cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17632/xk562w9hm6.2
title: Oregano supplementation in laying hens

description: This study aimed to explore the effects of oregano oil supplementation on performance, blood lipid profile, antioxidant capacity, and egg quality in Hy-line Brown layers during the peak laying phase
DOI: 10.17632/tczmkxmfgp.1
title: Supplementary Material

description: This supplementary material contains data about refugees' categories, NIEM integration values and detailed experiment results related to the paper "Optimizing the Assignment Decisions in the Refugee Resettlement Process".
DOI: 10.17632/tczmkxmfgp.2
title: Supplementary Material

description: This supplementary material contains data about refugees' categories, NIEM integration values, detailed experiment results and examples related to the paper "Optimizing the Assignment Decisions in the Refugee Resettlement Process".
DOI: 10.6084/m9.figshare.c.3612983_d4.v1
title: Additional file 5: Table S2. of Long-term balancing selection at the Phosphorus Starvation Tolerance 1 (PSTOL1) locus in wild, domesticated and weedy rice (Oryza)

description: PSTOL1 primers used in PCR genotyping and sequencing. (XLSX 8 kb)
DOI: 10.17632/dxrznmd7hf.1
title: Enhanced Image Segmentation using Double Hybrid DEGA and PSO-SA

description: Enhanced Image Segmentation using Double Hybrid DEGA and PSO-SA
DOI: 10.5519/qd.qhn86123
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (44 records)
DOI: 10.6084/m9.figshare.c.3612989_d1.v1
title: Additional file 5: of PFA toolbox: a MATLAB tool for Metabolic Flux Analysis

description: Stoichiometric matrix and experimental data for Escherichia coli. A Microsoft Excel spreadsheet file with i) the stoichiometric matrix of E. coli and ii) the experimental datasets taken from the literature. This includes measurements of biomass, glycerol, OUR, CPR and pyruvate. (XLSX 62 kb)
DOI: 10.6084/m9.figshare.c.3612959_d7.v1
title: Additional file 8: of Changes in the composition of the RNA virome mark evolutionary transitions in green plants

description: Alignment (Phylip format) of RdRP from viruses in order Tymovirales. (TXT 11 kb)
DOI: 10.6084/m9.figshare.c.3612992_d2.v1
title: Additional file 6: of Whole genome re-sequencing reveals genome-wide variations among parental lines of 16 mapping populations in chickpea (Cicer arietinum L.)

description: Summary of homozygous and heterozygous SNPs identified in 35 chickpea genotypes. (XLSX 11Â kb)
DOI: 10.6084/m9.figshare.c.3612989_d3.v1
title: Additional file 3: of PFA toolbox: a MATLAB tool for Metabolic Flux Analysis

description: Stoichiometric matrix and experimental data for Pichia pastoris. A Microsoft Excel spreadsheet file with i) the list of reactions and metabolites, ii) the stoichiometric matrix of P. pastoris and iii) the experimental datasets taken from the literature. This includes measurements of biomass, substrates uptakes (glycerol, glucose, and methanol), Oxygen Uptake Rate (OUR), CO2 production (CPR), and formation of byproducts (ethanol, citrate, and pyruvate). (XLSX 48 kb)
DOI: 10.6084/m9.figshare.c.3612992_d3.v1
title: Additional file 18: of Whole genome re-sequencing reveals genome-wide variations among parental lines of 16 mapping populations in chickpea (Cicer arietinum L.)

description: Classification of all SNPs using SNPEff program. (XLSX 10Â kb)
DOI: 10.6084/m9.figshare.c.3612989_d4.v1
title: Additional file 1: of PFA toolbox: a MATLAB tool for Metabolic Flux Analysis

description: Code for the examples A.rar file with the MATLAB files code to perform the examples described below with Example of flux estimation under data scarcity (a), P. pastoris (b) and E. coli (c). (RAR 5 kb)
DOI: 10.6084/m9.figshare.c.3613184_d7.v1
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.v1
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.v1
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.v1
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.v1
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.v1
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_d10.v1
title: Additional file 2: Table S2. of DNA methylation analysis of paediatric low-grade astrocytomas identifies a tumour-specific hypomethylation signature in pilocytic astrocytomas

description: Peak-corrected Infinium 450K methylation beta values for the test tumour set. Beta values are the ratios between the unmethylated (0) and methylated (1) signal intensities for the individual probes (ordered by Illumina probe ID). Normal brain controls: Foetal cerebellum, Foetal brain, Foetal frontal lobe, adult brain, human neural stem cells. Supratentorial pilocytic astrocytomas: PA1-PA6. Infratentorial pilocytic astrocytomas: PA7-PA17. Diffuse astrocytomas: DA1-DA10. (XLSX 173351 kb)
DOI: 10.6084/m9.figshare.c.3613235_d1.v1
title: Additional file 2: of A methodology for exploring biomarker â   phenotype associations: application to flow cytometry data and systemic sclerosis clinical manifestations

description: IRIS Data Set and R code. (ZIP 291 KB)
DOI: 10.6084/m9.figshare.c.3613415_d4.v1
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.v1
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.3613415_d6.v1
title: Additional file 5: Table S5. of Dormant non-culturable Mycobacterium tuberculosis retains stable low-abundant mRNA

description: Differential expression of protein-coding genes. The analysis of differential expression was performed with the edgeR software. Results for the following comparisons are shown: DE relative to Log, DM relative to DE, and DL relative to DM. Log2 fold change of gene expression, FDR-adjusted P-value for differential expression test, and M-value adjusted Log2 fold change are shown for every gene in each comparison. (XLSX 683 kb)
DOI: 10.6084/m9.figshare.c.3613439_d2.v1
title: MOESM4 of Classification and characterization of human endogenous retroviruses; mosaic forms are common

description: Additional file 4: List S4. HERV Env subgroup consensus sequences. The FASTA names contain 1. taxorder, 2. subgroup, 3. number of members in the subgroup, 4. 23-amino acid consensus immunosuppressive domain, 5. if present, the most highly related envelope protein from maximum likelihood (Fig. 6,  7) phylograms, and 6. the bootstrap value of the common branch of these envelope proteins.
DOI: 10.6084/m9.figshare.c.3613442_d1.v1
title: Additional file 3: of Tankyrase inhibition impairs directional migration and invasion of lung cancer cells by affecting microtubule dynamics and polarity signals

description: Raw data for Fig.Â 2 . (XLSX 128 kb)
DOI: 10.6084/m9.figshare.c.3613415_d7.v1
title: Additional file 6: Table S6. of Dormant non-culturable Mycobacterium tuberculosis retains stable low-abundant mRNA

description: Functional enrichments analysis. Functional enrichment analysis was performed using the GOseq package [76] and functional categories from the TubercuList and PATRIC databases [33, 34]. The lists of differentially expressed (up- and down-regulated) genes were generated by the comparison of the following samples: DE vs. Log, DM vs. DE, and DL vs. DM. For each functional category, the number of differentially expressed genes, the total number of genes in the category, and the adjusted p-value of overrepresentation are shown. (XLSX 38 kb)
DOI: 10.6084/m9.figshare.c.3613442_d2.v1
title: Additional file 11; of Tankyrase inhibition impairs directional migration and invasion of lung cancer cells by affecting microtubule dynamics and polarity signals

description: Raw data for Fig.Â 3 . (XLSX 37 kb)
DOI: 10.6084/m9.figshare.c.3613451_d1.v1
title: Additional file 1: Table 1. of Analysis of the frequency of EGFR, KRAS and ALK mutations in patients with lung adenocarcinoma in Croatia

description: Raw data. (XLSX 30 kb)
DOI: 10.6084/m9.figshare.c.3613679_d1.v1
title: Additional file 2: of Bloom and bust: intestinal microbiota dynamics in response to hospital exposures and Clostridium difficile colonization or infection

description: Table S2. Significant associations between medication use and intestinal microbiota families (univariable analysis). (XLSX 385 KB)
DOI: 10.6084/m9.figshare.c.3613682_d1.v1
title: Additional file 8: of Adjusting microbiome profiles for differences in microbial load by spike-in bacteria

description: ASCT experiment mapping file as used for reproduction. (TXT 1 kb)
DOI: 10.6084/m9.figshare.c.3613670_d3.v1
title: Additional file 1 of Exploiting HIV-1 protease and reverse transcriptase cross-resistance information for improved drug resistance prediction by means of multi-label classification

description: Sequence data. All sequences used in the study with information on cross-resistance. (XLS 402 kb)
DOI: 10.6084/m9.figshare.c.3613679_d2.v1
title: Additional file 1: of Bloom and bust: intestinal microbiota dynamics in response to hospital exposures and Clostridium difficile colonization or infection

description: Table S1. Significant associations between medication use and intestinal microbiota genera (univariable analysis). (XLSX 433 KB)
DOI: 10.6084/m9.figshare.c.3613682_d2.v1
title: Additional file 5: of Adjusting microbiome profiles for differences in microbial load by spike-in bacteria

description: 16S rDNA reference sequences of S. ruber, A. acidiphilus and R. radiobacter. (FASTA 4 kb)
DOI: 10.6084/m9.figshare.c.3613694_d1.v1
title: Additional file 1: of Sugammadex facilitates early recovery after surgery even in the absence of neuromuscular monitoring in patients undergoing laryngeal microsurgery: a single-center retrospective study

description: Available data. (XLSX 35Â kb)
DOI: 10.6084/m9.figshare.c.3613682_d3.v1
title: Additional file 12: of Adjusting microbiome profiles for differences in microbial load by spike-in bacteria

description: Spike-in concentrations by design as used for reproduction. (CSV 1 kb)
DOI: 10.6084/m9.figshare.c.3613892_d3.v1
title: Additional file 3: Table S3. of miRNA-dependent target regulation: functional characterization of single-nucleotide polymorphisms identified in genome-wide association studies of Alzheimer’s disease

description: Other miRNA targeting sites identified by less stringent analysis near rs7143400-C/G, rs2847655-T/C, rs610923-C/A and rs9909-G/C. A summary of the genes, PolymiRTSs, effects of minor alleles, targeting miRNAs and miRNA expression alterations observed in AD (when available; refer to the cited references). The grayed miRNAs were also found in the stringent screening described in Fig. 2a in the main text. (XLS 23 kb)
DOI: 10.6084/m9.figshare.c.3613886_d4.v1
title: Additional file 1: of A core phylogeny of Dictyostelia inferred from genomes representative of the eight major and minor taxonomic divisions of the group

description: Excel spreadsheet (.xlsx) listing assembly statistics of the six sequenced genomes before and filtering out of contamination with E.coli reads. (XLSX 16Â kb)
DOI: 10.6084/m9.figshare.c.3613886_d5.v1
title: Additional file 6: of A core phylogeny of Dictyostelia inferred from genomes representative of the eight major and minor taxonomic divisions of the group

description: Fasta file of the concatenated alignment of 47 proteins across 14 Amoebozoan taxa. (FAS 528Â kb)
DOI: 10.15468/dl.s4fhcy
title: Occurrence Download

description: A dataset containing 337 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is Inventario Nacional de Candelilla (Euphorbia antisyphilitica) Fase I.",
 "Geometry POLYGON((-131.52786 12.89340,-78.47214 12.89340,-78.47214 34.10660,-131.52786 34.10660,-131.52786 12.89340))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 337 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0037937-241126133413365/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.3613904_d1.v1
title: Additional file 1: of Equipment, measurement and doseâ  a survey for therapeutic ultrasound

description: Full set of anonymous responses to the survey. The file contains an overview sheet and 44 sheets for the 44 questions of the survey. (XLSX 154 kb)
DOI: 10.6084/m9.figshare.c.3614162_d1.v1
title: MOESM2 of The cnidarian Hydractinia echinata employs canonical and highly adapted histones to pack its DNA

description: Additional file 2. S2. List of primers used in this study.
DOI: 10.6084/m9.figshare.c.3614162_d2.v1
title: MOESM4 of The cnidarian Hydractinia echinata employs canonical and highly adapted histones to pack its DNA

description: Additional file 4. S4. Summary table of all experiments and results.
DOI: 10.6084/m9.figshare.c.3614177_d1.v1
title: Additional file 2 of Coevolutionary feedback elevates constitutive immune defence: a protein network model

description: C++ source code of the simulation programme. (ZIP 25.9 kb)
DOI: 10.6084/m9.figshare.c.3614186_d1.v1
title: Additional file 1: Table S1. of Stool microbiota composition is associated with the prospective risk of Plasmodium falciparum infection

description: Taxonomic composition of Dirichlet components DC1 and DC2. Table S2. Fit of DMM modeling for various values of K (the number of Dirichlet components). Best fit is highlighted in red. Table S3. Taxonomic composition of Dirichlet components CC1 through CC9. Table S4. Distribution of samples from the four cohorts (Mali, HMP, Malawi, and MSD) in the 9 Dirichlet components (CC1 through CC9). Table S5. Fit of DMM modeling for various values of K (the number of Dirichlet components) for P. falciparum infection status analysis. Best fit is highlighted in red. Table S6. Taxonomic composition of Dirichlet components PP1, PP2, PN1, and PN2. Table S7. Taxonomic composition of Dirichlet components FM1 and FM2. Table S8. Cox model of DMM Component: Time to Infection. Figure S1. Increase in microbial taxa diversity with age in the Malian cohort. For each stool microbiota sample, the alpha diversity on the y-axis was plotted against the individual’s age in years (x-axis). The blue lines are the linear model fits and all of them have positive slope (P
DOI: 10.6084/m9.figshare.c.3614192_d1.v1
title: Additional file 1: Table S1. of High-risk oral leukoplakia is associated with aberrant promoter methylation of multiple genes

description: List of primers for MSP. (XLSX 37 kb)
DOI: 10.6084/m9.figshare.c.3614411_d4.v1
title: Additional file 9: Table S6. of SNP discovery and genetic mapping using genotyping by sequencing of whole genome genomic DNA from a pea RIL population

description: Comparing polymorphism data in the 48 ‘Baccara’ x ‘PI180693’ RILs from a set of 953 SNP genotyped both in WGGBS and LGC Kasp™ assay methods, ordered according to their genetic position on the BP-WGGBS map. “A” corresponds to ‘Baccara’ homozygous parental genotype, “B” to ‘PI180693’ homozygous parental genotype, “H” to an heterozygous genotype, “-” indicates uncalled data. (XLSX 439 kb)
DOI: 10.6084/m9.figshare.c.3614411_d6.v1
title: Additional file 5: Table S4. of SNP discovery and genetic mapping using genotyping by sequencing of whole genome genomic DNA from a pea RIL population

description: Mapping data and polymorphism in the 48 ‘Baccara’ x ‘PI180693’ RILs of a set of 64,263 SNP markers mapped to the seven linkage groups of the BP-WGGBS map. (XLSX 17036 kb)
DOI: 10.6084/m9.figshare.c.3614411_d7.v1
title: Additional file 8: Table S5. of SNP discovery and genetic mapping using genotyping by sequencing of whole genome genomic DNA from a pea RIL population

description: Polymorphism data in the 8 sequenced pea parental lines and 4 F1 selected from a set of 953 SNP genotyped in LGC Kasp™ assay methods on 1438 different pea accessions. “A” corresponds to ‘Baccara’ homozygous parental genotype, “B” to ‘PI180693’ homozygous parental genotype, “H” to an heterozygous genotype, “-” indicates uncalled data. For each pea line, if available, different seed lots were genotyped (seed-DNA lot numbers in parenthesis). (XLSX 115 kb)
DOI: 10.6084/m9.figshare.c.3614411_d9.v1
title: Additional file 4: Table S3. of SNP discovery and genetic mapping using genotyping by sequencing of whole genome genomic DNA from a pea RIL population

description: Context sequences, genetic positions on pea linkage groups and genotyping data for eight P. sativum parental lines of mapping populations with a set of 63,353 newly developed SNP markers mapped to the seven linkage groups of the BP-WGGBS map. (XLSX 8728 kb)
DOI: 10.6084/m9.figshare.c.3614429_d1.v1
title: Additional file 6: Table S4. of Genome-wide identification of Drosophila dorso-ventral enhancers by differential histone acetylation analysis

description: Spreadsheet detailing the samples used in this study and the library preparation kits the libraries were created with, number of total reads, aligned reads, and MACS peaks for each sample. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.c.3614432_d1.v1
title: Additional file 1: Table S1. of Cross-sectional study of Fasciola gigantica and other trematode infections of cattle in Edu Local Government Area, Kwara State, north-central Nigeria

description: General characterisitics of households surveyed in Edu LGA, Kwara State. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.c.3614429_d3.v1
title: Additional file 5: Table S3. of Genome-wide identification of Drosophila dorso-ventral enhancers by differential histone acetylation analysis

description: Spreadsheet showing all identified DV enhancers that overlap a geneâ  s TSS, the assigned gene and its expression in the DV mutants, H3K27ac and transcription factor ChIP enrichment, and overlap with known DV enhancers and Vienna Tiles. (XLSX 147 kb)
DOI: 10.6084/m9.figshare.c.3614432_d2.v1
title: Additional file 2: Table S2. of Cross-sectional study of Fasciola gigantica and other trematode infections of cattle in Edu Local Government Area, Kwara State, north-central Nigeria

description: Univariate analysis of trematode infections in cattle based on household and cattle data in Edu, Kwara State, Nigeria. (XLSX 16 kb)
DOI: 10.6084/m9.figshare.c.3614429_d5.v1
title: Additional file 4: Table S2. of Genome-wide identification of Drosophila dorso-ventral enhancers by differential histone acetylation analysis

description: Spreadsheet of all distal identified DV enhancers, the assigned gene and its expression in the DV mutants, H3K27ac and transcription factor ChIP enrichment, overlap with known DV enhancers and Vienna Tiles, enrichment for transcription factor motifs, and classification as high confidence enhancers (used in Fig.5). (XLSX 256 kb)
DOI: 10.15468/dl.bsw95j
title: Occurrence Download

description: A dataset containing 107536 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Europe",
 "Country is Spain",
 "TaxonKey is Myiopsitta monachus (Boddaert, 1783)"
 ]
}

 The dataset includes 107536 records from 30 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0037936-241126133413365/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.3614648_d2.v1
title: Additional file 1: of Quantitative proteomics analysis of an ethanol- and a lactate-producing mutant strain of Synechocystis sp. PCC6803

description: Table S1. Strains used in this study. Table S2. A total of 1039 normalized protein 14N/15N isotopic ratios including their mascot scores from 3 biological replicates quantified in Synechocystis sp. PCC6803 wild-type (WT) strain, ethanol-forming strain (SAA012) and lactic acid-forming strain (SAW041). Table S3. List of primers used in RT-qPCR. Table S4. List of proteins quantified in SAA012 that were signifcantly changed and its p-value from z-test. Table S5. List of proteins quantified in SAW041 that were signifcantly changed and its p-value from z-test. Table S6. Results of KEGG pathway enrichment analyses of the significantly altered proteins quantified in the ethanol-producing strain (a) and the lactic acid-producing strain (b).
DOI: 10.6084/m9.figshare.c.3614672_d1.v1
title: Additional file 1: of Forecast analysis of any opportunistic infection among HIV positive individuals on antiretroviral therapy in Uganda

description: Data on monthly prevalence of any opportunistic infection among HIV positive individuals on HAART in TASO, Uganda (2004-2013). (XLS 34 kb)
DOI: 10.6084/m9.figshare.c.3614690_d1.v1
title: Additional file 4: Table S4. of Transcriptomic profiling of Melon necrotic spot virus-infected melon plants revealed virus strain and plant cultivar-specific alterations

description: Gene Ontology terms (GO terms) of the different clusters obtained in Planters Jumbo cotyledons. Significant GO terms from the different clusters obtained according to the differentially expressed gene pattern in Planters Jumbo cotyledons infected with MNSV-Mα5/3’264 in comparison to Tendral cotyledons infected with the same virus. % enrichment means the representation of the GO term in relation to the complete array. Genes belonging to each cluster are listed in contiguous spread sheets. A selection of genes from cluster 2 that had expression levels above 10 times as compared to their control (FC ≥ 10) is also listed in contiguous spreadsheets. (XLSX 263 kb)