cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.26181149
title: MIMOSA: a resource consisting of improved methylome prediction models increases power to identify DNA methylation-phenotype associations

description: Although DNA methylation (DNAm) has been implicated in the pathogenesis of numerous complex diseases, from cancer to cardiovascular disease to autoimmune disease, the exact methylation sites that play key roles in these processes remain elusive. One strategy to identify putative causal CpG sites and enhance disease etiology understanding is to conduct methylome-wide association studies (MWASs), in which predicted DNA methylation that is associated with complex diseases can be identified. However, current MWAS models are primarily trained using the data from single studies, thereby limiting the methylation prediction accuracy and the power of subsequent association studies. Here, we introduce a new resource, MWAS Imputing Methylome Obliging Summary-level mQTLs and Associated LD matrices (MIMOSA), a set of models that substantially improve the prediction accuracy of DNA methylation and subsequent MWAS power through the use of a large summary-level mQTL dataset provided by the Genetics of DNA Methylation Consortium (GoDMC). Through the analyses of GWAS (genome-wide association study) summary statistics for 28 complex traits and diseases, we demonstrate that MIMOSA considerably increases the accuracy of DNA methylation prediction in whole blood, crafts fruitful prediction models for low heritability CpG sites, and determines markedly more CpG site-phenotype associations than preceding methods. Finally, we use MIMOSA to conduct a case study on high cholesterol, pinpointing 146 putatively causal CpG sites.
DOI: 10.6084/m9.figshare.26181149.v1
title: MIMOSA: a resource consisting of improved methylome prediction models increases power to identify DNA methylation-phenotype associations

description: Although DNA methylation (DNAm) has been implicated in the pathogenesis of numerous complex diseases, from cancer to cardiovascular disease to autoimmune disease, the exact methylation sites that play key roles in these processes remain elusive. One strategy to identify putative causal CpG sites and enhance disease etiology understanding is to conduct methylome-wide association studies (MWASs), in which predicted DNA methylation that is associated with complex diseases can be identified. However, current MWAS models are primarily trained using the data from single studies, thereby limiting the methylation prediction accuracy and the power of subsequent association studies. Here, we introduce a new resource, MWAS Imputing Methylome Obliging Summary-level mQTLs and Associated LD matrices (MIMOSA), a set of models that substantially improve the prediction accuracy of DNA methylation and subsequent MWAS power through the use of a large summary-level mQTL dataset provided by the Genetics of DNA Methylation Consortium (GoDMC). Through the analyses of GWAS (genome-wide association study) summary statistics for 28 complex traits and diseases, we demonstrate that MIMOSA considerably increases the accuracy of DNA methylation prediction in whole blood, crafts fruitful prediction models for low heritability CpG sites, and determines markedly more CpG site-phenotype associations than preceding methods. Finally, we use MIMOSA to conduct a case study on high cholesterol, pinpointing 146 putatively causal CpG sites.
DOI: 10.6084/m9.figshare.25529486
title: Critical evaluation of the reliability of DNA methylation probes on the Illumina MethylationEPIC v1.0 BeadChip microarrays

description: DNA methylation (DNAm) plays a crucial role in a number of complex diseases. However, the reliability of DNAm levels measured using Illumina arrays varies across different probes. Previous research primarily assessed probe reliability by comparing duplicate samples between the 450k-450k or 450k-EPIC platforms, with limited investigations on Illumina EPIC v1.0 arrays. We conducted a comprehensive assessment of the EPIC v1.0 array probe reliability using 69 blood DNA samples, each measured twice, generated by the Alzheimer’s Disease Neuroimaging Initiative study. We observed higher reliability in probes with average methylation beta values of 0.2 to 0.8, and lower reliability in type I probes or those within the promoter and CpG island regions. Importantly, we found that probe reliability has significant implications in the analyses of Epigenome-wide Association Studies (EWAS). Higher reliability is associated with more consistent effect sizes in different studies, the identification of differentially methylated regions (DMRs) and methylation quantitative trait locus (mQTLs), and significant correlations with downstream gene expression. Moreover, blood DNAm measurements obtained from probes with higher reliability are more likely to show concordance with brain DNAm measurements. Our findings, which provide crucial reliability information for probes on the EPIC v1.0 array, will serve as a valuable resource for future DNAm studies.
DOI: 10.6084/m9.figshare.25529486.v1
title: Critical evaluation of the reliability of DNA methylation probes on the Illumina MethylationEPIC v1.0 BeadChip microarrays

description: DNA methylation (DNAm) plays a crucial role in a number of complex diseases. However, the reliability of DNAm levels measured using Illumina arrays varies across different probes. Previous research primarily assessed probe reliability by comparing duplicate samples between the 450k-450k or 450k-EPIC platforms, with limited investigations on Illumina EPIC v1.0 arrays. We conducted a comprehensive assessment of the EPIC v1.0 array probe reliability using 69 blood DNA samples, each measured twice, generated by the Alzheimer’s Disease Neuroimaging Initiative study. We observed higher reliability in probes with average methylation beta values of 0.2 to 0.8, and lower reliability in type I probes or those within the promoter and CpG island regions. Importantly, we found that probe reliability has significant implications in the analyses of Epigenome-wide Association Studies (EWAS). Higher reliability is associated with more consistent effect sizes in different studies, the identification of differentially methylated regions (DMRs) and methylation quantitative trait locus (mQTLs), and significant correlations with downstream gene expression. Moreover, blood DNAm measurements obtained from probes with higher reliability are more likely to show concordance with brain DNAm measurements. Our findings, which provide crucial reliability information for probes on the EPIC v1.0 array, will serve as a valuable resource for future DNAm studies.
DOI: 10.6084/m9.figshare.26889567
title: Identification and functional characterisation of DNA methylation differences between East- and West-originating Finns

description: Eastern and Western Finns show a striking difference in coronary heart disease-related mortality; genetics is a known contributor for this discrepancy. Here, we discuss the potential role of DNA methylation in mediating the discrepancy in cardiometabolic disease-risk phenotypes between the sub-populations. We used data from the Young Finns Study (<i>n</i> = 969) to compare the genome-wide DNA methylation levels of East- and West-originating Finns. We identified 21 differentially methylated loci (FDR &lt; 0.05; Δβ &gt;2.5%) and 7 regions (smoothed FDR &lt; 0.05; CpGs ≥ 5). Methylation at all loci and regions associates with genetic variants (<i>p</i> &lt; 5 × 10<sup>−8</sup>). Independently of genetics, methylation at 11 loci and 4 regions associates with transcript expression, including genes encoding zinc finger proteins. Similarly, methylation at 5 loci and 4 regions associates with cardiometabolic disease-risk phenotypes including triglycerides, glucose, cholesterol, as well as insulin treatment. This analysis was also performed in LURIC (<i>n</i> = 2371), a German cardiovascular patient cohort, and results replicated for the association of methylation at cg26740318 and DMR_11p15 with diabetes-related phenotypes and methylation at DMR_22q13 with triglyceride levels. Our results indicate that DNA methylation differences between East and West Finns may have a functional role in mediating the cardiometabolic disease discrepancy between the sub-populations.
DOI: 10.6084/m9.figshare.26889567.v1
title: Identification and functional characterisation of DNA methylation differences between East- and West-originating Finns

description: Eastern and Western Finns show a striking difference in coronary heart disease-related mortality; genetics is a known contributor for this discrepancy. Here, we discuss the potential role of DNA methylation in mediating the discrepancy in cardiometabolic disease-risk phenotypes between the sub-populations. We used data from the Young Finns Study (<i>n</i> = 969) to compare the genome-wide DNA methylation levels of East- and West-originating Finns. We identified 21 differentially methylated loci (FDR &lt; 0.05; Δβ &gt;2.5%) and 7 regions (smoothed FDR &lt; 0.05; CpGs ≥ 5). Methylation at all loci and regions associates with genetic variants (<i>p</i> &lt; 5 × 10<sup>−8</sup>). Independently of genetics, methylation at 11 loci and 4 regions associates with transcript expression, including genes encoding zinc finger proteins. Similarly, methylation at 5 loci and 4 regions associates with cardiometabolic disease-risk phenotypes including triglycerides, glucose, cholesterol, as well as insulin treatment. This analysis was also performed in LURIC (<i>n</i> = 2371), a German cardiovascular patient cohort, and results replicated for the association of methylation at cg26740318 and DMR_11p15 with diabetes-related phenotypes and methylation at DMR_22q13 with triglyceride levels. Our results indicate that DNA methylation differences between East and West Finns may have a functional role in mediating the cardiometabolic disease discrepancy between the sub-populations.
DOI: 10.6084/m9.figshare.26980537
title: Exploring fatty acids from royal jelly as a source of histone deacetylase inhibitors: from the hive to applications in human well-being and health

description: A differential diet with royal jelly (RJ) during early larval development in honeybees shapes the phenotype, which is probably mediated by epigenetic regulation of gene expression. Evidence indicates that small molecules in RJ can modulate gene expression in mammalian cells, such as the fatty acid 10-hydroxy-2-decenoic acid (10-HDA), previously associated with the inhibition of histone deacetylase enzymes (HDACs). Therefore, we combined computational (molecular docking simulations) and experimental approaches for the screening of potential HDAC inhibitors (HDACi) among 32 RJ-derived fatty acids. Biochemical assays and gene expression analyses (Reverse Transcriptase – quantitative Polymerase Chain Reaction) were performed to evaluate the functional effects of the major RJ fatty acids, 10-HDA and 10-HDAA (10-hydroxy-decanoic acid), in two human cancer cell lines (HCT116 and MDA-MB-231). The molecular docking simulations indicate that these fatty acids might interact with class I HDACs, specifically with the catalytic domain of human HDAC2, likewise well-known HDAC inhibitors (HDACi) such as SAHA (suberoylanilide hydroxamic acid) and TSA (Trichostatin A). In addition, the combined treatment with 10-HDA and 10-HDAA inhibits the activity of human nuclear HDACs and leads to a slight increase in the expression of HDAC-coding genes in cancer cells. Our findings indicate that royal jelly fatty acids collectively contribute to HDAC inhibition and that 10-HDA and 10-HDAA are weak HDACi that facilitate the acetylation of lysine residues of chromatin, triggering an increase in gene expression levels in cancer cells.
DOI: 10.6084/m9.figshare.26980537.v1
title: Exploring fatty acids from royal jelly as a source of histone deacetylase inhibitors: from the hive to applications in human well-being and health

description: A differential diet with royal jelly (RJ) during early larval development in honeybees shapes the phenotype, which is probably mediated by epigenetic regulation of gene expression. Evidence indicates that small molecules in RJ can modulate gene expression in mammalian cells, such as the fatty acid 10-hydroxy-2-decenoic acid (10-HDA), previously associated with the inhibition of histone deacetylase enzymes (HDACs). Therefore, we combined computational (molecular docking simulations) and experimental approaches for the screening of potential HDAC inhibitors (HDACi) among 32 RJ-derived fatty acids. Biochemical assays and gene expression analyses (Reverse Transcriptase – quantitative Polymerase Chain Reaction) were performed to evaluate the functional effects of the major RJ fatty acids, 10-HDA and 10-HDAA (10-hydroxy-decanoic acid), in two human cancer cell lines (HCT116 and MDA-MB-231). The molecular docking simulations indicate that these fatty acids might interact with class I HDACs, specifically with the catalytic domain of human HDAC2, likewise well-known HDAC inhibitors (HDACi) such as SAHA (suberoylanilide hydroxamic acid) and TSA (Trichostatin A). In addition, the combined treatment with 10-HDA and 10-HDAA inhibits the activity of human nuclear HDACs and leads to a slight increase in the expression of HDAC-coding genes in cancer cells. Our findings indicate that royal jelly fatty acids collectively contribute to HDAC inhibition and that 10-HDA and 10-HDAA are weak HDACi that facilitate the acetylation of lysine residues of chromatin, triggering an increase in gene expression levels in cancer cells.
DOI: 10.14272/zcjrwqdzpiiylm-uhfffaoysa-n/chmo0000593
title: 1H nuclear magnetic resonance spectroscopy (1H NMR) (2-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)aniline)
title: InChI=1S/C12H18BNO2/c1-11(2)12(3,4)16-13(15-11)9-7-5-6-8-10(9)14/h5-8H,14H2,1-4H3

description: dataset for 1H nuclear magnetic resonance spectroscopy (1H NMR)
DOI: 10.14272/zcjrwqdzpiiylm-uhfffaoysa-n/chmo0000599
title: correlation spectroscopy (COSY) (2-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)aniline)
title: InChI=1S/C12H18BNO2/c1-11(2)12(3,4)16-13(15-11)9-7-5-6-8-10(9)14/h5-8H,14H2,1-4H3

description: dataset for correlation spectroscopy (COSY)
DOI: 10.14272/zcjrwqdzpiiylm-uhfffaoysa-n/chmo0000601
title: heteronuclear multiple bond coherence (HMBC) (2-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)aniline)
title: InChI=1S/C12H18BNO2/c1-11(2)12(3,4)16-13(15-11)9-7-5-6-8-10(9)14/h5-8H,14H2,1-4H3

description: dataset for heteronuclear multiple bond coherence (HMBC)
DOI: 10.14272/zcjrwqdzpiiylm-uhfffaoysa-n/chmo0000604
title: heteronuclear single quantum coherence (HSQC) (2-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)aniline)
title: InChI=1S/C12H18BNO2/c1-11(2)12(3,4)16-13(15-11)9-7-5-6-8-10(9)14/h5-8H,14H2,1-4H3

description: dataset for heteronuclear single quantum coherence (HSQC)
DOI: 10.14272/zcjrwqdzpiiylm-uhfffaoysa-n/chmo0000596
title: distortionless enhancement with polarization transfer (DEPT) (2-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)aniline)
title: InChI=1S/C12H18BNO2/c1-11(2)12(3,4)16-13(15-11)9-7-5-6-8-10(9)14/h5-8H,14H2,1-4H3

description: dataset for distortionless enhancement with polarization transfer (DEPT)
DOI: 10.15468/dl.fq5qrr
title: Occurrence Download

description: A dataset containing 206 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Lophius litulon (Jordan, 1902)",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 206 records from 21 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025970-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.14272/zcjrwqdzpiiylm-uhfffaoysa-n.1
title: 2-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)aniline
title: InChI=1S/C12H18BNO2/c1-11(2)12(3,4)16-13(15-11)9-7-5-6-8-10(9)14/h5-8H,14H2,1-4H3

description: This is a physical chemical entity[CHEBI_24431] associated with a molecule[CHEBI_25367].
 The molecule[CHEBI_25367] can be described by the following structural desciptors[cheminf_000085]:
 InChI descriptor[cheminf_000113]: InChI=1S/C12H18BNO2/c1-11(2)12(3,4)16-13(15-11)9-7-5-6-8-10(9)14/h5-8H,14H2,1-4H3, and canonical SMILES descriptor[cheminf_000007]: Nc1ccccc1B1OC(C(O1)(C)C)(C)C, and by the IUPAC name[cheminf_000107]: 2-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)aniline.
 
 The physical chemical entity[CHEBI_24431] has a component solvent[CHEBI_46787] which is described by the canonical SMILES descriptor[cheminf_000007]:
 
 The physical chemical entity[CHEBI_24431] has the following Sample ID as registered in the research data repository chemotion (www.chemotion-repository.net, https://doi.org/10.25504/FAIRsharing.iagXcR): CRS-49392

 The physical chemical entity[CHEBI_24431] can be described by the physical descriptors [CHEMINF_000025]:
 Melting point descriptor[CHEMINF_000256]: 
 Boiling point descriptor[CHEMINF_000257]: 
 Refractive index descriptor[CHEMINF_000253]:

 The physical chemical entity[CHEBI_24431] can be further described by the following assays[OBI:0000070][CHMO:0001133]:
 
 CHMO:0000604 | heteronuclear single quantum coherence (HSQC)
 
 CHMO:0000596 | distortionless enhancement with polarization transfer (DEPT)
 
 CHMO:0000596 | distortionless enhancement with polarization transfer (DEPT)
 
 CHMO:0000599 | correlation spectroscopy (COSY)
 
 CHMO:0000595 | 13C nuclear magnetic resonance spectroscopy (13C NMR)
 
 CHMO:0000601 | heteronuclear multiple bond coherence (HMBC)
 
 CHMO:0000593 | 1H nuclear magnetic resonance spectroscopy (1H NMR)
 
 The physical chemical entity[CHEBI_24431] was deposited to the Molecule Archive of the Karlsruhe Insitute of Technology (KIT) with the following Sample ID: 

 Used ontologies:
 CHEBI - Chemical Entities of Biological Interest
 CHEMINF - chemical information ontology (information entities about chemical entities)
 CHMO - Chemical Methods Ontology
 OBI - Ontology for Biomedical Investigations
DOI: 10.14272/zcjrwqdzpiiylm-uhfffaoysa-n/chmo0000595
title: 13C nuclear magnetic resonance spectroscopy (13C NMR) (2-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)aniline)
title: InChI=1S/C12H18BNO2/c1-11(2)12(3,4)16-13(15-11)9-7-5-6-8-10(9)14/h5-8H,14H2,1-4H3

description: dataset for 13C nuclear magnetic resonance spectroscopy (13C NMR)
DOI: 10.14272/zcjrwqdzpiiylm-uhfffaoysa-n/chmo0000596.1
title: distortionless enhancement with polarization transfer (DEPT) (2-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)aniline)
title: InChI=1S/C12H18BNO2/c1-11(2)12(3,4)16-13(15-11)9-7-5-6-8-10(9)14/h5-8H,14H2,1-4H3

description: dataset for distortionless enhancement with polarization transfer (DEPT)
DOI: 10.5284/1124854
title: Data from an Archaeological Watching Brief at Nantwich Pool, Wall Lane, Nantwich, Cheshire, December 2012

description: This collection comprises data from an archaeological watching brief at Nantwich Pool, Wall Lane, Nantwich, Cheshire. This work was undertaken by Oxford Archaeology North in December 2012 during groundworks associated with the refurbishment and redesign of Nantwich Pool. The position of the site near to the town, which developed as a result of the salt workings since the Roman period, suggests that there was potential for archaeological finds and deposits. The watching brief comprised the monitoring of the excavation of three foundation trenches. The area around the buildings appeared to be extensively disturbed and any deposits that may have been of archaeological potential had been completely truncated. No archaeological finds or deposits were recorded and no waterlogged deposits were observed.
DOI: 10.15468/dl.pe3qey
title: Occurrence Download

description: A dataset containing 22972 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Plantae",
 "Year 1901-1920"
 ]
}

 The dataset includes 22972 records from 73 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025969-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14329549
title: Mechanical properties for 100kg PE/PA MNL film

description: Mechanical tensile properties for the 100kg PE/PA film made with Multinanolayer (MNL) process

Composition and process parameter in sheet 1, data in sheet 2.
DOI: 10.5281/zenodo.14329550
title: Mechanical properties for 100kg PE/PA MNL film

description: Mechanical tensile properties for the 100kg PE/PA film made with Multinanolayer (MNL) process

Composition and process parameter in sheet 1, data in sheet 2.
DOI: 10.15468/dl.thd3h7
title: Occurrence Download

description: A dataset containing 4670944 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Primulaceae"
 ]
}

 The dataset includes 4670944 records from 6103 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025964-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.3535/yzm-wrt-lk6
title: Goethite

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.25609029.v1
title: Multi-criteria optimization carbon dioxide through wood and bio-based construction materials

description: Decision making framework for multi-criteria analyzes generalized to construction material selection process.
DOI: 10.17632/6mpr2wnjtw
title: EXPLANATION OF INTENTION TO VACCINATE AGAINST COVID-19 AND THE AUTHORITIES' SUPPORT THROUGH THE THEORY OF PLANNED BEHAVIOR. AN EXPLORATORY STUDY IN ROMANIAN SAMPLE.

description: This study investigates the intention to vaccinate against Coronavirus and to support the authorities in limiting the effects of the pandemic from the perspective of the theory of planned behavior in a sample of 771 Romanian adults.

We intend to improve the prediction offered by the TPB model by constructing two alternative models that take into account additional variables such as irrational beliefs, past behavior, and risk perception. 
 
Data analysis involved performing hierarchical regressions and SEM modeling. Hierarchical regression analyzes show that the model based on demographic variables such as age and education and the constructs of the theory of planned behavior, attitude, social norms, and control beliefs best explain vaccination intention (75%) and support for authorities (29%).
This additional material presents the raw data used in the study, in SPSS type files. For SEM analysis the data are in JASP format.
DOI: 10.3535/936-sqc-p2r
title: Anhydrite

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/9gl-jqw-wcy
title: Sandstone

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.14371055.v2
title: Spreadsheet Data Extraction from Real-World Tables of SAUS (The 2010 Statistical Abstract of the United States): Case Study

description: This case study demonstrates how TabbyXL can be applied for extracting data items and their relationships from government statistics tables of SAUS (The 2010 Statistical Abstract of the United States) corpora.
DOI: 10.17632/96m659kfrp
title: SARS-CoV-2 mRNA vaccines foster potent antigen-specific germinal center responses associated with neutralizing antibody generation - Supplementary Material

description: Supplementary material for the manuscript titled: "SARS-CoV-2 mRNA vaccines foster potent antigen-specific germinal center responses associated with neutralizing antibody generation"
DOI: 10.17632/rf9csj2tcz
title: Photo-identification catalogue - Tonina Association

description: The photo-identification catalogue of Association Tonina, used for comparison purposes.
DOI: 10.3535/ked-7a2-vy6
title: Calcite

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.