cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.20626806.v1
title: Process-related GHG emissions in China (1990-2020).xlsx

description: This is the data file for review of the manuscript "China’s process-related greenhouse gas emission dataset 1990-2020" submitted to Scientific Data <br> Xiang Yu 1, 2, †, Chang Tan 3, †, * 1. University of Chinese Academy of Social Sciences, Beijing 102488, China 2. Research Institute for Eco-civilization (RIEco), Chinese Academy of Social Sciences, Beijing 100710, China 3. Department of Earth System Science, Ministry of Education Key Laboratory for Earth System Modeling, Institute for Global Change Studies, Tsinghua University, Beijing 100084, China *Corresponding author: Chang Tan (tanc21@mails.tsinghua.edu.cn) † These authors should be regarded as co-first authors.
DOI: 10.25578/hwn8ke
title: Lyon North realistic trip data set during the morning peak

description: The data contains the real departure time, arrival time, trip length, and estimated desired arrival time of all users. This data set represents two demand scenarios either with predefined departure time or predefined desired arrival time for the morning peak hours from 6:30 AM to 10:40 AM of the northern part of Lyon Metropolis (Lyon North), including 62,450 trips. Lyon North network covers 25 km2 and includes 1,883 nodes and 3,383 links.
DOI: 10.5281/zenodo.7024059
title: [Demo Input Data] for SCAFE: a software suite for analysis of transcribed cis-regulatory elements in single cells

description: This archive (input.tar.gz) contains the demo data for SCAFE v1.0.0 (on Zenodo or Github) <em>SCAFE</em> (Single Cell Analysis of Five-prime Ends) provides an end-to-end solution for processing of single cell 5’end RNA-seq data. It takes a read alignment file (*.bam) from single-cell RNA-5’end-sequencing (e.g. 10xGenomics Chromimum®), precisely maps the cDNA 5'ends (i.e. transcription start sites, TSS), filters for the artefacts and identifies genuine TSS clusters using logistic regression. Based on the TSS clusters, it defines transcribed cis-regulatory elements (tCRE) and annotated them to gene models. It then counts the UMI in tCRE in single cells and returns a tCRE UMI/cellbarcode matrix ready for downstream analyses, e.g. cell-type clustering, linking promoters to enhancers by co-activity <em>etc</em>. For details on installation, usage and test run on demo data, visit https://github.com/chung-lab/SCAFE
DOI: 10.5281/zenodo.7024060
title: [Demo Input Data] for SCAFE: a software suite for analysis of transcribed cis-regulatory elements in single cells

description: This archive (input.tar.gz) contains the demo data for SCAFE v1.0.0 (on Zenodo or Github) <em>SCAFE</em> (Single Cell Analysis of Five-prime Ends) provides an end-to-end solution for processing of single cell 5’end RNA-seq data. It takes a read alignment file (*.bam) from single-cell RNA-5’end-sequencing (e.g. 10xGenomics Chromimum®), precisely maps the cDNA 5'ends (i.e. transcription start sites, TSS), filters for the artefacts and identifies genuine TSS clusters using logistic regression. Based on the TSS clusters, it defines transcribed cis-regulatory elements (tCRE) and annotated them to gene models. It then counts the UMI in tCRE in single cells and returns a tCRE UMI/cellbarcode matrix ready for downstream analyses, e.g. cell-type clustering, linking promoters to enhancers by co-activity <em>etc</em>. For details on installation, usage and test run on demo data, visit https://github.com/chung-lab/SCAFE
DOI: 10.6084/m9.figshare.20655702
title: Explaining variation in reading comprehension in Northern Sotho-English bilingual children a Simple View of Reading perspective on longitudinal data.xlsx

description: Data sheet for the Simple View of Reading study in Northern Sotho-English (Grade2- Grade3) bilingual children. The study investigates the Simple View of Reading Theory in reading comprehension abilities of Northern Sotho first language speakers learning to read in a second language (English). A quantitative approach was used for data collection and analysis. Ethical approval was sought from Univesity of South Africa and the Department of Basic Education.
DOI: 10.6084/m9.figshare.20655702.v1
title: Explaining variation in reading comprehension in Northern Sotho-English bilingual children a Simple View of Reading perspective on longitudinal data.xlsx

description: Data sheet for the Simple View of Reading study in Northern Sotho-English (Grade2- Grade3) bilingual children. The study investigates the Simple View of Reading Theory in reading comprehension abilities of Northern Sotho first language speakers learning to read in a second language (English). A quantitative approach was used for data collection and analysis. Ethical approval was sought from Univesity of South Africa and the Department of Basic Education.
DOI: 10.5281/zenodo.5778942
title: Timeseries of lake margin, lake area, water level, mascon solutions of Lago Greve

description: These are the dataset of timeseries of lake extent, lake area, water level, and mass around the lake, of Lago Greve presented in the study. 1. Lake extent<br> Filename: LagoGreve.shp<br> Note: LagoGreve.cpg, LagoGreve.dbf, LagoGreve.prj, LagoGreve.shx are also needed. 2. Timeseries of lake area<br> Filename: LakeArea_LagoGreve.csv 3. Timeseries of water level<br> Filename: Lakelevel_LagoGreve.csv 4. Timeseries of grace mascon solution<br> Filename: MeanMasconLagoGreve_CSRv06.csv 5. Fitting model for mascon solution<br> Filename: MeanMasconFitting.csv
DOI: 10.34740/kaggle/dsv/4124307
title: YouTube Trending Video Dataset (updated daily)
DOI: 10.20372/aau_rdr/jahhhd/uiuojt
title: Raw data.docx

description: :unav
DOI: 10.20372/aau_rdr/jahhhd/qmytbi
title: 1234.tab

description: :unav
DOI: 10.20372/aau_rdr/jahhhd
title: ASSESEMENT OF E-MARKETING AND CRISIS MANAGEMENT PRACTICES OF STAR-RATED HOTELS IN ADDIS ABABA AMID COVID-19 AND ONGOING INTERNAL CONFLICT

description: The purpose of this study is to assess E-marketing and crisis management practices among star-rated hotels in Addis Ababa amid COVID 19 and on-going internal conflicts.
DOI: 10.34711/inptdat.572
title: Upscaling from single- to multi-filament dielectric barrier discharges in pulsed operation - Dataset

description: A study on the scalability of discharge characteristics of a single-filament dielectric barrier discharge (DBD) to a spatially one-dimensional multi-filament arrangement driven by the same high-voltage (HV) pulses was performed for a gas mixture of 0.1 vol% O2 in N2 at 1 bar. Both arrangements feature a 1 mm gap with dielectric-covered electrodes featuring two hemispherical alumina caps for the single-filament and two parallel alumina-tubes for the multi-filament arrangement. The DBDs were characterised by electrical measurements (for peak current, energy, and power) accompanied by iCCD and streak imaging to determine the filament number and the discharge development in the gas gap and on the surfaces. The dataset contains the data presented in the corresponding journal article.
DOI: 10.5517/ccdc.csd.cc25p4z0
title: CCDC 2016332: Experimental Crystal Structure Determination

description: Related Article: W. Clegg, R.W. Harrington|2020|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc27w16d
title: CCDC 2081563: Experimental Crystal Structure Determination

description: Related Article: W. Clegg, K. Guille|2021|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.6084/m9.figshare.12403550
title: Bioactive constituents of <i>Salvia przewalskii</i> and the molecular mechanism of its antihypoxia effects determined using quantitative proteomics

description: Environmental hypobaric hypoxia induces several physiological or pathological responses in individuals in high-altitude regions. <i>Salvia przewalskii</i> Maxim (Labiatae) (SPM) is a traditional Chinese herbal medicine and has known antibacterial, antiviral, antioxidant, anti-thrombotic, and anti-depressant activities. This study examined the antihypoxia effects of SPM <i>in vivo</i>. The dried and pulverised of SPM was extracted from root crude drug with 70% ethanol with ultrasound. Male Sprague-Dawley rats were divided into three groups (<i>n</i> = 10): normal group, hypoxia group (altitude of 4260 m), and hypoxia + SPM group (altitude of 4260 m, SPM of 1.0 g/kg/day). The experiment persisted for 4 weeks. The mean pulmonary arterial pressure (mPAP), hypoxia-inducible factor-1α (HIF-1α) mRNA, and lung pathology were analysed using pulmonary artery pressure recorder, quantitative polymerase chain reaction, and histopathological analysis. Moreover, the effects of SPM on lung proteomes during hypoxia were observed by a TMT-based proteomic approach. Pre-treatment with SPM decreased mPAP (24.86%) and HIF-1α (31.24%), and attenuated the pathological changes in lung tissues. In addition, a total of 28 proteins were differentially expressed in lung of hypoxia + SPM group (fold change &gt; ± 1.2 and <i>p</i> &lt; 0.05). The differentially altered proteins were primarily associated with antioxidative stress, as evidenced by the downregulated expression of Adh7, Cyp2d1, Plod2, Selenow, ND3, and Fabp1, and fructose metabolism, as evidenced by the downregulated expression of Khk and Aldob. These results suggested that SPM is a promising drug for antihypoxia. The mechanism of action might be related to increasing antioxidant capacity and inhibiting fructose metabolism.
DOI: 10.6084/m9.figshare.12403550.v1
title: Bioactive constituents of <i>Salvia przewalskii</i> and the molecular mechanism of its antihypoxia effects determined using quantitative proteomics

description: Environmental hypobaric hypoxia induces several physiological or pathological responses in individuals in high-altitude regions. <i>Salvia przewalskii</i> Maxim (Labiatae) (SPM) is a traditional Chinese herbal medicine and has known antibacterial, antiviral, antioxidant, anti-thrombotic, and anti-depressant activities. This study examined the antihypoxia effects of SPM <i>in vivo</i>. The dried and pulverised of SPM was extracted from root crude drug with 70% ethanol with ultrasound. Male Sprague-Dawley rats were divided into three groups (<i>n</i> = 10): normal group, hypoxia group (altitude of 4260 m), and hypoxia + SPM group (altitude of 4260 m, SPM of 1.0 g/kg/day). The experiment persisted for 4 weeks. The mean pulmonary arterial pressure (mPAP), hypoxia-inducible factor-1α (HIF-1α) mRNA, and lung pathology were analysed using pulmonary artery pressure recorder, quantitative polymerase chain reaction, and histopathological analysis. Moreover, the effects of SPM on lung proteomes during hypoxia were observed by a TMT-based proteomic approach. Pre-treatment with SPM decreased mPAP (24.86%) and HIF-1α (31.24%), and attenuated the pathological changes in lung tissues. In addition, a total of 28 proteins were differentially expressed in lung of hypoxia + SPM group (fold change &gt; ± 1.2 and <i>p</i> &lt; 0.05). The differentially altered proteins were primarily associated with antioxidative stress, as evidenced by the downregulated expression of Adh7, Cyp2d1, Plod2, Selenow, ND3, and Fabp1, and fructose metabolism, as evidenced by the downregulated expression of Khk and Aldob. These results suggested that SPM is a promising drug for antihypoxia. The mechanism of action might be related to increasing antioxidant capacity and inhibiting fructose metabolism.
DOI: 10.48490/55p5-v637
title: AR6 WGII Data for Figure TS.5(a): Latitudinal distribution of marine species richness
DOI: 10.48490/fnq2-gn02
title: AR6 WGII Data for Figure TS.5(b): Global distribution of marine species richness
DOI: 10.25574/14534
title: Chandra X-ray Observatory ObsId 14534

description: Wolf-Rayet Winds at High Spectral Resolution
DOI: 10.25574/14569
title: Chandra X-ray Observatory ObsId 14569

description: Occultation Measurements of the Embedded Wind Shock Distribution in the Nearest Eclipsing O-star Binary
DOI: 10.25574/14618
title: Chandra X-ray Observatory ObsId 14618

description: Transient LMXBs in Globular Clusters
DOI: 10.25574/14634
title: Chandra X-ray Observatory ObsId 14634

description: Accretion and Ejection in a Neutron Star Transient
DOI: 10.25574/14684
title: Chandra X-ray Observatory ObsId 14684

description: Pre-planned Target of Opportunity Observations of the Crab Nebula upon the Occurrence of a Gamma-Ray Flare
DOI: 10.25574/14687
title: Chandra X-ray Observatory ObsId 14687

description: Pre-planned Target of Opportunity Observations of the Crab Nebula upon the Occurrence of a Gamma-Ray Flare
DOI: 10.25574/14701
title: Chandra X-ray Observatory ObsId 14701

description: PROMPT STUDY OF MAGNETAR OUTBURSTS WITH CHANDRA
DOI: 10.6084/m9.figshare.20656707
title: Calculation results and algorithm

description: The basic logic of the algorithm
DOI: 10.6084/m9.figshare.20656707.v1
title: Calculation results and algorithm

description: The basic logic of the algorithm
DOI: 10.6084/m9.figshare.16586271
title: An IDH-independent mechanism of DNA hypermethylation upon VHL inactivation in cancer

description: Hypermethylation of tumour suppressors and other aberrations of DNA methylation in tumours play a significant role in cancer progression. DNA methylation can be affected by various environmental conditions, including hypoxia. The response to hypoxia is mainly achieved through activation of the transcriptional program associated with HIF1A transcription factor. Inactivation of Von Hippel-Lindau Tumour Suppressor gene (<i>VHL</i>) by genetic or epigenetic events, which also induces aberrant activation of HIF1A, is the most common driver event for renal cancer. With whole-genome bisulphite sequencing and LC-MS, we demonstrated that <i>VHL</i> inactivation induced global genome hypermethylation in human kidney cancer cells under normoxic conditions. This effect was reverted by exogenous expression of wild-type <i>VHL</i>. We showed that global genome hypermethylation in <i>VHL</i> mutants can be explained by transcriptional changes in <i>MDH</i> and <i>L2HGDH</i> genes that cause the accumulation of 2-hydroxyglutarate – a metabolite that inhibits DNA demethylation by TET enzymes. Unlike the known cases of DNA hypermethylation in cancer, 2-hydroxyglutarate was accumulated in the cells with the wild-type isocitrate dehydrogenases.
DOI: 10.6084/m9.figshare.16586271.v2
title: An IDH-independent mechanism of DNA hypermethylation upon VHL inactivation in cancer

description: Hypermethylation of tumour suppressors and other aberrations of DNA methylation in tumours play a significant role in cancer progression. DNA methylation can be affected by various environmental conditions, including hypoxia. The response to hypoxia is mainly achieved through activation of the transcriptional program associated with HIF1A transcription factor. Inactivation of Von Hippel-Lindau Tumour Suppressor gene (<i>VHL</i>) by genetic or epigenetic events, which also induces aberrant activation of HIF1A, is the most common driver event for renal cancer. With whole-genome bisulphite sequencing and LC-MS, we demonstrated that <i>VHL</i> inactivation induced global genome hypermethylation in human kidney cancer cells under normoxic conditions. This effect was reverted by exogenous expression of wild-type <i>VHL</i>. We showed that global genome hypermethylation in <i>VHL</i> mutants can be explained by transcriptional changes in <i>MDH</i> and <i>L2HGDH</i> genes that cause the accumulation of 2-hydroxyglutarate – a metabolite that inhibits DNA demethylation by TET enzymes. Unlike the known cases of DNA hypermethylation in cancer, 2-hydroxyglutarate was accumulated in the cells with the wild-type isocitrate dehydrogenases.
DOI: 10.6084/m9.figshare.16586271.v1
title: An IDH-independent mechanism of DNA hypermethylation upon VHL inactivation in cancer

description: Hypermethylation of tumour suppressors and other aberrations of DNA methylation in tumours play a significant role in cancer progression. DNA methylation can be affected by various environmental conditions, including hypoxia. The response to hypoxia is mainly achieved through activation of the transcriptional program associated with HIF1A transcription factor. Inactivation of Von Hippel-Lindau Tumour Suppressor gene (<i>VHL</i>) by genetic or epigenetic events, which also induces aberrant activation of HIF1A, is the most common driver event for renal cancer. With whole-genome bisulphite sequencing and LC-MS, we demonstrated that <i>VHL</i> inactivation induced global genome hypermethylation in human kidney cancer cells under normoxic conditions. This effect was reverted by exogenous expression of wild-type <i>VHL</i>. We showed that global genome hypermethylation in <i>VHL</i> mutants can be explained by transcriptional changes in <i>MDH</i> and <i>L2HGDH</i> genes that cause the accumulation of 2-hydroxyglutarate – a metabolite that inhibits DNA demethylation by TET enzymes. Unlike the known cases of DNA hypermethylation in cancer, 2-hydroxyglutarate was accumulated in the cells with the wild-type isocitrate dehydrogenases.
DOI: 10.6084/m9.figshare.15832008.v3
title: Disease-related blood-based differential methylation in cystic fibrosis and its representation in lung cancer revealed a regulatory locus in <i>PKP3</i> in lung epithelial cells

description: Cystic fibrosis (CF) is a monogenic disease, characterized by massive chronic lung inflammation. The observed variability in clinical phenotypes in monozygotic CF twins is likely associated with the extent of inflammation. This study sought to investigate inflammation-related aberrant DNA methylation in CF twins and to determine to what extent acquired methylation changes may be associated with lung cancer. Blood-based genome-wide DNA methylation analysis was performed to compare the DNA methylomes of monozygotic twins, from the European CF Twin and Sibling Study with various degrees of disease severity. Putatively inflammation-related and differentially methylated positions were selected from a large lung cancer case-control study and investigated in blood by targeted bisulphite next-generation-sequencing. An inflammation-related locus located in the <i>Plakophilin-3</i> (<i>PKP3</i>) gene was functionally analysed regarding promoter and enhancer activity in presence and absence of methylation using luciferase reporter assays. We confirmed in a unique cohort that monozygotic twins, even if clinically discordant, have only minor differences in global DNA methylation patterns and blood cell composition. Further, we determined the most differentially methylated positions, a high proportion of which are blood cell-type-specific, whereas others may be acquired and thus have potential relevance in the context of inflammation as lung cancer risk factors. We identified a sequence in the gene body of <i>PKP3</i> which is hypermethylated in blood from CF twins with severe phenotype and highly variably methylated in lung cancer patients and controls, independent of known clinical parameters, and showed that this region exhibits methylation-dependent promoter activity in lung epithelial cells.
DOI: 10.6084/m9.figshare.19316702
title: Ultra-deep whole genome bisulfite sequencing reveals a single methylation hotspot in human brain mitochondrial DNA

description: While DNA methylation is established as a major regulator of gene expression in the nucleus, the existence of mitochondrial DNA (mtDNA) methylation remains controversial. Here, we characterized the mtDNA methylation landscape in the prefrontal cortex of neurological healthy individuals (<i>n</i>=26) and patients with Parkinson’s disease (<i>n</i>=27), using a combination of whole-genome bisulphite sequencing (WGBS) and bisulphite-independent methods. Accurate mtDNA mapping from WGBS data required alignment to an mtDNA reference only, to avoid misalignment to nuclear mitochondrial pseudogenes. Once correctly aligned, WGBS data provided ultra-deep mtDNA coverage (16,723 ± 7,711) and revealed overall very low levels of cytosine methylation. The highest methylation levels (5.49 ± 0.97%) were found on CpG position m.545, located in the heavy-strand promoter 1 region. The m.545 methylation was validated using a combination of methylation-sensitive DNA digestion and quantitative PCR analysis. We detected no association between mtDNA methylation profile and Parkinson’s disease. Interestingly, m.545 methylation correlated with the levels of mtDNA transcripts, suggesting a putative role in regulating mtDNA gene expression. In addition, we propose a robust framework for methylation analysis of mtDNA from WGBS data, which is less prone to false-positive findings due to misalignment of nuclear mitochondrial pseudogene sequences.
DOI: 10.6084/m9.figshare.19316702.v1
title: Ultra-deep whole genome bisulfite sequencing reveals a single methylation hotspot in human brain mitochondrial DNA

description: While DNA methylation is established as a major regulator of gene expression in the nucleus, the existence of mitochondrial DNA (mtDNA) methylation remains controversial. Here, we characterized the mtDNA methylation landscape in the prefrontal cortex of neurological healthy individuals (<i>n</i>=26) and patients with Parkinson’s disease (<i>n</i>=27), using a combination of whole-genome bisulphite sequencing (WGBS) and bisulphite-independent methods. Accurate mtDNA mapping from WGBS data required alignment to an mtDNA reference only, to avoid misalignment to nuclear mitochondrial pseudogenes. Once correctly aligned, WGBS data provided ultra-deep mtDNA coverage (16,723 ± 7,711) and revealed overall very low levels of cytosine methylation. The highest methylation levels (5.49 ± 0.97%) were found on CpG position m.545, located in the heavy-strand promoter 1 region. The m.545 methylation was validated using a combination of methylation-sensitive DNA digestion and quantitative PCR analysis. We detected no association between mtDNA methylation profile and Parkinson’s disease. Interestingly, m.545 methylation correlated with the levels of mtDNA transcripts, suggesting a putative role in regulating mtDNA gene expression. In addition, we propose a robust framework for methylation analysis of mtDNA from WGBS data, which is less prone to false-positive findings due to misalignment of nuclear mitochondrial pseudogene sequences.