cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1387714.v7
title: Seattle Streets, Renamed over time

description: This group contains datasets with tables of street names before and after particular ordinances.
DOI: 10.6084/m9.figshare.1386856
title: Sustainable Transport Communications Dataset

description: A collection of sustainable transport communications for use in analysis of behaviour management mechanisms in the wild.
DOI: 10.6084/m9.figshare.1386856.v1
title: Sustainable Transport Communications Dataset

description: A collection of sustainable transport communications for use in analysis of behaviour management mechanisms in the wild.
DOI: 10.6084/m9.figshare.1386855
title: Gaussian Job Archive for C6H6Br10

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1387714.v8
title: Seattle Streets, Renamed over time

description: This group contains datasets with tables of street names before and after particular ordinances.
DOI: 10.6084/m9.figshare.1386855.v1
title: Gaussian Job Archive for C6H6Br10

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1387714.v9
title: Seattle Streets, Renamed over time

description: This group contains datasets with tables of street names before and after particular ordinances.
DOI: 10.6084/m9.figshare.1386785
title: Optical map Staphylococcus aureus JKD6210

description: optical map image
DOI: 10.6084/m9.figshare.1386785.v1
title: Optical map Staphylococcus aureus JKD6210

description: optical map image
DOI: 10.6084/m9.figshare.1386731
title: S1_Dataset: Regional average cumulative degree days for different temperature threshold values for the period 1950-2010

description: T0= Temperature threshold Cumulative degree days are calculated for every day of the year from the 1st of January for the period 1950-2010 based on a threshold temperature value (T0) and the daily maximum (Tmax) and minimum (Tmin) temperature values in each grid cell of the study areas. The table shows the area average values among all the grid cells in the study areas.
DOI: 10.6084/m9.figshare.1386725
title: S4 Dataset Phytoestrogens

description: Supporting information for Table 3: Phytoestrogen concentrations in milk on dairy farms with organic production system (ORG) and short-term (ORG-SG) or long-term grassland management (ORG-LG) and dairy farms with conventional production system (CON) and short-term (CON-SG) or long-term grassland management (CON-LG) during indoor (IN) and outdoor-feeding periods (OUT)
DOI: 10.6084/m9.figshare.1386731.v5
title: S1_Dataset: Regional average cumulative degree days for different temperature threshold values for the period 1950-2010

description: T0= Temperature threshold Cumulative degree days are calculated for every day of the year from the 1st of January for the period 1950-2010 based on a threshold temperature value (T0) and the daily maximum (Tmax) and minimum (Tmin) temperature values in each grid cell of the study areas. The table shows the area average values among all the grid cells in the study areas.
DOI: 10.6084/m9.figshare.1386725.v1
title: S4 Dataset Phytoestrogens

description: Supporting information for Table 3: Phytoestrogen concentrations in milk on dairy farms with organic production system (ORG) and short-term (ORG-SG) or long-term grassland management (ORG-LG) and dairy farms with conventional production system (CON) and short-term (CON-SG) or long-term grassland management (CON-LG) during indoor (IN) and outdoor-feeding periods (OUT)
DOI: 10.6084/m9.figshare.1386731.v4
title: S1_Data: Regional average cumulative degree days for different temperature threshold values for the period 1950-2010

description: T0= Temperature threshold Cumulative degree days are calculated for every day of the year from the 1st of January for the period 1950-2010 based on a threshold temperature value (T0) and the daily maximum (Tmax) and minimum (Tmin) temperature values in each grid cell of the study areas. The table shows the area average values among all the grid cells in the study areas.
DOI: 10.6084/m9.figshare.1386685
title: Pajek file for F1000Prime readers at Mendeley

description: This file can be loaded into Pajek to see details of the network used in the paper http://dx.doi.org/10.12688/f1000research.6062.1
DOI: 10.6084/m9.figshare.1386697.v1
title: Bioacoustics Day 2013

description: Bioacoustics Day 2013
DOI: 10.6084/m9.figshare.1386631
title: Gravel Bars Can Be Critical for Biodiversity Conservation: A Case Study on Scaly-sided Merganser in South China

description: This dataset inlcudes occurrences of Scaly-sided Merganser <em>Mergus squamatus</em> along a 40 km river section of Yuan River, in Central China, for three consecutive winters, and the landscape metrics of river gravel bars from geo-rectified fine resolution (0.6 m) aerial image data. We built habitat suitability models (Generalized Linear Models - GLMs) with the dataset to study the effects of landscape metrics and human disturbance on Scaly-sided Merganser presence probability.
DOI: 10.6084/m9.figshare.1386631.v1
title: Gravel Bars Can Be Critical for Biodiversity Conservation: A Case Study on Scaly-sided Merganser in South China

description: This dataset inlcudes occurrences of Scaly-sided Merganser <em>Mergus squamatus</em> along a 40 km river section of Yuan River, in Central China, for three consecutive winters, and the landscape metrics of river gravel bars from geo-rectified fine resolution (0.6 m) aerial image data. We built habitat suitability models (Generalized Linear Models - GLMs) with the dataset to study the effects of landscape metrics and human disturbance on Scaly-sided Merganser presence probability.
DOI: 10.6084/m9.figshare.1385387
title: A novel approach to diagnosing Southern Hemisphere planetary wave activity and its influence on regional climate variability: supplementary metadata

description: This page contains supplementary material relating to the following paper: Irving D, Simmonds I (2015). A novel approach to diagnosing Southern Hemisphere planetary wave activity and its influence on regional climate variability. <em>Journal of Climate</em>. 28, 9041-9057. doi:10.1175/JCLI-D-15-0287.1 In particular, it contains metadata files (.met) for each of the figures in that paper, outlining the history of command line entries that were executed from initial data download right up to the generation of the figure. A snapshot of the code repository referred to in those .met files is also included (github_DamienIrving-climate-analysis.zip), however readers are encouraged to view that code at the GitHub repository linked to below instead (because then they can view an entire revision history of the code instead of just an instantaneous snapshot). It should be noted that it is my daily repository, meaning there is code in there that does not directly relate to the paper - the .met files explain which code is relevant. The motivation for this approach to publishing reproducible computational research is outlined at: Irving D (2016). A minimum standard for publishing computational results in the weather and climate sciences.<em> Bulletin of the American Meteorological Society.</em> 97, 1149-1158. doi:10.1175/BAMS-D-15-00010.1.
DOI: 10.6084/m9.figshare.1385381
title: Sophisticated flavonoid pathway map based on large scale flavonoid profile datasets in Arabidopsis

description: <strong>How to duplicate the process in the article</strong> Dependent software - Cytoscape 3.2.1 (http://cytoscape.org) - R 3.2.0 (http://www.r-project.org) Dependent R package - ggplot2 <strong>Reproducing Figure 2.<br></strong> 1. Install and run Cytoscape 3.2.1 2. Open figure3.cys with <em>Open Session</em> toolbar button. <strong>Reproducing Figure 4.<br></strong> 1. Install R and ggplot2. 2. Run <em>fig4.R</em> with R. This script generates barplot png images for <em>fig4.csv</em>. 3. We manually created a network in <em>fig4.cys</em>. Then we renamed the barplot png images and mapped the images in <em>fig4.cys</em>. Although <em>fig4.cys</em> already has the custom graphics in the network, you can remap it with Cytoscape custom graphics manager.
DOI: 10.6084/m9.figshare.1385381.v1
title: Sophisticated flavonoid pathway map based on large scale flavonoid profile datasets in Arabidopsis

description: <strong>How to duplicate the process in the article</strong> Dependent software - Cytoscape 3.2.1 (http://cytoscape.org) - R 3.2.0 (http://www.r-project.org) Dependent R package - ggplot2 <strong>Reproducing Figure 2.<br></strong> 1. Install and run Cytoscape 3.2.1 2. Open figure3.cys with <em>Open Session</em> toolbar button. <strong>Reproducing Figure 4.<br></strong> 1. Install R and ggplot2. 2. Run <em>fig4.R</em> with R. This script generates barplot png images for <em>fig4.csv</em>. 3. We manually created a network in <em>fig4.cys</em>. Then we renamed the barplot png images and mapped the images in <em>fig4.cys</em>. Although <em>fig4.cys</em> already has the custom graphics in the network, you can remap it with Cytoscape custom graphics manager.
DOI: 10.6084/m9.figshare.1385387.v2
title: Southern Hemisphere planetary wave activity and its influence on weather and climate extremes: supplementary metadata

description: This page contains supplementary material relating to the following paper: Irving D, Simmonds I (submitted). Southern Hemisphere planetary wave activity and its influence on weather and climate extremes. <em>Journal of Climate</em>. In particular, it contains metadata files (.met) for each of the figures in that paper, outlining the history of command line entries that were executed from initial data download right up to the generation of the figure. A snapshot of the code repository referred to in those .met files is also included (github-importFGCaby.zip), however readers are encouraged to view that code at the GitHub repository linked to below instead (because then they can view an entire revision history of the code instead of just an instantaneous snapshot). It should be noted that it is my daily repository, meaning there is code in there that does not directly relate to the paper - the .met files explain which code is relevant. Links are also included to a live online draft of the paper and also a separate paper outlining the motivation for this approach to publishing reproducible computational research.
DOI: 10.6084/m9.figshare.1385387.v3
title: A novel approach to diagnosing Southern Hemisphere planetary wave activity and its influence on regional climate variability: supplementary metadata

description: This page contains supplementary material relating to the following paper: Irving D, Simmonds I (submitted). A novel approach to diagnosing Southern Hemisphere planetary wave activity and its influence on regional climate variability. <em>Journal of Climate</em>. In particular, it contains metadata files (.met) for each of the figures in that paper, outlining the history of command line entries that were executed from initial data download right up to the generation of the figure. A snapshot of the code repository referred to in those .met files is also included (github_DamienIrving-climate-analysis.zip), however readers are encouraged to view that code at the GitHub repository linked to below instead (because then they can view an entire revision history of the code instead of just an instantaneous snapshot). It should be noted that it is my daily repository, meaning there is code in there that does not directly relate to the paper - the .met files explain which code is relevant. Links are also included to a live online draft of the paper and also a separate paper outlining the motivation for this approach to publishing reproducible computational research.
DOI: 10.6084/m9.figshare.1385387.v4
title: A novel approach to diagnosing Southern Hemisphere planetary wave activity and its influence on regional climate variability: supplementary metadata

description: This page contains supplementary material relating to the following paper: Irving D, Simmonds I (submitted). A novel approach to diagnosing Southern Hemisphere planetary wave activity and its influence on regional climate variability. <em>Journal of Climate</em>. In particular, it contains metadata files (.met) for each of the figures in that paper, outlining the history of command line entries that were executed from initial data download right up to the generation of the figure. A snapshot of the code repository referred to in those .met files is also included (github_DamienIrving-climate-analysis.zip), however readers are encouraged to view that code at the GitHub repository linked to below instead (because then they can view an entire revision history of the code instead of just an instantaneous snapshot). It should be noted that it is my daily repository, meaning there is code in there that does not directly relate to the paper - the .met files explain which code is relevant. Links are also included to a live online draft of the paper and also a separate paper outlining the motivation for this approach to publishing reproducible computational research.
DOI: 10.6084/m9.figshare.1385387.v5
title: A novel approach to diagnosing Southern Hemisphere planetary wave activity and its influence on regional climate variability: supplementary metadata

description: This page contains supplementary material relating to the following paper: Irving D, Simmonds I (submitted). A novel approach to diagnosing Southern Hemisphere planetary wave activity and its influence on regional climate variability. <em>Journal of Climate</em>. In particular, it contains metadata files (.met) for each of the figures in that paper, outlining the history of command line entries that were executed from initial data download right up to the generation of the figure. A snapshot of the code repository referred to in those .met files is also included (github_DamienIrving-climate-analysis.zip), however readers are encouraged to view that code at the GitHub repository linked to below instead (because then they can view an entire revision history of the code instead of just an instantaneous snapshot). It should be noted that it is my daily repository, meaning there is code in there that does not directly relate to the paper - the .met files explain which code is relevant. Links are also included to a live online draft of the paper and also a separate paper outlining the motivation for this approach to publishing reproducible computational research.
DOI: 10.6084/m9.figshare.1385387.v6
title: A novel approach to diagnosing Southern Hemisphere planetary wave activity and its influence on regional climate variability: supplementary metadata

description: This page contains supplementary material relating to the following paper: Irving D, Simmonds I (submitted). A novel approach to diagnosing Southern Hemisphere planetary wave activity and its influence on regional climate variability. <em>Journal of Climate</em>. In particular, it contains metadata files (.met) for each of the figures in that paper, outlining the history of command line entries that were executed from initial data download right up to the generation of the figure. A snapshot of the code repository referred to in those .met files is also included (github_DamienIrving-climate-analysis.zip), however readers are encouraged to view that code at the GitHub repository linked to below instead (because then they can view an entire revision history of the code instead of just an instantaneous snapshot). It should be noted that it is my daily repository, meaning there is code in there that does not directly relate to the paper - the .met files explain which code is relevant. Links are also included to a live online draft of the paper and also a separate paper outlining the motivation for this approach to publishing reproducible computational research.
DOI: 10.6084/m9.figshare.1385387.v7
title: A novel approach to diagnosing Southern Hemisphere planetary wave activity and its influence on regional climate variability: supplementary metadata

description: This page contains supplementary material relating to the following paper: Irving D, Simmonds I (submitted). A novel approach to diagnosing Southern Hemisphere planetary wave activity and its influence on regional climate variability. <em>Journal of Climate</em>. In particular, it contains metadata files (.met) for each of the figures in that paper, outlining the history of command line entries that were executed from initial data download right up to the generation of the figure. A snapshot of the code repository referred to in those .met files is also included (github_DamienIrving-climate-analysis.zip), however readers are encouraged to view that code at the GitHub repository linked to below instead (because then they can view an entire revision history of the code instead of just an instantaneous snapshot). It should be noted that it is my daily repository, meaning there is code in there that does not directly relate to the paper - the .met files explain which code is relevant. Links are also included to a live online draft of the paper and also a separate paper outlining the motivation for this approach to publishing reproducible computational research.
DOI: 10.6084/m9.figshare.1385357
title: NG gene annotations

description: NCBI Nucleotide sequence gene annotation. Ezewudo MN, Joseph SJ, Castillo-Ramirez S, Dean D, del Rio C, Didelot X, Dillon J, Selden RF, Shafer WM, Turingan RS, Unemo M, Read TD. (2015) Population structure of Neisseria gonorrhoeae based on whole genome data and its relationship with antibiotic resistance. PeerJ 3:e806https://dx.doi.org/10.7717/peerj.806
DOI: 10.6084/m9.figshare.1385358
title: UPR workshop: Processing TCGA mRNA expression data

description: Handout and figure from a workshop on processing data from The Cancer Genome Atlas project. Uses the RTCGAToolbox to access Broad Institute Firehose data, examine the data and produce plots. The workshop was given in San Juan, PR, at the University of Puerto Rico Medical School, on Friday, April 17, 2015. The workshop was sponsored by the UPR/MDACC Parnership for Excellence in Cancer Research and the Puerto Rico Clinical and Translational Research Consortium.
DOI: 10.6084/m9.figshare.1385356
title: HIV figures

description: Figures of the HIV mature virion and viral lifecycle
DOI: 10.6084/m9.figshare.1385357.v1
title: NG gene annotations

description: NCBI Nucleotide sequence gene annotation. Ezewudo MN, Joseph SJ, Castillo-Ramirez S, Dean D, del Rio C, Didelot X, Dillon J, Selden RF, Shafer WM, Turingan RS, Unemo M, Read TD. (2015) Population structure of Neisseria gonorrhoeae based on whole genome data and its relationship with antibiotic resistance. PeerJ 3:e806https://dx.doi.org/10.7717/peerj.806
DOI: 10.6084/m9.figshare.1385354
title: Assessment of the Acute and Chronic Health Hazards of Hydraulic Fracturing Fluids

description: There is growing concern about how hydraulic fracturing affects public health because this activity involves handling large volumes of fluids that contain toxic and carcinogenic constituents, which are injected under high pressure through wells into the subsurface to release oil and gas from tight shale formations. The constituents of hydraulic fracturing fluids (HFFs) present occupational health risks because workers may be directly exposed to them, and general public health risks because of potential air and water contamination. Hazard identification, which focuses on the types of toxicity that substances may cause, is an important step in the complex health risk assessment of hydraulic fracturing. This article presents a practical and adaptable tool for the hazard identification of HFF constituents, and its use in the analysis of HFF constituents reported to be used in 2,850 wells in North Dakota between December 2009 and November 2013. Of the 569 reported constituents, 347 could be identified by a Chemical Service Registration Number (CASRN) and matching constituent name. The remainder could not be identified either because of trade secret labeling (210) or because of an invalid CASRN (12). Eleven public databases were searched for health hazard information on thirteen health hazard endpoints for 168 identifiable constituents that had at least 25 reports of use. Health hazard counts were generated for chronic and acute endpoints, including those associated with oral, inhalation, ocular, and dermal exposure. Eleven of the constituents listed in the top 30 by total health hazard count were also listed in the top 30 by reports of use. This includes naphthalene, which along with benzyl chloride, has the highest health hazard count. The top 25 constituents reportedly used in North Dakota largely overlap with those reported for Texas and Pennsylvania, despite different geologic formations, target resources (oil vs. gas), and disclosure requirements. Altogether, this database provides a public health tool to help inform stakeholders about potential health hazards, and to aid in the reformulation of less hazardous HFFs.
DOI: 10.6084/m9.figshare.1385356.v2
title: HIV figures

description: Figures of the HIV mature virion and viral lifecycle
DOI: 10.6084/m9.figshare.1385354.v1
title: Assessment of the Acute and Chronic Health Hazards of Hydraulic Fracturing Fluids

description: ABSTRACTThere is growing concern about how hydraulic fracturing affects public health because this activity involves handling large volumes of fluids that contain toxic and carcinogenic constituents, which are injected under high pressure through wells into the subsurface to release oil and gas from tight shale formations. The constituents of hydraulic fracturing fluids (HFFs) present occupational health risks because workers may be directly exposed to them, and general public health risks because of potential air and water contamination. Hazard identification, which focuses on the types of toxicity that substances may cause, is an important step in the complex health risk assessment of hydraulic fracturing. This paper presents a practical and adaptable tool for the hazard identification of HFF constituents, and its use in the analysis of HFF constituents reported to be used in 2,850 wells in North Dakota between December 2009 and November 2013. Of the 569 reported constituents, 347 could be identified by a Chemical Service Registration Number (CASRN) and matching constituent name. The remainder could not be identified either because of trade secret labeling (210) or because of an invalid CASRN (12). Eleven public databases were searched for health hazard information on thirteen health hazard endpoints for 168 identifiable constituents that had at least 25 reports of use. Health hazard counts were generated for chronic and acute endpoints, including those associated with oral, inhalation, ocular, and dermal exposure. Eleven of the constituents listed in the top 30 by total health hazard count were also listed in the top 30 by reports of use. This includes naphthalene, which along with benzyl chloride, has the highest health hazard count. The top 25 constituents reportedly used in North Dakota largely overlap with those reported for Texas and Pennsylvania, despite different geologic formations, target resources (oil vs. gas), and disclosure requirements. Altogether, this database provides a public health tool to help inform stakeholders about potential health hazards, and to aid in the reformulation of less hazardous HFFs.
DOI: 10.6084/m9.figshare.1385356.v1
title: HIV figures

description: Figures of the HIV mature virion and viral lifecycle