cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.19254727
title: Additional file 6 of HyperChIP: identification of hypervariable signals across ChIP-seq or ATAC-seq samples

description: Additional file 6: Table S6. Significant HVRs and LVRs (BH-adjusted p-value&lt;0.1) identified by HyperChIP for each of the data sets in Table 1.
DOI: 10.6084/m9.figshare.20295600
title: Additional file 1 of Associations of visceral adipose tissue with bone mineral density and fracture: observational and Mendelian randomization studies

description: Additional file 1: Table 1. Baseline characteristics of the final application datasets by quartiles of VAT^ mass. Table 2. Baseline characteristics of the final application datasets by sex. Table 3. ICD-10 codes for fracture definition in the UK biobank. Table 4. Associations of VAT^ with heel BMD in men and women by BMI categories. Table 5. Associations of VAT^ with heel BMD in men and women by BMI categories after excluding participants with T2D, CVD or cancer at baseline. Table 6. Association of DXA-derived VAT mass with DXA-derived BMD among participants by BMI categories. Table 7. Associations of VAT^ with incident fractures in men and women by BMI categories. Table 8. Associations of VAT^ with incident fractures in men and women by BMI categories after excluding participants with T2D, CVD or cancer at baseline. Table 9. Schoenfeld residuals test of the Cox models. Table 10. Genetic variants associated with VAT^ in the UK Biobank. Table 11. MR estimates of the causal effects of VAT^ on DXA-derived BMD without excluding LM-associated SNPs. Table 12. MR estimates of the causal effects of VAT^ on fractures without excluding LM-associated SNPs. Table 13. MR Egger test of directional horizontal pleiotropy.
DOI: 10.6084/m9.figshare.16625444.v1
title: Additional file 1 of Dexamethasone enhances the efficacy of atorvastatin in inhibiting excessively inflammation-induced abnormal angiogenesis by regulating macrophages

description: Additional file 1: File S1. The inclusion and exclusion criteria. Table S1. RT-PCR Primers used in this study. Table S2. Baseline characteristics and outcome of CSDH patients treated with a combination regimen or ATO monotherapy. Table S3. Baseline characteristics and outcomes of conservatively treated patients who have good efficacy or switched to surgery. Table S4. The functions of these proteins identified, but not specifically discussed in the manuscript. Figure S1. o-ATO and p-ATO in CSDH patients. Figure S2. Concentrations of ATO and DEX in HUVEC. Figure S3. Effects of ATO and DEX on expression of drug transport and catabolism-related proteins in macrophages. Figure S4. Monocytes and macrophages in the haematoma of CSDH patients. Figure S5. The differentiation of THP-1 cells into macrophages stimulated by PMA. Figure S6. LPS can effectively simulate the effect of haematoma on THP-1 macrophages. Figure S7. Regulation of ATO and DEX on the morphological changes of THP-1 macrophages. Figure S8. The effect of ATO and DEX on the MFI of CD86 and CD163 in macrophages. Figure S9. The concentrations of ET-1 in the haematoma, serum and medium supernatant quantified by ELISA.
DOI: 10.6084/m9.figshare.14011938
title: Genome-wide identification and functional prediction of circular RNAs in response to heat stress in Chinese Holstein cows

description: Heat stress (HS) leads to substantial economic loss of dairy industry each year. The negative effect of HS in dairy cows is becoming one of the more urgent issue due to accelerating side-effects of global warming. Various genes are involved in HS response but the information about the role of noncoding RNAs, especially circular RNAs (circRNAs) is largely unknown. In our study, we aimed to investigate the different expression profile of circRNAs between HS and Non-heat-stressed condition (NC) of Chinese Holstein cow’s mammary gland. CircRNAs were identified using RNA sequencing and bioinformatics analysis. In total, 37405 circRNAs were detected and 95 were differentially expressed (DE), including 15 downregulated and 80 upregulated circRNAs in HS group compared to NC. Eight circRNAs were randomly selected to verify the RNA sequencing result. Further, Sanger sequencing validated the backsplicing site of the eight circRNAs. Moreover, results obtained from the Quantitative real time PCR (qRT-PCR) showed consistent expression trend with that of RNA sequencing. GO annotation and KEGG analysis suggested that these DE circRNAs probably involved in the energy metabolic regulation. Furthermore, we constructed ceRNA network and the result indicated that these DE circRNAs could regulate lactation through IGF1 and PRL signaling pathway.
DOI: 10.6084/m9.figshare.25251316
title: db.csv

description: This dataset is linked to the study: “Too much focus on your health might be bad for your health: Reddit user’s communication style predicts their Long COVID likelihood”(forthcoming) by Ludovica Segneri, Nandor Babina, Teresa Hammerschmidt, Andrea Fronzetti Colladon, Peter A. Gloor.The dataset comprises the variables employed in the paper for conducting statistical analysis. A comprehensive description of the variables will be available in the paper following its publication.<br>
DOI: 10.6084/m9.figshare.25251316.v1
title: db.csv

description: This dataset is linked to the study: “Too much focus on your health might be bad for your health: Reddit user’s communication style predicts their Long COVID likelihood”(forthcoming) by Ludovica Segneri, Nandor Babina, Teresa Hammerschmidt, Andrea Fronzetti Colladon, Peter A. Gloor.The dataset comprises the variables employed in the paper for conducting statistical analysis. A comprehensive description of the variables will be available in the paper following its publication.<br>
DOI: 10.15151/esrf-es-1532074550
title: Inhouse high throughput samples

description: Inhouse high throughput samples
DOI: 10.6084/m9.figshare.15065815
title: Socioeconomic status and fertility treatment outcomes in high-income countries: a review of the current literature

description: The association between socioeconomic status and fertility is a subject that has received much attention. Yet, little is known as to whether the socioeconomic status has an impact on the outcomes of fertility treatment. This systematic review aims to assess any possible relationship between socioeconomic deprivation and treatment outcomes. A database search was conducted of all publications in this field up to March 2021. Eleven studies were identified and six of these specifically investigated the impact of socioeconomic status on fertility treatment outcomes. Children conceived following assisted conception are more likely to be born to mothers of a higher socioeconomic status than those conceived naturally. Of the few studies investigating the impact of socioeconomic status on fertility treatment outcomes and the results are conflicting, making it difficult to draw robust conclusions as to its effect. It is unknown which, if any, marker of socioeconomic status is the most significant for fertility patients: whether it is the characteristics of the individual or that of their surroundings. Further research is urgently needed.
DOI: 10.6084/m9.figshare.19254721
title: Additional file 4 of HyperChIP: identification of hypervariable signals across ChIP-seq or ATAC-seq samples

description: Additional file 4: Table S4. Class-specific regulators identified from the TCGA pan-cancer ATAC-seq data set.
DOI: 10.6084/m9.figshare.13487594
title: Quantitative structure activity relationship studies of novel hydrazone derivatives as α-amylase inhibitors with index of ideality of correlation

description: The present manuscript describes the synthesis, <i>α</i>-amylase inhibition, <i>in silico</i> studies and in-depth quantitative structure–activity relationship (QSAR) of a library of aroyl hydrazones based on benzothiazole skeleton. All the compounds of the developed library are characterized by various spectral techniques. <i>α</i>‐Amylase inhibitory potential of all compounds has been explored, where compound <b>7n</b> exhibits remarkable <i>α</i>-amylase inhibition of 87.5% at 50 µg/mL. Robust QSAR models are made by using the balance of correlation method in CORAL software. The chemical structures at different concentration with optimal descriptors are represented by SMILES. A data set of 66 SMILES of 22 hydrazones at three distinct concentrations are prepared. The significance of the index of ideality of correlation (IIC) with applicability domain (AD) is also studied at depth. A QSAR model with best Rvalidation2 = 0.8587 for split 1 is considered as a leading model. The outliers and promoters of increase and decrease of endpoint are also extracted. The binding modes of the most active compound, that is, <b>7n</b> in the active site of <i>Aspergillus oryzae</i> α-amylase (<b>PDB ID: 7TAA</b>) are also explored by <i>in silico</i> molecular docking studies. Compound <b>7n</b> displays high resemblance in binding mode and pose with the standard drug acarbose. Molecular dynamics simulations performed on protein–ligand complex for 100 ns, the protein gets stabilised after 20 ns and remained below 2 Å for the remaining simulation. Moreover, the deviation observed in RMSF during simulation for each amino acid residue with respect to Cα carbon atom is insignificant. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.13487594.v1
title: Quantitative structure activity relationship studies of novel hydrazone derivatives as α-amylase inhibitors with index of ideality of correlation

description: The present manuscript describes the synthesis, <i>α</i>-amylase inhibition, <i>in silico</i> studies and in-depth quantitative structure–activity relationship (QSAR) of a library of aroyl hydrazones based on benzothiazole skeleton. All the compounds of the developed library are characterized by various spectral techniques. <i>α</i>‐Amylase inhibitory potential of all compounds has been explored, where compound <b>7n</b> exhibits remarkable <i>α</i>-amylase inhibition of 87.5% at 50 µg/mL. Robust QSAR models are made by using the balance of correlation method in CORAL software. The chemical structures at different concentration with optimal descriptors are represented by SMILES. A data set of 66 SMILES of 22 hydrazones at three distinct concentrations are prepared. The significance of the index of ideality of correlation (IIC) with applicability domain (AD) is also studied at depth. A QSAR model with best Rvalidation2 = 0.8587 for split 1 is considered as a leading model. The outliers and promoters of increase and decrease of endpoint are also extracted. The binding modes of the most active compound, that is, <b>7n</b> in the active site of <i>Aspergillus oryzae</i> α-amylase (<b>PDB ID: 7TAA</b>) are also explored by <i>in silico</i> molecular docking studies. Compound <b>7n</b> displays high resemblance in binding mode and pose with the standard drug acarbose. Molecular dynamics simulations performed on protein–ligand complex for 100 ns, the protein gets stabilised after 20 ns and remained below 2 Å for the remaining simulation. Moreover, the deviation observed in RMSF during simulation for each amino acid residue with respect to Cα carbon atom is insignificant. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.20295690
title: Additional file 5 of A de novo assembled high-quality chromosome-scale Trifolium pratense genome and fine-scale phylogenetic analysis

description: Additional file 5: Figure S1. Red clover and its closely related species synteny analysis. (a) The beginning of NC represents the chromosome of M.truncatula, while the beginning of CHR represents the chromosome of red clover. (b) The beginning of NC represents the chromosome of C.arietinum, while the beginning of CHR represents the chromosome of red clover. (c) The beginning of NC represents the chromosome of G.max, while the beginning of CHR represents the chromosome of red clover. (d) The beginning of NC represents the chromosome of V.radiata, while the beginning of CHR represents the chromosome of red clover.
DOI: 10.6084/m9.figshare.16633371.v1
title: Additional file 1 of A nomogram to predict stricture-free survival in patients with ureteral stricture after balloon dilation

description: Additional file 1: Table 1. Baseline characteristics of the study population.
DOI: 10.15468/dl.sp6rez
title: Occurrence Download

description: A dataset containing 80 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Lotus peczoricus Miniaev & Ulle"
 ]
}

 The dataset includes 80 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022027-250402121839773/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.c75iaa
title: Occurrence Download

description: A dataset containing 39910 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "BasisOfRecord is Observation",
 "BasisOfRecord is Human Observation"
 ]
 },
 {
 "or" : [
 "Country is United Kingdom of Great Britain and Northern Ireland",
 "Country is Sweden",
 "Country is Germany",
 "Country is Finland",
 "Country is Norway",
 "Country is Isle of Man",
 "Country is Ireland",
 "Country is Austria",
 "Country is Netherlands",
 "Country is Italy",
 "Country is France",
 "Country is Switzerland",
 "Country is Türkiye",
 "Country is Denmark"
 ]
 },
 {
 "or" : [
 "PublishingOrg is 60440ffc-f4b7-4cd3-88d3-33a8cd5a0660",
 "PublishingOrg is f0232402-8d37-45d6-a866-2fdbda1cb78b",
 "PublishingOrg is 47eaaa43-47c7-4754-8e7a-bfaf616da4df",
 "PublishingOrg is 0c392aa0-a452-4254-be5c-e49dd60e9b02",
 "PublishingOrg is b8323864-602a-4a7d-9127-bb903054e97d",
 "PublishingOrg is bb646dff-a905-4403-a49b-6d378c2cf0d9",
 "PublishingOrg is 7774fda0-457b-40da-8936-214f632ba991",
 "PublishingOrg is f0edcf5c-2a34-4a6b-b9bb-44d52ed50f7a",
 "PublishingOrg is 04fd2e13-6881-4e5c-9dd1-8fdd9ab993c1",
 "PublishingOrg is d3978a37-635a-4ae3-bb85-7b4d41bc0b88"
 ]
 },
 "Year 1950-2018",
 {
 "or" : [
 "DatasetKey is The ARC Rare Species Database",
 "DatasetKey is Reptile distribution within Broadland (2004-2011): based upon field signs and sightings",
 "DatasetKey is Miscellaneous records held on the Cofnod database",
 "DatasetKey is Reptiles and Amphibians Dataset",
 "DatasetKey is Artportalen (Swedish Species Observation System)",
 "DatasetKey is naturgucker",
 "DatasetKey is Isle of Man wildlife records from 01/01/2000 to 13/02/2017",
 "DatasetKey is Suffolk Biodiversity Information Service (SBIS) Dataset",
 "DatasetKey is Hatikka.fi observations",
 "DatasetKey is Norwegian Species Observation Service"
 ]
 },
 "TaxonKey is Lacerta agilis Linnaeus, 1758",
 {
 "or" : [
 "Month is January",
 "Month is February",
 "Month is March",
 "Month is April",
 "Month is June",
 "Month is May",
 "Month is July",
 "Month is August",
 "Month is September",
 "Month is October",
 "Month is November",
 "Month is December"
 ]
 },
 "Geometry POLYGON ((-27.773437499999996 29.099958217159173, 41.1328125 28.48376172857383, 41.484375 72.13656746256059, -17.578125 72.13656746256059, -34.453125 57.62517305502047, -27.773437499999996 29.099958217159173))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 39910 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004424-180131172636756/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.r7sent
title: Occurrence Download

description: A dataset containing 308 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Brazil",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Peixotoa tomentosa A.Juss."
 ]
}

 The dataset includes 308 records from 49 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0039141-231002084531237/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hufy2n
title: Occurrence Download

description: A dataset containing 41786793 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 {
 "or" : [
 "Geometry POLYGON((-180 -85.05113,180 -85.05113,180 85.05113,-180 85.05113,-180 -85.05113))",
 "Geometry POLYGON((-5.98206 37.30901,-6.39954 36.83567,-6.32263 36.61553,-6.06995 36.26199,-5.67444 36.03133,-5.3009 36.11125,-5.14709 36.4036,-4.71863 36.48314,-4.27917 36.64198,-4.00452 36.74769,-4.20227 37.42253,-4.8175 37.562,-5.69641 37.46614,-5.98206 37.30901))"
 ]
 },
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Plantae"
 ]
}

 The dataset includes 41786793 records from 1902 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017867-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15156/bio/sh0955859.10fu
title: SH0955859.10FU

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: 10.5281/zenodo.13576324
title: Clay tutorial videos

description: Clay tutorial videos
DOI: 10.5281/zenodo.13576325
title: Clay tutorial videos

description: Clay tutorial videos
DOI: 10.15156/bio/sh0955860.10fu
title: SH0955860.10FU

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: 10.15156/bio/sh0955861.10fu
title: SH0955861.10FU

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: 10.15156/bio/sh0955862.10fu
title: SH0955862.10FU

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: 10.15156/bio/sh0955863.10fu
title: SH0955863.10FU

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: 10.15156/bio/sh0955864.10fu
title: SH0955864.10FU

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.