cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.13192147.v1
title: Additional file 2 of Why clinicians overtest: development of a thematic framework

description: Additional file 2 Supplementary File 2 Initial Thematic Framework: Excel Spreadsheet of articles included in the narrative literature review, thematic analysis and incorporation into initial framework of direct/intrinsic and indirect/extrinsic factors.
DOI: 10.6084/m9.figshare.13192147
title: Additional file 2 of Why clinicians overtest: development of a thematic framework

description: Additional file 2 Supplementary File 2 Initial Thematic Framework: Excel Spreadsheet of articles included in the narrative literature review, thematic analysis and incorporation into initial framework of direct/intrinsic and indirect/extrinsic factors.
DOI: 10.6084/m9.figshare.13192228.v1
title: Additional file 2 of Cell-free DNA and circulating TERT promoter mutation for disease monitoring in newly-diagnosed glioblastoma

description: Additional file 2: Table S1. Comparison of cfDNA characteristics at different sampling times.
DOI: 10.6084/m9.figshare.13192228
title: Additional file 2 of Cell-free DNA and circulating TERT promoter mutation for disease monitoring in newly-diagnosed glioblastoma

description: Additional file 2: Table S1. Comparison of cfDNA characteristics at different sampling times.
DOI: 10.6084/m9.figshare.13192237
title: Additional file 4 of Cell-free DNA and circulating TERT promoter mutation for disease monitoring in newly-diagnosed glioblastoma

description: Additional file 4: Table S3. Raw data from TERTp C228T and C250T sequencing with 113bp and 88bp assays per patient in the entire cohort.
DOI: 10.6084/m9.figshare.13192234
title: Additional file 3 of Cell-free DNA and circulating TERT promoter mutation for disease monitoring in newly-diagnosed glioblastoma

description: Additional file 3: Table S2. Results of the Cox model for overall survival and progression-free survival.
DOI: 10.6084/m9.figshare.13192237.v1
title: Additional file 4 of Cell-free DNA and circulating TERT promoter mutation for disease monitoring in newly-diagnosed glioblastoma

description: Additional file 4: Table S3. Raw data from TERTp C228T and C250T sequencing with 113bp and 88bp assays per patient in the entire cohort.
DOI: 10.6084/m9.figshare.13192234.v1
title: Additional file 3 of Cell-free DNA and circulating TERT promoter mutation for disease monitoring in newly-diagnosed glioblastoma

description: Additional file 3: Table S2. Results of the Cox model for overall survival and progression-free survival.
DOI: 10.6084/m9.figshare.13192249
title: Additional file 1 of Lifestyle-associated health risk indicators across a wide range of occupational groups: a cross-sectional analysis in 72,855 workers

description: Additional file 1. a. Proportions of workers in minor occupational groups within major occupational groups 1 to 5 according to SSYK. (referred to as white collar occupations). b. Proportions of workers in minor occupational groups within major occupational groups 6 to 9 according to SSYK (referred to as blue collar occupations).
DOI: 10.6084/m9.figshare.13192249.v1
title: Additional file 1 of Lifestyle-associated health risk indicators across a wide range of occupational groups: a cross-sectional analysis in 72,855 workers

description: Additional file 1. a. Proportions of workers in minor occupational groups within major occupational groups 1 to 5 according to SSYK. (referred to as white collar occupations). b. Proportions of workers in minor occupational groups within major occupational groups 6 to 9 according to SSYK (referred to as blue collar occupations).
DOI: 10.6084/m9.figshare.13192270.v1
title: Additional file 1 of The PVT1 lncRNA is a novel epigenetic enhancer of MYC, and a promising risk-stratification biomarker in colorectal cancer

description: Additional file 1: Supplementary Table 1
DOI: 10.6084/m9.figshare.13192270
title: Additional file 1 of The PVT1 lncRNA is a novel epigenetic enhancer of MYC, and a promising risk-stratification biomarker in colorectal cancer

description: Additional file 1: Supplementary Table 1
DOI: 10.6084/m9.figshare.13192312.v1
title: Additional file 1 of Epigenome-wide association study for pesticide (Permethrin and DEET) induced DNA methylation epimutation biomarkers for specific transgenerational disease

description: Additional file 1K Supplemental Table S1. DMR Site List Prostate p
DOI: 10.6084/m9.figshare.13192312
title: Additional file 1 of Epigenome-wide association study for pesticide (Permethrin and DEET) induced DNA methylation epimutation biomarkers for specific transgenerational disease

description: Additional file 1K Supplemental Table S1. DMR Site List Prostate p
DOI: 10.6084/m9.figshare.13192321
title: Additional file 1 of Too sweet: cheminformatics for deglycosylation in natural products

description: Additional file 1. For the sugar moieties structures that have been used in the tests.
DOI: 10.6084/m9.figshare.13192323.v1
title: Additional file 2 of Metastatic and recurrent adrenocortical cancer is not defined by its genomic landscape

description: Additional file 2. Table 1: (Part 1) List of Most Mutated Genes validated in &gt;10% of 23 T/N pairs and &gt;10% of all 43 ACC patients. (Part 2) List of Validated Driver Mutations in &lt;10% of 43 ACC Patients. Table 2: A, Alterations in Chromatin Remodeling Genes or Genes Controlling Epigenetic Processes. B, Alterations in DNA Repair Genes. Table 3: 769 Differentially Expressed Genes (DEG), upregulated (289) and downregulated (480) in ACC compared to NA. Table 4: IPA prediction of upstream regulators based on microarray expression data comparing 57 ACC samples vs. 5 normal adrenal samples. Table 5: Top Differentially Expressed MicroRNAs (DEM), up- or down-regulated in ACC compared to NA.
DOI: 10.6084/m9.figshare.13192323
title: Additional file 2 of Metastatic and recurrent adrenocortical cancer is not defined by its genomic landscape

description: Additional file 2. Table 1: (Part 1) List of Most Mutated Genes validated in &gt;10% of 23 T/N pairs and &gt;10% of all 43 ACC patients. (Part 2) List of Validated Driver Mutations in &lt;10% of 43 ACC Patients. Table 2: A, Alterations in Chromatin Remodeling Genes or Genes Controlling Epigenetic Processes. B, Alterations in DNA Repair Genes. Table 3: 769 Differentially Expressed Genes (DEG), upregulated (289) and downregulated (480) in ACC compared to NA. Table 4: IPA prediction of upstream regulators based on microarray expression data comparing 57 ACC samples vs. 5 normal adrenal samples. Table 5: Top Differentially Expressed MicroRNAs (DEM), up- or down-regulated in ACC compared to NA.
DOI: 10.6084/m9.figshare.13192321.v1
title: Additional file 1 of Too sweet: cheminformatics for deglycosylation in natural products

description: Additional file 1. For the sugar moieties structures that have been used in the tests.
DOI: 10.6084/m9.figshare.13192329
title: Additional file 11 of Whole genome analysis of the koa wilt pathogen (Fusarium oxysporum f. sp. koae) and the development of molecular tools for early detection and monitoring

description: Additional file 11. GenBank accession numbers and collection locations for all isolates used in this study.
DOI: 10.6084/m9.figshare.13192350
title: Additional file 7 of Whole genome analysis of the koa wilt pathogen (Fusarium oxysporum f. sp. koae) and the development of molecular tools for early detection and monitoring

description: Additional file 7. Distribution and virulence ratings for 15 characterized and 85 uncharacterized Fusarium oxysporum isolates collected from Acacia koa roots used for haplotype and primer amplification analysis.
DOI: 10.6084/m9.figshare.13192350.v1
title: Additional file 7 of Whole genome analysis of the koa wilt pathogen (Fusarium oxysporum f. sp. koae) and the development of molecular tools for early detection and monitoring

description: Additional file 7. Distribution and virulence ratings for 15 characterized and 85 uncharacterized Fusarium oxysporum isolates collected from Acacia koa roots used for haplotype and primer amplification analysis.
DOI: 10.6084/m9.figshare.13192329.v1
title: Additional file 11 of Whole genome analysis of the koa wilt pathogen (Fusarium oxysporum f. sp. koae) and the development of molecular tools for early detection and monitoring

description: Additional file 11. GenBank accession numbers and collection locations for all isolates used in this study.
DOI: 10.6084/m9.figshare.13192380.v1
title: Additional file 3 of Differential responses in placenta and fetal thymus at 12 days post infection elucidate mechanisms of viral level and fetal compromise following PRRSV2 infection

description: Additional file 3 : Table S1. Gene names. A total of 286 test genes and 10 housekeeping genes were assayed for mRNA expression levels on the NanoString platform. Table S2. Differential expression analysis results for all genes and all contrasts. The results are organized by gene then by contrast group within tissue. The included columns are log2FC: the log2 fold change value in the test group compared to the contrast group, AveExpr: the average count expression value for the gene across all samples, t: the T statistic for a given gene and contrast, P Value: the calculated P value for a given gene and contrast, adj.P.Val: the P value adjusted for multiple testing using the Benjamini Yekutieli correction method, and B: The B statistic for the log odds that the gene is differentially expressed. Table S3. Principle component loading gene values for placenta and thymus. Table S4. The Activation Z scores for all recognized pathways in the IPA software. The results are organized by IPA pathway, then by contrast group within tissue. The core analysis was done on individual contrast groups using DEG as input. Table S5. Placenta normalized counts by gene. Table S6. Fetal thymus normalized counts by gene.
DOI: 10.6084/m9.figshare.13192380
title: Additional file 3 of Differential responses in placenta and fetal thymus at 12 days post infection elucidate mechanisms of viral level and fetal compromise following PRRSV2 infection

description: Additional file 3 : Table S1. Gene names. A total of 286 test genes and 10 housekeeping genes were assayed for mRNA expression levels on the NanoString platform. Table S2. Differential expression analysis results for all genes and all contrasts. The results are organized by gene then by contrast group within tissue. The included columns are log2FC: the log2 fold change value in the test group compared to the contrast group, AveExpr: the average count expression value for the gene across all samples, t: the T statistic for a given gene and contrast, P Value: the calculated P value for a given gene and contrast, adj.P.Val: the P value adjusted for multiple testing using the Benjamini Yekutieli correction method, and B: The B statistic for the log odds that the gene is differentially expressed. Table S3. Principle component loading gene values for placenta and thymus. Table S4. The Activation Z scores for all recognized pathways in the IPA software. The results are organized by IPA pathway, then by contrast group within tissue. The core analysis was done on individual contrast groups using DEG as input. Table S5. Placenta normalized counts by gene. Table S6. Fetal thymus normalized counts by gene.
DOI: 10.6084/m9.figshare.13192392
title: Additional file 1 of Changes in DNA methylation profiles of myalgic encephalomyelitis/chronic fatigue syndrome patients reflect systemic dysfunctions

description: Additional file 1: Excel file containing additional information for this study including sheets; ‘Patient_Background’, ‘Symptom_Presentation’, ‘DMAP_Diff_Fragments’, ‘MethylKit_Diff_Cytosines’, ‘Cluster_Data’, ‘MethylKit_Promoter_Full’, ‘DMAP_Gene_Full’, ‘MethylKit_Gene_Full’, ‘DMAP_Pathways’, ‘MethylKit_Pathways’ and ‘Genelist_Overlap’.
DOI: 10.6084/m9.figshare.13192392.v1
title: Additional file 1 of Changes in DNA methylation profiles of myalgic encephalomyelitis/chronic fatigue syndrome patients reflect systemic dysfunctions

description: Additional file 1: Excel file containing additional information for this study including sheets; ‘Patient_Background’, ‘Symptom_Presentation’, ‘DMAP_Diff_Fragments’, ‘MethylKit_Diff_Cytosines’, ‘Cluster_Data’, ‘MethylKit_Promoter_Full’, ‘DMAP_Gene_Full’, ‘MethylKit_Gene_Full’, ‘DMAP_Pathways’, ‘MethylKit_Pathways’ and ‘Genelist_Overlap’.
DOI: 10.6084/m9.figshare.13192426
title: Additional file 2 of Modified base-binding EVE and DCD domains: striking diversity of genomic contexts in prokaryotes and predicted involvement in a variety of cellular processes

description: Additional file 2. EVE domain sequences used for CLANS analysis.
DOI: 10.6084/m9.figshare.13192429.v1
title: Additional file 3 of Modified base-binding EVE and DCD domains: striking diversity of genomic contexts in prokaryotes and predicted involvement in a variety of cellular processes

description: Additional file 3. Predicted protein sequences from a choanoflagellate transcriptome sequencing dataset published by Richter et al. that contain extended Tudor domains and/or DCD domains.
DOI: 10.6084/m9.figshare.13192429
title: Additional file 3 of Modified base-binding EVE and DCD domains: striking diversity of genomic contexts in prokaryotes and predicted involvement in a variety of cellular processes

description: Additional file 3. Predicted protein sequences from a choanoflagellate transcriptome sequencing dataset published by Richter et al. that contain extended Tudor domains and/or DCD domains.
DOI: 10.6084/m9.figshare.13192426.v1
title: Additional file 2 of Modified base-binding EVE and DCD domains: striking diversity of genomic contexts in prokaryotes and predicted involvement in a variety of cellular processes

description: Additional file 2. EVE domain sequences used for CLANS analysis.
DOI: 10.6084/m9.figshare.13192533.v1
title: Additional file 2 of Knowledge of peri-menarcheal changes and a comparative analysis of the age at menarche among young adolescent school girls in urban and rural Cameroon

description: Additional file 2: Supporting information file (S2). Database containing “status quo” data on the age of menarche in rural and urban Cameroon.
DOI: 10.6084/m9.figshare.13192533
title: Additional file 2 of Knowledge of peri-menarcheal changes and a comparative analysis of the age at menarche among young adolescent school girls in urban and rural Cameroon

description: Additional file 2: Supporting information file (S2). Database containing “status quo” data on the age of menarche in rural and urban Cameroon.
DOI: 10.6084/m9.figshare.13190708.v1
title: Significant variants / genes

description: The variants, and linked genes, that are significantly associated with body weight at multiple ages, in both diet-independent and diet-dependent manners, are enumerated in these files.
DOI: 10.25345/c5kr3h
title: MassIVE MSV000086410 - GNPS.MASS.shengwujian.11.5.try
title: Life is a chess-board The chess-board is the world: the pieces are the phenomena of the universe; the rules of the game are what we call the laws of nature. The player on the other side is hidden from us. We know that his play is always fair, just and patient. But also we know, to our cost, that he never overlooks a mistake, or makes the smallest allowance for ignorance
DOI: 10.5439/1699389
title: pccpa.c1

description: Point Cloud of Cloud Points (PCCP) VAP provides a stereo reconstructed Point Cloud of Cloud Points (PCCP) that correspond to the x,y,z coordinates of cloud features detected from stereo image pairs genrated from a multi-view stereo system deployed to collect exclusive set of data on shallow cumulus clouds overhead.
DOI: 10.25817/5fa38903a9942
title: Krui Catchment Soil Organic Carbon Data
DOI: 10.6084/m9.figshare.13190708.v2
title: Significant variants / genes

description: The variants, and linked genes, that are significantly associated with body weight at multiple ages, in both diet-independent and diet-dependent manners, are enumerated in these files.
DOI: 10.6084/m9.figshare.13190702.v1
title: Phenotype data

description: These files contain body weight measurements of all mice in the study, up until 22 months of age1. the raw body weight measurements, measured every 10 days2. l1-trend filtered body weight estimates, every 10 days
DOI: 10.6084/m9.figshare.13190615.v1
title: Covariate data

description: These files tabulate the generation waves and the dietary interventions for each mouse in the study.
DOI: 10.25345/c5g19m
title: MassIVE MSV000086411 - Recombinant Protein DDA Library for low abundant proteins identificaion in plasma
title: Recombinant SWATH library for identification of low abundant human plasma proteins
DOI: 10.5281/zenodo.4245781
title: COVID-19 lockdown in Beijing

description: The data supporting the conclusions in "COVID-19" paper.
DOI: 10.6084/m9.figshare.13190735.v1
title: Genotype data

description: These data include 1. the genotypes for all mice at ~110,000 typed variants; genotypes are represented as a probability vector quantifying the founder of origin of each variant2. the kinship between all pairs of mice, both using all chromosomes, and leaving each chromosome out (for QTL mapping)
DOI: 10.6084/m9.figshare.13193132.v1
title: organizational culture and policy process

description: An original survey data of organizational culture and environmental policy process
DOI: 10.6084/m9.figshare.13193132
title: organizational culture and policy process

description: An original survey data of organizational culture and environmental policy process
DOI: 10.6084/m9.figshare.13193291
title: Supplementary Material for: Meta-Analysis of the Pharmacogenetics of <b><i>ARMS2</i></b> A69S Polymorphism and the Response to Advanced Age-Related Macular Degeneration

description: Age-related macular degeneration (AMD) causes irreversible vision loss, and targeted anti-vascular endothelial growth factor (VEGF) therapy is now the most common and effective treatment. The aim of this meta-analysis is to discuss whether genetic polymorphism of <i>ARMS2</i> A69S could confer susceptibility to advanced AMD with the response to anti-VEGF treatment. We performed a meta-analysis of relevant published studies selected through electronic databases. A total of 21 preferred studies regarding the association between <i>ARMS2</i> gene and anti-VEGF treatment response in advanced AMD were generally included in the meta-analysis. The pooled results demonstrated that the carriage of G allele for <i>ARMS2</i> A69S presented a better clinical prognosis for advanced AMD treated with anti-VEGF drugs (OR = 1.38, 95% CI = 1.13–1.69, <i>p</i> = 0.002). In addition, in the subgroup analysis based on ethnicity, <i>ARMS2</i> polymorphisms were more likely to be a positive responder for East Asian patients (OR = 1.67, 95% CI = 1.29–2.16, <i>p</i> &lt; 0.001). This meta-analysis through a series of rigorous methodology data demonstrated a significant association between <i>ARMS2</i> A69S polymorphism and the anti-VEGF treatment response in advanced AMD, especially among East Asian population. Numerous well-designed, randomized, multicenter clinical trials with large sample size are required to validate the association.
DOI: 10.6084/m9.figshare.13193291.v1
title: Supplementary Material for: Meta-Analysis of the Pharmacogenetics of <b><i>ARMS2</i></b> A69S Polymorphism and the Response to Advanced Age-Related Macular Degeneration

description: Age-related macular degeneration (AMD) causes irreversible vision loss, and targeted anti-vascular endothelial growth factor (VEGF) therapy is now the most common and effective treatment. The aim of this meta-analysis is to discuss whether genetic polymorphism of <i>ARMS2</i> A69S could confer susceptibility to advanced AMD with the response to anti-VEGF treatment. We performed a meta-analysis of relevant published studies selected through electronic databases. A total of 21 preferred studies regarding the association between <i>ARMS2</i> gene and anti-VEGF treatment response in advanced AMD were generally included in the meta-analysis. The pooled results demonstrated that the carriage of G allele for <i>ARMS2</i> A69S presented a better clinical prognosis for advanced AMD treated with anti-VEGF drugs (OR = 1.38, 95% CI = 1.13–1.69, <i>p</i> = 0.002). In addition, in the subgroup analysis based on ethnicity, <i>ARMS2</i> polymorphisms were more likely to be a positive responder for East Asian patients (OR = 1.67, 95% CI = 1.29–2.16, <i>p</i> &lt; 0.001). This meta-analysis through a series of rigorous methodology data demonstrated a significant association between <i>ARMS2</i> A69S polymorphism and the anti-VEGF treatment response in advanced AMD, especially among East Asian population. Numerous well-designed, randomized, multicenter clinical trials with large sample size are required to validate the association.
DOI: 10.5281/zenodo.4245737
title: Water Erosion Risk Assessment in the Eastern Rift Valley: The Case of Kenya Great Rift Valley Region

description: RUSLE Supplementary Materials Water Erosion Risk Assessment in the Eastern Rift Valley: The Case of Kenya Great Rift Valley Region
DOI: 10.5281/zenodo.4245736
title: Water Erosion Risk Assessment in the Eastern Rift Valley: The Case of Kenya Great Rift Valley Region

description: RUSLE Supplementary Materials Water Erosion Risk Assessment in the Eastern Rift Valley: The Case of Kenya Great Rift Valley Region
DOI: 10.5281/zenodo.3960040
title: Data for paper "Effects of inflow conditions on plunge points and vertical profiles of turbidity currents on sloping flume based on 3D numerical simulation"

description: This set of xlsx files, metadata of model results and Matlab code accompanies the manuscript "Effects of inflow conditions on plunge points and vertical profiles of turbidity currents on sloping flume based on 3D numerical simulation" by Ruoyin Zhang, Baosheng Wu, and Bangwen Zhang. This is the first release of the data.
DOI: 10.5281/zenodo.3960039
title: Data for paper "Effects of inflow conditions on plunge points and vertical profiles of turbidity currents on sloping flume based on 3D numerical simulation"

description: This set of xlsx files, metadata of model results and Matlab code accompanies the manuscript "Effects of inflow conditions on plunge points and vertical profiles of turbidity currents on sloping flume based on 3D numerical simulation" by Ruoyin Zhang, Baosheng Wu, and Bangwen Zhang. This is the first release of the data.
DOI: 10.5281/zenodo.4245392
title: Raw diffraction data from Acta Cryst. 2020, D76, 1057-1065 (Wuhan Asiatic toad influenza virus neuraminidase with lattice-translocation defects)

description: The ectodomain (residues 79–466) of the neuraminidase from the Wuhan Asiatic toad influenza virus (GenBank accession No. MG600049.1) was crystallized. X-ray diffraction data were collected on beamline BL17U1 at Shanghai Synchrotron Radiation Facility (SSRF) using a Dectris EIGER 16M detector. A total of 100 frames were recorded with an oscillation angle of 1.0 deg. Sharp–diffuse diffraction patterns and native Patterson peaks manifest the pathological imperfection: lattice-translocation defects.
DOI: 10.5281/zenodo.4245391
title: Raw diffraction data from Acta Cryst. 2020, D76, 1057-1065 (Wuhan Asiatic toad influenza virus neuraminidase with lattice-translocation defects)

description: The ectodomain (residues 79–466) of the neuraminidase from the Wuhan Asiatic toad influenza virus (GenBank accession No. MG600049.1) was crystallized. X-ray diffraction data were collected on beamline BL17U1 at Shanghai Synchrotron Radiation Facility (SSRF) using a Dectris EIGER 16M detector. A total of 100 frames were recorded with an oscillation angle of 1.0 deg. Sharp–diffuse diffraction patterns and native Patterson peaks manifest the pathological imperfection: lattice-translocation defects.