cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.9740516
title: Additional file 1 of An equivalence approach to the integrative analysis of feature lists

description: Comma separated file containg original data for the Kidney lists example. Each list is a collection of affymetrix probesets from hgu133plus2 arrays. The file was downloaded from the url: https://www.ualberta.ca/medicine/institutes-centres-groups/atagc/research/gene-lists . (TSV 61 kb)
DOI: 10.6084/m9.figshare.9740519.v1
title: Additional file 1: of Patterns and determinants of essential neonatal care utilization among underprivileged ethnic groups in Midwest Nepal: a mixed method study

description: Operational definition of variables for the study. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.9740516.v1
title: Additional file 1 of An equivalence approach to the integrative analysis of feature lists

description: Comma separated file containg original data for the Kidney lists example. Each list is a collection of affymetrix probesets from hgu133plus2 arrays. The file was downloaded from the url: https://www.ualberta.ca/medicine/institutes-centres-groups/atagc/research/gene-lists . (TSV 61 kb)
DOI: 10.6084/m9.figshare.9740420
title: Additional file 2: of Fossil fuels are harming our brains: identifying key messages about the health effects of air pollution from fossil fuels

description: This file contains all data underlying the analyses reported in this article. (CSV 11640 kb)
DOI: 10.6084/m9.figshare.9740408
title: Additional file 1: of Genome-wide identification and interactome analysis of members of two-component system in Banana

description: Table S1. Description of members of TCS gene family in different plants. Table S2. Motifs identified in promoter sequences of TCS genes in banana using PlantCare online tool. Table S3. Transcription factors identified in promoter region sequence of TCS genes of banana using Plantpan online tool. Table S4. De novo motifs identified in promoter region sequence of TCS genes using MEME tool. Table S5. Primer sequences of selected TCS genes for the qRT PCR analysis. (RAR 343 kb)
DOI: 10.6084/m9.figshare.9740411
title: Additional file 2: of Genome-wide identification and interactome analysis of members of two-component system in Banana

description: Figure S1. Domain architecture of TCS proteins in Musa acuminata and Musa balbisiana obtained using SMART domain detection tool. Figure S2. (A) Circular representation of gene duplication event of TCS gene family in Musa acuminata and Musa balbisiana, generated using reciprocal blast hits for tandem and segmental duplicates in MCScanX program. (B) Circular representation of gene duplication event with in TCS gene groups in Musa acuminata and Musa balbisiana, generated using reciprocal blast hits for tandem and segmental duplicates in MCScanX program. Figure S3. Bar representation of chromosomal position of TCS genes in Musa acuminata (A) and Musa balbisiana (B). Figure S5. Expression of RR-A, RR-B and PRR genes in ethylene treatment: (A), (C) and € represents Log2 transformed fold change values from Banana Genome Hub DB, for 40 days, 60 days, 90 days (normal and ethylene treatment). (B), (D) and (F) represent Log2fold change value for TCS genes from 4 day ripe pulp (after ethylene treatment). Figurfe S6. TCS gene expression analysis in fungal infection in corm and roots of banana plant, expression of Receptor CHK/HK and mediator HPT genes in fungal infection: joint panel of 3 groups represent the fungal infection in root at 3 h, 27 h, and 51 h by Foc1 & Foc4 strains. Corm represents Log2 transformed fold change values for receptors during infection in corm. Figure S7. Expression of RR-A, RR-B and PRR genes in fungal infection: Joint panel of 3 groups represent the fungal infection in root at 3 h, 27 h, and 51 h by Foc1 & Foc4 strains. Corm represents Log2 transformed fold change values for receptors during infection in corm. Figure S8. Co expression network of TCS genes in ethylene treatment (A) and in fungal infection (B), based on correlation value (r) of TCS genes as bait, with top 200 differentially expressing genes. Cytoscape program was used for calculation and visualization of the network. Figure S9. Pictorial representation of docked proteins in TCS complexes, obtained by molecular docking. (A) Represents, representative members of receptor proteins with MaHP1 and MaRR1. (B) Represents, representative members of receptor proteins with MaHP1 and MaRR21. (C) Represents representative members of receptor proteins with MaHP1 and MaPRR1. Figure S10. Gene structure for HK, HPT and RR genes of Musa acuminata and Musa balbisiana, generated using GSDS online tool from using the genomic coordinates of banana GFF. (RAR 4103 kb)
DOI: 10.6084/m9.figshare.9740420.v1
title: Additional file 2: of Fossil fuels are harming our brains: identifying key messages about the health effects of air pollution from fossil fuels

description: This file contains all data underlying the analyses reported in this article. (CSV 11640 kb)
DOI: 10.6084/m9.figshare.9740408.v1
title: Additional file 1: of Genome-wide identification and interactome analysis of members of two-component system in Banana

description: Table S1. Description of members of TCS gene family in different plants. Table S2. Motifs identified in promoter sequences of TCS genes in banana using PlantCare online tool. Table S3. Transcription factors identified in promoter region sequence of TCS genes of banana using Plantpan online tool. Table S4. De novo motifs identified in promoter region sequence of TCS genes using MEME tool. Table S5. Primer sequences of selected TCS genes for the qRT PCR analysis. (RAR 343 kb)
DOI: 10.6084/m9.figshare.9740411.v1
title: Additional file 2: of Genome-wide identification and interactome analysis of members of two-component system in Banana

description: Figure S1. Domain architecture of TCS proteins in Musa acuminata and Musa balbisiana obtained using SMART domain detection tool. Figure S2. (A) Circular representation of gene duplication event of TCS gene family in Musa acuminata and Musa balbisiana, generated using reciprocal blast hits for tandem and segmental duplicates in MCScanX program. (B) Circular representation of gene duplication event with in TCS gene groups in Musa acuminata and Musa balbisiana, generated using reciprocal blast hits for tandem and segmental duplicates in MCScanX program. Figure S3. Bar representation of chromosomal position of TCS genes in Musa acuminata (A) and Musa balbisiana (B). Figure S5. Expression of RR-A, RR-B and PRR genes in ethylene treatment: (A), (C) and € represents Log2 transformed fold change values from Banana Genome Hub DB, for 40 days, 60 days, 90 days (normal and ethylene treatment). (B), (D) and (F) represent Log2fold change value for TCS genes from 4 day ripe pulp (after ethylene treatment). Figurfe S6. TCS gene expression analysis in fungal infection in corm and roots of banana plant, expression of Receptor CHK/HK and mediator HPT genes in fungal infection: joint panel of 3 groups represent the fungal infection in root at 3 h, 27 h, and 51 h by Foc1 & Foc4 strains. Corm represents Log2 transformed fold change values for receptors during infection in corm. Figure S7. Expression of RR-A, RR-B and PRR genes in fungal infection: Joint panel of 3 groups represent the fungal infection in root at 3 h, 27 h, and 51 h by Foc1 & Foc4 strains. Corm represents Log2 transformed fold change values for receptors during infection in corm. Figure S8. Co expression network of TCS genes in ethylene treatment (A) and in fungal infection (B), based on correlation value (r) of TCS genes as bait, with top 200 differentially expressing genes. Cytoscape program was used for calculation and visualization of the network. Figure S9. Pictorial representation of docked proteins in TCS complexes, obtained by molecular docking. (A) Represents, representative members of receptor proteins with MaHP1 and MaRR1. (B) Represents, representative members of receptor proteins with MaHP1 and MaRR21. (C) Represents representative members of receptor proteins with MaHP1 and MaPRR1. Figure S10. Gene structure for HK, HPT and RR genes of Musa acuminata and Musa balbisiana, generated using GSDS online tool from using the genomic coordinates of banana GFF. (RAR 4103 kb)
DOI: 10.6084/m9.figshare.9740378
title: Additional file 3: of Childhood traumatization is associated with differences in TRPA1 promoter methylation in female patients with multisomatoform disorder with pain as the leading bodily symptom

description: Table S1. Spearman correlations for selected variables (XLSX 17 kb)
DOI: 10.6084/m9.figshare.9740378.v1
title: Additional file 3: of Childhood traumatization is associated with differences in TRPA1 promoter methylation in female patients with multisomatoform disorder with pain as the leading bodily symptom

description: Table S1. Spearman correlations for selected variables (XLSX 17 kb)
DOI: 10.6084/m9.figshare.9740357
title: Additional file 3: of Systematic review of dengue vaccine efficacy

description: Dataset_dengue. The complete systematic review dataset (CSV 1 kb)
DOI: 10.6084/m9.figshare.9740357.v1
title: Additional file 3: of Systematic review of dengue vaccine efficacy

description: Dataset_dengue. The complete systematic review dataset (CSV 1 kb)
DOI: 10.6084/m9.figshare.9740318
title: Additional file 1: of RNA-seq of eight different poplar clones reveals conserved up-regulation of gene expression in response to insect herbivory

description: Table S1. Number of RNA-seq reads and percentage of uniquely mapped reads. Table S2. Differential expression results from DESeq2. Table S3. Genes forming the co-expression module shown in Fig. 3. Table S4. PFAM enrichment analysis of the genes forming the co-expression module shown in Fig. 3. Table S5. Most strongly induced genes, defined as having top 10% adjusted p-values and log2 fold-changes. Data for the genes were extracted via the GeneList utility on popgenie.org . Table S6. Illumina adapter sequences for each RNA-seq sample. (XLSX 2557 kb)
DOI: 10.6084/m9.figshare.9740318.v1
title: Additional file 1: of RNA-seq of eight different poplar clones reveals conserved up-regulation of gene expression in response to insect herbivory

description: Table S1. Number of RNA-seq reads and percentage of uniquely mapped reads. Table S2. Differential expression results from DESeq2. Table S3. Genes forming the co-expression module shown in Fig. 3. Table S4. PFAM enrichment analysis of the genes forming the co-expression module shown in Fig. 3. Table S5. Most strongly induced genes, defined as having top 10% adjusted p-values and log2 fold-changes. Data for the genes were extracted via the GeneList utility on popgenie.org . Table S6. Illumina adapter sequences for each RNA-seq sample. (XLSX 2557 kb)
DOI: 10.6084/m9.figshare.9740279
title: Additional file 5: of An analysis of deficiencies in the data of interventional drug trials registered with Clinical Trials Registry - India

description: Expanded methods, used to generate the data in the following sections. Sections 7–16 provide details on (7) The 1331 categories of Type of Study in 12,673 trials, year-wise from 2007–2018; (8) Determining the truly foreign trials; (9) Determining the unambiguously Indian trials, and error rates over time; (10) Determining the unambiguously Multinational trials, and error rates over time; (11) Identifying the actual trials in the categories Foreign, Indian and Multinational: A summary. (12) 55 Interventional Indian cases with Phase listed as PMS, and error rates over time; (13) For the redefined Indian and Multinational sets (i) cases of confusion between PMS and Phase 4 trials; (ii) cases where Type of Trial is BA/BE but Phase is 1–4; and (iii) Sites of study: Incorrect listing of cities. Error rates over time for some of these; (14) Missing data in terms of (i) Name of the PI was missing; (ii) for the redefined Indian set, and the Multinational set, cases where Type of Study was not available, but Phase of Trial was Phase 1, 1/2, 2, 2/3, 3, 3/4 or 4; (iii) Name of Primary Sponsor was missing; and (iv) the state hosting a trial was not listed. Error rates over time for some of these; (15) Examples of types of variations in PIs’ names; and examples, or the entire listing, of problems with ethics committees; and (16) A brief on the 47 trials conducted at the Malpani Multispeciality Hospital, Jaipur, Rajasthan. (ZIP 596 kb)
DOI: 10.6084/m9.figshare.9740282
title: Additional file 6: of An analysis of deficiencies in the data of interventional drug trials registered with Clinical Trials Registry - India

description: The percentage of trials with errors, in 3-year time periods, for the several categories of errors. a The percentage of trials with errors, in 3-year time periods, for the following categories of errors: (i) Type of Study: Large number of categories, (ii) Errors in determining the unambiguously Indian trials, (iii) Errors in determining the unambiguously Multinational trials, (iv) Indian trials: Interventional cases with Phase listed as PMS, (v) Redefined Indian trials: Type of Trial was PMS, but Phase of Trial was Phase 4, and (vi) Redefined Indian trials: Type of Trial was BA/BE, but Phase was 1, 1/2, 2, 2/3, 3, 3/4, or 4. Columns of data using redefined datasets are shaded. b The percentage of trials with errors, in 3-year time periods, for the following categories of errors: (i) Indian trials: Incorrect listing of cities, (ii) Multinational trials: Incorrect listing of cities, (iii) Indian trials: PI names listed as null, (iv) Multinational trials: PI names listed as null, (v) Redefined Indian trials: Type of Study was NA, but Phase was 1, 1/2, 2, 2/3, 3, 3/4, or 4, and (vi) Indian trials: Primary sponsor name â nilâ . Columns of data using redefined datasets are shaded. c The percentage of trials with errors, in 3-year time periods, for the following categories of errors: (i) Indian trials: State of trial site missing, (ii) Multinational trials: State of trial site missing, (iii) Indian trials: More ethics committees than trial sites, and (iv) Multinational trials: More ethics committees than trial sites. (XLS 16 kb)
DOI: 10.6084/m9.figshare.9740279.v1
title: Additional file 5: of An analysis of deficiencies in the data of interventional drug trials registered with Clinical Trials Registry - India

description: Expanded methods, used to generate the data in the following sections. Sections 7–16 provide details on (7) The 1331 categories of Type of Study in 12,673 trials, year-wise from 2007–2018; (8) Determining the truly foreign trials; (9) Determining the unambiguously Indian trials, and error rates over time; (10) Determining the unambiguously Multinational trials, and error rates over time; (11) Identifying the actual trials in the categories Foreign, Indian and Multinational: A summary. (12) 55 Interventional Indian cases with Phase listed as PMS, and error rates over time; (13) For the redefined Indian and Multinational sets (i) cases of confusion between PMS and Phase 4 trials; (ii) cases where Type of Trial is BA/BE but Phase is 1–4; and (iii) Sites of study: Incorrect listing of cities. Error rates over time for some of these; (14) Missing data in terms of (i) Name of the PI was missing; (ii) for the redefined Indian set, and the Multinational set, cases where Type of Study was not available, but Phase of Trial was Phase 1, 1/2, 2, 2/3, 3, 3/4 or 4; (iii) Name of Primary Sponsor was missing; and (iv) the state hosting a trial was not listed. Error rates over time for some of these; (15) Examples of types of variations in PIs’ names; and examples, or the entire listing, of problems with ethics committees; and (16) A brief on the 47 trials conducted at the Malpani Multispeciality Hospital, Jaipur, Rajasthan. (ZIP 596 kb)
DOI: 10.6084/m9.figshare.9740282.v1
title: Additional file 6: of An analysis of deficiencies in the data of interventional drug trials registered with Clinical Trials Registry - India

description: The percentage of trials with errors, in 3-year time periods, for the several categories of errors. a The percentage of trials with errors, in 3-year time periods, for the following categories of errors: (i) Type of Study: Large number of categories, (ii) Errors in determining the unambiguously Indian trials, (iii) Errors in determining the unambiguously Multinational trials, (iv) Indian trials: Interventional cases with Phase listed as PMS, (v) Redefined Indian trials: Type of Trial was PMS, but Phase of Trial was Phase 4, and (vi) Redefined Indian trials: Type of Trial was BA/BE, but Phase was 1, 1/2, 2, 2/3, 3, 3/4, or 4. Columns of data using redefined datasets are shaded. b The percentage of trials with errors, in 3-year time periods, for the following categories of errors: (i) Indian trials: Incorrect listing of cities, (ii) Multinational trials: Incorrect listing of cities, (iii) Indian trials: PI names listed as null, (iv) Multinational trials: PI names listed as null, (v) Redefined Indian trials: Type of Study was NA, but Phase was 1, 1/2, 2, 2/3, 3, 3/4, or 4, and (vi) Indian trials: Primary sponsor name â nilâ . Columns of data using redefined datasets are shaded. c The percentage of trials with errors, in 3-year time periods, for the following categories of errors: (i) Indian trials: State of trial site missing, (ii) Multinational trials: State of trial site missing, (iii) Indian trials: More ethics committees than trial sites, and (iv) Multinational trials: More ethics committees than trial sites. (XLS 16 kb)
DOI: 10.6084/m9.figshare.9740264
title: Additional file 3: of An analysis of deficiencies in the data of interventional drug trials registered with Clinical Trials Registry - India

description: The SQLite database with details of 12,673 trial records from CTRI. (ZIP 20 mb)
DOI: 10.6084/m9.figshare.9740270
title: Additional file 4: of An analysis of deficiencies in the data of interventional drug trials registered with Clinical Trials Registry - India

description: The schema of the SQLite database. (XLS 13 kb)
DOI: 10.6084/m9.figshare.9740264.v1
title: Additional file 3: of An analysis of deficiencies in the data of interventional drug trials registered with Clinical Trials Registry - India

description: The SQLite database with details of 12,673 trial records from CTRI. (ZIP 20 mb)
DOI: 10.6084/m9.figshare.9740270.v1
title: Additional file 4: of An analysis of deficiencies in the data of interventional drug trials registered with Clinical Trials Registry - India

description: The schema of the SQLite database. (XLS 13 kb)
DOI: 10.6084/m9.figshare.12815903.v1
title: Allosteric hotspots in the main protease of SARS-CoV-2 dataset

description: On the top level the zip file contains two folders which are described in detail below: <br>Main results:contains two folders named after the PDB ID of the viral main protease apo structure. 1. SARS-CoV Mpro structure 2DUC2. SARS-CoV-2 Mpro structure 6Y2EEach directory contains the protonated structure and a subfolder for each run performed on it. The subfolders are named after the source residues. Each subfolder contains three files:1. source_residues.txt A file listing all source residues2. propensity_residue_results.csv This file contains the raw results of the Bond-to-bond propensity analysis. 3. transient_residue_results.csv This file contains the raw results of the Markov transient analysis.<br>Small fragments:Contains a folder for each small fragment structure in close proximity to the identified hotspots. Each subfolder contains the protonated structure as well as the three files described above.
DOI: 10.6084/m9.figshare.9740114
title: Additional file 2: of Proteomic informed by transcriptomic for salivary glands components of the camel tick Hyalomma dromedarii

description: Table S2. Classification of proteins identified in the salivary glands of Hyalomma dromedarii males. Description of additional files. Accession: protein ID in the database. %coverage: percentage Coverage_ The percentage of all the amino acids in the protein sequence that were covered by identified peptides detected in the sample. -10logP: the P-value is converted to -10log10 (P-value). In PEAKS, this value is denoted by -10lgP as lg is the ISO reserved notation for log10. By this conversion, a more significant match will have a higher -10lgP value. Additionally, a P-value of 1% is equivalent to -10lgP of 20. #Peptides: number of peptides identified following LC-MS/MS analysis for a single protein. #Unique: Unique peptides_peptides with the same amino acid sequence but different charges or with different modifications are grouped together and counted only once. Avg.Mass: the average mass of a single protein obtained by summing the average atomic masses of the constituent elements. Description: description of the identified proteins in the database. Class: housekeeping class (H); possibly secreted proteins (S); transporters (T); and unknown class (U). (XLSX 94 kb)
DOI: 10.6084/m9.figshare.9740108
title: Additional file 1: of Proteomic informed by transcriptomic for salivary glands components of the camel tick Hyalomma dromedarii

description: Table S1. Classification of proteins identified in the salivary glands of Hyalomma dromedarii females. (XLSX 98 kb)
DOI: 10.6084/m9.figshare.9740108.v1
title: Additional file 1: of Proteomic informed by transcriptomic for salivary glands components of the camel tick Hyalomma dromedarii

description: Table S1. Classification of proteins identified in the salivary glands of Hyalomma dromedarii females. (XLSX 98 kb)
DOI: 10.6084/m9.figshare.9740114.v1
title: Additional file 2: of Proteomic informed by transcriptomic for salivary glands components of the camel tick Hyalomma dromedarii

description: Table S2. Classification of proteins identified in the salivary glands of Hyalomma dromedarii males. Description of additional files. Accession: protein ID in the database. %coverage: percentage Coverage_ The percentage of all the amino acids in the protein sequence that were covered by identified peptides detected in the sample. -10logP: the P-value is converted to -10log10 (P-value). In PEAKS, this value is denoted by -10lgP as lg is the ISO reserved notation for log10. By this conversion, a more significant match will have a higher -10lgP value. Additionally, a P-value of 1% is equivalent to -10lgP of 20. #Peptides: number of peptides identified following LC-MS/MS analysis for a single protein. #Unique: Unique peptides_peptides with the same amino acid sequence but different charges or with different modifications are grouped together and counted only once. Avg.Mass: the average mass of a single protein obtained by summing the average atomic masses of the constituent elements. Description: description of the identified proteins in the database. Class: housekeeping class (H); possibly secreted proteins (S); transporters (T); and unknown class (U). (XLSX 94 kb)
DOI: 10.6084/m9.figshare.9740096
title: Additional file 9: of Systematic evaluation and validation of reference and library selection methods for deconvolution of cord blood DNA methylation data

description: Table S7. pickCompProbes reference library probes using filtered de Goede reference. (CSV 350 kb)
DOI: 10.6084/m9.figshare.9740087
title: Additional file 8: of Systematic evaluation and validation of reference and library selection methods for deconvolution of cord blood DNA methylation data

description: Table S6. pickCompProbes reference library probes using raw combined reference. (CSV 370 kb)
DOI: 10.6084/m9.figshare.9740096.v1
title: Additional file 9: of Systematic evaluation and validation of reference and library selection methods for deconvolution of cord blood DNA methylation data

description: Table S7. pickCompProbes reference library probes using filtered de Goede reference. (CSV 350 kb)
DOI: 10.6084/m9.figshare.9740087.v1
title: Additional file 8: of Systematic evaluation and validation of reference and library selection methods for deconvolution of cord blood DNA methylation data

description: Table S6. pickCompProbes reference library probes using raw combined reference. (CSV 370 kb)