cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3487733.v1
title: Structural analysis and molecular docking of trypanocidal aryloxy-quinones in trypanothione and glutathione reductases: a comparison with biochemical data

description: A set of aryloxy-quinones, previously synthesized and evaluated against <i>Trypanosoma cruzi</i> epimastigotes cultures, were found more potent and selective than nifurtimox. One of the possible mechanisms of the trypanocidal activity of these quinones could be inhibition of trypanothione reductase (TR). Considering that glutathione reductase (GR) is the equivalent of TR in humans, biochemical, kinetic, and molecular docking studies in TR and GR were envisaged and compared with the trypanocidal and cytotoxic data of a set of aryloxy-quinones. Biochemical assays indicated that three naphthoquinones (<b>Nq-h</b>, <b>Nq-g</b>, and <b>Nq-d</b>) selectively inhibit TR and the TR kinetic analyses indicated that <b>Nq-h</b> inhibit TR in a noncompetitive mechanism. Molecular dockings were performed in TR and GR in the following three putative binding sites: the catalytic site, the dimer interface, and the nicotinamide adenine dinucleotide phosphate-binding site. In TR and GR, the aryloxy-quinones were found to exhibit high affinity for a site near it cognate-binding site in a place in which the noncompetitive kinetics could be justified. Taking as examples the three compounds with TR specificity (TRS) (<b>Nq-h</b>, <b>Nq-g</b>, and <b>Nq-d</b>), the presence of a network of contacts with the quinonic ring sustained by the triad of Lys62, Met400′, Ser464′ residues, seems to contribute hardly to the TRS. Compound <b>Nq-b</b>, a naphthoquinone with nitrophenoxy substituent, proved to be the best scaffold for the design of trypanocidal compounds with low toxicity. However, the compound displayed only a poor and non-selective effect toward TR indicating that TR inhibition is not the main reason for the antiparasitic activity of the aryloxy-quinones.
DOI: 10.6084/m9.figshare.3487685
title: TCGA Pan-Cancer sample, expression, and mutation data for Project Cognoma

description: The following datasets were created for Project Cognoma:<br>`expression-matrix.tsv.bz2` is a sample × gene matrix indicating a gene's expression level for a given sample. This dataset will be the feature/x/predictor information for Project Cognoma.<br>`expression-genes.tsv` provides information and summary statistics for every gene in `expression-matrix.tsv.bz2`.<br>`mutation-matrix.tsv.bz2` is a sample × gene matrix indicating whether a gene is mutated for a given sample. Select columns (or unions of several columns) in this dataset will be the status/y/outcome for Project Cognoma.<br>`mutation-genes.tsv` provides information and summary statistics for every gene in `mutation-matrix.tsv.bz2`.<br>`samples.tsv` is a sample × attribute matrix providing sample information and clinical measures for each sample.<br>`covariates.tsv` is a sample × attribute matrix for modeling that encodes categorical variables in samples.tsv using dummies.<br>All datasets contain the same samples as rows (in the same order). No two samples correspond to the same patient.<br>The data was retrieved from the UCSC Xena Browser.<br>These datasets were created by the GitHub repository commit below. See the download directory of the cancer-data repository for metadata files with the version info for the Xena downloads this release is based on.<br>See the data/subset directory of the cancer-data repository on GitHub to browse small subsets of the expression and mutation datasets.
DOI: 10.6084/m9.figshare.3487685.v2
title: TCGA Pan-Cancer expression and mutation data for Project Cognoma

description: The following datasets were created for Project Cognoma:<br>`expression-matrix.tsv.bz2` is a sample × gene matrix indicating a gene's expression level for a given sample. This dataset will be the feature/x/predictor for Project Cognoma.<br>`mutation-matrix.tsv.bz2` is a sample × gene matrix indicating whether a gene is mutated for a given sample. Select columns (or unions of several columns) in this dataset will be the status/y/outcome for Project Cognoma.<br>These are preliminary datasets for development use and machine learning. The data was retrieved from the UCSC Xena Browser.<br>All original work in the data is released under CC0. However, the license of TCGA and Xena data is currently unclear.<br>These two datasets were created by the GitHub repository commit below, although they were not tracked due to large file size. See the download directory of the cancer-data repository for metadata files with the version info for the Xena downloads this release is based on.<br>See the data/subset directory of the cancer-data repository on GitHub to browse small subsets of these datasets.
DOI: 10.6084/m9.figshare.3487685.v4
title: TCGA Pan-Cancer sample, expression, and mutation data for Project Cognoma

description: The following datasets were created for Project Cognoma:<br>`expression-matrix.tsv.bz2` is a sample × gene matrix indicating a gene's expression level for a given sample. This dataset will be the feature/x/predictor information for Project Cognoma.<br>`mutation-matrix.tsv.bz2` is a sample × gene matrix indicating whether a gene is mutated for a given sample. Select columns (or unions of several columns) in this dataset will be the status/y/outcome for Project Cognoma.<br>`samples.tsv` is a sample × attribute matrix providing sample information and clinical measures for each sample.<br>All three datasets contain the same samples as rows (in the same order). No two samples correspond to the same patient.<br>The data was retrieved from the UCSC Xena Browser. All original work in the data is released under CC0 1.0. TCGA data is public domain and the license of Xena data is currently unclear.<br>These three datasets were created by the GitHub repository commit below, although the large files were not tracked due to file size. See the download directory of the cancer-data repository for metadata files with the version info for the Xena downloads this release is based on.<br>See the data/subset directory of the cancer-data repository on GitHub to browse small subsets of the expression and mutation datasets.
DOI: 10.6084/m9.figshare.3487685.v5
title: TCGA Pan-Cancer sample, expression, and mutation data for Project Cognoma

description: The following datasets were created for Project Cognoma:<br>`expression-matrix.tsv.bz2` is a sample × gene matrix indicating a gene's expression level for a given sample. This dataset will be the feature/x/predictor information for Project Cognoma.<br>`mutation-matrix.tsv.bz2` is a sample × gene matrix indicating whether a gene is mutated for a given sample. Select columns (or unions of several columns) in this dataset will be the status/y/outcome for Project Cognoma.<br>`samples.tsv` is a sample × attribute matrix providing sample information and clinical measures for each sample.<br>`covariates.tsv` is a sample × attribute matrix for modeling that encodes categorical variables in samples.tsv using dummies.<br>All datasets contain the same samples as rows (in the same order). No two samples correspond to the same patient.<br>The data was retrieved from the UCSC Xena Browser. All original work in the data is released under CC0 1.0. TCGA data is public domain and the license of Xena data is currently unclear.<br>These datasets were created by the GitHub repository commit below, although the large files were not tracked due to file size. See the download directory of the cancer-data repository for metadata files with the version info for the Xena downloads this release is based on.<br>See the data/subset directory of the cancer-data repository on GitHub to browse small subsets of the expression and mutation datasets.
DOI: 10.6084/m9.figshare.3487685.v6
title: TCGA Pan-Cancer sample, expression, and mutation data for Project Cognoma

description: The following datasets were created for Project Cognoma:<br>`expression-matrix.tsv.bz2` is a sample × gene matrix indicating a gene's expression level for a given sample. This dataset will be the feature/x/predictor information for Project Cognoma.<br>`expression-genes.tsv` provides information and summary statistics for every gene in `expression-matrix.tsv.bz2`.<br>`mutation-matrix.tsv.bz2` is a sample × gene matrix indicating whether a gene is mutated for a given sample. Select columns (or unions of several columns) in this dataset will be the status/y/outcome for Project Cognoma.<br>`mutation-genes.tsv` provides information and summary statistics for every gene in `mutation-matrix.tsv.bz2`.<br>`samples.tsv` is a sample × attribute matrix providing sample information and clinical measures for each sample.<br>`covariates.tsv` is a sample × attribute matrix for modeling that encodes categorical variables in samples.tsv using dummies.<br>All datasets contain the same samples as rows (in the same order). No two samples correspond to the same patient.<br>The data was retrieved from the UCSC Xena Browser.<br>These datasets were created by the GitHub repository commit below, although the large files were not tracked due to file size. See the download directory of the cancer-data repository for metadata files with the version info for the Xena downloads this release is based on.<br>See the data/subset directory of the cancer-data repository on GitHub to browse small subsets of the expression and mutation datasets.
DOI: 10.6084/m9.figshare.3487679
title: Genome-wide chromatin and gene expression profiling during memory formation and maintenance in adult mice. [CODE: support files]

description: This repository contains annotation files for mouse genome assembly mm10, including chromosome sizes, gene and exon annotations, mappability file and the R package chequeR used to generate enrichment statistics for ChIP-seq data. The files are used in the analyses of ChIP-, MeDIP- and RNA-seq data from mouse, as described by the run_scientific_data_analysis.pdf in the scripts repository (https://dx.doi.org/10.6084/m9.figshare.3490613)<br>
DOI: 10.6084/m9.figshare.3487652
title: Regulation of a polyamine transporter by the conserved 3′ UTR-derived sRNA SorX confers resistance to singlet oxygen and organic hydroperoxides in <i>Rhodobacter sphaeroides</i>

description: Singlet oxygen is generated by bacteriochlorophylls when light and oxygen are simultaneously present in <i>Rhodobacter sphaeroides</i>. Singlet oxygen triggers a specific response that is partly regulated by the alternative sigma factor RpoHI/HII. The sRNA RSs2461 has previously been identified as an RpoHI/HII-dependent sRNA and is derived from the 3′ UTR of the mRNA for an OmpR-type transcriptional regulator. Similar to the RpoHI/HII-dependent CcsR and SorY sRNAs, RSs2461 affects the resistance of <i>R. sphaeroides</i> against singlet oxygen and was therefore renamed here SorX. Furthermore, SorX has a strong impact on resistance against organic hydroperoxides that usually occur as secondary damages downstream of singlet oxygen. The 75-nt SorX 3′ fragment, which is generated by RNase E cleavage and highly conserved among related species, represents the functional entity. A target search identified <i>potA</i> mRNA, which encodes a subunit of a polyamine transporter, as a direct SorX target and stress resistance via SorX could be linked to <i>potA</i>. The PotABCD transporter is an uptake system for spermidine in <i>E. coli</i>. While spermidine is generally described as beneficial during oxidative stress, we observed significantly increased sensitivity of <i>R. sphaeroides</i> to organic hydroperoxides in the presence of spermidine. We therefore propose that the diminished import of spermidine, due to down-regulation of <i>potA</i> by SorX, counteracts oxidative stress. Together with results from other studies this underlines the importance of regulated transport to bacterial stress defense.
DOI: 10.6084/m9.figshare.3487652.v1
title: Regulation of a polyamine transporter by the conserved 3′ UTR-derived sRNA SorX confers resistance to singlet oxygen and organic hydroperoxides in <i>Rhodobacter sphaeroides</i>

description: Singlet oxygen is generated by bacteriochlorophylls when light and oxygen are simultaneously present in <i>Rhodobacter sphaeroides</i>. Singlet oxygen triggers a specific response that is partly regulated by the alternative sigma factor RpoHI/HII. The sRNA RSs2461 has previously been identified as an RpoHI/HII-dependent sRNA and is derived from the 3′ UTR of the mRNA for an OmpR-type transcriptional regulator. Similar to the RpoHI/HII-dependent CcsR and SorY sRNAs, RSs2461 affects the resistance of <i>R. sphaeroides</i> against singlet oxygen and was therefore renamed here SorX. Furthermore, SorX has a strong impact on resistance against organic hydroperoxides that usually occur as secondary damages downstream of singlet oxygen. The 75-nt SorX 3′ fragment, which is generated by RNase E cleavage and highly conserved among related species, represents the functional entity. A target search identified <i>potA</i> mRNA, which encodes a subunit of a polyamine transporter, as a direct SorX target and stress resistance via SorX could be linked to <i>potA</i>. The PotABCD transporter is an uptake system for spermidine in <i>E. coli</i>. While spermidine is generally described as beneficial during oxidative stress, we observed significantly increased sensitivity of <i>R. sphaeroides</i> to organic hydroperoxides in the presence of spermidine. We therefore propose that the diminished import of spermidine, due to down-regulation of <i>potA</i> by SorX, counteracts oxidative stress. Together with results from other studies this underlines the importance of regulated transport to bacterial stress defense.
DOI: 10.6084/m9.figshare.3487649
title: Identification of processing elements and interactors implicate SMN, coilin and the pseudogene-encoded coilp1 in telomerase and box C/D scaRNP biogenesis

description: Many cellular functions, such as translation, require ribonucleoproteins (RNPs). The biogenesis of RNPs is a multi-step process that, depending on the RNP, can take place in many cellular compartments. Here we examine 2 different RNPs: telomerase and small Cajal body-specific RNPs (scaRNPs). Both of these RNPs are enriched in the Cajal body (CB), which is a subnuclear domain that also has high concentrations of another RNP, small nuclear RNPs (snRNPs). SnRNPs are essential components of the spliceosome, and scaRNPs modify the snRNA component of the snRNP. The CB contains many proteins, including WRAP53, SMN and coilin, the CB marker protein. We show here that coilin, SMN and coilp1, a newly identified protein encoded by a pseudogene in human, associate with telomerase RNA and a subset of scaRNAs. We also have identified a processing element within box C/D scaRNA. Our findings thus further strengthen the connection between the CB proteins coilin and SMN in the biogenesis of telomeras e and box C/D scaRNPs, and reveal a new player, coilp1, that likely participates in this process.
DOI: 10.6084/m9.figshare.3487649.v1
title: Identification of processing elements and interactors implicate SMN, coilin and the pseudogene-encoded coilp1 in telomerase and box C/D scaRNP biogenesis

description: Many cellular functions, such as translation, require ribonucleoproteins (RNPs). The biogenesis of RNPs is a multi-step process that, depending on the RNP, can take place in many cellular compartments. Here we examine 2 different RNPs: telomerase and small Cajal body-specific RNPs (scaRNPs). Both of these RNPs are enriched in the Cajal body (CB), which is a subnuclear domain that also has high concentrations of another RNP, small nuclear RNPs (snRNPs). SnRNPs are essential components of the spliceosome, and scaRNPs modify the snRNA component of the snRNP. The CB contains many proteins, including WRAP53, SMN and coilin, the CB marker protein. We show here that coilin, SMN and coilp1, a newly identified protein encoded by a pseudogene in human, associate with telomerase RNA and a subset of scaRNAs. We also have identified a processing element within box C/D scaRNA. Our findings thus further strengthen the connection between the CB proteins coilin and SMN in the biogenesis of telomeras e and box C/D scaRNPs, and reveal a new player, coilp1, that likely participates in this process.
DOI: 10.6084/m9.figshare.3487595
title: Cdk3, a conjugation-specific cyclin-dependent kinase, is essential for the initiation of meiosis in Tetrahymena thermophila

description: Meiosis is an important process in sexual reproduction. Meiosis initiation has been found to be highly diverse among species. In yeast, it has been established that cyclin-dependent kinases (Cdks) and cyclins are essential components in the meiosis initiation pathway. In this study, we identified 4 Cdks in the model ciliate, <i>Tetrahymena thermophila</i>, and we found one of them, Cdk3, which is specifically expressed during early conjugation, to be essential for meiosis initiation. Cdk3 deletion led to arrest at the pair formation stage of conjugation. We then confirmed that Cdk3 acts upstream of double-strand break (DSB) formation. Moreover, we detected that Cdk3 is necessary for the expression of many genes involved in early meiotic events. Through proteomic quantification of phosphorylation, co-expression analysis and RNA-Seq analyses, we identified a conjugation-specific cyclin, Cyc2, which most likely partners with Cdk3 to initiate meiosis.
DOI: 10.6084/m9.figshare.3487595.v2
title: Cdk3, a conjugation-specific cyclin-dependent kinase, is essential for the initiation of meiosis in Tetrahymena thermophila

description: Meiosis is an important process in sexual reproduction. Meiosis initiation has been found to be highly diverse among species. In yeast, it has been established that cyclin-dependent kinases (Cdks) and cyclins are essential components in the meiosis initiation pathway. In this study, we identified 4 Cdks in the model ciliate, <i>Tetrahymena thermophila</i>, and we found one of them, Cdk3, which is specifically expressed during early conjugation, to be essential for meiosis initiation. Cdk3 deletion led to arrest at the pair formation stage of conjugation. We then confirmed that Cdk3 acts upstream of double-strand break (DSB) formation. Moreover, we detected that Cdk3 is necessary for the expression of many genes involved in early meiotic events. Through proteomic quantification of phosphorylation, co-expression analysis and RNA-Seq analyses, we identified a conjugation-specific cyclin, Cyc2, which most likely partners with Cdk3 to initiate meiosis.
DOI: 10.6084/m9.figshare.3487595.v1
title: Cdk3, a conjugation-specific cyclin-dependent kinase, is essential for the initiation of meiosis in <i>Tetrahymena thermophila</i>

description: Meiosis is an important process in sexual reproduction. Meiosis initiation has been found to be highly diverse among species. In yeast, it has been established that cyclin-dependent kinases (Cdks) and cyclins are essential components in the meiosis initiation pathway. In this study, we identified four Cdks in the model ciliate, <i>Tetrahymena thermophila</i>, and we found one of them, Cdk3, which is specifically expressed during early conjugation, to be essential for meiosis initiation. Cdk3 deletion led to arrest at the pair formation stage of conjugation. We then confirmed that Cdk3 acts upstream of double-strand break (DSB) formation. Moreover, we detected that Cdk3 is necessary for the expression of many genes involved in early meiotic events. Through proteomic quantification of phosphorylation, co-expression analysis and RNA-Seq analyses, we identified a conjugation-specific cyclin, Cyc2, which most likely partners with Cdk3 to initiate meiosis.
DOI: 10.6084/m9.figshare.3487568
title: Tests on Thin Reinforced Concrete Walls Subjected to In-plane and Out-of-plane Cyclic Loading - TW1 (2/3)

description: The present dataset describes an experimental campaign on five thin T-shaped reinforced concrete walls. The tests aimed at assessing the influence of wall thickness on member stability, the role of lap splices on damage distribution and displacement ductility, and the effects of the simultaneous application of out-of-plane loading on the member response. Further data can be downloaded from the links below. If you use the data, please cite: Almeida, J. P., O. Prodan, A. Rosso, and K. Beyer. 2016. Tests on Thin Reinforced Concrete Walls Subjected to in-Plane and out-of-Plane Cyclic Loading. <i>Earthquake Spectra</i>.
DOI: 10.6084/m9.figshare.3487433
title: Alan Turing Institute symposium on reproducibility for data-intensive research - Annex B, delegate list

description: Delegate list containing names and institutional affiliation for delegates to the Alan Turing Institute symposium on reproducibility for data-intensive research, 6-7 April 2016
DOI: 10.6084/m9.figshare.3487433.v1
title: Alan Turing Institute symposium on reproducibility for data-intensive research - Annex B, delegate list

description: Delegate list containing names and institutional affiliation for delegates to the Alan Turing Institute symposium on reproducibility for data-intensive research, 6-7 April 2016
DOI: 10.6084/m9.figshare.3487418.v1
title: Arti et Amicitiae

description: The objective of the workshop os twofold : to promote an understanding of the role of visual media as a research tool and to develop basic technical skills to record and document exhibitions using photography.
DOI: 10.6084/m9.figshare.3487418.v2
title: Arti et Amicitiae

description: The objective of the workshop os twofold : to promote an understanding of the role of visual media as a research tool and to develop basic technical skills to record and document exhibitions using photography.
DOI: 10.6084/m9.figshare.3487418.v3
title: Arti et Amicitiae Amsterdam

description: The objective of the workshop os twofold : to promote an understanding of the role of visual media as a research tool and to develop basic technical skills to record and document exhibitions using photography. <br><br>First Part : an overview of visual documentation of exhibitions both historiacal and current will be presented to highlight different strategies and discuss both positiveaspects and shortcomings as well as to establish the need to define a clear purpose when visually documenting an exhibition. <br>Second part : pratical training will take place at an actual exhibition. Divide into groups of two or three people, with your camera, choose one situation requiring one or more of the following methods : -selection and variation of framing, anglem exposure and viewpoint
DOI: 10.6084/m9.figshare.3487418.v4
title: Arti et Amicitiae Amsterdam

description: The objective of the workshop os twofold : to promote an understanding of the role of visual media as a research tool and to develop basic technical skills to record and document exhibitions using photography. <br><br>First Part : an overview of visual documentation of exhibitions both historiacal and current will be presented to highlight different strategies and discuss both positiveaspects and shortcomings as well as to establish the need to define a clear purpose when visually documenting an exhibition. <br>Second part : pratical training will take place at an actual exhibition. Divide into groups of two or three people, with your camera, choose one situation requiring one or more of the following methods : -selection and variation of framing, anglem exposure and viewpoint
DOI: 10.6084/m9.figshare.3487391
title: Genome-wide chromatin and gene expression profiling during memory formation and maintenance in adult mice. [CODE: example files]

description: This repository contains example ChIP-, MeDIP- and RNA-seq samples to illustrate how to run the analyses regarding those samples, as described by the run_scientific_data_analysis.pdf in the scripts repository (https://dx.doi.org/10.6084/m9.figshare.3490613). The files are tab-delimited with sample names in one column and links to SRA files from the GEO dataset repository in the second column. The file names correspond to the data type of the samples, i.e. "sra_chip.txt" contains ChIP-seq samples, "sra_medip.txt" contains MeDIP-seq samples and "sra_rna.txt" contains RNA-seq samples.<br>