cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.14182510.v1
title: Mass Spectrometry Metabolomics of Hot Steep Malt Extracts and Association to Sensory Traits

description: In the brewing industry, there is value in defining sensory attributes of malt, and recent protocols have been developed that enable analysis of aroma and taste. One method, the “hot steep,” is a hot water extract that is highly reproducible and able to distinguish malt flavor. However, the chemistry of the hot steep extracts has not been fully defined, and the links between specific metabolites of the hot steep and their resulting sensory attributes remains largely unknown. Here, a study was designed to describe the metabolite chemistry of hot steep extracts, and to characterize variation in this chemistry and corresponding sensory by comparative analysis of 12 commercial pale malts. Metabolomics was performed on the 12 malt hot steep extracts using three mass spectrometry platforms to detect volatiles (HS/SPME-GC-MS) and non-volatiles (UHPLC-TOF-MS and GC-MS). The analysis detected a total of 1,026 compounds including lipids, organic acids, esters, and Maillard Reaction Products (MRPs), of which 162 compounds (15.7%) varied among the 12 hot steep extracts. Sensory of the 12 hot steep extracts was performed using an integrated Check All That Apply and quantitative analysis method for 14 traits, and the data revealed <i>cereal, grassy,</i> and <i>dough</i> aromas were the attributes that varied. The metabolomics and sensory data were integrated using OPLS analysis. The analysis revealed 64 compounds strongly associated with <i>cereal</i> aroma and included MRPs. A total of 23 compounds were strongly associated with <i>grassy</i> aroma including alkane/alkenes, benzenoids, organic acids, lipids, and fatty acid esters. Taken together, these data highlight the utility of the hot steep extract to differentiate malt for flavor and chemistry and indicate specific compounds that drive the most dominant flavors observed in this population of pale malts.
DOI: 10.6084/m9.figshare.14676635.v1
title: Additional file 1 of The divergence of alternative splicing between ohnologs in teleost fishes

description: Additional file 1: Table S1. Genes used in this study, and their transcript numbers in Ensembl and alternative splicing forms based on RAN-seq data. Details of gene identification and selection could be found in Inoue et al. [33] and Guo [21]. Table S2. The number of ohnolog pairs and their singleton orthologs. Table S3. GO-like enrichment of anatomical terms analysis of ohologs with significantly asymmetric splicing forms in zebrafish using BgeeDB ( https://bgee.org/ ). Table S4. Information of RNA-seq data used in this study.
DOI: 10.6084/m9.figshare.14676635
title: Additional file 1 of The divergence of alternative splicing between ohnologs in teleost fishes

description: Additional file 1: Table S1. Genes used in this study, and their transcript numbers in Ensembl and alternative splicing forms based on RAN-seq data. Details of gene identification and selection could be found in Inoue et al. [33] and Guo [21]. Table S2. The number of ohnolog pairs and their singleton orthologs. Table S3. GO-like enrichment of anatomical terms analysis of ohologs with significantly asymmetric splicing forms in zebrafish using BgeeDB ( https://bgee.org/ ). Table S4. Information of RNA-seq data used in this study.
DOI: 10.25934/00002071.1
title: Available IPD datapackage for study 'A 24-week, Double-blind, Double-dummy, Randomized, Parallel-group Study to Investigate the Effects of Rosiglitazone (Extended Release Tablets), Donepezil, and Placebo as Monotherapy on Cognition and Overall Clinical Response in APOE ε4-stratified Subjects With Mild to Moderate Alzheimer's Disease. (REFLECT-1)'

description: Vivli is an independent, non-profit organization that has developed a global data-sharing and analytics platform to serve all elements of the international research community. Our mission is to promote, coordinate, and facilitate scientific sharing and reuse of clinical research data through the creation and implementation of a sustainable global data-sharing enterprise. The Vivli platform includes an independent data repository, in-depth search engine and a cloud-based, secure analytics platform.
DOI: 10.25934/00002071.2
title: IPD datapackage for study 'A 24-week, Double-blind, Double-dummy, Randomized, Parallel-group Study to Investigate the Effects of Rosiglitazone (Extended Release Tablets), Donepezil, and Placebo as Monotherapy on Cognition and Overall Clinical Response in APOE ε4-stratified Subjects With Mild to Moderate Alzheimer's Disease. (REFLECT-1)' and research request: 'A novel statistical approach to detect the efficacy of drugs that have heterogeneous treatment effects'

description: Vivli is an independent, non-profit organization that has developed a global data-sharing and analytics platform to serve all elements of the international research community. Our mission is to promote, coordinate, and facilitate scientific sharing and reuse of clinical research data through the creation and implementation of a sustainable global data-sharing enterprise. The Vivli platform includes an independent data repository, in-depth search engine and a cloud-based, secure analytics platform.
DOI: 10.6084/m9.figshare.13632587
title: Additional file 3 of Feasibility of using alternative swabs and storage solutions for paired SARS-CoV-2 detection and microbiome analysis in the hospital environment

description: Additional file 3:
DOI: 10.6084/m9.figshare.13632587.v1
title: Additional file 3 of Feasibility of using alternative swabs and storage solutions for paired SARS-CoV-2 detection and microbiome analysis in the hospital environment

description: Additional file 3:
DOI: 10.6084/m9.figshare.13632590
title: Additional file 4 of Feasibility of using alternative swabs and storage solutions for paired SARS-CoV-2 detection and microbiome analysis in the hospital environment

description: Additional file 4:
DOI: 10.6084/m9.figshare.13632590.v1
title: Additional file 4 of Feasibility of using alternative swabs and storage solutions for paired SARS-CoV-2 detection and microbiome analysis in the hospital environment

description: Additional file 4:
DOI: 10.6084/m9.figshare.14676670
title: Additional file 1 of Genetic variation at the Cyp6m2 putative insecticide resistance locus in Anopheles gambiae and Anopheles coluzzii

description: Additional file 1: List of An. gambiae and An. coluzzii genome samples and haplotypes from Ag1000G Phase 2-AR3. Table showing Ag1000G Phase 2-AR3 sample properties such as population, country, region, sex, species identity and haplotype cluster.
DOI: 10.6084/m9.figshare.14676670.v1
title: Additional file 1 of Genetic variation at the Cyp6m2 putative insecticide resistance locus in Anopheles gambiae and Anopheles coluzzii

description: Additional file 1: List of An. gambiae and An. coluzzii genome samples and haplotypes from Ag1000G Phase 2-AR3. Table showing Ag1000G Phase 2-AR3 sample properties such as population, country, region, sex, species identity and haplotype cluster.
DOI: 10.6084/m9.figshare.14676673.v1
title: Additional file 2 of Genetic variation at the Cyp6m2 putative insecticide resistance locus in Anopheles gambiae and Anopheles coluzzii

description: Additional file 2: List of synonymous and non-synonymous genetic variants in Cyp6m2. Table showing Ag1000G Phase 2-AR3 Cyp6m2 variant calls and variant properties stratified by population and effect.
DOI: 10.6084/m9.figshare.14676673
title: Additional file 2 of Genetic variation at the Cyp6m2 putative insecticide resistance locus in Anopheles gambiae and Anopheles coluzzii

description: Additional file 2: List of synonymous and non-synonymous genetic variants in Cyp6m2. Table showing Ag1000G Phase 2-AR3 Cyp6m2 variant calls and variant properties stratified by population and effect.
DOI: 10.6084/m9.figshare.14676713.v1
title: Additional file 10 of Chromosome-level genome assembly and manually-curated proteome of model necrotroph Parastagonospora nodorum Sn15 reveals a genome-wide trove of candidate effector homologs, and redundancy of virulence-related functions within an accessory chromosome

description: Additional file 10: Supplementary Table 7. Presence-absence variation (PAV) matrix for comparison of Parastagonospora nodorum Sn15 genes versus all other Parastagonospora spp. isolates included in this study.
DOI: 10.6084/m9.figshare.14676713
title: Additional file 10 of Chromosome-level genome assembly and manually-curated proteome of model necrotroph Parastagonospora nodorum Sn15 reveals a genome-wide trove of candidate effector homologs, and redundancy of virulence-related functions within an accessory chromosome

description: Additional file 10: Supplementary Table 7. Presence-absence variation (PAV) matrix for comparison of Parastagonospora nodorum Sn15 genes versus all other Parastagonospora spp. isolates included in this study.
DOI: 10.6084/m9.figshare.14676728
title: Additional file 15 of Chromosome-level genome assembly and manually-curated proteome of model necrotroph Parastagonospora nodorum Sn15 reveals a genome-wide trove of candidate effector homologs, and redundancy of virulence-related functions within an accessory chromosome

description: Additional file 15: Supplementary Table 12. Orthology comparison between gene predictions of P. nodorum Sn15 and Sn4, indicating Sn15 orthologs to Sn4 effector candidates under diversifying selection identified in Richards et al. 2019.
DOI: 10.6084/m9.figshare.14676728.v1
title: Additional file 15 of Chromosome-level genome assembly and manually-curated proteome of model necrotroph Parastagonospora nodorum Sn15 reveals a genome-wide trove of candidate effector homologs, and redundancy of virulence-related functions within an accessory chromosome

description: Additional file 15: Supplementary Table 12. Orthology comparison between gene predictions of P. nodorum Sn15 and Sn4, indicating Sn15 orthologs to Sn4 effector candidates under diversifying selection identified in Richards et al. 2019.
DOI: 10.6084/m9.figshare.14676752
title: Additional file 6 of Chromosome-level genome assembly and manually-curated proteome of model necrotroph Parastagonospora nodorum Sn15 reveals a genome-wide trove of candidate effector homologs, and redundancy of virulence-related functions within an accessory chromosome

description: Additional file 6: Supplementary Table 3. De novo repeat sequences predicted within the Parastagonospora nodorum Sn15 genome assembly.
DOI: 10.6084/m9.figshare.14676752.v1
title: Additional file 6 of Chromosome-level genome assembly and manually-curated proteome of model necrotroph Parastagonospora nodorum Sn15 reveals a genome-wide trove of candidate effector homologs, and redundancy of virulence-related functions within an accessory chromosome

description: Additional file 6: Supplementary Table 3. De novo repeat sequences predicted within the Parastagonospora nodorum Sn15 genome assembly.
DOI: 10.6084/m9.figshare.14676755
title: Additional file 7 of Chromosome-level genome assembly and manually-curated proteome of model necrotroph Parastagonospora nodorum Sn15 reveals a genome-wide trove of candidate effector homologs, and redundancy of virulence-related functions within an accessory chromosome

description: Additional file 7: Supplementary Table 4. Summary of Parastagonospora nodorum gene properties and predicted effector candidate genes.
DOI: 10.6084/m9.figshare.14676755.v1
title: Additional file 7 of Chromosome-level genome assembly and manually-curated proteome of model necrotroph Parastagonospora nodorum Sn15 reveals a genome-wide trove of candidate effector homologs, and redundancy of virulence-related functions within an accessory chromosome

description: Additional file 7: Supplementary Table 4. Summary of Parastagonospora nodorum gene properties and predicted effector candidate genes.
DOI: 10.6084/m9.figshare.14676794
title: Additional file 3 of GRiNCH: simultaneous smoothing and detection of topological units of genome organization from sparse chromatin contact count matrices with matrix factorization

description: Additional file 3 Supplementary_tables.xlsx. An Excel file containing Tables S1-3. Each spreadsheet tab includes table name and legend in the top rows.
DOI: 10.6084/m9.figshare.14676796
title: Additional file 3 of De novo transcriptome sequencing and anthocyanin metabolite analysis reveals leaf color of Acer pseudosieboldianum in autumn

description: Additional file 3: Table S2. KEGG pathway annotation in A. pseudosieboldianum unigenes.
DOI: 10.6084/m9.figshare.14676799.v1
title: Additional file 4 of De novo transcriptome sequencing and anthocyanin metabolite analysis reveals leaf color of Acer pseudosieboldianum in autumn

description: Additional file 4: Table S3. KEGG pathway enrichment analysis of DEGs between B and M.
DOI: 10.6084/m9.figshare.14676796.v1
title: Additional file 3 of De novo transcriptome sequencing and anthocyanin metabolite analysis reveals leaf color of Acer pseudosieboldianum in autumn

description: Additional file 3: Table S2. KEGG pathway annotation in A. pseudosieboldianum unigenes.
DOI: 10.6084/m9.figshare.14676799
title: Additional file 4 of De novo transcriptome sequencing and anthocyanin metabolite analysis reveals leaf color of Acer pseudosieboldianum in autumn

description: Additional file 4: Table S3. KEGG pathway enrichment analysis of DEGs between B and M.
DOI: 10.6084/m9.figshare.14676802
title: Additional file 5 of De novo transcriptome sequencing and anthocyanin metabolite analysis reveals leaf color of Acer pseudosieboldianum in autumn

description: Additional file 5: Table S4. KEGG pathway enrichment analysis of DEGs between B and A.
DOI: 10.6084/m9.figshare.14676808
title: Additional file 7 of De novo transcriptome sequencing and anthocyanin metabolite analysis reveals leaf color of Acer pseudosieboldianum in autumn

description: Additional file 7: Table S6. Designed primers for RT-qPCR.
DOI: 10.6084/m9.figshare.14676808.v1
title: Additional file 7 of De novo transcriptome sequencing and anthocyanin metabolite analysis reveals leaf color of Acer pseudosieboldianum in autumn

description: Additional file 7: Table S6. Designed primers for RT-qPCR.
DOI: 10.6084/m9.figshare.14676802.v1
title: Additional file 5 of De novo transcriptome sequencing and anthocyanin metabolite analysis reveals leaf color of Acer pseudosieboldianum in autumn

description: Additional file 5: Table S4. KEGG pathway enrichment analysis of DEGs between B and A.
DOI: 10.6084/m9.figshare.14676827.v1
title: Additional file 3 of Transcriptome analysis of potential candidate genes and molecular pathways in colitis-associated colorectal cancer of Mkp-1-deficient mice

description: Additional file 3. The list of DEGs for adenoma stage in wild type and Mkp-1 knockout mice.
DOI: 10.6084/m9.figshare.14676833
title: Additional file 5 of Transcriptome analysis of potential candidate genes and molecular pathways in colitis-associated colorectal cancer of Mkp-1-deficient mice

description: Additional file 5. The enrichment analysis for common DEGs between wild type and Mkp-1 knockout mice.
DOI: 10.6084/m9.figshare.14676827
title: Additional file 3 of Transcriptome analysis of potential candidate genes and molecular pathways in colitis-associated colorectal cancer of Mkp-1-deficient mice

description: Additional file 3. The list of DEGs for adenoma stage in wild type and Mkp-1 knockout mice.
DOI: 10.6084/m9.figshare.14676830.v1
title: Additional file 4 of Transcriptome analysis of potential candidate genes and molecular pathways in colitis-associated colorectal cancer of Mkp-1-deficient mice

description: Additional file 4. The list of DEGs for carcinoma stage in wild type and Mkp-1 knockout mice.
DOI: 10.6084/m9.figshare.14676836
title: Additional file 6 of Transcriptome analysis of potential candidate genes and molecular pathways in colitis-associated colorectal cancer of Mkp-1-deficient mice

description: Additional file 6. The list of GO terms and KEGG pathways wild type and Mkp-1 knockout mice.
DOI: 10.6084/m9.figshare.14676839
title: Additional file 7 of Transcriptome analysis of potential candidate genes and molecular pathways in colitis-associated colorectal cancer of Mkp-1-deficient mice

description: Additional file 7. The survival analysis of the overall and disease-free survival of colorectal cancer patients based on the PrognoScan database.
DOI: 10.6084/m9.figshare.14676839.v1
title: Additional file 7 of Transcriptome analysis of potential candidate genes and molecular pathways in colitis-associated colorectal cancer of Mkp-1-deficient mice

description: Additional file 7. The survival analysis of the overall and disease-free survival of colorectal cancer patients based on the PrognoScan database.
DOI: 10.6084/m9.figshare.14676833.v1
title: Additional file 5 of Transcriptome analysis of potential candidate genes and molecular pathways in colitis-associated colorectal cancer of Mkp-1-deficient mice

description: Additional file 5. The enrichment analysis for common DEGs between wild type and Mkp-1 knockout mice.
DOI: 10.6084/m9.figshare.14676836.v1
title: Additional file 6 of Transcriptome analysis of potential candidate genes and molecular pathways in colitis-associated colorectal cancer of Mkp-1-deficient mice

description: Additional file 6. The list of GO terms and KEGG pathways wild type and Mkp-1 knockout mice.
DOI: 10.6084/m9.figshare.14676579
title: agronomic.tsv

description: data for agronomic features of coconut: Number of racemes, number of coconuts, polar circumference of the fruit, equatorial circumference of the fruit, polar circumference of the nut, equatorial circumference of the nut, nut weight, copra weight, fiber weight, water.body,div,table,thead,tbody,tfoot,tr,th,td,p { font-family:"Arial"; font-size:x-small }a.comment-indicator:hover + comment { background:#ffd; position:absolute; display:block; border:1px solid black; padding:0.5em; }a.comment-indicator { background:red; display:inline-block; border:1px solid black; width:0.5em; height:0.5em; }comment { display:none; }
DOI: 10.6084/m9.figshare.14676579.v1
title: agronomic.tsv

description: data for agronomic features of coconut: Number of racemes, number of coconuts, polar circumference of the fruit, equatorial circumference of the fruit, polar circumference of the nut, equatorial circumference of the nut, nut weight, copra weight, fiber weight, water.body,div,table,thead,tbody,tfoot,tr,th,td,p { font-family:"Arial"; font-size:x-small }a.comment-indicator:hover + comment { background:#ffd; position:absolute; display:block; border:1px solid black; padding:0.5em; }a.comment-indicator { background:red; display:inline-block; border:1px solid black; width:0.5em; height:0.5em; }comment { display:none; }
DOI: 10.6084/m9.figshare.14676920
title: Additional file 1 of Comparison study of differential abundance testing methods using two large Parkinson disease gut microbiome datasets derived from 16S amplicon sequencing

description: Additional file 1. Results for t-tests when testing for differences between datasets for various metrics.
DOI: 10.6084/m9.figshare.14676923
title: Additional file 2 of Comparison study of differential abundance testing methods using two large Parkinson disease gut microbiome datasets derived from 16S amplicon sequencing

description: Additional file 2: Table S1. Method characteristics.
DOI: 10.6084/m9.figshare.14676923.v1
title: Additional file 2 of Comparison study of differential abundance testing methods using two large Parkinson disease gut microbiome datasets derived from 16S amplicon sequencing

description: Additional file 2: Table S1. Method characteristics.
DOI: 10.6084/m9.figshare.14676926
title: Additional file 3 of Comparison study of differential abundance testing methods using two large Parkinson disease gut microbiome datasets derived from 16S amplicon sequencing

description: Additional file 3: Table S2. List of chosen parameters for each function within each method that either differed from default, or did not have a set default (and therefore a choice had to be made). AIC: Akaike information criterion; FDR: False discovery rate; TMM: Trimmed mean of M-values; RLE: Relative log expression; LDA: Linear discriminant analysis.
DOI: 10.6084/m9.figshare.14676926.v1
title: Additional file 3 of Comparison study of differential abundance testing methods using two large Parkinson disease gut microbiome datasets derived from 16S amplicon sequencing

description: Additional file 3: Table S2. List of chosen parameters for each function within each method that either differed from default, or did not have a set default (and therefore a choice had to be made). AIC: Akaike information criterion; FDR: False discovery rate; TMM: Trimmed mean of M-values; RLE: Relative log expression; LDA: Linear discriminant analysis.
DOI: 10.6084/m9.figshare.14676932
title: Additional file 5 of Comparison study of differential abundance testing methods using two large Parkinson disease gut microbiome datasets derived from 16S amplicon sequencing

description: Additional file 5: Table S4. Dataset 2 false discovery rate (FDR) q-values for differential abundance methods when performed on unfiltered data. Dataset 2 FDR q-values for all differential abundance methods were aggregated into one table along with the mean relative abundance of each genus for PD patients (Case MRA) and control subjects (Control MRA) and the mean relative abundance ratio of Case MRA to Control MRA (MRAR). 323 PD patients and 184 controls were included in all analyses. All genera detected in dataset 2 (561 genera) were included in the analyses. If an analysis resulted in an "NA" for a result, or a result was not outputted by the method, a 1 was placed for the FDR q-value. Calculations for the number of detected DA signatures for each method are located at the bottom of the table. Calculations for the number of methods that detected or replicated a genus as differentially abundant are located to the right of the table.
DOI: 10.6084/m9.figshare.14676932.v1
title: Additional file 5 of Comparison study of differential abundance testing methods using two large Parkinson disease gut microbiome datasets derived from 16S amplicon sequencing

description: Additional file 5: Table S4. Dataset 2 false discovery rate (FDR) q-values for differential abundance methods when performed on unfiltered data. Dataset 2 FDR q-values for all differential abundance methods were aggregated into one table along with the mean relative abundance of each genus for PD patients (Case MRA) and control subjects (Control MRA) and the mean relative abundance ratio of Case MRA to Control MRA (MRAR). 323 PD patients and 184 controls were included in all analyses. All genera detected in dataset 2 (561 genera) were included in the analyses. If an analysis resulted in an "NA" for a result, or a result was not outputted by the method, a 1 was placed for the FDR q-value. Calculations for the number of detected DA signatures for each method are located at the bottom of the table. Calculations for the number of methods that detected or replicated a genus as differentially abundant are located to the right of the table.