cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.27950672
title: Multi-omics insights into the pathogenesis of diabetic cardiomyopathy: epigenetic and metabolic profiles

description: Diabetic cardiomyopathy (DbCM), a complex metabolic disease, greatly threatens human health due to therapeutic limitations. Multi-omics approaches facilitate the elucidation of its intrinsic pathological changes. Metabolomics, RNA-seq, proteomics, and assay of transposase-accessible chromatin (ATAC-seq) were utilized to elucidate multidimensional molecular alterations in DbCM. In the heart and plasma of mice with DbCM, metabolomic analysis demonstrated significant differences in branched-chain amino acids (BCAAs) and lipids. Subsequent RNA-seq and proteomics showed that the key genes, including BCKDHB, PPM1K, Cpt1b, Fabp4, Acadm, Acadl, Acadvl, HADH, HADHA, HADHB, Eci1, Eci2, PDK4, and HMGCS2, were aberrantly regulated, contributing to the disorder of BCAAs and fatty acids. ATAC-seq analysis underscored the pivotal role of epigenetic regulation by revealing dynamic shifts in chromatin accessibility and a robust positive correlation with gene expression patterns in diabetic cardiomyopathy mice. Furthermore, motif analysis identified that KLF15 as a critical transcription factor in DbCM, regulating the core genes implicated with BCAAs metabolism. Our research delved into the metabolic alterations and epigenetic landscape and revealed that KLF15 may be a promising candidate for therapeutic intervention in DbCM.
DOI: 10.6084/m9.figshare.27966827
title: Emergent properties of the lysine methylome reveal regulatory roles via protein interactions and histone mimicry

description: Epigenomics has significantly advanced through the incorporation of Systems Biology approaches. This study aims to investigate the human lysine methylome as a system, using a data-science approach to reveal its emergent properties, particularly focusing on histone mimicry and the broader implications of lysine methylation across the proteome. We employed a data-science-driven OMICS approach, leveraging high-dimensional proteomic data to study the lysine methylome. The analysis focused on identifying sequence-based recognition motifs of lysine methyltransferases and evaluating the prevalence and distribution of lysine methylation across the human proteome. Our analysis revealed that lysine methylation impacts 15% of the known proteome, with a notable bias toward mono-methylation. We identified sequence-based recognition motifs of 13 lysine methyltransferases, highlighting candidates for histone mimicry. These findings suggest that the selective inhibition of individual lysine methyltransferases could have systemic effects rather than merely targeting histone methylation. The lysine methylome has significant mechanistic value and should be considered in the design and testing of therapeutic strategies, particularly in precision oncology. The study underscores the importance of considering non-histone proteins involved in DNA damage and repair, cell signaling, metabolism, and cell cycle pathways when targeting lysine methyltransferases.
DOI: 10.6084/m9.figshare.27966827.v1
title: Emergent properties of the lysine methylome reveal regulatory roles via protein interactions and histone mimicry

description: Epigenomics has significantly advanced through the incorporation of Systems Biology approaches. This study aims to investigate the human lysine methylome as a system, using a data-science approach to reveal its emergent properties, particularly focusing on histone mimicry and the broader implications of lysine methylation across the proteome. We employed a data-science-driven OMICS approach, leveraging high-dimensional proteomic data to study the lysine methylome. The analysis focused on identifying sequence-based recognition motifs of lysine methyltransferases and evaluating the prevalence and distribution of lysine methylation across the human proteome. Our analysis revealed that lysine methylation impacts 15% of the known proteome, with a notable bias toward mono-methylation. We identified sequence-based recognition motifs of 13 lysine methyltransferases, highlighting candidates for histone mimicry. These findings suggest that the selective inhibition of individual lysine methyltransferases could have systemic effects rather than merely targeting histone methylation. The lysine methylome has significant mechanistic value and should be considered in the design and testing of therapeutic strategies, particularly in precision oncology. The study underscores the importance of considering non-histone proteins involved in DNA damage and repair, cell signaling, metabolism, and cell cycle pathways when targeting lysine methyltransferases.
DOI: 10.6084/m9.figshare.28000184.v1
title: Placental expression and methylation of angiogenic factors in assisted reproductive technology pregnancies from India

description: This study aims to examine the gene expression and DNA methylation patterns of angiogenic factors in the placentae of Indian women who underwent assisted reproductive technology (ART) procedures and their association with maternal one-carbon metabolites and birth outcome. Placental gene expression and DNA methylation of angiogenic factors (<i>VEGF</i>, <i>PlGF</i>, <i>FLT-1</i>, <i>KDR</i>) in Indian women who underwent ART procedures (<i>n</i> = 64) and women who conceived naturally (Non-ART) (<i>n</i> = 93) was investigated using RT-qPCR and Epitect Methyl-II PCR assay kits. Maternal plasma one-carbon metabolites were assessed by CMIA technology. Gene expression of <i>FLT-1</i> and <i>KDR</i> was higher (<i>p</i> &lt; 0.05) in the ART placentae. Placental global DNA methylation levels were higher (<i>p</i> &lt; 0.01) and DNA methylation levels of <i>VEGF</i> promoter were lower (<i>p</i> &lt; 0.05) in ART compared to non-ART women. Maternal plasma folate and vitamin B<sub>12</sub> levels were higher (<i>p</i> &lt; 0.01) in the ART group. Gene expression of <i>PlGF</i> was negatively associated with maternal plasma folate (<i>p</i> &lt; 0.05) whereas KDR was positively associated with maternal plasma homocysteine (<i>p</i> &lt; 0.05). Gene expression of <i>KDR</i> was positively associated with chest circumference of the baby (<i>p</i> &lt; 0.05). Hypomethylation of <i>VEGF</i> and increased expression of <i>FLT-1</i> and <i>KDR</i> was observed in the placentae of women who underwent ART procedure. Assisted reproductive technology (ART) procedures such as in vitro fertilization (IVF) and intrauterine insemination (IUI) are used as infertility treatments. In India, the rate of infertility is on the rise thereby increasing the demand for these treatments. ART procedures are undertaken during gametogenesis and early embryo development. These are important stages where epigenetic modifications like DNA methylation are established for normal fetal development. ART procedures overlap with these stages, potentially affecting gene activity which may influence the development of the placenta and fetus. Evidence suggests that ART techniques are associated with maldevelopment and dysfunction of the placenta that would affect the fetal growth and development. Vascular endothelial growth factor (VEGF), placental growth factor (PlGF), fms-like tyrosine kinase (FLT-1) and kinase domain receptor (KDR) are growth factors that play an important role in the process of angiogenesis defined as formation of new blood vessels from existing blood vessels. This process is essential for the growth and development of the placenta as well as fetus. This study reports lower DNA methylation of <i>VEGF</i> and higher expression of <i>FLT-1</i> and <i>KDR</i> in the placentae of Indian women who underwent ART procedures. These changes within the placenta are likely to influence angiogenesis, placental, and fetal growth.
DOI: 10.6084/m9.figshare.28000184
title: Placental expression and methylation of angiogenic factors in assisted reproductive technology pregnancies from India

description: This study aims to examine the gene expression and DNA methylation patterns of angiogenic factors in the placentae of Indian women who underwent assisted reproductive technology (ART) procedures and their association with maternal one-carbon metabolites and birth outcome. Placental gene expression and DNA methylation of angiogenic factors (<i>VEGF</i>, <i>PlGF</i>, <i>FLT-1</i>, <i>KDR</i>) in Indian women who underwent ART procedures (<i>n</i> = 64) and women who conceived naturally (Non-ART) (<i>n</i> = 93) was investigated using RT-qPCR and Epitect Methyl-II PCR assay kits. Maternal plasma one-carbon metabolites were assessed by CMIA technology. Gene expression of <i>FLT-1</i> and <i>KDR</i> was higher (<i>p</i> &lt; 0.05) in the ART placentae. Placental global DNA methylation levels were higher (<i>p</i> &lt; 0.01) and DNA methylation levels of <i>VEGF</i> promoter were lower (<i>p</i> &lt; 0.05) in ART compared to non-ART women. Maternal plasma folate and vitamin B<sub>12</sub> levels were higher (<i>p</i> &lt; 0.01) in the ART group. Gene expression of <i>PlGF</i> was negatively associated with maternal plasma folate (<i>p</i> &lt; 0.05) whereas KDR was positively associated with maternal plasma homocysteine (<i>p</i> &lt; 0.05). Gene expression of <i>KDR</i> was positively associated with chest circumference of the baby (<i>p</i> &lt; 0.05). Hypomethylation of <i>VEGF</i> and increased expression of <i>FLT-1</i> and <i>KDR</i> was observed in the placentae of women who underwent ART procedure. Assisted reproductive technology (ART) procedures such as in vitro fertilization (IVF) and intrauterine insemination (IUI) are used as infertility treatments. In India, the rate of infertility is on the rise thereby increasing the demand for these treatments. ART procedures are undertaken during gametogenesis and early embryo development. These are important stages where epigenetic modifications like DNA methylation are established for normal fetal development. ART procedures overlap with these stages, potentially affecting gene activity which may influence the development of the placenta and fetus. Evidence suggests that ART techniques are associated with maldevelopment and dysfunction of the placenta that would affect the fetal growth and development. Vascular endothelial growth factor (VEGF), placental growth factor (PlGF), fms-like tyrosine kinase (FLT-1) and kinase domain receptor (KDR) are growth factors that play an important role in the process of angiogenesis defined as formation of new blood vessels from existing blood vessels. This process is essential for the growth and development of the placenta as well as fetus. This study reports lower DNA methylation of <i>VEGF</i> and higher expression of <i>FLT-1</i> and <i>KDR</i> in the placentae of Indian women who underwent ART procedures. These changes within the placenta are likely to influence angiogenesis, placental, and fetal growth.
DOI: 10.15468/dl.arfuyv
title: Occurrence Download

description: A dataset containing 654053 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Argentina anserina (L.) Rydb."
 ]
}

 The dataset includes 654053 records from 1514 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0046672-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.11600544
title: Johann Nikolaus Ritter (r0634)

description: -- Documentation --Name: Johann Nikolaus RittermusiXplora-ID: r0634musiXplora-URI: https://musixplora.de/mxp/r0634Gender: mConfessions: evangelisch-lutherischDate of Birth: 26 March 1702Place of Birth: UndefinedDate of Death: 28 February 1782Place of Death: ErlangenFirst Mentioned: 1726Sectors: Hof, Kirche, OrgelbauProfessions (Historical): Hochfürstl. Brandenburg-Culmbachischer Hoforgel- und InstrumentenmacherProfessions (Musical): OrgelbauerMain Place of Activity: HofOther Places of Activity: Altenburg, Amsterdam, Bayreuth, Erfurt, Erlangen, Freiberg, KulmbachAusbildung:
GroupRoleNamemXp-IDLehrerInnen und AusbilderInnenLehrerFriedrich Heidenreichh0576LehrerInnen und AusbilderInnenSchülerGottfried Silbermanns4066Arbeitsumfeld:
GroupRoleNamemXp-IDArbeitgeberInnenArbeitnehmerGottfried Silbermanns4066ArbeitgeberInnenArbeitnehmerTobias Heinrich Gottfried Trostt0908KollegInnenKollegeJohann Jacob Graicheng0549VorgängerInnenVorgängerFriedrich Heidenreichh0576Personal:
GroupRoleNamemXp-IDLeitungsfunktionMitarbeiterGraichen & Ritter3030835Titel/Medien:
RoleSigelTitlemXp-IDRelatedBernhard 2003aOrgeldatenbank Bayern5001131RelatedFischer & Wohnhaas 1994Lexikon süddeutscher Orgelbauer5001133Changelog:  - v0.0.1: Initial Upload.
DOI: 10.5281/zenodo.11600545
title: Johann Nikolaus Ritter (r0634)

description: -- Documentation --Name: Johann Nikolaus RittermusiXplora-ID: r0634musiXplora-URI: https://musixplora.de/mxp/r0634Gender: mConfessions: evangelisch-lutherischDate of Birth: 26 March 1702Place of Birth: UndefinedDate of Death: 28 February 1782Place of Death: ErlangenFirst Mentioned: 1726Sectors: Hof, Kirche, OrgelbauProfessions (Historical): Hochfürstl. Brandenburg-Culmbachischer Hoforgel- und InstrumentenmacherProfessions (Musical): OrgelbauerMain Place of Activity: HofOther Places of Activity: Altenburg, Amsterdam, Bayreuth, Erfurt, Erlangen, Freiberg, KulmbachAusbildung:
GroupRoleNamemXp-IDLehrerInnen und AusbilderInnenLehrerFriedrich Heidenreichh0576LehrerInnen und AusbilderInnenSchülerGottfried Silbermanns4066Arbeitsumfeld:
GroupRoleNamemXp-IDArbeitgeberInnenArbeitnehmerGottfried Silbermanns4066ArbeitgeberInnenArbeitnehmerTobias Heinrich Gottfried Trostt0908KollegInnenKollegeJohann Jacob Graicheng0549VorgängerInnenVorgängerFriedrich Heidenreichh0576Personal:
GroupRoleNamemXp-IDLeitungsfunktionMitarbeiterGraichen & Ritter3030835Titel/Medien:
RoleSigelTitlemXp-IDRelatedBernhard 2003aOrgeldatenbank Bayern5001131RelatedFischer & Wohnhaas 1994Lexikon süddeutscher Orgelbauer5001133Changelog:  - v0.0.1: Initial Upload.
DOI: 10.5281/zenodo.11600546
title: C. W. Ritdershausen (r0636)

description: -- Documentation --Name: C. W. RitdershausenmusiXplora-ID: r0636musiXplora-URI: https://musixplora.de/mxp/r0636Gender: mFirst Mentioned: 1722Professions (Musical): SchlagzeugherstellerOther Places of Activity: EuropaChangelog:  - v0.0.1: Initial Upload.
DOI: 10.5281/zenodo.11600547
title: C. W. Ritdershausen (r0636)

description: -- Documentation --Name: C. W. RitdershausenmusiXplora-ID: r0636musiXplora-URI: https://musixplora.de/mxp/r0636Gender: mFirst Mentioned: 1722Professions (Musical): SchlagzeugherstellerOther Places of Activity: EuropaChangelog:  - v0.0.1: Initial Upload.
DOI: 10.15468/dl.rrpgwm
title: Occurrence Download

description: A dataset containing 7863256 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 7863256 records from 2734 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0093260-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.34740/kaggle/dsv/8545610
title: Layline Shareholder activism dataset
DOI: 10.15468/dl.zouiau
title: Occurrence Download

description: A dataset containing 288 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "BasisOfRecord is Specimen",
 "BasisOfRecord is Human Observation",
 "BasisOfRecord is Material sample",
 "BasisOfRecord is Machine Observation",
 "BasisOfRecord is Observation"
 ]
 },
 "HasCoordinate is true",
 "TaxonKey is Ichneumia I.Geoffroy Saint-Hilaire, 1837",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 288 records from 21 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0036284-180508205500799/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pafwm5
title: Occurrence Download

description: A dataset containing 1481 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Chaenopsis ocellata Poey, 1865"
 ]
}

 The dataset includes 1481 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0059267-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.akhfyi
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Barbados",
 "TaxonKey is Blattodea"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0036284-181108115102211/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zcef7u
title: Occurrence Download

description: A dataset containing 8678316 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "BasisOfRecord is Human Observation",
 "BasisOfRecord is Specimen"
 ]
 },
 "Country is Brazil",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "Year 1990-2020"
 ]
}

 The dataset includes 8678316 records from 1402 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0106449-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.0jjovp
title: Occurrence Download

description: A dataset containing 12 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Country is Colombia",
 "Year 2001-2001",
 "DatasetKey is EOD – eBird Observation Dataset",
 "HasCoordinate is true",
 "TaxonKey is Myiozetetes similis (Spix, 1825)",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 12 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0036287-181108115102211/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2n4aaj
title: Occurrence Download

description: A dataset listing the 3985487 species recorded in GBIF matching the query:
{ }

 The dataset's 3985487 records were derived from 62278 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0076264-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.13145/bacdive147899.20251217.10
title: Moraxella catarrhalis

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive147900.20241212.9.2
title: Neisseria sicca

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.15156/bio/sh0135921.10fu
title: SH0135921.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.13145/bacdive147900.20251217.10
title: Neisseria sicca

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive147901.20241212.9.2
title: Bacteroides fragilis

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.15156/bio/sh0135922.10fu
title: SH0135922.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.13145/bacdive147901.20251217.10
title: Bacteroides fragilis

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive147902.20241212.9.2
title: Bacillus licheniformis

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.15156/bio/sh0135923.10fu
title: SH0135923.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.13145/bacdive147902.20251217.10
title: Bacillus licheniformis

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.