cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.c.3741110_d16.v1
title: Additional file 2: Table S1. of Defining the transcriptomic landscape of the developing enteric nervous system and its cellular environment

description: List of differentially expressed genes between the two cell populations of the intestine. The list in the first sheet represents all the genes filtered based on their adjusted p-value (cutoff is 0.01) while the second sheet shows the genes further filtered based on log2foldchange (1.5). Sheets 3 and 4 show the separated gene lists from the second sheet into upregulated genes in the neuronal cells and downregulated genes in the neuronal cell population, respectively. The scatter plot and the heat map in the main paper (Fig.Â 3c and d) were generated using the data provided in this table. (XLSX 3109 kb)
DOI: 10.6084/m9.figshare.c.3742286_d1
title: Additional file 1: of goSTAG: gene ontology subtrees to tag and annotate genes within a set

description: GMT file containing the gene symbols from the cancer therapeutics gene expression DEGs. (GMT 114Â kb)
DOI: 10.6084/m9.figshare.c.3742331_d2
title: Additional file 2: of Higher neonatal growth rate and body condition score at 7 months are predictive factors of obesity in adult female Beagle dogs

description: Averaged AUCs at 7 months of age during a 150 min postprandial kinetic. Values are expressed as mean (standard deviation). Their comparison was assessed by a linear regression model analysis. I:G correspond to the ratio between plasma insulin and glucose. Letters a and b represent significant differences (p
DOI: 10.15468/dl.a32pvw
title: Occurrence Download

description: A dataset containing 12 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Specimen)",
 "Continent is Asia",
 "Country is one of (India, Nepal)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "IucnRedListCategory is NE",
 "TaxonKey is Saussurea obvallata (DC.) Edgew., 1846"
 ]
}

 The dataset includes 12 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038663-241126133413365/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.3743108_d2.v1
title: Additional file 2: of Natural selection drove metabolic specialization of the chromatophore in Paulinella chromatophora

description: Metabolic model of the chromatophore (iCV265). (XLSX 121 kb)
DOI: 10.6084/m9.figshare.c.3743108_d2
title: Additional file 2: of Natural selection drove metabolic specialization of the chromatophore in Paulinella chromatophora

description: Metabolic model of the chromatophore (iCV265). (XLSX 121 kb)
DOI: 10.5281/zenodo.14512426
title: Additional_data
DOI: 10.5281/zenodo.14512427
title: Additional_data
DOI: 10.6084/m9.figshare.c.3743357_d1.v1
title: Additional file 1: Table S1. of Poplar stem transcriptome is massively remodelled in response to single or repeated mechanical stimuli

description: List of genes differentially expressed probset in response to one or two bendings, as identified by microarray analysis. Affymetrix 61 k poplar microarrays (composed of 61,251 probesets) were used to detect differences in expression. Four comparisons between bent plants (b) vs. control plants (c) at different time points after the bending were realized: 0.5 h PB (1b0.5 h vs. C0.5 h), 2 h PB (1b2h vs. C2h), 24 h PB (1b24h vs. C24h) and 72 h PB (1b72h vs. C72h). To understand the effect of a second bending, we ran two comparisons (i) 0.5 h after the 2nd bending (with a time-lapse of 24 h between the two bendings) compared to 24 h after the 1st bending (2b0.5 h vs. 1b24h) and (ii) 0.5 h after the 2nd bending compared to 0.5 h after the 1st bending (2b0.5 h vs. 1b0.5 h). Expression was considered significantly different if the P-value from the Benjamini–Hochberg test (BH P-value) is below 0.05. (CSV 694 kb)
DOI: 10.6084/m9.figshare.c.3743303_d5.v1
title: Additional file 4: Table S4. of Genome-wide DNA methylation measurements in prostate tissues uncovers novel prostate cancer diagnostic biomarkers and transcription factor binding patterns

description: Coefficients, standard errors and performance statistics for the top diagnostic model and top hypermethylated CpG model. (XLSX 46Â kb)
DOI: 10.6084/m9.figshare.c.3743303_d5
title: Additional file 4: Table S4. of Genome-wide DNA methylation measurements in prostate tissues uncovers novel prostate cancer diagnostic biomarkers and transcription factor binding patterns

description: Coefficients, standard errors and performance statistics for the top diagnostic model and top hypermethylated CpG model. (XLSX 46Â kb)
DOI: 10.6084/m9.figshare.c.3743357_d1
title: Additional file 1: Table S1. of Poplar stem transcriptome is massively remodelled in response to single or repeated mechanical stimuli

description: List of genes differentially expressed probset in response to one or two bendings, as identified by microarray analysis. Affymetrix 61 k poplar microarrays (composed of 61,251 probesets) were used to detect differences in expression. Four comparisons between bent plants (b) vs. control plants (c) at different time points after the bending were realized: 0.5 h PB (1b0.5 h vs. C0.5 h), 2 h PB (1b2h vs. C2h), 24 h PB (1b24h vs. C24h) and 72 h PB (1b72h vs. C72h). To understand the effect of a second bending, we ran two comparisons (i) 0.5 h after the 2nd bending (with a time-lapse of 24 h between the two bendings) compared to 24 h after the 1st bending (2b0.5 h vs. 1b24h) and (ii) 0.5 h after the 2nd bending compared to 0.5 h after the 1st bending (2b0.5 h vs. 1b0.5 h). Expression was considered significantly different if the P-value from the Benjamini–Hochberg test (BH P-value) is below 0.05. (CSV 694 kb)
DOI: 10.5278/dcb02ffe-3948-435b-9dba-4db33567175d
title: Data til A stochastich approach to estimate distribution grid state with confidence regions
DOI: 10.6084/m9.figshare.c.3743357_d2.v1
title: Additional file 2: Table S2. of Poplar stem transcriptome is massively remodelled in response to single or repeated mechanical stimuli

description: List of the 10 most up- or down-regulated genes at each time-point. *gene_ID corresponds to the gene model found in Phytozome database [55] for poplar or Arabidopsis (Ath). The log2 expression fold-change is shown for the different time-points: 0.5 h (exp 0.5 h), 2 h (exp 2 h), 24 h (exp 24 h) and 72 h (exp 72 h). (XLSX 15 kb)
DOI: 10.6084/m9.figshare.c.3743357_d3.v1
title: Additional file 3: Table S3. of Poplar stem transcriptome is massively remodelled in response to single or repeated mechanical stimuli

description: Gene Ontology enrichment analysis applied to the clusters. The GO enrichment was performed using the Amigo (1.8) term enrichment tool [58]. The list of A. thaliana orthologs of each cluster was used, and the TAIR database was chosen as a background. The maximum P-value for the threshold was 0.01, except for clusters marked * and ** for which maximum P-value was set at 0.05 and 0.1, respectively. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.c.3743357_d2
title: Additional file 2: Table S2. of Poplar stem transcriptome is massively remodelled in response to single or repeated mechanical stimuli

description: List of the 10 most up- or down-regulated genes at each time-point. *gene_ID corresponds to the gene model found in Phytozome database [55] for poplar or Arabidopsis (Ath). The log2 expression fold-change is shown for the different time-points: 0.5 h (exp 0.5 h), 2 h (exp 2 h), 24 h (exp 24 h) and 72 h (exp 72 h). (XLSX 15 kb)
DOI: 10.6084/m9.figshare.c.3744245_d1.v1
title: Additional file 1: Table S1. of Detection of Histone H3 mutations in cerebrospinal fluid-derived tumor DNA from children with diffuse midline glioma

description: List of Histone H3 Primer Sequences. The sequences and properties of primers used in this study are described. Melting temperature (TM) was calculated at 0.4 ÎźM.fdg. (XLS 22 kb)
DOI: 10.6084/m9.figshare.c.3744245_d1
title: Additional file 1: Table S1. of Detection of Histone H3 mutations in cerebrospinal fluid-derived tumor DNA from children with diffuse midline glioma

description: List of Histone H3 Primer Sequences. The sequences and properties of primers used in this study are described. Melting temperature (TM) was calculated at 0.4 ÎźM.fdg. (XLS 22 kb)
DOI: 10.6084/m9.figshare.c.3745220_d8.v1
title: Additional file 8: Table S7. of Reduced changes in protein compared to mRNA levels across non-proliferating tissues

description: MMT Enrichments and Domain Specificity. Emerging terms in the enrichment analysis of the MMT dataset, and scoring of their specificity, to either the protein or the mRNA domain. (XLSX 1597Â kb)
DOI: 10.6084/m9.figshare.c.3745220_d8
title: Additional file 8: Table S7. of Reduced changes in protein compared to mRNA levels across non-proliferating tissues

description: MMT Enrichments and Domain Specificity. Emerging terms in the enrichment analysis of the MMT dataset, and scoring of their specificity, to either the protein or the mRNA domain. (XLSX 1597Â kb)
DOI: 10.6084/m9.figshare.c.3745220_d9.v1
title: Additional file 9: Table S8. of Reduced changes in protein compared to mRNA levels across non-proliferating tissues

description: Post-Transcriptional Repression. Statistics of the post-transcriptionally repressed genes analysis, and emerging terms in their enrichment analysis. (XLSX 63Â kb)
DOI: 10.6084/m9.figshare.c.3745220_d9
title: Additional file 9: Table S8. of Reduced changes in protein compared to mRNA levels across non-proliferating tissues

description: Post-Transcriptional Repression. Statistics of the post-transcriptionally repressed genes analysis, and emerging terms in their enrichment analysis. (XLSX 63Â kb)
DOI: 10.6084/m9.figshare.c.3745292_d1.v1
title: Additional file 1: of SSER: Species specific essential reactions database

description: All models and reactions in SSER. (RAR 3930Â kb)
DOI: 10.6084/m9.figshare.c.3745331_d2.v1
title: Additional file 2: of On the association analysis of CNV data: a fast and robust family-based association method

description: Simulated data with 2000 replicates for different values of Î˛ under WSC, when there are three copy number clusters. (ZIP 138685Â kb)
DOI: 10.6084/m9.figshare.c.3745313_d4
title: Additional file 4: of Intersect-then-combine approach: improving the performance of somatic variant calling in whole exome sequencing data using multiple aligners and callers

description: VEP annotation for mutations called using the ITC approach and not by the second best (Mutect2/Novocraft) in AB551 breast cancer sample. (XLSX 143Â kb)
DOI: 10.6084/m9.figshare.c.3745331_d2
title: Additional file 2: of On the association analysis of CNV data: a fast and robust family-based association method

description: Simulated data with 2000 replicates for different values of Î˛ under WSC, when there are three copy number clusters. (ZIP 138685Â kb)
DOI: 10.6084/m9.figshare.c.3745343_d2.v1
title: Additional file 2: of Operations research in global health: a scoping review with a focus on the themes of health equity and impact

description: Database of references included in review. Description: An Excel database of the 1099 references included in the global overview of this review paper, including columns for Authors, Title, Journal and/or Conference and/or Book Title, Year, Volume, Pages, Conference location and/or Place Published, and Abstract. (XLSX 893 kb)
DOI: 10.6084/m9.figshare.c.3745376_d9.v1
title: Additional file 3: Figure S1. of Distribution, genetic diversity and potential spatiotemporal scale of alien gene flow in crop wild relatives of rice (Oryza spp.) in Colombia

description: Hierarchical cluster dendrograms based on the Bruvo and Nei (the latter for O. glumaepatula only) genetic distances and the Unweighted Pair Group Method with Arithmetic Mean. To types of p-values are provided to quantify branch support: the AU (Approximately Unbiased) p-value and BP (Bootstrap Probability) value. According to Suzuki and Shimodaira (2015) “AU p-value, which is computed by multiscale bootstrap resampling, is a better approximation to unbiased p-value than BP value computed by normal bootstrap resampling”. Clusters with branch support &gt;95% are highlighted in boxes with different colors. (ZIP 572 kb)
DOI: 10.6084/m9.figshare.c.3745376_d9
title: Additional file 3: Figure S1. of Distribution, genetic diversity and potential spatiotemporal scale of alien gene flow in crop wild relatives of rice (Oryza spp.) in Colombia

description: Hierarchical cluster dendrograms based on the Bruvo and Nei (the latter for O. glumaepatula only) genetic distances and the Unweighted Pair Group Method with Arithmetic Mean. To types of p-values are provided to quantify branch support: the AU (Approximately Unbiased) p-value and BP (Bootstrap Probability) value. According to Suzuki and Shimodaira (2015) “AU p-value, which is computed by multiscale bootstrap resampling, is a better approximation to unbiased p-value than BP value computed by normal bootstrap resampling”. Clusters with branch support &gt;95% are highlighted in boxes with different colors. (ZIP 572 kb)
DOI: 10.6084/m9.figshare.c.3745400_d4.v1
title: Additional file 4: Figure S4. of Comparison of the mechanical properties of different skin sites for auricular and nasal reconstruction

description: Histological analysis of the different skin sites by H&E, Massons Trichome and Millers Elastin staining. [A] H&E [B]. Massons Trichome [C]. Millers and Elastin. Key; FH; Forehead, SN; Submandibular Neck, TP; Temporoparietal Neck, PM; Postauricular Mastoid, FA; Forearm. Scale bar = 50 μm. (ZIP 2133 kb)
DOI: 10.6084/m9.figshare.c.3746420_d1
title: Additional file 1 of Generalized 3D fragmentation index derived from lidar point clouds

description: Code for full reproducibility. This is a snapshot of the repository [58] provided for full reproducibility as a 7z archive file. It contains a Dockerfile, so by using Docker it can be turned into runtime environment for processing the data and creating the figures and plots. The detailed instructions are in the readme file. The code for the newly developed modules is included. (7Z 10,850 kb)
DOI: 10.6084/m9.figshare.c.3746426_d2.v1
title: Additional file 2: of AnkPlex: algorithmic structure for refinement of near-native ankyrin-protein docking

description: Supplementary datasets used in this study. (XLS 13646 kb)
DOI: 10.6084/m9.figshare.c.3746426_d2
title: Additional file 2: of AnkPlex: algorithmic structure for refinement of near-native ankyrin-protein docking

description: Supplementary datasets used in this study. (XLS 13646 kb)
DOI: 10.6084/m9.figshare.c.3746444_d1.v1
title: Additional file 1: of Insight into human pubertal growth by applying the QEPS growth model

description: The first two sections explain pubertal variables of the QEPS-model in more detail in texts, figures and tables for the general pubertal growth, section A.1:1 and the individual variation in pubertal growth, section A.1:2, and the PQ -ratio in A1:3. The construction of the mathematical selection criterion, MathSelect, is described in section A.2:1, in texts, figures and tables, and extreme possible values of the nine input variables corresponding with MathSelect values are computed in section A.2:2. (ZIP 4423Â kb)
DOI: 10.6084/m9.figshare.c.3747551_d1
title: Additional file 1: of Association between Fcγ receptor IIA, IIIA and IIIB genetic polymorphisms and susceptibility to severe malaria anemia in children in western Kenya

description: These are details of the raw data for the study participants (N=274) used in the analyses of results presented in the current paper. (XLS 222 kb)
DOI: 10.48493/e355-n288
title: Evidence for the catalytic role of humans in the assembly and evolution of European Late Pleistocene scavenger guilds
DOI: 10.15468/dl.z287uc
title: Occurrence Download

description: A dataset containing 21096 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Solenopsis invicta Buren, 1972"
 ]
}

 The dataset includes 21096 records from 54 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038664-241126133413365/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.3747611_d5.v1
title: Additional file 5: Table S5A. of Pan genome and CRISPR analyses of the bacterial fish pathogen Moritella viscosa

description: M. viscosa spacers matching prophage-like elements. Table S5B. M. viscosa spacers matching plasmid-like elements. (XLSX 18 kb)
DOI: 10.15468/dl.puafdw
title: Occurrence Download

description: A dataset containing 1407 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((3.08928 44.15669,3.25056 44.15669,3.25056 44.30032,3.08928 44.30032,3.08928 44.15669))",
 "HasCoordinate is true",
 "IucnRedListCategory is one of (NT, VU, EN, CR, DD)",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 1407 records from 82 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038665-241126133413365/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.3747611_d5
title: Additional file 5: Table S5A. of Pan genome and CRISPR analyses of the bacterial fish pathogen Moritella viscosa

description: M. viscosa spacers matching prophage-like elements. Table S5B. M. viscosa spacers matching plasmid-like elements. (XLSX 18 kb)
DOI: 10.6084/m9.figshare.c.3747635_d1.v1
title: Additional file 10: of Integrative modelling of TIR domain-containing adaptor molecule inducing interferon-Î˛ (TRIF) provides insights into its autoinhibited state

description: Figure S6a. Profile of hydrogen bonds between Asp 21 on the N-terminal domain and Gln 443 on the TIR domain of TRIF along the MD trajectory. Figure S6b. Hydrogen bonds between Asp 21 and Leu 442 along the trajectory. Figure S6c. Hydrogen bonds between Lys 22 and Gln 471 over the MD trajectory. Figure S6d. Hydrogen bonds between Gln 20 and BB loop residue Glu 429. (ZIP 4528Â kb)
DOI: 10.6084/m9.figshare.c.3747641_d3
title: Additional file 3: of Cord blood hematopoietic cells from preterm infants display altered DNA methylation patterns

description: Significantly enriched GO terms (corrected p value &lt;0.10) from ErmineJ analysis of prematurity-DM sites for each cell type, ordered by corrected p value. (XLSX 18Â kb)
DOI: 10.6084/m9.figshare.c.3747635_d4
title: Additional file 13: of Integrative modelling of TIR domain-containing adaptor molecule inducing interferon-Î˛ (TRIF) provides insights into its autoinhibited state

description: Model coordinates of the N-TIR complex are provided as a Supplementary Material. (PDB 236Â kb)
DOI: 10.6084/m9.figshare.c.3747656_d1.v1
title: Additional file 1: of Haplotype of non-synonymous mutations within IL-23R is associated with susceptibility to severe malaria anemia in a P. falciparum holoendemic transmission area of Kenya

description: These are details of the raw data for the study participants (N = 369) used in the analyses of results presented in the current paper. (XLS 384 kb)
DOI: 10.6084/m9.figshare.c.3747641_d4.v1
title: Additional file 4: of Cord blood hematopoietic cells from preterm infants display altered DNA methylation patterns

description: “Location and genomic context of cell type-DM sites”. Each sheet is a table summarizing cell type-DM sites (FDR  0.20) for each birth group/cell type combination. (XLSX 11523 kb)
DOI: 10.6084/m9.figshare.c.3747656_d1
title: Additional file 1: of Haplotype of non-synonymous mutations within IL-23R is associated with susceptibility to severe malaria anemia in a P. falciparum holoendemic transmission area of Kenya

description: These are details of the raw data for the study participants (N = 369) used in the analyses of results presented in the current paper. (XLS 384 kb)
DOI: 10.15468/dl.sb4n6k
title: Occurrence Download

description: A dataset containing 72 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Nycticebus pygmaeus Bonhote, 1907"
 ]
}

 The dataset includes 72 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038666-241126133413365/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.3747641_d4
title: Additional file 4: of Cord blood hematopoietic cells from preterm infants display altered DNA methylation patterns

description: “Location and genomic context of cell type-DM sites”. Each sheet is a table summarizing cell type-DM sites (FDR  0.20) for each birth group/cell type combination. (XLSX 11523 kb)
DOI: 10.6084/m9.figshare.c.3747641_d5.v1
title: Additional file 5: of Cord blood hematopoietic cells from preterm infants display altered DNA methylation patterns

description: DNAm-based estimates of gestational age (GA) using Knight et al.â  s [24] methods. (XLSX 10Â kb)
DOI: 10.6084/m9.figshare.c.3747641_d5
title: Additional file 5: of Cord blood hematopoietic cells from preterm infants display altered DNA methylation patterns

description: DNAm-based estimates of gestational age (GA) using Knight et al.â  s [24] methods. (XLSX 10Â kb)
DOI: 10.6084/m9.figshare.c.3747668_d1.v1
title: Additional file 10: Table S7. of Cross-disorder comparative analysis of comorbid conditions reveals novel autism candidate genes

description: Biological processes for which the Multi-disorder component of the autism gene set (MDAG) were enriched. Identities of the MDAG genes overrepresented in the processes as well as the corrected p-values for the enrichment scores are provided. Enrichment was calculated using the biological processes only found among the MDAG genes and not found among the sibling disorders. (XLSX 50Â kb)
DOI: 10.6084/m9.figshare.c.3747674_d1.v1
title: Additional file 1: of Comparative transcriptomics of mountain pine beetle pheromone-biosynthetic tissues and functional analysis of CYP6DE3

description: Primer Table: A list of primers used for qRT-PCR and CYP6DE3 cloning. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.c.3747668_d5.v1
title: Additional file 14: Table S10. of Cross-disorder comparative analysis of comorbid conditions reveals novel autism candidate genes

description: Complete list of genes present in the intersection of PBCâ ŠNBC, along with the biological processes where they are involved, MDAG interactors and comorbid disorders where they are present. Also, PBCâ ŠNBC significantly differentially expressed in each dataset and in all the three datasets. (XLSX 226Â kb)
DOI: 10.6084/m9.figshare.c.3747674_d4.v1
title: Additional file 4: of Comparative transcriptomics of mountain pine beetle pheromone-biosynthetic tissues and functional analysis of CYP6DE3

description: Differentially Expressed Genes for Each Comparison: A list of all the genes that have greater than two fold differential expression for each considered comparison of sex and feeding status. (XLSX 1704 kb)
DOI: 10.6084/m9.figshare.c.3747668_d4
title: Additional file 13: Table S9. of Cross-disorder comparative analysis of comorbid conditions reveals novel autism candidate genes

description: Complete list of NBC, along with their q-values, MDAG interactors and comorbid disorders where they are present. Also, NBC significantly differentially expressed in each dataset and in all the three datasets. (XLSX 185Â kb)
DOI: 10.6084/m9.figshare.c.3747668_d5
title: Additional file 14: Table S10. of Cross-disorder comparative analysis of comorbid conditions reveals novel autism candidate genes

description: Complete list of genes present in the intersection of PBCâ ŠNBC, along with the biological processes where they are involved, MDAG interactors and comorbid disorders where they are present. Also, PBCâ ŠNBC significantly differentially expressed in each dataset and in all the three datasets. (XLSX 226Â kb)