cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.20078635.v1
title: The function of Sphingosine-1-phosphate receptor 2 (S1PR2) in maintaining intestinal barrier and inducing ulcerative colitis

description: Sphingosine-1-phosphate receptor 2 (S1PR2) was highly expressed in intestinal epithelial cells (IECs) and facilitated the proliferation of IECs. However, the specific function of S1PR2 in intestinal diseases, such as ulcerative colitis (UC), remains unclear. Accordingly, the current study set out to investigate the function of S1PR2 in maintaining intestinal barrier and inducing UC. S1PR2-overexpressed and knockdown Caco-2 cells were established to explore the function of S1PR2 on the permeability of IECs barrier. The UC-like mouse model in which UC is induced by dextran sulfate sodium (DSS) was established and utilized to investigate the role for S1PR2. The results showed that S1PR2 functioned as a maintainer of IECs permeability and a pathogenic factor for UC. A series of in vitro and in vivo experiments were conducted, and it was found that S1PR2 played an important role in intestinal epithelial cell proliferation and maintenance of intestinal epithelial cell barrier, possibly by the regulation on the expression level of SphK2, HDAC1, HDAC2, and ERK1/2 signaling pathway. The expression of S1PR2 was upregulated in UC mice and the colonic pathological damage in UC mice could be alleviated by the inhibition of S1PR2. Collectively, these results suggest that S1PR2 functions as a maintainer of IECs permeability and a pathogenic factor for UC. The research suggests S1PR2 may be an effective target for developing therapeutic strategies against UC. <b>Abbreviations:</b> S1PR2, Sphingosine-1-phosphate receptor 2; UC, ulcerative colitis; IECs, intestinal epithelial cells; DSS, dextran sulfate sodium; IBD, inflammation bowel disease; CD, Crohn’s disease; S1P, sphingosin-1-phosphate; SphK, sphingosine kinase; HIECs, human IECs; siRNA, small interfering RNA; CCK-8, cell counting kit-8; TEER, transepithelial electrical resistance; TEM, transmission electron microscope; RT-PCR, real-time reverse transcriptase polymerase-chain reaction; ELISA, enzyme-linked immunosorbent assay; HE, hematoxylin and eosin.
DOI: 10.6084/m9.figshare.20078672
title: The complete chloroplast genome sequence of <i>Urtica fissa</i>

description: <i>Urtica fissa</i> E. Pritz is not only an important medicinal plant for rheumatism and cough relief, but it is also an important forage plant. In this study, the complete chloroplast genome of <i>U. fissa</i> was assembled for the first time and reported to be 146,837 base pairs (bp) long with a typical tetragonal structure and including a large single-copy of 79,657 bp, a small single-copy of 17,712 bp, and two inverted repeats of 24,734 bp each. It harbors 115 unique genes, including 70 protein-coding genes, 38 transfer RNA genes, and 7 ribosomal RNA genes. Phylogenetic analysis showed that <i>U. fissa</i> is closely related to <i>Urtica lobatifolia</i>. This study contributes to the understanding of the origin and evolution of <i>U. fissa</i>, as well as its genetic relationships with other species.
DOI: 10.6084/m9.figshare.20078672.v1
title: The complete chloroplast genome sequence of <i>Urtica fissa</i>

description: <i>Urtica fissa</i> E. Pritz is not only an important medicinal plant for rheumatism and cough relief, but it is also an important forage plant. In this study, the complete chloroplast genome of <i>U. fissa</i> was assembled for the first time and reported to be 146,837 base pairs (bp) long with a typical tetragonal structure and including a large single-copy of 79,657 bp, a small single-copy of 17,712 bp, and two inverted repeats of 24,734 bp each. It harbors 115 unique genes, including 70 protein-coding genes, 38 transfer RNA genes, and 7 ribosomal RNA genes. Phylogenetic analysis showed that <i>U. fissa</i> is closely related to <i>Urtica lobatifolia</i>. This study contributes to the understanding of the origin and evolution of <i>U. fissa</i>, as well as its genetic relationships with other species.
DOI: 10.5281/zenodo.10650901
title: Gender diversity: Understanding the needs of transgender and non-binary young people in physical education classes. A descriptive case study of a school in the Netherlands.

description: Data gathered in the context of a Master’s thesis (Educational Masters degree in Physical Education): Gender diversity: Understanding the needs of transgender and non-binary young people in physical education classes. A descriptive case study of a school in the Netherlands.
DOI: 10.5281/zenodo.10650902
title: Gender diversity: Understanding the needs of transgender and non-binary young people in physical education classes. A descriptive case study of a school in the Netherlands.

description: Data gathered in the context of a Master’s thesis (Educational Masters degree in Physical Education): Gender diversity: Understanding the needs of transgender and non-binary young people in physical education classes. A descriptive case study of a school in the Netherlands.
DOI: 10.5281/zenodo.8422186
title: Path Mixing VLN dataset

description: The R2R dataset consists of human annotated instructions corresponding to the paths in these graphs. Each path consists of a sequence of viewpoints encountered by the agent during navigation. A derived dataset, Fine-Grained R2R (FGR2R) [ 12] dataset, annotated parts of instructions with corresponding graph edges to obtain a fine-grained dataset. Existing works in VLN have shown that more instruction examples can improve an agent’s performance in<br> previously unseen environments. Hence to augment training data, we mix parts of paths from the FGR2R dataset to obtain additional instruction-trajectory pairs. The paths are mixed from other neighboring paths that are part of<br> same house which sustains both view and instruction consistency.<br> To mix paths we identify all the edges in the graph corresponding<br> to the start of navigation 𝜀𝑠𝑡𝑎𝑟𝑡 and end of navigational episodes<br> 𝜀𝑒𝑛𝑑 . These edges are important for mixing as they correspond<br> to micro-instructions (Walk away from the desk, Turn right etc.)<br> that refer to start and stop positions in the house while other edges<br> correspond to instructions that back reference to previous locations.<br> The remaining transition edges 𝜀𝑡𝑟𝑎𝑛𝑠 are mixed to obtain a path<br> 𝜀𝑠𝑡𝑎𝑟𝑡 → 𝜀𝑡𝑟𝑎𝑛𝑠 → 𝜀𝑒𝑛𝑑 . Not all edges are inter-connectable, as<br> some of the nodes could be spatially close to each other - reducing<br> the visual variety of viewpoints or resulting in the repetition of<br> micro-instructions (short but actionable instructions) in the final<br> instruction. Accordingly, the edges are connected based on the<br> following criteria: (1) the distance between any 2 nodes should be<br> greater than 3m and the angle between edges should not acute<br> to prevent navigating in loops (2) the distance between the start<br> and end nodes should be greater than 3m to ensure that the path<br> ends up in a different room (3) the start and end nodes cannot<br> have a common edge (4) micro-instructions from common edges<br> of different paths are chosen randomly. The final instruction is<br> the sequence of micro-instructions and the path is the sequence of<br> edges (Figure 2). Using this method, we generate 162k instruction-<br> trajectory pairs with path lengths between 5m and 30m. The final dataset<br> has on average 7.27 views per path, a mean of 14.4m trajectory<br> length and an average of 82 words per instruction.
DOI: 10.5281/zenodo.10610999
title: An Overview of Open Science in Italy - Data Set

description: Data sets accompanying the paper "An Overview of Open Science in Italy", an overview of the current state of open science implementation in Italy.

See the readme.txt for a detailed description of the data sets.

The data sets atenei.csv and altri-istituti-ricerca.csv document the organisation selection resulting from the list of Italian universities recognised by the Ministero dell'Università e della Ricerca, the aggregation of data from a crowdsourcing activity born within the Open Access Italia mailing list, from the catalogue of policies of the open-science.it portal, as well as from the survey by the Open Science Working Group of CoPER on the monitoring of institutional policies for the management of scientific data.

The data set policies.csv consists of the list of documents (among policies, guidelines and regulations) that are related to the observed organisations.

The data set ita_publications_openaire.csv.zip includes records about italian publications selected from the OpenAIRE Graph based on affiliation relationships. The data set is created via the Zeppelin Note available at 10.5281/zenodo.10640721.

The data set openaire_observatory_it.csv reports the aggregated data with respect to the Italian open access (OA) and closed research products, from 2015 to 2023, retrieved from the OpenAIRE Open Science Observatory.

The data set openaire_observatory_eu.csv consists of the aggregated data on the top eleven European countries for the OA research production (publications, data sets, software, and other research products), from 2015 to 2023, retrieved from the OpenAIRE Open Science Observatory.

The data set coki_years.csv consists of the aggregated indicators on the Italian OA production from 2000 to 2023.

The data set coki_it.csv consists of the selection of indicators on open and closed publications (from 2015 to 2023) from the coki_years.csv.

The data sets services_re3data.csv, services_opendoar.csv, services_eoscmarketplace.csv, and services_fairsharing.csv consist of the records identifying italian services for open science downloaded from re3data, OpenDOAR, the EOSC Marketplace, and FAIRsharing respectively.
DOI: 10.5281/zenodo.10611000
title: An Overview of Open Science in Italy - Data Set

description: Data sets accompanying the paper "An Overview of Open Science in Italy", an overview of the current state of open science implementation in Italy.

See the readme.txt for a detailed description of the data sets.

The data sets atenei.csv and altri-istituti-ricerca.csv document the organisation selection resulting from the list of Italian universities recognised by the Ministero dell'Università e della Ricerca, the aggregation of data from a crowdsourcing activity born within the Open Access Italia mailing list, from the catalogue of policies of the open-science.it portal, as well as from the survey by the Open Science Working Group of CoPER on the monitoring of institutional policies for the management of scientific data.

The data set policies.csv consists of the list of documents (among policies, guidelines and regulations) that are related to the observed organisations.

The data set ita_publications_openaire.csv.zip includes records about italian publications selected from the OpenAIRE Graph based on affiliation relationships. The data set is created via the Zeppelin Note available at 10.5281/zenodo.10640721.

The data set openaire_observatory_it.csv reports the aggregated data with respect to the Italian open access (OA) and closed research products, from 2015 to 2023, retrieved from the OpenAIRE Open Science Observatory.

The data set openaire_observatory_eu.csv consists of the aggregated data on the top eleven European countries for the OA research production (publications, data sets, software, and other research products), from 2015 to 2023, retrieved from the OpenAIRE Open Science Observatory.

The data set coki_years.csv consists of the aggregated indicators on the Italian OA production from 2000 to 2023.

The data set coki_it.csv consists of the selection of indicators on open and closed publications (from 2015 to 2023) from the coki_years.csv.

The data sets services_re3data.csv, services_opendoar.csv, services_eoscmarketplace.csv, and services_fairsharing.csv consist of the records identifying italian services for open science downloaded from re3data, OpenDOAR, the EOSC Marketplace, and FAIRsharing respectively.
DOI: 10.6084/m9.figshare.19028945.v1
title: Additional file 6 of Genome-wide annotation of protein-coding genes in pig

description: Additional file 6. Includes a list of a subset of orthologs with one parsimonious high confidence ortholog used in human-pig comparison analyses, a table of specificity classification for human and pig, indicating overlap in classification, and the inputs for hypergeometric test for assessing the classification overlap between pig and human tissues.
DOI: 10.6084/m9.figshare.19028948.v1
title: Additional file 7 of Genome-wide annotation of protein-coding genes in pig

description: Additional file 7. Includes a table indicating which antibodies have been used in each figure, table of antibody information including ID, targeted gene, and antigen sequence, and a table of staining reagents.
DOI: 10.6084/m9.figshare.19028951.v1
title: Additional file 8 of Genome-wide annotation of protein-coding genes in pig

description: Additional file 8. Includes a gene-wise comparison of Ensembl 92 and 103 gene IDs with comments on changes in gene type and status.
DOI: 10.6084/m9.figshare.19028936
title: Additional file 3 of Genome-wide annotation of protein-coding genes in pig

description: Additional file 3. Stratification of body-wide distribution and specificity of pig genes, including a list of specificity and distribution classification for all porcine genes.
DOI: 10.6084/m9.figshare.19028951
title: Additional file 8 of Genome-wide annotation of protein-coding genes in pig

description: Additional file 8. Includes a gene-wise comparison of Ensembl 92 and 103 gene IDs with comments on changes in gene type and status.
DOI: 10.6084/m9.figshare.19028936.v1
title: Additional file 3 of Genome-wide annotation of protein-coding genes in pig

description: Additional file 3. Stratification of body-wide distribution and specificity of pig genes, including a list of specificity and distribution classification for all porcine genes.
DOI: 10.6084/m9.figshare.19028939.v1
title: Additional file 4 of Genome-wide annotation of protein-coding genes in pig

description: Additional file 4. List of genes in each UMAP cluster, as well as their specificity and distribution classification, and result from hypergeometric test for overlap in tissue specificity and cluster genes.
DOI: 10.6084/m9.figshare.19028942
title: Additional file 5 of Genome-wide annotation of protein-coding genes in pig

description: Additional file 5. Supplementary information for annotation of each UMAP cluster, including elevated tissues generated from the hypergeometric test (FDR &lt; 0.001 in sheet 3; Cluster tissue hypergeom), and list of gene set enrichment analysis (GSEA) analysis towards GO-terms.
DOI: 10.6084/m9.figshare.19028948
title: Additional file 7 of Genome-wide annotation of protein-coding genes in pig

description: Additional file 7. Includes a table indicating which antibodies have been used in each figure, table of antibody information including ID, targeted gene, and antigen sequence, and a table of staining reagents.
DOI: 10.6084/m9.figshare.13787334
title: Additional file 1 of TMT-based quantitative proteomic analysis reveals defense mechanism of wheat against the crown rot pathogen Fusarium pseudograminearum

description: Additional file 1: Table S1. GO functional enrichment of 366 DEPs.
DOI: 10.6084/m9.figshare.19029321
title: Additional file 1 of Case–control study on TP73 rs1801173 C &gt; T gene polymorphism and susceptibility to gastric cancer in a Chinese Han population

description: Additional file 1. Supplementary information file.
DOI: 10.6084/m9.figshare.19029321.v1
title: Additional file 1 of Case–control study on TP73 rs1801173 C &gt; T gene polymorphism and susceptibility to gastric cancer in a Chinese Han population

description: Additional file 1. Supplementary information file.
DOI: 10.6084/m9.figshare.19029492
title: Additional file 2 of IDEAS: individual level differential expression analysis for single-cell RNA-seq data

description: Additional file 2 GSEA results for COVID data analysis.
DOI: 10.6084/m9.figshare.19029515.v1
title: Additional file 3 of Open chromatin interaction maps reveal functional regulatory elements and chromatin architecture variations during wheat evolution

description: Additional file 3: Table S4 The intrachromosomal open chromatin loops.
DOI: 10.15468/dl.aste9a
title: Occurrence Download

description: A dataset containing 59770 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "SpeciesKey is Mustela erminea Linnaeus, 1758",
 "Year is greater than or equal to 2004",
 "Year is less than or equal to 2023"
 ]
}

 The dataset includes 59770 records from 478 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0104442-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.va28js
title: Occurrence Download

description: A dataset containing 714 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "SpeciesKey is Palliduphantes alutacius (Simon, 1884)",
 "Year is greater than or equal to 2004",
 "Year is less than or equal to 2023"
 ]
}

 The dataset includes 714 records from 49 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0104453-240626123714530/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.26846218
title: <b>Table S2 | AntiSMASH predicted biosynthetic gene clusters (BGCs) derived from mosquito-associated isolate and metagenome-assembled genomes. </b>

description: Table of AntiSMASH predicted BGCs for each assembly. The table gives information about each assembly and the start & end location of the BGC within each contig and the predicted product. Appended to this are also CheckM genome quality assurance metrics and taxonomic classifications predicted with GTDB-Tk.
DOI: 10.15468/dl.gkn387
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Cyrtodactylus jaegeri Luu, Calame, Bonkowski, Nguyen & Ziegler, 2014)",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 2000",
 "BasisOfRecord is one of (Human Observation, Observation, Machine Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than 100",
 "CoordinateUncertaintyInMeters is null"
 ]
 }
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0104454-240626123714530/datasets/export for details.
DOI: 10.15468/dl.w7ybz9
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "SpeciesKey is Chrysolina relucens (Rosenhauer, 1847)",
 "Year is greater than or equal to 2004",
 "Year is less than or equal to 2023"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0104455-240626123714530/datasets/export for details.
DOI: 10.15468/dl.ax34nu
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "SpeciesKey is Dicheirotrichus tscheresovae (Komarov, 1995)",
 "Year is greater than or equal to 2004",
 "Year is less than or equal to 2023"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0104456-240626123714530/datasets/export for details.
DOI: 10.15468/dl.bnmzup
title: Occurrence Download

description: A dataset containing 14988248 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is USA.10_1",
 "OccurrenceStatus is Present",
 "Year 2016-2019"
 ]
}

 The dataset includes 14988248 records from 268 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0104414-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pgmfn5
title: Occurrence Download

description: A dataset containing 1513 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "SpeciesKey is Palliduphantes ericaeus (Blackwall, 1853)",
 "Year is greater than or equal to 2004",
 "Year is less than or equal to 2023"
 ]
}

 The dataset includes 1513 records from 89 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0104457-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ut66ws
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Cyrtodactylus nigriocularis Sang, Orlov & Darevsky, 2006)",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 2000",
 "BasisOfRecord is one of (Human Observation, Observation, Machine Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than 100",
 "CoordinateUncertaintyInMeters is null"
 ]
 }
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0104458-240626123714530/datasets/export for details.
DOI: 10.15468/dl.9qjtw6
title: Occurrence Download

description: A dataset containing 84 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "SpeciesKey is Chrysolina lucida (Olivier, 1807)",
 "Year is greater than or equal to 2004",
 "Year is less than or equal to 2023"
 ]
}

 The dataset includes 84 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0104459-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cawp2e
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "SpeciesKey is Dicheirotrichus discolor (Faldermann, 1836)",
 "Year is greater than or equal to 2004",
 "Year is less than or equal to 2023"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0104460-240626123714530/datasets/export for details.