cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1437782.v2
title: Polycomb repressive complex 2 epigenomic signature defines age-associated hypermethylation and gene expression changes

description: Although age-associated gene expression and methylation changes have been reported throughout the literature, the unifying epigenomic principles of aging remain poorly understood. Recent explosion in availability and resolution of functional/regulatory genome annotation data (epigenomic data), such as that provided by the ENCODE and Roadmap Epigenomics projects, provides an opportunity for the identification of epigenomic mechanisms potentially altered by age-associated differentially methylated regions (aDMRs) and regulatory signatures in the promoters of age-associated genes (aGENs). In this study we found that aDMRs and aGENs identified in multiple independent studies share a common Polycomb Repressive Complex 2 signature marked by EZH2, SUZ12, CTCF binding sites, repressive H3K27me3, and activating H3K4me1 histone modification marks, and a “poised promoter” chromatin state. This signature is depleted in RNA Polymerase II-associated transcription factor binding sites, activating H3K79me2, H3K36me3, H3K27ac marks, and an “active promoter” chromatin state. The PRC2 signature was shown to be generally stable across cell types. When considering the directionality of methylation changes, we found the PRC2 signature to be associated with aDMRs hypermethylated with age, while hypomethylated aDMRs were associated with enhancers. In contrast, aGENs were associated with the PRC2 signature independently of the directionality of gene expression changes. In this study we demonstrate that the PRC2 signature is the common epigenomic context of genomic regions associated with hypermethylation and gene expression changes in aging.
DOI: 10.6084/m9.figshare.1437790.v7
title: The transcription factor Swi4 is target for PKA regulation of cell size at the G<sub>1</sub> to S transition in <i>Saccharomyces cerevisiae</i>

description: To investigate the specific target of PKA in the regulation of cell cycle progression and cell size we developed a new approach using the yeast strain GG104 bearing a deletion in adenylate cyclase gene and permeable to cAMP ( <i>cyr1</i>Δ, <i>pde2</i>Δ, <i>msn2</i>Δ, <i>msn4</i>Δ). In this strain the PKA activity is absent and can be activated by addition of cAMP in the medium, without any other change of the growth conditions. In the present work we show that the activation of PKA by exogenous cAMP in the GG104 strain exponentially growing in glucose medium caused a marked increase of cell size and perturbation of cell cycle with a transient arrest of cells in G<sub>1</sub>, followed by an accumulation of cells in G<sub>2</sub>/M phase with a minimal change in the growth rate. Deletion of <i>CLN1</i> gene, but not of <i>CLN2</i>, abolished the transient G<sub>1</sub> phase arrest. Consistently we found that PKA activation caused a transcriptional repression of <i>CLN1</i> gene. Transcription of <i>CLN1</i> is controlled by SBF and MBF dual-regulated promoter. We found that also the deletion of <i>SWI4</i> gene abolished the transient G<sub>1</sub> arrest suggesting that Swi4 is a target responsible for PKA modulation of G<sub>1</sub>/S phase transition. We generated a <i>SWI4</i> allele mutated in the consensus site for PKA (Swi4<sup>S159A</sup>) and we found that expression of Swi4<sup>S159A</sup> protein in the GG104-<i>Swi4</i>Δ strain did not restore the transient G<sub>1</sub> arrest induced by PKA activation, suggesting that Swi4 phosphorylation by PKA regulates <i>CLN1</i> gene expression and G<sub>1</sub>/S phase transition.
DOI: 10.6084/m9.figshare.1437790.v6
title: The transcription factor Swi4 is target for PKA regulation of cell size at the G<sub>1</sub> to S transition in <i>Saccharomyces cerevisiae</i>

description: To investigate the specific target of PKA in the regulation of cell cycle progression and cell size we developed a new approach using the yeast strain GG104 bearing a deletion in adenylate cyclase gene and permeable to cAMP ( <i>cyr1</i>Δ, <i>pde2</i>Δ, <i>msn2</i>Δ, <i>msn4</i>Δ). In this strain the PKA activity is absent and can be activated by addition of cAMP in the medium, without any other change of the growth conditions. In the present work we show that the activation of PKA by exogenous cAMP in the GG104 strain exponentially growing in glucose medium caused a marked increase of cell size and perturbation of cell cycle with a transient arrest of cells in G<sub>1</sub>, followed by an accumulation of cells in G<sub>2</sub>/M phase with a minimal change in the growth rate. Deletion of <i>CLN1</i> gene, but not of <i>CLN2</i>, abolished the transient G<sub>1</sub> phase arrest. Consistently we found that PKA activation caused a transcriptional repression of <i>CLN1</i> gene. Transcription of <i>CLN1</i> is controlled by SBF and MBF dual-regulated promoter. We found that also the deletion of <i>SWI4</i> gene abolished the transient G<sub>1</sub> arrest suggesting that Swi4 is a target responsible for PKA modulation of G<sub>1</sub>/S phase transition. We generated a <i>SWI4</i> allele mutated in the consensus site for PKA (Swi4<sup>S159A</sup>) and we found that expression of Swi4<sup>S159A</sup> protein in the GG104-<i>Swi4</i>Δ strain did not restore the transient G<sub>1</sub> arrest induced by PKA activation, suggesting that Swi4 phosphorylation by PKA regulates <i>CLN1</i> gene expression and G<sub>1</sub>/S phase transition.
DOI: 10.6084/m9.figshare.1437750
title: Recollection-based retrieval is influenced by contextual variation at encoding but not at retrieval

description: In this article, we investigated the effects of variations at encoding and retrieval on recollection. We argue that recollection is more likely to be affected by the processing that information undergoes at encoding than at retrieval. To date, manipulations shown to affect recollection were typically carried out at encoding. Therefore, an open question is whether these same manipulations would also affect recollection when carried out at retrieval, or whether there is an inherent connection between their effects on recollection and the encoding stage. We therefore manipulated, at either encoding or retrieval, fluency of processing (Experiment 1)—typically found not to affect recollection—and the amount of attentional resources available for processing (Experiments 2 and 3)—typically reported to affect recollection. We found that regardless of the type of manipulation, recollection was affected more by manipulations carried out at encoding and was essentially unaffected when these manipulations were carried out at retrieval. These findings suggest an inherent dependency between recollection-based retrieval and the encoding stage. It seems that because recollection is a contextual-based retrieval process, it is determined by the processing information undergoes at encoding—at the time when context is bound with the items—but not at retrieval—when context is only recovered.
DOI: 10.6084/m9.figshare.1437749
title: Dataset-pone

description: Supporting data underlying the results.
DOI: 10.6084/m9.figshare.1437750.v1
title: Recollection-based retrieval is influenced by contextual variation at encoding but not at retrieval

description: In this article, we investigated the effects of variations at encoding and retrieval on recollection. We argue that recollection is more likely to be affected by the processing that information undergoes at encoding than at retrieval. To date, manipulations shown to affect recollection were typically carried out at encoding. Therefore, an open question is whether these same manipulations would also affect recollection when carried out at retrieval, or whether there is an inherent connection between their effects on recollection and the encoding stage. We therefore manipulated, at either encoding or retrieval, fluency of processing (Experiment 1)—typically found not to affect recollection—and the amount of attentional resources available for processing (Experiments 2 and 3)—typically reported to affect recollection. We found that regardless of the type of manipulation, recollection was affected more by manipulations carried out at encoding and was essentially unaffected when these manipulations were carried out at retrieval. These findings suggest an inherent dependency between recollection-based retrieval and the encoding stage. It seems that because recollection is a contextual-based retrieval process, it is determined by the processing information undergoes at encoding—at the time when context is bound with the items—but not at retrieval—when context is only recovered.
DOI: 10.6084/m9.figshare.1437747
title: 'Electrical Knock-In' (EKI) study on GitHub

description: All code and data associated with the study described in: McKiernan EC. (2015) A genetic manipulation of motor neuron excitability does not alter locomotor output in Drosophila larvae. PeerJ PrePrints 3:e1062. (See links below.) Code is licensed under the MIT license, and data under the CC0 1.0 Universal license.
DOI: 10.6084/m9.figshare.1437748
title: Paired deer exclosure - control plots, forest understory vegetation, percent cover

description: Percent cover data for forest understory plants (2006-2013) collected from paired deer exclosure-control plots. Site: Dairymen's Club. Wisconsin, USA (46.15°N, 89.68°W). Data were used in our 2014 study published in AoB Plants--White-tailed deer are a biotic filter during community assembly, reducing species and phylogenetic diversity (linked below, open access), and my 2009 study published in Plant Ecology--High white-tailed deer densities benefit graminoids and contribute to biotic homogenization of forest ground-layer vegetation (linked below, paywall). Species are listed in rows. Voucher specimens are deposited at the Morton Arboretum (Illinois). Colums represent exclosure - years. Names refer to individual exclosures, numbers indicate the year, and T = exclosure, C = control plot. Values are % cover recorded along permanent transects using the line intercept method.
DOI: 10.6084/m9.figshare.1437748.v1
title: Paired deer exclosure - control plots, forest understory vegetation, percent cover

description: Percent cover data for forest understory plants (2006-2013) collected from paired deer exclosure-control plots. Site: Dairymen's Club. Wisconsin, USA (46.15°N, 89.68°W). Data were used in our 2014 study published in AoB Plants--White-tailed deer are a biotic filter during community assembly, reducing species and phylogenetic diversity (linked below, open access), and my 2009 study published in Plant Ecology--High white-tailed deer densities benefit graminoids and contribute to biotic homogenization of forest ground-layer vegetation (linked below, paywall). Species are listed in rows. Voucher specimens are deposited at the Morton Arboretum (Illinois). Colums represent exclosure - years. Names refer to individual exclosures, numbers indicate the year, and T = exclosure, C = control plot. Values are % cover recorded along permanent transects using the line intercept method.
DOI: 10.6084/m9.figshare.1437747.v2
title: EKI study on GitHub

description: All code and data associated with the study described in: McKiernan EC. (2015) A genetic manipulation of motor neuron excitability does not alter locomotor output in Drosophila larvae. PeerJ PrePrints 3:e1062
DOI: 10.6084/m9.figshare.1437740
title: Twitter activity data for Twitter-based analysis of the dynamics of collective attention to political parties (PLoS ONE, 2015)

description: This data-set contain dynamics of Twitter activity on political parties. Please see the main paper "Twitter-based analysis of the dynamics of collective attention to political parties (PLoS ONE, 2015)" for the details.
DOI: 10.6084/m9.figshare.1437747.v4
title: 'Electrical Knock-In' (EKI) study on GitHub

description: All code and data associated with the study described in: McKiernan EC. (2015) A genetic manipulation of motor neuron excitability does not alter locomotor output in Drosophila larvae. PeerJ PrePrints 3:e1062. (See links below.) Code is licensed under the MIT license, and data under the CC0 1.0 Universal license.
DOI: 10.6084/m9.figshare.1437747.v3
title: 'Ele study on GitHub

description: All code and data associated with the study described in: McKiernan EC. (2015) A genetic manipulation of motor neuron excitability does not alter locomotor output in Drosophila larvae. PeerJ PrePrints 3:e1062
DOI: 10.6084/m9.figshare.1437662
title: conserved CArGome BED annotation

description: conserved CArGome BED annotation
DOI: 10.6084/m9.figshare.1437667
title: CArGome BED annotation of mice

description: CArGome BED annotation of mice
DOI: 10.6084/m9.figshare.1437663
title: transcript GTF annotation of ICC in colon smooth muscle

description: transcript annotation of ICC in colon smooth muscle
DOI: 10.6084/m9.figshare.1437660
title: transcript GTF annotation of colon mucosa

description: transcript annotation of colon mucosa
DOI: 10.6084/m9.figshare.1437661
title: transcript GTF annotation of ICC in jejunum smooth muscle

description: transcript annotation of ICC in jejunum smooth muscle
DOI: 10.6084/m9.figshare.1437662.v2
title: conserved CArGome BED annotation

description: conserved CArGome BED annotation
DOI: 10.6084/m9.figshare.1437662.v1
title: conserved CarGome BED annotation

description: conserved CarGome BED annotation
DOI: 10.6084/m9.figshare.1437623
title: Common Data Elements

description: Common Data Elements to use in medical research
DOI: 10.6084/m9.figshare.1437661.v2
title: transcript GTF annotation of ICC in jejunum smooth muscle

description: transcript annotation of ICC in jejunum smooth muscle
DOI: 10.6084/m9.figshare.1437660.v2
title: transcript GTF annotation of colon mucosa

description: transcript annotation of colon mucosa
DOI: 10.6084/m9.figshare.1437661.v1
title: transcript annotation of ICC in jejunum smooth muscle

description: transcript annotation of ICC in jejunum smooth muscle
DOI: 10.6084/m9.figshare.1437663.v1
title: transcript annotation of ICC in colon smooth muscle

description: transcript annotation of ICC in colon smooth muscle
DOI: 10.6084/m9.figshare.1437667.v2
title: CArGome BED annotation of mice

description: CArGome BED annotation of mice
DOI: 10.6084/m9.figshare.1437616
title: Drosophila melanogaster wing landmarks and semi-landmarks for biometric analysis

description: This is an additional copy of the full set of landmarks for the paper An image database of Drosophila melanogaster wings for phenomic and biometric analysis<br>Anne Sonnenschein, David VanderZee, William R Pitchers, Sudarshan Chari and Ian Dworkin GigaScience 2015, 4:25 doi:10.1186/s13742-015-0065-6 All of the data is also available on the GigaDB http://dx.doi.org/10.5524/100141
DOI: 10.6084/m9.figshare.1437623.v1
title: Common Data Elements

description: Common Data Elements to use in medical research
DOI: 10.6084/m9.figshare.1437660.v1
title: transcript annotation of colon mucosa

description: transcript annotation of colon mucosa
DOI: 10.6084/m9.figshare.1437667.v1
title: CarGome BED annotation of mice

description: CarGome BED annotation of mice
DOI: 10.6084/m9.figshare.1437612
title: Figure07

description: Permanent radial deformation of the stem taper surface profile
DOI: 10.6084/m9.figshare.1437609
title: Yokohama Specie Bank flow-of-funds, 1893-1908 **corrected

description: The fileset contains networks graphs of the Yokohama Specie Bank interbranch 'flow-of-funds' for the period 1893-1908.
DOI: 10.6084/m9.figshare.1437610
title: Yokohama Specie Bank flow of-funds, 1893-1908 ***corrected

description: visualizations of the Yokohama Specie Bank 'flow-of-funds' for the period 1893-1908
DOI: 10.6084/m9.figshare.1437466
title: Ajuts concedits per la UB per publicar en accés obert 2013

description: Articles publicats durant l'any 2013 en revistes d'accés obert que han rebut ajut de la UB
DOI: 10.6084/m9.figshare.1437467
title: Ajuts concedits per la UB per publicar en accés obert 2012

description: Articles publicats durant l'any 2012 en revistes d'accés obert que han rebut ajut de la UB
DOI: 10.6084/m9.figshare.1437609.v1
title: Yokohama Specie Bank flow-of-funds, 1893-1908 **corrected

description: The fileset contains networks graphs of the Yokohama Specie Bank interbranch 'flow-of-funds' for the period 1893-1908.
DOI: 10.6084/m9.figshare.1437612.v1
title: Figure07

description: Permanent radial deformation of the stem taper surface profile
DOI: 10.6084/m9.figshare.1437465
title: Ajuts concedits per la UB per publicar en accés obert 2011

description: Articles publicats durant l'any 2011 en revistes d'accés obert que han rebut ajut de la UB
DOI: 10.6084/m9.figshare.1437455
title: Zeitreihendatensatz fuer Deutschland, 1834-2012, Programme und Metadaten

description: Programme zur Erzeugung des Datensatzes und der Dokumentation, SQL-Datenbank mit den Metadaten (Titel, Quellenangaben, etc.)
DOI: 10.6084/m9.figshare.1437466.v1
title: Ajuts per accés obert 2013

description: Articles publicats durant l'any 2013 en revistes d'accés obert que han rebut ajut de la UB
DOI: 10.6084/m9.figshare.1437465.v1
title: Ajuts per accés obert 2011

description: Articles publicats durant l'any 2011 en revistes d'accés obert que han rebut ajut de la UB
DOI: 10.6084/m9.figshare.1437467.v1
title: Ajuts per accés obert 2012

description: Articles publicats durant l'any 2012 en revistes d'accés obert que han rebut ajut de la UB
DOI: 10.6084/m9.figshare.1437467.v3
title: Ajuts concedits per la UB per publicar en accés obert 2012

description: Articles publicats durant l'any 2012 en revistes d'accés obert que han rebut ajut de la UB
DOI: 10.6084/m9.figshare.1437466.v3
title: Ajuts concedits per la UB per publicar en accés obert 2013

description: Articles publicats durant l'any 2013 en revistes d'accés obert que han rebut ajut de la UB
DOI: 10.6084/m9.figshare.1437465.v3
title: Ajuts concedits per la UB per publicar en accés obert 2011

description: Articles publicats durant l'any 2011 en revistes d'accés obert que han rebut ajut de la UB
DOI: 10.6084/m9.figshare.1437467.v2
title: Ajuts concedits per la UB per publicar en accés obert 2012

description: Articles publicats durant l'any 2012 en revistes d'accés obert que han rebut ajut de la UB
DOI: 10.6084/m9.figshare.1437455.v1
title: Zeitreihendatensatz für Deutschland, 1834-2012, Programme und Metadaten

description: Programme zur Erzeugung des Datensatzes und der Dokumentation, SQL-Datenbank mit den Metadaten (Titel, Quellenangaben, etc.)
DOI: 10.6084/m9.figshare.1437465.v2
title: Ajuts concedits per la UB per publicar en accés obert 2011

description: Articles publicats durant l'any 2011 en revistes d'accés obert que han rebut ajut de la UB
DOI: 10.6084/m9.figshare.1437466.v2
title: Ajuts concedits per la UB per publicar en accés obert 2013

description: Articles publicats durant l'any 2013 en revistes d'accés obert que han rebut ajut de la UB
DOI: 10.6084/m9.figshare.1437445
title: Threat of shock and Sustained Attention/Response Inhibition

description: First dataset exploring SART performance and startle response under threat of shock. Collected by Christian Grillon, Oliver Robinson and Marissa Krimsky at NIMH. In addition to data, please cite: Front. Hum. Neurosci., 07 March 2013 | http://dx.doi.org/10.3389/fnhum.2013.00069<br><em>The impact of induced anxiety on response inhibition <strong>Oliver J. Robinson, Marissa Krimsky and Christian Grillon</strong></em>
DOI: 10.6084/m9.figshare.1437449
title: MAGIC Maize RIL genotyping

description: Genotypic data for the MAGIC Maize (MM) RIL F6. lines. SNPs produced with Illumina MaizeSNP50. Individuals are given in rows, marker names in columns. The accompanying MAGIC maize paper can be found at doi:10.1186/s13059-015-0716-z
DOI: 10.6084/m9.figshare.1437451
title: Supplemental data for article: "Microbiome in low and high caries prevalence populations"

description: The oral microbiota was compared between Romanian adolescents with high caries prevalence and no dental care, and Swedish caries-active and caries-free adolescents in caries prevention programs with low caries prevalence. Biofilm samples were analyzed by FLX+-pyrosequencing of the v1−v4 hyper variable regions of 16S rRNA gene
DOI: 10.6084/m9.figshare.1437453
title: MAGIC Maize founders genotyping

description: Genotypic data for the MAGIC Maize (MM) founder lines: A632, B73, B96, F7, H99, HP301, Mo17, W153R, and for the backup founder CML91. SNPs produced with Illumina MaizeSNP50. Individuals are given in rows, marker names in columns. The MM founders have been genotyped twice, hence the naming (e.g., A632 and A632.1). The accompanying MAGIC maize paper can be found at doi:10.1186/s13059-015-0716-z
DOI: 10.6084/m9.figshare.1437449.v1
title: MAGIC Maize RIL genotyping

description: Genotypic data for the MAGIC Maize (MM) RIL F6. lines. SNPs produced with Illumina MaizeSNP50. Individuals are given in rows, marker names in columns. The accompanying MAGIC maize paper can be found at doi:10.1186/s13059-015-0716-z
DOI: 10.6084/m9.figshare.1437451.v1
title: Supplemental data for article: "Microbiome in low and high caries prevalence populations"

description: The oral microbiota was compared between Romanian adolescents with high caries prevalence and no dental care, and Swedish caries-active and caries-free adolescents in caries prevention programs with low caries prevalence. Biofilm samples were analyzed by FLX+-pyrosequencing of the v1−v4 hyper variable regions of 16S rRNA gene
DOI: 10.6084/m9.figshare.1436211
title: Andaman Islander humeral cross-sectional shape data extracted from virtual models

description: Data associated with the article: A Virtual Geometric Morphometric approach to the quantification of long bone bilateral asymmetry and cross-sectional shape. Geometric morphometric landmarks for cross sections extracted from virtual models of the human humerus. Virtual models were created from laser scans (surface scan). The sample comprised 20 individuals (left and right bones, N=40), and cross sections were extracted at 35%, 50%, and 65% bone length.
DOI: 10.6084/m9.figshare.1437412
title: Quantitative RT PCR data from imaginal wing discs of Drosophila sechellia and Drosophila simulans

description: This is some raw data from our quantitative RT PCR experiments of mature third instat wing imaginal discs from Drosophila sechellia and Drosophila simulans for a small number of key "wing" genes involved with anterior and posterior patterning and growth.
DOI: 10.6084/m9.figshare.1436211.v1
title: Andaman Islander humeral cross-sectional shape data extracted from virtual models

description: Data associated with the article: A Virtual Geometric Morphometric approach to the quantification of long bone bilateral asymmetry and cross-sectional shape. Geometric morphometric landmarks for cross sections extracted from virtual models of the human humerus. Virtual models were created from laser scans (surface scan). The sample comprised 20 individuals (left and right bones, N=40), and cross sections were extracted at 35%, 50%, and 65% bone length.
DOI: 10.6084/m9.figshare.1437445.v2
title: Threat of shock and Sustained Attention/Response Inhibition

description: First dataset exploring SART performance and startle response under threat of shock. Collected by Christian Grillon, Oliver Robinson and Marissa Krimsky at NIMH. In addition to data, please cite: Front. Hum. Neurosci., 07 March 2013 | http://dx.doi.org/10.3389/fnhum.2013.00069<br><em>The impact of induced anxiety on response inhibition <strong>Oliver J. Robinson, Marissa Krimsky and Christian Grillon</strong></em>
DOI: 10.6084/m9.figshare.1437445.v1
title: Stress and Go NoGo SART

description: First dataset exploring SART performance and startle response under threat of shock. Collected by Christian Grillon, Oliver Robinson and lab at NIMH. Please cite: Front. Hum. Neurosci., 07 March 2013 | http://dx.doi.org/10.3389/fnhum.2013.00069<br><em>The impact of induced anxiety on response inhibition <strong>Oliver J. Robinson, Marissa Krimsky and Christian Grillon</strong></em>