cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1311754.v3
title: Characterization of the UGA-recoding and SECIS-binding activities of SECIS-binding protein 2

description: Selenium, a micronutrient, is primarily incorporated into human physiology as selenocysteine (Sec). The 25 Sec-containing proteins in humans are known as selenoproteins. Their synthesis depends on the translational recoding of the UGA stop codon to allow Sec insertion. This requires a stem-loop structure in the 3’ untranslated region of eukaryotic mRNAs known as the Selenocysteine Insertion Sequence (SECIS). The SECIS is recognized by SECIS-binding protein 2 (SBP2) and this RNA:protein interaction is essential for UGA recoding to occur. Genetic mutations cause SBP2 deficiency in humans, resulting in a broad set of symptoms due to differential effects on individual selenoproteins. Progress on understanding the different phenotypes requires developing robust tools to investigate SBP2 structure and function. In this study we demonstrate that SBP2 protein produced by in vitro translation discriminates among SECIS elements in a competitive UGA recoding assay and has a much higher specific activity than bacterially expressed protein. We also show that a purified recombinant protein encompassing amino acids 517-777 of SBP2 binds to SECIS elements with high affinity and selectivity. The affinity of the SBP2:SECIS interaction correlated with the ability of a SECIS to compete for UGA recoding activity in vitro. The identification of a 250 amino acid sequence that mediates specific, selective SECIS-binding will facilitate future structural studies of the SBP2:SECIS complex. Finally, we identify an evolutionarily conserved core cysteine signature in SBP2 sequences from the vertebrate lineage. Mutation of multiple, but not single, cysteines impaired SECIS-binding but did not affect protein localization in cells.
DOI: 10.6084/m9.figshare.1311755.v3
title: Characterization of binding of LARP6 to the 5’ stem-loop of collagen mRNAs: Implications for synthesis of type I collagen

description: Type I collagen is composed of 2 polypeptides, α1(I) and α2(I), which fold into triple helix. Collagen α1(I) and α2(I) mRNAs have a conserved stem-loop structure in their 5’ UTRs, the 5’SL. LARP6 binds the 5’SL to regulate type I collagen expression. We show that 5 nucleotides within the single stranded regions of 5’SL contribute to the high affinity of LARP6 binding. Mutation of individual nucleotides abolishes the binding in gel mobility shift assay. LARP6 binding to 5’SL of collagen α2(I) mRNA is more stable than the binding to 5’SL of α1(I) mRNA, although the equilibrium binding constants are similar. The more stable binding to α2(I) mRNA may favor synthesis of the heterotrimeric type I collagen. LARP6 needs 2 domains to contact 5’SL, the La domain and the RRM. T133 in the La domain is critical for folding of the protein, while loop 3 in the RRM is critical for binding 5’SL. Loop 3 is also involved in the interaction of LARP6 and protein translocation channel SEC61. This interaction is essential for type I collagen synthesis, because LARP6 mutant which binds 5’SL but which does not interact with SEC61, suppresses collagen synthesis in a dominant negative manner. We postulate that LARP6 directly targets collagen mRNAs to the SEC61 translocons to facilitate coordinated translation of the 2 collagen mRNAs. The unique sequences of LARP6 identified in this work may have evolved to enable its role in type I collagen biosynthesis.
DOI: 10.6084/m9.figshare.1311753.v3
title: Splicing changes in SMA mouse motoneurons and SMN-depleted neuroblastoma cells: Evidence for involvement of splicing regulatory proteins

description: Spinal Muscular Atrophy (SMA) is caused by deletions or mutations in the Survival Motor Neuron 1 (<i>SMN1</i>) gene. The second gene copy, <i>SMN2</i>, produces some, but not enough, functional SMN protein. SMN is essential to assemble small nuclear ribonucleoproteins (snRNPs) that form the spliceosome. However, it is not clear whether SMA is caused by defects in this function that could lead to splicing changes in all tissues, or by the impairment of an additional, less well characterized, but motoneuron-specific SMN function. We addressed the first possibility by exon junction microarray analysis of motoneurons (MNs) isolated by laser capture microdissection from a severe SMA mouse model. This revealed changes in multiple U2-dependent splicing events. Moreover, splicing appeared to be more strongly affected in MNs than in other cells. By testing mutiple genes in a model of progressive SMN depletion in NB2a neuroblastoma cells, we obtained evidence that U2-dependent splicing changes occur earlier than U12-dependent ones. As several of these changes affect genes coding for splicing regulators, this may acerbate the splicing response induced by low SMN levels and induce secondary waves of splicing alterations.
DOI: 10.6084/m9.figshare.1312837.v5
title: Informatics

description: This fileset contains data relevant to AMIA 2015 submission titled: Process Mining of Growing Adoption of Genomic Precision Medicine Testing Using Commercial Claims and Encounters Database To facilitate comparison and execution on other datasets, we used R Markdown format designed for reproducible science that combines the analysis code with the resulting analytical report (see this fileset for code [*.Rmd] and output reports [*.docx]).
DOI: 10.6084/m9.figshare.1311752.v3
title: Positive correlation between ADAR expression and its targets suggests a complex regulation mediated by RNA editing in the human brain

description: A-to-I RNA editing by adenosine deaminases acting on RNA is a post-transcriptional modification that is crucial for normal life and development in vertebrates. RNA editing has been shown to be very abundant in the human transcriptome, specifically at the primate-specific Alu elements. The functional role of this wide-spread effect is still not clear; it is believed that editing of transcripts is a mechanism for their down-regulation via processes such as nuclear retention or RNA degradation. Here we combine 2 neural gene expression datasets with genome-level editing information to examine the relation between the expression of ADAR genes with the expression of their target genes. Specifically, we computed the spatial correlation across structures of post-mortem human brains between ADAR and a large set of targets that were found to be edited in their Alu repeats. Surprisingly, we found that a large fraction of the edited genes are positively correlated with ADAR, opposing the assumption that editing would reduce expression. When considering the correlations between ADAR and its targets over development, 2 gene subsets emerge, positively correlated and negatively correlated with ADAR expression. Specifically, in embryonic time points, ADAR is positively correlated with many genes related to RNA processing and regulation of gene expression. These findings imply that the suggested mechanism of regulation of expression by editing is probably not a global one; ADAR expression does not have a genome wide effect reducing the expression of editing targets. It is possible, however, that RNA editing by ADAR in non-coding regions of the gene might be a part of a more complex expression regulation mechanism.
DOI: 10.6084/m9.figshare.1312837.v6
title: Informatics

description: This fileset contains data relevant to AMIA 2015 submission titled: Process Mining of Growing Adoption of Genomic Precision Medicine Testing Using Commercial Claims and Encounters Database To facilitate comparison and execution on other datasets, we used R Markdown format designed for reproducible science that combines the analysis code with the resulting analytical report (see this fileset for code [*.Rmd] and output reports [*.docx]).
DOI: 10.6084/m9.figshare.1311751.v1
title: Comprehensive silencing of target-sharing microRNAs is a mechanism for SIRT1 overexpression in cancer

description: Overexpression of SIRT1 is frequently observed in various types of cancers, suggesting its potential role in malignancies. However, the molecular basis of how SIRT1 is elevated in cancer is less understood. Here we show that cancer-related SIRT1 overexpression is due to evasion of <i>Sirt1</i> mRNA from repression by a group of <i>Sirt1</i>-targeting microRNAs (miRNAs) that might be robustly silenced in cancer. Our comprehensive library-based screening and subsequent miRNA gene profiling revealed a housekeeping gene-like broad expression pattern and strong CpG island-association of the <i>Sirt1</i>-targeting miRNA genes. This suggests aberrant CpG DNA methylation as the mechanistic background for malignant SIRT1 elevation. Our work also provides an example where epigenetic mechanisms cause the group-wide regulation of miRNAs sharing a common key target.
DOI: 10.6084/m9.figshare.1312837.v7
title: Informatics

description: This fileset contains data relevant to AMIA 2015 submission titled: Process Mining of Growing Adoption of Genomic Precision Medicine Testing Using Commercial Claims and Encounters Database To facilitate comparison and execution on other datasets, we used R Markdown format designed for reproducible science that combines the analysis code with the resulting analytical report (see this fileset for code [*.Rmd] and output reports [*.docx]).
DOI: 10.6084/m9.figshare.1311751.v2
title: Comprehensive silencing of target-sharing microRNAs is a mechanism for SIRT1 overexpression in cancer

description: Overexpression of SIRT1 is frequently observed in various types of cancers, suggesting its potential role in malignancies. However, the molecular basis of how SIRT1 is elevated in cancer is less understood. Here we show that cancer-related SIRT1 overexpression is due to evasion of <i>Sirt1</i> mRNA from repression by a group of <i>Sirt1</i>-targeting microRNAs (miRNAs) that might be robustly silenced in cancer. Our comprehensive library-based screening and subsequent miRNA gene profiling revealed a housekeeping gene-like broad expression pattern and strong CpG island-association of the <i>Sirt1</i>-targeting miRNA genes. This suggests aberrant CpG DNA methylation as the mechanistic background for malignant SIRT1 elevation. Our work also provides an example where epigenetic mechanisms cause the group-wide regulation of miRNAs sharing a common key target.
DOI: 10.6084/m9.figshare.1312837.v8
title: Informatics

description: This fileset contains data relevant to AMIA 2015 submission titled: Process Mining of Growing Adoption of Genomic Precision Medicine Testing Using Commercial Claims and Encounters Database To facilitate comparison and execution on other datasets, we used R Markdown format designed for reproducible science that combines the analysis code with the resulting analytical report (see this fileset for code [*.Rmd] and output reports [*.docx]).
DOI: 10.6084/m9.figshare.1312837.v10
title: Informatics

description: This fileset contains data relevant to AMIA 2015 submission titled: Process Mining of Growing Adoption of Genomic Precision Medicine Testing Using Commercial Claims and Encounters Database To facilitate comparison and execution on other datasets, we used R Markdown format designed for reproducible science that combines the analysis code with the resulting analytical report (see this fileset for code [*.Rmd] and output reports [*.docx]).
DOI: 10.6084/m9.figshare.1312837.v9
title: Informatics

description: This fileset contains data relevant to AMIA 2015 submission titled: Process Mining of Growing Adoption of Genomic Precision Medicine Testing Using Commercial Claims and Encounters Database To facilitate comparison and execution on other datasets, we used R Markdown format designed for reproducible science that combines the analysis code with the resulting analytical report (see this fileset for code [*.Rmd] and output reports [*.docx]).
DOI: 10.6084/m9.figshare.1311743
title: Forensic analysis of the microbiome of phones and shoes

description: In this study, 2 participants sampled the front and back of their cell phones, four different locations on the soles of their shoes, and the floor beneath them every waking hour over a 2 day period. A further 89 participants took individual samples of their shoes and phones at three different scientific conferences. Due to FigShare’s limit on file size, the read file and index file were split into 102 and 23 files respectively. They can be concatenated using the “cat” command in Unix before passing to split libraries in QIIME. The OTU table (rarified to 1000 reads per sample) and mapping file used in the study are also provided. Requests for further data or information should be sent to Simon Lax at simonlax@uchicago.edu
DOI: 10.6084/m9.figshare.1311743.v1
title: Forensic analysis of the microbiome of phones and shoes

description: In this study, 2 participants sampled the front and back of their cell phones, four different locations on the soles of their shoes, and the floor beneath them every waking hour over a 2 day period. A further 89 participants took individual samples of their shoes and phones at three different scientific conferences.
DOI: 10.6084/m9.figshare.1311743.v2
title: Forensic analysis of the microbiome of phones and shoes

description: In this study, 2 participants sampled the front and back of their cell phones, four different locations on the soles of their shoes, and the floor beneath them every waking hour over a 2 day period. A further 89 participants took individual samples of their shoes and phones at three different scientific conferences.
DOI: 10.6084/m9.figshare.1311726
title: S1 Dataset

description: Financial log-returns at both the daily and intraday frequency and implied volatility of an index option.
DOI: 10.6084/m9.figshare.1311718
title: 2014 09 13 Field Notes

description: Field notes including image and/or video records.<br>Project order 41a<br>
DOI: 10.6084/m9.figshare.1311724
title: Shoe and Phone Microbiome

description: In this study, 2 participants sampled the front and back of their cell phones, four different locations on the soles of their shoes, and the floor beneath them every waking hour over a 2 day period. A further 89 participants took individual samples of their shoes and phones at three different scientific conferences.
DOI: 10.6084/m9.figshare.1311724.v1
title: Shoe and Phone Microbiome

description: In this study, 2 participants sampled the front and back of their cell phones, four different locations on the soles of their shoes, and the floor beneath them every waking hour over a 2 day period. A further 89 participants took individual samples of their shoes and phones at three different scientific conferences.
DOI: 10.6084/m9.figshare.1311672
title: Aggregated APC data 2014

description: This spreadsheet contains two tables and three charts which explore aggregated data of 6,741 article processing charges (APCs) paid by 22 UK higher education institutions during 2014. The data was collected as part of Jisc's APC data collection project to address the Total Cost of Ownership of scholarly communication (https://www.jisc-collections.ac.uk/Jisc-Monitor/APC-data-collection/). Now updated to include two more institutions, as well as article-level APC data.
DOI: 10.6084/m9.figshare.1311684
title: FigShare harvested dataset licenses at 31-12-2014

description: This dataset contains the output of a script harvester we run against FigShare to gather the licenses associated to the dataset it contains. For each figShare dataset page URL we show the license associated (and we count them) Example: 1,http://figshare.com/articles/Computed_List_of_H2D_Lines/1282524,CC-BY
DOI: 10.6084/m9.figshare.1311684.v1
title: FigShare harvested dataset licenses at 31-12-2014

description: This dataset contains the output of a script harvester we run against FigShare to gather the licenses associated to the dataset it contains. For each figShare dataset page URL we show the license associated (and we count them) Example: 1,http://figshare.com/articles/Computed_List_of_H2D_Lines/1282524,CC-BY
DOI: 10.6084/m9.figshare.1311718.v1
title: 13 September 2014 Field Notes

description: Field notes including image and/or video records.
DOI: 10.6084/m9.figshare.1311670
title: 2014 09 12 Field Notes

description: Field notes including image and/or video records.<br>Project order 40a<br>
DOI: 10.6084/m9.figshare.1311718.v3
title: 2014 09 13 Field Notes

description: Field notes including image and/or video records.<br>Project order 41a<br>
DOI: 10.6084/m9.figshare.1311718.v2
title: 2014 09 13 Field Notes

description: Field notes including image and/or video records.
DOI: 10.6084/m9.figshare.1311670.v1
title: 12 September 2014 Field Notes

description: Field notes including image and/or video records.
DOI: 10.6084/m9.figshare.1311672.v1
title: APC data 2014

description: This spreadsheet contains two tables and three charts which explore aggregated data of 6,061 article processing charges (APCs) paid by 20 UK higher education institutions during 2014. The data was collected as part of Jisc's APC data collection project to address the Total Cost of Ownership of scholarly communication (https://www.jisc-collections.ac.uk/Jisc-Monitor/APC-data-collection/).
DOI: 10.6084/m9.figshare.1311670.v3
title: 2014 09 12 Field Notes

description: Field notes including image and/or video records.<br>Project order 40a<br>
DOI: 10.6084/m9.figshare.1311647
title: Effects of visual fidelity on curve negotiation, gaze behaviour and simulator discomfort

description: Technological developments have led to increased visual fidelity of driving simulators. However, simplified visuals have potential advantages, such as improved experimental control, reduced simulator discomfort and increased generalisability of results. In this driving simulator study, we evaluated the effects of visual fidelity on driving performance, gaze behaviour and subjective discomfort ratings. Twenty-four participants drove a track with 90° corners in (1) a high fidelity, textured environment, (2) a medium fidelity, non-textured environment without scenery objects and (3) a low-fidelity monochrome environment that only showed lane markers. The high fidelity level resulted in higher steering activity on straight road segments, higher driving speeds and higher gaze variance than the lower fidelity levels. No differences were found between the two lower fidelity levels. In conclusion, textures and objects were found to affect steering activity and driving performance; however, gaze behaviour during curve negotiation and self-reported simulator discomfort were unaffected.<b>Practitioner Summary</b>: In a driving simulator study, three levels of visual fidelity were evaluated. The results indicate that the highest fidelity level, characterised by a textured environment, resulted in higher steering activity, higher driving speeds and higher variance of horizontal gaze than the two lower fidelity levels without textures.
DOI: 10.6084/m9.figshare.1311672.v2
title: Aggregated APC data 2014

description: This spreadsheet contains two tables and three charts which explore aggregated data of 6,061 article processing charges (APCs) paid by 20 UK higher education institutions during 2014. The data was collected as part of Jisc's APC data collection project to address the Total Cost of Ownership of scholarly communication (https://www.jisc-collections.ac.uk/Jisc-Monitor/APC-data-collection/).
DOI: 10.6084/m9.figshare.1311647.v2
title: Effects of visual fidelity on curve negotiation, gaze behaviour and simulator discomfort

description: Technological developments have led to increased visual fidelity of driving simulators. However, simplified visuals have potential advantages, such as improved experimental control, reduced simulator discomfort and increased generalisability of results. In this driving simulator study, we evaluated the effects of visual fidelity on driving performance, gaze behaviour and subjective discomfort ratings. Twenty-four participants drove a track with 90° corners in (1) a high fidelity, textured environment, (2) a medium fidelity, non-textured environment without scenery objects and (3) a low-fidelity monochrome environment that only showed lane markers. The high fidelity level resulted in higher steering activity on straight road segments, higher driving speeds and higher gaze variance than the lower fidelity levels. No differences were found between the two lower fidelity levels. In conclusion, textures and objects were found to affect steering activity and driving performance; however, gaze behaviour during curve negotiation and self-reported simulator discomfort were unaffected.<b>Practitioner Summary</b>: In a driving simulator study, three levels of visual fidelity were evaluated. The results indicate that the highest fidelity level, characterised by a textured environment, resulted in higher steering activity, higher driving speeds and higher variance of horizontal gaze than the two lower fidelity levels without textures.
DOI: 10.6084/m9.figshare.1311670.v2
title: 2014 09 12 Field Notes

description: Field notes including image and/or video records.
DOI: 10.6084/m9.figshare.1311672.v4
title: Aggregated APC data 2014

description: This spreadsheet contains two tables and three charts which explore aggregated data of 6,741 article processing charges (APCs) paid by 22 UK higher education institutions during 2014. The data was collected as part of Jisc's APC data collection project to address the Total Cost of Ownership of scholarly communication (https://www.jisc-collections.ac.uk/Jisc-Monitor/APC-data-collection/). Now updated to include two more institutions, as well as article-level APC data.
DOI: 10.6084/m9.figshare.1311647.v1
title: Effects of visual fidelity on curve negotiation, gaze behaviour and simulator discomfort

description: Technological developments have led to increased visual fidelity of driving simulators. However, simplified visuals have potential advantages, such as improved experimental control, reduced simulator discomfort and increased generalisability of results. In this driving simulator study, we evaluated the effects of visual fidelity on driving performance, gaze behaviour and subjective discomfort ratings. Twenty-four participants drove a track with 90° corners in (1) a high fidelity, textured environment, (2) a medium fidelity, non-textured environment without scenery objects and (3) a low-fidelity monochrome environment that only showed lane markers. The high fidelity level resulted in higher steering activity on straight road segments, higher driving speeds and higher gaze variance than the lower fidelity levels. No differences were found between the two lower fidelity levels. In conclusion, textures and objects were found to affect steering activity and driving performance; however, gaze behaviour during curve negotiation and self-reported simulator discomfort were unaffected.<b>Practitioner Summary</b>: In a driving simulator study, three levels of visual fidelity were evaluated. The results indicate that the highest fidelity level, characterised by a textured environment, resulted in higher steering activity, higher driving speeds and higher variance of horizontal gaze than the two lower fidelity levels without textures.
DOI: 10.6084/m9.figshare.1311672.v3
title: Aggregated APC data 2014

description: This spreadsheet contains two tables and three charts which explore aggregated data of 6,741 article processing charges (APCs) paid by 22 UK higher education institutions during 2014. The data was collected as part of Jisc's APC data collection project to address the Total Cost of Ownership of scholarly communication (https://www.jisc-collections.ac.uk/Jisc-Monitor/APC-data-collection/). Now updated to include two more institutions, as well as article-level APC data.