cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.14850734.v1
title: Additional file 5 of Reliable wolf-dog hybrid detection in Europe using a reduced SNP panel developed for non-invasively collected samples

description: Additional file 5: Table S5. The first tab contains names, locations and sampling dates for the samples that were genotyped in this study. Column named “Replicates” in the first tab shows how many times the same sample was genotyped, and the number in the parenthesis shows how many times the same individual was genotyped. Samples that were not included in the analysis are indicated. The second tab contains names, locations and sampling dates for the samples from the wolves from Italy and the Iberian Peninsula that were genotyped with the CanineHD Whole-Genome BeadChip (Illumina). The third tab contains sample names and breeds for the dog samples that were genotyped with the Illumina CanineHD chip. In each tab, there are results from the STRUCTURE and NEWHYBRIDS runs, with all possible prior combinations, for all the individuals included in the runs. When the result differed between the runs, several results were included. If the analysis was been done using a consensus genotype based on several samples from the same individual, the same result is indicated for all samples.
DOI: 10.6084/m9.figshare.14850731.v1
title: Additional file 4 of Reliable wolf-dog hybrid detection in Europe using a reduced SNP panel developed for non-invasively collected samples

description: Additional file 4: Table S4. FST values for dogs and wolves grouped based on the sampling location, except for Italian immigrants that were sampled in Germany. Analysis was performed also without Italian immigrants (n = 7) and Russian wolves (n = 4) due to low sample sizes in these groups. However, the FST values between the remaining groups were the same. When all wolves were combined as one group (n = 288), the overall FST to dogs (without wolf-dog breeds, n = 300) was 0.72 (p
DOI: 10.6084/m9.figshare.14850728.v1
title: Additional file 3 of Reliable wolf-dog hybrid detection in Europe using a reduced SNP panel developed for non-invasively collected samples

description: Additional file 3: Table S3. Genotyping success (proportion of successfully scored loci over all SNP loci) for samples from species that are potential sources of DNA in non-invasively collected samples.
DOI: 10.6084/m9.figshare.14850725.v1
title: Additional file 2 of Reliable wolf-dog hybrid detection in Europe using a reduced SNP panel developed for non-invasively collected samples

description: Additional file 2: Table S2. Comparison of genotypes from same individuals genotyped with CanineHD chip (Illumina) and microfluidic array (Fluidigm). We assumed Illumina genotype as the true genotype of individual. False allele: an allele seen in Fluidigm genotype but not in corresponding Illumina genotype; Missing allele: an allele seen in Illumina genotype but not in Fluidigm genotype; Hom: homozygous; Het: heterozygous.
DOI: 10.6084/m9.figshare.14850722.v1
title: Additional file 1 of Reliable wolf-dog hybrid detection in Europe using a reduced SNP panel developed for non-invasively collected samples

description: Additional file 1: Table S1. Comparison of non-invasive samples to the consensus of corresponding invasive samples. Corresponding samples are on the same row. False allele: an allele seen in non-invasive sample but not in corresponding invasive sample; Missing allele: an allele seen in invasive sample but not detected in the corresponding non-invasive sample; Missing data: sample didn’t produce readable genotype, Hom: homozygous, Het: heterozygous.
DOI: 10.6084/m9.figshare.14850698.v1
title: Additional file 12 of Reliable wolf-dog hybrid detection in Europe using a reduced SNP panel developed for non-invasively collected samples

description: Additional file 12: Table S12. Description of SNPs and primer sequences used in this study. Allele frequencies for the 93 SNPs are also reported. The first tab contains 96 SNPs that were included in the final SNP panel. Three SNPs that were removed before the analysis are indicated. The remaining SNPs that were tested but not included in the final panel and their corresponding primer sequences are in the second tab.
DOI: 10.6084/m9.figshare.14850695.v1
title: Additional file 11 of Reliable wolf-dog hybrid detection in Europe using a reduced SNP panel developed for non-invasively collected samples

description: Additional file 11: Table S11. Assignment accuracy for the selected 93 SNPs to categorize simulated individuals between dog and Iberian wolves for 8 different hybrid classes to the correct category (&gt; 0.5) or assign it to any hybrid category (sum of assignments to hybrid categories &gt; 0.7) by the software NEWHYBRIDS. Analysis was run with the four possible prior combinations. Range of results from different runs is indicated.
DOI: 10.6084/m9.figshare.14850692.v1
title: Additional file 10 of Reliable wolf-dog hybrid detection in Europe using a reduced SNP panel developed for non-invasively collected samples

description: Additional file 10: Table S10. Assignment accuracy for the selected 93 SNPs to categorize simulated individuals between dog and Italian wolves from 8 different hybrid classes to the correct category (&gt; 0.5) or assign it to any hybrid category (sum of assignments to hybrid categories &gt; 0.7) by the software NEWHYBRIDS. Analysis was run with the four possible prior combinations. Range of results from different runs is indicated.
DOI: 10.6084/m9.figshare.14850677.v1
title: Additional file 3 of SCAPP: an algorithm for improved plasmid assembly in metagenomes

description: Tab-separated list of the human gut-specific reference genomes used in the simulations.
DOI: 10.6084/m9.figshare.14850670.v1
title: Additional file 2 of MicroPIPE: validating an end-to-end workflow for high-quality complete bacterial genome construction

description: Additional file 2. Strain list 1: ST131 data used for validation (including accessions for complete genomes, raw ONT data and Illumina read data). Strain list 2: Accession and metadata for the eight publicly available ONT assemblies used in subsequent validation. Execution parameters: Specific commands used for each tool in this study. Guppy 3.4.3 vs. Guppy 3.6.1 remaining variants: List of variant positions and genetic context for Guppy v3.4.3 and v3.6.1 based on comparison to the EC958 reference genome standard. MicroPIPE metrics: Pipeline run times and memory metrics for 12 ST131 strains.
DOI: 10.6084/m9.figshare.14850661.v1
title: Additional file 1 of Comparative insights into genome signatures of ferric iron oxide- and anode-stimulated Desulfuromonas spp. strains

description: Additional file 1.
DOI: 10.6084/m9.figshare.14850650.v1
title: Additional file 4 of Genetic variation in recombination rate in the pig

description: Additional file 4: Table S3. Sex-averaged map of the landscape of pig recombination rate in 1-Mb windows.
DOI: 10.6084/m9.figshare.14850647.v1
title: Additional file 3 of Genetic variation in recombination rate in the pig

description: Additional file 3: Table S2. Female map of the landscape of pig recombination rate in 1-Mb windows.
DOI: 10.6084/m9.figshare.14850644.v1
title: Additional file 2 of Genetic variation in recombination rate in the pig

description: Additional file 2: Table S1. Male map of the landscape of pig recombination rate in 1-Mb windows
DOI: 10.6084/m9.figshare.14850635.v1
title: Additional file 2 of Pathological correlates of impaired self-awareness of memory function in Alzheimer’s disease

description: Additional file 2.
DOI: 10.6084/m9.figshare.14850631.v1
title: Additional file 2 of A proteomic network approach resolves stage-specific molecular phenotypes in chronic traumatic encephalopathy

description: Additional file 2. Table S1. Demographics and traits: Cases are grouped according to diagnosis. Case number is either Emory (letter followed by numbers) or Boston University (4-digit number). Age, Sex, PMI (postmortem interval), and brain region are shown for each case. Batch indicates the TMT batch numbers (1–10). Channel within batch is listed in 2 columns, both as a single number and as a 3-digit number with letter. Platform designates which mass spectrometer was utilized, either the Fusion 1 or Lumos. Demographic summary chart is also included. Table S2. ANOVA output for CTE/FTLD-MAPT dataset: ANOVA data for 6713 proteins without missing values across 10 batches. All combinations are shown between control and neurodegenerative diseases including p-values and differential expression. Corresponding data from the AD TMT dataset for each of the proteins is also included in columns BK and BJ. Table S3. Significantly enriched proteins identified in AD, CTE 4 and FTLD-MAPT and Gene Ontology for Biological Process, Molecular Function and Cellular Component. Table S4. kME Values for proteins within each module following WGCNA of the CTE/FTLD-MAPT TMT dataset. Table S5. Raw abundance data from CTE/FTLD-MAPT TMT Proteome. Table S6. WGCNA module number, color and size.
DOI: 10.6084/m9.figshare.14850911
title: Additional file 1 of Application of deep learning-based neural networks using theoretical seismograms as training data for locating earthquakes in the Hakone volcanic region, Japan

description: Additional file 1: Table S1. Comparisons of Root Mean Square Errors (RMSE) of hypocentral parameters estimated by 3DCNN and 3DCNN with the latitude grid size of the learning data set to be doubled.
DOI: 10.6084/m9.figshare.14850881
title: Additional file 3 of In silico analysis of differentially expressed genesets in metastatic breast cancer identifies potential prognostic biomarkers

description: Additional file 3:. Table S2. Twelve raw datasets with under-expressed genes.
DOI: 10.6084/m9.figshare.14850878
title: Additional file 2 of In silico analysis of differentially expressed genesets in metastatic breast cancer identifies potential prognostic biomarkers

description: Additional file 2:. Table S1. Twelve raw datasets with over-expressed genes.
DOI: 10.6084/m9.figshare.14850875
title: Additional file 1 of In silico analysis of differentially expressed genesets in metastatic breast cancer identifies potential prognostic biomarkers

description: Additional file 1: Supplementary Figure S1. KIF2C and ESR1 are hub genes the most significantly co-expressed with the potential biomarker candidate genes. (A and B) Shown are Pearson's pairwise correlation plots of RNA-seq gene expression between four DOE-A (A) or three DUE-A genes (B) and their most significantly co-expressed hub genes identified from PPI networks. Statistical analyses were performed by the pre-set analytic method of bc-GenExMiner. Supplementary Figure S2. Comparison of mRNA expression of the two most significantly co-expressed hub genes (KIF2C and ESR1) between basal-like or triple-negative breast cancer and other subtypes of breast cancer. (A and B) RNA-seq data of KIF2C and ESR1 were obtained from the Cancer Cell Line Encyclopedia (CCLE) and analyzed. N = 31 in BL/TNBC and N = 26 in luminal type cell lines. (C and D) RNA-seq data of KIF2C and ESR1 from The Cancer Genome Atlas (TCGA) [58] were analyzed at bc-GenExMiner v4.3. N = 97 in BL/TNBC and N = 736 in non-BL/TNBC type breast cancer patient samples. Statistical significance in A and B was determined by unpaired t-tests and those in C and D were determined by the pre-set analytic method of bc-GenExMiner. Supplementary Figure S3. Correlation between the expression levels of two co-expressed hub genes (KIF2C and ESR1) and patient survivals. (A and B) Relapse-free, overall, distant metastasis-free, and post-progression survival of two co-expressed hub genes (KIF2C in (A); ESR1 in (B)) were stratified by the expression levels of each gene (low or high). Expression data were analyzed by KM plotter ( http://kmplot.com/ ). JetSet best probes were selected and patients (for KIF2C, N = 3951 in RFS, = 1402 in OS, = 1746 in DMFS and = 414 in PPS; for ESR1, N = 3951 in RFS, = 1402 in OS, = 1746 in DMFS and = 414 in PPS) were split by median expression. (C) Metastatic relapse-free survival of KIF2C and ESR1 was stratified by the expression levels of each gene (low or high). Microarray expression data were analyzed by bc-GenExMiner v4.3 ( http://bcgenex.centregauducheau.fr/ ). Patients (KIF2C, N = 4533; ESR1, N = 4785) were split by median expression. Statistical analyses were performed by pre-set analytic methods. HRs (hazardous ratios) and 95% CIs (confidence intervals) are indicated.
DOI: 10.6084/m9.figshare.14850848
title: Additional file 1 of The Retornus-2 study: impact of respiratory muscle training in subacute stroke patients with dysphagia, study protocol of a double-blind randomized controlled trial

description: Additional file 1. A: Informed consent. B: Informed consent.
DOI: 10.6084/m9.figshare.14850847
title: Additional file 2 of Vertical clinging and leaping induced evolutionary rate shifts in postcranial evolution of tamarins and marmosets (Primates, Callitrichidae)

description: Additional file 2. Details on specimens, scanning resolution, scanning apparatus and operators.
DOI: 10.6084/m9.figshare.14850844
title: Additional file 1 of Vertical clinging and leaping induced evolutionary rate shifts in postcranial evolution of tamarins and marmosets (Primates, Callitrichidae)

description: Additional file 1: Table S1. Designation of the anatomical landmarks used for the humerus. Fig. S1. Location of the anatomical landmarks used for the humerus. Table S2. Designation of the anatomical landmarks used for the femur. Fig. S2. Location of the anatomical landmarks used for the femur. Table S3. Number of curve sliding landmarks per curve for humerus and femur. Fig. S3. Deformations associated with PCA axes. Table S4. Test for evolutive rate shift in shape across the phylogeny. Fig. S4. Node numbering used in the Table S4.
DOI: 10.6084/m9.figshare.14850829
title: Additional file 7 of OLIG2 regulates lncRNAs and its own expression during oligodendrocyte lineage formation

description: Additional file 7: Table S5. A list of statistically significant targets in OLIG2 RIP-Seq experiments
DOI: 10.6084/m9.figshare.14850820
title: Additional file 5 of OLIG2 regulates lncRNAs and its own expression during oligodendrocyte lineage formation

description: Additional file 5: Table S4. The annotation of ‘K4 only’, ‘K27 only’, and bivalent domains in NSCs, OPCs and NFOs (upstream and downstream 2 kb of TSS).
DOI: 10.6084/m9.figshare.14850814
title: Additional file 3 of OLIG2 regulates lncRNAs and its own expression during oligodendrocyte lineage formation

description: Additional file 3: Table S3. The gene expression patterns of lncRNA bound by OLIG2 in NSCs, OPCs and NFOs.
DOI: 10.6084/m9.figshare.14850811
title: Additional file 2 of OLIG2 regulates lncRNAs and its own expression during oligodendrocyte lineage formation

description: Additional file 2: Table S2. The differentiation expressed genes of OPCs vs. NSCs and NFOs vs. OPCs (At least one sample's (NSCs/OPCs/NFOs) FPKM&gt; 1, FDR 1).
DOI: 10.6084/m9.figshare.14850808
title: Additional file 1 of OLIG2 regulates lncRNAs and its own expression during oligodendrocyte lineage formation

description: Additional file 1: Table S1. The annotation of Olig2 binding peaks in NSCs, OPCs, and NFOs (upstream 5 kb plus genebody).
DOI: 10.6084/m9.figshare.14850794
title: Additional file 9 of A synbiotic intervention modulates meta-omics signatures of gut redox potential and acidity in elective caesarean born infants

description: Additional file 9: Supplementary Table 8. Non-parametric Mann-Whitney U tests performed at each time point on each pair of study group combination at genus level.
DOI: 10.6084/m9.figshare.14850791
title: Additional file 8 of A synbiotic intervention modulates meta-omics signatures of gut redox potential and acidity in elective caesarean born infants

description: Additional file 8: Supplementary Table 7. Non-parametric Mann-Whitney U tests performed at each time point on each pair of study group combination at family level.
DOI: 10.6084/m9.figshare.14850788
title: Additional file 7 of A synbiotic intervention modulates meta-omics signatures of gut redox potential and acidity in elective caesarean born infants

description: Additional file 7: Supplementary Table 6. 16S rRNA Species data (Mean and SD) per group and time point.
DOI: 10.6084/m9.figshare.14850785
title: Additional file 6 of A synbiotic intervention modulates meta-omics signatures of gut redox potential and acidity in elective caesarean born infants

description: Additional file 6: Supplementary Table 5. 16S rRNA Genus data (Mean and SD) per group and time point.
DOI: 10.6084/m9.figshare.14850782
title: Additional file 5 of A synbiotic intervention modulates meta-omics signatures of gut redox potential and acidity in elective caesarean born infants

description: Additional file 5: Supplementary Table 4. 16S rRNA Family data (Mean and SD) per group and time point.
DOI: 10.6084/m9.figshare.14850779
title: Additional file 4 of A synbiotic intervention modulates meta-omics signatures of gut redox potential and acidity in elective caesarean born infants

description: Additional file 4: Supplementary Table 3. Permutational Multivariate Analysis of Variance (PERMANOVA) tests.
DOI: 10.6084/m9.figshare.14850776
title: Additional file 3 of A synbiotic intervention modulates meta-omics signatures of gut redox potential and acidity in elective caesarean born infants

description: Additional file 3: Supplementary Table 2. 16S rRNA sequencing outputs.
DOI: 10.6084/m9.figshare.14850773
title: Additional file 2 of A synbiotic intervention modulates meta-omics signatures of gut redox potential and acidity in elective caesarean born infants

description: Additional file 2: Supplementary Table 1. Number of subjects per group and number of 16S rRNA samples per group and time point.
DOI: 10.6084/m9.figshare.14850769
title: Additional file 1 of Studying visual search without an eye tracker: an assessment of artificial foveation

description: Additional file 1. Example of artificial foveation technique implemented in E-Prime 3.0.
DOI: 10.6084/m9.figshare.14850767
title: Additional file 13 of A synbiotic intervention modulates meta-omics signatures of gut redox potential and acidity in elective caesarean born infants

description: Additional file 13: Supplementary Table 12. SEED functional annotation.
DOI: 10.6084/m9.figshare.14850764
title: Additional file 12 of A synbiotic intervention modulates meta-omics signatures of gut redox potential and acidity in elective caesarean born infants

description: Additional file 12: Supplementary Table 11. KEGG functional annotation.
DOI: 10.6084/m9.figshare.14850761
title: Additional file 11 of A synbiotic intervention modulates meta-omics signatures of gut redox potential and acidity in elective caesarean born infants

description: Additional file 11: Supplementary Table 10. Categorization of bacterial families into functional groups (anaerobic/aerobic metabolism and Lactic Acid Bacteria).
DOI: 10.6084/m9.figshare.14850758
title: Additional file 10 of A synbiotic intervention modulates meta-omics signatures of gut redox potential and acidity in elective caesarean born infants

description: Additional file 10: Supplementary Table 9. Non-parametric Mann-Whitney U tests performed at each time point on each pair of study group combination at species level.
DOI: 10.6084/m9.figshare.14850746
title: Additional file 9 of Reliable wolf-dog hybrid detection in Europe using a reduced SNP panel developed for non-invasively collected samples

description: Additional file 9: Table S9. NEWHYBRIDS and STRUCTURE results for other canid species that successfully amplified with the SNP panel.
DOI: 10.6084/m9.figshare.14850743
title: Additional file 8 of Reliable wolf-dog hybrid detection in Europe using a reduced SNP panel developed for non-invasively collected samples

description: Additional file 8: Table S8. NEWHYBRIDS and STRUCTURE results for wolves living in two animal parks in Germany.
DOI: 10.6084/m9.figshare.14850740
title: Additional file 7 of Reliable wolf-dog hybrid detection in Europe using a reduced SNP panel developed for non-invasively collected samples

description: Additional file 7: Table S7. NEWHYBRIDS and STRUCTURE results for Finnish museum samples categorized in different time periods as in Jansson et al. [54].
DOI: 10.6084/m9.figshare.14850737
title: Additional file 6 of Reliable wolf-dog hybrid detection in Europe using a reduced SNP panel developed for non-invasively collected samples

description: Additional file 6: Table S6. Description of suspected hybrid samples and discussion of the corresponding results. Microsatellite results, used for comparison, are unpublished.
DOI: 10.5281/zenodo.4587089
title: Smart Contract Code Summarization Dataset

description: The Paper has been accepted by ICPC'21. If you find this dataset useful, please cite our paper, here's the link: https://arxiv.org/abs/2103.07164 The whole data includes: <strong>(1)</strong> <strong>contracts:</strong> 347,410 smart contract &lt;method, comment&gt; pair raw data. <strong>(2)</strong> <strong>dataset:</strong> <em>a.</em> dictionaries: the dictionary of each sequence. <em> b.</em> token_idx: each input that has translated to digital index. <em> c. </em>dataset.pkl: 317,680 (SBT sequence, nodes equence, adjacency matrix, comment) tuples.
DOI: 10.5281/zenodo.4451875
title: Smart Contract Code Summarization Dataset

description: The Paper has been accepted by ICPC'21. If you find this dataset useful, please cite our paper, here's the link: https://arxiv.org/abs/2103.07164 The whole data includes: <strong>(1)</strong> <strong>contracts:</strong> 347,410 smart contract &lt;method, comment&gt; pair raw data. <strong>(2)</strong> <strong>dataset:</strong> <em>a.</em> dictionaries: the dictionary of each sequence. <em> b.</em> token_idx: each input that has translated to digital index. <em> c. </em>dataset.pkl: 317,680 (SBT sequence, nodes equence, adjacency matrix, comment) tuples.
DOI: 10.6084/m9.figshare.14850734
title: Additional file 5 of Reliable wolf-dog hybrid detection in Europe using a reduced SNP panel developed for non-invasively collected samples

description: Additional file 5: Table S5. The first tab contains names, locations and sampling dates for the samples that were genotyped in this study. Column named “Replicates” in the first tab shows how many times the same sample was genotyped, and the number in the parenthesis shows how many times the same individual was genotyped. Samples that were not included in the analysis are indicated. The second tab contains names, locations and sampling dates for the samples from the wolves from Italy and the Iberian Peninsula that were genotyped with the CanineHD Whole-Genome BeadChip (Illumina). The third tab contains sample names and breeds for the dog samples that were genotyped with the Illumina CanineHD chip. In each tab, there are results from the STRUCTURE and NEWHYBRIDS runs, with all possible prior combinations, for all the individuals included in the runs. When the result differed between the runs, several results were included. If the analysis was been done using a consensus genotype based on several samples from the same individual, the same result is indicated for all samples.
DOI: 10.6084/m9.figshare.14850731
title: Additional file 4 of Reliable wolf-dog hybrid detection in Europe using a reduced SNP panel developed for non-invasively collected samples

description: Additional file 4: Table S4. FST values for dogs and wolves grouped based on the sampling location, except for Italian immigrants that were sampled in Germany. Analysis was performed also without Italian immigrants (n = 7) and Russian wolves (n = 4) due to low sample sizes in these groups. However, the FST values between the remaining groups were the same. When all wolves were combined as one group (n = 288), the overall FST to dogs (without wolf-dog breeds, n = 300) was 0.72 (p