cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1288837
title: R script to perform a biogeographical regionalisation of the Adriatic Sea based on phylogenetic beta diversity

description: This R code provides a computational framework to perform a biogeographical regionalisation based on phylogenetic beta diversity. For this purpose, we will use two data sets: -Distribution_Data.csv: a csv file with 1323 observations (sites located on the Adreatic Sea) on 161 binary variables (species). -Phylogenetic_Data.trd: a phylogenetic tree of 363 Mediterranean teleost species (see Meynard et al., 2012 for details: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0036443). Two external functions are also required: -beta_pd_decompo.r: R function to quantify phylogenetic beta diversity (PBD) and its 'true' turnover and phylogenetic diversity (PD) components based on the UniFrac and PhyloSor indices. -A2R.r: R function for generating colored dendrograms which you can download here http://addictedtor.free.fr/packages/A2R/lastVersion/R/code.R.<br><br>For more details about this topic you can read the original article: Hattab, T., Albouy, C., Ben Rais Lasram, F., Le Loc'h, F., Guilhaumon, F., Leprieur, F. (2015), A biogeographical regionalization of coastal Mediterranean fishes. Journal of Biogeography. doi: 10.1111/jbi.12505 1.Put all the documents in a single folder (this becomes your working directory) 2. Install the necessary packages in R (see first part of the script) 3. Define the working directory in the script (setwd(“C:/…/”), as indicated in the script) 4. Run the script in R
DOI: 10.6084/m9.figshare.1288858.v1
title: Linear measurements of insectivore mammals' skulls

description: Linear measurements of insectivore mammals' skulls and mandibles
DOI: 10.6084/m9.figshare.1288777
title: Supplementary figures, tables and texts for FANTOM 5 phase 2

description: Supplementary figures, tables, auxiliary files and tables as in Arner et al (Science 2005)
DOI: 10.6084/m9.figshare.1288777.v1
title: Supplementary figures, tables and texts for FANTOM 5 phase 2

description: Supplementary figures, tables, auxiliary files and tables as in Arner et al (Science 2005)
DOI: 10.6084/m9.figshare.1288837.v1
title: R script to perform a biogeographical regionalisation of the Adriatic Sea based on phylogenetic beta diversity

description: R function to perform a biogeographical regionalisation based on phylogenetic beta diversity<br>#<br># Date 13 January 2015<br># Copyright: Hattab et al, 2015<br># License: GPL-3<br>This R code provides a computational framework to perform a biogeographical regionalisation based on phylogenetic beta diversity. For this purpose, we will use two data sets: -Distribution_Data.csv: a csv file with 1323 observations (sites located on the Adreatic Sea) on 161 binary variables (species).<br>-Phylogenetic_Data.trd: a phylogenetic tree of 363 Mediterranean teleost species (see Meynard et al., 2012 for details: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0036443). Two external functions are also required: -beta_pd_decompo.r: R function to quantify phylogenetic beta diversity (PBD) and its 'true' turnover and phylogenetic diversity (PD)<br> components based on the UniFrac and PhyloSor indices.<br>-A2R.r: R function for generating colored dendrograms which you can download here http://addictedtor.free.fr/packages/A2R/lastVersion/R/code.R.<br><br>For more details about this topic you can read the original article:<br>Tarek H, Albouy C, Ben Rais Lasram F, Le Loc'h F, Guilhaumon F, Leprieur F,(submited to Journal of Biogeography). A biogeographic regionalisation of coastal Mediterranean fishes. 1.Put all the documents in a single folder (this becomes your working directory) 2. Install the necessary packages in R (see first part of the script) 3. Define the working directory in the script (setwd(“C:/…/”), as indicated in the script) 4. Run the script in R
DOI: 10.6084/m9.figshare.1288855.v1
title: Franck-Condon factors (bound-bound) between 3He-4He+ and 3He-4He++

description: Franck-Condon factors and eigenvalues for bound to bound transitions between the helium molecular ion and the helium molecular dication for the case of 3He-4He+ (ion) and 3He-4He++ (dication).<br>Reduced mass of ions 3134.328 in units of electron mass.The eigenvalues are given in atomic units. The potential energies used are described in J. F. Babb and M. L. Du, Chem. Phys. Letters 167 (1990), 273. doi:10.1016/0009-2614(90)87167-P
DOI: 10.6084/m9.figshare.1288710
title: JIPA_supplementary_data

description: Supplementary data of the paper for the Journal of Indo-Pacific Archaeology
DOI: 10.6084/m9.figshare.1288737
title: Data of GWAS associated SNPs in regulatory regions

description: Data file 1: DNase I hotspot samples included in FORGE analysis. A list of DNase I hotspot samples included in FORGE analysis is shown.The table lists details of the 125 ENCODE and 299 Roadmap Epigenome samples. The fields are File: file name; Lab: data-generating lab. One of UW (University of Washington, John Stamatoyannopoulos lab), Duke:UNC:UTA (Duke University, Greg Crawford lab) or combined representing a merged dataset from both labs; Experiment type: always DNase-seq in the current implementation; Project: Either ENCODE or Roadmap; Cell: cell type; Tissue: tissue name derived as described above; Data type: always hotspots in the current implementation; Short name: a short sample used for plotting; Individual: either the code for the individual sample as described in Biosamples or NA if not available; GEO accession: the GEO accession where found, or “Not found” if it could not be deconvoluted. Data file 2: List of phenotypes analysed. The list of phenotypes analysed, with non-redundant SNP counts and Pubmed identifiers for the studies involved is shown. This table is also available in the data directory of the GitHub release,https://github.com/iandunham/Forge.
DOI: 10.6084/m9.figshare.1288618
title: Kasprak et al. 2015, JGR-Earth Surface Data

description: Topographic and sediment data used in the Kasprak et al. (2015) paper in Journal of Geophysical Resarch: Earth Surface (The relationship between particle travel distance and channel morphology: Results fromphysical models of braided rivers).
DOI: 10.6084/m9.figshare.1288687
title: aas wise

description: asdfasdf
DOI: 10.6084/m9.figshare.1288610
title: 2 Nov 2012 processed data

description: Processed images for 2 Nov 2012 time-lapse run.
DOI: 10.6084/m9.figshare.1288618.v1
title: Kasprak et al. 2015, JGR-Earth Surface Data

description: Topographic and sediment data used in the Kasprak et al. (2015) paper in Journal of Geophysical Resarch: Earth Surface (The relationship between particle travel distance and channel morphology: Results fromphysical models of braided rivers).
DOI: 10.6084/m9.figshare.1288687.v1
title: aas wise

description: asdfasdf
DOI: 10.6084/m9.figshare.1288710.v7
title: JIPA_supplementary_data

description: Supplementary data of the paper for the Journal of Indo-Pacific Archaeology
DOI: 10.6084/m9.figshare.1288609
title: Processed images - 2 Nov 2012 time lapse

description: Processed images for 2 Nov 2012 time-lapse run.
DOI: 10.6084/m9.figshare.1288710.v6
title: JIPA_supplementary_data

description: Supplementary data of the paper for the Journal of Indo-Pacific Archaeology
DOI: 10.6084/m9.figshare.1287817
title: Shh Phosphatome Screen

description: Table 1-Phosphatome Screen-Shh Signaling. The individual genes tested in primary screen for phosphatases involved in Shh signaling. Gene symbol, gene name and identifier and the target sequence are shown. Four or five target sequences were used for each gene. Table 2- Phosphatome Screen. Individual genes were identified as positive hits in an shRNA screen for phosphatases that affect Shh signaling in ShhlightII cells as assessed by Gli promoter-luciferase expression. Table 5- Phosphatome Screen-Primary Data. Results of phosphatome screen for Shh signaling in ShhlightII cells. For each targeting sequence the gene targeted, the average value for Firefly/Renilla luciferase, the In of that ratio and the robust z score are shown. Each sequence was tested in control conditions (vehicle), with SAG stimulation (300nM) and with Shh stimulation (300ng/ml) and results for each are shown.
DOI: 10.6084/m9.figshare.1288610.v2
title: 2 Nov 2012 processed data

description: Processed images for 2 Nov 2012 time-lapse run.
DOI: 10.6084/m9.figshare.1287817.v1
title: Shh Phosphatome Screen

description: Table 1-Phosphatome Screen-Shh Signaling. The individual genes tested in primary screen for phosphatases involved in Shh signaling. Gene symbol, gene name and identifier and the target sequence are shown. Four or five target sequences were used for each gene. Table 2- Phosphatome Screen. Individual genes were identified as positive hits in an shRNA screen for phosphatases that affect Shh signaling in ShhlightII cells as assessed by Gli promoter-luciferase expression. Table 5- Phosphatome Screen-Primary Data. Results of phosphatome screen for Shh signaling in ShhlightII cells. For each targeting sequence the gene targeted, the average value for Firefly/Renilla luciferase, the In of that ratio and the robust z score are shown. Each sequence was tested in control conditions (vehicle), with SAG stimulation (300nM) and with Shh stimulation (300ng/ml) and results for each are shown.
DOI: 10.6084/m9.figshare.1288610.v1
title: NikonTimeLapse

description: Processed images for 2 Nov 2012 time-lapse run.
DOI: 10.6084/m9.figshare.1288609.v1
title: ProcessedImages

description: Processed images for 2 Nov 2012 time-lapse run.
DOI: 10.6084/m9.figshare.1288609.v3
title: Processed images - 2 Nov 2012 time lapse

description: Processed images for 2 Nov 2012 time-lapse run.
DOI: 10.6084/m9.figshare.1287793
title: Comparison of genome-wide and gene-specific DNA methylation between ART and naturally conceived pregnancies

description: Data linking assisted reproductive technologies (ART) with aberrant DNA methylation is limited and inconclusive. In addition, most studies to date have analyzed only a small number of CpG sites and focused on methylation changes in placentas, while data on cord blood are scarce. Our aim was to compare DNA methylation in cord blood samples from ART (N = 10) and control pregnancies (N = 8) using a genome-wide approach with the Illumina® Infinium Human Methylation27 array, which interrogates 27,578 CpG sites. A total of 733 (2.7%) of the CpG sites were significantly differentially methylated between the 2 groups (<i>P</i> &lt; 0.05), with an overall relative hypomethylation in the ART group (<i>P</i> &lt; 0.001). Differences in DNA methylation were more pronounced for CpG sites in certain types of genomic locations and were related to baseline methylation levels and distance from CpG islands and transcription start sites. ART was associated with significantly higher variation in DNA methylation, suggesting that differences in DNA methylation between cases and controls may result from stochastic (or random) genome-wide changes in DNA methylation in ART pregnancies. We identified 24 candidate genes with 2 or more CpG sites that were significantly different between the IVF and control groups. The current study provides support for the hypothesis that ART or associated subfertility may be associated with genome-wide changes in DNA methylation, and these changes appear to be, at least in part, due to epigenetic instability in ART pregnancies. Further studies are required in order to determine the extent to which such ART-related epigenetic instability may have phenotypic consequences.
DOI: 10.6084/m9.figshare.1288609.v2
title: Processed images - 2 Nov 2012 time lapse

description: Processed images for 2 Nov 2012 time-lapse run.
DOI: 10.6084/m9.figshare.1287792
title: Survey of human-wildlife conflict, resource use and attitudes towards conservation and sustainable development in the Kanuku Mountains, Rupununi, Guyana

description: Raw data, metadata and summaries from surveys of human-wildlife conflict, subsistence and commercial resource use, attitudes towards wildlife, research and conservation, knowledge of regional wildlife, agricultural and livestock management practices, regional demographics and regional social issues in six indigenous communities surrounding the Kanuku Mountains, Guyana.
DOI: 10.6084/m9.figshare.1287793.v1
title: Comparison of Genome-Wide and Gene-Specific DNA Methylation between ART and Naturally Conceived Pregnancies

description: ABSTRACTData linking assisted reproductive technologies (ART) with aberrant DNA methylation is limited and inconclusive. In addition, most studies to date have analyzed only a small number of CpG sites and focused on methylation changes in placentas, while data on cord blood are scarce. Our aim was to compare DNA methylation in cord blood samples from ART (N = 10) and control pregnancies (N = 8) using a genome-wide approach with the Illumina® Infinium Human Methylation27 array, which interrogates 27,578 CpG sites. A total of 733 (2.7%) of the CpG sites were significantly differentially methylated between the two groups (<i>P</i> &lt; 0.05), with an overall relative hypomethylation in the ART group (<i>P</i> &lt; 0.001). Differences in DNA methylation were more pronounced for CpG sites in certain types of genomic locations and were related to baseline methylation levels and distance from CpG islands and transcription start sites. ART was associated with significantly higher variation in DNA methylation, suggesting that differences in DNA methylation between cases and controls may result from a stochastic increase in genome-wide DNA methylation in IVF pregnancies. We identified 24 candidate genes with 2 or more CpG sites that were significantly different between the IVF and control groups. The current study provides support for the hypothesis that ART-associated subfertility may be associated with genome-wide changes in DNA methylation, and these changes appear to be, at least in part, due to epigenetic instability in ART pregnancies. Further studies are required in order to determine the extent to which such ART-related epigenetic instability may have phenotypic consequences.
DOI: 10.6084/m9.figshare.1287792.v1
title: Survey of human-wildlife conflict, resource use and attitudes towards conservation and sustainable development in the Kanuku Mountains, Rupununi, Guyana

description: Metadata and data summaries from surveys of human-wildlife conflict, subsistence and commercial resource use, attitudes towards wildlife, research and conservation, knowledge of regional wildlife, agricultural and livestock management practices, regional demographics and regional social issues in six indigenous communities surrounding the Kanuku Mountains, Guyana.
DOI: 10.6084/m9.figshare.1287781
title: Paleoneuroanatomy of the European lambeosaurine dinosaur Arenysaurus ardevoli.

description: CT scans from the braincase of the lambeosaurine dinosaur Arenysaurus ardevoli. CT-scans in two parts. See the original article for more information: Cruzado-Caballero, P., Fortuny, J., Llacer, S., Canudo, J.I., Paleoneuroanatomy of the European lambeosaurine dinosaur Arenysaurus ardevoli. Peerj.. .
DOI: 10.6084/m9.figshare.1287793.v2
title: Comparison of genome-wide and gene-specific DNA methylation between ART and naturally conceived pregnancies

description: Data linking assisted reproductive technologies (ART) with aberrant DNA methylation is limited and inconclusive. In addition, most studies to date have analyzed only a small number of CpG sites and focused on methylation changes in placentas, while data on cord blood are scarce. Our aim was to compare DNA methylation in cord blood samples from ART (N = 10) and control pregnancies (N = 8) using a genome-wide approach with the Illumina® Infinium Human Methylation27 array, which interrogates 27,578 CpG sites. A total of 733 (2.7%) of the CpG sites were significantly differentially methylated between the 2 groups (<i>P</i> &lt; 0.05), with an overall relative hypomethylation in the ART group (<i>P</i> &lt; 0.001). Differences in DNA methylation were more pronounced for CpG sites in certain types of genomic locations and were related to baseline methylation levels and distance from CpG islands and transcription start sites. ART was associated with significantly higher variation in DNA methylation, suggesting that differences in DNA methylation between cases and controls may result from stochastic (or random) genome-wide changes in DNA methylation in ART pregnancies. We identified 24 candidate genes with 2 or more CpG sites that were significantly different between the IVF and control groups. The current study provides support for the hypothesis that ART or associated subfertility may be associated with genome-wide changes in DNA methylation, and these changes appear to be, at least in part, due to epigenetic instability in ART pregnancies. Further studies are required in order to determine the extent to which such ART-related epigenetic instability may have phenotypic consequences.
DOI: 10.6084/m9.figshare.1287793.v3
title: Comparison of genome-wide and gene-specific DNA methylation between ART and naturally conceived pregnancies

description: Data linking assisted reproductive technologies (ART) with aberrant DNA methylation is limited and inconclusive. In addition, most studies to date have analyzed only a small number of CpG sites and focused on methylation changes in placentas, while data on cord blood are scarce. Our aim was to compare DNA methylation in cord blood samples from ART (N = 10) and control pregnancies (N = 8) using a genome-wide approach with the Illumina® Infinium Human Methylation27 array, which interrogates 27,578 CpG sites. A total of 733 (2.7%) of the CpG sites were significantly differentially methylated between the 2 groups (<i>P</i> &lt; 0.05), with an overall relative hypomethylation in the ART group (<i>P</i> &lt; 0.001). Differences in DNA methylation were more pronounced for CpG sites in certain types of genomic locations and were related to baseline methylation levels and distance from CpG islands and transcription start sites. ART was associated with significantly higher variation in DNA methylation, suggesting that differences in DNA methylation between cases and controls may result from stochastic (or random) genome-wide changes in DNA methylation in ART pregnancies. We identified 24 candidate genes with 2 or more CpG sites that were significantly different between the IVF and control groups. The current study provides support for the hypothesis that ART or associated subfertility may be associated with genome-wide changes in DNA methylation, and these changes appear to be, at least in part, due to epigenetic instability in ART pregnancies. Further studies are required in order to determine the extent to which such ART-related epigenetic instability may have phenotypic consequences.
DOI: 10.6084/m9.figshare.1287779
title: Paleoneuroanatomy of the European lambeosaurine dinosaur Arenysaurus ardevoli

description: CT scans from the braincase of the lambeosaurine dinosaur Arenysaurus ardevoli. CT-scans in two parts. See the original article for more information: Cruzado-Caballero, P., Fortuny, J., Llacer, S., Canudo, J.I., Paleoneuroanatomy of the European lambeosaurine dinosaur Arenysaurus ardevoli. Peerj
DOI: 10.6084/m9.figshare.1287793.v5
title: Comparison of genome-wide and gene-specific DNA methylation between ART and naturally conceived pregnancies

description: Data linking assisted reproductive technologies (ART) with aberrant DNA methylation is limited and inconclusive. In addition, most studies to date have analyzed only a small number of CpG sites and focused on methylation changes in placentas, while data on cord blood are scarce. Our aim was to compare DNA methylation in cord blood samples from ART (N = 10) and control pregnancies (N = 8) using a genome-wide approach with the Illumina® Infinium Human Methylation27 array, which interrogates 27,578 CpG sites. A total of 733 (2.7%) of the CpG sites were significantly differentially methylated between the 2 groups (<i>P</i> &lt; 0.05), with an overall relative hypomethylation in the ART group (<i>P</i> &lt; 0.001). Differences in DNA methylation were more pronounced for CpG sites in certain types of genomic locations and were related to baseline methylation levels and distance from CpG islands and transcription start sites. ART was associated with significantly higher variation in DNA methylation, suggesting that differences in DNA methylation between cases and controls may result from stochastic (or random) genome-wide changes in DNA methylation in ART pregnancies. We identified 24 candidate genes with 2 or more CpG sites that were significantly different between the IVF and control groups. The current study provides support for the hypothesis that ART or associated subfertility may be associated with genome-wide changes in DNA methylation, and these changes appear to be, at least in part, due to epigenetic instability in ART pregnancies. Further studies are required in order to determine the extent to which such ART-related epigenetic instability may have phenotypic consequences.
DOI: 10.6084/m9.figshare.1287793.v4
title: Comparison of genome-wide and gene-specific DNA methylation between ART and naturally conceived pregnancies

description: Data linking assisted reproductive technologies (ART) with aberrant DNA methylation is limited and inconclusive. In addition, most studies to date have analyzed only a small number of CpG sites and focused on methylation changes in placentas, while data on cord blood are scarce. Our aim was to compare DNA methylation in cord blood samples from ART (N = 10) and control pregnancies (N = 8) using a genome-wide approach with the Illumina® Infinium Human Methylation27 array, which interrogates 27,578 CpG sites. A total of 733 (2.7%) of the CpG sites were significantly differentially methylated between the 2 groups (<i>P</i> &lt; 0.05), with an overall relative hypomethylation in the ART group (<i>P</i> &lt; 0.001). Differences in DNA methylation were more pronounced for CpG sites in certain types of genomic locations and were related to baseline methylation levels and distance from CpG islands and transcription start sites. ART was associated with significantly higher variation in DNA methylation, suggesting that differences in DNA methylation between cases and controls may result from stochastic (or random) genome-wide changes in DNA methylation in ART pregnancies. We identified 24 candidate genes with 2 or more CpG sites that were significantly different between the IVF and control groups. The current study provides support for the hypothesis that ART or associated subfertility may be associated with genome-wide changes in DNA methylation, and these changes appear to be, at least in part, due to epigenetic instability in ART pregnancies. Further studies are required in order to determine the extent to which such ART-related epigenetic instability may have phenotypic consequences.
DOI: 10.6084/m9.figshare.1287743
title: Household clustering of dengue in Vietnam (DTA)

description: Data underlying analyses published in Anders et al (2015) 'Households as foci for dengue transmission in highly urban Vietnam' <em>PLoS NTD</em>
DOI: 10.6084/m9.figshare.1287764
title: Calcium time series from OGB labeled V1 neurons in awake or anesthesized mice.

description: Calcium time series from OGB labeled V1 neurons in awake or anesthesized mice. Data published in: Pieter M. Goltstein, Jorrit S. Montijn, Cyriel M.A. Pennartz. (2015). Effects of isoflurane anesthesia on ensemble patterns of Ca2+ activity in mouse V1: Reduced direction selectivity independent of increased correlations in cellular activity. PLOS ONE.
DOI: 10.6084/m9.figshare.1287764.v1
title: Calcium time series from OGB labeled V1 neurons in awake or anesthesized mice.

description: Calcium time series from OGB labeled V1 neurons in awake or anesthesized mice. Data published in: Pieter M. Goltstein, Jorrit S. Montijn, Cyriel M.A. Pennartz. (2015). Effects of isoflurane anesthesia on ensemble patterns of Ca2+ activity in mouse V1: Reduced direction selectivity independent of increased correlations in cellular activity. PLOS ONE.