cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1604826.v1
title: miR-155 targets Caspase-3 mRNA in activated macrophages

description: To secure the functionality of activated macrophages in the innate immune response, efficient life span control is required. Recognition of bacterial lipopolysaccharides (LPS) by toll-like receptor 4 (TLR4) induces downstream signaling pathways, which merge to induce the expression of cytokine genes and anti-apoptotic genes. MicroRNAs (miRNAs) have emerged as important inflammatory response modulators, but information about their functional impact on apoptosis is scarce. To identify miRNAs differentially expressed in response to LPS, cDNA libraries from untreated and LPS-activated murine macrophages were analyzed by deep sequencing and regulated miRNA expression was verified by Northern blotting and qPCR. Employing TargetScan<sup>TM</sup> we identified CASPASE-3 (CASP-3) mRNA that encodes a key player in apoptosis as potential target of LPS-induced miR-155. LPS-dependent primary macrophage activation revealed TLR4-mediated enhancement of miR-155 expression and CASP-3 mRNA reduction. Endogenous CASP-3 and cleaved CASP-3 protein declined in LPS-activated macrophages. Accumulation of miR-155 and CASP-3 mRNA in miRNA-induced silencing complexes (miRISC) was demonstrated by ARGONAUTE 2 (AGO2) immunoprecipitation. Importantly, specific antagomir transfection effectively reduced mature miR-155 and resulted in significantly elevated CASP-3 mRNA levels in activated macrophages. <i>In vitro</i> translation assays demonstrated that the target site in the CASP-3 mRNA 3'UTR mediates miR-155-dependent Luciferase reporter mRNA destabilization. Strikingly, Annexin V staining of macrophages transfected with antagomir-155 and stimulated with LPS prior to staurosporine (SSP) treatment implied that LPS-induced miR-155 prevents apoptosis through CASP-3 mRNA down-regulation. In conclusion, we report that miR-155-mediated CASP-3 mRNA destabilization in LPS-activated RAW 264.7 macrophages suppresses apoptosis, as a prerequisite to maintain their crucial function in inflammation.
DOI: 10.6084/m9.figshare.1604827.v1
title: Semi-supervised Multi-View Learning for Gene Network Reconstruction

description: Semi-supervised Multi-View Learning for Gene Network Reconstruction
DOI: 10.6084/m9.figshare.1604827.v2
title: Semi-supervised Multi-View Learning for Gene Network Reconstruction

description: Semi-supervised Multi-View Learning for Gene Network Reconstruction SynTReN Data: E.coli and Yeast sub-networks, generated expression data and gold standards (Input_Datasets.zip) Interactions predicted by base methods (Base_Method_Predictions.zip) Interactions predicted by our approach - Clustering performed with PCA (Predictions.zip) Interactions predicted by our approach - Clustering performed with K-means (PredictionsK.zip)
DOI: 10.6084/m9.figshare.1604791
title: Extremely low frequency electromagnetic fields affect proliferation and mitochondrial activity of human cancer cell lines

description: <i>Purpose</i>: To date, the effects of electromagnetic fields on cell metabolism have been overlooked. The objective of the present study was to investigate the influence of extremely low frequency electromagnetic fields (ELF-EMF) over mitochondrial metabolism and the consequent impact on cancer cell growth.<i>Materials and methods</i>: The effects of ELF-EMF on cancer growth were investigated in several human cancer cell lines by crystal violet assay. The modulation of mitochondrial activity was assessed by cytofluorimetric evaluation of membrane potential and by real-time quantification of mitochondrial transcription. Moreover the expression of several mitochondrial proteins and their levels in the organelle were evaluated.<i>Results</i>: The long-term exposure to ELF-EMF reduced the proliferation of several cancer cell lines and the effect was associated to an increased mitochondrial activity without evident changes in ATP levels. The results of our experiments excluded a transcriptional modulation of mitochondrial respiratory complexes, rather suggesting that ELF-EMF increased the energy demand. The altered mitochondrial metabolism led to changes in mitochondrial protein profile. In fact we found a downregulated expression of mitochondrial phospho-ERK, p53 and cytochrome c.<i>Conclusion</i>: The results of the present study indicate that ELF-EMF can negatively modulate cancer cell growth increasing respiratory activity of cells and altering mitochondrial protein expression.
DOI: 10.6084/m9.figshare.1604827.v3
title: Semi-supervised Multi-View Learning for Gene Network Reconstruction

description: Semi-supervised Multi-View Learning for Gene Network Reconstruction SynTReN Data: E.coli and Yeast sub-networks, generated expression data and gold standards (Input_Datasets.zip) Interactions predicted by base methods (Base_Method_Predictions.zip) Interactions predicted by our approach - Clustering performed with PCA (Predictions.zip) Interactions predicted by our approach - Clustering performed with K-means (PredictionsK.zip)
DOI: 10.6084/m9.figshare.1604791.v1
title: Extremely low frequency electromagnetic fields affect proliferation and mitochondrial activity of human cancer cell lines

description: <i>Purpose</i>: To date, the effects of electromagnetic fields on cell metabolism have been overlooked. The objective of the present study was to investigate the influence of extremely low frequency electromagnetic fields (ELF-EMF) over mitochondrial metabolism and the consequent impact on cancer cell growth.<i>Materials and methods</i>: The effects of ELF-EMF on cancer growth were investigated in several human cancer cell lines by crystal violet assay. The modulation of mitochondrial activity was assessed by cytofluorimetric evaluation of membrane potential and by real-time quantification of mitochondrial transcription. Moreover the expression of several mitochondrial proteins and their levels in the organelle were evaluated.<i>Results</i>: The long-term exposure to ELF-EMF reduced the proliferation of several cancer cell lines and the effect was associated to an increased mitochondrial activity without evident changes in ATP levels. The results of our experiments excluded a transcriptional modulation of mitochondrial respiratory complexes, rather suggesting that ELF-EMF increased the energy demand. The altered mitochondrial metabolism led to changes in mitochondrial protein profile. In fact we found a downregulated expression of mitochondrial phospho-ERK, p53 and cytochrome c.<i>Conclusion</i>: The results of the present study indicate that ELF-EMF can negatively modulate cancer cell growth increasing respiratory activity of cells and altering mitochondrial protein expression.
DOI: 10.6084/m9.figshare.1604827.v4
title: Semi-supervised Multi-View Learning for Gene Network Reconstruction

description: Semi-supervised Multi-View Learning for Gene Network Reconstruction SynTReN Data: E.coli and Yeast sub-networks, generated expression data and gold standards (Input_Datasets.zip) Interactions predicted by base methods (Base_Method_Predictions.zip) Interactions predicted by our approach - Clustering performed with PCA (Predictions.zip) Interactions predicted by our approach - Clustering performed with K-means (PredictionsK.zip)
DOI: 10.6084/m9.figshare.1604772
title: PLOS One ANN Data

description: Clinical and gait analysis data of 56 older adults.
DOI: 10.6084/m9.figshare.1604773
title: Gaussian Job Archive for C6H20O8

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1604770
title: Gaussian Job Archive for C6H20O8

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1604772.v1
title: PLOS One ANN Data

description: Clinical and gait analysis data of 56 older adults.
DOI: 10.6084/m9.figshare.1604827.v5
title: Semi-supervised Multi-View Learning for Gene Network Reconstruction

description: Semi-supervised Multi-View Learning for Gene Network Reconstruction SynTReN Data: E.coli and Yeast sub-networks, generated expression data and gold standards (Input_Datasets.zip) Interactions predicted by base methods (Base_Method_Predictions.zip) Interactions predicted by our approach - Clustering performed with PCA (Predictions.zip) Interactions predicted by our approach - Clustering performed with K-means (PredictionsK.zip) Dream5 Data: Expression data and gold standards provided by Marbach et al. 2012 [1] (Input_Datasets_D5.zip) Interactions predicted by the considered DREAM5 base methods provided by Marbach et al. 2012 [1] (Base_Method_Predictions_D5.zip) Interactions predicted by our approach - Clustering performed with PCA (Predictions_D5.zip) Interactions predicted by our approach - Clustering performed with K-means (PredictionsK_D5.zip) <em>[1] Marbach, D., Costello, J. C., Kuffner, R., Vega, N. M., Prill, R. J., Camacho, D. M., Allison, K. R., Kellis, M., Collins, J. J., and Stolovitzky, G., Wisdom of crowds for robust gene network inference, Nature Methods, 9, 796-804, 2012.</em>
DOI: 10.6084/m9.figshare.1604773.v1
title: Gaussian Job Archive for C6H20O8

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1604769
title: Gaussian Job Archive for C6H16O6

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1604770.v1
title: Gaussian Job Archive for C6H20O8

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1604769.v1
title: Gaussian Job Archive for C6H16O6

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1604765
title: Evaluation of 309 molecules as inducers of CYP3A4, CYP2B6, CYP1A2, OATP1B1, OCT1, MDR1, MRP2, MRP3 and BCRP in cryopreserved human hepatocytes in sandwich culture

description: 1. Regulation of hepatic metabolism or transport may lead to increase in drug clearance and compromise efficacy or safety. In this study, cryopreserved human hepatocytes were used to assess the effect of 309 compounds on the activity and mRNA expression (using qPCR techniques) of CYP1A2, CYP2B6 and CYP3A4, as well as mRNA expression of six hepatic transport proteins: OATP1B1 (SCLO1B1), OCT1 (SLC22A1), MDR1 (ABCB1), MRP2 (ABCC2), MRP3 (ABCC3) and BCRP (ABCG2).2. The results showed that 6% of compounds induced CYP1A2 activity (1.5-fold increase); 30% induced CYP2B6 while 23% induced CYP3A4. qPCR data identified 16, 33 or 32% inducers of CYP1A2, CYP2B6 or CYP3A4, respectively. MRP2 was induced by 27 compounds followed by MDR1 (16) &gt; BCRP (9) &gt; OCT1 (8) &gt; OATP1B1 (5) &gt; MRP3 (2).3. CYP3A4 appeared to be down-regulated (≥2-fold decrease in mRNA expression) by 53 compounds, 10 for CYP2B6, 6 for OCT1, 4 for BCRP, 2 for CYP1A2 and OATP1B1 and 1 for MDR1 and MRP2.4. Structure–activity relationship analysis showed that CYP2B6 and CYP3A4 inducers are bulky lipophilic molecules with a higher number of heavy atoms and a lower number of hydrogen bond donors. Finally, a strategy for testing CYP inducers in drug discovery is proposed.
DOI: 10.6084/m9.figshare.1604768
title: Gaussian Job Archive for C6H18O7

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1604827.v6
title: Semi-supervised Multi-View Learning for Gene Network Reconstruction

description: Semi-supervised Multi-View Learning for Gene Network Reconstruction SynTReN Data: E.coli and Yeast sub-networks, generated expression data and gold standards (Input_Datasets.zip) Interactions predicted by base methods (Base_Method_Predictions.zip) Interactions predicted by our approach - Clustering performed with PCA (Predictions.zip) Interactions predicted by our approach - Clustering performed with K-means (PredictionsK.zip) Dream5 Data: Expression data and gold standards provided by Marbach et al. 2012 [1] (Input_Datasets_D5.zip) Interactions predicted by the considered DREAM5 base methods provided by Marbach et al. 2012 [1] (Base_Method_Predictions_D5.zip) Interactions predicted by our approach - Clustering performed with PCA (Predictions_D5.zip) Interactions predicted by our approach - Clustering performed with K-means (PredictionsK_D5.zip) <em>[1] Marbach, D., Costello, J. C., Kuffner, R., Vega, N. M., Prill, R. J., Camacho, D. M., Allison, K. R., Kellis, M., Collins, J. J., and Stolovitzky, G., Wisdom of crowds for robust gene network inference, Nature Methods, 9, 796-804, 2012.</em>
DOI: 10.6084/m9.figshare.1604765.v1
title: Evaluation of 309 molecules as inducers of CYP3A4, CYP2B6, CYP1A2, OATP1B1, OCT1, MDR1, MRP2, MRP3 and BCRP in cryopreserved human hepatocytes in sandwich culture

description: 1. Regulation of hepatic metabolism or transport may lead to increase in drug clearance and compromise efficacy or safety. In this study, cryopreserved human hepatocytes were used to assess the effect of 309 compounds on the activity and mRNA expression (using qPCR techniques) of CYP1A2, CYP2B6 and CYP3A4, as well as mRNA expression of six hepatic transport proteins: OATP1B1 (SCLO1B1), OCT1 (SLC22A1), MDR1 (ABCB1), MRP2 (ABCC2), MRP3 (ABCC3) and BCRP (ABCG2).2. The results showed that 6% of compounds induced CYP1A2 activity (1.5-fold increase); 30% induced CYP2B6 while 23% induced CYP3A4. qPCR data identified 16, 33 or 32% inducers of CYP1A2, CYP2B6 or CYP3A4, respectively. MRP2 was induced by 27 compounds followed by MDR1 (16) &gt; BCRP (9) &gt; OCT1 (8) &gt; OATP1B1 (5) &gt; MRP3 (2).3. CYP3A4 appeared to be down-regulated (≥2-fold decrease in mRNA expression) by 53 compounds, 10 for CYP2B6, 6 for OCT1, 4 for BCRP, 2 for CYP1A2 and OATP1B1 and 1 for MDR1 and MRP2.4. Structure–activity relationship analysis showed that CYP2B6 and CYP3A4 inducers are bulky lipophilic molecules with a higher number of heavy atoms and a lower number of hydrogen bond donors. Finally, a strategy for testing CYP inducers in drug discovery is proposed.
DOI: 10.6084/m9.figshare.1603884
title: Cuando SEC Data

description: SEC data used to build Cuando archive.
DOI: 10.6084/m9.figshare.1604768.v1
title: Gaussian Job Archive for C6H18O7

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1603555
title: Particle pollution estimation based on image analysis

description: Phoenix data 4
DOI: 10.6084/m9.figshare.1603553
title: Particle pollution estimation based on image analysis

description: Phoenix data 3
DOI: 10.6084/m9.figshare.1604827.v7
title: Semi-supervised Multi-View Learning for Gene Network Reconstruction

description: Semi-supervised Multi-View Learning for Gene Network Reconstruction SynTReN Data: E.coli and Yeast sub-networks, generated expression data and gold standards (Input_Datasets.zip) Interactions predicted by base methods (Base_Method_Predictions.zip) Interactions predicted by our approach - Clustering performed with PCA (Predictions.zip) Interactions predicted by our approach - Clustering performed with K-means (PredictionsK.zip) Dream5 Data: Expression data and gold standards provided by Marbach et al. 2012 [1] (Input_Datasets_D5.zip) Interactions predicted by the considered DREAM5 base methods provided by Marbach et al. 2012 [1] (Base_Method_Predictions_D5.zip) Interactions predicted by our approach - Clustering performed with PCA (Predictions_D5.zip) Interactions predicted by our approach - Clustering performed with K-means (PredictionsK_D5.zip) <em>[1] Marbach, D., Costello, J. C., Kuffner, R., Vega, N. M., Prill, R. J., Camacho, D. M., Allison, K. R., Kellis, M., Collins, J. J., and Stolovitzky, G., Wisdom of crowds for robust gene network inference, Nature Methods, 9, 796-804, 2012.</em>
DOI: 10.6084/m9.figshare.1603552
title: Particle pollution estimation based on image analysis

description: Phoenix data 1
DOI: 10.6084/m9.figshare.1603551
title: Particle pollution estimation based on image analysis

description: Phoenix data 2
DOI: 10.6084/m9.figshare.1603553.v1
title: Particle pollution estimation based on image analysis

description: Phoenix data 3
DOI: 10.6084/m9.figshare.1603550
title: Particle pollution estimation based on image analysis

description: Shanghai data 2
DOI: 10.6084/m9.figshare.1603551.v1
title: Particle pollution estimation based on image analysis

description: Phoenix data 2
DOI: 10.6084/m9.figshare.1603552.v1
title: Particle pollution estimation based on image analysis

description: Phoenix data 1
DOI: 10.6084/m9.figshare.1603556.v1
title: Particle pollution estimation based on image analysis

description: Beijing, Shanghai & Phoenix dataset
DOI: 10.6084/m9.figshare.1603548
title: Particle pollution estimation based on image analysis

description: Shanghai data 3
DOI: 10.6084/m9.figshare.1603549
title: Particle pollution estimation based on image analysis

description: Shanghai data 2
DOI: 10.6084/m9.figshare.1603884.v1
title: Cuando SEC Data

description: SEC data used to build Cuando archive.
DOI: 10.6084/m9.figshare.1603549.v1
title: Particle pollution estimation based on image analysis

description: Shanghai data 2
DOI: 10.6084/m9.figshare.1603550.v1
title: Particle pollution estimation based on image analysis

description: Shanghai data 2
DOI: 10.6084/m9.figshare.1603546
title: U–Pb zircon age of the Walloon Coal Measures in the Surat Basin, southeast Queensland: implications for paleogeography and basin subsidence

description: The Jurassic Walloon Coal Measures of the Surat Basin were previously estimated to be of Middle Jurassic age, ranging from Aalenian to Callovian, based on an uncalibrated eastern Australian biostratigraphic framework. New U–Pb dates of 162.55 ± 0.05 Ma and 158.86 ± 0.04 Ma obtained from zircons in ash-fall volcanic tuffs now place the Walloon Coal Measures of the Surat Basin in the Upper Jurassic Oxfordian. The new dates have several implications for the interpretation of the Jurassic strata in the Surat Basin. First-order subsidence rates of 61 m/Myr for the Walloon Coal Measures are more akin to those of foreland basins than the previously assumed intracratonic setting. The dates also imply deposition of the Walloon coals in substantially higher latitudes than previously assumed and that they accumulated as peats in mires that experienced more than three months’ continual darkness each winter. Zircon dating of tuffs and associated geochemistry should assist with the correlation of the laterally impersistent coals, fluvial sandstone and mudstone of the Walloon Coal Measures, which are currently difficult to correlate over distances of more than a few kilometres. Dating of the palynostratigraphic zones APJ4.2 to APJ5 (<i>Aequitriradites norrisii</i> Association Zone to <i>Murospora florida</i> Association Zone) will also need to be recalibrated.
DOI: 10.6084/m9.figshare.1603547
title: <i>Kutjamarcoot brevirostrum</i> gen. et sp. nov., a new short-snouted, early Miocene bandicoot (Marsupialia: Peramelemorphia) from the Kutjamarpu Local Fauna (Wipajiri Formation) in South Australia

description: Chamberlain, P.M., Travouillon, K.J., Archer, M. & Hand, S.J., November 2015. <i>Kutjamarcoot brevirostrum</i> gen. et sp. nov., a new short-snouted, early Miocene bandicoot (Marsupialia: Peramelemorphia) from the Kutjamarpu Local Fauna (Wipajiri Formation) in South Australia. <i>Alcheringa 40</i>, XX–XX. ISSN 0311-5518. A new bandicoot species, <i>Kutjamarcoot brevirostrum</i> gen. et sp. nov. (Peramelemorphia), is described here from the Leaf Locality, Kutjamarpu Local Fauna (LF), Wipajiri Formation (South Australia). The age of the fossil deposit is interpreted as early Miocene on the basis of biocorrelation between multiple species in the Kutjamarpu LF and local faunas from the Riversleigh World Heritage Area (WHA). <i>Kutjamarcoot brevirostrum</i> is represented by isolated teeth and three partial dentaries and appears to have been short-snouted with an estimated mass of 920 g. Phylogenetic analyses place <i>K. brevirostrum</i> in a clade with extant Australian bandicoots and the extinct <i>Madju</i>, but potentially exclude the extant New Guinean bandicoots. Morphometric analysis infers close similarity between <i>K. brevirostrum</i> and species of <i>Galadi</i> in both size and rostral length. They, thus, potentially occupied compatible ecological niches with competitive exclusion perhaps explaining geographical segregation between these broadly coeval lineages. <i>Philippa M. Chamberlain [</i>philippa.chamberlain@uq.net.au<i>], School of Earth Sciences, University of Queensland, St Lucia, Queensland 4072, Australia; Kenny J. Travouillon [</i>kenny.travouillon@museum.wa.gov.au<i>;</i>kennytravouillon@hotmail.com<i>], Western Australian Museum, Locked Bag 49, Welshpool DC, WA, 6986, and School of Earth Sciences, University of Queensland, St Lucia, Queensland, 4072, Australia; Michael Archer [</i>m.archer@unsw.edu.au<i>] and Suzanne J. Hand [</i>s.hand@unsw.edu.au<i>], School of Biological, Earth and Environmental Sciences, University of New South Wales, New South Wales, 2052, Australia.</i>
DOI: 10.6084/m9.figshare.1603547.v1
title: <i>Kutjamarcoot brevirostrum</i> gen. et sp. nov., a new short-snouted, early Miocene bandicoot (Marsupialia: Peramelemorphia) from the Kutjamarpu Local Fauna (Wipajiri Formation) in South Australia

description: Chamberlain, P.M., Travouillon, K.J., Archer, M. & Hand, S.J., November 2015. <i>Kutjamarcoot brevirostrum</i> gen. et sp. nov., a new short-snouted, early Miocene bandicoot (Marsupialia: Peramelemorphia) from the Kutjamarpu Local Fauna (Wipajiri Formation) in South Australia. <i>Alcheringa 40</i>, XX–XX. ISSN 0311-5518. A new bandicoot species, <i>Kutjamarcoot brevirostrum</i> gen. et sp. nov. (Peramelemorphia), is described here from the Leaf Locality, Kutjamarpu Local Fauna (LF), Wipajiri Formation (South Australia). The age of the fossil deposit is interpreted as early Miocene on the basis of biocorrelation between multiple species in the Kutjamarpu LF and local faunas from the Riversleigh World Heritage Area (WHA). <i>Kutjamarcoot brevirostrum</i> is represented by isolated teeth and three partial dentaries and appears to have been short-snouted with an estimated mass of 920 g. Phylogenetic analyses place <i>K. brevirostrum</i> in a clade with extant Australian bandicoots and the extinct <i>Madju</i>, but potentially exclude the extant New Guinean bandicoots. Morphometric analysis infers close similarity between <i>K. brevirostrum</i> and species of <i>Galadi</i> in both size and rostral length. They, thus, potentially occupied compatible ecological niches with competitive exclusion perhaps explaining geographical segregation between these broadly coeval lineages. <i>Philippa M. Chamberlain [</i>philippa.chamberlain@uq.net.au<i>], School of Earth Sciences, University of Queensland, St Lucia, Queensland 4072, Australia; Kenny J. Travouillon [</i>kenny.travouillon@museum.wa.gov.au<i>;</i>kennytravouillon@hotmail.com<i>], Western Australian Museum, Locked Bag 49, Welshpool DC, WA, 6986, and School of Earth Sciences, University of Queensland, St Lucia, Queensland, 4072, Australia; Michael Archer [</i>m.archer@unsw.edu.au<i>] and Suzanne J. Hand [</i>s.hand@unsw.edu.au<i>], School of Biological, Earth and Environmental Sciences, University of New South Wales, New South Wales, 2052, Australia.</i>
DOI: 10.6084/m9.figshare.1603548.v1
title: Particle pollution estimation based on image analysis

description: Shanghai data 3
DOI: 10.6084/m9.figshare.1603545
title: AARE 2015

description: Papers and media from our symposium presentation at the Australian Association for Reserch in Education (AARE) conference 2015, Freemantle, WA.