cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1441195.v7
title: Nuf2 is required for chromosome segregation during mouse oocyte meiotic maturation

description: Nuf2 plays an important role in kinetochore-microtubule attachment and thus is involved in regulation of the spindle assembly checkpoint in mitosis. In this study, we examined the localization and function of Nuf2 during mouse oocyte meiotic maturation. Myc<sub>6</sub>-Nuf2 mRNA injection and immunofluorescent staining showed that Nuf2 localized to kinetochores from germinal vesicle breakdown to metaphase I stages, while it disappeared from the kinetochores at the anaphase I stage, but relocated to kinetochores at the MII stage. Overexpression of Nuf2 caused defective spindles, misaligned chromosomes, and activated spindle assembly checkpoint, and thus inhibited chromosome segregation and metaphase-anaphase transition in oocyte meiosis. Conversely, precocious polar body extrusion was observed in the presence of misaligned chromosomes and abnormal spindle formation in Nuf2 knock-down oocytes, causing aneuploidy. Our data suggest that Nuf2 is a critical regulator of meiotic cell cycle progression in mammalian oocytes.
DOI: 10.6084/m9.figshare.1441195.v6
title: Nuf2 is required for chromosome segregation during mouse oocyte meiotic maturation

description: Nuf2 plays an important role in kinetochore-microtubule attachment and thus is involved in regulation of the spindle assembly checkpoint in mitosis. In this study, we examined the localization and function of Nuf2 during mouse oocyte meiotic maturation. Myc<sub>6</sub>-Nuf2 mRNA injection and immunofluorescent staining showed that Nuf2 localized to kinetochores from germinal vesicle breakdown to metaphase I stages, while it disappeared from the kinetochores at the anaphase I stage, but relocated to kinetochores at the MII stage. Overexpression of Nuf2 caused defective spindles, misaligned chromosomes, and activated spindle assembly checkpoint, and thus inhibited chromosome segregation and metaphase-anaphase transition in oocyte meiosis. Conversely, precocious polar body extrusion was observed in the presence of misaligned chromosomes and abnormal spindle formation in Nuf2 knock-down oocytes, causing aneuploidy. Our data suggest that Nuf2 is a critical regulator of meiotic cell cycle progression in mammalian oocytes.
DOI: 10.6084/m9.figshare.1439793
title: IASSIST 2015 Sketchnotes

description: Kristin Briney's sketchnotes from IASSIST 2015 in Minneapolis, MN. I attended and made notes from concurrent sessions: A5, B5, C3, D1, E5, F5, G2. I also sketchnoted the 3 plenaries.
DOI: 10.6084/m9.figshare.1439794
title: ODIN test and co-location data

description: Supplementary data files for the manuscript <em>"The Outdoor Dust Information Node (ODIN) - Development and performance assessment of a low cost ambient dust sensor"</em> submitted to Atmospheric Measurement Techniques. June 2015. <strong>odin01_24July_14August_2014.tsv</strong>: Tab separated data from the Outdoor Dust Information Node during its co-location with PM10/PM2.5 instruments <strong>StAlbans24July_14August_2014.tsv</strong>: Tab separated air quality data from Environment Canterbury's monitoring station. <strong>StAlbans24July_14August_2014_WIND.tsv:</strong> Tab separated wind data from Environment Canterbury's monitoring station. <strong>sharp_baseline_test.tsv</strong>: Tab separated data from the baseline test of the Sharp Dust Sensor. <strong>sharp_baseline_temperature_Nov2014.tsv</strong>: Tab separated data from the baseline temperature response of the Sharp Dust Sensor. November 2014.
DOI: 10.6084/m9.figshare.1441095.v2
title: Zooplankton DNA barcode library

description: Capture barcode sequences from hundreds of zooplankton specimens simultaneously using NGS platforms
DOI: 10.6084/m9.figshare.1439793.v1
title: IASSIST 2015 Sketchnotes

description: Kristin Briney's sketchnotes from IASSIST 2015 in Minneapolis, MN. I attended and made notes from concurrent sessions: A5, B5, C3, D1, E5, F5, G2. I also sketchnoted the 3 plenaries.
DOI: 10.6084/m9.figshare.1441095.v1
title: Zooplankton DNA barcode library

description: Capture barcode sequences from hundreds of zooplankton specimens simultaneously using NGS platforms
DOI: 10.6084/m9.figshare.1439794.v1
title: ODIN test and co-location data

description: Supplementary data files for the manuscript <em>"The Outdoor Dust Information Node (ODIN) - Development and performance assessment of a low cost ambient dust sensor"</em> submitted to Atmospheric Measurement Techniques. June 2015. <strong>odin01_24July_14August_2014.tsv</strong>: Tab separated data from the Outdoor Dust Information Node during its co-location with PM10/PM2.5 instruments <strong>StAlbans24July_14August_2014.tsv</strong>: Tab separated data from Environment Canterbury's air quality monitoring station. <strong>sharp_baseline_test.tsv</strong>: Tab separated data from the baseline test of the Sharp Dust Sensor. <strong>sharp_baseline_temperature_Nov2014.tsv</strong>: Tab separated data from the baseline temperature response of the Sharp Dust Sensor. November 2014.
DOI: 10.6084/m9.figshare.1439794.v3
title: ODIN test and co-location data

description: Supplementary data files for the manuscript <em>"The Outdoor Dust Information Node (ODIN) - Development and performance assessment of a low cost ambient dust sensor"</em> submitted to Atmospheric Measurement Techniques. June 2015. <strong>odin01_24July_14August_2014.tsv</strong>: Tab separated data from the Outdoor Dust Information Node during its co-location with PM10/PM2.5 instruments <strong>StAlbans24July_14August_2014.tsv</strong>: Tab separated air quality data from Environment Canterbury's monitoring station. <strong>StAlbans24July_14August_2014_WIND.tsv:</strong> Tab separated wind data from Environment Canterbury's monitoring station. <strong>sharp_baseline_test.tsv</strong>: Tab separated data from the baseline test of the Sharp Dust Sensor. <strong>sharp_baseline_temperature_Nov2014.tsv</strong>: Tab separated data from the baseline temperature response of the Sharp Dust Sensor. November 2014.
DOI: 10.6084/m9.figshare.1439794.v2
title: ODIN test and co-location data

description: Supplementary data files for the manuscript <em>"The Outdoor Dust Information Node (ODIN) - Development and performance assessment of a low cost ambient dust sensor"</em> submitted to Atmospheric Measurement Techniques. June 2015. <strong>odin01_24July_14August_2014.tsv</strong>: Tab separated data from the Outdoor Dust Information Node during its co-location with PM10/PM2.5 instruments <strong>StAlbans24July_14August_2014.tsv</strong>: Tab separated data from Environment Canterbury's air quality monitoring station. <strong>sharp_baseline_test.tsv</strong>: Tab separated data from the baseline test of the Sharp Dust Sensor. <strong>sharp_baseline_temperature_Nov2014.tsv</strong>: Tab separated data from the baseline temperature response of the Sharp Dust Sensor. November 2014.
DOI: 10.6084/m9.figshare.1439773
title: Validation Dataset

description: This dataset was used to validate the model created with training data from the pilot study using only chinese restaurants in San Francisco
DOI: 10.6084/m9.figshare.1439772
title: Training data used to generate predictive model

description: This dataset was used to create the predictive model applied to all other datasets.
DOI: 10.6084/m9.figshare.1439774
title: A Novel Approach for Efficient Submission of Research Data to the National Database for Autism Research (NDAR) (Poster)

description: Researchers seeking to share their data with coordinating centers such as the National Database for Autism Research (NDAR), face numerous barriers to establishing new connections and maintaining existing ones. We sought to dramatically reduce the time and money required to establish and maintain the interoperability of data between research centers, by establishing a process where manual recoding of data is replaced by data sharing instructions in the form of extraction and transformation scripts. Over the course of seven typical (20-60 subjects, 400-1000 fields each) data submissions to NDAR, the need for duplication, retranscription, or restructuring of the source data was fully eliminated. Separating the extraction and transformation scripts from data files also eradicated the impact of additional data collection on the time required to repeat successful transmissions. Revision controlled management of these scripts also provided a new benefit: traceability of the transformation process itself. Now, point-in-time retrieval of extraction scripts and explanations for modifications to the data sharing interface are possible. This method has proven to be successful and efficient for interfacing research data with NDAR. It presents little-to-no impact to transmitting investigators’ data, ensures high data integrity, trivializes the complexities of repeatedly modifying a growing dataset over time, and introduces traceability to the collaborative process of integrating two collections of data with one another.
DOI: 10.6084/m9.figshare.1439779
title: Linking CMEs to Associated Solar Phenomena

description: Invited talk on connecting interplanetary coronal mass ejections to other solar phenomena at the HELCATS First Annual Open Workshop: Heliospheric Imaging – A new era of space science and space weather observations. Göttingen, May 19-22, 2015 (http://www.affects-fp7.eu/helcats-meeting/)
DOI: 10.6084/m9.figshare.1439772.v1
title: Training data used to generate predictive model

description: This dataset was used to create the predictive model applied to all other datasets.
DOI: 10.6084/m9.figshare.1439779.v1
title: Linking CMEs to Associated Solar Phenomena

description: Invited talk on connecting interplanetary coronal mass ejections to other solar phenomena at the HELCATS First Annual Open Workshop: Heliospheric Imaging – A new era of space science and space weather observations. Göttingen, May 19-22, 2015 (http://www.affects-fp7.eu/helcats-meeting/)
DOI: 10.6084/m9.figshare.1439769
title: San Francisco Dataset without cuisine exclusion

description: Dataset of tags and keywords for restaurants in san Francisco on Yelp.com.
DOI: 10.6084/m9.figshare.1439770
title: New York City Dataset

description: Dataset of Yelp tags and keywords for New York City
DOI: 10.6084/m9.figshare.1439774.v2
title: A Novel Approach for Efficient Submission of Research Data to the National Database for Autism Research (NDAR) (Poster)

description: Researchers seeking to share their data with coordinating centers such as the National Database for Autism Research (NDAR), face numerous barriers to establishing new connections and maintaining existing ones. We sought to dramatically reduce the time and money required to establish and maintain the interoperability of data between research centers, by establishing a process where manual recoding of data is replaced by data sharing instructions in the form of extraction and transformation scripts. Over the course of seven typical (20-60 subjects, 400-1000 fields each) data submissions to NDAR, the need for duplication, retranscription, or restructuring of the source data was fully eliminated. Separating the extraction and transformation scripts from data files also eradicated the impact of additional data collection on the time required to repeat successful transmissions. Revision controlled management of these scripts also provided a new benefit: traceability of the transformation process itself. Now, point-in-time retrieval of extraction scripts and explanations for modifications to the data sharing interface are possible. This method has proven to be successful and efficient for interfacing research data with NDAR. It presents little-to-no impact to transmitting investigators’ data, ensures high data integrity, trivializes the complexities of repeatedly modifying a growing dataset over time, and introduces traceability to the collaborative process of integrating two collections of data with one another.
DOI: 10.6084/m9.figshare.1439769.v1
title: San Francisco Dataset without cuisine exclusion

description: Dataset of tags and keywords for restaurants in san Francisco on Yelp.com.
DOI: 10.6084/m9.figshare.1439774.v1
title: A Novel Approach for Efficient Submission of Research Data to the National Database for Autism Research (NDAR)

description: Researchers seeking to share their data with coordinating centers such as the National Database for Autism Research (NDAR), face numerous barriers to establishing new connections and maintaining existing ones. We sought to dramatically reduce the time and money required to establish and maintain the interoperability of data between research centers, by establishing a process where manual recoding of data is replaced by data sharing instructions in the form of extraction and transformation scripts. Over the course of seven typical (20-60 subjects, 400-1000 fields each) data submissions to NDAR, the need for duplication, retranscription, or restructuring of the source data was fully eliminated. Separating the extraction and transformation scripts from data files also eradicated the impact of additional data collection on the time required to repeat successful transmissions. Revision controlled management of these scripts also provided a new benefit: traceability of the transformation process itself. Now, point-in-time retrieval of extraction scripts and explanations for modifications to the data sharing interface are possible. This method has proven to be successful and efficient for interfacing research data with NDAR. It presents little-to-no impact to transmitting investigators’ data, ensures high data integrity, trivializes the complexities of repeatedly modifying a growing dataset over time, and introduces traceability to the collaborative process of integrating two collections of data with one another.
DOI: 10.6084/m9.figshare.1439767
title: Gaussian Job Archive for C20H20Cl2O6

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1439753
title: Export of Wikipedia recent changes

description: This Dataset contains about 600.000 Recent-Changes fetched from the Wikipadia API. All entries are dated between 2015-05-01 and 2015-06-07. No Minor- or Bot-Changes are collected. This data is a zip-compressed export of a Mongo DB. MD5 zipped: 77b5bfb4e9b47ce2dc02240f7cf2e9d2<br>MD5 unzipped: 98ca302cdc604052b66ceed781630452
DOI: 10.6084/m9.figshare.1439753.v1
title: Export of Wikipedia recent changes

description: This Dataset contains about 600.000 Recent-Changes fetched from the Wikipadia API. All entries are dated between 2015-05-01 and 2015-06-07. No Minor- or Bot-Changes are collected. This data is a zip-compressed export of a Mongo DB. MD5 zipped: 77b5bfb4e9b47ce2dc02240f7cf2e9d2<br>MD5 unzipped: 98ca302cdc604052b66ceed781630452
DOI: 10.6084/m9.figshare.1439767.v1
title: Gaussian Job Archive for C20H20Cl2O6

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1439742
title: Better-Than-Average Effect

description: Better Than Average, Or Better Than the Average Joe? The Better-Than-Average Effect Reconsidered
DOI: 10.6084/m9.figshare.1439749
title: A FreeSurfer view of the cortical transcriptome generated from the Allen Human Brain Atlas

description: The Allen Human Brain Atlas provides an anatomically detailed view of gene expression in the brain. This full transcriptomic dataset contains over 200 million expression values. To facilitate use of this resource, we distilled the data into a matrix of 20,737 genes by 68 cortical regions that represent the automatically segmented FreeSurfer regions (Desikan-Killiany parcellation). In this data report, we describe the Allen-FreeSurfer mapping, sampling information and provide regional values of gene expression. The resulting cortical transcriptome facilitates interpretation of human neuroimaging findings by providing a molecular context. Read the full data report at: http://journal.frontiersin.org/article/10.3389/fnins.2015.00323/full AllenHBA_to_DKRegion_Map.xls - Excel file containing the mapping from Allen Brain Atlas samples to the FreeSurfer cortical regions. Each sample is referenced with a unique identifier by combining the donor ID with the x, y and z MNI152 coordinates (“10021_5.1_27.1_28.6“ for example). DKRegionStatistics.tsv - Tab separated file characterizing the FreeSurfer cortical regions. This file lists how many donors contribute to each region, Allen Brain Atlas samples per region and alternative identifiers. AllenHBA_DK_ExpessionMatrix.tsv - tab separated file containing correlation to the median values across the donors (left hemisphere only, column named ”Average donor correlation to median”) and gene expression values across the 68 FreeSurfer cortical regions (columns). This file can be opened with read.table in R or as a tab separated file in a spreadsheet program. ConsistentGOGroups.tsv – Gene Ontology enrichment analyses results for the consistency measure. InconsistentGOGroups.tsv – Gene Ontology enrichment analyses results for the consistency measure (with high ranked groups showing more inconsistency). CreateExpressionLUT.r - This R script provides the method to load and convert expression values for a specific gene into a color lookup table that can be used to visualize the averaged expression values in FreeSurfer. CreateColorBar.r - This R script will create a color bar to complement the TKSurfer generated images.
DOI: 10.6084/m9.figshare.1439742.v2
title: Better-Than-Average Effect

description: Better Than Average, Or Better Than the Average Joe? The Better-Than-Average Effect Reconsidered
DOI: 10.6084/m9.figshare.1439742.v1
title: Better-Than-Average Effect

description: Better Than Average, Or Better Than the Average Joe? The Better-Than-Average Effect Reconsidered
DOI: 10.6084/m9.figshare.1439749.v5
title: A FreeSurfer view of the cortical transcriptome generated from the Allen Human Brain Atlas

description: The Allen Human Brain Atlas provides an anatomically detailed view of gene expression in the brain. This full transcriptomic dataset contains over 200 million expression values. To facilitate use of this resource, we distilled the data into a matrix of 20,737 genes by 68 cortical regions that represent the automatically segmented FreeSurfer regions (Desikan-Killiany parcellation). In this data report, we describe the Allen-FreeSurfer mapping, sampling information and provide regional values of gene expression. The resulting cortical transcriptome facilitates interpretation of human neuroimaging findings by providing a molecular context. AllenHBA_to_DKRegion_Map.xls - Excel file containing the mapping from Allen Brain Atlas samples to the FreeSurfer cortical regions. Each sample is referenced with a unique identifier by combining the donor ID with the x, y and z MNI152 coordinates (“10021_5.1_27.1_28.6“ for example). DKRegionStatistics.tsv - Tab separated file characterizing the FreeSurfer cortical regions. This file lists how many donors contribute to each region, Allen Brain Atlas samples per region and alternative identifiers. AllenHBA_DK_ExpessionMatrix.tsv - tab separated file containing correlation to the median values across the donors (left hemisphere only, column named ”Average donor correlation to median”) and gene expression values across the 68 FreeSurfer cortical regions (columns). This file can be opened with read.table in R or as a tab separated file in a spreadsheet program. ConsistentGOGroups.tsv – Gene Ontology enrichment analyses results for the consistency measure. InconsistentGOGroups.tsv – Gene Ontology enrichment analyses results for the consistency measure (with high ranked groups showing more inconsistency). CreateExpressionLUT.r - This R script provides the method to load and convert expression values for a specific gene into a color lookup table that can be used to visualize the averaged expression values in FreeSurfer.
DOI: 10.6084/m9.figshare.1439709
title: Single-Gene Analyses

description: Best tree from RaxML analysis single-gene amino acid sequence alignments for 208 single-copy genes from 35 Agaricales taxa plus four outgroups (Newick format). Includes: -Best-scoring ML tree with branch lengths (RAxML_bestTree.Copci1_XXX.phy) -Best-scoring ML tree with support values (RAxML_bipartitions.Copci1_XXX.phy) -Best-scoring ML tree with branch lengths and support values as branch labels (RAxML_bipartitionsBranchLabels.Copci1_XXX.phy) -Best-scoring ML trees from each bootstrap replicate (RAxML_bootstrap.Copci1_XXX.phy) -Info about analysis (RAxML_info.Copci1_XXX.phy)
DOI: 10.6084/m9.figshare.1439710
title: Agaricales Genomics

description: Datasets created for Dentinger et al. 2015. Tales from the crypt: genome mining from fungarium specimens improves resolution of the mushroom tree of life. Biological Journal of the Linnean Society. <strong>Contents</strong> Untrimmed Single-Gene Alignments: Raw untrimmed amino acid alignments of 210 single-copy genes from 35 Agaricales taxa, plus 5 five outgroups (relaxed Phylip format). Trimmed Single-Gene Alignments: Trimmed amino acid alignments of 208 single-copy genes from 35 Agaricales taxa, plus 5 five outgroups (relaxed Phylip format). Single-Gene Analyses: Best tree from RaxML analysis single-gene amino acid sequence alignments for 208 single-copy genes from 35 Agaricales taxa plus four outgroups (Newick format). Concatinated Alignment: Final trimmed, concatinated amino acid alignment of 208 single-copy genes from 35 Agaricales taxa, plus 5 five outgroups (relaxed Phylip format) Unpartitioned Analysis: Best tree from unpartitioned RaxML analysis of concatinated alignment of amino acid sequences for 208 single-copy genes from 35 Agaricales taxa plus four outgroups (Newick format). Partition Info for Concatinated Alignment: Partition information for concatinated amino acid alignment of 208 single-copy genes from 35 Agaricales taxa, plus four outgroups. Gene names are based on Coprinopsis cinerea locus IDs Partitioned Analysis: Best tree from partitioned RaxML analysis of concatinated alignment of amino acid sequences for 208 single-copy genes from 35 Agaricales taxa plus four outgroups (Newick format).
DOI: 10.6084/m9.figshare.1439702
title: Partitioned Analysis

description: Best tree from partitioned RaxML analysis of concatinated alignment of amino acid sequences for 208 single-copy genes from 35 Agaricales taxa plus four outgroups (Newick format). Includes: -Best-scoring ML tree with branch lengths (RAxML_bestTree.AllConcatinatedProt.phy_partitioned) -Best-scoring ML tree with support values (RAxML_bipartitions.AllConcatinatedProt.phy_partitioned) -Best-scoring ML tree with branch lengths and support values as branch labels (RAxML_bipartitionsBranchLabels.AllConcatinatedProt.phy_partitioned) -Best-scoring ML trees from each bootstrap replicate (RAxML_bootstrap.AllConcatinatedProt.phy_partitioned) -Info about analysis (RAxML_info.AllConcatinatedProt.phy_partitioned)