cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.13650863
title: metadata.zip

description: This folder contains the associated metadata for running the data analysis to explore tissue dependent associations in PSC-IBD:<br>metadata_microbiome_filtered.tsv - metadata for microbiome data after filtering out poor quality samples <br>metadata_rnaseq.tsv - metadata for RNA-seq analysis after filtering out poor quality samples<br>metadata_microbiome.tsv - metadata for microbiome analysis metadata_unfiltered_rnaseq.tsv - metadata for RNA-seq analysis before any filtering of samples<br><br><br><br>
DOI: 10.6084/m9.figshare.13650863.v2
title: metadata.zip

description: This folder contains the associated metadata for running the data analysis to explore tissue dependent associations in PSC-IBD:<br>metadata_microbiome_filtered.tsv - metadata for microbiome data after filtering out poor quality samples <br>metadata_rnaseq.tsv - metadata for RNA-seq analysis after filtering out poor quality samples<br>metadata_microbiome.tsv - metadata for microbiome analysis metadata_unfiltered_rnaseq.tsv - metadata for RNA-seq analysis before any filtering of samples<br><br><br><br>
DOI: 10.6084/m9.figshare.13650863.v1
title: metadata.zip

description: This folder contains the associated metadata for running the data analysis to explore tissue dependent associations in PSC-IBD:<br>metadata_microbiome_filtered.tsv - metadata for microbiome data after filtering out poor quality samples <br>metadata_rnaseq.tsv - metadata for RNA-seq analysis after filtering out poor quality samples<br>metadata_microbiome.tsv - metadata for microbiome analysis metadata_unfiltered_rnaseq.tsv - metadata for RNA-seq analysis before any filtering of samples<br><br><br><br>
DOI: 10.6084/m9.figshare.13655915
title: counts.zip

description: This folder contains the processed data i.e. counts tables for ensembl genes in the RNA-seq analysis and the genus counts for the microbiome data:<br>genes.tsv.gz - ensembl gene countsclass_abundance.tsv - class level taxon counts<br>genus_abundance.tsv - genus level taxon counts<br>phylum_abundance.tsv - phylum level taxon counts<br>family_abundance.tsv - family level taxon counts<br>GSE125970_raw_UMIcounts.txt - scRNA-seq data from intestinal eputhelium with accession number as in the filename<br>species_abundance.tsv - species level taxon counts<br>order_abundance.tsv - order level taxon counts taxa_abundances.tsv - amplicon sequence variant (ASV) level counts<br><br><br>
DOI: 10.6084/m9.figshare.13655915.v2
title: counts.zip

description: This folder contains the processed data i.e. counts tables for ensembl genes in the RNA-seq analysis and the genus counts for the microbiome data:<br>genes.tsv.gz - ensembl gene countsclass_abundance.tsv - class level taxon counts<br>genus_abundance.tsv - genus level taxon counts<br>phylum_abundance.tsv - phylum level taxon counts<br>family_abundance.tsv - family level taxon counts<br>GSE125970_raw_UMIcounts.txt - scRNA-seq data from intestinal eputhelium with accession number as in the filename<br>species_abundance.tsv - species level taxon counts<br>order_abundance.tsv - order level taxon counts taxa_abundances.tsv - amplicon sequence variant (ASV) level counts<br><br><br>
DOI: 10.6084/m9.figshare.13655915.v1
title: counts.zip

description: This folder contains the processed data i.e. counts tables for ensembl genes in the RNA-seq analysis and the genus counts for the microbiome data:<br>genes.tsv.gz - ensembl gene countsclass_abundance.tsv - class level taxon counts<br>genus_abundance.tsv - genus level taxon counts<br>phylum_abundance.tsv - phylum level taxon counts<br>family_abundance.tsv - family level taxon counts<br>GSE125970_raw_UMIcounts.txt - scRNA-seq data from intestinal eputhelium with accession number as in the filename<br>species_abundance.tsv - species level taxon counts<br>order_abundance.tsv - order level taxon counts taxa_abundances.tsv - amplicon sequence variant (ASV) level counts<br><br><br>
DOI: 10.6084/m9.figshare.13651250
title: annotations.zip

description: This folder contains data required to re-run the data analysis. It is annotations data that includes:<br>c2.cp.reactome.v6.1.symbols.tsv - reactome pathways (MSigDB) <br>gene_id2gene_name - Ensembl gene id to gene name mapping<br>c3.tft.v6.1.symbols.tsv - transcription factor gene sets (MSigDB)<br>geneset_all.gtf.gz - Ensembl hg38 build 91 gtf annotation<br>c5.bp.v6.1.symbols.tsv - GO biological pathway genesets (MSigDB)<br>teichmann_fractions.txt - Cell fractions estimated usig scRNAseq from https://www.gutcellatlas.org/<br>
DOI: 10.6084/m9.figshare.13651250.v1
title: annotations.zip

description: This folder contains data required to re-run the data analysis. It is annotations data that includes:<br>c2.cp.reactome.v6.1.symbols.tsv - reactome pathways (MSigDB) <br>gene_id2gene_name - Ensembl gene id to gene name mapping<br>c3.tft.v6.1.symbols.tsv - transcription factor gene sets (MSigDB)<br>geneset_all.gtf.gz - Ensembl hg38 build 91 gtf annotation<br>c5.bp.v6.1.symbols.tsv - GO biological pathway genesets (MSigDB)<br>teichmann_fractions.txt - Cell fractions estimated usig scRNAseq from https://www.gutcellatlas.org/<br>
DOI: 10.6084/m9.figshare.14546283
title: Supplementary Material for: Impact of Sleep Duration on Mortality and Quality of Life in Chronic Kidney Disease: Results from the 2007–2015 KNHANES

description: <b><i>Introduction:</i></b> In the general population, short and long sleep durations have been associated with adverse health outcomes. However, this association remains unclear in patients with chronic kidney disease (CKD). We examined the relationship of sleep duration to mortality and health-related quality of life (HRQOL) in individuals with CKD. <b><i>Methods:</i></b> A total of 1,783 adults with CKD who participated in the 2007–2015 Korea National Health and Nutrition Examination Survey were analyzed. CKD was defined as an estimated glomerular filtration rate of &lt;60 mL/min per 1.73 m<sup>2</sup>. Participants were categorized into 3 groups according to self-reported sleep duration: &lt;6 h (short sleepers), 6–8 h, and &gt;8 h (long sleepers). The outcome variables were all-cause mortality and HRQOL. HRQOL was assessed using the European Quality of Life-5 Dimensions (EQ-5D) index. <b><i>Results:</i></b> During a median of 6.4 years, 481 (27%) deaths occurred. In unadjusted Cox regression analysis, long sleepers with CKD had an increased risk of death (hazard ratio [HR], 1.62; 95% confidence interval [CI]: 1.26–2.09). This significant association remained after adjusting for age, sex, and BMI (HR, 1.36; 95% CI: 1.05–1.75); however, it was lost after adjusting for CKD stage, social and lifestyle factors, and presence of comorbidities (HR, 1.15; 95% CI: 0.89–1.49). Compared with 6- to 8-h sleepers with CKD, long sleepers with CKD had significantly worse HRQOL in multivariable linear regression models. The adjusted means of the EQ-5D index were 0.80 (95% CI: 0.77–0.82) for short sleepers, 0.81 (95% CI: 0.80–0.82) for 6- to 8-h sleepers, and 0.76 (95% CI: 0.73–0.79) for long sleepers (<i>p</i> = 0.01). <b><i>Discussion/Conclusion:</i></b> Long sleep duration is associated with poor HRQOL in Korean adults with CKD. The weak association between long sleep duration and mortality was attenuated after multivariable adjustment in this study.
DOI: 10.6084/m9.figshare.14546301
title: China’s monthly SO2 emissions during COVID-19 in 2020

description: China’s monthly SO2 emissions by source sector and by province
DOI: 10.6084/m9.figshare.14546316
title: China’s monthly NOx emissions during COVID-19 in 2020

description: China’s monthly NOx emissions by source sector and by province
DOI: 10.6084/m9.figshare.14546319
title: China’s monthly CO emissions during COVID-19 in 2020

description: China’s monthly CO emissions by source sector and by province
DOI: 10.34740/kaggle/dsv/2200202
title: Molecular modelling
DOI: 10.34740/kaggle/dsv/2200203
title: Molecular modelling
DOI: 10.5255/ukda-sn-854716
title: Supporting and Engaging Schools in Decision-Making and Multi-Agency Working for the Protection of Children, 2017-2019

description: To investigate the engagement of schools in decision-making and multi-agency working in relation to child protection four data sets were collected during three phases of the research. The first data set is 17 transcripts taken from 'scoping' interviews with local authority education and children's social care staff. The findings of these interviews were used to inform the second phase of data collection involving national surveys of: (a) local authority education safeguarding leads; (b) children's social care leads; and (c) Local Safeguarding Children Boards (LSCBs). This is the second data set. The third phase of the project involved interviews with key staff involved in safeguarding and child protection work in 50 schools spread across 5 local authority areas. Staff were also asked to complete the Organisational Social Context questionnaire. The interview transcripts and questionnaire results from these case studies are included here as the third and forth data sets.
DOI: 10.5517/ccdc.csd.cc23p6vw
title: CCDC 1956808: Experimental Crystal Structure Determination

description: Related Article: Yu Shang, Rui-Kang Huang, Shao-Li Chen, Chun-Ting He, Zhi-Hong Yu, Zi-Ming Ye, Wei-Xiong Zhang, Xiao-Ming Chen|2020|Cryst.Growth Des.|20|1891|doi:10.1021/acs.cgd.9b01592
DOI: 10.5517/ccdc.csd.cc23wd3j
title: CCDC 1962737: Experimental Crystal Structure Determination

description: Related Article: Yi Han, Zibo Xue, Guangwu Li, Yanwei Gu, Yong Ni, Shaoqiang Dong, Chunyan Chi|2020|Angew.Chem.,Int.Ed.|59|9026|doi:10.1002/anie.201915327
DOI: 10.6084/m9.figshare.14546331
title: China’s monthly NMVOCs emissions during COVID-19 in 2020

description: China’s monthly NMVOCs emissions by source sector and by province
DOI: 10.5517/ccdc.csd.cc1zk1sc
title: CCDC 1833643: Experimental Crystal Structure Determination

description: Related Article: Wei-Peng Chen,  Pei-Qin Liao,  Peng-Bo Jin,  Lei Zhang,  Bo-Kai Ling,  Shi-Cheng Wang,  Yi-Tsu Chan,  Xiao-Ming Chen,  Yan-Zhen Zheng|2020|J.Am.Chem.Soc.|142|4663|doi:10.1021/jacs.9b11543
DOI: 10.6084/m9.figshare.14546331.v1
title: China’s monthly NMVOCs emissions during COVID-19 in 2020

description: China’s monthly NMVOCs emissions by source sector and by province
DOI: 10.5517/ccdc.csd.cc271vnt
title: CCDC 2057366: Experimental Crystal Structure Determination

description: Related Article: Takashi Kurogi, Kazuhiko Takai|2021|CSD Communication|||
DOI: 10.5517/ccdc.csd.cc271w8g
title: CCDC 2057385: Experimental Crystal Structure Determination

description: Related Article: xulong qin|2021|CSD Communication|||
DOI: 10.5517/ccdc.csd.cc271xv2
title: CCDC 2057434: Experimental Crystal Structure Determination

description: Related Article: Thomas Fellowes, Angela Qin, Jackson Smith|2021|CSD Communication|||
DOI: 10.6084/m9.figshare.14546340
title: China’s monthly PM2.5 emissions during COVID-19 in 2020

description: China’s monthly PM2.5 emissions by source sector and by province
DOI: 10.34740/kaggle/dsv/2071483
title: Used Mercedes Vehicle Features in Turkey Market
DOI: 10.6084/m9.figshare.14546346
title: China’s monthly BC emissions during COVID-19 in 2020

description: China’s monthly BC emissions by source sector and by province
DOI: 10.15161/oar.it/73768
title: CovidStat project data

description: This record contains the daily updated data of the CovidStat project. CovidStat is a project carried out by the CovidStat Working Group at INFN, whose creation was promoted within the Italian National Institute of Nuclear Physics with the aim of making a statistical analysis of the data provided daily by the Civil Protection on the spread of the pandemic in Italy. CovidStat data can interactively be browsed at https://covid19.infn.it.
description: The software to process this Root TTree is in the related identifier. Be sure to use the right corresponding version, based on the data in which Root TTree was generated.
DOI: 10.17638/datacat.liverpool.ac.uk/1047
title: Discovery of a low thermal conductivity oxide guided by probe structure prediction and machine learning

description: See Readme file.
DOI: 10.11583/dtu.14541297
title: Turbulence measurements from the Tarifa mast

description: This dataset consists of raw time series and 10-minute statistics of wind speed and wind direction measurements from two 40m mast in the Tarifa area, Spain. The period includes more than 280 hours of turbulence measurements during spring 1997.<br>Detailed site documentation is available here.<br><br><br><b>Public data</b><br><br><b>Run statistics </b>stored as NetCDF format1) tarifa_all.nc2) tarifa_concurrent.nc<br><b>Raw time series</b> (ascii), each with a duration of 600 sec, sampled with 4 Hz.:3) Cabauw.zip<br>
DOI: 10.5519/qd.2j634mky
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (4777632 records)
DOI: 10.5445/ir/1000131913
title: IMK/IAA MIPAS temperature retrieval version 8: nominal measurements

description: The data set comprises temperature data of the Earth's middle atmosphere region for the years 2002-2012 as rerieved from the nominal mode mid infrared spectra measurements collected by the MIPAS instrument on board of the Envisat satellite. The data version is V8.
DOI: 10.6084/m9.figshare.14546271
title: Ketoreductase sequences and alignment

description: Ketoreductase amino acid sequences and Muscle alignment associated with Fazal et al. 2021. ACS Chem Biol, submitted.
DOI: 10.5281/zenodo.4297322
title: Studied disinfectant substances against SARS-CoV-2 and other coronaviruses

description: This data-sheet covers those disinfectants tested against SARS-CoV-2 or other coronaviruses. Data were extracted from several research articles indicated in the reference row. The data-sheet comprises a total of 11 fields with info regarding the virus (virus and strain/isolate names), formulation (substance(s) and its concentration in percentage) and test characteristics (suspension or surface tested, kind of surface, use dilution before testing, disinfectant and inoculum volumes, organic load type and concentrations and contact time) as well as their results, normalized in terms of Log<sub>10 </sub>viral infectivity reduction. Data is included and comented in the following journal article: https://doi.org/10.3390/foods10020283 Please reference also to this publication if using the data-sheet.
description: This research was funded by RTI2018-093560-J-I00 (MCIU/AEI/FEDER, UE) and IN606A-2020/028 (Xunta de Galicia predoctoral grant)
DOI: 10.5281/zenodo.4297015
title: Studied disinfectant substances against SARS-CoV-2 and other coronaviruses

description: This data-sheet covers those disinfectants tested against SARS-CoV-2 or other coronaviruses. Data were extracted from several research articles indicated in the reference row. The data-sheet comprises a total of 11 fields with info regarding the virus (virus and strain/isolate names), formulation (substance(s) and its concentration in percentage) and test characteristics (suspension or surface tested, kind of surface, use dilution before testing, disinfectant and inoculum volumes, organic load type and concentrations and contact time) as well as their results, normalized in terms of Log<sub>10 </sub>viral infectivity reduction. Data is included and comented in the following journal article: https://doi.org/10.3390/foods10020283 Please reference also to this publication if using the data-sheet.
description: This research was funded by RTI2018-093560-J-I00 (MCIU/AEI/FEDER, UE) and IN606A-2020/028 (Xunta de Galicia predoctoral grant)
DOI: 10.5255/ukda-sn-854550
title: Formation of the Action Research Collective, 2016-2020

description: This deposit contains 29 documents. This includes two documents used to promote the Jam and Justice project and generate initial interest in joining the Action Research Collective (ARC). The second bundle of documents are those relating to the formation of the ARC. The project methodology aimed to bring together academic and non-academic researchers – with different knowledge, skills and resources interested in making devolution matter in Greater Manchester – to test and learn about the theory and practice of co-production in research. This selected group would be known as the ARC whose primary role was to initiate, develop and undertake comparative learning from action research projects. Documents deposited are the ARC application form, the marking criteria used by the Principle Investigators to select ARC members, profile information sheet for ARC members and the consent form for ARC members to participate. The ARC members Co-designed 10 social experiment projects and all of the final project reports from these and the Jam and Justice final report are included. The power point presentation slides used at the final report launch in July 2019 are also deposited. A number of administrative documents are deposited, namely the agreement of services for individual ARC projects and payment approval sign off records used to ensure projects were on track and meeting milestones. Finally, there is a document that details all of the short project videos generated with links to view them online.
DOI: 10.6084/m9.figshare.8293439
title: A two-step probing method to compare lysine accessibility across macromolecular complex conformations

description: Structural models of large and dynamic molecular complexes are appearing in increasing numbers, in large part because of recent technical advances in cryo-electron microscopy. However, the inherent complexity of such biological assemblies comprising dozens of moving parts often limits the resolution of structural models and leaves the puzzle as to how each functional configuration transitions to the next. Orthogonal biochemical information is crucial to understanding the molecular interactions that drive those rearrangements. We present a two-step method for chemical probing detected by tandem mass-spectrometry to globally assess the reactivity of lysine residues within purified macromolecular complexes. Because lysine side chains often balance the negative charge of RNA in ribonucleoprotein complexes, the method is especially useful for detecting changes in protein-RNA interactions. By probing the <i>E. coli</i> 30S ribosome subunit, we established that the reactivity pattern of lysine residues quantitatively reflects structure models derived from X-ray crystallography. We also used the strategy to assess differences in three conformations of purified human spliceosomes in the context of recent cryo-electron microscopy models. Our results demonstrate that the probing method yields powerful biochemical information that helps contextualize architectural rearrangements of intermediate resolution structures of macromolecular complexes, often solved in multiple conformations.
DOI: 10.6084/m9.figshare.8293439.v3
title: A two-step probing method to compare lysine accessibility across macromolecular complex conformations

description: Structural models of large and dynamic molecular complexes are appearing in increasing numbers, in large part because of recent technical advances in cryo-electron microscopy. However, the inherent complexity of such biological assemblies comprising dozens of moving parts often limits the resolution of structural models and leaves the puzzle as to how each functional configuration transitions to the next. Orthogonal biochemical information is crucial to understanding the molecular interactions that drive those rearrangements. We present a two-step method for chemical probing detected by tandem mass-spectrometry to globally assess the reactivity of lysine residues within purified macromolecular complexes. Because lysine side chains often balance the negative charge of RNA in ribonucleoprotein complexes, the method is especially useful for detecting changes in protein-RNA interactions. By probing the <i>E. coli</i> 30S ribosome subunit, we established that the reactivity pattern of lysine residues quantitatively reflects structure models derived from X-ray crystallography. We also used the strategy to assess differences in three conformations of purified human spliceosomes in the context of recent cryo-electron microscopy models. Our results demonstrate that the probing method yields powerful biochemical information that helps contextualize architectural rearrangements of intermediate resolution structures of macromolecular complexes, often solved in multiple conformations.
DOI: 10.6084/m9.figshare.8343428
title: Low level of exosomal long non-coding RNA <i>HOTTIP</i> is a prognostic biomarker in colorectal cancer

description: Molecular risk stratification of colorectal cancer can improve patient outcome. A panel of lncRNAs (<i>H19, HOTTIP, HULC</i> and <i>MALAT1</i>) derived from serum exosomes of patients with non-metastatic CRC and healthy donors was analyzed. Exosomes from healthy donors carried significantly more <i>H19, HULC</i> and <i>HOTTIP</i> transcripts in comparison to CRC patients. Correlation analysis between lncRNAs and clinical data revealed a statistical significance between low levels of exosomal <i>HOTTIP</i> and poor overall survival. This was confirmed by multivariate analysis that <i>HOTTIP</i> is an independent prognostic marker for overall survival (HR: 4.5, CI: 1.69–11.98, p = 0.0027). Here, <i>HOTTIP</i> poses to be a valid biomarker for patients with a CRC to predict post-surgical survival time.
DOI: 10.6084/m9.figshare.8792606
title: Multiple origins of reverse transcriptases linked to CRISPR-Cas systems

description: Prokaryotic genomes harbour a plethora of uncharacterized reverse transcriptases (RTs). RTs phylogenetically related to those encoded by group-II introns have been found associated with type III CRISPR-Cas systems, adjacent or fused at the C-terminus to Cas1. It is thought that these RTs may have a relevant function in the CRISPR immune response mediating spacer acquisition from RNA molecules. The origin and relationships of these RTs and the ways in which the various protein domains evolved remain matters of debate. We carried out a large survey of annotated RTs in databases (198,760 sequences) and constructed a large dataset of unique representative sequences (9,141). The combined phylogenetic reconstruction and identification of the RTs and their various protein domains in the vicinity of CRISPR adaptation and effector modules revealed three different origins for these RTs, consistent with their emergence on multiple occasions: a larger group that have evolved from group-II intron RTs, and two minor lineages that may have arisen more recently from Retron/retron-like sequences and Abi-P2 RTs, the latter associated with type I-C systems. We also identified a particular group of RTs associated with CRISPR-<i>cas</i> loci in clade 12, fused C-terminally to an archaeo-eukaryotic primase (AEP), a protein domain (AE-Prim_S_like) forming a particular family within the AEP proper clade. Together, these data provide new insight into the evolution of CRISPR-Cas/RT systems.