cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.13151964.v1
title: Additional file 1 of Blood-based epigenetic estimators of chronological age in human adults using DNA methylation data from the Illumina MethylationEPIC array

description: Additional file 1. This file includes CpG sites for ABEC, eABEC, and cABEC, their corresponding coefficients, overlap with the other published clocks, genomic locations, neighboring genes, presence in the Illumina HumanMethylation450K and 27 K array, and the SNP annotations generated by Zhou et al. [38] (with the suffix of “Zhou”) and McCartney et al. [39] (with the suffix of “McCartney”).
DOI: 10.6084/m9.figshare.13151964
title: Additional file 1 of Blood-based epigenetic estimators of chronological age in human adults using DNA methylation data from the Illumina MethylationEPIC array

description: Additional file 1. This file includes CpG sites for ABEC, eABEC, and cABEC, their corresponding coefficients, overlap with the other published clocks, genomic locations, neighboring genes, presence in the Illumina HumanMethylation450K and 27 K array, and the SNP annotations generated by Zhou et al. [38] (with the suffix of “Zhou”) and McCartney et al. [39] (with the suffix of “McCartney”).
DOI: 10.6084/m9.figshare.13151992.v1
title: Additional file 5 of Chromatin accessibility dynamics of Chlamydia-infected epithelial cells

description: Additional file 5. Time specific regions. The list of time-specific differential chromatin-accessible regions. It should be noted that some genes in these lists are repeated at each time due to multiple peaks occurring at an annotated interval, that enhancers can affect more than one gene, and single genes can be affected by more than one enhancer.
DOI: 10.6084/m9.figshare.13151980.v1
title: Additional file 1 of Chromatin accessibility dynamics of Chlamydia-infected epithelial cells

description: Additional file 1. Summary of mapped reads by time and condition. Table summarising the number of mapped reads for each time and infection condition.
DOI: 10.6084/m9.figshare.13151986
title: Additional file 3 of Chromatin accessibility dynamics of Chlamydia-infected epithelial cells

description: Additional file 3. Annotation of all significant peaks. Annotation of all the significant peaks, with tabs separating genomic features and fold-change regulation.
DOI: 10.6084/m9.figshare.13151986.v1
title: Additional file 3 of Chromatin accessibility dynamics of Chlamydia-infected epithelial cells

description: Additional file 3. Annotation of all significant peaks. Annotation of all the significant peaks, with tabs separating genomic features and fold-change regulation.
DOI: 10.6084/m9.figshare.13151995
title: Additional file 6 of Chromatin accessibility dynamics of Chlamydia-infected epithelial cells

description: Additional file 6. Complete list of motifs and transcription factors. The complete list of significant motifs and enriched transcription factors.
DOI: 10.6084/m9.figshare.13151995.v1
title: Additional file 6 of Chromatin accessibility dynamics of Chlamydia-infected epithelial cells

description: Additional file 6. Complete list of motifs and transcription factors. The complete list of significant motifs and enriched transcription factors.
DOI: 10.6084/m9.figshare.13151992
title: Additional file 5 of Chromatin accessibility dynamics of Chlamydia-infected epithelial cells

description: Additional file 5. Time specific regions. The list of time-specific differential chromatin-accessible regions. It should be noted that some genes in these lists are repeated at each time due to multiple peaks occurring at an annotated interval, that enhancers can affect more than one gene, and single genes can be affected by more than one enhancer.
DOI: 10.6084/m9.figshare.13151980
title: Additional file 1 of Chromatin accessibility dynamics of Chlamydia-infected epithelial cells

description: Additional file 1. Summary of mapped reads by time and condition. Table summarising the number of mapped reads for each time and infection condition.
DOI: 10.6084/m9.figshare.13152052
title: Additional file 2 of Impact of extracellular matrix stiffness on genomic heterogeneity in MYCN-amplified neuroblastoma cell line

description: Additional file 2: Table S1: Log2 Ratio and copy number of each segmental chromosome aberration -SCA-, and aberrant cell percentage of each sample from SK-N-BE(2) cell line. These parameters were estimated using ChAS software.
DOI: 10.6084/m9.figshare.13152055.v1
title: Additional file 3 of Impact of extracellular matrix stiffness on genomic heterogeneity in MYCN-amplified neuroblastoma cell line

description: Additional file 3: Table S2: Genomic variants detected by next generation sequencing (NGS) in the sequenced samples from (A) SK-N-BE(2) cells or (B) SH-SY5Y cells, filtered by mean allelic frequencies equal to or over 0.1, and a coverage equal to or over 100x. XenofilteR and Disambiguate software were applied to remove variants from mice genome and SW10 cells. (C) Genomic regions included in NB-mechanopanel.
DOI: 10.6084/m9.figshare.13152055
title: Additional file 3 of Impact of extracellular matrix stiffness on genomic heterogeneity in MYCN-amplified neuroblastoma cell line

description: Additional file 3: Table S2: Genomic variants detected by next generation sequencing (NGS) in the sequenced samples from (A) SK-N-BE(2) cells or (B) SH-SY5Y cells, filtered by mean allelic frequencies equal to or over 0.1, and a coverage equal to or over 100x. XenofilteR and Disambiguate software were applied to remove variants from mice genome and SW10 cells. (C) Genomic regions included in NB-mechanopanel.
DOI: 10.6084/m9.figshare.13152058
title: Additional file 1 of Identification of potential causal variants for premature ovarian failure by whole exome sequencing

description: Additional file 1: Table S1. List of POF/POI genes (131). List of candidate POF genes obtained from four public databases (DisGeNET, Monarch, MalaCards and NCBI:Gene) that collect genes and variants associated with human disease. Table S2. Primers used for confirming selected variants. Table S3. Genes with identical rare variants (MAF ≤ 0.01) detected in more than one individual. Table S4. Identical coding variants found in two or more individuals via whole-exome sequencing. VEST analysis generates values between 0 and 1, and scores ≥ 0.5 were classified as pathogenic variants and those
DOI: 10.6084/m9.figshare.13152052.v1
title: Additional file 2 of Impact of extracellular matrix stiffness on genomic heterogeneity in MYCN-amplified neuroblastoma cell line

description: Additional file 2: Table S1: Log2 Ratio and copy number of each segmental chromosome aberration -SCA-, and aberrant cell percentage of each sample from SK-N-BE(2) cell line. These parameters were estimated using ChAS software.
DOI: 10.6084/m9.figshare.13152058.v1
title: Additional file 1 of Identification of potential causal variants for premature ovarian failure by whole exome sequencing

description: Additional file 1: Table S1. List of POF/POI genes (131). List of candidate POF genes obtained from four public databases (DisGeNET, Monarch, MalaCards and NCBI:Gene) that collect genes and variants associated with human disease. Table S2. Primers used for confirming selected variants. Table S3. Genes with identical rare variants (MAF ≤ 0.01) detected in more than one individual. Table S4. Identical coding variants found in two or more individuals via whole-exome sequencing. VEST analysis generates values between 0 and 1, and scores ≥ 0.5 were classified as pathogenic variants and those
DOI: 10.6084/m9.figshare.13152063.v1
title: Additional file 11 of Healthy diets can create environmental trade-offs, depending on how diet quality is measured

description: Additional file 11: Supplemental Table 9. Annual amount of pesticides used to produce Total Food Demand, by land use category and Healthy Eating Index-2015 quintile Total Food Demand represents the sum of retail waste, consumer waste, inedible portions, and consumed food. Higher quintiles represent higher diet quality. Pesticides include herbicides, insecticides, and fungicides. HEI-2015, Health Eating Index-2015. NA, not applicable. 1Test for linear trend across quintiles 1 through 5.
DOI: 10.6084/m9.figshare.13152066
title: Additional file 12 of Healthy diets can create environmental trade-offs, depending on how diet quality is measured

description: Additional file 12: Supplemental Table 10. Annual amount of irrigation water used to produce Total Food Demand, by land use category and Healthy Eating Index-2015 quintile Total Food Demand represents the sum of retail waste, consumer waste, inedible portions, and consumed food. Higher quintiles represent higher diet quality. HEI-2015, Healthy Eating Index-2015. 1Test for linear trend across quintiles 1 through 5.
DOI: 10.6084/m9.figshare.13152066.v1
title: Additional file 12 of Healthy diets can create environmental trade-offs, depending on how diet quality is measured

description: Additional file 12: Supplemental Table 10. Annual amount of irrigation water used to produce Total Food Demand, by land use category and Healthy Eating Index-2015 quintile Total Food Demand represents the sum of retail waste, consumer waste, inedible portions, and consumed food. Higher quintiles represent higher diet quality. HEI-2015, Healthy Eating Index-2015. 1Test for linear trend across quintiles 1 through 5.
DOI: 10.6084/m9.figshare.13152075.v1
title: Additional file 15 of Healthy diets can create environmental trade-offs, depending on how diet quality is measured

description: Additional file 15: Supplemental Table 13. Annual amount of pesticides used to produce Total Food Demand, by Alternative Healthy Eating Index-2010 quintile Total Food Demand represents the sum of retail waste, consumer waste, inedible portions, and consumed food. Higher quintiles represent higher diet quality. Pesticides include herbicides, insecticides, and fungicides. AHEI-2010, Health Eating Index-2010. NA, not applicable. 1Test for linear trend across quintiles 1 through 5.
DOI: 10.6084/m9.figshare.13152060.v1
title: Additional file 10 of Healthy diets can create environmental trade-offs, depending on how diet quality is measured

description: Additional file 10: Supplemental Table 8. Annual amount of fertilizer nutrients used to produce Total Food Demand, by land use category and Healthy Eating Index-2015 quintile Total Food Demand represents the sum of retail waste, consumer waste, inedible portions, and consumed food. Higher quintiles represent higher diet quality. Fertilizers nutrients represents the sum of nitrogen, phosphorus (P2O5), and potash (K2O). HEI-2015, Health Eating Index-2015. NA, not applicable. 1Test for linear trend across quintiles 1 through 5.
DOI: 10.6084/m9.figshare.13152063
title: Additional file 11 of Healthy diets can create environmental trade-offs, depending on how diet quality is measured

description: Additional file 11: Supplemental Table 9. Annual amount of pesticides used to produce Total Food Demand, by land use category and Healthy Eating Index-2015 quintile Total Food Demand represents the sum of retail waste, consumer waste, inedible portions, and consumed food. Higher quintiles represent higher diet quality. Pesticides include herbicides, insecticides, and fungicides. HEI-2015, Health Eating Index-2015. NA, not applicable. 1Test for linear trend across quintiles 1 through 5.
DOI: 10.6084/m9.figshare.13152069
title: Additional file 13 of Healthy diets can create environmental trade-offs, depending on how diet quality is measured

description: Additional file 13: Supplemental Table 11. Annual amount of agricultural land used to produce Total Food Demand, by Alternative Healthy Eating Index-2010 quintile Total Food Demand represents the sum of retail waste, consumer waste, inedible portions, and consumed food. Higher quintiles represent higher diet quality. AHEI-2010, Alternative Healthy Eating Index-2010. 1Test for linear trend across quintiles 1 through 5.
DOI: 10.6084/m9.figshare.13152072.v1
title: Additional file 14 of Healthy diets can create environmental trade-offs, depending on how diet quality is measured

description: Additional file 14: Supplemental Table 12. Annual amount of fertilizer nutrients used to produce Total Food Demand, by Alternative Healthy Eating Index-2010 quintile Total Food Demand represents the sum of retail waste, consumer waste, inedible portions, and consumed food. Higher quintiles represent higher diet quality. Fertilizers include nitrogen, phosphorus (P2O5), and potash (K2O). AHEI-2010, Alternative Healthy Eating Index-2010. NA, not applicable. 1Test for linear trend across quintiles 1 through 5.
DOI: 10.6084/m9.figshare.13152078.v1
title: Additional file 16 of Healthy diets can create environmental trade-offs, depending on how diet quality is measured

description: Additional file 16: Supplemental Table 14. Annual amount of irrigation water used to produce Total Food Demand, by Healthy Eating Index-2010 quintile Total Food Demand represents the sum of retail waste, consumer waste, inedible portions, and consumed food. Higher quintiles represent higher diet quality. AHEI-2010, Alternative Healthy Eating Index-2010. 1Test for linear trend across quintiles 1 through 5.
DOI: 10.6084/m9.figshare.13152084
title: Additional file 18 of Healthy diets can create environmental trade-offs, depending on how diet quality is measured

description: Additional file 18: Supplemental Table 16. Unadjusted and adjusted Alternative Healthy Eating Index-2010 scores (2005–2016). Adjusted scores reflect two changes to the Alternative Healthy Eating Index-2010 scoring algorithm to adapt this instrument to a population that includes individuals
DOI: 10.6084/m9.figshare.13152069.v1
title: Additional file 13 of Healthy diets can create environmental trade-offs, depending on how diet quality is measured

description: Additional file 13: Supplemental Table 11. Annual amount of agricultural land used to produce Total Food Demand, by Alternative Healthy Eating Index-2010 quintile Total Food Demand represents the sum of retail waste, consumer waste, inedible portions, and consumed food. Higher quintiles represent higher diet quality. AHEI-2010, Alternative Healthy Eating Index-2010. 1Test for linear trend across quintiles 1 through 5.
DOI: 10.6084/m9.figshare.13152084.v1
title: Additional file 18 of Healthy diets can create environmental trade-offs, depending on how diet quality is measured

description: Additional file 18: Supplemental Table 16. Unadjusted and adjusted Alternative Healthy Eating Index-2010 scores (2005–2016). Adjusted scores reflect two changes to the Alternative Healthy Eating Index-2010 scoring algorithm to adapt this instrument to a population that includes individuals
DOI: 10.6084/m9.figshare.13152072
title: Additional file 14 of Healthy diets can create environmental trade-offs, depending on how diet quality is measured

description: Additional file 14: Supplemental Table 12. Annual amount of fertilizer nutrients used to produce Total Food Demand, by Alternative Healthy Eating Index-2010 quintile Total Food Demand represents the sum of retail waste, consumer waste, inedible portions, and consumed food. Higher quintiles represent higher diet quality. Fertilizers include nitrogen, phosphorus (P2O5), and potash (K2O). AHEI-2010, Alternative Healthy Eating Index-2010. NA, not applicable. 1Test for linear trend across quintiles 1 through 5.
DOI: 10.6084/m9.figshare.13152081
title: Additional file 17 of Healthy diets can create environmental trade-offs, depending on how diet quality is measured

description: Additional file 17: Supplemental Table 15. Daily per capita Total Food Demand by time period. HEI-2015, Healthy Eating Index. AHEI-2010, Alternative Healthy Eating Index. Total Food Demand includes retail loss, inedible, consumer waste, and consumption.. 1Z-tests with P
DOI: 10.6084/m9.figshare.13152081.v1
title: Additional file 17 of Healthy diets can create environmental trade-offs, depending on how diet quality is measured

description: Additional file 17: Supplemental Table 15. Daily per capita Total Food Demand by time period. HEI-2015, Healthy Eating Index. AHEI-2010, Alternative Healthy Eating Index. Total Food Demand includes retail loss, inedible, consumer waste, and consumption.. 1Z-tests with P
DOI: 10.6084/m9.figshare.13152093
title: Additional file 3 of Healthy diets can create environmental trade-offs, depending on how diet quality is measured

description: Additional file 3: Supplemental Table 1. Scoring standards for each component of the Healthy Eating Index-2015 (HEI-2015) and Alternative Healthy Eating Index-2010 (AHEI-2010) EPA, eicosapentaenoic acid (20:5, n-3). DHA, docosahexaenoic acid (22:6, n-3). 1Development and validation available at https://epi.grants.cancer.gov/hei/developing.html#2005 2Energy-adjusted to 1000 kcal, except for unsaturated fatty acids, saturated fatty acids, and added sugars. 3Cup equivalents and ounce equivalents were obtained from the USDA Food Pattern Equivalents Database ( https://www.ars.usda.gov/northeast-area/beltsville-md-bhnrc/beltsville-human-nutrition-research-center/food-surveys-research-group/docs/fped-overview/ ). 4Development, validation, scoring standards, cup equivalents, and ounce equivalents from Chiuve et al. (2012). Alternative dietary indices both strongly predict risk of chronic disease. Journal of Nutrition, 142:1009–1018. To adapt the scoring standards for children, modifications were made to the scores for sodium and alcohol (see relevant footnotes for details), and the scores for the other components were energy-adjusted to 1849 kcal, which reflects the mean energy intake of the source population from which this index was constructed (from Chiuve et al., 2012). 5To adapt the scoring standards for children, scores were energy-adjusted to 1849 kcal, which reflects the mean energy intake of the source population from Chiuvre et al. (2012). Alternative dietary indices both strongly predict risk of chronic disease. Journal of Nutrition, 142:1009–1018. 6Beverages with ≥15 g of added sugar per 8 oz serving. 7Age categories (years): 1–3, 4–8, 9–13, 14–18, 19–30, 31–50, 51–70, ≥70. 8Adult non-drinkers received 2.5 points. Children (
DOI: 10.6084/m9.figshare.13152093.v1
title: Additional file 3 of Healthy diets can create environmental trade-offs, depending on how diet quality is measured

description: Additional file 3: Supplemental Table 1. Scoring standards for each component of the Healthy Eating Index-2015 (HEI-2015) and Alternative Healthy Eating Index-2010 (AHEI-2010) EPA, eicosapentaenoic acid (20:5, n-3). DHA, docosahexaenoic acid (22:6, n-3). 1Development and validation available at https://epi.grants.cancer.gov/hei/developing.html#2005 2Energy-adjusted to 1000 kcal, except for unsaturated fatty acids, saturated fatty acids, and added sugars. 3Cup equivalents and ounce equivalents were obtained from the USDA Food Pattern Equivalents Database ( https://www.ars.usda.gov/northeast-area/beltsville-md-bhnrc/beltsville-human-nutrition-research-center/food-surveys-research-group/docs/fped-overview/ ). 4Development, validation, scoring standards, cup equivalents, and ounce equivalents from Chiuve et al. (2012). Alternative dietary indices both strongly predict risk of chronic disease. Journal of Nutrition, 142:1009–1018. To adapt the scoring standards for children, modifications were made to the scores for sodium and alcohol (see relevant footnotes for details), and the scores for the other components were energy-adjusted to 1849 kcal, which reflects the mean energy intake of the source population from which this index was constructed (from Chiuve et al., 2012). 5To adapt the scoring standards for children, scores were energy-adjusted to 1849 kcal, which reflects the mean energy intake of the source population from Chiuvre et al. (2012). Alternative dietary indices both strongly predict risk of chronic disease. Journal of Nutrition, 142:1009–1018. 6Beverages with ≥15 g of added sugar per 8 oz serving. 7Age categories (years): 1–3, 4–8, 9–13, 14–18, 19–30, 31–50, 51–70, ≥70. 8Adult non-drinkers received 2.5 points. Children (
DOI: 10.6084/m9.figshare.13152078
title: Additional file 16 of Healthy diets can create environmental trade-offs, depending on how diet quality is measured

description: Additional file 16: Supplemental Table 14. Annual amount of irrigation water used to produce Total Food Demand, by Healthy Eating Index-2010 quintile Total Food Demand represents the sum of retail waste, consumer waste, inedible portions, and consumed food. Higher quintiles represent higher diet quality. AHEI-2010, Alternative Healthy Eating Index-2010. 1Test for linear trend across quintiles 1 through 5.
DOI: 10.6084/m9.figshare.13152099
title: Additional file 5 of Healthy diets can create environmental trade-offs, depending on how diet quality is measured

description: Additional file 5: Supplemental Table 3. Healthy Eating Index-2015 component scores, National Health and Nutrition Examination Survey, 2005–2016 (n = 50,014) Includes individuals ≥2 years of age.
DOI: 10.6084/m9.figshare.13152111
title: Additional file 9 of Healthy diets can create environmental trade-offs, depending on how diet quality is measured

description: Additional file 9: Supplemental Table 7. Annual amount of agricultural land used to produce Total Food Demand, by land use category and Healthy Eating Index-2015 quintile Total Food Demand represents the sum of retail waste, consumer waste, inedible portions, and consumed food. Higher quintiles represent higher diet quality. HEI-2015, Healthy Eating Index-2015. 1Test for linear trend across quintiles 1 through 5.
DOI: 10.6084/m9.figshare.13152096
title: Additional file 4 of Healthy diets can create environmental trade-offs, depending on how diet quality is measured

description: Additional file 4: Supplemental Table 2. Characteristics of study population, National Health and Nutrition Examination Survey (2005–2016) 1Sample sizes are unweighted. 2Percentages within each column adjusted for survey weight.
DOI: 10.6084/m9.figshare.13152096.v1
title: Additional file 4 of Healthy diets can create environmental trade-offs, depending on how diet quality is measured

description: Additional file 4: Supplemental Table 2. Characteristics of study population, National Health and Nutrition Examination Survey (2005–2016) 1Sample sizes are unweighted. 2Percentages within each column adjusted for survey weight.
DOI: 10.6084/m9.figshare.13152105
title: Additional file 7 of Healthy diets can create environmental trade-offs, depending on how diet quality is measured

description: Additional file 7: Supplemental Table 5. Daily per capita Total Food Demand (2005–2016), by Healthy Eating Index-2015 quintile (n = 50,014) Higher quintiles represent higher diet quality. 1Test for linear trend across quintiles 1 through 5, not adjusted for covariates. 2Test for linear trend across quintiles 1 through 5, adjusted for age (continuous) and sex (male/female). 3Includes vegetable juice. 4Mostly candy, soft drinks, and other beverages.
DOI: 10.6084/m9.figshare.13152060
title: Additional file 10 of Healthy diets can create environmental trade-offs, depending on how diet quality is measured

description: Additional file 10: Supplemental Table 8. Annual amount of fertilizer nutrients used to produce Total Food Demand, by land use category and Healthy Eating Index-2015 quintile Total Food Demand represents the sum of retail waste, consumer waste, inedible portions, and consumed food. Higher quintiles represent higher diet quality. Fertilizers nutrients represents the sum of nitrogen, phosphorus (P2O5), and potash (K2O). HEI-2015, Health Eating Index-2015. NA, not applicable. 1Test for linear trend across quintiles 1 through 5.