cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1295513.v1
title: Aberrant CpG methylation of the <i>TFAP2A</i> gene constitutes a mechanism for loss of <i>TFAP2A</i> expression in human metastatic melanoma

description: Metastatic melanoma is a deadly treatment-resistant form of skin cancer whose global incidence is on the rise. During melanocyte transformation and melanoma progression the expression profile of many genes changes. Among these, a gene implicated in several steps of melanocyte development, <i>TFAP2A</i>, is frequently silenced; however, the molecular mechanism of <i>TFAP2A</i> silencing in human melanoma remains unknown. In this study, we measured <i>TFAP2A</i> mRNA expression in primary human melanocytes compared to 11 human melanoma samples by quantitative real-time RT-PCR. In addition, we assessed CpG DNA methylation of the <i>TFAP2A</i> promoter in these samples using bisulfite sequencing. Compared to primary melanocytes, which showed high <i>TFAP2A</i> mRNA expression and no promoter methylation, human melanoma samples showed decreased <i>TFAP2A</i> mRNA expression and increased promoter methylation. We further show that increased CpG methylation correlates with decreased <i>TFAP2A</i> mRNA expression. Using The Cancer Genome Atlas, we further identified <i>TFAP2A</i> as a gene displaying among the most decreased expression in stage 4 melanomas vs. non-stage 4 melanomas, and whose CpG methylation was frequently associated with lack of mRNA expression. Based on our data, we conclude that <i>TFAP2A</i> expression in human melanomas can be silenced by aberrant CpG methylation of the <i>TFAP2A</i> promoter. We have identified aberrant CpG DNA methylation as an epigenetic mark associated with TFAP2A silencing in human melanoma that could have significant implications for the therapy of human melanoma using epigenetic modifying drugs.
DOI: 10.6084/m9.figshare.1295505
title: IPython Tricks

description: This IPython notebook demonstrates some tricks that can be used within notebooks.
DOI: 10.6084/m9.figshare.1295512.v1
title: <i>OASIS/CREB3L1</i> is epigenetically silenced in human bladder cancer facilitating tumor cell spreading and migration <i>in vitro</i>

description: <i>CREB3L1</i> has been recently proposed as a novel metastasis suppressor gene in breast cancer. Our current study highlights CREB3L1 expression, regulation, and function in bladder cancer. We demonstrate a significant downregulation of <i>CREB3L1</i> mRNA expression (n = 64) in primary bladder cancer tissues caused by tumor-specific <i>CREB3L1</i> promoter hypermethylation (n = 51). Based on pyrosequencing <i>CREB3L1</i> methylation was shown to be potentially associated with a more aggressive phenotype of bladder cancer. These findings were verified by an independent public data set containing data from 184 bladder tumors. In addition, immunohistochemical evaluation showed that CREB3L1 protein expression is decreased in bladder cancer tissues as well. Interestingly, protein loss is predominately observed in the nuclei of aggressive tumor cells. Based on <i>in vitro</i> models we clearly show that CREB3L1 re-expression mediates suppression of tumor cell migration and colony growth of high grade and invasive bladder cancer cells. The candidate tumor suppressor and TGF-β signaling inhibitor HTRA3 was furthermore identified as putative target gene of CREB3L1 in both invasive J82 bladder cells and primary bladder tumors. Hence, our data provide for the first time evidence that the transcription factor CREB3L1 may have an important role as a putative tumor suppressor in bladder cancer.
DOI: 10.6084/m9.figshare.1295494
title: Late Permian–Triassic siliciclastic provenance, palaeogeography, and crustal growth of the Songpan terrane, eastern Tibetan Plateau: evidence from U–Pb ages, trace elements, and Hf isotopes of detrital zircons

description: In order to constrain the detrital provenance of the siliciclastic rocks, palaeogeographic variations, and crustal growth history of central China, we carried out simultaneously <i>in situ</i> U–Pb dating and trace element and Hf isotope analyses on 368 detrital zircons obtained from upper Permian–Triassic sandstones of the Songpan terrane, eastern Tibetan Plateau. Two groups of detrital zircons, i.e. magmatic and metamorphic in origin, have been identified based on cathodoluminescence images, zircon Ti-temperatures, and Th/U ratios. Our data suggest that the derivation of siliciclastic rocks in the Songpan terrane was mainly from the Qinling, Qilian, and Kunlun orogens, whereas the Yangtze and North China Cratons served as minor source areas during late Permian–Triassic times. The detrital zircons from Middle–Late Triassic siliciclastic rocks exhibit wide age spectra with two dominant populations of 230–600 Ma and &gt;1600 Ma, peaking at ~1.8–1.9 Ga and ~2.4–2.5 Ga, suggestive of a derivation from the Qinling, Qilian, and Kunlun orogens and the Yangtze Craton being the minor source area. The proportions of detrital zircon populations from the northern Qinling, Qilian, and Kunlun orogens distinctly decreased during Middle–Late Triassic time, demonstrating that the initial uplift of the western Qinling occurred then and it could have blocked most of the detritus from the Qilian–northern Qinling orogens and North China Cratons into the main Songpan–Ganzi depositional basin. The relatively detrital zircon proportions of the Yangtze Craton source decreased during Early-Middle Late Triassic time, indicating that the Longmenshan orogen was probably being elevated, since the early Late Triassic and gradually formed a barrier between the Yangtze Craton and the Songpan terrane. In addition, our Lu–Hf isotopic results also reveal that the Phanerozoic magmatic rocks in central China had been the primary products of crustal reworking with insignificant formation of a juvenile crust.
DOI: 10.6084/m9.figshare.1295493
title: Newton Presentation

description: This is a presentation that Jason Harris and I gave to get students in GST comfortable with some of the computing resources available.
DOI: 10.6084/m9.figshare.1295505.v2
title: IPython Tricks

description: This IPython notebook demonstrates some tricks that can be used within notebooks.
DOI: 10.6084/m9.figshare.1295493.v1
title: Newton Presentation

description: This is a presentation that Jason Harris and I gave to get students in GST comfortable with some of the computing resources available.
DOI: 10.6084/m9.figshare.1295494.v1
title: Late Permian–Triassic siliciclastic provenance, palaeogeography, and crustal growth of the Songpan terrane, eastern Tibetan Plateau: evidence from U–Pb ages, trace elements, and Hf isotopes of detrital zircons

description: In order to constrain the detrital provenance of the siliciclastic rocks, palaeogeographic variations, and crustal growth history of central China, we carried out simultaneously <i>in situ</i> U–Pb dating and trace element and Hf isotope analyses on 368 detrital zircons obtained from upper Permian–Triassic sandstones of the Songpan terrane, eastern Tibetan Plateau. Two groups of detrital zircons, i.e. magmatic and metamorphic in origin, have been identified based on cathodoluminescence images, zircon Ti-temperatures, and Th/U ratios. Our data suggest that the derivation of siliciclastic rocks in the Songpan terrane was mainly from the Qinling, Qilian, and Kunlun orogens, whereas the Yangtze and North China Cratons served as minor source areas during late Permian–Triassic times. The detrital zircons from Middle–Late Triassic siliciclastic rocks exhibit wide age spectra with two dominant populations of 230–600 Ma and &gt;1600 Ma, peaking at ~1.8–1.9 Ga and ~2.4–2.5 Ga, suggestive of a derivation from the Qinling, Qilian, and Kunlun orogens and the Yangtze Craton being the minor source area. The proportions of detrital zircon populations from the northern Qinling, Qilian, and Kunlun orogens distinctly decreased during Middle–Late Triassic time, demonstrating that the initial uplift of the western Qinling occurred then and it could have blocked most of the detritus from the Qilian–northern Qinling orogens and North China Cratons into the main Songpan–Ganzi depositional basin. The relatively detrital zircon proportions of the Yangtze Craton source decreased during Early-Middle Late Triassic time, indicating that the Longmenshan orogen was probably being elevated, since the early Late Triassic and gradually formed a barrier between the Yangtze Craton and the Songpan terrane. In addition, our Lu–Hf isotopic results also reveal that the Phanerozoic magmatic rocks in central China had been the primary products of crustal reworking with insignificant formation of a juvenile crust.
DOI: 10.6084/m9.figshare.1295505.v1
title: IPython Tips

description: This IPython notebook demonstrates some tricks that can be used within notebooks.
DOI: 10.6084/m9.figshare.1295469
title: Chikungunya Epidemic Data Readme File

description: Information about the spreadsheet (variable names, data source(s), important notes)
DOI: 10.6084/m9.figshare.1295464
title: Chikungunya Epidemic Data (extracted from PAHO)

description: Spreadsheet containing data on cumulative 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.
DOI: 10.6084/m9.figshare.1295466
title: stroop paper

description: stroop paper
DOI: 10.6084/m9.figshare.1295463
title: Multilocus phylogeny and taxonomic revision of the <i>Hemidactylus robustus</i> species group (Reptilia, Gekkonidae) with descriptions of three new species from Yemen and Ethiopia

description: The gecko genus <i>Hemidactylus</i>, with its 132 currently recognized species, ranks among the most species-rich reptile genera. Recent phylogenetic studies disclosed unexpectedly high genetic variability and complex biogeographic history within its arid clade distributed in the Mediterranean, Northeast Africa, Middle East and the Indian subcontinent. Particularly, the species from the Arabian Peninsula have been lately the subject of many taxonomic revisions that have resulted in the descriptions of 16 new taxa. Yet not all detected cryptic lineages have been treated taxonomically and thoroughly investigated morphologically. Based on phylogenetic analyses of two mtDNA (<i>12S</i>, <i>cytb</i>) and four nDNA (<i>cmos</i>, <i>mc1r</i>, <i>rag1</i>, <i>rag2</i>) gene fragments of a total length of 4015 bp in combination with analysis of morphological characters, we reinvestigate the systematics of the <i>H. robustus</i> species group consisting of the widespread <i>H. robustus</i> and three undescribed species, two of which occur in Southwest Yemen and one in central Ethiopia. By comparing two phylogenetic inference methods, concatenated gene trees and species-tree estimation, we reconstruct the phylogeny of the <i>H. robustus</i> species group. The coalescent-based species-tree estimation resulted in different tree topology than the concatenation approach, being probably a result of incomplete lineage sorting of ancestral polymorphism, suggesting that the <i>H. robustus</i> species group is in a stage of incipient speciation. The degree of differentiation of the characters examined within the <i>H. robustus</i> species group allowed us to provide a redescription of <i>H. robustus</i> and formally describe three new species of <i>Hemidactylus</i> – <i>H. adensis</i> sp. nov. and <i>H. mandebensis</i> sp. nov. from Yemen and <i>H. awashensis</i> sp. nov. from Ethiopia.
DOI: 10.6084/m9.figshare.1295466.v1
title: stroop paper

description: stroop paper
DOI: 10.6084/m9.figshare.1295463.v2
title: Multilocus phylogeny and taxonomic revision of the <i>Hemidactylus robustus</i> species group (Reptilia, Gekkonidae) with descriptions of three new species from Yemen and Ethiopia

description: The gecko genus <i>Hemidactylus</i>, with its 132 currently recognized species, ranks among the most species-rich reptile genera. Recent phylogenetic studies disclosed unexpectedly high genetic variability and complex biogeographic history within its arid clade distributed in the Mediterranean, Northeast Africa, Middle East and the Indian subcontinent. Particularly, the species from the Arabian Peninsula have been lately the subject of many taxonomic revisions that have resulted in the descriptions of 16 new taxa. Yet not all detected cryptic lineages have been treated taxonomically and thoroughly investigated morphologically. Based on phylogenetic analyses of two mtDNA (<i>12S</i>, <i>cytb</i>) and four nDNA (<i>cmos</i>, <i>mc1r</i>, <i>rag1</i>, <i>rag2</i>) gene fragments of a total length of 4015 bp in combination with analysis of morphological characters, we reinvestigate the systematics of the <i>H. robustus</i> species group consisting of the widespread <i>H. robustus</i> and three undescribed species, two of which occur in Southwest Yemen and one in central Ethiopia. By comparing two phylogenetic inference methods, concatenated gene trees and species-tree estimation, we reconstruct the phylogeny of the <i>H. robustus</i> species group. The coalescent-based species-tree estimation resulted in different tree topology than the concatenation approach, being probably a result of incomplete lineage sorting of ancestral polymorphism, suggesting that the <i>H. robustus</i> species group is in a stage of incipient speciation. The degree of differentiation of the characters examined within the <i>H. robustus</i> species group allowed us to provide a redescription of <i>H. robustus</i> and formally describe three new species of <i>Hemidactylus</i> – <i>H. adensis</i> sp. nov. and <i>H. mandebensis</i> sp. nov. from Yemen and <i>H. awashensis</i> sp. nov. from Ethiopia.
DOI: 10.6084/m9.figshare.1295454
title: Contraceptive use in Sweden

description: This is a database of 1000 women and their contraceptive use and experience of unintended pregnancy in Sweden 2012
DOI: 10.6084/m9.figshare.1295463.v1
title: Multilocus phylogeny and taxonomic revision of the <i>Hemidactylus robustus</i> species group (Reptilia, Gekkonidae) with descriptions of three new species from Yemen and Ethiopia

description: The gecko genus <i>Hemidactylus</i>, with its 132 currently recognized species, ranks among the most species-rich reptile genera. Recent phylogenetic studies disclosed unexpectedly high genetic variability and complex biogeographic history within its arid clade distributed in the Mediterranean, Northeast Africa, Middle East and the Indian subcontinent. Particularly, the species from the Arabian Peninsula have been lately the subject of many taxonomic revisions that have resulted in the descriptions of 16 new taxa. Yet not all detected cryptic lineages have been treated taxonomically and thoroughly investigated morphologically. Based on phylogenetic analyses of two mtDNA (<i>12S</i>, <i>cytb</i>) and four nDNA (<i>cmos</i>, <i>mc1r</i>, <i>rag1</i>, <i>rag2</i>) gene fragments of a total length of 4015 bp in combination with analysis of morphological characters, we reinvestigate the systematics of the <i>H. robustus</i> species group consisting of the widespread <i>H. robustus</i> and three undescribed species, two of which occur in Southwest Yemen and one in central Ethiopia. By comparing two phylogenetic inference methods, concatenated gene trees and species-tree estimation, we reconstruct the phylogeny of the <i>H. robustus</i> species group. The coalescent-based species-tree estimation resulted in different tree topology than the concatenation approach, being probably a result of incomplete lineage sorting of ancestral polymorphism, suggesting that the <i>H. robustus</i> species group is in a stage of incipient speciation. The degree of differentiation of the characters examined within the <i>H. robustus</i> species group allowed us to provide a redescription of <i>H. robustus</i> and formally describe three new species of <i>Hemidactylus</i> – <i>H. adensis</i> sp. nov. and <i>H. mandebensis</i> sp. nov. from Yemen and <i>H. awashensis</i> sp. nov. from Ethiopia.
DOI: 10.6084/m9.figshare.1295411
title: Crowdsourced geo-referenced image data (2014)

description: Crowdsourced georeference data for over three thousand maps, annotated online by participants in the BL Georeferencer project. http://britishlibrary.typepad.co.uk/magnificentmaps/2014/08/success.html <em>"In just 28 days from release, 3,220 maps have been geo-located online by participants in the BL Georeferencer project. For this quantity of maps to be completed at such a speed is truly impressive, and testifies to much scrutiny of maps and online research by many people."</em> NB The image identifier refers to its Flickr identifier. "11000447924" refers to the image located at https://flickr.com/photos/biritishlibrary/11000447924
DOI: 10.6084/m9.figshare.1295447
title: 1

description: 1
DOI: 10.6084/m9.figshare.1295411.v1
title: Crowdsourced geo-referenced image data (2014)

description: Crowdsourced georeference data for over three thousand maps, annotated online by participants in the BL Georeferencer project. http://britishlibrary.typepad.co.uk/magnificentmaps/2014/08/success.html <em>"In just 28 days from release, 3,220 maps have been geo-located online by participants in the BL Georeferencer project. For this quantity of maps to be completed at such a speed is truly impressive, and testifies to much scrutiny of maps and online research by many people."</em> NB The image identifier refers to its Flickr identifier. "11000447924" refers to the image located at https://flickr.com/photos/biritishlibrary/11000447924
DOI: 10.6084/m9.figshare.1295407
title: plos one "Optogenetic Activation of CA1 Pyramidal Neurons at the Dorsal and Ventral Hippocampus Evokes Distinct Brain-wide Responses Revealed by Mouse fMRI"

description: Brain activation by dorsal and ventral hippocampus
DOI: 10.7925/drs1.duchas_4955114
title: Blessed Virgin and the Corn

description: Story collected by Sioban Cuddihy, a student at Baile Roibín, Knocktopher school (Newmarket, Co. Kilkenny) from informant an unidentified informant.
description: Collected as part of the Schools' Folklore scheme, 1937-1938, under the supervision of teacher Ss. Ó Súilleabháin.
description: Supported by funding from the Department of Arts, Heritage and the Gaeltacht (Ireland), University College Dublin, and the National Folklore Foundation (Fondúireacht Bhéaloideas Éireann), 2014-2016.
DOI: 10.7925/drs1.duchas_4955117
title: Customs of May Eve

description: Story collected by Sioban Cuddihy, a student at Baile Roibín, Knocktopher school (Newmarket, Co. Kilkenny) from informant an unidentified informant.
description: Collected as part of the Schools' Folklore scheme, 1937-1938, under the supervision of teacher Ss. Ó Súilleabháin.
description: Supported by funding from the Department of Arts, Heritage and the Gaeltacht (Ireland), University College Dublin, and the National Folklore Foundation (Fondúireacht Bhéaloideas Éireann), 2014-2016.
DOI: 10.7925/drs1.duchas_4955119
title: Proverbs

description: Story collected by Sioban Cuddihy, a student at Baile Roibín, Knocktopher school (Newmarket, Co. Kilkenny) from informant an unidentified informant.
description: Collected as part of the Schools' Folklore scheme, 1937-1938, under the supervision of teacher Ss. Ó Súilleabháin.
description: Supported by funding from the Department of Arts, Heritage and the Gaeltacht (Ireland), University College Dublin, and the National Folklore Foundation (Fondúireacht Bhéaloideas Éireann), 2014-2016.
DOI: 10.7925/drs1.duchas_4955120
title: May Bush

description: Story collected by Sioban Cuddihy, a student at Baile Roibín, Knocktopher school (Newmarket, Co. Kilkenny) from informant an unidentified informant.
description: Collected as part of the Schools' Folklore scheme, 1937-1938, under the supervision of teacher Ss. Ó Súilleabháin.
description: Supported by funding from the Department of Arts, Heritage and the Gaeltacht (Ireland), University College Dublin, and the National Folklore Foundation (Fondúireacht Bhéaloideas Éireann), 2014-2016.
DOI: 10.7925/drs1.duchas_4955121
title: Prayers

description: Story collected by a student at Baile Roibín, Knocktopher school (Newmarket, Co. Kilkenny) (no informant identified).
description: Collected as part of the Schools' Folklore scheme, 1937-1938, under the supervision of teacher Ss. Ó Súilleabháin.
description: Supported by funding from the Department of Arts, Heritage and the Gaeltacht (Ireland), University College Dublin, and the National Folklore Foundation (Fondúireacht Bhéaloideas Éireann), 2014-2016.
DOI: 10.7925/drs1.duchas_4955125
title: Riddles

description: Story collected by Cristina Corcoran, a student at Baile Roibín, Knocktopher school (Newmarket, Co. Kilkenny) (no informant identified).
description: Collected as part of the Schools' Folklore scheme, 1937-1938, under the supervision of teacher Ss. Ó Súilleabháin.
description: Supported by funding from the Department of Arts, Heritage and the Gaeltacht (Ireland), University College Dublin, and the National Folklore Foundation (Fondúireacht Bhéaloideas Éireann), 2014-2016.
DOI: 10.7925/drs1.duchas_4955127
title: Riddles

description: Story collected by Nellie Deloughry, a student at Baile Roibín, Knocktopher school (Newmarket, Co. Kilkenny) (no informant identified).
description: Collected as part of the Schools' Folklore scheme, 1937-1938, under the supervision of teacher Ss. Ó Súilleabháin.
description: Supported by funding from the Department of Arts, Heritage and the Gaeltacht (Ireland), University College Dublin, and the National Folklore Foundation (Fondúireacht Bhéaloideas Éireann), 2014-2016.
DOI: 10.7925/drs1.duchas_4955130
title: Story

description: Story collected by James Holden, a student at Baile Roibín, Knocktopher school (Newmarket, Co. Kilkenny) from informant an unidentified informant.
description: Collected as part of the Schools' Folklore scheme, 1937-1938, under the supervision of teacher Ss. Ó Súilleabháin.
description: Supported by funding from the Department of Arts, Heritage and the Gaeltacht (Ireland), University College Dublin, and the National Folklore Foundation (Fondúireacht Bhéaloideas Éireann), 2014-2016.
DOI: 10.7925/drs1.duchas_4955132
title: Game

description: Story collected by James Holden, a student at Baile Roibín, Knocktopher school (Newmarket, Co. Kilkenny) (no informant identified).
description: Collected as part of the Schools' Folklore scheme, 1937-1938, under the supervision of teacher Ss. Ó Súilleabháin.
description: Supported by funding from the Department of Arts, Heritage and the Gaeltacht (Ireland), University College Dublin, and the National Folklore Foundation (Fondúireacht Bhéaloideas Éireann), 2014-2016.
DOI: 10.7925/drs1.duchas_4955137
title: Game - the Ghost in the Garden

description: Story collected by Sioban Cuddihy, a student at Baile Roibín, Knocktopher school (Newmarket, Co. Kilkenny) (no informant identified).
description: Collected as part of the Schools' Folklore scheme, 1937-1938, under the supervision of teacher Ss. Ó Súilleabháin.
description: Supported by funding from the Department of Arts, Heritage and the Gaeltacht (Ireland), University College Dublin, and the National Folklore Foundation (Fondúireacht Bhéaloideas Éireann), 2014-2016.
DOI: 10.7925/drs1.duchas_4955140
title: Game - Four Corners

description: Story collected by Edward Dwyer, a student at Baile Roibín, Knocktopher school (Newmarket, Co. Kilkenny) (no informant identified).
description: Collected as part of the Schools' Folklore scheme, 1937-1938, under the supervision of teacher Ss. Ó Súilleabháin.
description: Supported by funding from the Department of Arts, Heritage and the Gaeltacht (Ireland), University College Dublin, and the National Folklore Foundation (Fondúireacht Bhéaloideas Éireann), 2014-2016.