07–1.31). Our meta-analysis demonstrated LAN exposure is associated with increased risk of overweight/obesity, hypertension, and diabetes.
DOI: 10.6084/m9.figshare.26311089.v1
title: Exposure to light at night (LAN) and risk of overweight/obesity, hypertension, and diabetes: a systematic review and meta-analysis

description: Current studies have presented conflicting findings regarding the associations between light at night (LAN) exposure and the risk of overweight/obesity, hypertension, and diabetes. Our study systematically summarized the evidence of the association between LAN exposure and the risk of overweight/obesity, hypertension, and diabetes. We searched five databases (PubMed, Web of Science, Embase, Scopus, and Cochrane) for observational studies published up to 1 August 2023. The pooled odds ratio (ORs) and 95% confidence intervals (CIs) were estimated by random-effects models for the association. Eighteen studies were included in the meta-analysis. Compared with the group with the lowest level of LAN, the group with the highest level of LAN is associated with an increased risk of overweight/obesity (pooled OR = 1.19, 95%CI: 1.13–1.26), hypertension (pooled OR: 1.86, 95% CI:1.28–2.72), and diabetes (pooled OR = 1.21, 95%CI: 1.07–1.31). Our meta-analysis demonstrated LAN exposure is associated with increased risk of overweight/obesity, hypertension, and diabetes.
DOI: 10.6084/m9.figshare.26300538.v1
title: Historical cosmetic talc consumption and incidence of mesothelioma in the United States

description: Jointpoint Regression Software from the National Cancer Institute was used to model age-adjusted male and female pleural and peritoneal mesothelioma rates in the surveillance, epidemiology, and end results (SEER) 8, SEER 12, and SEER 22 cancer registries. Linear mixed models were then used to determine if there was a statistical association between U.S. cosmetic talc consumption and the 30-year lagged age-adjusted mesothelioma rates (1) over the reporting period for each registry and (2) for the periods of time identified by the jointpoint model where changes in the rate of mesothelioma occurred. Regardless of the SEER registry used, from the early-1980s through 2020, rates of peritoneal mesothelioma have remained steady or declined. Female pleural mesothelioma rates were unchanged from the early-1980s until 2017 when rates declined, while male rates peaked in the early 1990s and have since declined. Cosmetic talc consumption was not statistically associated with an increased rate of pleural or peritoneal mesothelioma in males or females, suggesting that the use of cosmetic talc products is not associated with the development of mesothelioma.
DOI: 10.15468/dl.hbgau6
title: Occurrence Download

description: A dataset containing 11 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Denekia capensis Thunb.",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((20.7576 -24.3688,20.529 -24.0715,20.509 -24.0715,20.509 -28.5786,25.5395 -28.5786,25.5395 -24.0715,25.1306 -24.0715,24.9333 -24.4571,23.8962 -24.2467,22.8065 -24.295,22.3719 -24.7207,22.2323 -25.547,22.0387 -25.7188,21.7833 -25.7784,21.5388 -25.7113,21.3553 -25.5415,20.7576 -24.3688))"
 ]
}

 The dataset includes 11 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0046133-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2zhqfx
title: Occurrence Download

description: A dataset containing 46049544 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is North America",
 "License is CC-BY 4.0",
 "Month is one of (June, July)",
 "Year 2022-2023"
 ]
}

 The dataset includes 46049544 records from 177 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0046123-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.7302/8057
title: Literature searches for extracorporeal life support in pregnancy

description: These searches were used to support a systematic review on extracorporeal life support in pregnancy. The searches were designed to work in the following databases: Ovid MEDLINE, Elsevier Embase, Clarivate Web of Science, and EBSCOhost CINAHL. The searches can be repurposed for other databases as long as the syntax is appropriately altered.
DOI: 10.15468/dl.b87phz
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Denekia capensis Thunb.",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((20.529 -24.0715,20.509 -24.0455,20.509 -24.0715,20.529 -24.0715))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0046134-250525065834625/datasets/export for details.
DOI: 10.34740/kaggle/dsv/12164993
title: Peer-to-Peer Boliviano (BOB) Exchange Data
DOI: 10.15468/dl.42msyd
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Denekia capensis Thunb.",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((25.5395 -23.2724,25.1306 -24.0715,25.5395 -24.0715,25.5395 -23.2724))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0046135-250525065834625/datasets/export for details.
DOI: 10.5281/zenodo.15663711
title: Immune Escape Potential of SARS-CoV-2 Spike Mutations L452W, F486P, D614G  (Q1 2025)

description: This dataset contains a comprehensive mutation profile analysis of the SARS-CoV-2 Spike protein from sequences collected during Q1 of 2025 . Using alignment-based mutation calling via Nextclade and functional annotation using Biopython tools locally, I identified the most frequent Spike mutation patters such as L452W, F486P, D614G. These mutations were observed across multiple lineages including JN.1, KP.2, LB.1

Each of these mutations has been previously associated with immune escape properties, enhanced ACE2 binding, and reduced neutralization by monoclonal antibodies and vaccine-induced immunity.

Functional Mutation Analysis

L452W is located within receptor Binding Domain (RBD), position 452. It enhances ACE2 affinity and reduces neutralization by therapeutic antibodies such as Bamlanivimab and C135. As described by Zhou et al., Nature 2022 that L452R/W mutations are linked to immune evasion and increased transmissibility this study confirms this pattern.  

F486P located within RBD, position 486 disrupts antibody binding at a conserved epitope; may impact neutralization by class 1 and class 2 antibodies. The F486 substitutions reduce binding by potent neutralizing antibodies targeting the ACE2 interface as described by McCallum et al., Science 2022.

D614G is located within Spike S1 domain it stabilizes Spike trimer, enhances fusion efficiency, and increases viral infectivity. D614G increases SARS-CoV-2 spike flexibility (Gobeil et al., PNAS 2021) and ACE2 receptor engagement is also enhanced.

Together, this mutation profile suggests a potential escape mechanism from both vaccine-induced immunity and therapeutic monoclonal antibodies, while maintaining high ACE2 binding affinity and transmission fitness.

Methods Overview

Sequences obtained from NCBI/GISAID EpiCoV databases

Mutation profiles extracted using Nextclade and iVar.

Lineage classification via Pangolin

Mutation annotations mapped to Wuhan-Hu-1 reference genome

Immune escape prediction based on known antibody epitopes from CoV-AbDab and structural studies

All methods are fully reproducible and generated fasta file is included with this dataset.

References

1. Zhou, D., et al. (2022).    Evidence of escape of SARS-CoV-2 variant BQ.1.1 from vaccine and therapeutic antibody protection. Nature.   - https://doi.org/10.1038/s41586-022-04967-2 

2. McCallum, M., et al. (2022).    Structural basis of potent antibody responses to SARS-CoV-2 variants   . Science.   - https://doi.org/10.1126/science.abq2652 

3. Gobeil, S.M.C., et al. (2021).    Effect of the D614G substitution on the structure of the spike glycoprotein of SARS-CoV-2. PNAS.   - https://doi.org/10.1073/pnas.2106524118 

4. Wang, Q., et al. (2023).    Antibody resistance of XBB.1.5 and related variants. Cell Reports.   - https://doi.org/10.1016/j.celrep.2023.112322 

5. WHO.    Tracking SARS-CoV-2 variants: Omicron sublineages and recombinants.   - https://www.who.int/publications/m/item/tracking-sars-cov-2-variants
DOI: 10.5281/zenodo.15663712
title: Immune Escape Potential of SARS-CoV-2 Spike Mutations L452W, F486P, D614G  (Q1 2025)

description: This dataset contains a comprehensive mutation profile analysis of the SARS-CoV-2 Spike protein from sequences collected during Q1 of 2025 . Using alignment-based mutation calling via Nextclade and functional annotation using Biopython tools locally, I identified the most frequent Spike mutation patters such as L452W, F486P, D614G. These mutations were observed across multiple lineages including JN.1, KP.2, LB.1

Each of these mutations has been previously associated with immune escape properties, enhanced ACE2 binding, and reduced neutralization by monoclonal antibodies and vaccine-induced immunity.

Functional Mutation Analysis

L452W is located within receptor Binding Domain (RBD), position 452. It enhances ACE2 affinity and reduces neutralization by therapeutic antibodies such as Bamlanivimab and C135. As described by Zhou et al., Nature 2022 that L452R/W mutations are linked to immune evasion and increased transmissibility this study confirms this pattern.  

F486P located within RBD, position 486 disrupts antibody binding at a conserved epitope; may impact neutralization by class 1 and class 2 antibodies. The F486 substitutions reduce binding by potent neutralizing antibodies targeting the ACE2 interface as described by McCallum et al., Science 2022.

D614G is located within Spike S1 domain it stabilizes Spike trimer, enhances fusion efficiency, and increases viral infectivity. D614G increases SARS-CoV-2 spike flexibility (Gobeil et al., PNAS 2021) and ACE2 receptor engagement is also enhanced.

Together, this mutation profile suggests a potential escape mechanism from both vaccine-induced immunity and therapeutic monoclonal antibodies, while maintaining high ACE2 binding affinity and transmission fitness.

Methods Overview

Sequences obtained from NCBI/GISAID EpiCoV databases

Mutation profiles extracted using Nextclade and iVar.

Lineage classification via Pangolin

Mutation annotations mapped to Wuhan-Hu-1 reference genome

Immune escape prediction based on known antibody epitopes from CoV-AbDab and structural studies

All methods are fully reproducible and generated fasta file is included with this dataset.

References

1. Zhou, D., et al. (2022).    Evidence of escape of SARS-CoV-2 variant BQ.1.1 from vaccine and therapeutic antibody protection. Nature.   - https://doi.org/10.1038/s41586-022-04967-2 

2. McCallum, M., et al. (2022).    Structural basis of potent antibody responses to SARS-CoV-2 variants   . Science.   - https://doi.org/10.1126/science.abq2652 

3. Gobeil, S.M.C., et al. (2021).    Effect of the D614G substitution on the structure of the spike glycoprotein of SARS-CoV-2. PNAS.   - https://doi.org/10.1073/pnas.2106524118 

4. Wang, Q., et al. (2023).    Antibody resistance of XBB.1.5 and related variants. Cell Reports.   - https://doi.org/10.1016/j.celrep.2023.112322 

5. WHO.    Tracking SARS-CoV-2 variants: Omicron sublineages and recombinants.   - https://www.who.int/publications/m/item/tracking-sars-cov-2-variants
DOI: 10.15468/dl.872ed5
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Denekia capensis Thunb.",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((20.2855 -34.7533,20.509 -34.5676,20.509 -32.9007,17.7723 -32.9007,17.8156 -33.0786,18.3471 -33.7176,18.3748 -33.8287,18.2181 -34.0492,18.3197 -34.3408,18.4452 -34.429,18.5435 -34.4213,18.5872 -34.3667,18.5363 -34.167,18.7345 -34.1508,18.7216 -34.3637,18.7808 -34.4521,19.0289 -34.4206,19.0831 -34.4835,19.2655 -34.5017,19.2032 -34.6157,19.2394 -34.6926,19.375 -34.6963,19.6091 -34.8524,19.8251 -34.8396,19.9798 -34.9064,20.1081 -34.8731,20.1517 -34.7847,20.2855 -34.7533))"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0046137-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6hztxp
title: Occurrence Download

description: A dataset containing 1631 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-77.5 -70.5,-55 -70.5,-55 -60,-77.5 -60,-77.5 -70.5))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Month is one of (January, February, March, December)",
 "OccurrenceStatus is Present",
 "TaxonKey is Euphausia superba Dana, 1850",
 "Year 2003-2025"
 ]
}

 The dataset includes 1631 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0046138-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.amdveg
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Denekia capensis Thunb.",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((35.628 -23.023,35.6007 -22.9702,35.6007 -23.165,35.628 -23.023))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0046139-250525065834625/datasets/export for details.
DOI: 10.15468/dl.kkkj63
title: Occurrence Download

description: A dataset containing 41084644 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is North America",
 "License is CC-BY 4.0",
 "Month is one of (August, September)",
 "Year 2022-2023"
 ]
}

 The dataset includes 41084644 records from 155 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0046131-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dwnk64
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Denekia capensis Thunb.",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((35.6306 -23.844,35.6007 -23.8125,35.6007 -24.0157,35.6306 -23.844))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0046140-250525065834625/datasets/export for details.
DOI: 10.5281/zenodo.15663752
title: Deepfake Ethics Paper References
DOI: 10.5281/zenodo.15663753
title: Deepfake Ethics Paper References
DOI: 10.15468/dl.8jcphq
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Romulea aquatica G.J.Lewis",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((30.0251 -31.3959,30.5701 -30.7329,30.5701 -28.5786,25.5395 -28.5786,25.5395 -32.9007,28.2048 -32.9007,28.5753 -32.6569,29.4902 -31.7517,30.0251 -31.3959))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0046141-250525065834625/datasets/export for details.
DOI: 10.5281/zenodo.15603489
title: Codebook Motif Explorer Supplementary Dataset

description: This is the supplementary dataset of the GRECO-BIT/Codebook Motif Explorer (MEX),which is a detailed online catalog of DNA motifs built using a huge collection of experimental data produced by the Codebook Consortium to annotate the binding specificities of human transcription factors, see Vorontsov et al. (bioRxiv).

Motif discovery for MEX was performed with multiple software tools, and the resulting motifs were rigorously benchmarked against held-out test data. Here you can find detailed benchmarking results, complete motif sets, and the benchmarking-ready preprocessed experimental data. 

Further details are provided in README.

*The version update resolves minor file naming issues in the original upload. The files contents remain the same.

Note: There are two extra accompanying Zenodo datasets, namely,doi:10.5281/zenodo.8327477 (MEX HT-SELEX data) and doi:10.5281/zenodo.8327970 (MEX GHT-SELEX data).

 

Update 2025: replaced files for TFs whose datasets were partially mislabeled in the original upload.

Affected TFs: CHCHD3, CPXCR1, MYRFL, PRDM5, TIGD4, TIGD5, TTF1, ZBED5, ZBTB5, ZNF578.

Note: PBM and SMS datasets were not affected and the respective files remain the same as in the previous upload.

This repository now also provides the set of reference artifact motifs used to filter the MEX results in a variety of commonly accepted formats (TRANSFAC, MEME, JASPAR, plain text).
DOI: 10.15468/dl.p5k5gy
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Romulea aquatica G.J.Lewis",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((30.5701 -24.0715,25.5395 -24.0715,25.5395 -28.5786,30.5701 -28.5786,30.5701 -24.0715))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0046143-250525065834625/datasets/export for details.
DOI: 10.15468/dl.vbjspq
title: Occurrence Download

description: A dataset containing 143 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-103.17716 -18.76346,-21.82284 -18.76346,-21.82284 13.76346,-103.17716 13.76346,-103.17716 -18.76346))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Brachyplatystoma filamentosum (Lichtenstein, 1819)"
 ]
}

 The dataset includes 143 records from 30 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0046142-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.83jwq8
title: Occurrence Download

description: A dataset containing 93 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-96.10287 -16.93503,-28.89713 -16.93503,-28.89713 9.93503,-96.10287 9.93503,-96.10287 -16.93503))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Brachyplatystoma rousseauxii (Castelnau, 1855)"
 ]
}

 The dataset includes 93 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0046144-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qeabnn
title: Occurrence Download

description: A dataset containing 768808 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Saxifragaceae"
 ]
}

 The dataset includes 768808 records from 908 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002936-190621201848488/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4dr8x5
title: Occurrence Download

description: A dataset containing 1724 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Bactericera cockerelli (Šulc, 1909)"
 ]
}

 The dataset includes 1724 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0034824-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tfvpys
title: Occurrence Download

description: A dataset containing 194 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Karelinia caspia (Pall.) Less."
 ]
}

 The dataset includes 194 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0034825-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6g6mqj
title: Occurrence Download

description: A dataset containing 2518 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((113.14733 -44.26429,158.61403 -44.26429,158.61403 3.61846,113.14733 3.61846,113.14733 -44.26429))",
 "OccurrenceStatus is Present",
 "TaxonKey is Hypseleotris compressa (Krefft, 1864)"
 ]
}

 The dataset includes 2518 records from 26 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0034826-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.