cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7861784.v1
title: Prediction and integration of semantics during L2 and L1 listening

description: Using the visual world paradigm, we tested whether Dutch-English bilinguals predict upcoming semantic information in auditory sentence comprehension to the same extent in their native (L1) and second language (L2). Participants listened to sentences in L1 and L2 while their eye-movements were measured. A display containing a picture of either a target word or a semantic competitor, and three unrelated objects was shown before the onset of the auditory target word in the sentence. There were more fixations on the target and competitor pictures relative to the unrelated pictures in both languages, before hearing the target word could affect fixations. Also, semantically stronger related competitors attracted more fixations. This relatedness effect was stronger, and it started earlier in the L1 than in the L2. These results suggest that bilinguals predict semantics in the L2, but the spread of semantic activation during prediction is slower and weaker than in the L1.
DOI: 10.6084/m9.figshare.7861757
title: Hybrid Decay: A Transgenerational Epigenetic Decline in Vigor and Viability Triggered in Backcross Populations of Teosinte with Maize

description: The genotype files are coded in Hapmap format, and can be read by TASSEL (https://www.maizegenetics.net/tassel) or any programs that recognize tab-delimited files (e.g. R). The "Hybrid_Decay_GBS_merge.hmp.txt" file contains 18 individuals and 955,690 non-imputed SNP markersderived from more than 60,000 samples (http://www.panzea.org/). <br>This fileset contains the genotype file used in the following manuscript: Wei Xue, et al. (2019) Hybrid Decay: A Transgenerational Epigenetic Decline in Vigor and Viability Triggered in Backcross Populations of Teosinte with Maize. Genetics. The genotype file is coded in Hapmap format, and can be read by TASSEL (https://www.maizegenetics.net/tassel) or any programs that recognize tab-delimited files (e.g. R). The "Hybrid_Decay_GBS_merge.hmp.txt" file contains 18 individuals and 955,690 non-imputed SNP markersderived from more than 60,000 samples (http://www.panzea.org/).
DOI: 10.6084/m9.figshare.7861757.v1
title: Hybrid Decay: A Transgenerational Epigenetic Decline in Vigor and Viability Triggered in Backcross Populations of Teosinte with Maize

description: The genotype files are coded in Hapmap format, and can be read by TASSEL (https://www.maizegenetics.net/tassel) or any programs that recognize tab-delimited files (e.g. R). The "Hybrid_Decay_GBS_merge.hmp.txt" file contains 18 individuals and 955,690 non-imputed SNP markersderived from more than 60,000 samples (http://www.panzea.org/). <br>
DOI: 10.6084/m9.figshare.7861628
title: MOESM1 of Comparison of msp genotyping and a 24 SNP molecular assay for differentiating Plasmodium falciparum recrudescence from reinfection

description: Additional file 1. R code for generating truncated bar code.
DOI: 10.6084/m9.figshare.7861613
title: Additional file 4: of Fecal metatranscriptomics of macaques with idiopathic chronic diarrhea reveals altered mucin degradation and fucose utilization

description: Campylobacter_Subsystems_DESeq_results. This Excel spreadsheet contains the differential expression by SEED Subsystems hierarchies between ICD and control samples for Campylobacter-specific transcriptome (only those reads mapping to Campylobacter). The first tab contains a description of all hierarchies included in the analyses. The remaining tabs contain results corresponding to the level 1, level 2, and level 3 hierarchies. The controlMean refers to mean counts of the control samples. ExperimentalMean refers to mean counts of the ICD samples. Log2 fold changes refer to ICD relative to control. The p values are adjusted for multiple hypothesis testing. (XLSX 409 kb)
DOI: 10.6084/m9.figshare.7861628.v1
title: MOESM1 of Comparison of msp genotyping and a 24 SNP molecular assay for differentiating Plasmodium falciparum recrudescence from reinfection

description: Additional file 1. R code for generating truncated bar code.
DOI: 10.6084/m9.figshare.7861613.v1
title: Additional file 4: of Fecal metatranscriptomics of macaques with idiopathic chronic diarrhea reveals altered mucin degradation and fucose utilization

description: Campylobacter_Subsystems_DESeq_results. This Excel spreadsheet contains the differential expression by SEED Subsystems hierarchies between ICD and control samples for Campylobacter-specific transcriptome (only those reads mapping to Campylobacter). The first tab contains a description of all hierarchies included in the analyses. The remaining tabs contain results corresponding to the level 1, level 2, and level 3 hierarchies. The controlMean refers to mean counts of the control samples. ExperimentalMean refers to mean counts of the ICD samples. Log2 fold changes refer to ICD relative to control. The p values are adjusted for multiple hypothesis testing. (XLSX 409 kb)
DOI: 10.6084/m9.figshare.7861598
title: Additional file 2: of Fecal metatranscriptomics of macaques with idiopathic chronic diarrhea reveals altered mucin degradation and fucose utilization

description: All_bacteria_Subsystems_DESeq_results. This Excel spreadsheet contains the differential expression by SEED Subsystem hierarchies between ICD and control samples for community-wide metatranscriptomes. The first tab contains a description of all hierarchies included in the analyses. The remaining tabs contain results corresponding to the level 1, level 2, and level 3 hierarchies. The controlMean refers to mean counts of the control samples. ExperimentalMean refers to mean counts of the ICD samples. Log2 fold changes refer to ICD relative to control. The p values are adjusted for multiple hypothesis testing. (XLSX 444 kb)
DOI: 10.6084/m9.figshare.7861601
title: Additional file 3: of Fecal metatranscriptomics of macaques with idiopathic chronic diarrhea reveals altered mucin degradation and fucose utilization

description: Prevotella_Subsystems_DESeq_results. This Excel spreadsheet contains the differential expression by SEED Subsystem hierarchies between ICD and control samples for Prevotella-specific transcriptome (only those reads mapping to Prevotella). The first tab contains a description of all hierarchies included in the analyses. The remaining tabs contain results corresponding to the level 1, level 2, and level 3 hierarchies. The controlMean refers to mean counts of the control samples. ExperimentalMean refers to mean counts of the ICD samples. Log2 fold changes refer to ICD relative to control. The p values are adjusted for multiple hypothesis testing. (XLSX 365 kb)
DOI: 10.6084/m9.figshare.7861589
title: Additional file 3: of Genome-wide association study and scan for signatures of selection point to candidate genes for body temperature maintenance under the cold stress in Siberian cattle populations

description: Putatively selected regions of the cattle genome in the Hereford and Kazakh Whiteheaded breeds as reported by the DCMS statistics. (XLSX 16 kb)
DOI: 10.6084/m9.figshare.7861592
title: Additional file 1: of Fecal metatranscriptomics of macaques with idiopathic chronic diarrhea reveals altered mucin degradation and fucose utilization

description: Macaque_bacteria_genus_DESeq_results. This tab-separated file contains the DESeq2 output of differential bacterial gene expression at the genus level between ICD and control samples, with adjusted p values. The controlMean refers to mean counts of the control samples. ExperimentalMean refers to mean counts of the ICD samples. Log2 fold changes refer to ICD relative to control. The p values are adjusted for multiple hypothesis testing. (TSV 149 kb)
DOI: 10.6084/m9.figshare.7861598.v1
title: Additional file 2: of Fecal metatranscriptomics of macaques with idiopathic chronic diarrhea reveals altered mucin degradation and fucose utilization

description: All_bacteria_Subsystems_DESeq_results. This Excel spreadsheet contains the differential expression by SEED Subsystem hierarchies between ICD and control samples for community-wide metatranscriptomes. The first tab contains a description of all hierarchies included in the analyses. The remaining tabs contain results corresponding to the level 1, level 2, and level 3 hierarchies. The controlMean refers to mean counts of the control samples. ExperimentalMean refers to mean counts of the ICD samples. Log2 fold changes refer to ICD relative to control. The p values are adjusted for multiple hypothesis testing. (XLSX 444 kb)
DOI: 10.6084/m9.figshare.7861601.v1
title: Additional file 3: of Fecal metatranscriptomics of macaques with idiopathic chronic diarrhea reveals altered mucin degradation and fucose utilization

description: Prevotella_Subsystems_DESeq_results. This Excel spreadsheet contains the differential expression by SEED Subsystem hierarchies between ICD and control samples for Prevotella-specific transcriptome (only those reads mapping to Prevotella). The first tab contains a description of all hierarchies included in the analyses. The remaining tabs contain results corresponding to the level 1, level 2, and level 3 hierarchies. The controlMean refers to mean counts of the control samples. ExperimentalMean refers to mean counts of the ICD samples. Log2 fold changes refer to ICD relative to control. The p values are adjusted for multiple hypothesis testing. (XLSX 365 kb)
DOI: 10.6084/m9.figshare.7861580
title: Additional file 2: of Genome-wide association study and scan for signatures of selection point to candidate genes for body temperature maintenance under the cold stress in Siberian cattle populations

description: Description of the experimental dataset: breeds, sex, phenotype. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.7861589.v1
title: Additional file 3: of Genome-wide association study and scan for signatures of selection point to candidate genes for body temperature maintenance under the cold stress in Siberian cattle populations

description: Putatively selected regions of the cattle genome in the Hereford and Kazakh Whiteheaded breeds as reported by the DCMS statistics. (XLSX 16 kb)
DOI: 10.6084/m9.figshare.7861592.v1
title: Additional file 1: of Fecal metatranscriptomics of macaques with idiopathic chronic diarrhea reveals altered mucin degradation and fucose utilization

description: Macaque_bacteria_genus_DESeq_results. This tab-separated file contains the DESeq2 output of differential bacterial gene expression at the genus level between ICD and control samples, with adjusted p values. The controlMean refers to mean counts of the control samples. ExperimentalMean refers to mean counts of the ICD samples. Log2 fold changes refer to ICD relative to control. The p values are adjusted for multiple hypothesis testing. (TSV 149 kb)
DOI: 10.6084/m9.figshare.7861580.v1
title: Additional file 2: of Genome-wide association study and scan for signatures of selection point to candidate genes for body temperature maintenance under the cold stress in Siberian cattle populations

description: Description of the experimental dataset: breeds, sex, phenotype. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.7861445
title: Additional file 1: of Probabilistic independent component analysis of dynamic susceptibility contrast perfusion MRI in metastatic brain tumors

description: Table S1. Histopathology of primary lesion for â Otherâ cohort. Primary lesion site and number of case. (XLSX 8 kb)
DOI: 10.6084/m9.figshare.7861445.v1
title: Additional file 1: of Probabilistic independent component analysis of dynamic susceptibility contrast perfusion MRI in metastatic brain tumors

description: Table S1. Histopathology of primary lesion for â Otherâ cohort. Primary lesion site and number of case. (XLSX 8 kb)
DOI: 10.6084/m9.figshare.7861304
title: Additional file 8: of MGSEA â a multivariate Gene set enrichment analysis

description: Table S5. Mann-Whitney p-values of 16 pairwise random walk comparisons among the 676 functional categories in the TCGA GBM data. Mann-Whitney p-values of 16 pairwise random walk comparisons among the 676 significant gene sets in the TCGA GBM data. (XLSX 118 kb)
DOI: 10.6084/m9.figshare.7861310
title: Additional file 9: of MGSEA â a multivariate Gene set enrichment analysis

description: Table S6. Dominant and combinatorial features of enrichment in 676 functional classes of TCGA GBM data. The table shows the full list of significantly enriched gene sets and their combinatorial relations for TCGA GBM data. The reduced functional category for each gene set is also reported. An NA entry denotes that the gene set and its reduced functional category are identical. (XLSX 38 kb)
DOI: 10.6084/m9.figshare.7861301
title: Additional file 2: of Long-read based assembly and synteny analysis of a reference Drosophila subobscura genome reveals signatures of structural evolution driven by inversions recombination-suppression effects

description: Table S2. Genetic markers used for validation, and physical anchoring, ordering and orientation of scaffolds. In total, 683 markers were considered, of which 621 were used. 62 markers were not used because they showed inconsistencies as to their localization with respect to markers from other studies and our own data. The MS Excel file contains eight spreadsheets, including one for this title, one for each of the five major pseudochromosomes (i.e., A, J, U, E and O), one with a summary, and one with the references for the marker data. For each pseudochromosome, markers are listed in column “A”, including used cytological (numbered, black), used linkage (numbered, blue), and nonused (nonnumbered, red) markers. For each marker, information relative to its name, cytological localization, authors, corresponding D. pseudoobscura “GA” gene model name, inconsistency where it applies, coordinates in the pseudochromosome, scaffold name, scaffold orientation and cytological span, and BLASTn statistics is provided in subsequent columns, from “B” to “Y”. Column “X” provides the number of used marker per scaffold. Alternating color in the background denotes different scaffolds. Cytological coordinates are always relative to the Kunze-Mühl and Müller [12] standard reference map. From the summary spreadsheet, most of the inconsistencies (72%) come from one (Laayouni et al. 2007) out of the total 26 cited works. Excluding that study, the total percent of inconsistencies is only 2.85% (i.e, 17 out of 638 markers). (XLSX 168 kb)
DOI: 10.6084/m9.figshare.7861298
title: Additional file 7: of MGSEA â a multivariate Gene set enrichment analysis

description: Table S4. Dominant and combinatorial features of enrichment in 434 functional classes of TCGA breast cancer data. The table shows the full list of significantly enriched gene sets and their combinatorial relations for TCGA breast cancer data. The reduced functional category for each gene set is also reported. An NA entry denotes that the gene set and its reduced functional category are identical. (XLSX 28 kb)
DOI: 10.6084/m9.figshare.7861301.v1
title: Additional file 2: of Long-read based assembly and synteny analysis of a reference Drosophila subobscura genome reveals signatures of structural evolution driven by inversions recombination-suppression effects

description: Table S2. Genetic markers used for validation, and physical anchoring, ordering and orientation of scaffolds. In total, 683 markers were considered, of which 621 were used. 62 markers were not used because they showed inconsistencies as to their localization with respect to markers from other studies and our own data. The MS Excel file contains eight spreadsheets, including one for this title, one for each of the five major pseudochromosomes (i.e., A, J, U, E and O), one with a summary, and one with the references for the marker data. For each pseudochromosome, markers are listed in column “A”, including used cytological (numbered, black), used linkage (numbered, blue), and nonused (nonnumbered, red) markers. For each marker, information relative to its name, cytological localization, authors, corresponding D. pseudoobscura “GA” gene model name, inconsistency where it applies, coordinates in the pseudochromosome, scaffold name, scaffold orientation and cytological span, and BLASTn statistics is provided in subsequent columns, from “B” to “Y”. Column “X” provides the number of used marker per scaffold. Alternating color in the background denotes different scaffolds. Cytological coordinates are always relative to the Kunze-Mühl and Müller [12] standard reference map. From the summary spreadsheet, most of the inconsistencies (72%) come from one (Laayouni et al. 2007) out of the total 26 cited works. Excluding that study, the total percent of inconsistencies is only 2.85% (i.e, 17 out of 638 markers). (XLSX 168 kb)
DOI: 10.6084/m9.figshare.7861304.v1
title: Additional file 8: of MGSEA â a multivariate Gene set enrichment analysis

description: Table S5. Mann-Whitney p-values of 16 pairwise random walk comparisons among the 676 functional categories in the TCGA GBM data. Mann-Whitney p-values of 16 pairwise random walk comparisons among the 676 significant gene sets in the TCGA GBM data. (XLSX 118 kb)
DOI: 10.6084/m9.figshare.7861310.v1
title: Additional file 9: of MGSEA â a multivariate Gene set enrichment analysis

description: Table S6. Dominant and combinatorial features of enrichment in 676 functional classes of TCGA GBM data. The table shows the full list of significantly enriched gene sets and their combinatorial relations for TCGA GBM data. The reduced functional category for each gene set is also reported. An NA entry denotes that the gene set and its reduced functional category are identical. (XLSX 38 kb)
DOI: 10.6084/m9.figshare.7861292
title: Additional file 6: of MGSEA â a multivariate Gene set enrichment analysis

description: Table S3. Mann-Whitney p-values of 16 pairwise random walk comparisons among the 434 functional categories in the TCGA breast cancer data. The table shows the Mann-Whitney p-values of 16 pairwise random walk comparisons among the 434 significant gene sets in the TCGA breast cancer data. (XLSX 79 kb)
DOI: 10.6084/m9.figshare.7861295
title: Additional file 21: of Long-read based assembly and synteny analysis of a reference Drosophila subobscura genome reveals signatures of structural evolution driven by inversions recombination-suppression effects

description: Table S10. Synteny analysis of inversion breakpoints. Provided is breakpoint information for 12 inversions, including six from pseudochromosome A (h1, h2, h3, h4, 5 and 6), one from J (ST), two from U (1 and 2), two from E (g1 and ST), and one from O (ms). The MS Excel file contains six spreadsheets, including one for this title, and one for each of the five major pseudochromosomes (i.e., A, J, U, E and O). For each pseudochromosome, inversions are listed in column “A”. For each inversion, information about the three protein coding genes flanking each side of each breakpoint in three species, including D. melanogaster, D. guanche and D. subobscura is provided in subsequent columns, from “B” to “Q”. This information includes species names, names and pseudochromosome coordinates of the three coding gene markers on both sides of each distal and proximal breakpoint, and the size of the pseudochromosome segment spanned by the breakpoints in Mb. Also provided is, for each breakpoint, its cytological and estimated pseudochromosome coordinates, and its hypothetical originating mechanism with the length of the associated duplication where it applies. Cells color background indicate contiguity (brown) or altered (yellow) order of the markers relative to the outgroup (D. melanogaster/D. pseudoobscura). For example, in the case of hypothetical inversion 1 of the A chromosome (i.e., h1) in D. subobscura, the three markers downstream the proximal breakpoint and upstream the distal breakpoint are in reverse order relative to D. guanche, which shows the markers ordered as in D. melanogaster. Reciprocal BLASTn searches with each breakpoint did not detect evidence of duplication, suggesting that the most likely originating mechanism of inversion Ah1 (depicted in yellow) is simple, or nearly straight breaks. (XLSX 31 kb)
DOI: 10.6084/m9.figshare.7861286
title: Additional file 5: of MGSEA â a multivariate Gene set enrichment analysis

description: Table S2. Parameters settings for analysis presented in this study. The table shows the parameters used for MGSEA and REVIGO in the analysis. (XLSX 8 kb)
DOI: 10.6084/m9.figshare.7861292.v1
title: Additional file 6: of MGSEA â a multivariate Gene set enrichment analysis

description: Table S3. Mann-Whitney p-values of 16 pairwise random walk comparisons among the 434 functional categories in the TCGA breast cancer data. The table shows the Mann-Whitney p-values of 16 pairwise random walk comparisons among the 434 significant gene sets in the TCGA breast cancer data. (XLSX 79 kb)
DOI: 10.6084/m9.figshare.7861295.v1
title: Additional file 21: of Long-read based assembly and synteny analysis of a reference Drosophila subobscura genome reveals signatures of structural evolution driven by inversions recombination-suppression effects

description: Table S10. Synteny analysis of inversion breakpoints. Provided is breakpoint information for 12 inversions, including six from pseudochromosome A (h1, h2, h3, h4, 5 and 6), one from J (ST), two from U (1 and 2), two from E (g1 and ST), and one from O (ms). The MS Excel file contains six spreadsheets, including one for this title, and one for each of the five major pseudochromosomes (i.e., A, J, U, E and O). For each pseudochromosome, inversions are listed in column “A”. For each inversion, information about the three protein coding genes flanking each side of each breakpoint in three species, including D. melanogaster, D. guanche and D. subobscura is provided in subsequent columns, from “B” to “Q”. This information includes species names, names and pseudochromosome coordinates of the three coding gene markers on both sides of each distal and proximal breakpoint, and the size of the pseudochromosome segment spanned by the breakpoints in Mb. Also provided is, for each breakpoint, its cytological and estimated pseudochromosome coordinates, and its hypothetical originating mechanism with the length of the associated duplication where it applies. Cells color background indicate contiguity (brown) or altered (yellow) order of the markers relative to the outgroup (D. melanogaster/D. pseudoobscura). For example, in the case of hypothetical inversion 1 of the A chromosome (i.e., h1) in D. subobscura, the three markers downstream the proximal breakpoint and upstream the distal breakpoint are in reverse order relative to D. guanche, which shows the markers ordered as in D. melanogaster. Reciprocal BLASTn searches with each breakpoint did not detect evidence of duplication, suggesting that the most likely originating mechanism of inversion Ah1 (depicted in yellow) is simple, or nearly straight breaks. (XLSX 31 kb)
DOI: 10.6084/m9.figshare.7861298.v1
title: Additional file 7: of MGSEA â a multivariate Gene set enrichment analysis

description: Table S4. Dominant and combinatorial features of enrichment in 434 functional classes of TCGA breast cancer data. The table shows the full list of significantly enriched gene sets and their combinatorial relations for TCGA breast cancer data. The reduced functional category for each gene set is also reported. An NA entry denotes that the gene set and its reduced functional category are identical. (XLSX 28 kb)
DOI: 10.6084/m9.figshare.7861280
title: Additional file 4: of MGSEA – a multivariate Gene set enrichment analysis

description: Table S1. Number of significantly enriched gene sets using top 100 genes from each feature score. The table shows the number of significantly enriched gene sets by querying top 100 genes from each feature score. A gene set is significantly enriched if the p-value of the Fisher’s exact test &lt;0.05. (XLSX 8 kb)