cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1384855.v5
title: SMAD signaling and redox imbalance cooperate to induce prostate cancer cell dormancy

description: Metastasis involves the dissemination of single or small clumps of cancer cells through blood or lymphatic vessels and their extravasation into distant organs. Despite the strong regulation of metastases development by a cell dormancy phenomenon, the dormant state of cancer cells remains poorly characterized due to the difficulty of <i>in vivo</i> studies. We have recently shown <i>in vitro</i> that clonogenicity of prostate cancer cells is regulated by a dormancy phenomenon that is strongly induced when cells are cultured both at low cell density and in a slightly hypertonic medium. Here, we characterized by RT-qPCR a genetic expression signature of this dormant state which combines the presence of both stemness and differentiation markers. We showed that both TFGβ/BMP signaling and redox imbalance are required for the full induction of this dormancy signature and cell quiescence. Moreover, reconstruction experiments showed that TFGβ/BMP signaling and redox imbalance are sufficient to generate a pattern of genetic expression displaying all characteristic features of the dormancy signature. Finally, we observed that low cell density was sufficient to activate TGFβ/BMP signaling and to generate a slight redox imbalance thus priming cells for dormancy that can be attained with a co-stimulus like hypertonicity, most likely through an increased redox imbalance. The identification of a dual regulation of dormancy provides a framework for the interpretation of previous reports showing a restricted ability of BMP signaling to regulate cancer cell dormancy <i>in vivo</i> and draws attention on the role of oxidative stress in the metastatic process.
DOI: 10.6084/m9.figshare.1384846.v1
title: Covariance Partition Priors: A Bayesian Approach to Simultaneous Covariance Estimation for Longitudinal Data

description: The estimation of the covariance matrix is a key concern in the analysis of longitudinal data. When data consists of multiple groups, it is often assumed the covariance matrices are either equal across groups or are completely distinct. We seek methodology to allow borrowing of strength across potentially similar groups to improve estimation. To that end, we introduce a covariance partition prior which proposes a partition of the groups at each measurement time. Groups in the same set of the partition share dependence parameters for the distribution of the current measurement given the preceding ones, and the sequence of partitions is modeled as a Markov chain to encourage similar structure at nearby measurement times. This approach additionally encourages a lower-dimensional structure of the covariance matrices by shrinking the parameters of the Cholesky decomposition toward zero. We demonstrate the performance of our model through two simulation studies and the analysis of data from a depression study. This article includes Supplementary Material available online.
DOI: 10.6084/m9.figshare.1384855.v4
title: SMAD signaling and redox imbalance cooperate to induce prostate cancer cell dormancy

description: Metastasis involves the dissemination of single or small clumps of cancer cells through blood or lymphatic vessels and their extravasation into distant organs. Despite the strong regulation of metastases development by a cell dormancy phenomenon, the dormant state of cancer cells remains poorly characterized due to the difficulty of <i>in vivo</i> studies. We have recently shown <i>in vitro</i> that clonogenicity of prostate cancer cells is regulated by a dormancy phenomenon that is strongly induced when cells are cultured both at low cell density and in a slightly hypertonic medium. Here, we characterized by RT-qPCR a genetic expression signature of this dormant state which combines the presence of both stemness and differentiation markers. We showed that both TFGβ/BMP signaling and redox imbalance are required for the full induction of this dormancy signature and cell quiescence. Moreover, reconstruction experiments showed that TFGβ/BMP signaling and redox imbalance are sufficient to generate a pattern of genetic expression displaying all characteristic features of the dormancy signature. Finally, we observed that low cell density was sufficient to activate TGFβ/BMP signaling and to generate a slight redox imbalance thus priming cells for dormancy that can be attained with a co-stimulus like hypertonicity, most likely through an increased redox imbalance. The identification of a dual regulation of dormancy provides a framework for the interpretation of previous reports showing a restricted ability of BMP signaling to regulate cancer cell dormancy <i>in vivo</i> and draws attention on the role of oxidative stress in the metastatic process.
DOI: 10.6084/m9.figshare.1384845
title: The 3'-5' exoribonuclease Dis3 regulates the expression of specific microRNAs in <i>Drosophila</i> wing imaginal discs

description: Dis3 is a highly conserved exoribonuclease which degrades RNAs in the 3'-5' direction. Mutations in Dis3 are associated with a number of human cancers including multiple myeloma and acute myeloid leukemia. In this work, we have assessed the effect of a Dis3 knockdown on <i>Drosophila</i> imaginal disc development and on expression of mature microRNAs. We find that Dis3 knockdown severely disrupts the development of wing imaginal discs in that the flies have a “no wing” phenotype. Use of RNA-seq to quantify the effect of Dis3 knockdown on microRNA expression shows that Dis3 normally regulates a small subset of microRNAs, with only 11 (10.1%) increasing in level ≥2-fold and 6 (5.5%) decreasing in level ≥2-fold. Of these microRNAs, <i>miR-252–5p</i> is increased 2.1-fold in Dis3-depleted cells compared to controls while the level of the <i>miR-252</i> precursor is unchanged, suggesting that Dis3 can act in the cytoplasm to specifically degrade this mature miRNA. Furthermore, our experiments suggest that Dis3 normally interacts with the exosomal subunit Rrp40 in the cytoplasm to target <i>miR-252–5p</i> for degradation during normal wing development. Another microRNA, <i>miR-982–5p</i>, is expressed at lower levels in Dis3 knockdown cells, while the <i>miR-982</i> precursor remains unchanged, indicating that Dis3 is involved in its processing. Our study therefore reveals an unexpected specificity for this ribonuclease toward microRNA regulation, which is likely to be conserved in other eukaryotes and may be relevant to understanding its role in human disease.
DOI: 10.6084/m9.figshare.1384845.v1
title: The 3’-5’ exoribonuclease Dis3 regulates the expression of specific microRNAs in <i>Drosophila</i> wing imaginal discs

description: Dis3 is a highly conserved exoribonuclease which degrades RNAs in the 3'-5' direction. Mutations in Dis3 are associated with a number of human cancers including multiple myeloma and acute myeloid leukaemia. In this work, we have assessed the effect of a Dis3 knockdown on <i>Drosophila</i> imaginal disc development and on expression of mature microRNAs. We find that Dis3 knockdown severely disrupts the development of wing imaginal discs in that the flies have a “no wing” phenotype. Use of RNA-seq to quantify the effect of Dis3 knockdown on microRNA expression shows that Dis3 normally regulates a small subset of microRNAs, with only 11 (10.1%) increasing in level &gt; 2-fold and 6 (5.5%) decreasing in level &gt;2-fold. Of these microRNAs, <i>miR–252–5p</i> is increased 2.1-fold in Dis3-depleted cells compared to controls while the level of the <i>miR–252</i> precursor is unchanged, suggesting that Dis3 can act in the cytoplasm to specifically degrade this mature miRNA. Furthermore, our experiments suggest that Dis3 normally interacts with the exosomal subunit Rrp40 in the cytoplasm to target <i>miR–252–5p</i> for degradation during normal wing development. Another microRNA, <i>miR–982–5p</i>, is expressed at lower levels in Dis3 knockdown cells, while the <i>miR–982</i> precursor remains unchanged, indicating that Dis3 is involved in its processing. Our study therefore reveals an unexpected specificity for this ribonuclease towards microRNA regulation, which is likely to be conserved in other eukaryotes and may be relevant to understanding its role in human disease.
DOI: 10.6084/m9.figshare.1384833
title: Supplemental data for article " Maturation of oral microbiota in children with or without dental caries"

description: Supplemental data for article " Maturation of oral microbiota in children with or without dental caries" PLOS ONE PONE-D-15-10554 corresponding author Pernilla Lif Holgerson pernilla.lif@umu.se
DOI: 10.6084/m9.figshare.1384833.v1
title: Supplemental data for article " Maturation of oral microbiota in children with or without dental caries"

description: Supplemental data for article " Maturation of oral microbiota in children with or without dental caries" PLOS ONE PONE-D-15-10554 corresponding author Pernilla Lif Holgerson pernilla.lif@umu.se
DOI: 10.6084/m9.figshare.1384845.v3
title: The 3'-5' exoribonuclease Dis3 regulates the expression of specific microRNAs in <i>Drosophila</i> wing imaginal discs

description: Dis3 is a highly conserved exoribonuclease which degrades RNAs in the 3'-5' direction. Mutations in Dis3 are associated with a number of human cancers including multiple myeloma and acute myeloid leukemia. In this work, we have assessed the effect of a Dis3 knockdown on <i>Drosophila</i> imaginal disc development and on expression of mature microRNAs. We find that Dis3 knockdown severely disrupts the development of wing imaginal discs in that the flies have a “no wing” phenotype. Use of RNA-seq to quantify the effect of Dis3 knockdown on microRNA expression shows that Dis3 normally regulates a small subset of microRNAs, with only 11 (10.1%) increasing in level ≥2-fold and 6 (5.5%) decreasing in level ≥2-fold. Of these microRNAs, <i>miR-252–5p</i> is increased 2.1-fold in Dis3-depleted cells compared to controls while the level of the <i>miR-252</i> precursor is unchanged, suggesting that Dis3 can act in the cytoplasm to specifically degrade this mature miRNA. Furthermore, our experiments suggest that Dis3 normally interacts with the exosomal subunit Rrp40 in the cytoplasm to target <i>miR-252–5p</i> for degradation during normal wing development. Another microRNA, <i>miR-982–5p</i>, is expressed at lower levels in Dis3 knockdown cells, while the <i>miR-982</i> precursor remains unchanged, indicating that Dis3 is involved in its processing. Our study therefore reveals an unexpected specificity for this ribonuclease toward microRNA regulation, which is likely to be conserved in other eukaryotes and may be relevant to understanding its role in human disease.
DOI: 10.6084/m9.figshare.1384832
title: Supplemental information for article "Maturation of oral microbiota in children with or without dental caries"

description: Supplemental information for article "Maturation of oral microbiota in children with or without dental caries" PLOS ONE PONE-D-15-10554 corresponding author: Pernilla Lif Holgerson pernilla.lif@umu.se
DOI: 10.6084/m9.figshare.1384832.v1
title: Supplemental information for article "Maturation of oral microbiota in children with or without dental caries"

description: Supplemental information for article "Maturation of oral microbiota in children with or without dental caries" PLOS ONE PONE-D-15-10554 corresponding author: Pernilla Lif Holgerson pernilla.lif@umu.se
DOI: 10.6084/m9.figshare.1384845.v2
title: The 3'-5' exoribonuclease Dis3 regulates the expression of specific microRNAs in <i>Drosophila</i> wing imaginal discs

description: Dis3 is a highly conserved exoribonuclease which degrades RNAs in the 3'-5' direction. Mutations in Dis3 are associated with a number of human cancers including multiple myeloma and acute myeloid leukemia. In this work, we have assessed the effect of a Dis3 knockdown on <i>Drosophila</i> imaginal disc development and on expression of mature microRNAs. We find that Dis3 knockdown severely disrupts the development of wing imaginal discs in that the flies have a “no wing” phenotype. Use of RNA-seq to quantify the effect of Dis3 knockdown on microRNA expression shows that Dis3 normally regulates a small subset of microRNAs, with only 11 (10.1%) increasing in level ≥2-fold and 6 (5.5%) decreasing in level ≥2-fold. Of these microRNAs, <i>miR-252–5p</i> is increased 2.1-fold in Dis3-depleted cells compared to controls while the level of the <i>miR-252</i> precursor is unchanged, suggesting that Dis3 can act in the cytoplasm to specifically degrade this mature miRNA. Furthermore, our experiments suggest that Dis3 normally interacts with the exosomal subunit Rrp40 in the cytoplasm to target <i>miR-252–5p</i> for degradation during normal wing development. Another microRNA, <i>miR-982–5p</i>, is expressed at lower levels in Dis3 knockdown cells, while the <i>miR-982</i> precursor remains unchanged, indicating that Dis3 is involved in its processing. Our study therefore reveals an unexpected specificity for this ribonuclease toward microRNA regulation, which is likely to be conserved in other eukaryotes and may be relevant to understanding its role in human disease.
DOI: 10.6084/m9.figshare.1384769
title: Gaussian Job Archive for C6H6Br6

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1384769.v1
title: Gaussian Job Archive for C6H6Br6

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1384768
title: Gaussian Job Archive for C6H6Br6

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1384767
title: Snow zonation on Hielo Patagónico Sur, southern Patagonia, derived from Landsat 5 TM data

description: This dataset contains the classification of glacier surface of the South Patagonian Icefield published in: <em><strong>De Angelis, Hernán, Frank Rau, and Pedro Skvarca. "Snow zonation on Hielo Patagónico Sur, southern Patagonia, derived from Landsat 5 TM data." Global and Planetary Change 59.1 (2007): 149-158.</strong></em> The dataset contains four files: DeAngelis-Rau-Skvarca_2007_SnowZonationOnHieloPatagonicoSur_ClassifiedImage.tif A geographically enabled RGB file that can be displayed in any browser. DeAngelis-Rau-Skvarca_2007_SnowZonationOnHieloPatagonicoSur_DataImage.tif A GeoTiff image with the classification itself, suitable for analysis. DeAngelis-Rau-Skvarca_2007_SnowZonationOnHieloPatagonicoSur_OverviewMap.png An overview map, for visualization and presentation. DeAngelis-Rau-Skvarca_2007_SnowZonationOnHieloPatagonicoSur_ClassificationReport.txt The original classification report. <strong>Use of these files is subject to the conditions of the license, meaning that users are free to use, modify and redistribute, with the condition to cite the source article and authors.</strong>
DOI: 10.6084/m9.figshare.1384768.v1
title: Gaussian Job Archive for C6H6Br6

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1383961
title: Phytogeographical affinities at the crossroads of two continents: Distribution patterns of Lamiaceae in Chios Island (East Aegean Islands, Greece) and Çeşme–Karaburun Peninsula (West Anatolia, Turkey)

description: The East Aegean (East Aegean Islands, Greece and West Anatolia, Turkey) is a biogeographically transitional region, where biodiversity elements from Europe and Asia join. However, affinities in the region were until recently scarcely explored. We assess biogeographical affinities in the East Aegean focusing on distribution patterns of Lamiaceae plants in Chios Island and its adjacent Çeşme–Karaburun Peninsula. Detailed <i>in-situ</i> record was acquired for 48 native species. These were grouped based on their habitat and geological substrate preference, their distribution was mapped in grid cells and distribution patterns were analysed in relation to species groupings. In both Chios and Çeşme–Karaburun, species follow five distribution patterns: widespread, locally widespread, locally restricted, sporadic and rare. Fifty to 62% of the species exhibit similar distribution patterns, trends in habitat and geological substrate preference in Chios and Çeşme–Karaburun, results complying with previous evidence of close biogeographical affinities of the East Aegean Islands and neighbouring Anatolia. Differences observed between the two regions may be attributed to insularity effects, human impact and the melange, an old rock matrix known for its key role in elucidating regional geodynamic evolution. Distributions of widespread and locally widespread species in Chios give evidence of density compensation and niche shifts responses, however, the actual occurrence of these phenomena in island plant populations is still to be elucidated. Overall, the species distribution patterns, particularly those of rare ones, reflect the complex geological history, palaeogeography and human influence in the Aegean region.
DOI: 10.6084/m9.figshare.1383587
title: Interspecies quantitative structure–activity–activity relationships (QSAARs) for prediction of acute aquatic toxicity of aromatic amines and phenols

description: We propose interspecies quantitative structure–activity–activity relationships (QSAARs), that is, QSARs with descriptors, to estimate species-specific acute aquatic toxicity. Using training datasets consisting of more than 100 aromatic amines and phenols, we found that the descriptors that predicted acute toxicities to fish (<i>Oryzias latipes</i>) and algae were daphnia toxicity, molecular weight (an indicator of molecular size and uptake) and selected indicator variables that discriminated between the absence or presence of various substructures. Molecular weight and the selected indicator variables improved the goodness-of-fit of the fish and algae toxicity prediction models. External validations of the QSAARs proved that algae toxicity could be predicted within 1.0 log unit and revealed structural profiles of outlier chemicals with respect to fish toxicity. In addition, applicability domains based on leverage values provided structural alerts for the predicted fish toxicity of chemicals with more than one hydroxyl or amino group attached to an aromatic ring, but not for fluoroanilines, which were not included in the training dataset. Although these simple QSAARs have limitations, their applicability is defined so clearly that they may be practical for screening chemicals with molecular weights of ≤364.9.
DOI: 10.6084/m9.figshare.1383587.v4
title: Interspecies quantitative structure–activity–activity relationships (QSAARs) for prediction of acute aquatic toxicity of aromatic amines and phenols

description: We propose interspecies quantitative structure–activity–activity relationships (QSAARs), that is, QSARs with descriptors, to estimate species-specific acute aquatic toxicity. Using training datasets consisting of more than 100 aromatic amines and phenols, we found that the descriptors that predicted acute toxicities to fish (<i>Oryzias latipes</i>) and algae were daphnia toxicity, molecular weight (an indicator of molecular size and uptake) and selected indicator variables that discriminated between the absence or presence of various substructures. Molecular weight and the selected indicator variables improved the goodness-of-fit of the fish and algae toxicity prediction models. External validations of the QSAARs proved that algae toxicity could be predicted within 1.0 log unit and revealed structural profiles of outlier chemicals with respect to fish toxicity. In addition, applicability domains based on leverage values provided structural alerts for the predicted fish toxicity of chemicals with more than one hydroxyl or amino group attached to an aromatic ring, but not for fluoroanilines, which were not included in the training dataset. Although these simple QSAARs have limitations, their applicability is defined so clearly that they may be practical for screening chemicals with molecular weights of ≤364.9.
DOI: 10.6084/m9.figshare.1383587.v3
title: Interspecies quantitative structure–activity–activity relationships (QSAARs) for prediction of acute aquatic toxicity of aromatic amines and phenols

description: We propose interspecies quantitative structure–activity–activity relationships (QSAARs), that is, QSARs with descriptors, to estimate species-specific acute aquatic toxicity. Using training datasets consisting of more than 100 aromatic amines and phenols, we found that the descriptors that predicted acute toxicities to fish (<em>Oryzias latipes</em>) and algae were daphnia toxicity, molecular weight (an indicator of molecular size and uptake) and selected indicator variables that discriminated between the absence or presence of various substructures. Molecular weight and the selected indicator variables improved the goodness-of-fit of the fish and algae toxicity prediction models. External validations of the QSAARs proved that algae toxicity could be predicted within 1.0 log unit and revealed structural profiles of outlier chemicals with respect to fish toxicity. In addition, applicability domains based on leverage values provided structural alerts for the predicted fish toxicity of chemicals with more than one hydroxyl or amino group attached to an aromatic ring, but not for fluoroanilines, which were not included in the training dataset. Although these simple QSAARs have limitations, their applicability is defined so clearly that they may be practical for screening chemicals with molecular weights of ≤364.9.
DOI: 10.6084/m9.figshare.1383961.v2
title: Phytogeographical affinities at the crossroads of two continents: Distribution patterns of Lamiaceae in Chios Island (East Aegean Islands, Greece) and Çeşme–Karaburun Peninsula (West Anatolia, Turkey)

description: The East Aegean (East Aegean Islands, Greece and West Anatolia, Turkey) is a biogeographically transitional region, where biodiversity elements from Europe and Asia join. However, affinities in the region were until recently scarcely explored. We assess biogeographical affinities in the East Aegean focusing on distribution patterns of Lamiaceae plants in Chios Island and its adjacent Çeşme–Karaburun Peninsula. Detailed <i>in-situ</i> record was acquired for 48 native species. These were grouped based on their habitat and geological substrate preference, their distribution was mapped in grid cells and distribution patterns were analysed in relation to species groupings. In both Chios and Çeşme–Karaburun, species follow five distribution patterns: widespread, locally widespread, locally restricted, sporadic and rare. Fifty to 62% of the species exhibit similar distribution patterns, trends in habitat and geological substrate preference in Chios and Çeşme–Karaburun, results complying with previous evidence of close biogeographical affinities of the East Aegean Islands and neighbouring Anatolia. Differences observed between the two regions may be attributed to insularity effects, human impact and the melange, an old rock matrix known for its key role in elucidating regional geodynamic evolution. Distributions of widespread and locally widespread species in Chios give evidence of density compensation and niche shifts responses, however, the actual occurrence of these phenomena in island plant populations is still to be elucidated. Overall, the species distribution patterns, particularly those of rare ones, reflect the complex geological history, palaeogeography and human influence in the Aegean region.