cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.c.3870532_d10
title: Additional file 7: of Members of the Candidate Phyla Radiation are functionally differentiated by carbon- and nitrogen-cycling capabilities

description: Maximum-likelihood rps3 tree file. (TREE 419Â kb)
DOI: 10.6084/m9.figshare.c.3870532_d11.v1
title: Additional file 8: of Members of the Candidate Phyla Radiation are functionally differentiated by carbon- and nitrogen-cycling capabilities

description: Maximum-likelihood 16S rRNA tree file. (TREE 102Â kb)
DOI: 10.6084/m9.figshare.c.3870532_d11
title: Additional file 8: of Members of the Candidate Phyla Radiation are functionally differentiated by carbon- and nitrogen-cycling capabilities

description: Maximum-likelihood 16S rRNA tree file. (TREE 102Â kb)
DOI: 10.6084/m9.figshare.c.3870532_d12.v1
title: Additional file 9: of Members of the Candidate Phyla Radiation are functionally differentiated by carbon- and nitrogen-cycling capabilities

description: Maximum-likelihood gyrA tree file. (TREE 294Â kb)
DOI: 10.6084/m9.figshare.c.3870532_d12
title: Additional file 9: of Members of the Candidate Phyla Radiation are functionally differentiated by carbon- and nitrogen-cycling capabilities

description: Maximum-likelihood gyrA tree file. (TREE 294Â kb)
DOI: 10.6084/m9.figshare.c.3870595_d1.v1
title: Additional file 1: Table S1. of Computational discovery and functional validation of novel fluoroquinolone resistance genes in public metagenomic data sets

description: Annotations for matches in NCBI nt and bacterial genomes. Best hit annotations for sequences matched by the hidden Markov model in NCBI nt and bacterial genome sequences. (XLSX 15Â kb)
DOI: 10.6084/m9.figshare.c.3870604_d7
title: MOESM16 of Genome-wide computational analysis of potential long noncoding RNA mediated DNA:DNA:RNA triplexes in the human genome

description: Additional file 16. Complete list for possible Hi-C (Hi-C_PTS_CCHiC-HeLaS3CCL2p2-G1-0.25F) interaction domains with PTS sites.
DOI: 10.6084/m9.figshare.c.3870604_d9.v1
title: MOESM18 of Genome-wide computational analysis of potential long noncoding RNA mediated DNA:DNA:RNA triplexes in the human genome

description: Additional file 18. Complete list for possible Hi-C (CCHiC-HeLaS3CCL2p2-M-0.25FA) interaction domains with PTS sites.
DOI: 10.6084/m9.figshare.c.3870604_d10.v1
title: MOESM19 of Genome-wide computational analysis of potential long noncoding RNA mediated DNA:DNA:RNA triplexes in the human genome

description: Additional file 19. Complete list for possible Hi-C (CCHiC-HeLaS3CCL2p2-M-1FA) interaction domains with PTS sites.
DOI: 10.6084/m9.figshare.c.3870604_d8
title: MOESM17 of Genome-wide computational analysis of potential long noncoding RNA mediated DNA:DNA:RNA triplexes in the human genome

description: Additional file 17. Complete list for possible Hi-C (CCHiC-HeLaS3CCL2p2-G1-1FA) interaction domains with PTS sites.
DOI: 10.6084/m9.figshare.c.3870604_d9
title: MOESM18 of Genome-wide computational analysis of potential long noncoding RNA mediated DNA:DNA:RNA triplexes in the human genome

description: Additional file 18. Complete list for possible Hi-C (CCHiC-HeLaS3CCL2p2-M-0.25FA) interaction domains with PTS sites.
DOI: 10.6084/m9.figshare.c.3870604_d13.v1
title: MOESM21 of Genome-wide computational analysis of potential long noncoding RNA mediated DNA:DNA:RNA triplexes in the human genome

description: Additional file 21. Complete list for possible Hi-C (CCHiC-K562-M-R1) interaction domains with PTS sites.
DOI: 10.6084/m9.figshare.c.3870604_d10
title: MOESM19 of Genome-wide computational analysis of potential long noncoding RNA mediated DNA:DNA:RNA triplexes in the human genome

description: Additional file 19. Complete list for possible Hi-C (CCHiC-HeLaS3CCL2p2-M-1FA) interaction domains with PTS sites.
DOI: 10.6084/m9.figshare.c.3870604_d12.v1
title: MOESM20 of Genome-wide computational analysis of potential long noncoding RNA mediated DNA:DNA:RNA triplexes in the human genome

description: Additional file 20. Complete list for possible Hi-C (CCHiC-HeLaS3CCL2p2-M-98percent) interaction domains with PTS sites.
DOI: 10.6084/m9.figshare.c.3870604_d12
title: MOESM20 of Genome-wide computational analysis of potential long noncoding RNA mediated DNA:DNA:RNA triplexes in the human genome

description: Additional file 20. Complete list for possible Hi-C (CCHiC-HeLaS3CCL2p2-M-98percent) interaction domains with PTS sites.
DOI: 10.6084/m9.figshare.c.3870604_d13
title: MOESM21 of Genome-wide computational analysis of potential long noncoding RNA mediated DNA:DNA:RNA triplexes in the human genome

description: Additional file 21. Complete list for possible Hi-C (CCHiC-K562-M-R1) interaction domains with PTS sites.
DOI: 10.6084/m9.figshare.c.3870604_d18.v1
title: MOESM3 of Genome-wide computational analysis of potential long noncoding RNA mediated DNA:DNA:RNA triplexes in the human genome

description: Additional file 3. The complete list of coordinates of PTS for the four lncRNA viz. MALAT1, HOTAIR and DHFR.
DOI: 10.6084/m9.figshare.c.3870604_d21.v1
title: MOESM6 of Genome-wide computational analysis of potential long noncoding RNA mediated DNA:DNA:RNA triplexes in the human genome

description: Additional file 6. List of predicted lncRNAs forming Pyrimidine motif (Y) with the human reference genome. The file consists of lncRNA transcript id, lncRNA gene name, lncRNA length, TFO start, TFO stop, chromosome number of TTS, TTS start, TTS stop, motif type, strand orientation and guanine-rate.
DOI: 10.6084/m9.figshare.c.3870604_d20.v1
title: MOESM5 of Genome-wide computational analysis of potential long noncoding RNA mediated DNA:DNA:RNA triplexes in the human genome

description: Additional file 5. List of predicted lncRNAs forming Purine motif (R) motif with the human reference genome. The file consists of lncRNA transcript id, lncRNA gene name, lncRNA length, TFO start, TFO stop, chromosome number of TTS, TTS start, TTS stop, motif type, strand orientation and guanine-rate.
DOI: 10.6084/m9.figshare.c.3870604_d22.v1
title: MOESM7 of Genome-wide computational analysis of potential long noncoding RNA mediated DNA:DNA:RNA triplexes in the human genome

description: Additional file 7. List of predicted lncRNAs forming Purine-Pyrimidine motif (M) motif with the human reference genome. The file consists of lncRNA transcript id, lncRNA gene name, lncRNA length, TFO start, TFO stop, chromosome number of TTS, TTS start, TTS stop, motif type, strand orientation and guanine-rate.
DOI: 10.6084/m9.figshare.28053845
title: PROTECTiO_db_v1_0_0.tar.gz

description: <pre>This is the complete PROTECTiO Database (version v1.0.0), providing Tissue-specific RNA off-target risk induced by CBEs.</pre>
DOI: 10.6084/m9.figshare.c.3870667_d1.v1
title: Additional file 1: Table S1. of Mutations in the gene of the GÎą subunit of the heterotrimeric G protein are the cause for the brachytic1 semi-dwarf phenotype in barley and applicable for practical breeding

description: SNP and mutation information for Brh1 mutant lines and original background cultivars. (XLSX 121Â kb)
DOI: 10.15468/dl.jwhbqa
title: Occurrence Download

description: A dataset containing 407 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "TaxonKey is one of (Ambystoma annulatum Cope, 1886)"
 ]
}

 The dataset includes 407 records from 23 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0039340-241126133413365/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.c.3870661_d1.v1
title: Additional file 1: Table S4. of Genomic regions and pathways associated with gastrointestinal parasites resistance in Santa Inês breed adapted to tropical climate

description: Genomic regions associated with egg counts per gram of feces (EPGlog) in Santa Inês sheep; Table S5. Genomic regions associated with famacha (FAM) in Santa Inês sheep; Table S6. Genomic regions associated with blood cell count (WBC) in Santa Inês sheep; Table S7. Genomic regions associated with red blood cells (RBC) in Santa Inês sheep; Table S8. Genomic regions associated with platelet (PLT) in Santa Inês sheep; Table S9. Genomic regions associated with hematocrit (HCT) in Santa Inês sheep; Table S10. Genomic regions associated with blood cell count (HGB) in Santa Inês sheep. (XLS 74 kb)
DOI: 10.6084/m9.figshare.c.3870661_d1
title: Additional file 1: Table S4. of Genomic regions and pathways associated with gastrointestinal parasites resistance in Santa Inês breed adapted to tropical climate

description: Genomic regions associated with egg counts per gram of feces (EPGlog) in Santa Inês sheep; Table S5. Genomic regions associated with famacha (FAM) in Santa Inês sheep; Table S6. Genomic regions associated with blood cell count (WBC) in Santa Inês sheep; Table S7. Genomic regions associated with red blood cells (RBC) in Santa Inês sheep; Table S8. Genomic regions associated with platelet (PLT) in Santa Inês sheep; Table S9. Genomic regions associated with hematocrit (HCT) in Santa Inês sheep; Table S10. Genomic regions associated with blood cell count (HGB) in Santa Inês sheep. (XLS 74 kb)
DOI: 10.6084/m9.figshare.c.3870667_d1
title: Additional file 1: Table S1. of Mutations in the gene of the GÎą subunit of the heterotrimeric G protein are the cause for the brachytic1 semi-dwarf phenotype in barley and applicable for practical breeding

description: SNP and mutation information for Brh1 mutant lines and original background cultivars. (XLSX 121Â kb)
DOI: 10.6084/m9.figshare.c.3870685_d1.v1
title: Additional file 1: of Collection of non-meconium stool on fecal occult blood cards is an effective method for fecal microbiota studies in infants

description: Table S1: Software and R libraries used in the analysis. Table S2: P values from Adonis tests for different contrasts with different rarefaction cutoffs and different distance measures. Figure S1A: Rarefaction plot of number of assigned OTUs versus number of sequences from different storage conditions in meconium samples. The vertical line indicates the number of sequences used for the single rarefaction in analyses. Figure S1B: Rarefaction plot of number of assigned OTUs versus number of sequences from different storage conditions in stool samples. The vertical line indicates the number of sequences used for the single rarefaction in analyses. Figure S2: PCoA plots for all samples. Figure S3A. PCoA plots with Bray–Curtis, Jensen–Shannon divergence, unweighted UniFrac, and weighted UniFrac distance measures for meconium samples. Figure S3B. PCoA plots with Bray–Curtis, Jensen–Shannon divergence, unweighted UniFrac, and weighted UniFrac distance measures for stool samples. Compressed OTU file with all the samples at Family level: stoolAndMeconiumOTUByFamily.csv.zip. Compressed OTU file with all the samples at Genus level: stoolAndMeconiumOTUByGenus.csv.zip. (ZIP 3263 kb)
DOI: 10.6084/m9.figshare.c.3870676_d1.v1
title: Additional file 10: of Enrichment of beneficial bacteria in the skin microbiota of bats persisting with white-nose syndrome

description: OTU table resulting from the analysis of 66 bat skin microbiota samples and 11 environmental samples.
DOI: 10.6084/m9.figshare.c.3870676_d1
title: Additional file 10: of Enrichment of beneficial bacteria in the skin microbiota of bats persisting with white-nose syndrome

description: OTU table resulting from the analysis of 66 bat skin microbiota samples and 11 environmental samples.
DOI: 10.6084/m9.figshare.c.3870685_d1
title: Additional file 1: of Collection of non-meconium stool on fecal occult blood cards is an effective method for fecal microbiota studies in infants

description: Table S1: Software and R libraries used in the analysis. Table S2: P values from Adonis tests for different contrasts with different rarefaction cutoffs and different distance measures. Figure S1A: Rarefaction plot of number of assigned OTUs versus number of sequences from different storage conditions in meconium samples. The vertical line indicates the number of sequences used for the single rarefaction in analyses. Figure S1B: Rarefaction plot of number of assigned OTUs versus number of sequences from different storage conditions in stool samples. The vertical line indicates the number of sequences used for the single rarefaction in analyses. Figure S2: PCoA plots for all samples. Figure S3A. PCoA plots with Bray–Curtis, Jensen–Shannon divergence, unweighted UniFrac, and weighted UniFrac distance measures for meconium samples. Figure S3B. PCoA plots with Bray–Curtis, Jensen–Shannon divergence, unweighted UniFrac, and weighted UniFrac distance measures for stool samples. Compressed OTU file with all the samples at Family level: stoolAndMeconiumOTUByFamily.csv.zip. Compressed OTU file with all the samples at Genus level: stoolAndMeconiumOTUByGenus.csv.zip. (ZIP 3263 kb)
DOI: 10.6084/m9.figshare.c.3870661_d2.v1
title: Additional file 2: Table S11. of Genomic regions and pathways associated with gastrointestinal parasites resistance in Santa Inês breed adapted to tropical climate

description: KEGG pathways (P
DOI: 10.5281/zenodo.14515128
title: The potential of in situ Raman spectroscopy in the study of the health of cement-based materials of modern buildings during restoration works
DOI: 10.5281/zenodo.14515129
title: The potential of in situ Raman spectroscopy in the study of the health of cement-based materials of modern buildings during restoration works
DOI: 10.6084/m9.figshare.c.3870676_d4.v1
title: Additional file 3: of Enrichment of beneficial bacteria in the skin microbiota of bats persisting with white-nose syndrome

description: Main taxa relative abundance (&gt;â  0.1%) in negative control samples. File 1 presents DNA extraction control samples, file 2 the library control, file 3 the negative site controls, and file 4 presents all controls together.
DOI: 10.6084/m9.figshare.c.3870709_d2.v1
title: Additional file 11: Table S8a. of Chromosome contacts in activated T cells identify autoimmune disease candidate genes

description: GTF file with definitions for all Ensembl 75 genomic features plus CD4-specific regulatory regions inferred from chromatin states. These regulatory regions have been named with identifiers containing a CD4R prefix, assigned a regulatory biotype and marked as pertaining to both genomic strands due to their bi-directional transcription potential. (GZ 39807 kb)
DOI: 10.6084/m9.figshare.c.3870676_d4
title: Additional file 3: of Enrichment of beneficial bacteria in the skin microbiota of bats persisting with white-nose syndrome

description: Main taxa relative abundance (&gt;â  0.1%) in negative control samples. File 1 presents DNA extraction control samples, file 2 the library control, file 3 the negative site controls, and file 4 presents all controls together.
DOI: 10.6084/m9.figshare.c.3870709_d2
title: Additional file 11: Table S8a. of Chromosome contacts in activated T cells identify autoimmune disease candidate genes

description: GTF file with definitions for all Ensembl 75 genomic features plus CD4-specific regulatory regions inferred from chromatin states. These regulatory regions have been named with identifiers containing a CD4R prefix, assigned a regulatory biotype and marked as pertaining to both genomic strands due to their bi-directional transcription potential. (GZ 39807 kb)
DOI: 10.6084/m9.figshare.c.3870697_d3.v1
title: Additional file 3: Table S2. of Evolution of mobile genetic element composition in an epidemic methicillin-resistant Staphylococcus aureus: temporal changes correlated with frequent loss and gain events

description: Summary of MGEs identified in 923 MRSA CC22 isolates, describing distribution across the CC22 and non-CC22 isolates. (XLSX 39 kb)
DOI: 10.6084/m9.figshare.c.3870697_d3
title: Additional file 3: Table S2. of Evolution of mobile genetic element composition in an epidemic methicillin-resistant Staphylococcus aureus: temporal changes correlated with frequent loss and gain events

description: Summary of MGEs identified in 923 MRSA CC22 isolates, describing distribution across the CC22 and non-CC22 isolates. (XLSX 39 kb)
DOI: 10.6084/m9.figshare.c.3870712_d2.v1
title: Additional file 2: Table S2. of Permanent draft genome sequence of Frankia sp. NRRL B-16219 reveals the presence of canonical nod genes, which are highly homologous to those detected in Candidatus Frankia Dg1 genome

description: Percent similarities based on amino acid sequence for NodA, B, C and H between Frankia sp. NRRL B-16219, Candidatus Frankia Dg1 and Dg2, and other rhizobial strains. (XLSX 308Â kb)
DOI: 10.6084/m9.figshare.c.3870709_d3.v1
title: Additional file 12: Table S8b. of Chromosome contacts in activated T cells identify autoimmune disease candidate genes

description: Whole-genome segmentation of non-activated and activated CD4 T cells into 15 states obtained from a CHROMHMM analysis using ChIP-seq data for activated CD4+ T cells. (GZ 1551 kb)
DOI: 10.25625/zdun53
title: Counseling and disclosure practices in predictive Alzheimer's disease diagnostics: A scoping review

description: New possibilities of biomarker-based predictive technologies for Alzheimer's disease (AD) have become more reliable as well as more accessible. Standardized clinical recommendations and guidance for counseling and disclosure in this context are not yet well developed. Our scoping review identified publications from database searches in PubMed, PsycINFO, LIVIVO, and Web of Science. Inclusion criteria were: (1) information or counseling, (2) biomarkers and a type of cognitive impairment or AD, and (3) published between 2005 and 2024. We identified 63 articles and synthesized them along the categories of staged information provision: pre-test counseling, disclosure, and post-disclosure follow-up. Most publications referred to the context of disclosure (48), followed by pre-test counseling (33), and post-disclosure follow-up (31). Some publications referred to all stages of counseling (17). Our findings highlight the need to further develop and specify comprehensive and standardized guidelines for counseling, disclosure, and post-disclosure follow-up in the context of AD biomarker testing.
DOI: 10.25625/zdun53/t7soqs
title: Alzheimer's Dementia - 2024 - Perry - Counseling and disclosure practices in predictive Alzheimer s disease diagnostics .pdf

description: :unav
DOI: 10.6084/m9.figshare.c.3870730_d1
title: Additional file 1: Figure S1. of Maintenance of stemness is associated with the interation of LRP6 and heparin-binding protein CCN2 autocrined by hepatocellular carcinoma

description: Expression of CCN2 and LRP6 was analyzed in 144-paired HCC samples and adjacent nontumor liver samples in training cohorts. (A) Upregulation of CCN2 in HCC samples. (B) Upregulation of LRP6 in HCC samples. Figure S2. Up-regulation of CCN2 and LRP6 correlates with poor prognosis and in HCC patients. Kaplan-Meier’s curves for OS and TTR according to CCN2 and LRP6 expression in the validation cohort (n=144). Figure S3. Expression of CCN2 and LRP6 was analyzed in 374-paired HCC samples and adjacent nontumor liver samples in validation cohorts by tissue microarrays. Figure S4. Oxaliplatin-treated HCC cell lines and subcutaneous tumor tissues showed increased expression of CCN2 and LRP6. (A) Upregulation of CCN2 and LRP6 in Oxaliplatin-treated HCC cell lines. (B) Upregulation of CCN2 and LRP6 in Oxaliplatin-treated subcutaneous tumor tissues. Figure S5. Expression of CCN2 and LRP6 from the gene expression profiles of 30-paired HCC samples with or without metastasis was analyzed. LRP6 was significantly upregulated in HCC with metastasis, while no significant association was found in the expression of CCN2. Figure S6. LMWH demonstrate no significant inhibitory effect on the in vitro proliferation of MHCC-97H for 24, 48, 72h, with the IC50 645±99.33, 699±87.88, and 469±72.77 U/ml respectively. Figure S7. The synergetic effect of LMWH combined with chemotherapy was evaluated, and LMWH (2 U/ml) significantly increased the sensitivity MHCC-97H cells to oxaliplatin. (ZIP 8918 kb)
DOI: 10.6084/m9.figshare.c.3870709_d9.v1
title: Additional file 3: Table S2. of Chromosome contacts in activated T cells identify autoimmune disease candidate genes

description: Results of differential expression analysis on RNA-seq data. Features are defined in the GTF file in Additional file 11: Table S8a. (GZ 835 kb)
DOI: 10.6084/m9.figshare.c.3870709_d9
title: Additional file 3: Table S2. of Chromosome contacts in activated T cells identify autoimmune disease candidate genes

description: Results of differential expression analysis on RNA-seq data. Features are defined in the GTF file in Additional file 11: Table S8a. (GZ 835 kb)
DOI: 10.6084/m9.figshare.c.3870709_d10.v1
title: Additional file 4: Table S3. of Chromosome contacts in activated T cells identify autoimmune disease candidate genes

description: Baited HindIII fragments used for capture of Hi-C libraries, annotated with Ensembl annotated genes. (GZ 572 kb)
DOI: 10.6084/m9.figshare.c.3870709_d10
title: Additional file 4: Table S3. of Chromosome contacts in activated T cells identify autoimmune disease candidate genes

description: Baited HindIII fragments used for capture of Hi-C libraries, annotated with Ensembl annotated genes. (GZ 572 kb)
DOI: 10.6084/m9.figshare.c.3870709_d11.v1
title: Additional file 5: Table S4. of Chromosome contacts in activated T cells identify autoimmune disease candidate genes

description: PCHi-C interactions called with the CHiCAGO pipeline. Annotation for baited fragments is given in Additional file 4: Table S3. PIRs are called other ends (‘oe’). CHICAGO scores for activated (‘Total_CD4_Activated’) and non-activated (‘Total_CD4_NonActivated’) CD4+ T cells were considered called with confidence if above 5. We also conducted differential analysis, and the read counts input into that are given by the columns P1.non - P3.act, with the results summarised by their log fold change (logFC) and FDR. Bait-PIR pairs are shown only if the CHiCAGO score is ≥ 5 for at least one CD4+ T cell. (GZ 14529 kb)
DOI: 10.6084/m9.figshare.28053213
title: pwacsf

description: A modification of atomic centered symmetry functions (ACSF) for predicting birefringence of nonlinear optical crystalshttps://github.com/manualmouse/pwacsf
DOI: 10.6084/m9.figshare.28053213.v1
title: pwacsf

description: A modification of atomic centered symmetry functions (ACSF) for predicting birefringence of nonlinear optical crystalshttps://github.com/manualmouse/pwacsf
DOI: 10.6084/m9.figshare.c.3870736_d6
title: Additional file 6: Table S1. of Dual RNA-seq reveals no plastic transcriptional response of the coccidian parasite Eimeria falciformis to host immune defenses

description: GO terms enriched in Mm-clusters in Fig. 2b. (CSV 50 kb)
DOI: 10.6084/m9.figshare.c.3870709_d14
title: Additional file 8: Table S6b. of Chromosome contacts in activated T cells identify autoimmune disease candidate genes

description: Results of GWAS summary statistic fine-mapping. (GZ 2833 kb)
DOI: 10.6084/m9.figshare.c.3870736_d7.v1
title: Additional file 7: Table S2. of Dual RNA-seq reveals no plastic transcriptional response of the coccidian parasite Eimeria falciformis to host immune defenses

description: GO terms enriched in Ef-clusters in Fig. 4b. (CSV 18 kb)
DOI: 10.6084/m9.figshare.c.3870709_d15.v1
title: Additional file 9: Table S7a. of Chromosome contacts in activated T cells identify autoimmune disease candidate genes

description: Autoimmune disease COGS gene prioritisation. Overall COGS gene scores (COGS_Overall_Gene_Score) for each gene and autoimmune disease are shown together with the prioritised category and score associated with that category (COGS_Category_Gene_Score) (Fig. 3). The ‘analysis’ column describes whether the input data was GWAS or ImmunoChip (ICHIP) and whether summary statistic (SS) or GUESSFM (GF) fine-mapping was used. ‘diff.expr’ indicates whether the gene was not expressed (NA) or, if expressed, whether there was differential expression at the FDR  0.5 that are analysed in this paper. (GZ 37 kb)