cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.11627175.v1
title: Simulated mean wave direction (monthly, 150a) from FIO-ESM v2.0 1pctCO2 experiment r1i1p1f1

description: Simulated mean wave direction (monthly, 150a) from FIO-ESM v2.0 1pctCO2 experiment (CO2 prescribed to increase at 1% per year) r1i1p1f1, which is branch from Jan 1, 301 of piControl experiment. The grid, named gx1v6, is the displaced pole (the North Pole displaced to the Greenland) grid with 1.1 degree in longitude and 0.27-0.54 degree in latitude.
DOI: 10.6084/m9.figshare.11627148
title: Supplementary Material for: Next Generation Sequencing-Based Fetal ABO Blood Group Prediction by Analysis of Cell-Free DNA from Maternal Plasma

description: <b><i>Introduction:</i></b> ABO blood group incompatibility between a pregnant woman and her fetus as a cause of morbidity or mortality of the fetus or newborn remains an important, albeit rare, risk. When a pregnant woman has a high level of anti-A or anti-B IgG antibodies, the child may be at risk for hemolytic disease of the fetus and newborn (HDFN). Performing a direct prenatal determination of the fetal ABO blood group can provide valuable clinical information. <b><i>Objective:</i></b> Here, we report a next generation sequencing (NGS)-based assay for predicting the prenatal ABO blood group. <b><i>Materials and Methods:</i></b> A total of 26 plasma samples from 26 pregnant women were tested from gestational weeks 12 to 35. Of these samples, 20 were clinical samples and 6 were test samples. Extracted cell-free DNA was PCR-amplified using 2 primer sets followed by NGS. NGS data were analyzed by 2 different methods, FASTQ analysis and a grep search, to ensure robust results. The fetal ABO prediction was compared with the known serological infant ABO type, which was available for 19 samples. <b><i>Results:</i></b> There was concordance for 19 of 19 predictable samples where the phenotype information was available and when the analysis was done by the 2 methods. For immunized pregnant women (<i>n</i> = 20), the risk of HDFN was predicted for 12 fetuses, and no risk was predicted for 7 fetuses; one result of the clinical samples was indeterminable. Cloning and sequencing revealed a novel variant harboring the same single nucleotide variations as <i>ABO</i>*<i>O.01.24</i> with an additional c.220C&gt;T substitution. An additional indeterminable result was found among the 6 test samples and was caused by maternal heterozygosity. The 2 indeterminable samples demonstrated limitations to the assay due to hybrid ABO genes or maternal heterozygosity. <b><i>Conclusions:</i></b> We pioneered an NGS-based fetal ABO prediction assay based on a cell-free DNA analysis from maternal plasma and demonstrated its application in a small number of samples. Based on the calculations of variant frequencies and <i>ABO</i>*<i>O.01/ABO</i>*<i>O.02</i> heterozygote frequency, we estimate that we can assign a reliable fetal ABO type in approximately 95% of the forthcoming clinical samples of type O pregnant women. Despite the vast genetic variations underlying the ABO blood groups, many variants are rare, and prenatal ABO prediction is possible and adds valuable early information for the prevention of ABO HDFN.
DOI: 10.6084/m9.figshare.11627154
title: Simulated significant wave height (monthly, 150a) from FIO-ESM v2.0 1pctCO2 experiment r1i1p1f1

description: Simulated significant wave height (monthly, 150a) from FIO-ESM v2.0 1pctCO2 experiment (CO2 prescribed to increase at 1% per year) r1i1p1f1, which is branch from Jan 1, 301 of piControl experiment. The grid, named gx1v6, is the displaced pole (the North Pole displaced to the Greenland) grid with 1.1 degree in longitude and 0.27-0.54 degree in latitude.
DOI: 10.6084/m9.figshare.11627148.v1
title: Supplementary Material for: Next Generation Sequencing-Based Fetal ABO Blood Group Prediction by Analysis of Cell-Free DNA from Maternal Plasma

description: <b><i>Introduction:</i></b> ABO blood group incompatibility between a pregnant woman and her fetus as a cause of morbidity or mortality of the fetus or newborn remains an important, albeit rare, risk. When a pregnant woman has a high level of anti-A or anti-B IgG antibodies, the child may be at risk for hemolytic disease of the fetus and newborn (HDFN). Performing a direct prenatal determination of the fetal ABO blood group can provide valuable clinical information. <b><i>Objective:</i></b> Here, we report a next generation sequencing (NGS)-based assay for predicting the prenatal ABO blood group. <b><i>Materials and Methods:</i></b> A total of 26 plasma samples from 26 pregnant women were tested from gestational weeks 12 to 35. Of these samples, 20 were clinical samples and 6 were test samples. Extracted cell-free DNA was PCR-amplified using 2 primer sets followed by NGS. NGS data were analyzed by 2 different methods, FASTQ analysis and a grep search, to ensure robust results. The fetal ABO prediction was compared with the known serological infant ABO type, which was available for 19 samples. <b><i>Results:</i></b> There was concordance for 19 of 19 predictable samples where the phenotype information was available and when the analysis was done by the 2 methods. For immunized pregnant women (<i>n</i> = 20), the risk of HDFN was predicted for 12 fetuses, and no risk was predicted for 7 fetuses; one result of the clinical samples was indeterminable. Cloning and sequencing revealed a novel variant harboring the same single nucleotide variations as <i>ABO</i>*<i>O.01.24</i> with an additional c.220C&gt;T substitution. An additional indeterminable result was found among the 6 test samples and was caused by maternal heterozygosity. The 2 indeterminable samples demonstrated limitations to the assay due to hybrid ABO genes or maternal heterozygosity. <b><i>Conclusions:</i></b> We pioneered an NGS-based fetal ABO prediction assay based on a cell-free DNA analysis from maternal plasma and demonstrated its application in a small number of samples. Based on the calculations of variant frequencies and <i>ABO</i>*<i>O.01/ABO</i>*<i>O.02</i> heterozygote frequency, we estimate that we can assign a reliable fetal ABO type in approximately 95% of the forthcoming clinical samples of type O pregnant women. Despite the vast genetic variations underlying the ABO blood groups, many variants are rare, and prenatal ABO prediction is possible and adds valuable early information for the prevention of ABO HDFN.
DOI: 10.6084/m9.figshare.11627154.v1
title: Simulated significant wave height (monthly, 150a) from FIO-ESM v2.0 1pctCO2 experiment r1i1p1f1

description: Simulated significant wave height (monthly, 150a) from FIO-ESM v2.0 1pctCO2 experiment (CO2 prescribed to increase at 1% per year) r1i1p1f1, which is branch from Jan 1, 301 of piControl experiment. The grid, named gx1v6, is the displaced pole (the North Pole displaced to the Greenland) grid with 1.1 degree in longitude and 0.27-0.54 degree in latitude.
DOI: 10.6084/m9.figshare.11627139
title: pcr microarray

description: pcr microarray dataset
DOI: 10.6084/m9.figshare.11627139.v1
title: pcr microarray

description: pcr microarray dataset
DOI: 10.6084/m9.figshare.11627124
title: Coupled effects of moisture sources and convection on stable isotopes in precipitation across East Asia: Implications for paleoclimate reconstruction

description: The meteorological and isotopic data are used in the paper titled "Coupled effects of moisture sources and convection on stable isotopes in precipitation across East Asia: Implications for paleoclimate reconstruction".
DOI: 10.6084/m9.figshare.11627082
title: Supplementary Material for: Steroid 17-Hydroxyprogesterone in Hair Is a Potential Long-Term Biomarker of Androgen Control in Congenital Adrenal Hyperplasia due to 21-Hydroxylase Deficiency

description: <b><i>Introduction:</i></b> To evaluate scalp hair steroid concentrations as a monitoring tool for androgen control and metabolic outcomes in adults with congenital adrenal hyperplasia (CAH) due to 21-hydroxylase deficiency. <b><i>Methods:</i></b> 17-hydroxyprogesterone (17-OHP), androstenedione, testosterone, cortisol, cortisone, progesterone, prednisolone, and prednisone concentrations were measured in scalp hair by means of LC-MS/MS in 27 women and 15 men with CAH and controls (37 women, 42 men). <b><i>Results:</i></b> In CAH men and women, 17-OHP levels in hair showed a significant positive correlation with corresponding levels in serum (ρ = 0.654; <i>p</i> = 0.01; ρ = 0.553, <i>p</i> = 0.003 respectively), while total testosterone levels were only significantly correlated in CAH men (ρ = 0.543; <i>p</i> = 0.036). Androstenedione levels did not show a significant correlation. Receiver-operating characteristic (ROC) curve analysis indicated that a cutoff value of 21.7 pg/mg for 17-OHP in hair provided a sensitivity of 100% and a specificity of 88.9% for identifying men with elevated serum androstenedione. Hair 17-OHP in women showed a poorer performance in terms of identifying those with elevated androstenedione serum levels. However, when applying a cutoff value of 5.5 for the free androgen index as a marker of significant hyperandrogenism in CAH women, 17-OHP &gt;27.6 pg/mg in hair provided a sensitivity of 100% and a specificity of 95.8% (AUC 0.986, 95% CI 0.945–1.000; <i>p</i> &lt; 0.001). Neither hair cortisol nor markers of adrenal androgen control in hair showed significant associations with cardiometabolic outcome or bone health. <b><i>Conclusion:</i></b> This study shows that scalp hair 17-OHP concentrations may be a promising noninvasive long-term parameter for treatment monitoring in adult patients with CAH.
DOI: 10.6084/m9.figshare.11627124.v1
title: Coupled effects of moisture sources and convection on stable isotopes in precipitation across East Asia: Implications for paleoclimate reconstruction

description: The meteorological and isotopic data are used in the paper titled "Coupled effects of moisture sources and convection on stable isotopes in precipitation across East Asia: Implications for paleoclimate reconstruction".
DOI: 10.6084/m9.figshare.11627067
title: HKE Intonation as Indexical Markers of Identities

description: This article studies the social meaning of intonational variation in Hong Kong English (HKE) and its contribution to sociolinguistic research. In 21st-century, globalised Hong Kong, the local HKE accent, though still stigmatised, can be stylistically manipulated for indexical purposes through its prosody. Adopting a unified, variationist approach, the study examines how intonational variation in HKE from the global accent to the local accent is utilised as a marker of local identity. 36 university students, half HKE speakers and half non-HKE, are invited to perform 4 spontaneous dyad discussion tasks, on HK culture topics and neutral topics. The spontaneous use of local intonation by polycentric speakers with access to both accents is demonstrated to index social meanings such as highlighting their local identity and sounding sarcastic. Non-polycentric speakers, though confined to local intonation only, can switch from the core HKE tones to original Cantonese tones for similar purposes.
DOI: 10.6084/m9.figshare.11627064
title: Supplementary Material for: OBEDIS Core Variables Project: European Expert Guidelines on a Minimal Core Set of Variables to Include in Randomized, Controlled Clinical Trials of Obesity Interventions

description: Heterogeneity of interindividual and intraindividual responses to interventions is often observed in randomized, controlled trials for obesity. To address the global epidemic of obesity and move toward more personalized treatment regimens, the global research community must come together to identify factors that may drive these heterogeneous responses to interventions. This project, called OBEDIS (OBEsity Diverse Interventions Sharing – focusing on dietary and other interventions), provides a set of European guidelines for a minimal set of variables to include in future clinical trials on obesity, regardless of the specific endpoints. Broad adoption of these guidelines will enable researchers to harmonize and merge data from multiple intervention studies, allowing stratification of patients according to precise phenotyping criteria which are measured using standardized methods. In this way, studies across Europe may be pooled for better prediction of individuals’ responses to an intervention for obesity – ultimately leading to better patient care and improved obesity outcomes.
DOI: 10.6084/m9.figshare.11627124.v2
title: Coupled effects of moisture sources and convection on stable isotopes in precipitation across East Asia: Implications for paleoclimate reconstruction

description: The meteorological and isotopic data are used in the paper titled "Coupled effects of moisture sources and convection on stable isotopes in precipitation across East Asia: Implications for paleoclimate reconstruction".
DOI: 10.6084/m9.figshare.11627064.v1
title: Supplementary Material for: OBEDIS Core Variables Project: European Expert Guidelines on a Minimal Core Set of Variables to Include in Randomized, Controlled Clinical Trials of Obesity Interventions

description: Heterogeneity of interindividual and intraindividual responses to interventions is often observed in randomized, controlled trials for obesity. To address the global epidemic of obesity and move toward more personalized treatment regimens, the global research community must come together to identify factors that may drive these heterogeneous responses to interventions. This project, called OBEDIS (OBEsity Diverse Interventions Sharing – focusing on dietary and other interventions), provides a set of European guidelines for a minimal set of variables to include in future clinical trials on obesity, regardless of the specific endpoints. Broad adoption of these guidelines will enable researchers to harmonize and merge data from multiple intervention studies, allowing stratification of patients according to precise phenotyping criteria which are measured using standardized methods. In this way, studies across Europe may be pooled for better prediction of individuals’ responses to an intervention for obesity – ultimately leading to better patient care and improved obesity outcomes.
DOI: 10.6084/m9.figshare.11627124.v3
title: Coupled effects of moisture sources and convection on stable isotopes in precipitation across East Asia: Implications for paleoclimate reconstruction

description: The meteorological and isotopic data are used in the paper titled "Coupled effects of moisture sources and convection on stable isotopes in precipitation across East Asia: Implications for paleoclimate reconstruction".
DOI: 10.6084/m9.figshare.11627124.v4
title: Coupled effects of moisture sources and convection on stable isotopes in precipitation across East Asia: Implications for paleoclimate reconstruction

description: The meteorological and isotopic data are used in the paper titled "Coupled effects of moisture sources and convection on stable isotopes in precipitation across East Asia: Implications for paleoclimate reconstruction".
DOI: 10.6084/m9.figshare.11627124.v6
title: Coupled effects of moisture sources and convection on stable isotopes in precipitation across East Asia: Implications for paleoclimate reconstruction

description: The meteorological and isotopic data are used in the paper titled "Coupled effects of moisture sources and convection on stable isotopes in precipitation across East Asia: Implications for paleoclimate reconstruction".
DOI: 10.6084/m9.figshare.11627124.v5
title: Coupled effects of moisture sources and convection on stable isotopes in precipitation across East Asia: Implications for paleoclimate reconstruction

description: The meteorological and isotopic data are used in the paper titled "Coupled effects of moisture sources and convection on stable isotopes in precipitation across East Asia: Implications for paleoclimate reconstruction".
DOI: 10.6084/m9.figshare.11626914
title: MOESM4 of Therapeutic use of cannabis and cannabinoids: an evidence mapping and appraisal of systematic reviews

description: Additional file 4: PICOs included on systematic reviews.
DOI: 10.6084/m9.figshare.11626914.v1
title: MOESM4 of Therapeutic use of cannabis and cannabinoids: an evidence mapping and appraisal of systematic reviews

description: Additional file 4: PICOs included on systematic reviews.
DOI: 10.6084/m9.figshare.11626908
title: MOESM3 of Therapeutic use of cannabis and cannabinoids: an evidence mapping and appraisal of systematic reviews

description: Additional file 3: Characteristics of individual studies included in systematic reviews.
DOI: 10.6084/m9.figshare.11626908.v1
title: MOESM3 of Therapeutic use of cannabis and cannabinoids: an evidence mapping and appraisal of systematic reviews

description: Additional file 3: Characteristics of individual studies included in systematic reviews.
DOI: 10.6084/m9.figshare.11626872
title: MOESM4 of PRAP: Pan Resistome analysis pipeline

description: Additional file 4. Archive containing results of analysis for nucleotide sequences of 26â€‰S. enterica genomes annotated by the ResFinder database.
DOI: 10.6084/m9.figshare.11626869
title: MOESM3 of PRAP: Pan Resistome analysis pipeline

description: Additional file 3. Archive containing results of annotation of different formats of genome files for 26â€‰S. enterica genomes based on both the CARD and ResFinder databases.
DOI: 10.6084/m9.figshare.11626872.v1
title: MOESM4 of PRAP: Pan Resistome analysis pipeline

description: Additional file 4. Archive containing results of analysis for nucleotide sequences of 26â€‰S. enterica genomes annotated by the ResFinder database.
DOI: 10.6084/m9.figshare.11626869.v1
title: MOESM3 of PRAP: Pan Resistome analysis pipeline

description: Additional file 3. Archive containing results of annotation of different formats of genome files for 26â€‰S. enterica genomes based on both the CARD and ResFinder databases.
DOI: 10.6084/m9.figshare.11626857
title: MOESM2 of PRAP: Pan Resistome analysis pipeline

description: Additional file 2. Archive containing files for evaluation k-mer performance and scoring generated by the k-mer method.
DOI: 10.6084/m9.figshare.11626857.v1
title: MOESM2 of PRAP: Pan Resistome analysis pipeline

description: Additional file 2. Archive containing files for evaluation k-mer performance and scoring generated by the k-mer method.
DOI: 10.6084/m9.figshare.11626851
title: MOESM1 of PRAP: Pan Resistome analysis pipeline

description: Additional file 1. Information for 26â€‰S. enterica genomes.
DOI: 10.6084/m9.figshare.11626851.v1
title: MOESM1 of PRAP: Pan Resistome analysis pipeline

description: Additional file 1. Information for 26â€‰S. enterica genomes.
DOI: 10.6084/m9.figshare.11626785
title: MOESM10 of Deficiency of Gankyrin in the small intestine is associated with augmented colitis accompanied by altered bacterial composition of intestinal microbiota

description: Additional file 10: Table S2. Number of sequence reads analyzed during the 16S rRNA amplicon analysis conducted to understand the intestinal microbiota in the co-housed mice groups
DOI: 10.6084/m9.figshare.11626779
title: MOESM1 of Genome-resolved metagenomics analysis provides insights into the ecological role of Thaumarchaeota in the Amazon River and its plume

description: Additional file 1: Dataset S1. provides GenBank accession numbers and ribosomal gene sequences for the genomes used to construct the phylogenetic tree.
DOI: 10.6084/m9.figshare.11626785.v1
title: MOESM10 of Deficiency of Gankyrin in the small intestine is associated with augmented colitis accompanied by altered bacterial composition of intestinal microbiota

description: Additional file 10: Table S2. Number of sequence reads analyzed during the 16S rRNA amplicon analysis conducted to understand the intestinal microbiota in the co-housed mice groups
DOI: 10.6084/m9.figshare.11626779.v1
title: MOESM1 of Genome-resolved metagenomics analysis provides insights into the ecological role of Thaumarchaeota in the Amazon River and its plume

description: Additional file 1: Dataset S1. provides GenBank accession numbers and ribosomal gene sequences for the genomes used to construct the phylogenetic tree.
DOI: 10.6084/m9.figshare.11626722
title: MOESM1 of Delineating significant genome-wide associations of variants with antipsychotic and antidepressant treatment response: implications for clinical pharmacogenomics

description: Additional file 1: Table S1. Summary information for the identified drug SNP-correlations. Table S2. List of the antipsychotic/antidepressant drug-SNP correlations that have been reported once (duplicates removed) in the assessed 20 studies deposited in the GWAS catalog.
DOI: 10.6084/m9.figshare.11626722.v1
title: MOESM1 of Delineating significant genome-wide associations of variants with antipsychotic and antidepressant treatment response: implications for clinical pharmacogenomics

description: Additional file 1: Table S1. Summary information for the identified drug SNP-correlations. Table S2. List of the antipsychotic/antidepressant drug-SNP correlations that have been reported once (duplicates removed) in the assessed 20 studies deposited in the GWAS catalog.
DOI: 10.6084/m9.figshare.11626695
title: MOESM1 of The changing epidemiology of hepatitis B and C infections in Nanoro, rural Burkina Faso: a random sampling survey

description: Additional file 1. Questionnaires used in the study. Appendix 1a is questionnaire for children and appendix 1b for mothers. These questionnaires were solely developed for this study and it mainly included the demographic information, vaccination status of the children, general knowledge on the hepatitis B virus infection and the available of vaccination.
DOI: 10.6084/m9.figshare.11626689
title: MOESM1 of Model-based exploration of the impact of glucose metabolism on the estrous cycle dynamics in dairy cows

description: Additional file 1 The Matlab code contains the three m-files BovSys_para.m, BovSys_equa.m and BovSys_run.m. To start simulations, one has to run BovSys_run.m, which guides the user through different simulation scenarios (lactating/non-lactating with different diets). In addition, there are four data files containing the data for IGF (Data_IGF_Hol.mat), P4 (Data_P4_Hol.mat), milk (ML.mat), and DMI (DM.mat), that are needed as input files to run the model.
DOI: 10.6084/m9.figshare.11626695.v1
title: MOESM1 of The changing epidemiology of hepatitis B and C infections in Nanoro, rural Burkina Faso: a random sampling survey

description: Additional file 1. Questionnaires used in the study. Appendix 1a is questionnaire for children and appendix 1b for mothers. These questionnaires were solely developed for this study and it mainly included the demographic information, vaccination status of the children, general knowledge on the hepatitis B virus infection and the available of vaccination.
DOI: 10.6084/m9.figshare.11626689.v1
title: MOESM1 of Model-based exploration of the impact of glucose metabolism on the estrous cycle dynamics in dairy cows

description: Additional file 1 The Matlab code contains the three m-files BovSys_para.m, BovSys_equa.m and BovSys_run.m. To start simulations, one has to run BovSys_run.m, which guides the user through different simulation scenarios (lactating/non-lactating with different diets). In addition, there are four data files containing the data for IGF (Data_IGF_Hol.mat), P4 (Data_P4_Hol.mat), milk (ML.mat), and DMI (DM.mat), that are needed as input files to run the model.
DOI: 10.6084/m9.figshare.11626569
title: MOESM1 of Proteomics profiling and pathway analysis of hippocampal aging in rhesus monkeys

description: Additional file 1: Table S1. All differentially expressed proteins detected.
DOI: 10.6084/m9.figshare.11626569.v1
title: MOESM1 of Proteomics profiling and pathway analysis of hippocampal aging in rhesus monkeys

description: Additional file 1: Table S1. All differentially expressed proteins detected.