cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.16545820.v2
title: Novel DNA methylation loci and genes showing pleiotropic association with Alzheimer’s dementia: a network Mendelian randomization analysis

description: Previous genome-wide association studies (GWAS) have identified potential genetic variants involved in the risk of Alzheimer’s dementia, but their underlying biological interpretation remains largely unclear. In addition, the effects of DNA methylation and gene expression on Alzheimer’s dementia are not well understood. A network summary data-based Mendelian randomization (SMR) analysis was performed integrating cis- DNA methylation quantitative trait loci (mQTL) /cis- gene expression QTL (eQTL) data in the brain and blood, as well as GWAS summarized data for Alzheimer’s dementia to evaluate the pleiotropic associations of DNA methylation and gene expression with Alzheimer’s dementia and to explore the complex mechanisms underpinning Alzheimer’s dementia. After correction for multiple testing (false discovery rate [FDR] <i>P</i> &lt; 0.05) and filtering using the heterogeneity in dependent instruments (HEIDI) test (<i>P</i><sub>HEIDI</sub>&gt;0.01), we identified dozens of DNA methylation sites and genes showing pleiotropic associations with Alzheimer’s dementia. We found 22 and 16 potentially causal pathways of Alzheimer’s dementia (i.e., SNP→DNA methylation→Gene expression→Alzheimer’s dementia) in the brain and blood, respectively. Approximately two-thirds of the identified DNA methylation sites had an influence on gene expression and the expression of almost all the identified genes was regulated by DNA methylation. Our network SMR analysis provided evidence supporting the pleiotropic association of some novel DNA methylation sites and genes with Alzheimer’s dementia and revealed possible causal pathways underlying the pathogenesis of Alzheimer’s dementia. Our findings shed light on the role of DNA methylation in gene expression and in the development of Alzheimer’s dementia.
DOI: 10.6084/m9.figshare.16545820
title: Novel DNA methylation loci and genes showing pleiotropic association with Alzheimer’s dementia: a network Mendelian randomization analysis

description: Previous genome-wide association studies (GWAS) have identified potential genetic variants involved in the risk of Alzheimer’s dementia, but their underlying biological interpretation remains largely unclear. In addition, the effects of DNA methylation and gene expression on Alzheimer’s dementia are not well understood. A network summary data-based Mendelian randomization (SMR) analysis was performed integrating cis- DNA methylation quantitative trait loci (mQTL) /cis- gene expression QTL (eQTL) data in the brain and blood, as well as GWAS summarized data for Alzheimer’s dementia to evaluate the pleiotropic associations of DNA methylation and gene expression with Alzheimer’s dementia and to explore the complex mechanisms underpinning Alzheimer’s dementia. After correction for multiple testing (false discovery rate [FDR] <i>P</i> &lt; 0.05) and filtering using the heterogeneity in dependent instruments (HEIDI) test (<i>P</i><sub>HEIDI</sub>&gt;0.01), we identified dozens of DNA methylation sites and genes showing pleiotropic associations with Alzheimer’s dementia. We found 22 and 16 potentially causal pathways of Alzheimer’s dementia (i.e., SNP→DNA methylation→Gene expression→Alzheimer’s dementia) in the brain and blood, respectively. Approximately two-thirds of the identified DNA methylation sites had an influence on gene expression and the expression of almost all the identified genes was regulated by DNA methylation. Our network SMR analysis provided evidence supporting the pleiotropic association of some novel DNA methylation sites and genes with Alzheimer’s dementia and revealed possible causal pathways underlying the pathogenesis of Alzheimer’s dementia. Our findings shed light on the role of DNA methylation in gene expression and in the development of Alzheimer’s dementia.
DOI: 10.6084/m9.figshare.8157137
title: Additional file 1: of Transcriptional reference map of hormone responses in wheat spikes

description: Table S1. List of genes differentially expressed in wheat spikes in response to seven hormones. Table S2. Gene enrichment analysis of DEGs in response to various hormones. Table S3. List of 1599 DEGs responsive to both F. graminearum and hormone treatments. Table S4. Gene enrichment analysis of DEGs commonly regulated by hormones (ABA, MeJA, or IAA) and F. graminearum. Table. S5. List of 157 DEGs responsive to water deficit stress in the glume and hormone treatments. Table S6. List of 29 genes that exhibited the opposite expression patterns in response to water deficit stress and IAA. Table S7. Details regarding the qRT-PCR primers. (XLSX 583 kb)
DOI: 10.25549/one-ouc17552590
title: Mattachine Society, California Society of Employment and Rehabilitation (1961)
DOI: 10.6084/m9.figshare.8157227.v1
title: Additional file 8: of Detection of circular RNA expression and related quantitative trait loci in the human dorsolateral prefrontal cortex

description: Table S7. The detail of circQTL SNPs located in the splicing site. (XLSX 17 kb)
DOI: 10.5281/zenodo.10667092
title: Dataset related to article "Mapping Tumor Heterogeneity via Local Entropy Assessment: Making Biomarkers Visible "

description: This record contains raw data related to article “Mapping Tumor Heterogeneity via Local Entropy Assessment: Making Biomarkers Visible "

Abstract



Advanced imaging and analysis improve prediction of pathology data and outcomes in several tumors, with entropy-based measures being among the most promising biomarkers. However, entropy is often perceived as statistical data lacking clinical significance. We aimed to generate a voxel-by-voxel visual map of local tumor entropy, thus allowing to (1) make entropy explainable and accessible to clinicians; (2) disclose and quantitively characterize any intra-tumoral entropy heterogeneity; (3) evaluate associations between entropy and pathology data. We analyzed the portal phase of preoperative CT of 20 patients undergoing liver surgery for colorectal metastases. A three-dimensional core kernel (5 × 5 × 5 voxels) was created and used to compute the local entropy value for each voxel of the tumor. The map was encoded with a color palette. We performed two analyses: (a) qualitative assessment of tumors' detectability and pattern of entropy distribution; (b) quantitative analysis of the entropy values distribution. The latter data were compared with standard Hounsfield data as predictors of post-chemotherapy tumor regression grade (TRG). Entropy maps were successfully built for all tumors. Metastases were qualitatively hyper-entropic compared to surrounding parenchyma. In four cases hyper-entropic areas exceeded the tumor margin visible at CT. We identified four "entropic" patterns: homogeneous, inhomogeneous, peripheral rim, and mixed. At quantitative analysis, entropy-derived data (percentiles/mean/median/root mean square) predicted TRG (p < 0.05) better than Hounsfield-derived ones (p = n.s.). We present a standardized imaging technique to visualize tumor heterogeneity built on a voxel-by-voxel entropy assessment. The association of local entropy with pathology data supports its role as a biomarker.
DOI: 10.5281/zenodo.10667093
title: Dataset related to article "Mapping Tumor Heterogeneity via Local Entropy Assessment: Making Biomarkers Visible "

description: This record contains raw data related to article “Mapping Tumor Heterogeneity via Local Entropy Assessment: Making Biomarkers Visible "

Abstract



Advanced imaging and analysis improve prediction of pathology data and outcomes in several tumors, with entropy-based measures being among the most promising biomarkers. However, entropy is often perceived as statistical data lacking clinical significance. We aimed to generate a voxel-by-voxel visual map of local tumor entropy, thus allowing to (1) make entropy explainable and accessible to clinicians; (2) disclose and quantitively characterize any intra-tumoral entropy heterogeneity; (3) evaluate associations between entropy and pathology data. We analyzed the portal phase of preoperative CT of 20 patients undergoing liver surgery for colorectal metastases. A three-dimensional core kernel (5 × 5 × 5 voxels) was created and used to compute the local entropy value for each voxel of the tumor. The map was encoded with a color palette. We performed two analyses: (a) qualitative assessment of tumors' detectability and pattern of entropy distribution; (b) quantitative analysis of the entropy values distribution. The latter data were compared with standard Hounsfield data as predictors of post-chemotherapy tumor regression grade (TRG). Entropy maps were successfully built for all tumors. Metastases were qualitatively hyper-entropic compared to surrounding parenchyma. In four cases hyper-entropic areas exceeded the tumor margin visible at CT. We identified four "entropic" patterns: homogeneous, inhomogeneous, peripheral rim, and mixed. At quantitative analysis, entropy-derived data (percentiles/mean/median/root mean square) predicted TRG (p < 0.05) better than Hounsfield-derived ones (p = n.s.). We present a standardized imaging technique to visualize tumor heterogeneity built on a voxel-by-voxel entropy assessment. The association of local entropy with pathology data supports its role as a biomarker.
DOI: 10.6084/m9.figshare.12872150.v1
title: Additional file 3 of Identification of drought tolerant mechanisms in a drought-tolerant maize mutant based on physiological, biochemical and transcriptomic analyses

description: Additional file 3 : Table S3 The common DEGs shared by C7–2 and C7–2t.
DOI: 10.25549/one-ouc17551380
title: Mattachine Society, correspondence, Gonzalo (Tony) Segura, Jr. (1956-1961)
DOI: 10.25549/one-ouc17551381
title: Mattachine Society, correspondence, Donald Stewart Lucas (1956-1965)
DOI: 10.6084/m9.figshare.12872153
title: Additional file 4 of Identification of drought tolerant mechanisms in a drought-tolerant maize mutant based on physiological, biochemical and transcriptomic analyses

description: Additional file 4 : Table S4 The DEGs specific to C7–2 and C7–2t.
DOI: 10.25549/one-ouc17555585
title: Mattachine Society, Tay-Bush legal defense fund (1961-1962)
DOI: 10.6084/m9.figshare.14444866.v1
title: Additional file 5 of Global analysis of HBV-mediated host proteome and ubiquitylome change in HepG2.2.15 human hepatoblastoma cell line

description: Additional file 5: Table S1. Total identified and quantified proteins in response to HBV integration in HepG2.2.15 cells.
DOI: 10.6084/m9.figshare.12872156
title: Additional file 5 of Identification of drought tolerant mechanisms in a drought-tolerant maize mutant based on physiological, biochemical and transcriptomic analyses

description: Additional file 5 : Table S5 GO enrichment analysis of the DEGs in C7–2 and C7–2t.
DOI: 10.25549/one-ouc17551383
title: Mattachine Society, correspondence, Donald Stewart Lucas (1956-1965)
DOI: 10.6084/m9.figshare.8157218
title: Additional file 6: of Detection of circular RNA expression and related quantitative trait loci in the human dorsolateral prefrontal cortex

description: Table S5. List of circRNAs associated with age of death at an FDRâ &lt;â 0.05. (XLSX 30 kb)
DOI: 10.25549/one-ouc17551389
title: Mattachine Society, correspondence, Wallace O. Maxey (1953-1961)
DOI: 10.25549/one-ouc17551384
title: Mattachine Society, correspondence, Donald Stewart Lucas (1956-1965)
DOI: 10.6084/m9.figshare.8157248.v1
title: MOESM2 of Plasma proteomic and autoantibody profiles reveal the proteomic characteristics involved in longevity families in Bama, China

description: Additional file 2. Table S2. Proteins (autoantigens) recognized by plasma autoantibodies of the longevous and normal groups, identified by human proteome microarray.
DOI: 10.25549/one-ouc17551387
title: Mattachine Society, correspondence, Donald Stewart Lucas (1956-1965)
DOI: 10.6084/m9.figshare.12872147.v1
title: Additional file 2 of Identification of drought tolerant mechanisms in a drought-tolerant maize mutant based on physiological, biochemical and transcriptomic analyses

description: Additional file 2 : Table S2 The DEGs detected in C7–2 and C7–2t.
DOI: 10.5281/zenodo.7066504
title: Wikidata68K

description: Wikidata68K is a benchmark dataset extracted from Wikidata and Wikipedia for inductive link prediction in knowledge graphs.
DOI: 10.5281/zenodo.7066503
title: Wikidata68K

description: Wikidata68K is a benchmark dataset extracted from Wikidata and Wikipedia for inductive link prediction in knowledge graphs.
DOI: 10.5281/zenodo.7225382
title: Graphs of redirection: an examination of URIs in identity graphs

description: This is the dataset for our paper <strong>What does it mean when your URIs are redirected? Examining identity and redirection in the LOD cloud</strong> Redirection of URIs is widely used in the LOD cloud, and is even part of the best practice guidelines as an approach to the ``curation problem'' on the semantic web (i.e. how to repair imperfections). When dereferencing, one URI is redirected to another URI. Such a redirection could be the result of an update of the namespace, a different encoding scheme, or some other reasons. In this paper, we study the semantics of redirection and examine if redirection indicates how entities in the LOD cloud evolve. More specifically, we focus on entities in the identity graphs: subgraphs in the semantic web restricted to identity links. The entities we study are from sameAs.cc, an identity graph extracted from a crawl of the semantic web in 2015. Our analytical results include an examination of edges and chains of redirection as well as a statistical analysis of the redirection behavior of sampled entities. Additionally, we present properties of the graphs formed by redirection relations. The dataset contains the redirect relations of four sets of sampled entities. These sampled files are: ite_uniform... the edges of redirection graph corresponding to uniform samplings cc_sample_2... the sampling regarding connected components of size 2, 3-10, 10+, respectively. The Python scripts are open source online at: https://github.com/shuaiwangvu/redirection The paper is attached. In case of any questions, please contact Shuai Wang at shuai.wang@vu.nl.
DOI: 10.5281/zenodo.7225383
title: Graphs of redirection: an examination of URIs in identity graphs

description: This is the dataset for our paper <strong>What does it mean when your URIs are redirected? Examining identity and redirection in the LOD cloud</strong> Redirection of URIs is widely used in the LOD cloud, and is even part of the best practice guidelines as an approach to the ``curation problem'' on the semantic web (i.e. how to repair imperfections). When dereferencing, one URI is redirected to another URI. Such a redirection could be the result of an update of the namespace, a different encoding scheme, or some other reasons. In this paper, we study the semantics of redirection and examine if redirection indicates how entities in the LOD cloud evolve. More specifically, we focus on entities in the identity graphs: subgraphs in the semantic web restricted to identity links. The entities we study are from sameAs.cc, an identity graph extracted from a crawl of the semantic web in 2015. Our analytical results include an examination of edges and chains of redirection as well as a statistical analysis of the redirection behavior of sampled entities. Additionally, we present properties of the graphs formed by redirection relations. The dataset contains the redirect relations of four sets of sampled entities. These sampled files are: ite_uniform... the edges of redirection graph corresponding to uniform samplings cc_sample_2... the sampling regarding connected components of size 2, 3-10, 10+, respectively. The Python scripts are open source online at: https://github.com/shuaiwangvu/redirection The paper is attached. In case of any questions, please contact Shuai Wang at shuai.wang@vu.nl.
DOI: 10.34740/kaggle/dsv/4482334
title: Global Genomic Neurofibromatosis Neoplasia
DOI: 10.5281/zenodo.6556310
title: A Genome-Wide Evolutionary Simulation of the Transcription-Supercoiling Coupling: extended version

description: Data set used for the Artificial Life journal paper <em>A Genome-Wide Evolutionary Simulation of the Transcription-Supercoiling Coupling: extended version</em>. A preprint of the paper is also available here. This data is also used in Chapter 4 of my PhD thesis.
DOI: 10.5281/zenodo.6556309
title: A Genome-Wide Evolutionary Simulation of the Transcription-Supercoiling Coupling: extended version

description: Data set used for the Artificial Life journal paper <em>A Genome-Wide Evolutionary Simulation of the Transcription-Supercoiling Coupling: extended version</em>. A preprint of the paper is also available here. This data is also used in Chapter 4 of my PhD thesis.
DOI: 10.57992/nmrxiv.p13
title: Menthol
DOI: 10.57992/nmrxiv.p13.s.d470
title: 1
DOI: 10.57992/nmrxiv.p13.s.d471
title: 5
DOI: 10.57992/nmrxiv.p13.s.d472
title: 2
DOI: 10.57992/nmrxiv.p13.s.d473
title: 4
DOI: 10.57992/nmrxiv.p13.s.d474
title: 6
DOI: 10.57992/nmrxiv.p13.s.d475
title: 8
DOI: 10.57992/nmrxiv.p13.s.d476
title: 7
DOI: 10.57992/nmrxiv.p13.s80
title: Jena_2216-51-5_light
DOI: 10.5519/qd.lonpwb7e
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (3955 records)
DOI: 10.6084/m9.figshare.21268572
title: CONSORT checklist and flow chart for ‘Respiratory and diarrhoeal pathogens in Malawian children hospitalised with diarrhoea and association with short-term growth’

description: CONSORT checklist and flow chart for ‘Respiratory and diarrhoeal pathogens in Malawian children hospitalised with diarrhoea and association with short-term growth’
DOI: 10.6084/m9.figshare.21268572.v1
title: CONSORT checklist and flow chart for ‘Respiratory and diarrhoeal pathogens in Malawian children hospitalised with diarrhoea and association with short-term growth’

description: CONSORT checklist and flow chart for ‘Respiratory and diarrhoeal pathogens in Malawian children hospitalised with diarrhoea and association with short-term growth’
DOI: 10.6084/m9.figshare.21268572.v2
title: CONSORT checklist and flow chart for ‘Respiratory and diarrhoeal pathogens in Malawian children hospitalised with diarrhoea and association with short-term growth’

description: CONSORT checklist and flow chart for ‘Respiratory and diarrhoeal pathogens in Malawian children hospitalised with diarrhoea and association with short-term growth’
DOI: 10.3886/e182902
title: Serial deleterious effects of cybervictimization among college students over two years: From hostile rumination to moral disengagement

description: The longitudinal data of this study were collected based on convenience sampling by the whole class, as a part of a large longitudinal survey among college students from six universities in five Chinese cities.
DOI: 10.3886/e182902v1
title: Serial deleterious effects of cybervictimization among college students over two years: From hostile rumination to moral disengagement

description: The longitudinal data of this study were collected based on convenience sampling by the whole class, as a part of a large longitudinal survey among college students from six universities in five Chinese cities.
DOI: 10.5281/zenodo.6973687
title: DATASET: Nanoporous Au Formation on Au Substrates via High Voltage Electrolysis

description: This folder contains all the data shown in the figures of the manuscript or SI titled<br> "Nanoporous Au Formation on Au Substrates via High Voltage Electrolysis" (doi:10.26434/chemrxiv-2022-mx2qd).<br> For each figure, a folder is created here where the corresponding data can be found.
DOI: 10.5281/zenodo.6973686
title: DATASET: Nanoporous Au Formation on Au Substrates via High Voltage Electrolysis

description: This folder contains all the data shown in the figures of the manuscript or SI titled<br> "Nanoporous Au Formation on Au Substrates via High Voltage Electrolysis" (doi:10.26434/chemrxiv-2022-mx2qd).<br> For each figure, a folder is created here where the corresponding data can be found.
DOI: 10.5255/ukda-sn-856047
title: Perception Spillover From Fracking, 2022

description: Public opposition to new energy technology can harm the chances of successful deployment. Less is known about knock-on effects on the wider energy system, including whether such opposition impacts public perceptions of other technologies. Here we present a mixed-methods study into ‘perception spillover’, examining whether the controversy over fracking for oil and gas affects public attitudes to two novel low-carbon energy technologies: deep ‘enhanced’ geothermal systems, and ‘green’ hydrogen. We argue that perception spillover is multi-faceted, and we conceptualise and test spontaneous, prompted and primed forms, examining how and why particular types occur. Using a nationally-representative UK survey and two focus groups, we show that perception spillover from fracking could lead to widespread negative perceptions of deep geothermal energy, influencing the conditions which deep geothermal would be expected to meet. Conversely, a minority of participants expressed more positive perceptions of green hydrogen because they deemed it dissimilar to fracking.
DOI: 10.14459/10.14459/2022mp1691120
title: Optically Induced Long-Lived Chirality Memory in the Color-Tunable Chiral Lead-Free Semiconductor (R)/(S)‑CHEA4Bi2BrxI10−x (x = 0−10)

description: Hybrid organic-inorganic perovskites are optoelectronic materials with tunable chemical and electronic structures. Incorporating chiral organic molecules into perovskite networks has attracted great attention due to their potential in lighting applications and optical communication. Here, we introduce chiral organic molecules (R)/(S)-1-cyclohexylethylamine (R/S-CHEA) into bismuth-based materials with a perovskite-related motif, to synthesize chiral lead-free (R)/(S)-CHEA4Bi2BrxI10-x crystals and thin films. We perform single-crystal XRD measurements and density-functional theory (DFT) calculations to identify their crystal and electronic band structures. We investigate their optical properties, and find circular dichroism, which we tune over a wide wavelength range from 300 - 500 nm by changing the bromide-to-iodide ratio. Further, we employ transient absorption and time-resolved PL spectroscopy to investigate charge carrier dynamics, which show long-lived excitations with optically-induced chirality memory up to microsecond timescales. Our demonstration of color-tunable and chiral lead-free perovskites opens a new avenue for the discovery of high performance lead-free spintronic materials with optical functionalities.
DOI: 10.34740/kaggle/dsv/4482545
title: YouTube Trending Video Dataset (updated daily)
DOI: 10.14459/2022mp1691120
title: Optically Induced Long-Lived Chirality Memory in the Color-Tunable Chiral Lead-Free Semiconductor (R)/(S)‑CHEA4Bi2BrxI10−x (x = 0−10)

description: Hybrid organic-inorganic perovskites are optoelectronic materials with tunable chemical and electronic structures. Incorporating chiral organic molecules into perovskite networks has attracted great attention due to their potential in lighting applications and optical communication. Here, we introduce chiral organic molecules (R)/(S)-1-cyclohexylethylamine (R/S-CHEA) into bismuth-based materials with a perovskite-related motif, to synthesize chiral lead-free (R)/(S)-CHEA4Bi2BrxI10-x crystals and thin films. We perform single-crystal XRD measurements and density-functional theory (DFT) calculations to identify their crystal and electronic band structures. We investigate their optical properties, and find circular dichroism, which we tune over a wide wavelength range from 300 - 500 nm by changing the bromide-to-iodide ratio. Further, we employ transient absorption and time-resolved PL spectroscopy to investigate charge carrier dynamics, which show long-lived excitations with optically-induced chirality memory up to microsecond timescales. Our demonstration of color-tunable and chiral lead-free perovskites opens a new avenue for the discovery of high performance lead-free spintronic materials with optical functionalities.