cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.ted24w
title: Occurrence Download

description: A dataset containing 67 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Asia",
 "Country is Malaysia",
 "OccurrenceStatus is Present",
 "TaxonKey is Ficus racemosa L."
 ]
}

 The dataset includes 67 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021365-250402121839773/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qmkrhg
title: Occurrence Download

description: A dataset containing 793 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Melilotus officinalis (L.) Lam."
 ]
}

 The dataset includes 793 records from 23 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021366-250402121839773/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.13684865.v1
title: Additional file 1 of Dynamic characteristics and functional analysis provide new insights into long non-coding RNA responsive to Verticillium dahliae infection in Gossypium hirsutum

description: Additional file 1: Table S1. Summary of RNA -seq data.
DOI: 10.6084/m9.figshare.19976665.v1
title: Additional file 4 of Establish an allele-specific real-time PCR for Leishmania species identification

description: Additional file 4: Table S4. Precision of intra and inter-assay of allele-specific real-time PCR assay.
DOI: 10.6084/m9.figshare.22598578
title: Additional file 1 of Variants of a putative baseplate wedge protein extend the host range of Pseudomonas phage K8

description: Additional file 1: Supplementary Table S1. Bacteria, plasmids, and phages used in this study. Supplementary Table S2. Primers used in this study. Supplementary Table S3. Molar mass of GP075 and its derivatives. Supplementary Table S4. Possible protein interactions identified by the bacterial two-hybrid system a. Supplementary Table S5. Mutations of the gp075 gene of the 41 isolated K8 mutants a. Supplementary Figure S1. Protein structure modelling by using the online server SWISS-MODEL. The amino acid sequences of the wild-type protein GP075 and its two variants GP075m and GP075-D7 were uploaded for structural template searching and model building. The upper panels showed the brief descriptions of the secondary structure parameters of each protein. The bottom panels displayed the 3D structure images of the indicated proteins. Supplementary Figure S2. SDS-PAGE of the purified viral proteins. GP076: 670 amino acids. GP075: 243 amino acids. GP075m: GP075 with one amino acid substitution T239A. GP075-D7: GP075 with one copy of the 7-aa duplication (APWYSVG). GP075-D14: GP075 with two identical copies of the 7-aa duplication. GP075-D21: GP075 with three identical copies of the 7-aa duplication. M: Premixed Protein Marker (Low) from Takara. Supplementary Figure S3. Native-PAGE of the purified viral proteins. GP075: 243 amino acids. GP075m: GP075 with one amino acid substitution T239A. The protein samples for electrophoresis were treated before loading as follows: 1 and 5, the protein samples were mixed with 2×loading buffer (without SDS); 2 and 6, the protein samples were mixed with 2×loading buffer (without SDS) and incubated at 100°C for 10 min. 3 and 7: the protein samples were mixed with 2×loading buffer (containing 4% SDS). 4 and 8: the protein samples were mixed with 2×loading buffer (containing 4% SDS) and incubated at 100°C for 10 min. M: Premixed Protein Marker (Low) from Takara. Supplementary Figure S4. Thermostability of the K8 mutants. a. Amino acids sequences alignments of the GP075-like proteins from the isolated K8 mutants. Red letters represent the amino acids duplication or the substitutions. Numbers represent the positions of amino acid residuals in the GP075 protein. b. Thermostability of the K8 mutants. Phages were treated at various temperatures for 1 h before determination of the live phages. The phage titers obtained at the treatment at 4°C were used as controls to calculate the survival percentages. The experiments were independently replicated three times. One-way ANOVA followed by a Tamhane T2 test was performed to compare the means of the groups treated at 70°C. Supplementary Dataset 1. LC-MS data. Supplementary Dataset 2. Ampliconsequencing data. Supplementary Dataset 3.Homologs of GP075.
DOI: 10.6084/m9.figshare.13161320
title: Additional file 1 of Identification of the subtypes of gastric cancer based on DNA methylation and the prediction of prognosis

description: Additional file 1: Supplementary Table 1. 406 patients' information and the follow-up data.
DOI: 10.6084/m9.figshare.13161335
title: Additional file 6 of Identification of the subtypes of gastric cancer based on DNA methylation and the prediction of prognosis

description: Additional file 6: Supplementary Table 6. Mehylation sites used in the Cox proportional hazard model and their coefficients.
DOI: 10.6084/m9.figshare.13161335.v1
title: Additional file 6 of Identification of the subtypes of gastric cancer based on DNA methylation and the prediction of prognosis

description: Additional file 6: Supplementary Table 6. Mehylation sites used in the Cox proportional hazard model and their coefficients.
DOI: 10.6084/m9.figshare.13684880
title: Additional file 6 of Dynamic characteristics and functional analysis provide new insights into long non-coding RNA responsive to Verticillium dahliae infection in Gossypium hirsutum

description: Additional file 6: Table S3. List of PCR primers used in this study.
DOI: 10.6084/m9.figshare.13684871.v1
title: Additional file 3 of Dynamic characteristics and functional analysis provide new insights into long non-coding RNA responsive to Verticillium dahliae infection in Gossypium hirsutum

description: Additional file 3: Table S2. Correlation analysis of lncRNA-mRNA pairs related to JA biosynthesis pathway in cotton.
DOI: 10.6084/m9.figshare.13684880.v1
title: Additional file 6 of Dynamic characteristics and functional analysis provide new insights into long non-coding RNA responsive to Verticillium dahliae infection in Gossypium hirsutum

description: Additional file 6: Table S3. List of PCR primers used in this study.
DOI: 10.6084/m9.figshare.13684871
title: Additional file 3 of Dynamic characteristics and functional analysis provide new insights into long non-coding RNA responsive to Verticillium dahliae infection in Gossypium hirsutum

description: Additional file 3: Table S2. Correlation analysis of lncRNA-mRNA pairs related to JA biosynthesis pathway in cotton.
DOI: 10.6084/m9.figshare.13684865
title: Additional file 1 of Dynamic characteristics and functional analysis provide new insights into long non-coding RNA responsive to Verticillium dahliae infection in Gossypium hirsutum

description: Additional file 1: Table S1. Summary of RNA -seq data.
DOI: 10.6084/m9.figshare.16305930.v1
title: Additional file 2 of Prevotella copri increases fat accumulation in pigs fed with formula diets

description: Additional file 2.
DOI: 10.6084/m9.figshare.22598782.v1
title: Additional file 2 of Molecular subtypes based on cuproptosis-related genes and tumor microenvironment infiltration characteristics in pancreatic adenocarcinoma

description: Additional file 2: Table S1. Primers used in this study. Table S2. The association between CRG expression and drug sensitivity. Table S3. Data set information included in this study for cuproptosis classification. Table S4. Univariate Cox regression analysis of CRGs in PAAD patients. Table S5. Univariate Cox regression analysis of differentially expressed genes (DEGs) in PAAD patients. Table S6. Multivariate Cox regression analysis for the cuproptosis signature based on 10 DEGs. Table S7. The activation states of biological pathways between the two cuproptosis score group by GSVA enrichment analysis. Table S8. Gene set enrichment KEGG analysis results based on the signature in the TCGA cohort. Table S9. Correlations between DLAT expression and clinicopathologic characteristics of PAAD patients. Table S10. Univariate and multivariate Cox regression analyses of prognostic variables in PAAD patients.
DOI: 10.6084/m9.figshare.22598578.v1
title: Additional file 1 of Variants of a putative baseplate wedge protein extend the host range of Pseudomonas phage K8

description: Additional file 1: Supplementary Table S1. Bacteria, plasmids, and phages used in this study. Supplementary Table S2. Primers used in this study. Supplementary Table S3. Molar mass of GP075 and its derivatives. Supplementary Table S4. Possible protein interactions identified by the bacterial two-hybrid system a. Supplementary Table S5. Mutations of the gp075 gene of the 41 isolated K8 mutants a. Supplementary Figure S1. Protein structure modelling by using the online server SWISS-MODEL. The amino acid sequences of the wild-type protein GP075 and its two variants GP075m and GP075-D7 were uploaded for structural template searching and model building. The upper panels showed the brief descriptions of the secondary structure parameters of each protein. The bottom panels displayed the 3D structure images of the indicated proteins. Supplementary Figure S2. SDS-PAGE of the purified viral proteins. GP076: 670 amino acids. GP075: 243 amino acids. GP075m: GP075 with one amino acid substitution T239A. GP075-D7: GP075 with one copy of the 7-aa duplication (APWYSVG). GP075-D14: GP075 with two identical copies of the 7-aa duplication. GP075-D21: GP075 with three identical copies of the 7-aa duplication. M: Premixed Protein Marker (Low) from Takara. Supplementary Figure S3. Native-PAGE of the purified viral proteins. GP075: 243 amino acids. GP075m: GP075 with one amino acid substitution T239A. The protein samples for electrophoresis were treated before loading as follows: 1 and 5, the protein samples were mixed with 2×loading buffer (without SDS); 2 and 6, the protein samples were mixed with 2×loading buffer (without SDS) and incubated at 100°C for 10 min. 3 and 7: the protein samples were mixed with 2×loading buffer (containing 4% SDS). 4 and 8: the protein samples were mixed with 2×loading buffer (containing 4% SDS) and incubated at 100°C for 10 min. M: Premixed Protein Marker (Low) from Takara. Supplementary Figure S4. Thermostability of the K8 mutants. a. Amino acids sequences alignments of the GP075-like proteins from the isolated K8 mutants. Red letters represent the amino acids duplication or the substitutions. Numbers represent the positions of amino acid residuals in the GP075 protein. b. Thermostability of the K8 mutants. Phages were treated at various temperatures for 1 h before determination of the live phages. The phage titers obtained at the treatment at 4°C were used as controls to calculate the survival percentages. The experiments were independently replicated three times. One-way ANOVA followed by a Tamhane T2 test was performed to compare the means of the groups treated at 70°C. Supplementary Dataset 1. LC-MS data. Supplementary Dataset 2. Ampliconsequencing data. Supplementary Dataset 3.Homologs of GP075.
DOI: 10.6084/m9.figshare.22598653.v1
title: Additional file 1 of Ultra-low-coverage genome-wide association study—insights into gestational age using 17,844 embryo samples with preimplantation genetic testing

description: Additional file 1: Table S1. Genotype imputation performance at different ultra-low coverages and sample sizes. Table S2. WGA methods and sequencing platforms used in the PGT experiments. Table S3. The summary of 40 significant SNPs satisfying Bonferroni-corrected significant level of 4.526e-8. Table S4. The list of candidate SNPs. Table S5. Nonsynonymous candidate SNPs. Table S6. The reported genomic risk loci from GWAS catalog that were detected in our dataset. Table S7. A list of 166 mapped genes by positional, eQTL, and chromatin interaction mappings. Table S8. Data sources of genome-wide mRNA expression in Preterm birth, infant disease and breast cancer. Table S9. A list of the 166 mapped genes that were also identified by differentially expressed genes (DEGs) derived from analyzing the genome-wide gene expression datasets listed.
DOI: 10.6084/m9.figshare.13161311
title: Additional file 11 of Identification of the subtypes of gastric cancer based on DNA methylation and the prediction of prognosis

description: Additional file 11: Supplementary Table 10. Functional enrichment analysis of site genes.
DOI: 10.6084/m9.figshare.16305930
title: Additional file 2 of Prevotella copri increases fat accumulation in pigs fed with formula diets

description: Additional file 2.
DOI: 10.6084/m9.figshare.22598653
title: Additional file 1 of Ultra-low-coverage genome-wide association study—insights into gestational age using 17,844 embryo samples with preimplantation genetic testing

description: Additional file 1: Table S1. Genotype imputation performance at different ultra-low coverages and sample sizes. Table S2. WGA methods and sequencing platforms used in the PGT experiments. Table S3. The summary of 40 significant SNPs satisfying Bonferroni-corrected significant level of 4.526e-8. Table S4. The list of candidate SNPs. Table S5. Nonsynonymous candidate SNPs. Table S6. The reported genomic risk loci from GWAS catalog that were detected in our dataset. Table S7. A list of 166 mapped genes by positional, eQTL, and chromatin interaction mappings. Table S8. Data sources of genome-wide mRNA expression in Preterm birth, infant disease and breast cancer. Table S9. A list of the 166 mapped genes that were also identified by differentially expressed genes (DEGs) derived from analyzing the genome-wide gene expression datasets listed.
DOI: 10.5281/zenodo.10628549
title: AORTIC STENOSIS

description: The database includes 467 patients (mean age 80.6 ± 8.2 years; 51% men) with at least moderate aortic stenosis, and sinus rhythm. The primary study endpoint was the composite of all-cause mortality and hospitalizations for heart failure. The eligibility criteria were: 1. outpatient transthoracic echocardiogram performed between January 2019 and June 2022; 2. at least moderate AS by quantitively echocardiographic criteria(maximum aortic velocity ≥3 m/s or mean gradient≥30 mmHg or AVA ≤ 1.5 cm2).  Exclusion criteria were moderate-to-severe mitral stenosis (MS), severe aortic regurgitation (AR), previous aortic valve surgery/transcatheter interventions, any established diagnosis of cardiomyopathy, missing relevant clinical data, and poor quality echocardiographic study unsuitable for a speckle tracking evaluation. Atrial fibrillation was also an exclusion criterion as it independently impact LA mechanics.
DOI: 10.5281/zenodo.10628550
title: AORTIC STENOSIS

description: The database includes 467 patients (mean age 80.6 ± 8.2 years; 51% men) with at least moderate aortic stenosis, and sinus rhythm. The primary study endpoint was the composite of all-cause mortality and hospitalizations for heart failure. The eligibility criteria were: 1. outpatient transthoracic echocardiogram performed between January 2019 and June 2022; 2. at least moderate AS by quantitively echocardiographic criteria(maximum aortic velocity ≥3 m/s or mean gradient≥30 mmHg or AVA ≤ 1.5 cm2).  Exclusion criteria were moderate-to-severe mitral stenosis (MS), severe aortic regurgitation (AR), previous aortic valve surgery/transcatheter interventions, any established diagnosis of cardiomyopathy, missing relevant clinical data, and poor quality echocardiographic study unsuitable for a speckle tracking evaluation. Atrial fibrillation was also an exclusion criterion as it independently impact LA mechanics.
DOI: 10.6084/m9.figshare.6871067
title: Prediction of matrix metal proteinases-12 inhibitors by machine learning approaches

description: Matrix metal proteinases-12 (MMP-12) is a hot pharmaceutical target on the treatment of many human diseases. There’s a crying need for designing and finding new MMP-12 inhibitors. In this work, four machine learning approaches, support vector machine, k-nearest neighbor, C4.5 decision tree, and random forest, were employed to derive statistical models from datasets with well distributed biological activities and predict a compound whether it is a MMP-12 inhibitor. The prediction accuracies of the models are in the range of 96.15–98.08% for sensitivity, 87.23–100.00% for specificity, 91.92–98.99% for the overall prediction accuracy and 0.8401–0.9800 for Matthews correlation coefficient, all producing satisfactory results. By means of diverse feature selection methods, several sets of critical descriptors with key information of inhibitory properties were selected by different models, accelerating the classification for MMP-12 inhibitors and non-inhibitors. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.6871067.v2
title: Prediction of matrix metal proteinases-12 inhibitors by machine learning approaches

description: Matrix metal proteinases-12 (MMP-12) is a hot pharmaceutical target on the treatment of many human diseases. There’s a crying need for designing and finding new MMP-12 inhibitors. In this work, four machine learning approaches, support vector machine, k-nearest neighbor, C4.5 decision tree, and random forest, were employed to derive statistical models from datasets with well distributed biological activities and predict a compound whether it is a MMP-12 inhibitor. The prediction accuracies of the models are in the range of 96.15–98.08% for sensitivity, 87.23–100.00% for specificity, 91.92–98.99% for the overall prediction accuracy and 0.8401–0.9800 for Matthews correlation coefficient, all producing satisfactory results. By means of diverse feature selection methods, several sets of critical descriptors with key information of inhibitory properties were selected by different models, accelerating the classification for MMP-12 inhibitors and non-inhibitors. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.23647480.v1
title: Additional file 1 of Aberrant mechanical loading induces annulus fibrosus cells apoptosis in intervertebral disc degeneration via mechanosensitive ion channel Piezo1

description: Additional file 1: Figure S1. The expression of Piezo2 in AF tissue and AFCs. (a) Representative immunofluorescent staining pictures detecting the expression of Piezo2 channel in AF tissue of the Ctrl group and IVDD group (scale bar = 150 μm). Piezo2 appeared green and nuclei were counterstained with Hoechst 33358 (blue). (b) Representative immunofluorescent staining pictures detecting the expression of Piezo2 channel in AFCs of the Ctrl group and CMS group (scale bar = 50 μm). Piezo2 appeared green and nuclei were counterstained with Hoechst 33358 (blue). Figure S2. Verification of Piezo1 knockdown by Lv-Piezo1 (n = 3). Verification of Calpain1 and Calpain2 knockdown by si-CAPN1 and siCAPN2 (n = 3). Figure S3. Statistic data of western blotting. (a-d) Western blotting analysis showing the Calpain1, Calpain2, Bax, Cleaved-Caspase3 expression in the Ctrl group, CMS group, CMS + Lv-Ctrl group, and CMS + Lv-Piezo1 group (n = 3). (e-f) Western blotting analysis showing the Bax, Cleaved-Caspase3 expression in the CMS + Yoda1 group, CMS + Yoda1 + si-Ctrl group, CMS + Yoda1 + si-CAPN1 group, and CMS + Yoda1 + si-CAPN2 group (n = 3). **P&lt;0.01, ***P&lt;0.001, ****P&lt;0.0001. Table S1. Histological grading scale system.
DOI: 10.6084/m9.figshare.23647529.v1
title: Additional file 2 of Genome-wide systematic characterization of the NRT2 gene family and its expression profile in wheat (Triticum aestivum L.) during plant growth and in response to nitrate deficiency

description: Additional file 2. The NRT2 genes information in wheat.
DOI: 10.6084/m9.figshare.22599044
title: Additional file 2 of Detection and genomic analysis of BRAF fusions in Juvenile Pilocytic Astrocytoma through the combination and integration of multi-omic data

description: Additional file 2.
DOI: 10.6084/m9.figshare.22599065.v1
title: Additional file 8 of Detection and genomic analysis of BRAF fusions in Juvenile Pilocytic Astrocytoma through the combination and integration of multi-omic data

description: Additional file 8.
DOI: 10.6084/m9.figshare.23647538.v1
title: Additional file 5 of Genome-wide systematic characterization of the NRT2 gene family and its expression profile in wheat (Triticum aestivum L.) during plant growth and in response to nitrate deficiency

description: Additional file 5. The raw data of transcriptome in shoot under nitrogen deficiency condition.
DOI: 10.25549/one-ouc17003332
title: David S., letter (1969)

description: David S., letter requesting sample publication (1969)
DOI: 10.15156/bio/sh1306981.08fu
title: SH1306981.08FU

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/sh1306982.08fu
title: SH1306982.08FU

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/sh1306983.08fu
title: SH1306983.08FU

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.