cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5517/ccdc.csd.cc29clgr
title: CCDC 2126304: Experimental Crystal Structure Determination

description: Related Article: Xi-Li Li, Ailing Wang, Minghui Cui, Congli Gao, Xiaojing Yu, Bing Su, Liming Zhou, Cai-Ming Liu, Hong-Ping Xiao, Yi-Quan Zhang|2022|Inorg.Chem.|61|9283|doi:10.1021/acs.inorgchem.2c01031
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.cc2bbdwz
title: CCDC 2154961: Experimental Crystal Structure Determination

description: Related Article: Lucía Mato-López, Antía Sar-Rañó, Miguel Riopedre Fernández, María Luz Díaz-Prado, Adrià Gil, Ángel Sánchez-González, Natalia Fernández-Bertólez, Josefina Méndez, Vanessa Valdiglesias, Fernando Avecilla|2022|J.Inorg.Biochem.|235|111937|doi:10.1016/j.jinorgbio.2022.111937
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.cc2bbdx0
title: CCDC 2154962: Experimental Crystal Structure Determination

description: Related Article: Lucía Mato-López, Antía Sar-Rañó, Miguel Riopedre Fernández, María Luz Díaz-Prado, Adrià Gil, Ángel Sánchez-González, Natalia Fernández-Bertólez, Josefina Méndez, Vanessa Valdiglesias, Fernando Avecilla|2022|J.Inorg.Biochem.|235|111937|doi:10.1016/j.jinorgbio.2022.111937
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.cc2bmx2z
title: CCDC 2164081: Experimental Crystal Structure Determination

description: Related Article: Arun K. Ghosh, John P. Gulliver|2022|Tetrahedron Lett.|102|153954|doi:10.1016/j.tetlet.2022.153954
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.cc2bsr41
title: CCDC 2168733: Experimental Crystal Structure Determination

description: Related Article: Jun Ni, Wei-Jie Qi, Shu-Qin Liu, Jian-Jun Zhang|2022|Dyes Pigm.|205|110567|doi:10.1016/j.dyepig.2022.110567
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.cc2bsr52
title: CCDC 2168734: Experimental Crystal Structure Determination

description: Related Article: Jun Ni, Wei-Jie Qi, Shu-Qin Liu, Jian-Jun Zhang|2022|Dyes Pigm.|205|110567|doi:10.1016/j.dyepig.2022.110567
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: 10.17045/sthlmuni.19174268.v1
title: Factors_Affecting_Notetaking_Data

description: This data set includes survey data related to factors affecting notetaking provided by students in five countries. The data set includes responses to the survey item: What factors affect your ability to take notes? Students were allowed to choose multiple options from a list provided. This data set is presented by country. A paper utilizing this data has been accepted for publication in the International Journal of Listening and is currently being revised. Once published, the doi will be provided.
DOI: 10.25403/upresearchdata.20318076
title: Assessments of children's reading difficulties

description: The data used in this qualitative research study is secondary data from the client files of the children who were assessed at the training facility of an institution of higher learning. Deductive content analysis was used to analyse the data which consist of all the sections that were used for analysis from the client reports.These sections include the observations of the assessors when standardised reading assessments and dynamic assessment of reading was conducted. They demonstrate the value of dynamic assessment in providing additional information of a child's reading ability, in comparison to the information gained from using standardised assessments only. Pseudonyms were used in order to protect the identities and maintain confidentiality of the children whose reading assessments were analysed.
DOI: 10.25403/upresearchdata.20318076.v1
title: Assessments of children's reading difficulties

description: The data used in this qualitative research study is secondary data from the client files of the children who were assessed at the training facility of an institution of higher learning. Deductive content analysis was used to analyse the data which consist of all the sections that were used for analysis from the client reports.These sections include the observations of the assessors when standardised reading assessments and dynamic assessment of reading was conducted. They demonstrate the value of dynamic assessment in providing additional information of a child's reading ability, in comparison to the information gained from using standardised assessments only. Pseudonyms were used in order to protect the identities and maintain confidentiality of the children whose reading assessments were analysed.
DOI: 10.17045/sthlmuni.19174268
title: Factors_Affecting_Notetaking_Data

description: This data set includes survey data related to factors affecting notetaking provided by students in five countries. The data set includes responses to the survey item: What factors affect your ability to take notes? Students were allowed to choose multiple options from a list provided. This data set is presented by country. A paper utilizing this data has been published in the International Journal of Listening and is available for open access at: https://www.tandfonline.com/doi/full/10.1080/10904018.2022.2059484
DOI: 10.17045/sthlmuni.19174268.v3
title: Factors_Affecting_Notetaking_Data

description: This data set includes survey data related to factors affecting notetaking provided by students in five countries. The data set includes responses to the survey item: What factors affect your ability to take notes? Students were allowed to choose multiple options from a list provided. This data set is presented by country. A paper utilizing this data has been published in the International Journal of Listening and is available for open access at: https://www.tandfonline.com/doi/full/10.1080/10904018.2022.2059484
DOI: 10.17045/sthlmuni.19174268.v2
title: Factors_Affecting_Notetaking_Data

description: This data set includes survey data related to factors affecting notetaking provided by students in five countries. The data set includes responses to the survey item: What factors affect your ability to take notes? Students were allowed to choose multiple options from a list provided. This data set is presented by country. A paper utilizing this data has been published in the International Journal of Listening and is available for open access at: https://www.tandfonline.com/doi/full/10.1080/10904018.2022.2059484
DOI: 10.5281/zenodo.5643551
title: Summary Statistics from "Meta-GWAS of PCSK9 levels detects two novel loci at APOB and TM6SF2"

description: GWAMA summary statistics of PCSK9 levels using fixed-effect model. Genome-wide data is given for Europeans with statin adjustment and Europeans without statin treatment only (subset of the population). In addition, locus-wide data of the PCSK9 gene locus for African-Americans without statin treatment is listed. When using this data, please cite: Pott J, Gadin J, Theusch E, et al.. Meta-GWAS of PCSK9 levels detects two novel loci at APOB and TM6SF2. Hum Mol Genet. 2021 Sep 30:ddab279. doi: 10.1093/hmg/ddab279. PMID: 34590679 All txt files contain the following columns: markername chr bp_hg19 (base position according to hg19) ea (effect allele) oa (other allele) eaf (effect allele frequency) info (minimal info score across all used studies) nSamples (sample size per SNP) nStudies (number of studies) beta (effect estimate) se (standard error) p (p-value) I2 (SNP heterogeneity across studies) phenotype (phenotyp setting)
description: {"references": ["Pott J, Gadin J, Theusch E, Kleber ME, Delgado GE, Kirsten H, Hauck SM, Burkhardt R, Scharnagl H, Krauss RM, Loeffler M, M\u00e4rz W, Thiery J, Silveira A, Vant Hooft FM, Scholz M. Meta-GWAS of PCSK9 levels detects two novel loci at APOB and TM6SF2. Hum Mol Genet. 2021 Sep 30:ddab279. doi: 10.1093/hmg/ddab279"]}
DOI: 10.6084/m9.figshare.14754195
title: Synergistic roles for human U1 snRNA stem-loops in pre-mRNA splicing

description: During spliceosome assembly, interactions that bring the 5′ and 3′ ends of an intron in proximity are critical for the production of mature mRNA. Here, we report synergistic roles for the stem-loops 3 (SL3) and 4 (SL4) of the human U1 small nuclear RNA (snRNA) in maintaining the optimal U1 snRNP function, and formation of cross-intron contact with the U2 snRNP. We find that SL3 and SL4 bind distinct spliceosomal proteins and combining a U1 snRNA activity assay with siRNA-mediated knockdown, we demonstrate that SL3 and SL4 act through the RNA helicase UAP56 and the U2 protein SF3A1, respectively. <i>In vitro</i> analysis using UV crosslinking and splicing assays indicated that SL3 likely promotes the SL4-SF3A1 interaction leading to enhancement of A complex formation and pre-mRNA splicing. Overall, these results highlight the vital role of the distinct contacts of SL3 and SL4 in bridging the pre-mRNA bound U1 and U2 snRNPs during the early steps of human spliceosome assembly.
DOI: 10.6084/m9.figshare.14754195.v1
title: Synergistic roles for human U1 snRNA stem-loops in pre-mRNA splicing

description: During spliceosome assembly, interactions that bring the 5′ and 3′ ends of an intron in proximity are critical for the production of mature mRNA. Here, we report synergistic roles for the stem-loops 3 (SL3) and 4 (SL4) of the human U1 small nuclear RNA (snRNA) in maintaining the optimal U1 snRNP function, and formation of cross-intron contact with the U2 snRNP. We find that SL3 and SL4 bind distinct spliceosomal proteins and combining a U1 snRNA activity assay with siRNA-mediated knockdown, we demonstrate that SL3 and SL4 act through the RNA helicase UAP56 and the U2 protein SF3A1, respectively. <i>In vitro</i> analysis using UV crosslinking and splicing assays indicated that SL3 likely promotes the SL4-SF3A1 interaction leading to enhancement of A complex formation and pre-mRNA splicing. Overall, these results highlight the vital role of the distinct contacts of SL3 and SL4 in bridging the pre-mRNA bound U1 and U2 snRNPs during the early steps of human spliceosome assembly.
DOI: 10.6084/m9.figshare.14587077
title: Bisulphite miRNA-seq reveals widespread CpG and non-CpG 5-(hydroxy)methyl-Cytosine in human microRNAs

description: In the last decade, the field of epitranscriptomics highlighted a wide array of post-transcriptional modifications in human RNAs, including microRNAs (miRNAs). Recent reports showed that human miRNAs undergo cytosine methylation. We describe the first high-throughput NGS-based method (BS-miRNA-seq) and an analysis pipeline (MAmBA) to attain high-resolution mapping of (hydroxy)-methyl-5-cytosine ((h)m5C) modifications in human miRNAs. Our method uncovers that miRNAs undergo widespread cytosine modification in various sequence contexts. Furthermore, validation of our data with specific antibodies reveals both m5C and hm5C residues in human mature miRNAs. BS-miRNA-seq and MAmBA may contribute to the precise mapping of (h)m5C on miRNAs in various cell types and tissues, a key achievement towards the understanding of the functional implications of this modification in miRNAs. MAmBA is available for download at https://github.com/flcvlr/MAmBA
DOI: 10.6084/m9.figshare.14560724.v1
title: A DNA intercalating dye-based RT-qPCR alternative to diagnose SARS-CoV-2

description: Early detection of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been proven crucial during the efforts to mitigate the effects of the COVID-19 pandemic. Several diagnostic methods have emerged in the past few months, each with different shortcomings and limitations. The current gold standard, RT-qPCR using fluorescent probes, relies on demanding equipment requirements plus the high costs of the probes and specific reaction mixes. To broaden the possibilities of reagents and thermocyclers that could be allocated towards this task, we have optimized an alternative strategy for RT-qPCR diagnosis. This is based on a widely used DNA-intercalating dye and can be implemented with several different qPCR reagents and instruments. Remarkably, the proposed qPCR method performs similarly to the broadly used TaqMan-based detection, in terms of specificity and sensitivity, thus representing a reliable tool. We think that, through enabling the use of vast range of thermocycler models and laboratory facilities for SARS-CoV-2 diagnosis, the alternative proposed here can increase dramatically the testing capability, especially in countries with limited access to costly technology and reagents.
DOI: 10.6084/m9.figshare.14560724
title: A DNA intercalating dye-based RT-qPCR alternative to diagnose SARS-CoV-2

description: Early detection of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been proven crucial during the efforts to mitigate the effects of the COVID-19 pandemic. Several diagnostic methods have emerged in the past few months, each with different shortcomings and limitations. The current gold standard, RT-qPCR using fluorescent probes, relies on demanding equipment requirements plus the high costs of the probes and specific reaction mixes. To broaden the possibilities of reagents and thermocyclers that could be allocated towards this task, we have optimized an alternative strategy for RT-qPCR diagnosis. This is based on a widely used DNA-intercalating dye and can be implemented with several different qPCR reagents and instruments. Remarkably, the proposed qPCR method performs similarly to the broadly used TaqMan-based detection, in terms of specificity and sensitivity, thus representing a reliable tool. We think that, through enabling the use of vast range of thermocycler models and laboratory facilities for SARS-CoV-2 diagnosis, the alternative proposed here can increase dramatically the testing capability, especially in countries with limited access to costly technology and reagents.
DOI: 10.6084/m9.figshare.14587077.v1
title: Bisulfite miRNA-seq reveals widespread CpG and non-CpG 5-(hydroxy)methyl-Cytosine in human microRNAs

description: In the last decade, the field of epitranscriptomics highlighted a wide array of post-transcriptional modifications in human RNAs, including microRNAs (miRNAs). Recent reports showed that human miRNAs undergo cytosine methylation. We describe the first high-throughput NGS based method (BS-miRNA-seq) and an analysis pipeline (MAmBA) to attain high-resolution mapping of (hydroxy)-methyl-5-cytosine ((h)m5C) modifications in human miRNAs. Our method uncovers that miRNAs undergo widespread cytosine modification in various sequence contexts. Furthermore, validation of our data with specific antibodies reveals both m5C and hm5C residues in human mature miRNAs. BS-miRNA-seq and MAmBA may contribute to the precise mapping of (h)m5C on miRNAs in various cell types and tissues, a key achievement towards the understanding of the functional implications of this modification in miRNAs. MAmBA is available for download at https://github.com/flcvlr/MAmBA
DOI: 10.6084/m9.figshare.14685427
title: Comprehensive characterization of mRNAs associated with yeast cytosolic aminoacyl-tRNA synthetases

description: Aminoacyl-tRNA synthetases (aaRSs) are a conserved family of enzymes with an essential role in protein synthesis: ligating amino acids to cognate tRNA molecules for translation. In addition to their role in tRNA charging, aaRSs have acquired non-canonical functions, including post-transcriptional regulation of mRNA expression. Yet, the extent and mechanisms of these post-transcriptional functions are largely unknown. Herein, we performed a comprehensive transcriptome analysis to define the mRNAs that are associated with almost all aaRSs present in <i>S. cerevisiae</i> cytosol. Nineteen (out of twenty) isogenic strains of GFP-tagged cytosolic aaRSs were subjected to immunoprecipitation with anti-GFP beads along with an untagged control. mRNAs associated with each aaRS were then identified by RNA-seq. The extent of mRNA association varied significantly between aaRSs, from MetRS in which none appeared to be statistically significant, to PheRS that binds hundreds of different mRNAs. Interestingly, many target mRNAs are bound by multiple aaRSs, suggesting co-regulation by this family of enzymes. Gene Ontology analyses for aaRSs with a considerable number of target mRNAs discovered an enrichment for pathways of amino acid metabolism and of ribosome biosynthesis. Furthermore, sequence and structure motif analysis revealed for some aaRSs an enrichment for motifs that resemble the anticodon stem loop of cognate tRNAs. These data suggest that aaRSs coordinate mRNA expression in response to amino acid availability and may utilize RNA elements that mimic their canonical tRNA binding partners.
DOI: 10.6084/m9.figshare.14685427.v1
title: Comprehensive characterization of mRNAs associated with yeast cytosolic aminoacyl-tRNA synthetases

description: Aminoacyl-tRNA synthetases (aaRSs) are a conserved family of enzymes with an essential role in protein synthesis: ligating amino acids to cognate tRNA molecules for translation. In addition to their role in tRNA charging, aaRSs have acquired non-canonical functions, including post-transcriptional regulation of mRNA expression. Yet, the extent and mechanisms of these post-transcriptional functions are largely unknown. Herein, we performed a comprehensive transcriptome analysis to define the mRNAs that are associated with almost all aaRSs present in <i>S. cerevisiae</i> cytosol. Nineteen (out of twenty) isogenic strains of GFP-tagged cytosolic aaRSs were subjected to immunoprecipitation with anti-GFP beads along with an untagged control. mRNAs associated with each aaRS were then identified by RNA-seq. The extent of mRNA association varied significantly between aaRSs, from MetRS in which none appeared to be statistically significant, to PheRS that binds hundreds of different mRNAs. Interestingly, many target mRNAs are bound by multiple aaRSs, suggesting co-regulation by this family of enzymes. Gene Ontology analyses for aaRSs with a considerable number of target mRNAs discovered an enrichment for pathways of amino acid metabolism and of ribosome biosynthesis. Furthermore, sequence and structure motif analysis revealed for some aaRSs an enrichment for motifs that resemble the anticodon stem loop of cognate tRNAs. These data suggest that aaRSs coordinate mRNA expression in response to amino acid availability and may utilize RNA elements that mimic their canonical tRNA binding partners.
DOI: 10.6084/m9.figshare.16651916
title: <i>In vivo</i> discovery of RNA proximal proteins via proximity-dependent biotinylation

description: RNA molecules function as messenger RNAs (mRNAs) that encode proteins and noncoding transcripts that serve as adaptor molecules, structural components, and regulators of genome organization and gene expression. Their function and regulation are largely mediated by RNA binding proteins (RBPs). Here we present RNA proximity labelling (RPL), an RNA-centric method comprising the endonuclease-deficient Type VI CRISPR-Cas protein dCas13b fused to engineered ascorbate peroxidase APEX2. RPL discovers target RNA proximal proteins <i>in vivo</i> via proximity-based biotinylation. RPL applied to <i>U1</i> identified proteins involved in both <i>U1</i> canonical and noncanonical functions. Profiling of poly(A) tail proximal proteins uncovered expected categories of RBPs and provided additional evidence for 5ʹ-3ʹ proximity and unexplored subcellular localizations of poly(A)<sup>+</sup> RNA. Our results suggest that RPL allows rapid identification of target RNA binding proteins in native cellular contexts, and is expected to pave the way for discovery of novel RNA–protein interactions important for health and disease.
DOI: 10.6084/m9.figshare.14507167
title: RGG-motif containing mRNA export factor Gbp2 acts as a translation repressor

description: Complex cascades of RNA-binding proteins regulate the mRNA metabolism and influence gene expression. Several distinct proteins act at different stages of mRNA life cycle. SR family proteins in yeast are implicated in mRNA processing and nuclear export. In this report, we uncover the role of an SR/RGG-motif containing mRNA export factor Gbp2 in mRNA translation regulation. We demonstrate that Gbp2 localizes to cytoplasmic granules upon heat shock and oxidative stress. Our pull-down assays demonstrate that Gbp2 directly binds to the conserved translation factor eIF4G1 via its RGG motif. We further mapped the region on eIF4G1 to which Gbp2 binds and observed that the binding region overlaps with another translation repressor Sbp1. We found that the RGG-motif deletion mutant is defective in localizing to polysome fractions. Upon tethering Gbp2 to a GFP reporter mRNA <i>in vivo</i>, translation of GFP reporter decreased significantly indicating that Gbp2 acts as a translation repressor. Consistent with these results, we show that Gbp2 can directly repress mRNA translation in the <i>in vitro</i> translation systems in an RGG-motif dependent manner. Taken together, our results establish that the mRNA export factor Gbp2 has a vital role in repressing translation of mRNA. We propose that Gbp2 is a multifaceted RGG-motif protein responsible for translational repression without affecting mRNA levels.