cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.29625369
title: EWAS in COPD by biomass-burning smoke exposure identifies low levels of endothelin-1 by hypermethylation of EDN1

description: Exposure to smoke from biomass combustion is a significant environmental risk factor for chronic obstructive pulmonary disease (COPD). Through epigenome-wide association studies (EWAS), changes in DNA methylation levels associated with pathological conditions can be identified. We aimed to determine the methylation patterns in genes involved in the development of COPD resulting from exposure to biomass-burning smoke (COPD-BBS). EWAS was conducted on induced sputum samples from 45 women with stable COPD (COPD-BBS) exposure and 45 women exposed to BBS but without the disease (BBES). Proteins whose genes showed significant differences in methylation and were soluble in the induced sputum supernatant were quantified. 205 CpG sites were found differentially hypomethylated, and 420 were hypermethylated. The top 50 show genes associated with lung remodeling (<i>FOXP1 p</i> = 0.002, <i>FMOD p</i> = 0.012, <i>EDN1 p</i> = 0.044), the immune system (<i>ALOX5 p</i> = 0.005, <i>IL19 p</i> = 0.047), mucus production (<i>MUC19 p</i> = 0.04), and xenobiotic metabolism (<i>GSTO2 p</i> = 0.02). Of the proteins evaluated, endothelin-1 was decreased in the reference group compared to patients (<i>p</i> = 0.00054). Gene methylation changes are linked to lung remodeling, immune response, mucus production, and xenobiotic metabolism. Hypermethylation of the cg08450425 site (<i>EDN1</i>) is significant in women with COPD and associated with low endothelin-1 levels. DNA modifications not present in the sequence contribute to COPD in women exposed to biomass-burning smoke. In both rural and urban areas, using biomass (firewood) for cooking and heating homes is quite common. Unfortunately, the smoke produced from burning firewood contains substances harmful to the respiratory system. The primary population affected is women, leading some to develop lung disease. The aim of this study was to assess the changes that genetic material can exhibit and their impact on the production of proteins involved in the disease. We found a significant effect on genes that play roles in inflammation and detoxification processes in the body. Notably, our findings highlight the influence on the endothelin gene, which encodes a protein that regulates inflammatory responses and manages high blood pressure in the pulmonary arteries. These results will enable us to explore additional pathways that have not been previously analyzed to gain further insight into the disease.
DOI: 10.6084/m9.figshare.29625369.v1
title: EWAS in COPD by biomass-burning smoke exposure identifies low levels of endothelin-1 by hypermethylation of EDN1

description: Exposure to smoke from biomass combustion is a significant environmental risk factor for chronic obstructive pulmonary disease (COPD). Through epigenome-wide association studies (EWAS), changes in DNA methylation levels associated with pathological conditions can be identified. We aimed to determine the methylation patterns in genes involved in the development of COPD resulting from exposure to biomass-burning smoke (COPD-BBS). EWAS was conducted on induced sputum samples from 45 women with stable COPD (COPD-BBS) exposure and 45 women exposed to BBS but without the disease (BBES). Proteins whose genes showed significant differences in methylation and were soluble in the induced sputum supernatant were quantified. 205 CpG sites were found differentially hypomethylated, and 420 were hypermethylated. The top 50 show genes associated with lung remodeling (<i>FOXP1 p</i> = 0.002, <i>FMOD p</i> = 0.012, <i>EDN1 p</i> = 0.044), the immune system (<i>ALOX5 p</i> = 0.005, <i>IL19 p</i> = 0.047), mucus production (<i>MUC19 p</i> = 0.04), and xenobiotic metabolism (<i>GSTO2 p</i> = 0.02). Of the proteins evaluated, endothelin-1 was decreased in the reference group compared to patients (<i>p</i> = 0.00054). Gene methylation changes are linked to lung remodeling, immune response, mucus production, and xenobiotic metabolism. Hypermethylation of the cg08450425 site (<i>EDN1</i>) is significant in women with COPD and associated with low endothelin-1 levels. DNA modifications not present in the sequence contribute to COPD in women exposed to biomass-burning smoke. In both rural and urban areas, using biomass (firewood) for cooking and heating homes is quite common. Unfortunately, the smoke produced from burning firewood contains substances harmful to the respiratory system. The primary population affected is women, leading some to develop lung disease. The aim of this study was to assess the changes that genetic material can exhibit and their impact on the production of proteins involved in the disease. We found a significant effect on genes that play roles in inflammation and detoxification processes in the body. Notably, our findings highlight the influence on the endothelin gene, which encodes a protein that regulates inflammatory responses and manages high blood pressure in the pulmonary arteries. These results will enable us to explore additional pathways that have not been previously analyzed to gain further insight into the disease.
DOI: 10.15468/dl.bxzwcg
title: Occurrence Download

description: A dataset containing 1 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 (Didelphis marsupialis)",
 "Country is one of (Bermuda, Canada, Greenland, Saint Pierre and Miquelon, United States of America)"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020360-250802193616735/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.29839520
title: SFPDADL.rar

description: 一种耦合数据同化和深度学习模型（SFPDADL）的亚热带森林物候反演模型，以提高物候估计精度。
DOI: 10.6084/m9.figshare.29839520.v1
title: SFPDADL.rar

description: 一种耦合数据同化和深度学习模型（SFPDADL）的亚热带森林物候反演模型，以提高物候估计精度。
DOI: 10.15468/dl.ucge9f
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Casuarina glauca",
 "Country is Papua New Guinea",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020359-250802193616735/datasets/export for details.
DOI: 10.5281/zenodo.15273992
title: Dataset from "Delayed and Displaced: The impact of binary interactions on core-collapse supernova feedback"

description: This archive contains the dataset associated with our paper on the impact of binary interactions on core-collapse supernovae. Each HDF5 file represents a cogsworth population (https://cogsworth.readthedocs.io/en/latest/) which can be loaded with cogsworth.pop.load(FILE_PATH). The addition sn_positions files give the position of each supernova for each variation.

All code for reproducing simulations and plots is included in the github repo here (https://github.com/TomWagg/supernova-feedback/), which is also archived here.
DOI: 10.5281/zenodo.15273993
title: Dataset from "Delayed and Displaced: The impact of binary interactions on core-collapse supernova feedback"

description: This archive contains the dataset associated with our paper on the impact of binary interactions on core-collapse supernovae. Each HDF5 file represents a cogsworth population (https://cogsworth.readthedocs.io/en/latest/) which can be loaded with cogsworth.pop.load(FILE_PATH). The addition sn_positions files give the position of each supernova for each variation.

All code for reproducing simulations and plots is included in the github repo here (https://github.com/TomWagg/supernova-feedback/), which is also archived here.
DOI: 10.15468/dl.t75epg
title: Occurrence Download

description: A dataset containing 24883 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 (Didelphis marsupialis)",
 "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 24883 records from 396 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020361-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.95szrx
title: Occurrence Download

description: A dataset containing 0 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 (Didelphis marsupialis)",
 "Country is one of (Afghanistan, Armenia, Azerbaijan, Bahrain, Bangladesh, Bhutan, Brunei Darussalam, Cambodia, China, Cyprus, Georgia, Hong Kong, India, Indonesia, Iran (Islamic Republic of), Iraq, Israel, Japan, Jordan, Kazakhstan, Korea (Democratic People’s Republic of), Korea, Republic of, Kuwait, Kyrgyzstan, Lao People’s Democratic Republic, Lebanon, Macao, Malaysia, Maldives, Mongolia, Myanmar, Nepal, Oman, Pakistan, Palestine, State of, Philippines, Qatar, Saudi Arabia, Singapore, Sri Lanka, Syrian Arab Republic, Tajikistan, Thailand, Timor-Leste, Türkiye, Turkmenistan, United Arab Emirates, Uzbekistan, Viet Nam, Yemen)"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020362-250802193616735/datasets/export for details.
DOI: 10.15468/dl.35krnx
title: Occurrence Download

description: A dataset containing 349837 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is USA.10_1",
 "TaxonKey is one of (Squamata, Crocodylia, Testudines)"
 ]
}

 The dataset includes 349837 records from 127 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020324-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vcmsae
title: Occurrence Download

description: A dataset containing 1283 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Phoeniculus somaliensis)",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "License is one of (CC-BY 4.0, CC0 1.0)"
 ]
}

 The dataset includes 1283 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020364-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vgdwpw
title: Occurrence Download

description: A dataset containing 5 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Silhouettea dotui)",
 "BasisOfRecord is one of (Specimen, Literature Occurrence, Human Observation, Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1991",
 "Year is less than or equal to 2025"
 ]
}

 The dataset includes 5 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020367-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25345/c58c9rh20
title: MassIVE MSV000098742 - 4D-DIA Proteomic Analysis of Pochonia chlamydosporia During Nematode Egg Infection
title: Pochonia chlamydosporia is an egg-parasitic fungus widely studied for its potential in the biological control of nematode pests. However, the protein-level mechanisms involved in its infection process remain poorly understood. In this study, we employed four-dimensional data-independent acquisition (4D-DIA) proteomic sequencing to investigate dynamic proteomic changes in P. chlamydosporia mycelia at different infection stages of nematode eggs. The dataset provides insights into the temporal regulation of protein expression during egg invasion and could support future studies in biocontrol mechanisms and fungal-nematode interactions.
DOI: 10.15468/dl.p5fuzf
title: Occurrence Download

description: A dataset containing 519 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Takydromus septentrionalis",
 "Country is China",
 "HasCoordinate is true"
 ]
}

 The dataset includes 519 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020363-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25392/leicester.data.29264864
title: COPD Viromes

description: <br><br>The vOTU catalogue for “Bacteriophage diversity declines with COPD severity in the respiratory microbiome”, and an excel workbook with four supplementary tables. Supplementary Table 1: Sample data. Supplementary Table 2: vOTU characteristics. Supplementary Table 3: vOTU abundance table (CPM). Supplementary Table 4: Bacterial abundance table.<br><br>COPD_virome_supplemental_script.R includes statistical analyses described in the manuscript<br>Figure_1.R reproduces panels for the figure 1 - generated using ggplot2 in R studio<br>Figure_2.R reproduced panels for the Figure 2 etc , etc
DOI: 10.25392/leicester.data.29264864.v2
title: COPD Viromes

description: <br><br>The vOTU catalogue for “Bacteriophage diversity declines with COPD severity in the respiratory microbiome”, and an excel workbook with four supplementary tables. Supplementary Table 1: Sample data. Supplementary Table 2: vOTU characteristics. Supplementary Table 3: vOTU abundance table (CPM). Supplementary Table 4: Bacterial abundance table.<br><br>COPD_virome_supplemental_script.R includes statistical analyses described in the manuscript<br>Figure_1.R reproduces panels for the figure 1 - generated using ggplot2 in R studio<br>Figure_2.R reproduced panels for the Figure 2 etc , etc
DOI: 10.25392/leicester.data.29264864.v1
title: COPD Viromes

description: <br><br>The vOTU catalogue for “Bacteriophage diversity declines with COPD severity in the respiratory microbiome”, and an excel workbook with four supplementary tables. Supplementary Table 1: Sample data. Supplementary Table 2: vOTU characteristics. Supplementary Table 3: vOTU abundance table (CPM). Supplementary Table 4: Bacterial abundance table.
DOI: 10.15468/dl.dyve4v
title: Occurrence Download

description: A dataset containing 290 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Phoenicurus bicolor)",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "License is one of (CC-BY 4.0, CC0 1.0)"
 ]
}

 The dataset includes 290 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020365-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.yw7pa3
title: Occurrence Download

description: A dataset containing 9029 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((7.69914 48.55101,9.06817 48.55101,9.06817 49.44914,7.69914 49.44914,7.69914 48.55101))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is one of (Linum usitatissimum, Cannabis sativa, Urtica dioica, Tilia, Phragmites, Triticum, Hordeum, Secale)"
 ]
}

 The dataset includes 9029 records from 89 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020368-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.k7jmps
title: Occurrence Download

description: A dataset containing 0 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 (Didelphis marsupialis)",
 "Country is one of (Åland Islands, Albania, Andorra, Austria, Belarus, Belgium, Bosnia and Herzegovina, Bulgaria, Croatia, Czechia, Denmark, Estonia, Faroe Islands, Finland, France, Germany, Gibraltar, Greece, Guernsey, Holy See, Hungary, Iceland, Ireland, Isle of Man, Italy, Jersey, Latvia, Liechtenstein, Lithuania, Luxembourg, Malta, Moldova, Republic of, Monaco, Montenegro, Netherlands, North Macedonia, Norway, Poland, Portugal, Romania, Russian Federation, San Marino, Serbia, Slovakia, Slovenia, Spain, Svalbard and Jan Mayen, Sweden, Switzerland, Ukraine, United Kingdom of Great Britain and Northern Ireland)"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020369-250802193616735/datasets/export for details.
DOI: 10.15468/dl.jn7zaj
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Casuarina glauca",
 "Country is Paraguay",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020370-250802193616735/datasets/export for details.
DOI: 10.17866/rd.salford.3409126
title: Educational signs ranking for research sites within Manchester and Salford

description: This file contains the Educational Signs ranking.  The ranking criteria is as follows:  0 = not present; 1 = present but poorly maintained signs which explains only one or two aspects of the site and/or not easily readable or visible; 2 = present and well-maintained signs which explain multiple aspects of the site.
DOI: 10.17866/rd.salford.3409126.v1
title: Educational signs ranking for research sites within Manchester and Salford

description: This file contains the Educational Signs ranking.  The ranking criteria is as follows:  0 = not present; 1 = present but poorly maintained signs which explains only one or two aspects of the site and/or not easily readable or visible; 2 = present and well-maintained signs which explain multiple aspects of the site.
DOI: 10.48723/fr58-f782
title: Transcriptomics profiling of human PSC cultured under different conditions
title: Transkriptomikdata på humana PSC odlade under olika förhållanden

description: This study has used transcriptome data derived for quality testing of pluripotent stem cells to investigate how different culture conditions affect gene expression. All pluripotent stem cells in the study have passed pluritest testing.
Data contains transcriptomics signatures of pluripotent stem cell lines originating from human donors, measured with Illumina Gene Expression HT12 Direct Hybridization assay (Illumina HT 12v.4). Human induced pluripotent stem cells (iPSCs) and embryonic stem cells (ESCs) were cultured under either undefined culture conditions or defined and xenofree culture conditions, or transferred from the undefined to defined condition. These are labeled as feeder, laminin and transfer in the sample table, respectively. Skin biopsy samples were collected with informed consent from donors for creating models for studying human development. Donor samples were reprogrammed to iPSC and transcriptome analyses were performed for quality testing of the pluripotent cells.

The dataset consists of 115 files in IDAT format and one in CSV format.
The total size of the dataset is approximately 335 MB.
description: Den här studien har använt transkkriptomikdata från kvalitetstestning av pluripotenta stamceller för att undersöka hur olika odlingsförhållanden påverkar genuttryck. Alla pluripotenta stamceller i studien har klarat test av pluripotens.
Data innehåller transkriptomiska signaturer av pluripotenta stamcell-linjer från humana donatorer, uppmätta med Illumina Gene Expression HT12 Direct Hybridization assay (Illumina HT 12v.4). Humana inducerade pluripotenta stamceller (iPSC) och embryonala stamceller (ESC) odlades under antingen odefinierad eller definierad och xenofri kultur, eller överförd från odefinierade till definierade kultur. Dessa benämns som feeder, laminin och transfer tabellen över proverna, respektive. Hudbiopsier samlades in efter samtycke från donatorer för modellering av tidig human utveckling. Donatorproverna omprogrammerades till iPCS och transkriptomanalyser utfördes för att kvalitetstesta de pluripotenta stamcellerna.

Datasetet består av 115 filer i IDAT-format och en i CSV-format.
Datasetets totala storlek är ungefär 335 MB.
DOI: 10.48723/0a55-ab34
title: Transcriptomics profiling of human PSC cultured under different conditions
title: Transkriptomikdata på humana PSC odlade under olika förhållanden

description: This study has used transcriptome data derived for quality testing of pluripotent stem cells to investigate how different culture conditions affect gene expression. All pluripotent stem cells in the study have passed pluritest testing.
Data contains transcriptomics signatures of pluripotent stem cell lines originating from human donors, measured with Illumina Gene Expression HT12 Direct Hybridization assay (Illumina HT 12v.4). Human induced pluripotent stem cells (iPSCs) and embryonic stem cells (ESCs) were cultured under either undefined culture conditions or defined and xenofree culture conditions, or transferred from the undefined to defined condition. These are labeled as feeder, laminin and transfer in the sample table, respectively. Skin biopsy samples were collected with informed consent from donors for creating models for studying human development. Donor samples were reprogrammed to iPSC and transcriptome analyses were performed for quality testing of the pluripotent cells.

The dataset consists of 115 files in IDAT format and one in CSV format.
The total size of the dataset is approximately 335 MB.
description: Den här studien har använt transkkriptomikdata från kvalitetstestning av pluripotenta stamceller för att undersöka hur olika odlingsförhållanden påverkar genuttryck. Alla pluripotenta stamceller i studien har klarat test av pluripotens.
Data innehåller transkriptomiska signaturer av pluripotenta stamcell-linjer från humana donatorer, uppmätta med Illumina Gene Expression HT12 Direct Hybridization assay (Illumina HT 12v.4). Humana inducerade pluripotenta stamceller (iPSC) och embryonala stamceller (ESC) odlades under antingen odefinierad eller definierad och xenofri kultur, eller överförd från odefinierade till definierade kultur. Dessa benämns som feeder, laminin och transfer tabellen över proverna, respektive. Hudbiopsier samlades in efter samtycke från donatorer för modellering av tidig human utveckling. Donatorproverna omprogrammerades till iPCS och transkriptomanalyser utfördes för att kvalitetstesta de pluripotenta stamcellerna.

Datasetet består av 115 filer i IDAT-format och en i CSV-format.
Datasetets totala storlek är ungefär 335 MB.