cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1296276.v1
title: Ubiquitination and proteasomal degradation of ATG12 regulates its proapoptotic activity

description: During macroautophagy, conjugation of ATG12 to ATG5 is essential for LC3 lipidation and autophagosome formation. Additionally, ATG12 has ATG5-independent functions in diverse processes including mitochondrial fusion and mitochondrial-dependent apoptosis. In this study, we investigated the regulation of free ATG12. In stark contrast to the stable ATG12–ATG5 conjugate, we find that free ATG12 is highly unstable and rapidly degraded in a proteasome-dependent manner. Surprisingly, ATG12, itself a ubiquitin-like protein, is directly ubiquitinated and this promotes its proteasomal degradation. As a functional consequence of its turnover, accumulation of free ATG12 contributes to proteasome inhibitor-mediated apoptosis, a finding that may be clinically important given the use of proteasome inhibitors as anticancer agents. Collectively, our results reveal a novel interconnection between autophagy, proteasome activity, and cell death mediated by the ubiquitin-like properties of ATG12.
DOI: 10.6084/m9.figshare.1296276.v3
title: Ubiquitination and proteasomal degradation of ATG12 regulates its proapoptotic activity

description: During macroautophagy, conjugation of ATG12 to ATG5 is essential for LC3 lipidation and autophagosome formation. Additionally, ATG12 has ATG5-independent functions in diverse processes including mitochondrial fusion and mitochondrial-dependent apoptosis. In this study, we investigated the regulation of free ATG12. In stark contrast to the stable ATG12–ATG5 conjugate, we find that free ATG12 is highly unstable and rapidly degraded in a proteasome-dependent manner. Surprisingly, ATG12, itself a ubiquitin-like protein, is directly ubiquitinated and this promotes its proteasomal degradation. As a functional consequence of its turnover, accumulation of free ATG12 contributes to proteasome inhibitor-mediated apoptosis, a finding that may be clinically important given the use of proteasome inhibitors as anticancer agents. Collectively, our results reveal a novel interconnection between autophagy, proteasome activity, and cell death mediated by the ubiquitin-like properties of ATG12.
DOI: 10.6084/m9.figshare.1296278.v2
title: A novel cytostatic form of autophagy in sensitization of non-small cell lung cancer cells to radiation by vitamin D and the vitamin D analog, EB 1089

description: The standard of care for unresectable lung cancer is chemoradiation. However, therapeutic options are limited and patients are rarely cured. We have previously shown that vitamin D and vitamin D analogs such as EB 1089 can enhance the response to radiation in breast cancer through the promotion of a cytotoxic form of autophagy. In A549 and H460 non-small cell lung cancer (NSCLC) cells, 1,25-D<sub>3</sub> (the hormonally active form of vitamin D) and EB 1089 prolonged the growth arrest induced by radiation alone and suppressed proliferative recovery, which translated to a significant reduction in clonogenic survival. In H838 or H358 NSCLC cells, which lack VDR/vitamin D receptor or functional TP53, respectively, 1,25-D<sub>3</sub> failed to modify the extent of radiation-induced growth arrest or suppress proliferative recovery post-irradiation. Sensitization to radiation in H1299 NSCLC cells was evident only when TP53 was induced in otherwise <i>tp53</i>-null H1299 NSCLC cells. Sensitization was not associated with increased DNA damage, decreased DNA repair or an increase in apoptosis, necrosis, or senescence. Instead sensitization appeared to be a consequence of the conversion of the cytoprotective autophagy induced by radiation alone to a novel cytostatic form of autophagy by the combination of 1,25-D<sub>3</sub> or EB 1089 with radiation. While both pharmacological and genetic suppression of autophagy or inhibition of AMPK phosphorylation sensitized the NSCLC cells to radiation alone, inhibition of the cytostatic autophagy induced by the combination treatment reversed sensitization. Evidence for selectivity was provided by lack of radiosensitization in normal human bronchial cells and cardiomyocytes. Taken together, these studies have identified a unique cytostatic function of autophagy that appears to be mediated by VDR, TP53, and possibly AMPK in the promotion of an enhanced response to radiation by 1,25-D<sub>3</sub> and EB 1089 in NSCLC.
DOI: 10.6084/m9.figshare.1296270
title: Comprehensive analysis of small RNA-seq data reveals that combination of miRNA with its isomiRs increase the accuracy of target prediction in <i>Arabidopsis thaliana</i>

description: Along with the canonical miRNA, distinct miRNA-like sequences called sibling miRNAs (sib-miRs) are generated from the same pre-miRNA. Among them, isomeric sequences featuring slight variations at the terminals, relative to the canonical miRNA, constitute a pool of isomeric sibling miRNAs (isomiRs). Despite the high prevalence of isomiRs in eukaryotes, their features and relevance remain elusive. In this study, we performed a comprehensive analysis of mature precursor miRNA (pre-miRNA) sequences from <i>Arabidopsis</i> to understand their features and regulatory targets. The influence of isomiR terminal heterogeneity in target binding was examined comprehensively. Our comprehensive analyses suggested a novel computational strategy that utilizes miRNA and its isomiRs to enhance the accuracy of their regulatory target prediction in <i>Arabidopsis</i>. A few targets are shared by several members of isomiRs; however, this phenomenon was not typical. Gene Ontology (GO) enrichment analysis showed that commonly targeted mRNAs were enriched for certain GO terms. Moreover, comparison of these commonly targeted genes with validated targets from published data demonstrated that the validated targets are bound by most isomiRs and not only the canonical miRNA. Furthermore, the biological role of isomiRs in target cleavage was supported by degradome data. Incorporating this finding, we predicted potential target genes of several miRNAs and confirmed them by experimental assays. This study proposes a novel strategy to improve the accuracy of predicting miRNA targets through combined use of miRNA with its isomiRs.
DOI: 10.6084/m9.figshare.1296276.v2
title: Ubiquitination and proteasomal degradation of ATG12 regulates its proapoptotic activity

description: During macroautophagy, conjugation of ATG12 to ATG5 is essential for LC3 lipidation and autophagosome formation. Additionally, ATG12 has ATG5-independent functions in diverse processes including mitochondrial fusion and mitochondrial-dependent apoptosis. In this study, we investigated the regulation of free ATG12. In stark contrast to the stable ATG12–ATG5 conjugate, we find that free ATG12 is highly unstable and rapidly degraded in a proteasome-dependent manner. Surprisingly, ATG12, itself a ubiquitin-like protein, is directly ubiquitinated and this promotes its proteasomal degradation. As a functional consequence of its turnover, accumulation of free ATG12 contributes to proteasome inhibitor-mediated apoptosis, a finding that may be clinically important given the use of proteasome inhibitors as anticancer agents. Collectively, our results reveal a novel interconnection between autophagy, proteasome activity, and cell death mediated by the ubiquitin-like properties of ATG12.
DOI: 10.6084/m9.figshare.1296261
title: Chikungunya Epidemic Dataset

description: Spreadsheet containing data on confirmed and suspected cumulative cases of chikungunya as well as deaths in 6 regions: North America, Central American Isthmus, Latin Caribbean, Andean Area, Southern Cone, and Non-Latin Caribbean. Read me file contains information about the spreadsheet (variable names, data source(s), important notes). Data obtained from the Pan American Health Organization.
DOI: 10.6084/m9.figshare.1296262
title: VExtractor_ontologies_and_semtypes.txt

description: Outline of the ontologies and semantic types used in the VExtractor algorithm
DOI: 10.6084/m9.figshare.1296270.v1
title: Comprehensive analysis of small RNA-seq data reveals that combination of miRNA with its isomiRs increase the accuracy of target prediction in <i>Arabidopsis</i>

description: ABSTRACTAlong with the canonical miRNA, distinct miRNA-like sequences called sibling miRNAs (sib-miRs) are generated from the same pre-miRNA. Among them, isomeric sequences featuring slight variations at the terminals, relative to the canonical miRNA, constitute a pool of isomeric sibling miRNAs (isomiRs). Despite the high prevalence of isomiRs in eukaryotes, their features and relevance remain elusive. In this study, we performed a comprehensive analysis of mature precursor miRNA (pre-miRNA) sequences from <i>Arabidopsis</i> to understand their features and regulatory targets. The influence of isomiR terminal heterogeneity in target binding was examined comprehensively. Our comprehensive analyses suggested a novel computational strategy that utilizes miRNA and its isomiRs to enhance the accuracy of their regulatory target prediction in <i>Arabidopsis</i>. A few targets are shared by several members of isomiRs; however, this phenomenon was not typical. Gene Ontology (GO) enrichment analysis showed that commonly targeted mRNAs were enriched for certain GO terms. Moreover, comparison of these commonly targeted genes with validated targets from published data demonstrated that the validated targets are bound by most isomiRs and not only the canonical miRNA. Furthermore, the biological role of isomiRs in target cleavage was supported by degradome data. Incorporating this finding, we predicted potential target genes of several miRNAs and confirmed them by experimental assays. This study proposes a novel strategy to improve the accuracy of predicting miRNA targets through combined use of miRNA with its isomiRs.
DOI: 10.6084/m9.figshare.1296232
title: University of Warwick APCs 2014

description: This spreadsheet contains details of article processing charges (APCs) paid by the University of Warwick during 2014. The data is being 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/) and has been released with permission of the University of Warwick Library.
DOI: 10.6084/m9.figshare.1296270.v2
title: Comprehensive analysis of small RNA-seq data reveals that combination of miRNA with its isomiRs increase the accuracy of target prediction in <i>Arabidopsis thaliana</i>

description: Along with the canonical miRNA, distinct miRNA-like sequences called sibling miRNAs (sib-miRs) are generated from the same pre-miRNA. Among them, isomeric sequences featuring slight variations at the terminals, relative to the canonical miRNA, constitute a pool of isomeric sibling miRNAs (isomiRs). Despite the high prevalence of isomiRs in eukaryotes, their features and relevance remain elusive. In this study, we performed a comprehensive analysis of mature precursor miRNA (pre-miRNA) sequences from <i>Arabidopsis</i> to understand their features and regulatory targets. The influence of isomiR terminal heterogeneity in target binding was examined comprehensively. Our comprehensive analyses suggested a novel computational strategy that utilizes miRNA and its isomiRs to enhance the accuracy of their regulatory target prediction in <i>Arabidopsis</i>. A few targets are shared by several members of isomiRs; however, this phenomenon was not typical. Gene Ontology (GO) enrichment analysis showed that commonly targeted mRNAs were enriched for certain GO terms. Moreover, comparison of these commonly targeted genes with validated targets from published data demonstrated that the validated targets are bound by most isomiRs and not only the canonical miRNA. Furthermore, the biological role of isomiRs in target cleavage was supported by degradome data. Incorporating this finding, we predicted potential target genes of several miRNAs and confirmed them by experimental assays. This study proposes a novel strategy to improve the accuracy of predicting miRNA targets through combined use of miRNA with its isomiRs.
DOI: 10.6084/m9.figshare.1296229
title: Pesticide toxicity in honey bee via wing contact

description: Dataset of the mortalities induced by thorax and wings contact with pesticides, 120 hours after contamination.
DOI: 10.6084/m9.figshare.1296270.v3
title: Comprehensive analysis of small RNA-seq data reveals that combination of miRNA with its isomiRs increase the accuracy of target prediction in <i>Arabidopsis thaliana</i>

description: Along with the canonical miRNA, distinct miRNA-like sequences called sibling miRNAs (sib-miRs) are generated from the same pre-miRNA. Among them, isomeric sequences featuring slight variations at the terminals, relative to the canonical miRNA, constitute a pool of isomeric sibling miRNAs (isomiRs). Despite the high prevalence of isomiRs in eukaryotes, their features and relevance remain elusive. In this study, we performed a comprehensive analysis of mature precursor miRNA (pre-miRNA) sequences from <i>Arabidopsis</i> to understand their features and regulatory targets. The influence of isomiR terminal heterogeneity in target binding was examined comprehensively. Our comprehensive analyses suggested a novel computational strategy that utilizes miRNA and its isomiRs to enhance the accuracy of their regulatory target prediction in <i>Arabidopsis</i>. A few targets are shared by several members of isomiRs; however, this phenomenon was not typical. Gene Ontology (GO) enrichment analysis showed that commonly targeted mRNAs were enriched for certain GO terms. Moreover, comparison of these commonly targeted genes with validated targets from published data demonstrated that the validated targets are bound by most isomiRs and not only the canonical miRNA. Furthermore, the biological role of isomiRs in target cleavage was supported by degradome data. Incorporating this finding, we predicted potential target genes of several miRNAs and confirmed them by experimental assays. This study proposes a novel strategy to improve the accuracy of predicting miRNA targets through combined use of miRNA with its isomiRs.
DOI: 10.6084/m9.figshare.1296229.v1
title: Pesticide toxicity in honey bee via wing contact

description: Dataset of the mortalities induced by thorax and wings contact with pesticides, 120 hours after contamination.
DOI: 10.6084/m9.figshare.1296156
title: Does the type of event influence how user interactions evolve on Twitter?

description: Set of graphs that represents interactions among Twitter users related to scheduled events.
DOI: 10.6084/m9.figshare.1296216
title: Spatial and temporal variation of community composition and species cover following dune restoration in the Devesa de Albufera (Valencia, Spain).

description: Plant populations were reintroduced to the coastal dune bar of the Devesa de Albufera from 1988 to 2004; different coastline sections received different species composition and cover. With the aim to detect spatial and temporal variation of floristic diversity, we compared current species composition and cover across the length of the Devesa and across the dune bar with those imposed at the time of restoration. Non-metric multidimensional scaling (NMDS) detected significant differences both across the dune faces and across the coast sections. Differences across the dune faces reflect the sea-inland ecological gradient and resulted from a spatial rearrangement of plant populations: <i>Calystegia soldanella</i>, <i>Achillea maritima</i> and <i>Polygonum maritimum</i> prefer the windward face; <i>Malcolmia littorea</i> and <i>Lagurus ovatus</i> the leeward. Differences across coast sections are related to those at restoration time, with a slow trend towards the homogenization of plant communities. At the current level of anthropic pressure, the plant cover is likely to evolve following the trends pointed out in this research.
DOI: 10.6084/m9.figshare.1296216.v2
title: Spatial and temporal variation of community composition and species cover following dune restoration in the Devesa de Albufera (Valencia, Spain).

description: Plant populations were reintroduced to the coastal dune bar of the Devesa de Albufera from 1988 to 2004; different coastline sections received different species composition and cover. With the aim to detect spatial and temporal variation of floristic diversity, we compared current species composition and cover across the length of the Devesa and across the dune bar with those imposed at the time of restoration. Non-metric multidimensional scaling (NMDS) detected significant differences both across the dune faces and across the coast sections. Differences across the dune faces reflect the sea-inland ecological gradient and resulted from a spatial rearrangement of plant populations: <i>Calystegia soldanella</i>, <i>Achillea maritima</i> and <i>Polygonum maritimum</i> prefer the windward face; <i>Malcolmia littorea</i> and <i>Lagurus ovatus</i> the leeward. Differences across coast sections are related to those at restoration time, with a slow trend towards the homogenization of plant communities. At the current level of anthropic pressure, the plant cover is likely to evolve following the trends pointed out in this research.
DOI: 10.6084/m9.figshare.1296270.v5
title: Comprehensive analysis of small RNA-seq data reveals that combination of miRNA with its isomiRs increase the accuracy of target prediction in <i>Arabidopsis thaliana</i>

description: Along with the canonical miRNA, distinct miRNA-like sequences called sibling miRNAs (sib-miRs) are generated from the same pre-miRNA. Among them, isomeric sequences featuring slight variations at the terminals, relative to the canonical miRNA, constitute a pool of isomeric sibling miRNAs (isomiRs). Despite the high prevalence of isomiRs in eukaryotes, their features and relevance remain elusive. In this study, we performed a comprehensive analysis of mature precursor miRNA (pre-miRNA) sequences from <i>Arabidopsis</i> to understand their features and regulatory targets. The influence of isomiR terminal heterogeneity in target binding was examined comprehensively. Our comprehensive analyses suggested a novel computational strategy that utilizes miRNA and its isomiRs to enhance the accuracy of their regulatory target prediction in <i>Arabidopsis</i>. A few targets are shared by several members of isomiRs; however, this phenomenon was not typical. Gene Ontology (GO) enrichment analysis showed that commonly targeted mRNAs were enriched for certain GO terms. Moreover, comparison of these commonly targeted genes with validated targets from published data demonstrated that the validated targets are bound by most isomiRs and not only the canonical miRNA. Furthermore, the biological role of isomiRs in target cleavage was supported by degradome data. Incorporating this finding, we predicted potential target genes of several miRNAs and confirmed them by experimental assays. This study proposes a novel strategy to improve the accuracy of predicting miRNA targets through combined use of miRNA with its isomiRs.
DOI: 10.6084/m9.figshare.1296156.v1
title: Does the type of event influence how user interactions evolve on Twitter?

description: Set of graphs that represents interactions among Twitter users related to scheduled events.
DOI: 10.6084/m9.figshare.1296216.v1
title: Spatial and temporal variation of community composition and species cover following dune restoration in the Devesa de Albufera (Valencia, Spain)

description: Plant populations were reintroduced to the coastal dune bar of the Devesa de Albufera from 1988 to 2004; different coastline sections received different species composition and cover. With the aim to detect spatial and temporal variation of floristic diversity, we compared current species composition and cover across the length of the Devesa and across the dune bar with those imposed at the time of restoration.
DOI: 10.6084/m9.figshare.1296270.v4
title: Comprehensive analysis of small RNA-seq data reveals that combination of miRNA with its isomiRs increase the accuracy of target prediction in <i>Arabidopsis thaliana</i>

description: Along with the canonical miRNA, distinct miRNA-like sequences called sibling miRNAs (sib-miRs) are generated from the same pre-miRNA. Among them, isomeric sequences featuring slight variations at the terminals, relative to the canonical miRNA, constitute a pool of isomeric sibling miRNAs (isomiRs). Despite the high prevalence of isomiRs in eukaryotes, their features and relevance remain elusive. In this study, we performed a comprehensive analysis of mature precursor miRNA (pre-miRNA) sequences from <i>Arabidopsis</i> to understand their features and regulatory targets. The influence of isomiR terminal heterogeneity in target binding was examined comprehensively. Our comprehensive analyses suggested a novel computational strategy that utilizes miRNA and its isomiRs to enhance the accuracy of their regulatory target prediction in <i>Arabidopsis</i>. A few targets are shared by several members of isomiRs; however, this phenomenon was not typical. Gene Ontology (GO) enrichment analysis showed that commonly targeted mRNAs were enriched for certain GO terms. Moreover, comparison of these commonly targeted genes with validated targets from published data demonstrated that the validated targets are bound by most isomiRs and not only the canonical miRNA. Furthermore, the biological role of isomiRs in target cleavage was supported by degradome data. Incorporating this finding, we predicted potential target genes of several miRNAs and confirmed them by experimental assays. This study proposes a novel strategy to improve the accuracy of predicting miRNA targets through combined use of miRNA with its isomiRs.
DOI: 10.6084/m9.figshare.1296151
title: Data from: Molecular evolution and island colonisation

description: For details of the contents of the fileset, please see the README file.
DOI: 10.6084/m9.figshare.1296151.v1
title: Data from: Molecular evolution and island colonisation

description: For details of the contents of the fileset, please see the README file.
DOI: 10.6084/m9.figshare.1296110
title: The St. John’s Hospital Cemetery and Environs, Cambridge: Contextualizing the Medieval Urban Dead

description: The excavation of four hundred complete and partial <i>in situ</i> burials from the Hospital of St. John the Evangelist, Cambridge, represented one of the largest medieval hospital osteoarchaeological assemblages from the British Isles. The significance of the group is enhanced by the detailed investigation of a carefully maintained network of pathways associated with the cemetery, the archaeological sequence that pre- and post-dated its use and a number of contemporary properties that were situated immediately outside its bounds. This evidence allows the cemetery to be placed within its urban context in a way that is rarely possible. The overwhelming majority of the burials were extended west-east aligned supine inhumations without grave-goods. Atypical burials included examples aligned east-west and south-north, a double burial, a prone burial and individuals buried with a jet crucifix and a brooch. Other significant finds included a nearby pit with four bodies in it, an anthropomorphic bone handle and a reused cruciform horse harness pendant. The proportion of males and females in the burial population is similar, whilst individuals who died under the age of sixteen are relatively uncommon and individuals aged under five are completely absent.
DOI: 10.6084/m9.figshare.1296109
title: Protein Folding and Non-Covalent Interactions Lectures

description: These six lectures examine the different non-covalent interactions present in proteins, such as hydrogen bonding, van der Waals interactions and the htdrophobic effect, and how these lead to proteins folding repeatability into unique structures.