cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.11406462
title: Supplementary Material for: Novel Model Predicts Diabetic Nephropathy in Type 2 Diabetes

description: <b><i>Background:</i></b> Clinical indicators for accurately distinguishing diabetic nephropathy (DN) from non-diabetic renal disease in type 2 diabetes (T2D) are lacking. This study aimed to develop and validate a nomogram for predicting DN in T2D patients with kidney disease. <b><i>Methods:</i></b> A total of 302 consecutive patients with T2D who underwent renal biopsy at China-Japan Friendship Hospital between January 2014 and June 2019 were included in the study. The data were randomly split into a training set containing 70% of the patients (<i>n</i> = 214) and a validation set containing the remaining 30% of patients (<i>n</i> = 88). Multivariable logistic regression analyses were applied to develop a prediction nomogram incorporating the candidates selected in the least absolute shrinkage and selection operator regression model. Discrimination, calibration, and clinical usefulness of the prediction model were assessed using a concordance index (C-index), calibration plot, and decision curve analysis. Both internal and external validations were assessed. <b><i>Results:</i></b> A multivariable model that included gender, diabetes duration, diabetic retinopathy, hematuria, glycated hemoglobin A1c, anemia, blood pressure, urinary protein excretion, and estimated glomerular filtration rate was represented as the nomogram. The model demonstrated very good discrimination with a C-index of 0.934 (95% CI 0.904–0.964). The calibration plot diagram of predicted probabilities against observed DN rates indicated excellent concordance. The C-index value was 0.91 for internal validation and 0.875 for external validation. Decision curve analysis demonstrated that the novel nomogram was clinically useful. <b><i>Conclusion:</i></b> The novel model was very useful for predicting DN in patients with T2D and kidney disease, and thereby could be used by clinicians either in triage or as a replacement for biopsy.
DOI: 10.6084/m9.figshare.11406447
title: MOESM1 of Nuclear factor erythroid 2 – related factor 2 and its relationship with cellular response in nickel exposure: a systems biology analysis

description: Additional file . clusters ontology analysis.
DOI: 10.6084/m9.figshare.11406447.v1
title: MOESM1 of Nuclear factor erythroid 2 – related factor 2 and its relationship with cellular response in nickel exposure: a systems biology analysis

description: Additional file . clusters ontology analysis.
DOI: 10.6084/m9.figshare.11406432
title: MOESM8 of Osa-miR7695 enhances transcriptional priming in defense responses against the rice blast fungus

description: Additional file 8: Table S5. DEGs in MIR7695-Ac versus WT-Az plants.
DOI: 10.6084/m9.figshare.11406432.v1
title: MOESM8 of Osa-miR7695 enhances transcriptional priming in defense responses against the rice blast fungus

description: Additional file 8: Table S5. DEGs in MIR7695-Ac versus WT-Az plants.
DOI: 10.6084/m9.figshare.11406429
title: MOESM7 of Osa-miR7695 enhances transcriptional priming in defense responses against the rice blast fungus

description: Additional file 7: Table S4. Gene Ontology terms enriched in MIR7695-Ac versus WT-Az plants according to molecular function.
DOI: 10.6084/m9.figshare.11406429.v1
title: MOESM7 of Osa-miR7695 enhances transcriptional priming in defense responses against the rice blast fungus

description: Additional file 7: Table S4. Gene Ontology terms enriched in MIR7695-Ac versus WT-Az plants according to molecular function.
DOI: 10.6084/m9.figshare.11406423
title: MOESM6 of Osa-miR7695 enhances transcriptional priming in defense responses against the rice blast fungus

description: Additional file 6: Table S3. Differentially expressed genes (DEGs) in MIR7695-Ac plants relative to wild-type azygous (WT-Az) plants (MIR7695-Ac vs WT-Az).
DOI: 10.6084/m9.figshare.11406423.v1
title: MOESM6 of Osa-miR7695 enhances transcriptional priming in defense responses against the rice blast fungus

description: Additional file 6: Table S3. Differentially expressed genes (DEGs) in MIR7695-Ac plants relative to wild-type azygous (WT-Az) plants (MIR7695-Ac vs WT-Az).
DOI: 10.6084/m9.figshare.11406408
title: MOESM3 of Osa-miR7695 enhances transcriptional priming in defense responses against the rice blast fungus

description: Additional file 3: Table S2. qPCR of T-DNA copy number in MIR7695-Ac mutant plants with the sucrose phosphate synthase (SPS) gene as an endogenous reference.
DOI: 10.6084/m9.figshare.11406408.v1
title: MOESM3 of Osa-miR7695 enhances transcriptional priming in defense responses against the rice blast fungus

description: Additional file 3: Table S2. qPCR of T-DNA copy number in MIR7695-Ac mutant plants with the sucrose phosphate synthase (SPS) gene as an endogenous reference.
DOI: 10.6084/m9.figshare.11406402
title: MOESM2 of Osa-miR7695 enhances transcriptional priming in defense responses against the rice blast fungus

description: Additional file 2: Table S1. Oligonucleotides used in this study
DOI: 10.6084/m9.figshare.11406402.v1
title: MOESM2 of Osa-miR7695 enhances transcriptional priming in defense responses against the rice blast fungus

description: Additional file 2: Table S1. Oligonucleotides used in this study
DOI: 10.6084/m9.figshare.11406375
title: MOESM14 of Osa-miR7695 enhances transcriptional priming in defense responses against the rice blast fungus

description: Additional file 14: Table S10. DEGs in the top GO categories that are overrepresented in MIR7695-Ac with M. oryzae infection (bifactorial analysis).
DOI: 10.6084/m9.figshare.11406375.v1
title: MOESM14 of Osa-miR7695 enhances transcriptional priming in defense responses against the rice blast fungus

description: Additional file 14: Table S10. DEGs in the top GO categories that are overrepresented in MIR7695-Ac with M. oryzae infection (bifactorial analysis).
DOI: 10.6084/m9.figshare.11406372
title: MOESM13 of Osa-miR7695 enhances transcriptional priming in defense responses against the rice blast fungus

description: Additional file 13: Table S9. DEGs in bifactorial analysis.
DOI: 10.6084/m9.figshare.11406372.v1
title: MOESM13 of Osa-miR7695 enhances transcriptional priming in defense responses against the rice blast fungus

description: Additional file 13: Table S9. DEGs in bifactorial analysis.
DOI: 10.6084/m9.figshare.11406363
title: MOESM12 of Osa-miR7695 enhances transcriptional priming in defense responses against the rice blast fungus

description: Additional file 12: Table S8. Pathogenesis-related (PR) gene expression in WT-Az and MIR7695-Ac plants during M. oryzae infection at 48 hpi.
DOI: 10.6084/m9.figshare.11406363.v1
title: MOESM12 of Osa-miR7695 enhances transcriptional priming in defense responses against the rice blast fungus

description: Additional file 12: Table S8. Pathogenesis-related (PR) gene expression in WT-Az and MIR7695-Ac plants during M. oryzae infection at 48 hpi.
DOI: 10.6084/m9.figshare.11406354
title: MOESM11 of Osa-miR7695 enhances transcriptional priming in defense responses against the rice blast fungus

description: Additional file 11: Table S7. DEGs in MIR7695-Ac plants after infection with M. oryzae (48 hpi) (INF-MIR7695-Ac vs. MIR7695-Ac).
DOI: 10.6084/m9.figshare.11406354.v1
title: MOESM11 of Osa-miR7695 enhances transcriptional priming in defense responses against the rice blast fungus

description: Additional file 11: Table S7. DEGs in MIR7695-Ac plants after infection with M. oryzae (48 hpi) (INF-MIR7695-Ac vs. MIR7695-Ac).
DOI: 10.6084/m9.figshare.11406348
title: MOESM10 of Osa-miR7695 enhances transcriptional priming in defense responses against the rice blast fungus

description: Additional file 10: Table S6. DEGs in WT plants after infection with M. oryzae (48 h post-infection [hpi]) (INF-WT-Az vs. WT-Az).
DOI: 10.6084/m9.figshare.11406348.v1
title: MOESM10 of Osa-miR7695 enhances transcriptional priming in defense responses against the rice blast fungus

description: Additional file 10: Table S6. DEGs in WT plants after infection with M. oryzae (48 h post-infection [hpi]) (INF-WT-Az vs. WT-Az).
DOI: 10.6084/m9.figshare.11406336
title: MOESM9 of Novel findings to the biosynthetic pathway of magnoflorine and taspine through transcriptomic and metabolomic analysis of Croton draco (Euphorbiaceae)

description: Additional file 9: Table S14: Putative identification of magnoflorine and taspine, and some of their immediate precursors identified by ion search and HRMS analysis. Table S15. Primers used in RT-qPCR assays
DOI: 10.6084/m9.figshare.11406336.v1
title: MOESM9 of Novel findings to the biosynthetic pathway of magnoflorine and taspine through transcriptomic and metabolomic analysis of Croton draco (Euphorbiaceae)

description: Additional file 9: Table S14: Putative identification of magnoflorine and taspine, and some of their immediate precursors identified by ion search and HRMS analysis. Table S15. Primers used in RT-qPCR assays
DOI: 10.6084/m9.figshare.11406327
title: MOESM8 of Novel findings to the biosynthetic pathway of magnoflorine and taspine through transcriptomic and metabolomic analysis of Croton draco (Euphorbiaceae)

description: Additional file 8: Matrices of percentage identity of every pair of proteins identified as orthologs to the reference proteins: tyrosine decarboxylase (Table S7, (S)-norcoclaurine synthase Table S8 and Table S9), (S)-norcoclaurine 6′-O-methyltransferase Table S10), (S)-coclaurine N-methyltransferase (Table S11), (S)-N-methylcoclaurine 3′-hydroxylase (Table S12), (S)-corytuberine synthase (Table S13).
DOI: 10.6084/m9.figshare.11406327.v1
title: MOESM8 of Novel findings to the biosynthetic pathway of magnoflorine and taspine through transcriptomic and metabolomic analysis of Croton draco (Euphorbiaceae)

description: Additional file 8: Matrices of percentage identity of every pair of proteins identified as orthologs to the reference proteins: tyrosine decarboxylase (Table S7, (S)-norcoclaurine synthase Table S8 and Table S9), (S)-norcoclaurine 6′-O-methyltransferase Table S10), (S)-coclaurine N-methyltransferase (Table S11), (S)-N-methylcoclaurine 3′-hydroxylase (Table S12), (S)-corytuberine synthase (Table S13).
DOI: 10.6084/m9.figshare.11406321
title: MOESM7 of Novel findings to the biosynthetic pathway of magnoflorine and taspine through transcriptomic and metabolomic analysis of Croton draco (Euphorbiaceae)

description: Additional file 7: Table S4. Expression profile matrix of C. draco unigenes. Table S5. Expression profiles of preferentially expressed genes. Table S6. OrthoMCL-defined protein families (orthogroups).
DOI: 10.6084/m9.figshare.11406321.v1
title: MOESM7 of Novel findings to the biosynthetic pathway of magnoflorine and taspine through transcriptomic and metabolomic analysis of Croton draco (Euphorbiaceae)

description: Additional file 7: Table S4. Expression profile matrix of C. draco unigenes. Table S5. Expression profiles of preferentially expressed genes. Table S6. OrthoMCL-defined protein families (orthogroups).
DOI: 10.6084/m9.figshare.11406309
title: MOESM5 of Novel findings to the biosynthetic pathway of magnoflorine and taspine through transcriptomic and metabolomic analysis of Croton draco (Euphorbiaceae)

description: Additional file 5: Table S2. Annotation of C. draco non-redundant (nr) unigenes.
DOI: 10.6084/m9.figshare.11406312
title: MOESM6 of Novel findings to the biosynthetic pathway of magnoflorine and taspine through transcriptomic and metabolomic analysis of Croton draco (Euphorbiaceae)

description: Additional file 6: Table S3. Functional categorization of C. draco unigenes.
DOI: 10.6084/m9.figshare.11406312.v1
title: MOESM6 of Novel findings to the biosynthetic pathway of magnoflorine and taspine through transcriptomic and metabolomic analysis of Croton draco (Euphorbiaceae)

description: Additional file 6: Table S3. Functional categorization of C. draco unigenes.
DOI: 10.6084/m9.figshare.11406309.v1
title: MOESM5 of Novel findings to the biosynthetic pathway of magnoflorine and taspine through transcriptomic and metabolomic analysis of Croton draco (Euphorbiaceae)

description: Additional file 5: Table S2. Annotation of C. draco non-redundant (nr) unigenes.
DOI: 10.6084/m9.figshare.11406297
title: MOESM3 of Novel findings to the biosynthetic pathway of magnoflorine and taspine through transcriptomic and metabolomic analysis of Croton draco (Euphorbiaceae)

description: Additional file 3:. Unigene sequences shorter than 1000 bp. (FASTA 67268 kb)
DOI: 10.6084/m9.figshare.11406297.v1
title: MOESM3 of Novel findings to the biosynthetic pathway of magnoflorine and taspine through transcriptomic and metabolomic analysis of Croton draco (Euphorbiaceae)

description: Additional file 3:. Unigene sequences shorter than 1000 bp. (FASTA 67268 kb)
DOI: 10.6084/m9.figshare.11406285
title: MOESM2 of Novel findings to the biosynthetic pathway of magnoflorine and taspine through transcriptomic and metabolomic analysis of Croton draco (Euphorbiaceae)

description: Additional file 2:. Unigene sequences longer than 1000 bp. (FASTA 51035 kb)
DOI: 10.6084/m9.figshare.11406285.v1
title: MOESM2 of Novel findings to the biosynthetic pathway of magnoflorine and taspine through transcriptomic and metabolomic analysis of Croton draco (Euphorbiaceae)

description: Additional file 2:. Unigene sequences longer than 1000 bp. (FASTA 51035 kb)
DOI: 10.6084/m9.figshare.11406276
title: MOESM1 of Novel findings to the biosynthetic pathway of magnoflorine and taspine through transcriptomic and metabolomic analysis of Croton draco (Euphorbiaceae)

description: Additional file 1: Table S1. Summary of sequencing data generated from Croton draco.
DOI: 10.6084/m9.figshare.11406276.v1
title: MOESM1 of Novel findings to the biosynthetic pathway of magnoflorine and taspine through transcriptomic and metabolomic analysis of Croton draco (Euphorbiaceae)

description: Additional file 1: Table S1. Summary of sequencing data generated from Croton draco.
DOI: 10.6084/m9.figshare.11406255
title: MOESM8 of Early cold stress responses in post-meiotic anthers from tolerant and sensitive rice cultivars

description: Additional file 8: Table S4. Expression values of known anther development and starch accumulation genes.
DOI: 10.6084/m9.figshare.11406249
title: MOESM7 of Early cold stress responses in post-meiotic anthers from tolerant and sensitive rice cultivars

description: Additional file 7: Table S3. List of transcription factors upregulated in cold stress.
DOI: 10.6084/m9.figshare.11406255.v1
title: MOESM8 of Early cold stress responses in post-meiotic anthers from tolerant and sensitive rice cultivars

description: Additional file 8: Table S4. Expression values of known anther development and starch accumulation genes.
DOI: 10.6084/m9.figshare.11406246
title: MOESM6 of Early cold stress responses in post-meiotic anthers from tolerant and sensitive rice cultivars

description: Additional file 6: Table S2. Gene ontology of DEGs obtained from RNA-seq data
DOI: 10.6084/m9.figshare.11406246.v1
title: MOESM6 of Early cold stress responses in post-meiotic anthers from tolerant and sensitive rice cultivars

description: Additional file 6: Table S2. Gene ontology of DEGs obtained from RNA-seq data
DOI: 10.6084/m9.figshare.11406249.v1
title: MOESM7 of Early cold stress responses in post-meiotic anthers from tolerant and sensitive rice cultivars

description: Additional file 7: Table S3. List of transcription factors upregulated in cold stress.
DOI: 10.6084/m9.figshare.11406240
title: MOESM5 of Early cold stress responses in post-meiotic anthers from tolerant and sensitive rice cultivars

description: Additional file 5: Table S1. List of DEGs from RNA-seq data.
DOI: 10.6084/m9.figshare.11406243
title: MOESM2 of Overexpression of rice jacalin-related mannose-binding lectin (OsJAC1) enhances resistance to ionizing radiation in Arabidopsis

description: Additional file 2: Table S1. Expression levels of anotated transciprts in OsJAC1-overexpressing Arabidopsis lines.
DOI: 10.6084/m9.figshare.11406240.v1
title: MOESM5 of Early cold stress responses in post-meiotic anthers from tolerant and sensitive rice cultivars

description: Additional file 5: Table S1. List of DEGs from RNA-seq data.
DOI: 10.6084/m9.figshare.11406243.v1
title: MOESM2 of Overexpression of rice jacalin-related mannose-binding lectin (OsJAC1) enhances resistance to ionizing radiation in Arabidopsis

description: Additional file 2: Table S1. Expression levels of anotated transciprts in OsJAC1-overexpressing Arabidopsis lines.
DOI: 10.6084/m9.figshare.11406213
title: MOESM3 of Quantitative proteome analysis of Merkel cell carcinoma cell lines using SILAC

description: Additional file 3. Table S2. Lists all proteins that are shown in the Venn diagram (Fig. 3). First each cell line was compared to the reference cell line HaCaT. Then the cell line specific proteins of each cell line (MCC13, MKL-1, MKL-2, PeTa and WaGa) were related in a Venn diagram to show similarities and differences.
DOI: 10.6084/m9.figshare.11406213.v1
title: MOESM3 of Quantitative proteome analysis of Merkel cell carcinoma cell lines using SILAC

description: Additional file 3. Table S2. Lists all proteins that are shown in the Venn diagram (Fig. 3). First each cell line was compared to the reference cell line HaCaT. Then the cell line specific proteins of each cell line (MCC13, MKL-1, MKL-2, PeTa and WaGa) were related in a Venn diagram to show similarities and differences.
DOI: 10.6084/m9.figshare.11406207
title: MOESM2 of Quantitative proteome analysis of Merkel cell carcinoma cell lines using SILAC

description: Additional file 2: Table S1. Shows overlapping and specific proteins for each cell line.
DOI: 10.6084/m9.figshare.11406204
title: MOESM10 of Early cold stress responses in post-meiotic anthers from tolerant and sensitive rice cultivars

description: Additional file 10: Table S6. List of Mapman bins, and DEGs within, specifically de-regulated in each cultivar.
DOI: 10.6084/m9.figshare.11406207.v1
title: MOESM2 of Quantitative proteome analysis of Merkel cell carcinoma cell lines using SILAC

description: Additional file 2: Table S1. Shows overlapping and specific proteins for each cell line.
DOI: 10.6084/m9.figshare.11406204.v1
title: MOESM10 of Early cold stress responses in post-meiotic anthers from tolerant and sensitive rice cultivars

description: Additional file 10: Table S6. List of Mapman bins, and DEGs within, specifically de-regulated in each cultivar.
DOI: 10.6084/m9.figshare.11406162.v1
title: MOESM4 of A comprehensive proteomics profiling identifies NRP1 as a novel identity marker of human bone marrow mesenchymal stromal cell-derived small extracellular vesicles

description: Additional file 4: Table S1. hBM-MSC characterization for surface identity markers, differentiation potential to mesodermal lineage and population doublings.
DOI: 10.5281/zenodo.4001362
title: Ensemble filtering experiments with HYSPLIT

description: This dataset contains ensembles of HYSPLIT dispersion model concentration outputs for 14 different case studies. The ensemble members have been filtered using VOLCAT satellite retrievals obtained for the 14 case studies (http://doi.org/10.5281/zenodo.3579613).
DOI: 10.5281/zenodo.4001361
title: Ensemble filtering experiments with HYSPLIT

description: This dataset contains ensembles of HYSPLIT dispersion model concentration outputs for 14 different case studies. The ensemble members have been filtered using VOLCAT satellite retrievals obtained for the 14 case studies (http://doi.org/10.5281/zenodo.3579613).
DOI: 10.6084/m9.figshare.11406108.v1
title: MOESM2 of Within-species contamination of bacterial whole-genome sequence data has a greater influence on clustering analyses than between-species contamination

description: Additional file 2: Table S4. ConFindr results from analysis of 10,000 Listeria monocytogenes, Salmonella enterica, and Escherichia coli fastq datasets. (XLS 7913 kb)
DOI: 10.6084/m9.figshare.11405964
title: MOESM3 of Novel human sex-typing strategies based on the autism candidate gene NLGN4X and its male-specific gametologue NLGN4Y

description: Additional file 3. Quantitative PCR-results on SNP_C
DOI: 10.6084/m9.figshare.11405964.v1
title: MOESM3 of Novel human sex-typing strategies based on the autism candidate gene NLGN4X and its male-specific gametologue NLGN4Y

description: Additional file 3. Quantitative PCR-results on SNP_C
DOI: 10.6084/m9.figshare.11405898
title: MOESM1 of Bi-allelic mutations in uncoordinated mutant number-45 myosin chaperone B are a cause for congenital myopathy

description: Additional file 1: Figure S1. Further myopathological, electron microscopical and phenotypic findings in our patient with UNC45B variant. Figure S2. Gene and isoform expression of UNC45B in various tissues and a possible disease model scheme.
DOI: 10.6084/m9.figshare.11405898.v1
title: MOESM1 of Bi-allelic mutations in uncoordinated mutant number-45 myosin chaperone B are a cause for congenital myopathy

description: Additional file 1: Figure S1. Further myopathological, electron microscopical and phenotypic findings in our patient with UNC45B variant. Figure S2. Gene and isoform expression of UNC45B in various tissues and a possible disease model scheme.
DOI: 10.6084/m9.figshare.11405733
title: MOESM3 of Whole genome DNA sequencing provides an atlas of somatic mutagenesis in healthy human cells and identifies a tumor-prone cell type

description: Additional file 3. Lists of somatic mutations detected on the X chromosome of female donors (KD05, KD06 and KD11). Not used in the analyses.
DOI: 10.6084/m9.figshare.11405733.v1
title: MOESM3 of Whole genome DNA sequencing provides an atlas of somatic mutagenesis in healthy human cells and identifies a tumor-prone cell type

description: Additional file 3. Lists of somatic mutations detected on the X chromosome of female donors (KD05, KD06 and KD11). Not used in the analyses.
DOI: 10.6084/m9.figshare.11405724
title: MOESM2 of Whole genome DNA sequencing provides an atlas of somatic mutagenesis in healthy human cells and identifies a tumor-prone cell type

description: Additional file 2. Lists of somatic mutations detected on autosomes of 69 clones from 6 healthy donors and grouped per tissue
DOI: 10.6084/m9.figshare.11405724.v1
title: MOESM2 of Whole genome DNA sequencing provides an atlas of somatic mutagenesis in healthy human cells and identifies a tumor-prone cell type

description: Additional file 2. Lists of somatic mutations detected on autosomes of 69 clones from 6 healthy donors and grouped per tissue
DOI: 10.6084/m9.figshare.12865580
title: Appendix BEH 3626

description: More specific pairwise comparisons to explore differences in NND at different time points.
DOI: 10.6084/m9.figshare.12865580.v1
title: Appendix BEH 3626

description: More specific pairwise comparisons to explore differences in NND at different time points.
DOI: 10.6084/m9.figshare.11405622
title: MOESM2 of Genetic diversity of Listeria monocytogenes strains in ruminant abortion and rhombencephalitis cases in comparison with the natural environment

description: Additional file 2: Table S2. A complete database of Listeria monocytogenes isolates from the natural environment.
DOI: 10.6084/m9.figshare.11405616
title: MOESM1 of Genetic diversity of Listeria monocytogenes strains in ruminant abortion and rhombencephalitis cases in comparison with the natural environment

description: Additional file 1: Table S1. A complete database of Listeria monocytogenes isolates from the animal clinical cases.
DOI: 10.6084/m9.figshare.11405622.v1
title: MOESM2 of Genetic diversity of Listeria monocytogenes strains in ruminant abortion and rhombencephalitis cases in comparison with the natural environment

description: Additional file 2: Table S2. A complete database of Listeria monocytogenes isolates from the natural environment.
DOI: 10.6084/m9.figshare.11405616.v1
title: MOESM1 of Genetic diversity of Listeria monocytogenes strains in ruminant abortion and rhombencephalitis cases in comparison with the natural environment

description: Additional file 1: Table S1. A complete database of Listeria monocytogenes isolates from the animal clinical cases.