cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.c.3627719_d2
title: Additional file 3: of Analysis of a spatial gene expression database for sea anemone Nematostella vectensis during early development

description: Subsequent expression domains of genes from an expression database. Pairs of subsequently available expression domains (third and fourth columns) are ordered in a Microsoft Excel spreadsheet table by their initial and final stages of development (first and second columns, respectively). The percentages (sixth column) are the relative frequencies (from the gene counts in the fifth column) for each pair of expression domains. A change from cylindrical expression pattern symmetry to biradial or bilateral symmetry is indicated in the seventh column with “symmetry break”. Changes of expression over major regions are indicated in the eighth column (appeared = expression is observed only in the second stage, major change = expression moved to another major region, minor change = expression in the second stage is limited to the same major region(s) as in the first stage, none = no expression is observed in both stages, vanished = expression is observed only in the first stage). (XLSX 21 kb)
DOI: 10.6084/m9.figshare.c.3627653_d12
title: Additional file 7: of LRR-RLK family from two Citrus species: genome-wide identification and evolutionary aspects

description: Pairwise list of orthologues LRR-XII subfamily members of C. clementina and C. sinensis. The colors represent the gene position in the same phylogenetic group (Fig.Â  2 ). * represents genes in clusters. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.c.3627698_d6
title: Additional file 5: of Transcriptomic responses of the basidiomycete yeast Sporobolomyces sp. to the mycotoxin patulin

description: Unprocessed Cuffdiff output of the RNAseq experiments performed for Sporobolomyces grown in the presence of 5 μg/ml of PAT. Where no Sporobolomyces gene models are indicated based on the previous JGI annotation (column C), it indicates a novel transcript identified following the transcriptomic analysis presented in this study. (XLSX 1622 kb)
DOI: 10.6084/m9.figshare.c.3627719_d3
title: Additional file 2: of Analysis of a spatial gene expression database for sea anemone Nematostella vectensis during early development

description: Observed expression domains of genes with in situ hybridizations stored for multiple stages of embryonic development. The pattern descriptions are ordered in a Microsoft Access database spreadsheet. Shorthand notations: base = base of tentacle; cells = individual cells; syphonoglyph = syphonoglyph side; tuft = apical tuft; wall = body wall. “N/A” means no hybridization image and description are currently provided for this developmental stage. “?” means an entry in the expression summary is provided without a corresponding hybridization image. “none” means no gene expression is observed. “band” means expression is observed in a ring between the oral and aboral ends. “full” means expression is observed in the complete tissue layer. “biradial” means two disconnected expression domains are observed on opposite sides (suggesting a biradially symmetric pattern). “octoradial?” means expression is observed in eight separate domains, possibly suggesting octoradial symmetry. “one side” means expression is present in one side of the embryo, but this side (either the syphonoglyph side or the non-syphonoglyph side) is not indicated. (ACCDB 5268 kb)
DOI: 10.6084/m9.figshare.c.3627653_d13
title: Additional file 8: of LRR-RLK family from two Citrus species: genome-wide identification and evolutionary aspects

description: Classification of kinases from C. clementina and C. sinensis LRR-RLK as RD, non-RD and ACF. The kinases classification was done according to the presence or absence of the Arg (R) in the conserved HRD motif. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.c.3627698_d8
title: Additional file 2: of Transcriptomic responses of the basidiomycete yeast Sporobolomyces sp. to the mycotoxin patulin

description: All new assembled Sporobolomyces sp. isoforms used for BLAST analyses. (TXT 34275Â kb)
DOI: 10.6084/m9.figshare.c.3627770_d2
title: Additional file 5: Table S4. of Genome-wide transcription start site profiling in biofilm-grown Burkholderia cenocepacia J2315

description: Promoter motifs in sequences upstream of TSS based on Improbizer [13] analysis. The last nt of all sequences is position +1 of the transcript, the TSS. Motifs with scores &gt;2 were regarded as positive matches. Motif sequences are indicated in capital letters. (XLSX 436ย�kb)
DOI: 10.6084/m9.figshare.c.3627770_d3
title: Additional file 2: Table S2. of Genome-wide transcription start site profiling in biofilm-grown Burkholderia cenocepacia J2315

description: Transcription start sites identified by differential RNA sequencing and automated annotation. (XLSX 489Â kb)
DOI: 10.6084/m9.figshare.c.3627779_d2
title: Additional file 4: of Bacterial small RNAs in the Genus Rickettsia

description: List of Rickettsia species and strains used throughout this work. The list has been categorized into the rickettsial groups with the RefSeq ID listed in the next column. (XLSX 46 kb)
DOI: 10.6084/m9.figshare.c.3627770_d4
title: Additional file 11: Table S10. of Genome-wide transcription start site profiling in biofilm-grown Burkholderia cenocepacia J2315

description: Genes with antisense transcripts. (XLSX 20Â kb)
DOI: 10.6084/m9.figshare.c.3627779_d3
title: Additional file 5: of Bacterial small RNAs in the Genus Rickettsia

description: List of primers used for amplification of R. prowazekii predicted sRNAs. (XLSX 49 kb)
DOI: 10.6084/m9.figshare.c.3627770_d5
title: Additional file 10: Table S9. of Genome-wide transcription start site profiling in biofilm-grown Burkholderia cenocepacia J2315

description: Number of mapped reads and RPKM values sense and antisense for all genes of the B. cenocepacia J2315 genome. (XLSX 2108Â kb)
DOI: 10.6084/m9.figshare.c.3627779_d4
title: Additional file 1: of Bacterial small RNAs in the Genus Rickettsia

description: List of predicted sRNAs via rickettsial species. (XLSX 595 kb)
DOI: 10.6084/m9.figshare.c.3627803_d1
title: MOESM2 of PCSK5 mutation in a patient with the VACTERL association

description: Additional file 2: Table S2. Summary of the mutations identified in the subjects and database.
DOI: 10.6084/m9.figshare.c.3627770_d11
title: Additional file 8: Table S7. of Genome-wide transcription start site profiling in biofilm-grown Burkholderia cenocepacia J2315

description: Genes belonging to enriched functionally related gene groups among leaderless transcripts and among transcripts with a 5′UTR longer than 150 nt. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.c.3627842_d2
title: Additional file 3: of RepeatAnalyzer: a tool for analysing and managing short-sequence repeat data

description: A table including all SSRs extracted from the S. pneumoniae samples. Each SSR is identified by a number. (XLS 28 kb)
DOI: 10.6084/m9.figshare.c.3627770_d12
title: Additional file 9: Table S8. of Genome-wide transcription start site profiling in biofilm-grown Burkholderia cenocepacia J2315

description: Amino acid sequences associated with orphan TSS or internal antisense TSS and with homologues in the non-redundant protein sequence database. (XLSX 18Â kb)
DOI: 10.6084/m9.figshare.c.3627827_d4
title: MOESM10 of Maintenance-energy requirements and robustness of Saccharomyces cerevisiae at aerobic near-zero specific growth rates

description: Additional file 10. See Additional file 8 caption.
DOI: 10.6084/m9.figshare.c.3627827_d6
title: MOESM11 of Maintenance-energy requirements and robustness of Saccharomyces cerevisiae at aerobic near-zero specific growth rates

description: Additional file 11. See Additional file 8 caption.
DOI: 10.6084/m9.figshare.c.3627827_d7
title: MOESM9 of Maintenance-energy requirements and robustness of Saccharomyces cerevisiae at aerobic near-zero specific growth rates

description: Additional file 9. See Additional file 8 caption.
DOI: 10.6084/m9.figshare.c.3627827_d8
title: MOESM14 of Maintenance-energy requirements and robustness of Saccharomyces cerevisiae at aerobic near-zero specific growth rates

description: Additional file 14. List of gene-groups described in literature that were mined for enrichment among differentially expressed genes identified in clusters 1 and 2 in Fig.Â 6.
DOI: 10.6084/m9.figshare.c.3627827_d9
title: MOESM12 of Maintenance-energy requirements and robustness of Saccharomyces cerevisiae at aerobic near-zero specific growth rates

description: Additional file 12. See Additional file 8 caption.
DOI: 10.6084/m9.figshare.c.3627827_d10
title: MOESM3 of Maintenance-energy requirements and robustness of Saccharomyces cerevisiae at aerobic near-zero specific growth rates

description: Additional file 3. Genes with significant growth-rate dependent gene expression in aerobic and anaerobic cultures between specific growth rates of 0.1 h-1 and below 0.001 h-1 (see Fig.Â 6).
DOI: 10.6084/m9.figshare.c.3627905_d1
title: Additional file 1: of Discrepancies between qualitative and quantitative evaluation of randomised controlled trial results: achieving clarity through mixed methods triangulation

description: Convergence coding matrix. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.c.3627881_d5
title: Additional file 3: Table S2. of A mutation in the low voltage-gated calcium channel CACNA1G alters the physiological properties of the channel, causing spinocerebellar ataxia

description: Candidate variants. (XLSX 35Â kb)
DOI: 10.6084/m9.figshare.c.3627923_d1
title: Additional file 1: of A hierarchical method to automatically encode Chinese diagnoses through semantic similarity estimation

description: Coding performance under all settings. The detailed precision, recall, and F-score of the proposed algorithm under two encoding methods, three semantic similarity measures, and various word similarity thresholds. (XLSX 53 kb)
DOI: 10.6084/m9.figshare.c.3627929_d1
title: Additional file 1: Table S1. of Central obesity associates with renal hyperfiltration in the non-diabetic general population: a cross-sectional study

description: Regression models for the alternative renal hyperfiltration definitions. Table S2. mGFR cut-off points for renal hyperfiltration in male and female subjects from the study cohort with average height, weight and age. Table S3. Odds ratio for RHFheight, with body weight added as an independent variable. Table S4. Multiple linear regression with measured GFR and continuous obesity variables. (XLSX 22Â kb)
DOI: 10.6084/m9.figshare.c.3627926_d3
title: Additional file 1: of The native microbiome of the nematode Caenorhabditis elegans: gateway to a new host-microbiome model

description: Data and results from statistical analysis of the native and experimental microbiome of C. elegans. This document contains a total of 23 tables as sheets of an Excel file, which summarize the material used and the results of the statistical analyses. Table S1-1. List of samples used for analysis of the Caenorhabditis native microbiome. Table S1-2. Summary of sample numbers used for analysis of the Caenorhabditis native microbiome. Table S1-3. Top 100 operational taxonomic units (OTUs) of the native microbiome of Caenorhabditis elegans. Table S1-4. Top 100 OTUs of the native microbiome of Caenorhabditis remanei. Table S1-5. Top 100 OTUs of the native microbiome of Caenorhabditis briggsae. Table S1-6. Statistical comparison of bacterial taxa abundances among sample types for the native Caenorhabditis microbiome. Table S1-7. Statistical evaluation of the factors for the canonical correspondence analysis of the native Caenorhabditis microbiome. Table S1-8. Statistical evaluation of the factors for the multivariate analysis of variance of the native Caenorhabditis microbiome. Table S1-9. List of bacterial and fungal isolates from natural C. elegans samples or corresponding substrates. Table S1-10. Overview of sample sizes for analysis of the experimental microbiome. Table S1-11. Overview of included and excluded samples in the analysis of the experimental microbiome. Table S1-12. Statistical comparison of bacterial taxa abundances among sample types for the experimental C. elegans microbiome. Table S1-13. Statistical evaluation of the factors for the canonical correspondence analysis of the experimental C. elegans microbiome. Table S1-14. Statistical evaluation of the factors for the multivariate analysis of variance of the experimental C. elegans microbiome. Table S1-15. Statistical comparison of bacterial taxa abundances among sample types for the second experiment with the experimental C. elegans microbiome. Table S1-16. Statistical evaluation of the factors for the canonical correspondence analysis of the second experiment with the experimental C. elegans microbiome. Table S1-17. Raw data for the bacterial colonization experiment. Table S1-18. Raw data for the population growth experiment with the experimental microbiome under different conditions. Table S1-19. Statistical analysis of C. elegans population growth on the experimental microbiome under different conditions. Table S1-20. Raw data for the population growth experiment with individual bacterial isolates. Table S1-21. Statistical analysis of C. elegans population growth on individual bacterial isolates. Table S1-22. Raw data for the analysis of bacterial effects on fungal growth. Table S1-23. General linear model analysis of antifungal effects of three Pseudomonas isolates. Table S1-24. Raw data for the bacterial effect on Drechmeria-induced worm killing. Table S1-25. Statistical analysis of an in vivo antifungal effect of Pseudomonas MYb11. (XLSX 116 kb)
DOI: 10.6084/m9.figshare.c.3627935_d2
title: Additional file 6: Table S2. of Ancient pathogen-driven adaptation triggers increased susceptibility to non-celiac wheat sensitivity in present-day European populations

description: SNPs showing exceptionally high differentiation at the genomic level. (XLSX 11Â kb)
DOI: 10.6084/m9.figshare.c.3627914_d6
title: Additional file 1: Table S1. of Loss of maternal ANNEXIN A10 via a 34-kb deleted-type copy number variation is associated with embryonic mortality in Japanese Black cattle

description: Detailed features of deleted-type CNVRs on autosomes in this study. Positions are based on the UMD3.1 assembly of the bovine genome. 1 Multiple: CNVR contained more than one CNV in the same animal. Table S2. CNVR_322 with genome-wide associations with embryonic mortality. Embryonic mortality was defined by cows that received a second round of AI at 18–29 days (D), 30–60 D, 61–90 D, 91–140 D, and 141 D–parturition after the 1st AI. Table S3. Detailed features of CNVR_322 and the surrounding SNPs. Positions are based on the UMD3.1 assembly of the bovine genome. Table S4. Primer information for identification of CNVR_322 breakpoint. Positions are based on the UMD3.1 assembly of the bovine genome. Table S5. Genotype frequencies of CNVR_322 in 6364 cows and 2391 steers. Table S6. P-value of association between CNVR_322 and meat traits in 1156 Japanese Black cattle. 1 YE (%) = 69.419 + 0.13REA + 0.667RT - 0.025CW - 0.896SFT. Table S7. Number of corpora lutea and implantation sites in Anxa10 -/- and Anxa10 +/+ female mice. Table S8. Primers and probes for CNVR_322. Positions are based on the UMD3.1 assembly of the bovine genome. Table S9. Primers and probes for basic transcriptional factor 3. Positions are based on the UMD3.1 assembly of the bovine genome. Table S10. Information for multiplex PCR primers for CNVR_322. Positions are based on the UMD3.1 assembly of the bovine genome. Table S11. Primer and probe for bovine ANXA10 and mouse Anxa10 expression. Table S12. Primer information for exons 1 to 2 and exons 1 to 7 of ANXA10. (XLSX 37 kb)
DOI: 10.6084/m9.figshare.c.3627935_d3
title: Additional file 7: Table S3. of Ancient pathogen-driven adaptation triggers increased susceptibility to non-celiac wheat sensitivity in present-day European populations

description: Haplogroup frequencies in the NCWS and reference samples. (XLSX 10Â kb)
DOI: 10.6084/m9.figshare.28027712
title: Data and script from Nicotinamide mononucleotide restores impaired metabolism, endothelial cell proliferation and angiogenesis in old sedentary male mice, published in iScience.

description: Aging is accompanied by a decline in neovascularisation potential and increased susceptibility to ischemic injury. Here, we confirm the age-related impaired neovascularization following ischemic leg injury and impaired angiogenesis. The age-related deficits in angiogenesis arose primarily from diminished EC proliferation capacity, but not migration or VEGF sensitivity. Aged EC harvested from the mouse skeletal muscle displayed a pro-angiogenic gene expression phenotype, along with considerable changes in metabolic genes. Metabolomics analysis and <sup>13</sup>C<sub> </sub>glucose tracing revealed impaired ATP production and blockade in glycolysis and TCA cycle in late passage HUVECs, which occurred at nicotinamide adenine dinucleotide (NAD⁺)-dependent steps, along with NAD<sup>+</sup> depletion. Supplementation with nicotinamide mononucleotide (NMN), a precursor of NAD⁺, enhances late-passage EC proliferation and sprouting angiogenesis from aged mice aortas. Taken together, our study illustrates the importance of NAD<sup>+</sup>-dependent metabolism in the maintenance of EC proliferation capacity with age, and the therapeutic potential of NAD precursors.
DOI: 10.6084/m9.figshare.c.3627989_d6
title: Additional file 6: of Prognostic impact of circulating tumor cell apoptosis and clusters in serial blood samples from patients with metastatic breast cancer in a prospective observational cohort

description: Supporting data. (XLS 73 kb)
DOI: 10.6084/m9.figshare.c.3628016_d2
title: Additional file 2 of Tools and pipelines for BioNano data: molecule assembly pipeline and FASTA super scaffolding tool

description: Cumulative length and number of single molecule maps per BNX file for T. castaneum data generated over time. Detailed metrics for molecule maps per BNX file (cumulative length and number of maps). Columns include cumulative length of molecule maps &gt; 150 kb, number of molecule maps &gt; 150 kb and date that BNX file was generated. (CSV 4.11 kb)
DOI: 10.6084/m9.figshare.c.3628016_d3
title: Additional file 1 of Tools and pipelines for BioNano data: molecule assembly pipeline and FASTA super scaffolding tool

description: Single molecule map stretch per scan in recent flowcells. Bases per pixel (bpp) is plotted for scans 1..n for each flowcell of mouse lemur molecules (purple). The first scan of each flowcell is indicated with a grey dashed line. The pre-adjusted molecule map stretch was determined by aligning molecule maps to the in silico maps. Data made available by P.A. Larsen, J. Rogers, A.D. Yoder and the Duke Lemur Center. (ZIP 55 kb)
DOI: 10.6084/m9.figshare.c.3628016_d4
title: Additional file 3 of Tools and pipelines for BioNano data: molecule assembly pipeline and FASTA super scaffolding tool

description: Single molecule map metrics and histograms from T. castaneum DNA. Detailed metrics for molecule maps including map N50, cumulative length and number of maps. Figures show histograms of per molecule map quality metrics including length, molecule map SNR and intensity, label count, label SNR and label intensity. Molecule maps are filter for minimum molecule lengths of 100, 150 or 180 kb. (ZIP 39.8 kb)
DOI: 10.6084/m9.figshare.c.3628025_d2
title: Additional file 4 of Interactive knowledge discovery and data mining on genomic expression data with numeric formal concept analysis

description: CSV file of GO terms’ information for gene enrichment from WebGeneKFCA. A sample print-out from WebGeneKFCA with the information about the GO terms and their p-values computed as described in http://www.biomedcentral.com/content/supplementary/10.1186/s12859-016-1234-z-S2.pdfAdditional file 2 for the bicluster with intent MalePS, Parental NoDox, Clone 1 NoDox and Clone 3 NoDox from Fig. 4. It can also be obtained on-line at https://webgenekfca.com/webgenekfca/kfcaresultses/9 . (CSV 24 kb)
DOI: 10.5066/p9zfzk0l
title: Geospatial datasets and hydraulic model for flood-inundation maps for the Cuyahoga River in and near the City of Independence, Ohio

description: Digital flood-inundation maps for a 9.9-mile reach of the Cuyahoga River near Independence, Ohio, were created by the U.S. Geological Survey (USGS) in cooperation with the Northeast Ohio Regional Sewer District Board of Trustees. Flood profiles were computed for the stream reach by means of a one-dimensional step-backwater model. The model was calibrated to the current (rating number 42) stage-discharge relation at the U.S. Geological Survey streamgage Cuyahoga River at Independence, Ohio (station number 04208000). The hydraulic model was then used to compute 13 total water-surface profiles for flood stages ranging from 14 to 26 ft. The overall range in stages are from “action stage” to above “major flood stage” as reported by the National Weather Service. The simulated water-surface profiles were then used in combination with a geographic information system digital elevation model derived from light detection and ranging data to delineate the areas flooded at each water level. The model produced by this study could be used to assess possible flood mitigation options and define flood hazard areas that could contribute to the protection of life and property. The availability of these maps, along with internet information regarding current stage from the USGS streamgage and forecasted high-flow stages from the National Weather Service, could provide emergency management personnel and residents with information that is critical for flood response activities such as evacuations and road closures, as well as for post-flood recovery efforts.
DOI: 10.6084/m9.figshare.c.3628073_d1
title: Additional file 1: of Integration of multi-omics data for prediction of phenotypic traits using random forest

description: List of the data sets used in this article. (XLSX 14739Â kb)
DOI: 10.6084/m9.figshare.c.3628088_d1
title: Additional file 4: of Molecular profile of dissociative drug ketamine in relation to its rapid antidepressant action

description: The lists of probe IDs and gene names obtained in the comparison between tissues based on two-way ANOVA results (at p  0.3 at least at one of the time points). Transcripts regulated by drug treatment in the hippocampus or striatum specifically and a list of genes altered in both tissues are presented. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.c.3628088_d3
title: Additional file 1: of Molecular profile of dissociative drug ketamine in relation to its rapid antidepressant action

description: Results from three-way ANOVA for 52 drug-responsive transcripts (FDR for drug factor  0.5 at least at one time point for any substance) are included. For each transcript a p-value and percent FDR for drug, time and tissue factors and all the interactions are presented. (XLSX 19 kb)
DOI: 10.6084/m9.figshare.c.3628088_d4
title: Additional file 6: of Molecular profile of dissociative drug ketamine in relation to its rapid antidepressant action

description: The table summarizing results of gene expression profiling of ketamine effects in the mouse striatum using RNA-seq (n = 4). In the first sheet 23 genes regulated by ketamine selected from the microarray profiling are listed with their chromosome location, fold change over control, p-value and FDR. The second sheet presents a list of the 15 selected genes with significant differences in expression between ketamine-treated and saline controls (p
DOI: 10.6084/m9.figshare.c.3628088_d5
title: Additional file 2: of Molecular profile of dissociative drug ketamine in relation to its rapid antidepressant action

description: The lists of transcript IDs and gene names corresponding to Venn diagrams for the hippocampus and striatum are presented in the first and second sheet respectively. Column names indicate which drugs alter the expression of listed transcripts. In case where only one substance name is listed, the altered expression level is drug-specific (at p  0.3 at least at one of the time points in the analyzed tissue). (XLSX 12 kb)