cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12769856.v2
title: 1. Dataset 1 Raw data from a survey mental health status and quality of life among Cambodian migrant workers in Thailand.xlsx

description: This study was approved by the Khon Kaen University (KKU) committee for research ethics in human research (Reference no. HE602361), Khon Kaen, Thailand.
DOI: 10.6084/m9.figshare.12769826.v1
title: Bone health in patients with asthma: A systematic review and meta-analysis

description: Form used to extract all the relevant data from each eligible article.
DOI: 10.6084/m9.figshare.12769778.v1
title: Data of transcripts,ORFs and phenology

description: 1. transcripts and ORFAntu_transcript_ORF.tar.gz # Antu sampleDongfeng1_transcript_ORF.tar.gz # Dongfeng1 sampleDongfeng2_transcript_ORF.tar.gz # Dongfeng2 sampleDunhua1_transcript_ORF.tar.gz # Dunhua1 sampleDunhua2_transcript_ORF.tar.gz # Dunhua2 sampleWangqing_transcript_ORF.tar.gz # Wangqing sample<br>Data of each sample includes three files, '*.fasta' (sequences of transcript), '*.cds' (ORFs of transcripts, nucleotide sequences), and '*.pep' (ORFs of transcripts, amino acids). For example, files of Wangqing sample are:Wangqing.ORF.cdsWangqing.ORF.pepWangqing.transcript.fasta<br>2. sequences (amino acids) of single-copy genes for constructing the phylogeny (phylogeny_data.tar.gz)105gene_align_16species.fa # concatenated amino acids of 105 genes105gene_align_16species.Gblock.fa # removed ambiguous sequences in '105gene_align_16species.fa' using Gblock method, this data was used for constructing phylogenetic tree<br>
DOI: 10.6084/m9.figshare.12769826.v2
title: Bone health in patients with asthma: A systematic review and meta-analysis

description: Form used to extract all the relevant data from each eligible article.
DOI: 10.6084/m9.figshare.12769826.v3
title: Bone health in patients with asthma: A systematic review and meta-analysis

description: Form used to extract all the relevant data from each eligible article.
DOI: 10.6084/m9.figshare.12768995
title: Additional file 1 of Multilayer approach reveals organizational principles disrupted in breast cancer co-expression networks

description: Additional file 1 Supplementary Figure 1: Distribution of each structural parameter in 1000 random GCNs conserving chromosomal connectivity of layer 0. The real values in layer 0 of healthy and Basal GCNs are added as vertical dotted lines. Supplementary Figure 2: Degree distribution of layers 95 to 100 of healthy and Basal GCNs. Supplementary Figure 3: Degree distribution of core nodes of layer 100 and a control group in layers 95 to 100 of healthy and Basal GCNs. Supplementary Figure 4: Cumulative conservation rates (ccr) in core nodes of Basal and healthy tissues considering layer 94 as the reference to compute ccr.
DOI: 10.6084/m9.figshare.12768995.v1
title: Additional file 1 of Multilayer approach reveals organizational principles disrupted in breast cancer co-expression networks

description: Additional file 1 Supplementary Figure 1: Distribution of each structural parameter in 1000 random GCNs conserving chromosomal connectivity of layer 0. The real values in layer 0 of healthy and Basal GCNs are added as vertical dotted lines. Supplementary Figure 2: Degree distribution of layers 95 to 100 of healthy and Basal GCNs. Supplementary Figure 3: Degree distribution of core nodes of layer 100 and a control group in layers 95 to 100 of healthy and Basal GCNs. Supplementary Figure 4: Cumulative conservation rates (ccr) in core nodes of Basal and healthy tissues considering layer 94 as the reference to compute ccr.
DOI: 10.6084/m9.figshare.12768983
title: Additional file 2 of Effect of phosphorus supply on root traits of two Brassica oleracea L. genotypes

description: Additional file 2 Table S1. Two-way analysis of variance (ANOVA) table with p values (those less than 5% are highlighted in bold) and means squares (in italics) for response variables in two Brassica oleracea accessions (C6 and F103) grown hydroponically for 2 weeks in solutions containing 0.025 mM P (Low P) or 0.25 mM P (High P); Zn, zinc. Table S2. Relative concentration of polar metabolites detected in root exudates of two Brassica oleracea accessions (C6 and F103) grown hydroponically for 2 weeks in solutions containing 0.025 mM P (Low P) or 0.25 mM P (High P). * indicates metabolites for which fold change could not be calculated, as it was not detected in one of the treatments in both accessions. Table S3. Two-way analysis of variance (ANOVA) table with p values (those less than 5% are highlighted in bold) and means squares (in italics) for main root length and ANOVA on Ranks for lateral root length along the main root length, divided into quartiles, in two Brassica oleracea accessions (C6 and F103) grown in the high throughput root phenotyping system with Low phosphorus (P) and High P treatments (four groups in total) for 2 weeks. Table S4. All differentially expressed P-responsive genes and their expression in FPKM, in roots of two Brassica oleracea accessions (C6 and F103) grown hydroponically for 2 weeks in solutions containing 0.025 mM P (Low P; LP) and 0.25 mM P (High P; HP). Differentially expressed genes were defined by comparing the gene expression in the Low P treatment with the gene expression in the High P treatment for each of the B. oleracea accession. Table S5. Gene ontology enrichment analysis for all differentially expressed genes in roots of two Brassica oleracea accessions (the C6 and the F103) grown in solutions containing 0.025 mM P (Low P) and 0.25 mM P (High P) for 2 weeks (n = 3 for each accession and each treatment). Bonferroni corrected p-values were used to determine significantly enriched categories and a corrected p-value of 0.05 was used as a cut-off. Table S6. P-responsive genes with orthologues in Arabidopsis thaliana. The table shows the gene expression of all P-responsive genes in the roots of two Brassica oleracea accessions (C6 and F103) grown hydroponically for 2 weeks in solutions containing 0.025 mM P (Low P) and 0.25 mM P (High P) which have A. thaliana ortholouges. Table S7. Shoot fresh weight, phosphorus (P) and zinc (Zn) concentrations and P efficiency ratio (calculated as Yieldlow / (Plow × Yieldlow) or Yieldhigh / (Phigh × Yieldhigh)) of the two Brassica oleracea accessions (C6 and F103) grown in a peat-based compost amended with Low P (5.25 mg L− 1) and High P (15.75 mg L− 1) used in the experiments. Data for fresh weight, shoot P concentration and P efficiency ratio are from [1] and shoot Zn concentrations are from [2]; DM, dry matter.
DOI: 10.6084/m9.figshare.12768983.v1
title: Additional file 2 of Effect of phosphorus supply on root traits of two Brassica oleracea L. genotypes

description: Additional file 2 Table S1. Two-way analysis of variance (ANOVA) table with p values (those less than 5% are highlighted in bold) and means squares (in italics) for response variables in two Brassica oleracea accessions (C6 and F103) grown hydroponically for 2 weeks in solutions containing 0.025 mM P (Low P) or 0.25 mM P (High P); Zn, zinc. Table S2. Relative concentration of polar metabolites detected in root exudates of two Brassica oleracea accessions (C6 and F103) grown hydroponically for 2 weeks in solutions containing 0.025 mM P (Low P) or 0.25 mM P (High P). * indicates metabolites for which fold change could not be calculated, as it was not detected in one of the treatments in both accessions. Table S3. Two-way analysis of variance (ANOVA) table with p values (those less than 5% are highlighted in bold) and means squares (in italics) for main root length and ANOVA on Ranks for lateral root length along the main root length, divided into quartiles, in two Brassica oleracea accessions (C6 and F103) grown in the high throughput root phenotyping system with Low phosphorus (P) and High P treatments (four groups in total) for 2 weeks. Table S4. All differentially expressed P-responsive genes and their expression in FPKM, in roots of two Brassica oleracea accessions (C6 and F103) grown hydroponically for 2 weeks in solutions containing 0.025 mM P (Low P; LP) and 0.25 mM P (High P; HP). Differentially expressed genes were defined by comparing the gene expression in the Low P treatment with the gene expression in the High P treatment for each of the B. oleracea accession. Table S5. Gene ontology enrichment analysis for all differentially expressed genes in roots of two Brassica oleracea accessions (the C6 and the F103) grown in solutions containing 0.025 mM P (Low P) and 0.25 mM P (High P) for 2 weeks (n = 3 for each accession and each treatment). Bonferroni corrected p-values were used to determine significantly enriched categories and a corrected p-value of 0.05 was used as a cut-off. Table S6. P-responsive genes with orthologues in Arabidopsis thaliana. The table shows the gene expression of all P-responsive genes in the roots of two Brassica oleracea accessions (C6 and F103) grown hydroponically for 2 weeks in solutions containing 0.025 mM P (Low P) and 0.25 mM P (High P) which have A. thaliana ortholouges. Table S7. Shoot fresh weight, phosphorus (P) and zinc (Zn) concentrations and P efficiency ratio (calculated as Yieldlow / (Plow × Yieldlow) or Yieldhigh / (Phigh × Yieldhigh)) of the two Brassica oleracea accessions (C6 and F103) grown in a peat-based compost amended with Low P (5.25 mg L− 1) and High P (15.75 mg L− 1) used in the experiments. Data for fresh weight, shoot P concentration and P efficiency ratio are from [1] and shoot Zn concentrations are from [2]; DM, dry matter.
DOI: 10.6084/m9.figshare.12768964
title: Additional file 18 of Comparative transcriptome analyses reveal different mechanism of high- and low-tillering genotypes controlling tiller growth in orchardgrass (Dactylis glomerata L.)

description: Additional file 18 : Supplemental Table 8 The expression of key genes regulating tillering
DOI: 10.6084/m9.figshare.12768961
title: Additional file 17 of Comparative transcriptome analyses reveal different mechanism of high- and low-tillering genotypes controlling tiller growth in orchardgrass (Dactylis glomerata L.)

description: Additional file 17 : Supplemental Table 7 The detail information of KEGG in A(h)_L vs D(l)_L
DOI: 10.6084/m9.figshare.12768958
title: Additional file 16 of Comparative transcriptome analyses reveal different mechanism of high- and low-tillering genotypes controlling tiller growth in orchardgrass (Dactylis glomerata L.)

description: Additional file 16 : Supplemental Table 6 The detail information of KEGG in A(h)_S vs D(l)_S
DOI: 10.6084/m9.figshare.12768961.v1
title: Additional file 17 of Comparative transcriptome analyses reveal different mechanism of high- and low-tillering genotypes controlling tiller growth in orchardgrass (Dactylis glomerata L.)

description: Additional file 17 : Supplemental Table 7 The detail information of KEGG in A(h)_L vs D(l)_L
DOI: 10.6084/m9.figshare.12768964.v1
title: Additional file 18 of Comparative transcriptome analyses reveal different mechanism of high- and low-tillering genotypes controlling tiller growth in orchardgrass (Dactylis glomerata L.)

description: Additional file 18 : Supplemental Table 8 The expression of key genes regulating tillering
DOI: 10.6084/m9.figshare.12768955
title: Additional file 15 of Comparative transcriptome analyses reveal different mechanism of high- and low-tillering genotypes controlling tiller growth in orchardgrass (Dactylis glomerata L.)

description: Additional file 15 : Supplemental Table 5 Percent of genome regions
DOI: 10.6084/m9.figshare.12768958.v1
title: Additional file 16 of Comparative transcriptome analyses reveal different mechanism of high- and low-tillering genotypes controlling tiller growth in orchardgrass (Dactylis glomerata L.)

description: Additional file 16 : Supplemental Table 6 The detail information of KEGG in A(h)_S vs D(l)_S
DOI: 10.6084/m9.figshare.12768943
title: Additional file 11 of Comparative transcriptome analyses reveal different mechanism of high- and low-tillering genotypes controlling tiller growth in orchardgrass (Dactylis glomerata L.)

description: Additional file 11 : Supplemental Table 1 The data of initial field selection
DOI: 10.6084/m9.figshare.12768949
title: Additional file 13 of Comparative transcriptome analyses reveal different mechanism of high- and low-tillering genotypes controlling tiller growth in orchardgrass (Dactylis glomerata L.)

description: Additional file 13 : Supplemental Table 3 RNA-seq statistics
DOI: 10.6084/m9.figshare.12768949.v1
title: Additional file 13 of Comparative transcriptome analyses reveal different mechanism of high- and low-tillering genotypes controlling tiller growth in orchardgrass (Dactylis glomerata L.)

description: Additional file 13 : Supplemental Table 3 RNA-seq statistics
DOI: 10.6084/m9.figshare.12768952
title: Additional file 14 of Comparative transcriptome analyses reveal different mechanism of high- and low-tillering genotypes controlling tiller growth in orchardgrass (Dactylis glomerata L.)

description: Additional file 14 : Supplemental Table 4 Statistics of annotation analysis of unigenes
DOI: 10.6084/m9.figshare.12768955.v1
title: Additional file 15 of Comparative transcriptome analyses reveal different mechanism of high- and low-tillering genotypes controlling tiller growth in orchardgrass (Dactylis glomerata L.)

description: Additional file 15 : Supplemental Table 5 Percent of genome regions
DOI: 10.6084/m9.figshare.12768943.v1
title: Additional file 11 of Comparative transcriptome analyses reveal different mechanism of high- and low-tillering genotypes controlling tiller growth in orchardgrass (Dactylis glomerata L.)

description: Additional file 11 : Supplemental Table 1 The data of initial field selection
DOI: 10.6084/m9.figshare.12768946
title: Additional file 12 of Comparative transcriptome analyses reveal different mechanism of high- and low-tillering genotypes controlling tiller growth in orchardgrass (Dactylis glomerata L.)

description: Additional file 12 : Supplemental Table 2 The primers information for qRT-PCR
DOI: 10.6084/m9.figshare.12768952.v1
title: Additional file 14 of Comparative transcriptome analyses reveal different mechanism of high- and low-tillering genotypes controlling tiller growth in orchardgrass (Dactylis glomerata L.)

description: Additional file 14 : Supplemental Table 4 Statistics of annotation analysis of unigenes
DOI: 10.6084/m9.figshare.12768946.v1
title: Additional file 12 of Comparative transcriptome analyses reveal different mechanism of high- and low-tillering genotypes controlling tiller growth in orchardgrass (Dactylis glomerata L.)

description: Additional file 12 : Supplemental Table 2 The primers information for qRT-PCR
DOI: 10.6084/m9.figshare.12768919
title: Additional file 6 of Genetic Dissection of Seed Dormancy in Rice (Oryza sativa L.) by Using Two Mapping Populations Derived from Common Parents

description: Additional file 6: Table S4. Bin map information of Nipponbare × 9311 BILs.
DOI: 10.6084/m9.figshare.12768916
title: Additional file 5 of Genetic Dissection of Seed Dormancy in Rice (Oryza sativa L.) by Using Two Mapping Populations Derived from Common Parents

description: Additional file 5: Table S3. Bin map information of Nipponbare × 9311 CSSLs.
DOI: 10.6084/m9.figshare.12768919.v1
title: Additional file 6 of Genetic Dissection of Seed Dormancy in Rice (Oryza sativa L.) by Using Two Mapping Populations Derived from Common Parents

description: Additional file 6: Table S4. Bin map information of Nipponbare × 9311 BILs.
DOI: 10.6084/m9.figshare.12768916.v1
title: Additional file 5 of Genetic Dissection of Seed Dormancy in Rice (Oryza sativa L.) by Using Two Mapping Populations Derived from Common Parents

description: Additional file 5: Table S3. Bin map information of Nipponbare × 9311 CSSLs.
DOI: 10.6084/m9.figshare.12768901
title: Additional file 11 of Genetic Dissection of Seed Dormancy in Rice (Oryza sativa L.) by Using Two Mapping Populations Derived from Common Parents

description: Additional file 11: Table S8. The putative candidate genes for four major loci: qSD3.1, qSD3.2, qSD5.2 and qSD11.2.
DOI: 10.6084/m9.figshare.12768901.v1
title: Additional file 11 of Genetic Dissection of Seed Dormancy in Rice (Oryza sativa L.) by Using Two Mapping Populations Derived from Common Parents

description: Additional file 11: Table S8. The putative candidate genes for four major loci: qSD3.1, qSD3.2, qSD5.2 and qSD11.2.
DOI: 10.6084/m9.figshare.12768872
title: Additional file 2 of Loss of AA13 LPMOs impairs degradation of resistant starch and reduces the growth of Aspergillus nidulans

description: Additional file 2: Label-free Proteomics.
DOI: 10.6084/m9.figshare.12768872.v1
title: Additional file 2 of Loss of AA13 LPMOs impairs degradation of resistant starch and reduces the growth of Aspergillus nidulans

description: Additional file 2: Label-free Proteomics.
DOI: 10.6084/m9.figshare.12768856
title: Additional file 7 of Comparative gene expression profiling between optic nerve and spinal cord injury in Xenopus laevis reveals a core set of genes inherent in successful regeneration of vertebrate central nervous system axons

description: Additional file 7. KEGG pathway analysis of the DESR gene lists revealed that 60% (69/115) of the Adipocytokine signaling pathway genes were differentially expressed in at least one tissue at one time point (p
DOI: 10.6084/m9.figshare.12768847
title: Additional file 4 of Comparative gene expression profiling between optic nerve and spinal cord injury in Xenopus laevis reveals a core set of genes inherent in successful regeneration of vertebrate central nervous system axons

description: Additional file 4. Manually Curated DESR Gene Data (Cuffdiff2). DESR gene lists were manually curated and parsed into eleven functional categories using a literature search. Tabs: 3 Day DESR, 11 Day 1 WK DESR, 3 WK DESR: Manually curated spreadsheets for each time point, 3 days, 11 days/1 week, and 3 weeks, respectively, providing Cuffdiff2 data for each gene for tadpole SCI hindbrain (even numbered rows) and juvenile frog ONC (odd numbered rows). Column A, surgical condition; Columns B - N, relevant Cuffdiff2 data for each gene under each surgical condition (see Additional_File1_Differential_Expression_Analysis_by_Cuffdif.xlsm for abbreviations and column annotations). Gene symbols (Column B) in green and red were up-regulated and down-regulated, respectively, in successfully regenerative tissues relative to controls. Column O, primary functional category (NA, gene has not been assigned a human ortholog); Column P, secondary functional category, if relevant; Column Q, Manually curated notes, providing additional information on the expression behaviors of the other homeologs of this gene (even numbered rows), and a statement on the function of the gene that lead to its being placed in a particular functional category, followed by the literature reference supporting it.
DOI: 10.6084/m9.figshare.12768856.v1
title: Additional file 7 of Comparative gene expression profiling between optic nerve and spinal cord injury in Xenopus laevis reveals a core set of genes inherent in successful regeneration of vertebrate central nervous system axons

description: Additional file 7. KEGG pathway analysis of the DESR gene lists revealed that 60% (69/115) of the Adipocytokine signaling pathway genes were differentially expressed in at least one tissue at one time point (p
DOI: 10.6084/m9.figshare.12768841
title: Additional file 2 of Comparative gene expression profiling between optic nerve and spinal cord injury in Xenopus laevis reveals a core set of genes inherent in successful regeneration of vertebrate central nervous system axons

description: Additional file 2. DESeq2 differential expression data. Tabs are for each injury condition and time point vs. their relevant controls (N = 3 biological replicates, each). Tabs PW1–3) Tadpole spinal cord injury (SCI) hindbrain vs. age-matched, unoperated control hindbrain at 3 days, 1 week, and 3 weeks, respectively; PW4–6) Juvenile frog SCI hindbrain at 3 days, 1 week, and 3 weeks vs. unoperated control hindbrain; PW7–9) juvenile frog optic nerve crush (ONC) eye vs. the contralateral unoperated eye at 3 days, 11 days, and 3 weeks, respectively. Columns: A - Gene Name; B, baseMean - mean counts of all samples, normalized for sequencing depth. It does not take into account gene length and is used for estimating the dispersion of a gene; C, log2FoldChange - log2(control/experimental); in this analysis, negative values represent injury induced increases relative to control); D, lfcSE - Standard Error of the log2 fold change; E, stat - log2FoldChange/lfcSE; F, pvalue - the probability of the null hypothesis for an individual gene (i.e., variance among replicates = variance between conditions); G, padj - false discovery rate-adjusted (FDR) p-value.
DOI: 10.6084/m9.figshare.12768847.v1
title: Additional file 4 of Comparative gene expression profiling between optic nerve and spinal cord injury in Xenopus laevis reveals a core set of genes inherent in successful regeneration of vertebrate central nervous system axons

description: Additional file 4. Manually Curated DESR Gene Data (Cuffdiff2). DESR gene lists were manually curated and parsed into eleven functional categories using a literature search. Tabs: 3 Day DESR, 11 Day 1 WK DESR, 3 WK DESR: Manually curated spreadsheets for each time point, 3 days, 11 days/1 week, and 3 weeks, respectively, providing Cuffdiff2 data for each gene for tadpole SCI hindbrain (even numbered rows) and juvenile frog ONC (odd numbered rows). Column A, surgical condition; Columns B - N, relevant Cuffdiff2 data for each gene under each surgical condition (see Additional_File1_Differential_Expression_Analysis_by_Cuffdif.xlsm for abbreviations and column annotations). Gene symbols (Column B) in green and red were up-regulated and down-regulated, respectively, in successfully regenerative tissues relative to controls. Column O, primary functional category (NA, gene has not been assigned a human ortholog); Column P, secondary functional category, if relevant; Column Q, Manually curated notes, providing additional information on the expression behaviors of the other homeologs of this gene (even numbered rows), and a statement on the function of the gene that lead to its being placed in a particular functional category, followed by the literature reference supporting it.
DOI: 10.6084/m9.figshare.12768842
title: Additional file 3 of Tuberculosis active case-finding interventions and approaches for prisoners in sub-Saharan Africa: a systematic scoping review

description: Additional file 3: Supplementary file 3: Quality appraisal tool
DOI: 10.6084/m9.figshare.12768841.v1
title: Additional file 2 of Comparative gene expression profiling between optic nerve and spinal cord injury in Xenopus laevis reveals a core set of genes inherent in successful regeneration of vertebrate central nervous system axons

description: Additional file 2. DESeq2 differential expression data. Tabs are for each injury condition and time point vs. their relevant controls (N = 3 biological replicates, each). Tabs PW1–3) Tadpole spinal cord injury (SCI) hindbrain vs. age-matched, unoperated control hindbrain at 3 days, 1 week, and 3 weeks, respectively; PW4–6) Juvenile frog SCI hindbrain at 3 days, 1 week, and 3 weeks vs. unoperated control hindbrain; PW7–9) juvenile frog optic nerve crush (ONC) eye vs. the contralateral unoperated eye at 3 days, 11 days, and 3 weeks, respectively. Columns: A - Gene Name; B, baseMean - mean counts of all samples, normalized for sequencing depth. It does not take into account gene length and is used for estimating the dispersion of a gene; C, log2FoldChange - log2(control/experimental); in this analysis, negative values represent injury induced increases relative to control); D, lfcSE - Standard Error of the log2 fold change; E, stat - log2FoldChange/lfcSE; F, pvalue - the probability of the null hypothesis for an individual gene (i.e., variance among replicates = variance between conditions); G, padj - false discovery rate-adjusted (FDR) p-value.