cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.8983766.v1
title: Supplementary Material for: The Genetic Relevance of Human Induced Pluripotent Stem Cell-Derived Microglia to Alzheimer’s Disease and Major Neuropsychiatric Disorders

description: Microglia are the primary innate immune cell type in the brain that have been implicated in the pathogenesis of several neurodegenerative and neuropsychiatric disorders, most notably Alzheimer’s disease (AD) and schizophrenia. Microglia generated from human induced pluripotent stem cells (hiPSCs) represent a promising in vitro cellular model for studying the neuroimmune interactions involved in these disorders. Among several methods of generating ­hiPSC-derived microglia (iMG) – varying in duration and resultant purity – a recent protocol by Brownjohn et al. [Stem Cell Reports. 2018 Apr;10(4):1294–307] is particularly simple and efficient. However, the replicability of this method, transcriptomic similarity of these iMG to primary adult microglia, and their genetic relevance to disease (i.e., enrichment of disease risk loci in genes preferentially expressed in these cells) remains unclear. Using two hiPSC lines, we demonstrated that Brownjohn’s protocol can rapidly generate iMG that morphologically and functionally resembled microglia. The iMG cells we generated were found to be transcriptionally similar to previously reported iMG, as well as fetal and adult microglia. Furthermore, by using cell type-specific gene expression to partition disease heritability, we showed that iMG cells are genetically relevant to AD but found no significant enrichments of risk loci of Parkinson’s disease, schizophrenia, major depressive disorder, bipolar disorder, autism spectrum disorder, or body mass index. Across a range of neuronal and immune cell types, we found only iMG, primary microglia, and microglia-like cell types exhibited a significant enrichment for AD heritability. Our results thus support the use of iMG as a human cellular model for understanding AD biology and underlying genetic factors, as well as for developing and efficiently screening new therapeutics.
DOI: 10.6084/m9.figshare.8983751
title: Data for Figures 2 and 4 from Simultaneous normal form transformation and model-order reduction for systems of coupled nonlinear oscillators

description: In this paper, we describe a direct normal form decomposition for systems of coupled nonlinear oscillators. We demonstrate how the order of the system can be reduced during this type of normal form transformation process. Two specific examples are considered to demonstrate particular challenges that can occur in this type of analysis. The first is a 2 d.f. system with both quadratic and cubic nonlinearities, where there is no internal resonance, but the nonlinear terms are not necessarily <i>ɛ</i><sup>1</sup>-order small. To obtain an accurate solution, the direct normal form expansion is extended to <i>ɛ</i><sup>2</sup>-order to capture the nonlinear dynamic behaviour, while simultaneously reducing the order of the system from 2 to 1 d.f. The second example is a thin plate with nonlinearities that are <i>ɛ</i><sup>1</sup>-order small, but with an internal resonance in the set of ordinary differential equations used to model the low-frequency vibration response of the system. In this case, we show how a direct normal form transformation can be applied to further reduce the order of the system while simultaneously obtaining the normal form, which is used as a model for the internal resonance. The results are verified by comparison with numerically computed results using a continuation software.
DOI: 10.6084/m9.figshare.8983751.v1
title: Data for Figures 2 and 4 from Simultaneous normal form transformation and model-order reduction for systems of coupled nonlinear oscillators

description: In this paper, we describe a direct normal form decomposition for systems of coupled nonlinear oscillators. We demonstrate how the order of the system can be reduced during this type of normal form transformation process. Two specific examples are considered to demonstrate particular challenges that can occur in this type of analysis. The first is a 2 d.f. system with both quadratic and cubic nonlinearities, where there is no internal resonance, but the nonlinear terms are not necessarily <i>ɛ</i><sup>1</sup>-order small. To obtain an accurate solution, the direct normal form expansion is extended to <i>ɛ</i><sup>2</sup>-order to capture the nonlinear dynamic behaviour, while simultaneously reducing the order of the system from 2 to 1 d.f. The second example is a thin plate with nonlinearities that are <i>ɛ</i><sup>1</sup>-order small, but with an internal resonance in the set of ordinary differential equations used to model the low-frequency vibration response of the system. In this case, we show how a direct normal form transformation can be applied to further reduce the order of the system while simultaneously obtaining the normal form, which is used as a model for the internal resonance. The results are verified by comparison with numerically computed results using a continuation software.
DOI: 10.6084/m9.figshare.8983586
title: Secondary structures of the training set of group II introns

description: Secondary structures of the training set of eukaryotic group II introns
DOI: 10.6084/m9.figshare.8983586.v2
title: Secondary structures of the training set of group II introns

description: Secondary structures of the training set of eukaryotic group II introns
DOI: 10.6084/m9.figshare.8983586.v1
title: Secondary structures of the training set of group II introns

description: Secondary structures of the training set of mobile group II introns
DOI: 10.6084/m9.figshare.8982683
title: Raw data 2: chicken reads from amplicons generated with a naive primer set

description: These are the compressed, raw, paired-end read files generated in a Illumina MiSeq platform with a naive set of primers.Each individual is encoded in the name of file pairs by all characters before the first "_". The "R1" and "R2" at the end of file names indicate their origin as forward or reverse reads, respectively.
DOI: 10.6084/m9.figshare.8982674
title: Raw data 1: chicken reads from amplicons generated with optimal primers

description: These are the compressed, raw, paired-end read files generated in a Illumina MiSeq platform with optimal primers. Each individual is encoded in the name of file pairs by all characters before the first "_". The "R1" and "R2" at the end of file names indicate their origin as forward or reverse reads, respectively.
DOI: 10.6084/m9.figshare.8982674.v1
title: Raw data 1: chicken reads from amplicons generated with optimal primers

description: These are the compressed, raw, paired-end read files generated in a Illumina MiSeq platform with optimal primers. Each individual is encoded in the name of file pairs by all characters before the first "_". The "R1" and "R2" at the end of file names indicate their origin as forward or reverse reads, respectively.
DOI: 10.6084/m9.figshare.8982500
title: Efficacy of a Modified Treat-and-Extend Regimen of Aflibercept for Macular Oedema from Branch Retinal Vein Occlusion: 1-year prospective study outcomes

description: Raw data of "Efficacy of a Modified Treat-and-Extend Regimen of Aflibercept for Macular Oedema from Branch Retinal Vein Occlusion: 1-year prospective study outcomes"
DOI: 10.6084/m9.figshare.8982500.v1
title: Efficacy of a Modified Treat-and-Extend Regimen of Aflibercept for Macular Oedema from Branch Retinal Vein Occlusion: 1-year prospective study outcomes

description: Raw data of "Efficacy of a Modified Treat-and-Extend Regimen of Aflibercept for Macular Oedema from Branch Retinal Vein Occlusion: 1-year prospective study outcomes"
DOI: 10.6084/m9.figshare.8982380
title: Tables with differentialy expressed genes from transcriptomic analysis

description: Tables listing deferentially expressed genes from transcriptomic analysis from macrophages and endothelial cells
DOI: 10.6084/m9.figshare.8982380.v2
title: Tables with differentialy expressed genes from transcriptomic analysis

description: Tables listing deferentially expressed genes from transcriptomic analysis from macrophages and endothelial cells
DOI: 10.6084/m9.figshare.8982347
title: Dataset for: Effective coupling of Rapid-Freeze Quench to High-Frequency Electron Paramagnetic Resonance

description: This dataset is relative to the paper with the same name to be published. It contains:- 275 GHz EPR spectra- X-band EPR spectra<br>- Python files used for data analysis and to generate the figures<br>All the experimental conditions are illustrated in detail in the paper.
DOI: 10.6084/m9.figshare.8982380.v1
title: Tables deferentially expressed genes transcriptomic analysis

description: Tables listing deferentially expressed genes from transcriptomic analysis from macrophages and endothelial cells
DOI: 10.6084/m9.figshare.8982335
title: Synthesis and Photoluminescence Properties of Silica-modified SiO2@ANA-Si-Tb@SiO2, SiO2@ANA-Si-Tb-L@SiO2 Core-Shell-Shell Nanostructured Composites

description: Three novel core–shell nanostructured composites SiO<sub>2</sub>@ANA-Si-Tb, SiO<sub>2</sub>@ANA-Si-Tb-L (L = second ligand) with SiO<sub>2</sub> as the core and terbium organic complex as the shell were successfully synthesized. The core and shell were connected together by covalent bonds. The terbium ion was coordinated with organic ligand-forming terbium organic complex in the shell layer. The organosilane (HOOCC<sub>5</sub>H<sub>4</sub>NN(CONH(CH<sub>2</sub>)<sub>3</sub>Si(OCH<sub>2</sub>CH<sub>3</sub>)<sub>3</sub>)<sub>2</sub> (abbreviated as ANA-Si) was used as the first ligand and 1, 10-phenanthroline (phen) or 2-thenoyltrifluoroacetone (TTA) was used as the second ligand. Furthermore, silica-modified SiO<sub>2</sub>@ANA-Si-Tb@SiO<sub>2</sub>, SiO<sub>2</sub>@ANA-Si-Tb-L@SiO<sub>2</sub> core–shell–shell nanostructured composites were also synthesized by sol–gel chemical route, which involved the hydrolysis and polycondensation processes of tetraethoxysilane (TEOS) using cetyltrimethyl ammonium bromide (CTAB) as a surface-active agent. An amorphous silica shell was coated around the SiO<sub>2</sub>@ANA-Si-Tb, SiO<sub>2</sub>@ANA-Si-Tb-L core–shell nanostructured composites. The core–shell and core–shell–shell nanostructured composites exhibited excellent luminescence in the solid state. Meanwhile, an improved luminescent stability property of the core–shell–shell nanostructured composites was observed for the aqueous solution. This type of core–shell–shell nanostructured composites exhibited bright luminescence, high stability and good solubility, which may present potential applications in the fields of optoelectronic devices, bio-imaging, medical diagnosis and study on the structure of function composite materials.
DOI: 10.6084/m9.figshare.8982335.v1
title: Synthesis and Photoluminescence Properties of Silica-modified SiO2@ANA-Si-Tb@SiO2, SiO2@ANA-Si-Tb-L@SiO2 Core-Shell-Shell Nanostructured Composites

description: Three novel core–shell nanostructured composites SiO<sub>2</sub>@ANA-Si-Tb, SiO<sub>2</sub>@ANA-Si-Tb-L (L = second ligand) with SiO<sub>2</sub> as the core and terbium organic complex as the shell were successfully synthesized. The core and shell were connected together by covalent bonds. The terbium ion was coordinated with organic ligand-forming terbium organic complex in the shell layer. The organosilane (HOOCC<sub>5</sub>H<sub>4</sub>NN(CONH(CH<sub>2</sub>)<sub>3</sub>Si(OCH<sub>2</sub>CH<sub>3</sub>)<sub>3</sub>)<sub>2</sub> (abbreviated as ANA-Si) was used as the first ligand and 1, 10-phenanthroline (phen) or 2-thenoyltrifluoroacetone (TTA) was used as the second ligand. Furthermore, silica-modified SiO<sub>2</sub>@ANA-Si-Tb@SiO<sub>2</sub>, SiO<sub>2</sub>@ANA-Si-Tb-L@SiO<sub>2</sub> core–shell–shell nanostructured composites were also synthesized by sol–gel chemical route, which involved the hydrolysis and polycondensation processes of tetraethoxysilane (TEOS) using cetyltrimethyl ammonium bromide (CTAB) as a surface-active agent. An amorphous silica shell was coated around the SiO<sub>2</sub>@ANA-Si-Tb, SiO<sub>2</sub>@ANA-Si-Tb-L core–shell nanostructured composites. The core–shell and core–shell–shell nanostructured composites exhibited excellent luminescence in the solid state. Meanwhile, an improved luminescent stability property of the core–shell–shell nanostructured composites was observed for the aqueous solution. This type of core–shell–shell nanostructured composites exhibited bright luminescence, high stability and good solubility, which may present potential applications in the fields of optoelectronic devices, bio-imaging, medical diagnosis and study on the structure of function composite materials.
DOI: 10.6084/m9.figshare.8982059
title: Gastroesophageal reflux GWAS identifies risk loci that also associate with subsequent severe esophageal diseases

description: Gastroesophageal reflux GWAS identifies risk loci that also associate with subsequent severe esophageal diseases
DOI: 10.6084/m9.figshare.8982059.v1
title: Gastroesophageal reflux GWAS identifies risk loci that also associate with subsequent severe esophageal diseases

description: Gastroesophageal reflux GWAS identifies risk loci that also associate with subsequent severe esophageal diseases
DOI: 10.6084/m9.figshare.8981888
title: Gastroesophageal reflux GWAS identifies risk loci that also associate with subsequent severe esophageal diseases

description: Gastroesophageal reflux GWAS identifies risk loci that also associate with subsequent severe esophageal diseases
DOI: 10.6084/m9.figshare.8981888.v2
title: Gastroesophageal reflux GWAS identifies risk loci that also associate with subsequent severe esophageal diseases

description: Gastroesophageal reflux GWAS identifies risk loci that also associate with subsequent severe esophageal diseases
DOI: 10.6084/m9.figshare.8981888.v1
title: GERD_UKBB_QSKIN.gwas.gz

description: It is a GWAS summary result dataset. The phenotype is GERD(Gastroesophageal reflux disease). The UK biobank and QSKIN data were used. The number of case and control are 69,964,244,802. BOLT-LMM and Metal were used to produce the data. The full paper was published in Nature communications (2019).
DOI: 10.6084/m9.figshare.8981762
title: MOESM4 of Crosstalk between chromatin structure, cohesin activity and transcription

description: Additional file 4: Table S4 List of misregulated genes from additional studies used for comparative analyses in Table 2.
DOI: 10.6084/m9.figshare.8981762.v1
title: MOESM4 of Crosstalk between chromatin structure, cohesin activity and transcription

description: Additional file 4: Table S4 List of misregulated genes from additional studies used for comparative analyses in Table 2.
DOI: 10.6084/m9.figshare.8981756
title: MOESM3 of Crosstalk between chromatin structure, cohesin activity and transcription

description: Additional file 3: Table S3. Misregulated genes in ssc1-73. Lists of up- and downregulated genes are shown.
DOI: 10.6084/m9.figshare.8981756.v1
title: MOESM3 of Crosstalk between chromatin structure, cohesin activity and transcription

description: Additional file 3: Table S3. Misregulated genes in ssc1-73. Lists of up- and downregulated genes are shown.
DOI: 10.6084/m9.figshare.8981741
title: ImTecho Survey Data set and Code book

description: The data represents the Cluster Randomized trial of mHealth intervention called " ImTECHO" (Improve Delivery of Maternal, Neonatal and Child Care services through Community Based Accredited Social Health Activists.
DOI: 10.6084/m9.figshare.8981708
title: Additional file 2: of A grey area: how does image hue affect unfamiliar face matching?

description: Data colour match Exp. 2 (SAV 13 kb)
DOI: 10.6084/m9.figshare.8981699
title: Additional file 1: of A grey area: how does image hue affect unfamiliar face matching?

description: Data colour match experiment (Exp.) 1 (SAV 6 kb)
DOI: 10.6084/m9.figshare.8981708.v1
title: Additional file 2: of A grey area: how does image hue affect unfamiliar face matching?

description: Data colour match Exp. 2 (SAV 13 kb)
DOI: 10.6084/m9.figshare.8981699.v1
title: Additional file 1: of A grey area: how does image hue affect unfamiliar face matching?

description: Data colour match experiment (Exp.) 1 (SAV 6 kb)
DOI: 10.6084/m9.figshare.8981684
title: MOESM2 of Prioritising site-specific micropollutants in surface water from LC-HRMS non-target screening data using a rarity score

description: Additional file 2. Calculated peak attributes for all sites and the intensities of peaks with high rarity scores for all sites.
DOI: 10.6084/m9.figshare.8981684.v1
title: MOESM2 of Prioritising site-specific micropollutants in surface water from LC-HRMS non-target screening data using a rarity score

description: Additional file 2. Calculated peak attributes for all sites and the intensities of peaks with high rarity scores for all sites.
DOI: 10.6084/m9.figshare.8981657
title: Additional file 7: of Genomic and epigenomic predictors of response to guadecitabine in relapsed/refractory acute myelogenous leukemia

description: Table S7. Comparison of the major 19 mutated genes in this study and TCGA tn-AML (n = 200). (p
DOI: 10.6084/m9.figshare.8981657.v1
title: Additional file 7: of Genomic and epigenomic predictors of response to guadecitabine in relapsed/refractory acute myelogenous leukemia

description: Table S7. Comparison of the major 19 mutated genes in this study and TCGA tn-AML (n = 200). (p
DOI: 10.6084/m9.figshare.8981651
title: Additional file 6: of Genomic and epigenomic predictors of response to guadecitabine in relapsed/refractory acute myelogenous leukemia

description: Table S6. Canonical pathway analysis (Ingenuity Pathway Analysis) of 121 genes with differentially methylated promoters from an analysis of 17,793 CpG sites (â Ľâ 20 reads). (XLSX 8 kb)
DOI: 10.6084/m9.figshare.8981648
title: Additional file 5: of Genomic and epigenomic predictors of response to guadecitabine in relapsed/refractory acute myelogenous leukemia

description: Table S5. Locations of 879 differentially methylated SmaI CpG sites correlated with complete response (CR) in the methylation analysis of a total of 17,793 CpG sites (≥ 20 reads) by DREAM analysis (empirical p
DOI: 10.6084/m9.figshare.8981651.v1
title: Additional file 6: of Genomic and epigenomic predictors of response to guadecitabine in relapsed/refractory acute myelogenous leukemia

description: Table S6. Canonical pathway analysis (Ingenuity Pathway Analysis) of 121 genes with differentially methylated promoters from an analysis of 17,793 CpG sites (â Ľâ 20 reads). (XLSX 8 kb)
DOI: 10.6084/m9.figshare.8981645
title: Additional file 4: of Genomic and epigenomic predictors of response to guadecitabine in relapsed/refractory acute myelogenous leukemia

description: Table S4. Clinical characteristics of relapsed/refractory AML patients at baseline, survival, and response in the CGI methylation clusters (XLSX 11 kb)
DOI: 10.6084/m9.figshare.8981639
title: Additional file 3: of Genomic and epigenomic predictors of response to guadecitabine in relapsed/refractory acute myelogenous leukemia

description: Table S3. Demographic and baseline characteristics of the analyzed r/r AML patients in phase I and II (XLSX 11 kb)
DOI: 10.6084/m9.figshare.8981648.v1
title: Additional file 5: of Genomic and epigenomic predictors of response to guadecitabine in relapsed/refractory acute myelogenous leukemia

description: Table S5. Locations of 879 differentially methylated SmaI CpG sites correlated with complete response (CR) in the methylation analysis of a total of 17,793 CpG sites (≥ 20 reads) by DREAM analysis (empirical p
DOI: 10.6084/m9.figshare.8981639.v1
title: Additional file 3: of Genomic and epigenomic predictors of response to guadecitabine in relapsed/refractory acute myelogenous leukemia

description: Table S3. Demographic and baseline characteristics of the analyzed r/r AML patients in phase I and II (XLSX 11 kb)
DOI: 10.6084/m9.figshare.8981645.v1
title: Additional file 4: of Genomic and epigenomic predictors of response to guadecitabine in relapsed/refractory acute myelogenous leukemia

description: Table S4. Clinical characteristics of relapsed/refractory AML patients at baseline, survival, and response in the CGI methylation clusters (XLSX 11 kb)
DOI: 10.6084/m9.figshare.8981630
title: Additional file 2: of Genomic and epigenomic predictors of response to guadecitabine in relapsed/refractory acute myelogenous leukemia

description: Table S2. List of TaqMan gene expression assays* used in this study. (XLSX 8 kb)
DOI: 10.6084/m9.figshare.8981627
title: Additional file 1: of Genomic and epigenomic predictors of response to guadecitabine in relapsed/refractory acute myelogenous leukemia

description: Table S1. Summary of studies reported in this paper (XLSX 8 kb)
DOI: 10.6084/m9.figshare.8981630.v1
title: Additional file 2: of Genomic and epigenomic predictors of response to guadecitabine in relapsed/refractory acute myelogenous leukemia

description: Table S2. List of TaqMan gene expression assays* used in this study. (XLSX 8 kb)
DOI: 10.6084/m9.figshare.8981627.v1
title: Additional file 1: of Genomic and epigenomic predictors of response to guadecitabine in relapsed/refractory acute myelogenous leukemia

description: Table S1. Summary of studies reported in this paper (XLSX 8 kb)
DOI: 10.6084/m9.figshare.8981615
title: Additional file 6: of A combined epigenome- and transcriptome-wide association study of the oral masticatory mucosa assigns CYP1B1 a central role for epithelial health in smokers

description: Results from the ANCOVA of OSCC samples in AHRR and CYP1B1. Listed are all CpGs within the genetic regions of AHRR and CYP1B1 (n = 202) to indicate absence of CpGs in the 450 k analysis of OSCC. CpGs passing the adjusted significance threshold are marked in red. (XLSX 8961 kb)
DOI: 10.6084/m9.figshare.8981606
title: Additional file 5: of A combined epigenome- and transcriptome-wide association study of the oral masticatory mucosa assigns CYP1B1 a central role for epithelial health in smokers

description: Correlation of associated CpGs with association of transcripts. Shown are all CpGs with q
DOI: 10.6084/m9.figshare.8981603
title: Additional file 11: of Genomic and epigenomic predictors of response to guadecitabine in relapsed/refractory acute myelogenous leukemia

description: Table S9. Characteristics of r/r AML patients by baseline gene expression cluster in phase II (XLSX 11 kb)
DOI: 10.6084/m9.figshare.8981615.v1
title: Additional file 6: of A combined epigenome- and transcriptome-wide association study of the oral masticatory mucosa assigns CYP1B1 a central role for epithelial health in smokers

description: Results from the ANCOVA of OSCC samples in AHRR and CYP1B1. Listed are all CpGs within the genetic regions of AHRR and CYP1B1 (n = 202) to indicate absence of CpGs in the 450 k analysis of OSCC. CpGs passing the adjusted significance threshold are marked in red. (XLSX 8961 kb)
DOI: 10.6084/m9.figshare.8981600
title: Additional file 4: of A combined epigenome- and transcriptome-wide association study of the oral masticatory mucosa assigns CYP1B1 a central role for epithelial health in smokers

description: Results from the KEGG and Reactome Pathway Analyses of Differentially Expressed Genes. (XLSX 76 kb)
DOI: 10.6084/m9.figshare.8981606.v1
title: Additional file 5: of A combined epigenome- and transcriptome-wide association study of the oral masticatory mucosa assigns CYP1B1 a central role for epithelial health in smokers

description: Correlation of associated CpGs with association of transcripts. Shown are all CpGs with q
DOI: 10.6084/m9.figshare.8981594
title: Additional file 3: of A combined epigenome- and transcriptome-wide association study of the oral masticatory mucosa assigns CYP1B1 a central role for epithelial health in smokers

description: Median TPM values from RNA-Sequencing. Transcripts were ranked according to their median TPM value in the EWAS samples, with the highest expressed genes on top. (XLSX 1299 kb)