cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.c.3639401_d1.v1
title: Additional file 3: of Induced pluripotent stem cell models of Zellweger spectrum disorder show impaired peroxisome assembly and cell type-specific lipid abnormalities

description: Lipid composition of cultured PBD-ZSD patient and control-derived cells. A complete list of all biochemical measurements pertinent to the lipid composition of the cells discussed herein is provided. (XLSX 61 kb)
DOI: 10.6084/m9.figshare.c.3639401_d3.v1
title: Additional file 6: of Induced pluripotent stem cell models of Zellweger spectrum disorder show impaired peroxisome assembly and cell type-specific lipid abnormalities

description: Copy number variation in PBD-ZSD patient and healthy control-derived iPSCs. A full list of copy number changes (CNCs) detected for iPSCs in this study is provided. (XLSX 17 kb)
DOI: 10.6084/m9.figshare.c.3639401_d5.v1
title: Additional file 1: of Induced pluripotent stem cell models of Zellweger spectrum disorder show impaired peroxisome assembly and cell type-specific lipid abnormalities

description: Characterization of candidate iPSCs. A complete listing of the protein, genetic, epigenetic, and cell differentiation assays performed on the iPSCs generated in this study is provided. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.c.3639401_d6.v1
title: Additional file 4: of Induced pluripotent stem cell models of Zellweger spectrum disorder show impaired peroxisome assembly and cell type-specific lipid abnormalities

description: Gene expression analysis of ASGPR-positive hepatocyte-like cell cultures. A complete list of log-transformed gene expression scores from PBD-ZSD patient and healthy donor control ASGPR-positive hepatocyte-like cell cultures is provided. (XLSX 3605 kb)
DOI: 10.6084/m9.figshare.c.3639401_d11.v1
title: Additional file 8: of Induced pluripotent stem cell models of Zellweger spectrum disorder show impaired peroxisome assembly and cell type-specific lipid abnormalities

description: Differentially expressed genes between PBD-ZSD patient and control healthy donor-derived iPSCs. A complete list of all gene expression scores and differentially expressed genes (DEGs) between PBD-ZSD patient and healthy donor control fibroblasts is provided. (XLSX 77 kb)
DOI: 10.6084/m9.figshare.c.3639401_d8.v1
title: Additional file 12: of Induced pluripotent stem cell models of Zellweger spectrum disorder show impaired peroxisome assembly and cell type-specific lipid abnormalities

description: Activities of hepatocyte-like cell cultures. Data relevant to the levels of albumin and urea produced in PBD-ZSD patient and healthy control hepatocyte-like cell cultures is provided. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.c.3639401_d9.v1
title: Additional file 9: of Induced pluripotent stem cell models of Zellweger spectrum disorder show impaired peroxisome assembly and cell type-specific lipid abnormalities

description: Pathway analysis of DEGS between PBD-ZSD patient and healthy donor-derived iPSCs. Gene Ontology (GO), KEGG, and IPA Pathway analyses of patient and healthy donor control fibroblasts are provided. (XLSX 546 kb)
DOI: 10.6084/m9.figshare.c.3639401_d10.v1
title: Additional file 2: of Induced pluripotent stem cell models of Zellweger spectrum disorder show impaired peroxisome assembly and cell type-specific lipid abnormalities

description: Log-transformed gene expression scores from PBD-ZSD patient and healthy donor control fibroblasts and iPSCs. A complete list of log-transformed gene expression scores from PBD-ZSD patient and healthy donor control fibroblasts and iPSCs is provided. (XLSX 11932 kb)
DOI: 10.6084/m9.figshare.c.3639419_d5.v1
title: MOESM1 of Serum-derived exosomes from non-viremic animals previously exposed to the porcine respiratory and reproductive virus contain antigenic viral proteins

description: Additional file 1. Codification and status of virus in blood and antibodies in porcine sera samples received. All samples were codified as soon as received in the laboratory and classified by virus and antibody status according to the RT-PCR and serology test for PRRSV.
DOI: 10.6084/m9.figshare.c.3639419_d4.v1
title: MOESM4 of Serum-derived exosomes from non-viremic animals previously exposed to the porcine respiratory and reproductive virus contain antigenic viral proteins

description: Additional file 4. Sus scrofa proteins identified by Maxquant/Andromeda analysis using nanoLC-MS/MS spectra. Porcine proteins were identified in exosomes by proteomic analyses and several molecular markers of exosomes are present in these samples such as CD5, CD9, CD81 and CD63.
DOI: 10.6084/m9.figshare.c.3639422_d3.v1
title: Additional file 3: of Sequence conservation analysis and in silico human leukocyte antigen-peptide binding predictions for the Mtb72F and M72 tuberculosis candidate vaccine antigens

description: Predicted 9-mer HLA class I peptide binding regions in Mtb72F. (XLSX 13Â kb)
DOI: 10.6084/m9.figshare.c.3639422_d2.v1
title: Additional file 1: of Sequence conservation analysis and in silico human leukocyte antigen-peptide binding predictions for the Mtb72F and M72 tuberculosis candidate vaccine antigens

description: Predicted HLA class II binding peptides in Mtb72F. (XLSX 15Â kb)
DOI: 10.6084/m9.figshare.c.3639479_d1.v1
title: Additinal file 3

description: Generated edge list. The CyNetworkBMA output consisting of a list of edges and their probabilities that represent a gene network generated from the example DREAM4 input data set (available as Additional file 2). This output file corresponding to Additional file 3 is a text file consisting of three columns: parent, child, posterior probabilities. Each line represents a directed edge from parent node to child node with the posterior probability in the third column. We provide this file so that the user can verify the examples shown in this manuscript. (CSV 345 kb)
DOI: 10.6084/m9.figshare.c.3639479_d2.v1
title: Additinal file 2

description: Sample input data file. This is a text file containing the dataset â   i n s i l i c o_s i z e100_1_t i m e s e r i e s.t x tâ   was derived from DREAM 4 Challenge 2 [32, 33], and is publicly available from our project home page ( http://webdatascience.github.io/CyNetworkBMA ). (TXT 204 kb)
DOI: 10.6084/m9.figshare.c.3639497_d1.v1
title: Additional file 2: of Phylogenetic and morphological characterization of trypanosomes from Brazilian armoured catfishes and leeches reveal high species diversity, mixed infections and a new fish trypanosome species

description: Morphometric analysis of the different in vitro cultured forms of Trypanosoma abeli n. sp. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.c.3639497_d2.v1
title: Additional file 3: of Phylogenetic and morphological characterization of trypanosomes from Brazilian armoured catfishes and leeches reveal high species diversity, mixed infections and a new fish trypanosome species

description: Morphometric analysis of bloodstream trypomastigotes. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.c.3639497_d3.v1
title: Additional file 1: of Phylogenetic and morphological characterization of trypanosomes from Brazilian armoured catfishes and leeches reveal high species diversity, mixed infections and a new fish trypanosome species

description: Trypanosome parasitemia in blood removed from organs of Hypostomus affinis and H. luetkeni armored catfish. (XLSX 8 kb)
DOI: 10.6084/m9.figshare.c.3639497_d4.v1
title: Additional file 4: of Phylogenetic and morphological characterization of trypanosomes from Brazilian armoured catfishes and leeches reveal high species diversity, mixed infections and a new fish trypanosome species

description: Morphometric analysis of the different developmental forms of trypanosomes found in leeches of the species Haementeria brasiliensis . (XLSX 9 kb)
DOI: 10.6084/m9.figshare.c.3639527_d13.v1
title: Additional file 3: of 
                     HOTAIR and its surrogate DNA methylation signature indicate carboplatin resistance in ovarian cancer

description: Normalised beta-value DNAme data matrix that was used to identify the 67 HOTAIR -associated CpGs. This data matrix has dimensions 5000 CpGs (the 5000 most variable positions) by 134 samples; samples are annotated according to whether they are HOTAIRâ  +â  ve/-ve and type of chemotherapy received. (XLSX 9331 kb)
DOI: 10.6084/m9.figshare.c.3639536_d2.v1
title: MOESM2 of Identification of potential protein biomarkers for early detection of pregnancy in cow urine using 2D DIGE and label free quantitation

description: Additional file 2: Table S1. List of identified proteins revealed by Max Quant Softawre.
DOI: 10.5519/qd.ne5juc17
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (167 records)
DOI: 10.6084/m9.figshare.c.3639653_d1.v1
title: MOESM1 of Immune protection of chickens conferred by a vaccine consisting of attenuated strains of Salmonella Enteritidis, Typhimurium and Infantis

description: Additional file 1. Expression of all the genes tested in this study and included in the calculation of the PCA plots for individual chickens. This file contains expressions of genes associated with chicken inflammatory response for each individual chicken. Expressions of slightly different subsets of genes were determined in the cecum or liver based on the maximal responsiveness of these genes in either of the tissues. Each line represents one chicken and expressions of genes normalized to average expression of GAPDH, TBP and UB.
DOI: 10.6084/m9.figshare.c.3639725_d4.v1
title: Additional file 2: of Focal exposure of limited lung volumes to high-dose irradiation down-regulated organ development-related functions and up-regulated the immune response in mouse pulmonary tissues

description: The full list of genes include in each pattern and associated with enriched pathways. (XLSX 1669 kb)
DOI: 10.6084/m9.figshare.c.3639731_d1.v1
title: Additional file 2: Table S2. of Genetic variation of naturally growing olive trees in Israel: from abandoned groves to feral and wild?

description: Raw microsatellite data. The fragment sizes (in base pairs) of the two alleles per individual for each locus are given as a and b (0 represents missing data). (XLSX 38 kb)
DOI: 10.6084/m9.figshare.c.3639731_d4.v1
title: Additional file 3: Table S3. of Genetic variation of naturally growing olive trees in Israel: from abandoned groves to feral and wild?

description: Number of olive trees assigned to different multi-locus lineages (MLLs). (XLSX 18 kb)
DOI: 10.6084/m9.figshare.c.3639785_d9.v1
title: Additional file 4: Table S4. of The impact of tumor profiling approaches and genomic data strategies for cancer precision medicine

description: All matched mutation calls (due to size, see Additional file 5: Table S5 for unmatched mutation calls). (XLSX 3746 kb)
DOI: 10.6084/m9.figshare.c.3639797_d3.v1
title: Additional file 3: Table S1. of The phenotypic signature of adaptation to thermal stress in Escherichia coli

description: The loadings for each Biolog test in the first nine principal component. (XLS 58Â kb)
DOI: 10.6084/m9.figshare.c.3639854_d1.v1
title: Additional file 1: of modPDZpep: a web resource for structure based analysis of human PDZ-mediated interaction networks

description: All Supplementary tables are merged into single Excel file. Table S1. ROC- and PR-AUC values for 14 Human PDZ domains with artificial negative interaction data. Approximately equal number of binder and nonbinder were considered in small sets and average AUC is calculated for each domain. For SCRIBBLE1_LAP4_3, PSCDBP and NHERF2_2, equal number of non-binder peptides were randomly selected and AUC is calculated. This is repeated twice to get average AUC. Table S2. List of 43 PDZ domains included in modPDzpep testset. PDZ domains which cannot be predicted by POW are marked as ‘N’, while those used in the training are marked ‘T’. The list of test set peptides for these 43 PDZ domains is available under Benchmark link of modPDZpep server. Table S3. List of phage display peptides which showed exact match in human C-terminal proteome Table S4. Amino acid variants present on human PDZ domains. (XLS 55 kb)
DOI: 10.6084/m9.figshare.c.3639860_d2.v1
title: Additional file 10: of A systematic review and meta-analysis of the effectiveness of food safety education interventions for consumers in developed countries

description: Detailed GRADE assessment results. (XLS 31Â kb)
DOI: 10.6084/m9.figshare.c.3639860_d4.v1
title: Additional file 7: of A systematic review and meta-analysis of the effectiveness of food safety education interventions for consumers in developed countries

description: Summary table of PICO characteristics for each relevant article. (XLS 65Â kb)
DOI: 10.6084/m9.figshare.c.3639860_d3.v1
title: Additional file 8: of A systematic review and meta-analysis of the effectiveness of food safety education interventions for consumers in developed countries

description: Detailed within-study risk-of-bias assessment results. (XLS 92Â kb)
DOI: 10.6084/m9.figshare.c.3639860_d6.v1
title: Additional file 6: of A systematic review and meta-analysis of the effectiveness of food safety education interventions for consumers in developed countries

description: Citation list of all 77 relevant articles. (XLS 44Â kb)
DOI: 10.6084/m9.figshare.c.3639860_d9.v1
title: Additional file 4: of A systematic review and meta-analysis of the effectiveness of food safety education interventions for consumers in developed countries

description: Correlation values from previous studies. (XLSX 11Â kb)
DOI: 10.6084/m9.figshare.c.3639860_d11.v1
title: Additional file 13: of A systematic review and meta-analysis of the effectiveness of food safety education interventions for consumers in developed countries

description: Sensitivity analysis of comparing meta-analysis estimates for pre-post vs. pre-follow-up measurements. (XLS 26Â kb)
DOI: 10.6084/m9.figshare.c.3639860_d12.v1
title: Additional file 11: of A systematic review and meta-analysis of the effectiveness of food safety education interventions for consumers in developed countries

description: Sensitivity analysis of imputing different correlations for combining multiple outcome measures within a study. (XLS 29Â kb)
DOI: 10.6084/m9.figshare.c.3639860_d13.v1
title: Additional file 12: of A systematic review and meta-analysis of the effectiveness of food safety education interventions for consumers in developed countries

description: Sensitivity analysis of imputing different pre-post correlations for paired meta-analyses. (XLS 27Â kb)
DOI: 10.6084/m9.figshare.c.3639863_d1.v1
title: Additional file 6: of Molecular pathways associated with the nutritional programming of plant-based diet acceptance in rainbow trout following an early feeding exposure

description: List of probes in pathways significantly enriched based on early nutritional history in the liver. The list of differentially expressed mRNA probes comprising the pathways intermediary metabolism; oxidation-reduction; zymogens; peptidyl-prolyl-isomerases; cytoskeleton; and cell cycle that are significantly enriched based on early nutritional history in the liver are outlined in separate worksheets. Probe names highlighted in yellow were selected for RT-PCR confirmation. (XLSX 28Â kb)
DOI: 10.6084/m9.figshare.c.3639863_d5.v1
title: Additional file 5: of Molecular pathways associated with the nutritional programming of plant-based diet acceptance in rainbow trout following an early feeding exposure

description: List of probes in pathways significantly enriched based on early nutritional history in the brain. The list of differentially expressed mRNA probes comprising the pathways neurological system process; homocysteine and methionine metabolism; and neuroendocrine peptides that are significantly enriched based on early nutritional history in the brain are outlined in separate worksheets. Probe names highlighted in yellow were selected for RT-PCR confirmation. (XLSX 18Â kb)
DOI: 10.6084/m9.figshare.c.3639863_d6.v1
title: Additional file 1: of Molecular pathways associated with the nutritional programming of plant-based diet acceptance in rainbow trout following an early feeding exposure

description: List of mRNA probes differentially expressed based on nutritional history in the brain and liver. The lists of 1787 (3-week + Brain) and of 924 (3-week + Liver) differentially expressed mRNA probes (fold change ≥ 1.5 and p [nutritional history] ≤ 0.05), both at the end of the early exposure (Fig. 1; 3-week, diet V vs. diet M) and in the brain or liver of juvenile trout at the end of the V-challenge (Fig. 1; V-his vs. M-his). The list of 159 probes with overlapping significant expression profiles in both brain and liver comparisons is shown in a separate worksheet. Probe names highlighted in yellow were selected for RT-PCR confirmation. (XLSX 216 kb)
DOI: 10.6084/m9.figshare.c.3639863_d7.v1
title: Additional file 8: of Molecular pathways associated with the nutritional programming of plant-based diet acceptance in rainbow trout following an early feeding exposure

description: List of primers used in real-time RT-PCR analysis for confirmation of differential expression of selected genes identified by the microarray analysis. (XLSX 11Â kb)
DOI: 10.6084/m9.figshare.c.3639911_d1.v1
title: Additional file 1: Table S1. of Proposed nomenclature for microhaplotypes

description: Proposed standardized symbols for the 31 microhaplotype loci in Kidd et al. [2]. The first column gives the symbol used in that paper. The second column lists the standardized microhaplotype locus symbol. The SNPs involved in these loci remain the same except for two. Microhaplotype mh01KK-001 has had two SNPs added (indicated by asterisks) extending the length to 259 bp. Microhaplotype mh01Nakahara (originally identified by Dr. Nakahara but not otherwise named by him) has one new SNP (also indicated by an asterisk) added by Kidd Lab; the new extent is 279Â bp. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.c.3639911_d2.v1
title: Additional file 2: Figure S1. of Proposed nomenclature for microhaplotypes

description: Haplotype frequencies for a region between ADH7 and ADH1C. (XLSX 1.00 mb)
DOI: 10.6084/m9.figshare.c.3639917_d1.v1
title: Additional file 1: Table S1. of Evidence of recent interspecies horizontal gene transfer regarding nucleopolyhedrovirus infection of Spodoptera frugiperda

description: Potentially expressed ORFs in the genome of SfMNPV ColA. In bold letter are indicated the core genes. (XLSX 32Â kb)
DOI: 10.6084/m9.figshare.c.3639932_d1.v1
title: Additional file 2:  of Merino and Merino-derived sheep breeds: a genome-wide intercontinental study

description: Figure S1. Distributions of the number of SNPs across frequency bins for all population samples. Breeds are ordered along the x-axis according to group membership (Merino and Merino-derived sheep, in blue; Spanish non-Merino sheep, in purple; Italian non-Merino sheep, in cyan blue; primitive North European sheep, in brown; feral sheep, in green; wild sheep, in red). Figure S2. ADMIXTURE cross-validation analysis. For each number of assumed clusters (K) ranging from 1 to 37, prediction errors were calculated from five independent runs. Figure S3. TREEMIX log-likelihood values for the dataset of 671 samples arranged in 37 populations and for different numbers of migrations. Figure S4. TREEMIX log-likelihood values for the aggregated dataset with populations arranged into six groups as specified in the Methods section, and for different numbers of migrations. Figure S5. Heat map showing the correlation of r for pairs of SNPs that are separated by 0 to10 kb. Figure S6. Heat map showing the correlation of r for pairs of SNPs that are separated by 10 to 25Â kb. Figure S7. Heat map showing the correlation of r for pairs of SNPs that are separated by 100 to 250Â kb distances. Figure S8. Heat map showing the pair-wise haplotype sharing distances, calculated as the logarithm of 1/(total length of shared segments across the genome).
DOI: 10.6084/m9.figshare.c.3639929_d2.v1
title: Additional file 3: Table S3. of Reduced BRCA1 transcript levels in freshly isolated blood leukocytes from BRCA1 mutation carriers is mutation specific

description: Pathway enrichment analysis of genes differentially expressed between BRCA1 mutation carriers and non-carriers. (XLS 205 kb)
DOI: 10.6084/m9.figshare.c.3639932_d2.v1
title: Additional file 1:  of Merino and Merino-derived sheep breeds: a genome-wide intercontinental study

description: Table S1. Breed and population details and within-population genetic diversity parameters. Table S1 provides, for each considered population, information concerning the species, the geographical origin, the membership of breeds to four groups, as specified in the Methods section, the number of individuals (N), the proportion of polymorphic loci (P p l ), a measure of gene diversity (H e ), and the inbreeding coefficient (F). Table S2. Within-population genetic diversity parameters estimated for rarefied samples. Table S2 provides the proportion of polymorphic loci (P p l ), a measure of gene diversity (H e ), and the inbreeding coefficient (F) for population samples rarefied to N = 10 each. The membership of breeds to four groups, as specified in the Methods section, is also indicated. Table S3. Breeds and populations involved in the migration events inferred by TREEMIX. Table S3 provides a list of breeds and populations for which TREEMIX detected possible migration events. The analysis was carried out using the dataset of 671 samples from 37 populations, assuming M = 40. Relative migration weights are indicated. Branches of trees are shown in the Newick format. Only migrations with weights greater than 0.1 are shown. Table S4. Groups of populations involved in the migration events inferred by TREEMIX. Table S4 shows the results of the TREEMIX analysis carried out after removal of the Merino-derived breeds (Chinese Merino, Merinolandschaf, Sopravissana, Gentile di Puglia and Merinizzata) and clustering of the considered breeds and populations into six arbitrary groups, as specified in the Methods section. Relative migration weights are indicated. Table S5. Groups of populations involved in the migration events inferred by TREEMIX, after removal of the Andalusian Merino, Arapawa and Macarthur Merino populations. Table S5 shows the results of the TREEMIX analysis carried out after removal of Andalusian Merino, Arapawa, Macarthur Merino and the Merino-derived breeds (Chinese Merino, Merinolandschaf, Sopravissana, Gentile di Puglia and Merinizzata) and clustering of the considered breeds and populations into six arbitrary groups, as specified in the Methods section. Relative migration weights are indicated. Table S6. Z-scores from the f4 test on the aggregated dataset. Table S6 shows the results of the f4 test carried out using the dataset aggregated into six arbitrary groups (wild, WIL; feral, FER; primitive, PRIM; Merino, MER; Spanish non-Merino, SPA; Italian non-Merino; ITA). Only trees with significant Z-scores (&gt;3) are shown. For each tree, the three possible four-population topologies are reported.
DOI: 10.60520/ieda/113589
title: SIMS analyses of olivine in kimberlites

description: To obtain estimates of primary H2O contents in kimberlite melts, we have examined the systematics of proton incorporation in olivine point defects (referred as H) in grains from eight representative kimberlites from Africa, Canada and Greenland.
DOI: 10.6084/m9.figshare.c.3640079_d2.v1
title: Additional file 3: of Tracing the origin of disseminated tumor cells in breast cancer using single-cell sequencing

description: Copy number calls for all single cells and bulk samples. (ZIP 631 kb)
DOI: 10.6084/m9.figshare.c.3640079_d3.v1
title: Additional file 2: of Tracing the origin of disseminated tumor cells in breast cancer using single-cell sequencing

description: Supplementary Tables S1â  S7. (XLSX 99 kb)