cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.9776543
title: Additional file 2: of The developmental origins of sex-biased expression in cardiac development

description: Table S2. Accession and metadata of all samples analyzed in this study (XLSX 10 kb)
DOI: 10.6084/m9.figshare.9776540.v1
title: Additional file 1: of Fast and accurate average genome size and 16S rRNA gene average copy number computation in metagenomic data

description: Single-copy genes universally present in prokaryotes. Table showing the COG number of the 35 single-copy genes identified by Raes et al. (2007), and the number of sequences included in each COG. (XLSX 42 kb)
DOI: 10.6084/m9.figshare.9776534.v1
title: Additional file 1: of The developmental origins of sex-biased expression in cardiac development

description: Table S1. List of antibodies used for ChIP-seq (XLSX 9 kb)
DOI: 10.6084/m9.figshare.9776543.v1
title: Additional file 2: of The developmental origins of sex-biased expression in cardiac development

description: Table S2. Accession and metadata of all samples analyzed in this study (XLSX 10 kb)
DOI: 10.6084/m9.figshare.9776525
title: Additional file 15: of The developmental origins of sex-biased expression in cardiac development

description: Dataset S9. Sex-biased Genes Shared between Human and Mouse Adult Hearts (XLSX 13 kb)
DOI: 10.6084/m9.figshare.9776531
title: Additional file 11: of Fast and accurate average genome size and 16S rRNA gene average copy number computation in metagenomic data

description: Exploring the variability of the AGS and ACN of TARA Oceans metagenomes. Table with details of the Pearson correlation tests between and among the AGS and ACN, and the functional and taxonomic richness of TARA Ocean metagenomes, and the water depth and temperature of the sampling sites. (XLSX 34 kb)
DOI: 10.6084/m9.figshare.9776522
title: Additional file 10: of Fast and accurate average genome size and 16S rRNA gene average copy number computation in metagenomic data

description: Comparing the AGS and ACN of TARA Oceans metagenomes between water layers. Table showing details of the Wilcoxon rank-sum tests, performed to evaluate the differentiation of TARA Oceans metagenomes from different water layers according to their AGS, and ACN. The comparisons were made on a matching subset of 63 metagenomes, obtained from the surface, deep chlorophyll maximum, and mesopelagic water layers (SRF, DCM, and MES, respectively), at 21 sampling sites. (XLSX 44 kb)
DOI: 10.6084/m9.figshare.9776519
title: Additional file 1: of Does mHealth voice messaging work for improving knowledge and practice of maternal and newborn healthcare?

description: Study questionnaires. (ZIP 380 kb)
DOI: 10.6084/m9.figshare.9776525.v1
title: Additional file 15: of The developmental origins of sex-biased expression in cardiac development

description: Dataset S9. Sex-biased Genes Shared between Human and Mouse Adult Hearts (XLSX 13 kb)
DOI: 10.6084/m9.figshare.9776519.v1
title: Additional file 1: of Does mHealth voice messaging work for improving knowledge and practice of maternal and newborn healthcare?

description: Study questionnaires. (ZIP 380 kb)
DOI: 10.6084/m9.figshare.9776531.v1
title: Additional file 11: of Fast and accurate average genome size and 16S rRNA gene average copy number computation in metagenomic data

description: Exploring the variability of the AGS and ACN of TARA Oceans metagenomes. Table with details of the Pearson correlation tests between and among the AGS and ACN, and the functional and taxonomic richness of TARA Ocean metagenomes, and the water depth and temperature of the sampling sites. (XLSX 34 kb)
DOI: 10.6084/m9.figshare.9776522.v1
title: Additional file 10: of Fast and accurate average genome size and 16S rRNA gene average copy number computation in metagenomic data

description: Comparing the AGS and ACN of TARA Oceans metagenomes between water layers. Table showing details of the Wilcoxon rank-sum tests, performed to evaluate the differentiation of TARA Oceans metagenomes from different water layers according to their AGS, and ACN. The comparisons were made on a matching subset of 63 metagenomes, obtained from the surface, deep chlorophyll maximum, and mesopelagic water layers (SRF, DCM, and MES, respectively), at 21 sampling sites. (XLSX 44 kb)
DOI: 10.6084/m9.figshare.9776513
title: Additional file 14: of The developmental origins of sex-biased expression in cardiac development

description: Datasets S7Â and S8. Ingenuity Pathway Analysis for sex-biased genes in adult heart (XLSX 19 kb)
DOI: 10.6084/m9.figshare.9776513.v1
title: Additional file 14: of The developmental origins of sex-biased expression in cardiac development

description: Datasets S7Â and S8. Ingenuity Pathway Analysis for sex-biased genes in adult heart (XLSX 19 kb)
DOI: 10.6084/m9.figshare.9776498
title: Additional file 11: of The developmental origins of sex-biased expression in cardiac development

description: Dataset S6. Sex Biases in Single Cell Data (XLSX 108 kb)
DOI: 10.6084/m9.figshare.9776501
title: Additional file 4: of Impaired glucose metabolism and altered gut microbiome despite calorie restriction of ob/ob mice

description: Table S1. Detailed information on when fresh fecal samples and cecum content were collected. Table S2. Associations between individual metabolic phenotypes and microbial alpha diversity measures using linear mixed models. Table S3. Testing for differences in the Shannon diversity index, observed ASVs, and Firmicutes to Bacteroidetes ratio between the groups during each week. FDR-adjusted p-values from Wilcoxon rank-sum test are reported. Table S4. Testing for differences in PC1 between groups during each week. FDR-adjusted p-values from Wilcoxon rank-sum test are reported. Table S5a-c. ASVs that are differentially abundant in pairwise comparisons of groups, consistently during W6-W9. Both p-values and Holm's sequential rejection-based adjusted p-values are reported. ASVs re-annotated with iMGMC are marked in the last column "Altered taxonomy". Table S6a-f. KEGG pathways (a-c) and orthologous groups (d-f) that are differentially abundant in pairwise comparisons of groups, consistently during W6-W9. Both p-values and Holm's sequential rejection-based adjusted p-values are reported. Table S7a-b. Spearman rank correlations between microbial taxa and one-time metabolic measurements, estimated separately for the groups. Taxa with at least one correlation with FDR-adjusted P
DOI: 10.6084/m9.figshare.9776501.v1
title: Additional file 4: of Impaired glucose metabolism and altered gut microbiome despite calorie restriction of ob/ob mice

description: Table S1. Detailed information on when fresh fecal samples and cecum content were collected. Table S2. Associations between individual metabolic phenotypes and microbial alpha diversity measures using linear mixed models. Table S3. Testing for differences in the Shannon diversity index, observed ASVs, and Firmicutes to Bacteroidetes ratio between the groups during each week. FDR-adjusted p-values from Wilcoxon rank-sum test are reported. Table S4. Testing for differences in PC1 between groups during each week. FDR-adjusted p-values from Wilcoxon rank-sum test are reported. Table S5a-c. ASVs that are differentially abundant in pairwise comparisons of groups, consistently during W6-W9. Both p-values and Holm's sequential rejection-based adjusted p-values are reported. ASVs re-annotated with iMGMC are marked in the last column "Altered taxonomy". Table S6a-f. KEGG pathways (a-c) and orthologous groups (d-f) that are differentially abundant in pairwise comparisons of groups, consistently during W6-W9. Both p-values and Holm's sequential rejection-based adjusted p-values are reported. Table S7a-b. Spearman rank correlations between microbial taxa and one-time metabolic measurements, estimated separately for the groups. Taxa with at least one correlation with FDR-adjusted P
DOI: 10.6084/m9.figshare.12782507
title: Fig5F_G_J_ZenKDsegmented_maps.tif

description: Segmented cartographic projections from a Tc-Zen1 knockdown light sheet timelapse movie
DOI: 10.6084/m9.figshare.12782507.v1
title: Fig5F_G_J_ZenKDsegmented_maps.tif

description: Segmented cartographic projections from a Tc-Zen1 knockdown light sheet timelapse movie
DOI: 10.6084/m9.figshare.9776498.v1
title: Additional file 11: of The developmental origins of sex-biased expression in cardiac development

description: Dataset S6. Sex Biases in Single Cell Data (XLSX 108 kb)
DOI: 10.6084/m9.figshare.9776399
title: Additional file 6: of Evidence of epistatic suppression of repeat fruiting in cultivated strawberry

description: Table S6. Segregating strawberry breeding families planted 2008 and evaluated the summers of 2008 and 2009. Parental and progeny phenotypes were classified as once-fruiting (jb) or repeat fruiting (RB) for each summer. Segregation ratios were calculated and tested for Chi-square goodness of fit. Chi-test probabilities over 0.000001 were highlighted in light green. The best fitting ratio or ratios were determined for the year of planting and for the subsequent year. Differences in segregation ratio from one year to the next occurred for several families. (XLSX 58 kb)
DOI: 10.6084/m9.figshare.9776399.v1
title: Additional file 6: of Evidence of epistatic suppression of repeat fruiting in cultivated strawberry

description: Table S6. Segregating strawberry breeding families planted 2008 and evaluated the summers of 2008 and 2009. Parental and progeny phenotypes were classified as once-fruiting (jb) or repeat fruiting (RB) for each summer. Segregation ratios were calculated and tested for Chi-square goodness of fit. Chi-test probabilities over 0.000001 were highlighted in light green. The best fitting ratio or ratios were determined for the year of planting and for the subsequent year. Differences in segregation ratio from one year to the next occurred for several families. (XLSX 58 kb)
DOI: 10.6084/m9.figshare.9776390
title: Additional file 5: of Evidence of epistatic suppression of repeat fruiting in cultivated strawberry

description: Table S5. Segregation ratios for progeny families from all possible phenotype/genotype parental combinations for a two-locus model to explain repeat fruiting vs once-fruiting of strawberry. Segregation ratios assume the primary, already mapped locus, has a dominant allele (RB) conferring repeat fruiting, and a recessive allele (jb) conferring once-fruiting. Repeat-fruiting parental phenotypes are highlighted in dull yellow, and once-fruiting phenotypes are highlighted in pale green. On the left of the grey vertical bar are segregations ratios that assume the presence of a second locus with a completely dominant allele (STOP) conferring epistatic suppression of the mapped locus when homozygous (STOP STOP) or heterozygous (STOP stop), and a recessive allele (stop) that does not affect the mapped locus). On the right of the grey vertical bar are segregation ratios that assume the presence of a second locus with a recessive allele (stop) conferring epistatic suppression of (or failure to support) the mapped locus when homozygous (stop stop), and a completely dominant allele (STOP) that does not change the phenotype conferred by the mapped locus. Horizontal grey and purple bars separate different genotypic parental-combination possibilities for similar phenotypic possibilities. Resulting progeny phenotypes are characterized as repeat-fruiting (RB) or once-fruiting (jb) similar to the mapped locus. Similar segregation ratios are highlighted in similar colors, and simplified to the right if appropriate, with non-segregation designated as RB for all repeat-fruiting, and jb for all once-fruiting. (XLSX 41 kb)
DOI: 10.6084/m9.figshare.9776390.v1
title: Additional file 5: of Evidence of epistatic suppression of repeat fruiting in cultivated strawberry

description: Table S5. Segregation ratios for progeny families from all possible phenotype/genotype parental combinations for a two-locus model to explain repeat fruiting vs once-fruiting of strawberry. Segregation ratios assume the primary, already mapped locus, has a dominant allele (RB) conferring repeat fruiting, and a recessive allele (jb) conferring once-fruiting. Repeat-fruiting parental phenotypes are highlighted in dull yellow, and once-fruiting phenotypes are highlighted in pale green. On the left of the grey vertical bar are segregations ratios that assume the presence of a second locus with a completely dominant allele (STOP) conferring epistatic suppression of the mapped locus when homozygous (STOP STOP) or heterozygous (STOP stop), and a recessive allele (stop) that does not affect the mapped locus). On the right of the grey vertical bar are segregation ratios that assume the presence of a second locus with a recessive allele (stop) conferring epistatic suppression of (or failure to support) the mapped locus when homozygous (stop stop), and a completely dominant allele (STOP) that does not change the phenotype conferred by the mapped locus. Horizontal grey and purple bars separate different genotypic parental-combination possibilities for similar phenotypic possibilities. Resulting progeny phenotypes are characterized as repeat-fruiting (RB) or once-fruiting (jb) similar to the mapped locus. Similar segregation ratios are highlighted in similar colors, and simplified to the right if appropriate, with non-segregation designated as RB for all repeat-fruiting, and jb for all once-fruiting. (XLSX 41 kb)
DOI: 10.6084/m9.figshare.9776372
title: Additional file 3: of Evidence of epistatic suppression of repeat fruiting in cultivated strawberry

description: Table S3. Breeding-parent marker profiles using all markers of Linkage Group IV, which is associated with repeat-fruiting in commercial strawberry (Fragaria Ă ananassa), that were amplified from the repeat-fruiting mapping parent and had a significant association with repeat fruiting when using the Kruskal-Wallis test. Markers are listed in order according to Kruskal-Wallis test value for mapping population generated by 'Tribute' Ă 'Honeoye'. Primer amplification of a product is designated by a "1", no amplification of the product when others were amplified by the primers is designated by a "0", and no amplification of any products from the primers was considered a failed reaction and designated by "m" for "missing". Marker products associated with once-fruiting are colored grey ("1" if the marker is in coupling, and "0" for the marker in repulsion). (XLSX 17 kb)
DOI: 10.6084/m9.figshare.9776378
title: Additional file 4: of Evidence of epistatic suppression of repeat fruiting in cultivated strawberry

description: Table S4. Calculations of segregation ratios for progeny families from all possible phenotype/genotype parental combinations for a two-locus model to explain repeat fruiting vs once-fruiting of strawberry. Calculations assume the primary, already mapped locus, has a dominant allele (RB) conferring repeat fruiting, and a recessive allele (jb) conferring once-fruiting. Repeat-fruiting parental and progeny phenotypes are highlighted in dull yellow, and once-fruiting phenotypes are highlighted in pale green. On the left of the grey vertical bar are calculations that assume the presence of a second locus with a completely dominant allele (STOP) conferring epistatic suppression of the mapped locus when homozygous (STOP STOP) or heterozygous (STOP stop), and a recessive allele (stop) that does not affect the mapped locus). On the right of the grey vertical bar are calculations that assume the presence of a second locus with a recessive allele (stop) conferring epistatic suppression of (or failure to support) the mapped locus when homozygous (stop stop), and a completely dominant allele (STOP) that does not change the phenotype conferred by the mapped locus. Horizontal grey and purple bars separate different genotypic parental-combination possibilities for similar phenotypic possibilities. Resulting progeny phenotypes are characterized as repeat-fruiting (RB) or once-fruiting (jb) similar to the mapped locus. Expected resulting segregation ratios are highlighted in bright yellow boxes. (XLSX 235 kb)
DOI: 10.6084/m9.figshare.9776372.v1
title: Additional file 3: of Evidence of epistatic suppression of repeat fruiting in cultivated strawberry

description: Table S3. Breeding-parent marker profiles using all markers of Linkage Group IV, which is associated with repeat-fruiting in commercial strawberry (Fragaria Ă ananassa), that were amplified from the repeat-fruiting mapping parent and had a significant association with repeat fruiting when using the Kruskal-Wallis test. Markers are listed in order according to Kruskal-Wallis test value for mapping population generated by 'Tribute' Ă 'Honeoye'. Primer amplification of a product is designated by a "1", no amplification of the product when others were amplified by the primers is designated by a "0", and no amplification of any products from the primers was considered a failed reaction and designated by "m" for "missing". Marker products associated with once-fruiting are colored grey ("1" if the marker is in coupling, and "0" for the marker in repulsion). (XLSX 17 kb)
DOI: 10.6084/m9.figshare.9776378.v1
title: Additional file 4: of Evidence of epistatic suppression of repeat fruiting in cultivated strawberry

description: Table S4. Calculations of segregation ratios for progeny families from all possible phenotype/genotype parental combinations for a two-locus model to explain repeat fruiting vs once-fruiting of strawberry. Calculations assume the primary, already mapped locus, has a dominant allele (RB) conferring repeat fruiting, and a recessive allele (jb) conferring once-fruiting. Repeat-fruiting parental and progeny phenotypes are highlighted in dull yellow, and once-fruiting phenotypes are highlighted in pale green. On the left of the grey vertical bar are calculations that assume the presence of a second locus with a completely dominant allele (STOP) conferring epistatic suppression of the mapped locus when homozygous (STOP STOP) or heterozygous (STOP stop), and a recessive allele (stop) that does not affect the mapped locus). On the right of the grey vertical bar are calculations that assume the presence of a second locus with a recessive allele (stop) conferring epistatic suppression of (or failure to support) the mapped locus when homozygous (stop stop), and a completely dominant allele (STOP) that does not change the phenotype conferred by the mapped locus. Horizontal grey and purple bars separate different genotypic parental-combination possibilities for similar phenotypic possibilities. Resulting progeny phenotypes are characterized as repeat-fruiting (RB) or once-fruiting (jb) similar to the mapped locus. Expected resulting segregation ratios are highlighted in bright yellow boxes. (XLSX 235 kb)
DOI: 10.6084/m9.figshare.9776342
title: MOESM4 of Reducing malaria burden and accelerating elimination with long-lasting systemic insecticides: a modelling study of three potential use cases

description: Additional file 4. Directions on how to obtain the software and scripts used to generate and analyse the data in this study.
DOI: 10.6084/m9.figshare.9776342.v1
title: MOESM4 of Reducing malaria burden and accelerating elimination with long-lasting systemic insecticides: a modelling study of three potential use cases

description: Additional file 4. Directions on how to obtain the software and scripts used to generate and analyse the data in this study.
DOI: 10.6084/m9.figshare.9776111
title: Datasets.xlsx

description: Quantitative data of T cell activation and function<br>
DOI: 10.6084/m9.figshare.9776126
title: T cells sense rigidity of microscale structures

description: Cells have the remarkable ability to sense the mechanical stiffness of their surroundings. This has been studied extensively in the context of cells interacting with planar surfaces, a conceptually elegant model that also has application in biomaterial design. However, physiological interfaces are spatially complex, exhibiting topographical features that are described over multiple scales. This report explores mechanosensing of microstructured elastomer surfaces by CD4+ T cells, key mediators of the adaptive immune response. We show that T cells form complex interactions with elastomer micropillar arrays, extending processes into spaces between structures and forming local areas of contraction and expansion dictated by the layout of microtubules within this interface. Conversely, cytoskeletal reorganization and intracellular signaling are sensitive to the pillar dimensions and flexibility. Unexpectedly, these measures show different responses to substrate rigidity, suggesting competing processes in overall T cell mechanosensing. The results of this study demonstrate that T cells sense the local rigidity of their environment, leading to new strategies for biomaterial design.<br>
DOI: 10.6084/m9.figshare.9776075
title: Data of: Differences in the structural chemical composition of the primary xylem of Cactaceae: a topochemical perspective

description: This data represent the gravimetric quantification of the structural chemical compounds of primary xylem of seedlings from Cactaceae, mean, standar deviation and coefficient of variation are part of the objectives. Ftir spectre of the eight seedling species are present too.
DOI: 10.6084/m9.figshare.9776030
title: condensed_species_GTDB v1.0.1

description: The condensed_species.csv dataset is the second data product from the data merger workflow. The trait data are mapped and aggregated to GTDB species level.
DOI: 10.6084/m9.figshare.9776033
title: High elevations of the Middle Miocene Qaidam Basin, northern Tibetan Plateau, revealed by a novel ostracod-based carbonate clumped-isotope thermometry

description: <b>Table S1.</b> Summary of clumped isotope data from the Qaidam Basin. <b>Table S2.</b> Compilation of modern summer lake surface temperature, lake level and thermocline depth data for modern lakes in Asia.<br>
DOI: 10.6084/m9.figshare.9776027
title: condensed_traits_GTDB v1.0.1

description: The condensed_traits.csv dataset is the first data product from the data merger workflow. It include species and strains, and the raw are in their clean, but raw, form. Use the GTDB taxonomy.<br>
DOI: 10.6084/m9.figshare.9776075.v1
title: Untitled Item

description: This data represent the gravimetric quantification of the structural chemical compounds of primary xylem of seedlings from Cactaceae, mean, standar deviation and coefficient of variation are part of the objectives. Ftir spectre of the eight seedling species are present too.
DOI: 10.6084/m9.figshare.9776030.v2
title: condensed_species_GTDB v1.0.0

description: The condensed_species.csv dataset is the second data product from the data merger workflow. The trait data are mapped and aggregated to GTDB species level.
DOI: 10.6084/m9.figshare.9776075.v3
title: Data of: Differences in the structural chemical composition of the primary xylem of Cactaceae: a topochemical perspective

description: This data represent the gravimetric quantification of the structural chemical compounds of primary xylem of seedlings from Cactaceae, mean, standar deviation and coefficient of variation are part of the objectives. Ftir spectre of the eight seedling species are present too.
DOI: 10.6084/m9.figshare.9776033.v2
title: High elevations of the Middle Miocene Qaidam Basin, northern Tibetan Plateau, revealed by a novel ostracod-based carbonate clumped-isotope thermometry

description: <b>Table S1.</b> Summary of clumped isotope data from the Qaidam Basin. <b>Table S2.</b> Compilation of modern summer lake surface temperature, lake level and thermocline depth data for modern lakes in Asia.<br>
DOI: 10.6084/m9.figshare.9776033.v1
title: High elevations of the Middle Miocene Qaidam Basin, northern Tibetan Plateau, revealed by a novel ostracod-based carbonate clumped-isotope thermometry

description: <b>Table S1.</b> Summary of clumped isotope data from the Qaidam Basin. <b>Table S2.</b> Compilation of modern summer lake surface temperature, lake level and thermocline depth data for modern lakes in Asia.<br>