cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.c.3613076_d6
title: Additional file 7: of Comparative genomics of 43 strains of Xanthomonas citri pv. citri reveals the evolutionary events giving rise to pathotypes with different host ranges

description: Examination of putative pathotype-specific genes from Zhang et al. [ 17 ]. Each strain in the dataset is represented as a column, and each row represents best reciprocal hits to genes identified as either unique to A strains or unique to Aw and A* strains by Zhang et al. [17] with a description of their status from our dataset, their distribution across all strains in our dataset, and whether they coincide with detected regions of recombination. The strains are highlighted based on their pathotype: A strains (blue), Aw strains (orange) and A* strains (purple). (XLSX 63 kb)
DOI: 10.6084/m9.figshare.c.3613076_d7
title: Additional file 4: of Comparative genomics of 43 strains of Xanthomonas citri pv. citri reveals the evolutionary events giving rise to pathotypes with different host ranges

description: Table of best reciprocal blast hit relationships for genes across all examined strains. Each strain in the dataset is represented as a column, and each row represents best reciprocal hits. The rows are ordered initially by the gene order from IAPAR 306, and then arbitrarily by different strains cycling through the A, Aw and A* pathotypes. The strains are highlighted based on their pathotype: A strains (blue), Aw strains (orange) and A* strains (purple). Additional information for certain genes are contained in parenthesis after the systematic gene name. (XLSX 2199 kb)
DOI: 10.6084/m9.figshare.c.3613154_d2
title: Additional file 4: of Genomic analysis of the multi-host pathogen Erysipelothrix rhusiopathiae reveals extensive recombination as well as the existence of three generalist clades with wide geographic distribution

description: File S1. Program versions and specific command line options. (TXT 4Â kb)
DOI: 10.6084/m9.figshare.c.3613154_d3
title: Additional file 3: Table S2. of Genomic analysis of the multi-host pathogen Erysipelothrix rhusiopathiae reveals extensive recombination as well as the existence of three generalist clades with wide geographic distribution

description: Excel spreadsheet presenting cluster statistics for host species, geographic location, and submitting laboratory, as output from the program BaTS. (XLSX 11Â kb)
DOI: 10.6084/m9.figshare.c.3613163_d2
title: Additional file 2: Table S1. of Spinal cord injury induces astroglial conversion towards neuronal lineage

description: Database of differential expression comparison of activated astrocyte RNA-Seq data relative to non-injured control astrocyte at 1 and 2Â weeks after hemisection and full transection injuries. (XLSX 90 kb)
DOI: 10.6084/m9.figshare.c.3613154_d4
title: Additional file 1: Table S1. of Genomic analysis of the multi-host pathogen Erysipelothrix rhusiopathiae reveals extensive recombination as well as the existence of three generalist clades with wide geographic distribution

description: Excel spreadsheet of the Erysipelothrix spp. isolates used in this study, including metadata and assembly statistics. (XLSX 24Â kb)
DOI: 10.6084/m9.figshare.c.3613181_d4
title: Additional file 1: Table S1. of Fully immunized child: coverage, timing and sequencing of routine immunization in an urban poor settlement in Nairobi, Kenya

description: Proportion of fully immunized children by 12Â months of age by different background factors. The file lists the vaccination coverage of each antigen by different background characteristics for children aged 12-23 months. (XLSX 14Â kb)
DOI: 10.6084/m9.figshare.c.3613184_d3
title: Additional file 5: Table S4. of DNA methylation analysis of paediatric low-grade astrocytomas identifies a tumour-specific hypomethylation signature in pilocytic astrocytomas

description: Normalized gene expression analysis for selected test tumours and controls. Expression analysis was performed using Affymetrix Human U133_plus2 arrays. Log-transformed expression values are shown for 18 tumour samples (10 diffuse astrocytomas and 8 pilocytic astrocytomas), and foetal and adult normal brain controls (foetal and adult diencephalon, cerebellum and cerebral cortex, adult medulla and thalamus). Affymetrix annotation is shown. Probes are ordered alphabetically according to the gene symbol. (XLSX 19307 kb)
DOI: 10.6084/m9.figshare.c.3613184_d5
title: Additional file 7: Table S6. of DNA methylation analysis of paediatric low-grade astrocytomas identifies a tumour-specific hypomethylation signature in pilocytic astrocytomas

description: Three-way comparison of the test tumour set of pilocytic and diffuse astrocytomas with normal brain control tissue. 993 CpG probes are shown where the difference between the average beta values of pilocytic and diffuse astrocytomas, or between either of these and the control samples is equal to or greater than 0.3 (δβ ≥ 0.3, Benjamini-Hochberg corrected p-value &lt;0.05), assessed by MethLAB. Illumina annotation is included. (XLSX 436 kb)
DOI: 10.6084/m9.figshare.c.3613184_d6
title: Additional file 16: Table S15. of DNA methylation analysis of paediatric low-grade astrocytomas identifies a tumour-specific hypomethylation signature in pilocytic astrocytomas

description: Differential expression of AP-1 target genes in pilocytic astrocytomas compared to normal brain controls and diffuse astrocytomas. 1_ List of published AP-1 target genes [Eferl and Wagner, Nature Rev Cancer 3(11):853-868, 2003; Li et al, J Genet Genomics 38(6):235-242, 2011] and predicted AP-1 target genes identified in the 315 differentially methylated sites. 2_ Table showing AP-1 target genes that are differentially expressed in pilocytic astrocytomas compared to normal brain controls and diffuse astrocytomas. For each gene, methylation and expression status, plus the normalized log2 transformed expression values for each sample are included. The data is ordered by correlation with FOS expression (positive to negative correlation). The colour coordination shows which genes were taken from the three lists. (XLSX 101 kb)
DOI: 10.6084/m9.figshare.c.3613184_d7
title: Additional file 6: Table S5. of DNA methylation analysis of paediatric low-grade astrocytomas identifies a tumour-specific hypomethylation signature in pilocytic astrocytomas

description: Pyrosequencing assays. Primers used for pyrosequencing (XLSX 72 kb)
DOI: 10.6084/m9.figshare.c.3613184_d8
title: Additional file 12: Table S11. of DNA methylation analysis of paediatric low-grade astrocytomas identifies a tumour-specific hypomethylation signature in pilocytic astrocytomas

description: Normalised log2 expression values for the genes associated with the 315 CpG sites. The Î´Î˛ values between the pilocytic and diffuse astrocytoma groups were obtained from the grouped averaged beta values. Genes with a differential gene expression â Ľ2 fold are highlighted in grey. Sorted alphabetically by gene symbol. (XLSX 370 kb)
DOI: 10.6084/m9.figshare.c.3613184_d9
title: Additional file 8: Table S7. of DNA methylation analysis of paediatric low-grade astrocytomas identifies a tumour-specific hypomethylation signature in pilocytic astrocytomas

description: Ingenuity Pathway Analysis (IPA) for genes associated with 993 differentially methylated sites identified in the three-way comparison of the test tumour set. IPA analysis shows significant biological and disease categories including functional annotation (p-value &lt;0.05), for 537 genes sorted by p-value. (XLSX 89 kb)
DOI: 10.6084/m9.figshare.c.3613232_d1
title: MOESM1 of Pipeline for amplifying and analyzing amplicons of the V1â  V3 region of the 16S rRNA gene

description: Additional file 1. FASTA file of 16S rRNA genes contained in the mock community.
DOI: 10.6084/m9.figshare.c.3613229_d1
title: Additional file 1: of Impact of clinical input variable uncertainties on ten-year atherosclerotic cardiovascular disease risk using new pooled cohort equations

description: Dataset: our detailed analysis dataset of NHANES data. (XLSX 319Â kb)
DOI: 10.6084/m9.figshare.c.3613232_d2
title: MOESM2 of Pipeline for amplifying and analyzing amplicons of the V1â  V3 region of the 16S rRNA gene

description: Additional file 2. Commands executed in mothur.
DOI: 10.6084/m9.figshare.c.3613184_d14
title: Additional file 18: Table S17. of DNA methylation analysis of paediatric low-grade astrocytomas identifies a tumour-specific hypomethylation signature in pilocytic astrocytomas

description: Ingenuity Pathway Analysis (IPA) of genes associated with differentially methylated sites in infratentorial pilocytic astrocytomas and normal cerebellum. IPA analysis of the top 20 significant biological and disease categories including their functional annotation (p-value &lt;0.05) identified for 161 genes that had ≤2 fold change in gene expression and δβ ≥ 0.3, sorted by p-value. (XLSX 71 kb)
DOI: 10.6084/m9.figshare.c.3613241_d8
title: MOESM13 of Network-based integration of molecular and physiological data elucidates regulatory mechanisms underlying adaptation to high-fat diet

description: Supplementary material 13 (CYS 488Â kb)
DOI: 10.6084/m9.figshare.c.3613241_d9
title: MOESM7 of Network-based integration of molecular and physiological data elucidates regulatory mechanisms underlying adaptation to high-fat diet

description: Supplementary material 7 (XLSX 25Â kb)
DOI: 10.6084/m9.figshare.c.3613226_d7
title: Additional file 5: Table S1. of Ligation-free ribosome profiling of cell type-specific translation in the brain

description: List of cell type-specific gene ontologies and their median TEs. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.c.3613241_d10
title: MOESM4 of Network-based integration of molecular and physiological data elucidates regulatory mechanisms underlying adaptation to high-fat diet

description: Supplementary material 4 (ZIP 6984Â kb)
DOI: 10.6084/m9.figshare.c.3613184_d17
title: Additional file 20: Table S19. of DNA methylation analysis of paediatric low-grade astrocytomas identifies a tumour-specific hypomethylation signature in pilocytic astrocytomas

description: Differentially methylated CpG sites identified between diffuse astrocytomas and cerebral cortex controls. 1_ MethLAB analysis identified 90,249 CpG sites that are significantly differentially methylated in supratentorial pilocytic astrocytomas, diffuse astrocytomas, glial component of the cerebral cortex, neuronal component of the cerebral cortex, adult cerebral cortex and foetal cerebral cortex (Benjamini-Hochberg corrected p-value &lt;0.05). The adult cerebral cortex controls (including the glial and neuronal components) were taken from [Guintivano et al, Epigenetics 8:290-302, 2013]. The number of differentially methylated sites (averaged beta values with a difference of δβ ≥ 0.3, Benjamini-Hochberg corrected p-value &lt;0.05) identified in tumour and all controls was 58 CpG sites for the diffuse astrocytomas. 2_ CpG sites hypermethylated and 3_ hypomethylated in diffuse astrocytomas compared to controls. 4_ Expression analysis for the genes that show differentially methylated CpG sites. Highlighted genes show ≤ 2 fold change in expression compared to controls. (XLSX 37720 kb)
DOI: 10.6084/m9.figshare.c.3613241_d11
title: MOESM11 of Network-based integration of molecular and physiological data elucidates regulatory mechanisms underlying adaptation to high-fat diet

description: Supplementary material 11 (XLSX 41550Â kb)
DOI: 10.6084/m9.figshare.c.3613184_d18
title: Additional file 21: Table S20. of DNA methylation analysis of paediatric low-grade astrocytomas identifies a tumour-specific hypomethylation signature in pilocytic astrocytomas

description: Differentially methylated CpG sites in infratentorial pilocytic astrocytomas, supratentorial astrocytomas and diffuse astrocytomas. 1_ MethLAB analysis identified 676 CpG sites that are significantly differentially methylated in infratentorial pilocytic, supratentorial pilocytic and diffuse astrocytomas (Benjamini-Hochberg corrected p-value &lt;0.05). 2_ The 72 differentially methylated CpG sites in supratentorial and infratentorial pilocytic astrocytomas. 3_ The 393 differentially methylated CpG sites for infratentorial pilocytic astrocytomas and diffuse astrocytomas (averaged beta values with δβ ≥ 0.3, Benjamini-Hochberg corrected p-value &lt;0.05). 4_ Genes that show differentially methylated CpG sites and expression between supratentorial and infratentorial pilocytic astrocytomas (genes with fold change ≥ 2 highlighted in grey). (XLSX 406 kb)
DOI: 10.6084/m9.figshare.c.3613241_d12
title: MOESM10 of Network-based integration of molecular and physiological data elucidates regulatory mechanisms underlying adaptation to high-fat diet

description: Supplementary material 10 (XLSX 39Â kb)
DOI: 10.6084/m9.figshare.c.3613184_d19
title: Additional file 19: Table S18. of DNA methylation analysis of paediatric low-grade astrocytomas identifies a tumour-specific hypomethylation signature in pilocytic astrocytomas

description: Differentially methylated CpG sites identified between supratentorial pilocytic astrocytomas and cerebral cortex controls. 1_ MethLAB analysis identified 90,249 CpG sites that are significantly differentially methylated in supratentorial pilocytic astrocytomas, diffuse astrocytomas, glial component of the cerebral cortex, neuronal component of the cerebral cortex, adult cerebral cortex and foetal cerebral cortex (Benjamini-Hochberg corrected p-value &lt;0.05). The adult cerebral cortex controls (including the glial and neuronal components) were taken from [Guintivano et al, Epigenetics 8:290-302, 2013]. The number of differentially methylated sites (averaged beta values with a difference of δβ ≥ 0.3, Benjamini-Hochberg corrected p-value &lt;0.05) identified in tumour and all controls was 382 CpG sites for supratentorial pilocytic astrocytomas. 2_ CpG sites hypermethylated and 3_ hypomethylated in pilocytic astrocytomas compared to controls. 4_ Expression analysis for the genes that show differentially methylated CpG sites. Highlighted genes show ≤ 2 fold change in expression compared to controls. (XLSX 37842 kb)
DOI: 10.6084/m9.figshare.c.3613184_d20
title: Additional file 15: Table S14. of DNA methylation analysis of paediatric low-grade astrocytomas identifies a tumour-specific hypomethylation signature in pilocytic astrocytomas

description: Predicted transcription factor binding sites for the 315 differentially methylated signature in low-grade astrocytomas. Table to show TRANSFAC predicted transcription factor binding sites within a 200Â bp region (100Â bp either side of the CpG site detected by the Illumina probe). Illumina annotation highlighted in grey and transcription factor binding predictions plus sequence highlighted in blue. List of the top predicted transcription factors and gene expression levels of the top predicted transcription factors for the low-grade astrocytomas are also shown. (XLSX 215 kb)
DOI: 10.6084/m9.figshare.c.3613241_d13
title: MOESM12 of Network-based integration of molecular and physiological data elucidates regulatory mechanisms underlying adaptation to high-fat diet

description: Supplementary material 12 (XLSX 12Â kb)
DOI: 10.6084/m9.figshare.c.3613241_d14
title: MOESM6 of Network-based integration of molecular and physiological data elucidates regulatory mechanisms underlying adaptation to high-fat diet

description: Supplementary material 6 (CYS 336Â kb)
DOI: 10.6084/m9.figshare.c.3613184_d21
title: Additional file 10: Table S9. of DNA methylation analysis of paediatric low-grade astrocytomas identifies a tumour-specific hypomethylation signature in pilocytic astrocytomas

description: Comparison of pilocytic astrocytomas with diffuse astrocytomas in the test tumour set. 315 CpG sites are shown where δβ ≥ 0.3 (Benjamini-Hochberg corrected p-value &lt;0.05), assessed by MethLAB. Illumina annotation is included. Rows highlighted in grey (42/315 CpG sites) were absent in the 993 differentially methylated CpG sites between tumours and normal brain control. Ordered by chromosomal location. (XLSX 205 kb)
DOI: 10.15468/dl.tbyngj
title: Occurrence Download

description: A dataset containing 1102 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is EOD – eBird Observation Dataset",
 "Geometry POLYGON((-385.08055 17.22223,-385.16885 17.19136,-385.3074 17.12747,-385.37417 17.08512,-385.36914 17.01405,-385.31961 16.90062,-385.19111 16.90421,-385.15091 16.93077,-385.07337 16.98677,-384.97574 17.04204,-384.94344 17.09158,-384.97502 17.15619,-385.08055 17.22223))"
 ]
}

 The dataset includes 1102 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032750-241126133413365/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.3613304_d1
title: Additional file 4: Figure S1. of Statistical correlation of nonconservative substitutions of HIV gp41 variable amino acid residues with the R5X4 HIV-1 phenotype

description: Gp41 coordinates - Homology model (PDB 598 kb)
DOI: 10.6084/m9.figshare.c.3613301_d1
title: Additional file 1: of Contact heat sensitivity and reports of unpleasantness in communicative people with mild to moderate cognitive impairment in Alzheimerâ  s disease: a cross-sectional study

description: Psychophysics Raw Data. (XLSX 17 KB)
DOI: 10.15468/dl.f58ggf
title: Occurrence Download

description: A dataset containing 34 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "TaxonKey is Rana kukunoris Nikolskii, 1918"
 ]
}

 The dataset includes 34 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032751-241126133413365/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.3613310_d2
title: Additional file 3: Table S3. of Staphylococcal species heterogeneity in the nasal microbiome following antibiotic prophylaxis revealed by tuf gene deep sequencing

description: Staphylococcal relative sequence abundance for all patient samples. (XLSX 23Â kb)
DOI: 10.6084/m9.figshare.c.3613349_d1
title: Additional file 1: of Identifying specific proteins involved in eggshell membrane formation using gene expression analysis and bioinformatics

description: Excel file (.xlsx) containing list of over-expressed transcripts (107 genes) in WI/Ma and WI/Ut contrasts. (XLSX 26Â kb)
DOI: 10.6084/m9.figshare.c.3613370_d1
title: Additional file 1: of HIV risk perception and testing behaviours among men having sex with men (MSM) reporting potential transmission risks in the previous 12Â months from a large online sample of MSM living in Germany

description: A subset of the survey dataset including the variables used for the analysis and the data analysis syntax (stata do-file) are provided as Additional File 1 (Zip-archive, including a CSV-data file and the do-file in txt-format). (7Z 111 kb)
DOI: 10.15468/dl.nnf66c
title: Occurrence Download

description: A dataset containing 2979 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is EOD – eBird Observation Dataset",
 "Geometry POLYGON((-24.94085 16.92916,-24.95462 16.93261,-24.98432 16.92787,-25.00627 16.90076,-25.04328 16.89043,-25.06523 16.87752,-25.0889 16.85385,-25.0932 16.82803,-25.06695 16.80866,-25.03295 16.78886,-24.99981 16.76261,-24.93224 16.77208,-24.86424 16.80221,-24.83756 16.8418,-24.86209 16.88785,-24.90255 16.92615,-24.94085 16.92916))"
 ]
}

 The dataset includes 2979 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032752-241126133413365/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.26241992
title: S-wave traveltimes & Vs anomaly model of SET

description: teleseismic S-wave relative traveltimes & Vs anomaly model of SET from the joint inversion of surface wave phase velocity and body wave traveltime
DOI: 10.6084/m9.figshare.26241992.v3
title: S-wave traveltimes & Vs anomaly model of SET

description: teleseismic S-wave relative traveltimes & Vs anomaly model of SET from the joint inversion of surface wave phase velocity and body wave traveltime
DOI: 10.6084/m9.figshare.c.3613415_d2
title: Additional file 8: Table S8. of Dormant non-culturable Mycobacterium tuberculosis retains stable low-abundant mRNA

description: Oligonucleotides used in the study. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.c.3613406_d3
title: Additional file 4: of Suppression of cell migration is promoted by miR-944 through targeting of SIAH1 and PTP4A1 in breast cancer cells

description: Raw data obtained from gene expression studies using DNA microarrays. (XLS 2.36 mb)
DOI: 10.6084/m9.figshare.c.3613415_d3
title: Additional file 1: Table S1. of Dormant non-culturable Mycobacterium tuberculosis retains stable low-abundant mRNA

description: Mapping statistics for each of the sequenced samples. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.c.3613415_d4
title: Additional file 3: Table S3. of Dormant non-culturable Mycobacterium tuberculosis retains stable low-abundant mRNA

description: Correlation between samples. Spearman coefficients of correlation between each of the sequenced samples are shown. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.c.3613415_d5
title: Additional file 4: Table S4. of Dormant non-culturable Mycobacterium tuberculosis retains stable low-abundant mRNA

description: Expression changes of selected genes and total mRNA transcriptome. (A) The expression of selected genes in the Log, DE, DM, and DL samples is presented as RPKM values (RNA-seq) and relative mRNA levels normalized to 16S rRNA (qPCR). (B) The expression of selected genes was determined by RNA-seq (RPKM values) and qPCR (relative to 16S rRNA) and presented as the ratio of the DE, DM, and DL values normalized to Log values. (C) Correlation between expression changes measured by RNA-seq and qRT-PCR. (D) Coefficient M representing the changes in the quantity of total mRNA relative to 16S rRNA. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.c.3613439_d6
title: MOESM6 of Classification and characterization of human endogenous retroviruses; mosaic forms are common

description: Additional file 6: Table S6. Translation table for HERV PBS sequences, taken from ReTe and hg19. The derivation and structure of this table is described in Methods.
DOI: 10.6084/m9.figshare.c.3613442_d5
title: Additional file 7: of Tankyrase inhibition impairs directional migration and invasion of lung cancer cells by affecting microtubule dynamics and polarity signals

description: Raw data for Fig. S2. (XLSX 48 kb)
DOI: 10.6084/m9.figshare.c.3613448_d4
title: Additional file 1: Figure-CT-case-1. of Malignant mesothelioma of the pleura with desmoplastic histology: a case series and literature review

description: Chest computed tomography of DMM lesions of Case 1. Figure-path-case-1 (a) Low-power image of case 1. (b) High-power image of case 1. (ZIP 10146 kb)
DOI: 10.15468/dl.c8xftg
title: Occurrence Download

description: A dataset containing 146 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is EOD – eBird Observation Dataset",
 "Geometry POLYGON((-24.77747 16.81274,-24.78538 16.8093,-24.79429 16.79005,-24.79543 16.76707,-24.78078 16.73834,-24.75838 16.73202,-24.72419 16.72369,-24.67766 16.72628,-24.67549 16.76535,-24.71772 16.77166,-24.74472 16.79407,-24.77747 16.81274))"
 ]
}

 The dataset includes 146 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032753-241126133413365/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.3613466_d3
title: MOESM2 of 
                     Clostridium thermocellum DSM 1313 transcriptional responses to redox perturbation

description: Additional file 2. Calculated differential expression and adjusted p values for genes showing significant (adjusted p valueÂ