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3,871 results for “quantitative”
Quantitative Content Analysis Data for Hand Labeling Road Surface Conditions in New York State Department of Transportation Camera Images
<p><strong>Foundational Codebook and Data: </strong></p> <p>Traffic camera images from the New York State Department of Transportation (511ny.org) are used to create a hand-labeled dataset of images classified into to one of six road surface conditions: 1) severe snow, 2) snow, 3) wet, 4) dry, 5) poor visibility, or 6) obstructed. Six labelers (authors Sutter, Wirz, Przybylo, Cains, Radford, and Evans) went through a series of four labeling trials where reliability across all six labelers were assessed using the Krippendorff’s alpha (KA) metric (Krippendorff, 2007). The online tool by Dr. Freelon (Freelon, 2013; Freelon, 2010) was used to calculate reliability metrics after each trial, and the group achieved inter-coder reliability with KA of 0.888 on the 4th trial. This process is known as quantitative content analysis, and three pieces of data used in this process are shared, including: 1) a PDF of the codebook which serves as a set of rules for labeling images, 2) images from each of the four labeling trials, including the use of New York State Mesonet weather observation data (Brotzge et al., 2020), and 3) an Excel spreadsheet including the calculated inter-coder reliability (ICR) metrics and other summaries used to asses reliability after each trial. The data are included in NYSDOT_quantitative_content_analysis.zip.</p> <p>The broader purpose of this work is that the six human labelers, after achieving inter-coder reliability, can then label large sets of images independently, each contributing to the creation of larger labeled dataset used for training supervised machine learning models to predict road surface conditions from camera images. The xCITE lab (xCITE, 2023) is used to store camera images from 511ny.org, and the lab provides computing resources for training machine learning models.</p> <p><strong>Obstructed Class Variation: </strong></p> <p>There are many applications for labeling roadside camera images, and as a variation of the foundational codebook, an addendum codebook provides another version of labeling the obstructed class. Specifically, this variation prioritizes labeling an image as “obstructed” only in extreme circumstances where there is a camera- or image- specific problem that prevents the assessment of any road surfaces. For labelers who want to use this version of the obstructed class (in this document) and also the other five weather-related classes (in the foundational codebook), the guidance is to use both documents in tandem, making sure to use the obstructed rules/definitions in this document while disregarding the obstructed rules/definitions in the foundational codebook. Alternatively, this codebook may be used alone in applications where the goal is to solely classify obstructed vs not obstructed. To ensure reliability and quality of this variation, quantitative content analysis was conducted on this addendum codebook, just as it was for the foundational codebook. Two labelers were tested with a sample of 30 images and achieved inter-coder reliability with Krippendorff's Alpha of 0.934 after one trial. The data, including the addendum codebook and labeling trial data (images and results) are included in ObstructedVariation_quantitative_content_analysis.zip.</p> <p>This material is based upon work supported by the U.S. National Science Foundation under Grant No. RISE-2019758.</p>
Pathogen lifestyle determines host genetic signature of quantitative disease resistance loci in oilseed rape (Brassica napus)
<p>Supplemental datasets associated with publication: Pathogen lifestyle determines host genetic signature of quantitative disease resistance loci in oilseed rape (<em>Brassica napus</em>)</p> <p><strong>Abstract</strong></p> <ul> <li>Crops are affected by several pathogens, but these are rarely studied in parallel to identify common and unique genetic factors controlling diseases. Broad-spectrum quantitative disease resistance (QDR) is desirable for crop breeding as it confers resistance to several pathogen species.</li> <li>Here, we use associative transcriptomics (AT) to identify candidate gene loci associated with <em>Brassica napus</em> constitutive QDR to four contrasting fungal pathogens: <em>Alternaria brassicicola</em>, <em>Botrytis cinerea</em>, <em>Pyrenopeziza</em><em> brassicae</em> and <em>Verticillium longisporum. </em>We did not identify any loci associated with broad-spectrum QDR to fungal pathogens with contrasting lifestyles. Instead, we observed QDR dependent on the lifestyle of the pathogen—hemibiotrophic and necrotrophic pathogens had distinct QDR responses and associated loci, including some loci associated with early immunity. Furthermore, we identify a genomic deletion associated with resistance to <em>V. longisporum </em>and potentially broad-spectrum QDR.</li> <li>This is the first time AT has been used for several pathosystems simultaneously to identify host genetic loci involved in broad-spectrum QDR. We highlight constitutively expressed candidate loci for broad-spectrum QDR with no antagonistic effects on susceptibility to the other pathogens studies as candidates for crop breeding. In conclusion, this study represents and advancement in our understanding if broad-spectrum QDR in <em>B. napus </em>and is a significant resource for the scientific community. </li> </ul> <p><strong>Description of data files</strong></p> <p><strong>Full dataset for input into AT analysis </strong>Full datasets (infection phenotypes for <em>A. brassicicola, B. cinerea, </em>or <em>V.longisporum, </em>ROS measurements for chitin, flg22, or elf18) and link to original <em>P. brassicae </em>dataset. These datasets were used for input into the Associative Transcriptomics pipeline (Nichols, 2022, <a href="https://github.com/bsnichols/GAGA. https://zenodo.org/badge/latestdoi/512807075">https://github.com/bsnichols/GAGA. https://zenodo.org/badge/latestdoi/512807075</a>). </p> <p><strong>Table S1 </strong>Mean, normalized phenotype data for resistance to pathogens (<em>Alternaria brassicicola, Botrytis cinerea, Pyrenopeziza brassicae </em>and <em>Verticillium longisporum</em>) and ROS response induced by PAMPS (chitin, flg22, and elf18). These data were used for association transcriptomic analysis.<strong> </strong></p> <p><strong>Table S2 </strong>Full list of single nucleotide polymorphism (SNP) markers and significance levels from genome-wide association (GWA) analyses for resistance to pathogens (<em>Alternaria brassicicola, Botrytis cinerea, Pyrenopeziza brassicae </em>and <em>Verticillium longisporum</em>) and ROS response induced by PAMPS (chitin, flg22, and elf18). Each excel tab contains the analyses for a single trait. The best fit model for GWA analysis is indicated in the tab title. Manhattan plots showing marker-trait association are included for data visualization; x-axis indicates SNP location along the chromosome; the y-axis indicates the -log10(p) (P value). Qqplots are included to demonstrate model fit.</p> <p><strong>Table S3</strong> Full list of gene expression markers (GEMs) and significance levels from GEM analyses for resistance to pathogens (<em>Alternaria brassicicola, Botrytis cinerea, Pyrenopeziza brassicae and Verticillium longisporum</em>) and ROS response induced by PAMPS (chitin, flg22, and elf18). Each excel tab contains the analyses for a single trait. Manhattan plots showing marker-trait association are included for data visualization; x-axis indicates GEM location along the chromosome; the y-axis indicates the -log10(p) (P value). </p> <p><strong>Table S4 </strong>184 gene expression markers (GEMs) associated with chitin-induced ROS compared with GEMs associated with resistance to pathogens (<em>Alternaria brassicicola, Botrytis cinerea, Pyrenopeziza brassicae </em>and<em> Verticillium longisporum</em>) and ROS response induced by flg22, and elf18. Lists correspond to Venn diagrams in Fig. 2. The first tab includes all 184 GEMs associated with chitin-induced ROS. The subsequent tabs include lists of shared GEMs associated with chitin-induced ROS response and each additional trait (quantitative disease resistance (QDR) to each fungal pathogen or additional PAMP-induced ROS responses). The title of each tab indicates the data included in each comparison and the number of shared GEMs. Predicted <em>Arabidopsis thaliana</em> orthologs and corresponding descriptions are shown where possible. </p> <p><strong>Table S5</strong> Enrichment analyses to determine if the number of gene expression markers (GEMs) shared between different lists is greater than the number of GEMs that would be expected by chance (e.g., lists of quantitative disease resistance (QDR) GEMs for two fungal pathogens). The representation factor is the number of overlapping GEMs divided by the expected number of overlapping GEMs drawn from two independent groups (traits), considering the total number of GEMs sequenced (53884). A representation factor > 1 indicates more overlap than expected of two groups, a representation factor < 1 indicates less overlap than expected, and a representation factor of 1 indicates that the two groups by the number of genes expected for independent groups of genes. </p> <p><strong>Table S6 R</strong>esults from Weighted Co-expression Gene Network Analysis (WGCNA). The first tab indicates significant modules from WGCNA analysis. Black and magenta modules are associated with antagonistic effects on resistance/susceptibility to all four pathogens. The second tab includes a full list of the GEM markers (Table S3), which are in significant WGCNA modules. The third, fourth and, fifth tabs indicate all significant GEMs in the black module, GO terms associated with GEMs in the black module, and all GO terms associated with the black module, respectively. The sixth, seventh and, eighth tabs indicate all significant GEMs in the magenta module, GO terms associated with GEMs in the magenta module, and all GO terms associated with the magenta module, respectively.</p> <p><strong>Table S7 </strong>Shared gene expression markers (GEMs) associated with resistance to different pathogens (<em>Alternaria brassicicola, Botrytis cinerea, Pyrenopeziza brassicae </em>and <em>Verticillium longisporum</em>). Lists correspond to matrices and Venn diagrams in Fig. 3. The first tab includes all GEMs associated quantitative disease resistance (QDR) to the fungal pathogens. The subsequent tabs include lists of shared GEMs associated with QDR to two or more fungal pathogens. The title of each tab indicates the data included in each comparison and the number of shared GEMs. Predicted <em>Arabidopsis thaliana</em> orthologs and corresponding descriptions are shown where possible. </p> <p><strong>Table S8 </strong>List of genes in linkage disequilibrium with the top marker for <em>Verticillium longisporum</em> resistance from genome-wide association (GWA) analysis on chromosome A09 (107 genes)(Tab 1) and the homoeologous region on C08 (Tab 2). Their percentage identity and query coverage in <em>Brassica napus</em> reference genotypes Quinta, Tapidor, Westar and Zhongshuang 11 compared to the <em>B. napus</em> pantranscriptome is indicated. Predicted <em>Arabidopsis thaliana</em> orthologs and corresponding descriptions are shown where possible. </p> <p> </p>
R Code and Re-analyzed Datasets for: Robust approaches for the quantitative analysis of genome formula variation in multipartite and segmented viruses
<p>This submission includes all the scripts and data analyzed in the manuscript "Robust approaches for the quantitative analysis of genome formula variation in multipartite and segmented viruses". This manuscript is a technical note on how genome formula data can be analyzed. There are no new experimental data in the manuscript, as published datasets are re-analyzed. Here we reproduce those datasets as formatted for our analysis, for the convenience of the reader. Please consult the README.txt file first.</p> <p>The corresponding paper was published in Viruses <em>16</em>(2): 270. (<a href="https://doi.org/10.3390/v16020270">https://doi.org/10.3390/v16020270</a>).</p> <p>This is the second version of the code, corresponding to the final version of the paper. The intial restricted version for review had a DOI 10.5281/zenodo.10355273.</p> <p> </p>
Two datasets to illustrate quantitative analysis methods for fluorescent calcium measurements
<p>Two datasets in HDF5 formats used for illustrating some quantitative data analysis methods.</p> <p><strong>CCD_calibration.hdf5</strong>: Imago/SensiCam CCD camera (Till Photonics) calibration data set. <br> Fluorescence measurments were made using a fluorescent plastic slide. 10 exposure times from 10 to 100 ms (each making an HDF5 group) were used. For each exposure time 100 exposures were performed (with 200 ms between each). The fluorescence measured in each of the 60 x 80 pixels of the camera are stored in the stack data set of each group. The time data set (a vector) of each group contains the time at which each illumination was done. These recordings were done by Andreas Pippow (Kloppenburg Laboratory Cologne University, http://cecad.uni-koeln.de/Prof-Peter-Kloppenburg.82.0.html). <br> They were used in: Sébastien Joucla, Andreas Pippow, Peter Kloppenburg and Christophe Pouzat (2010) Quantitative estimation of calcium dynamics from ratiometric measurements: A direct, non-ratioing, method. Journal of Neurophysiology 103: 1130-1144.</p> <p><strong>Data_POMC.hdf5</strong>: POMC data set recorded by Andreas Pippow (Kloppenburg Laboratory Cologne University, http://cecad.uni-koeln.de/Prof-Peter-Kloppenburg.82.0.html). 168 measurements performed with a CCD camera recording Fura-2 fluorescence (excitation wavelength: 340 nm). The size of the CCD chip is 60 x 80 pixels. A stimulation (depolarization induced calcium entry) comes at time 527. <br>Details about this data set can be found in: Joucla et al (2013) Estimating background-subtracted fluorescence transients in calcium imaging experiments: A quantitative approach. Cell Calcium. 54 (2): 71-85.</p> <p> </p>
Quantitative results of the analysis of human bioengineered tissues corresponding to the work "Development of novel squid gladius biomaterials for cornea tissue engineering"
<p>This dataset corresponds to the quantitative data generated in the work entitled "Development of novel squid gladius biomaterials for cornea tissue engineering".</p> <p>Cornea tissue engineering is strictly dependent on the development of biomaterials fulfilling the strict biocompatibility, biomechanical and optical requirements of this organ. In this work, we have generated novel biomaterials from the squid gladius (SG) and their application in cornea tissue engineering was evaluated. Results revealed that the native SG (N-SG) was biocompatible in laboratory animals, although a local inflammatory reaction was driven by the material. Cellularized biomaterials (C-SG) demonstrated that the SG provides an adequate substrate for cell attachment and growth, and corneal epithelial cells cultured on this biomaterial were able to express crystallin alpha, a marker for this type of cells. Biomechanical analyses showed that N-SG biomaterials have higher Young modulus and lower traction deformation than control native corneas (CTR), and C-SG showed similar Young modulus than CTR. Analysis of the optical properties of these samples revealed that the diffuse transmittance of N-SG and C-SG were higher than CTR, with the diffuse reflectance showing the opposite behavior. These results confirm the putative usefulness of this abundant marine-derived biomaterial that can be obtained as a byproduct of the fishing industry.</p>
Mangrove terrestrial laser scanning (TLS) point clouds and quantitative structural models (QSMs)
<p>Datasets for a publication entitled, "Terrestrial laser scanning for the estimation of above ground biomass of mangrove roots by modelling them as inverted trees."</p> <p>See the file "Data dictionary for Mangrove terrestrial laser scanning.pdf" for a description of the datasets included in the zipped folder. </p>
Data to "Phantom-based quality assurance for multicenter quantitative MRI in locally advanced cervical cancer"
<p>This record includes the DICOM images and analysed data that were used in the multicenter QA program for quantitative MRI in cervical cancer as published (<a href="https://www.sciencedirect.com/science/article/pii/S0167814020307854?via%3Dihub">https://doi.org/10.1016/j.radonc.2020.09.013</a> ).</p> <p>The DICOM data includes the acquired DICOM data for each institute selected to those that were used in the publication. Acquisitions that were not used were removed. Data was anonymized with conquest dicom server tools.</p> <p>The analyzed data files are included giving per measurement the estimated quantitative parameter values as well as the position of the ROIs and extracted signal intensity values per phantom sample. An explanation of the structure of the files is added in the readme file. The analysis was done with in-house written code in matlab.</p> <p>Included are a description of the sequence parameters for each institute (IQEMBRACE_PhantomQA_OverviewInstitutionalSequenceParameters_20241114) and details on the choices in the analysis of the data (IQEMBRACE_PhantomQA_OverviewPhantomData_20241114). As background also the description of the measurements was added, giving more information on how the measurements were performed.</p> <p>This work was in preparation for the IQ-EMBRACE trial (clinicaltrials.gov NCT03210428)</p>
The 2020 Comparison of Tools for the Analysis of Quantitative Formal Models: Results and Reproduction
<p>This archive contains detailed results from QComp 2020 as well as the necessary scripts and data to reproduce them.</p> <p>Visit http://qcomp.org for more information for QComp.</p> <p>Overview of Contents</p> <p>- `qcomp.org/` contains the state of our website from the timepoint of the competition. This includes:<br> - All benchmark files, browsable at `qcomp.org/benchmarks/index.html`<br> - Detailed competition results in a human-readable format, browsable at `https://qcomp.org/competition/2020/`<br> - `logs/` contains the raw logfiles and data gathered by our scripts<br> - `scripts/` contains scripts to replicate the whole competition<br> - `toolpackages/` contains a package for each participating tool which includes<br> - Instructions for obtaining and installing the tool<br> - a file `invocations.json` listing the commandlines used in QComp 2020<br> - a file `tool.py` providing functionalities to obtain the result from the tool output.</p>
Raw data supporting "mScarlet fluorescence lifetime reports lysosomal pH quantitatively"
<p>Original dataset and processing code supporting the preprint (scientific publication) "mScarlet fluorescence lifetime reports lysosomal pH quantitatively."</p> <p>Publication Abstract: The lysosome maintains a highly acidic pH, which is critical for successful lysosomal catabolism. Lysosomal pH (pHlys) is difficult to measure because of the simultaneous need for a sensor with large dynamic range, genetic targetability, low pKa, and a quantitative readout. Here, we demonstrate that the fluorescence lifetime of the mScarlet-LAMP1 fusion protein quantitatively reports lysosomal pH, exhibiting a large dynamic range and a pKa well-tuned for the lysosome. Because fluorescence lifetime is an intrinsic property, pH measurements can be achieved in a single fluorescence channel. mScarlet-LAMP1 lifetime allows for individual lysosome-resolved recordings, a critical advance in describing and understanding pHlys heterogeneity. Using this biosensor, we quantify heterogeneity of pHlys in cultured cells at rest and over time during drug treatment. We anticipate that mScarlet-LAMP1 will enable new insights into the diversity of lysosomal physiology and ionic milieu.</p>
Data for article: A quantitative framework to infer the effect of traits, diversity and environment on dispersal and extinction rates from fossils
<p>Supplementary information for:</p> <p><strong>A quantitative framework to infer the effect of traits, diversity and environment on dispersal and extinction rates from fossils</strong></p> <p>Torsten Hauffe, Mathias M. Pires, Tiago B. Quental, Thomas Wilke, and Daniele Silvestro</p> <p> </p><ul> <li> Simulations <ul> <li>Scripts <ul> <li>Scenario1_SamplingHeterogeneity.R: Script to simulate biogeographic histories with sampling heterogeneity</li> <li>Scenario3_SealevelInvasion.R: Script to simulate biogeographic histories where sea level facilitates dispersal and invasion induces extinction</li> <li>Scenario3_DiversityDependence.R: Script to simulate diversity-dependent biogeographic histories</li> <li>Scenario4_TraitDependence.R: Script to simulate trait-dependent biogeographic histories</li> <li>Scenario5_CategoricalTraitDependence.R: Script to simulate trait-dependent biogeographic histories</li> </ul> </li> <li>Results <ul> <li>Scenario1_SamplingHeterogenetiy_alpha05.txt: Results of simulations scenario 1 with a sampling heterogeneity of alpha = 0.5</li> <li>Scenario1_SamplingHeterogenetiy_alpha1.txt: Results of simulations scenario 1 with a sampling heterogeneity of alpha = 1</li> <li>Scenario1_SamplingHeterogenetiy_alpha2.txt: Results of simulations scenario 1 with a sampling heterogeneity of alpha = 2</li> <li>Scenario1_SamplingHeterogenetiy_alpha10.txt: Results of simulations scenario 1 with a sampling heterogeneity of alpha = 10</li> <li>Scenario2_Independent_dispersal_and_extinction.txt: Results of simulation scenario 2 with sea-level independent dispersal and no invasion induced extinction</li> <li>Scenario2_Sealevel_dependent_dispersal_and_independent_extinction.txt: Results of simulation scenario 2 with sea-level dependent dispersal and no invasion induced extinction</li> <li>Scenario2_Sealevel_independent_dispersal_and_invasion_induced_extinction.txt: Results of simulation scenario 2 with sea-level independent dispersal and invasion induced extinction</li> <li>Scenario2_Sealevel_dependent_dispersal_and_invasion_induced_extinction.txt: Results of simulation scenario 2 with sea-level dependent dispersal and invasion induced extinction</li> <li>Scenario3_Independent_dispersal_and_extinction.txt: Results of simulations scenario 3 with diversity-independent dispersal and extinction</li> <li>Scenario3_Diversity_dependent_dispersal_and_independent_extinction.txt: Results of simulations scenario 3 with diversity-dependent dispersal and diversity-independent extinction</li> <li>Scenario3_Independent_dispersal_and_Diversity_dependent_extinction.txt: Results of simulations scenario 3 with diversity-dependent dispersal and diversity-independent extinction</li> <li>Scenario3_Diversity_dependent_dispersal_and_extinction.txt: Results of simulations scenario 3 with diversity-dependent dispersal and extinction</li> <li>Scenario4_Independent_dispersal_and_extinction.txt: Results of scenario 4 with trait-independent dispersal and extinction</li> <li>Scenario4_Trait_dependent_dispersal_and_independent_extinction.txt: Results of scenario 4 with trait-dependent dispersal and independent extinction</li> <li>Scenario4_Independent_dispersal_and_trait_dependent_extinction.txt: Results of scenario 4 with independent dispersal and trait-dependent extinction</li> <li>Scenario4_trait_dependent_dispersal_and_extinction.txt: Results of scenario 4 with trait-dependent dispersal and extinction</li> <li>Scenario5_CatTrait_dependent_dispersal_and_independent_extinction.txt: Results of model 2 with categorical traits (e.g family) influence dispersal but no influence of a category-specific continuous traits</li> </ul> </li> </ul> </li> <li>Carnivora <ul> <li>BinnedOccurrence: Folder with 100 replicates of binned occurrences of max. 330 carnivoran genera throughout the Neogene</li> <li>BodyMass: Folder with 100 replicates of body mass for 330 carnivoran genera</li> <li>Sealevel: Folder with sea level through the Neogene</li> <li>Temperature: Folder with the temperature record of the Neogene</li> <li>Families: Folder with families as taxonomic proxy for phylogeny. FamilyGeneraNumeric.txt is the numeric coding used for the Bayesian analyses of carnivoran biogeography</li> </ul> </li> </ul> <p></p>
Relaxation anisotropy of quantitative MRI parameters in biological tissues
<p>Dataset for the manuscript "Relaxation anisotropy of quantitative MRI parameters in biological tissues" published in Scientific Reports 2022</p>
Semi-automated Quantitative Morphometric Analysis of E18 Rat Hippocampal Neurons from 0.5 to 6 Days In Vitro
<p>This is the dataset presented in "Semi-automated quantitatve evaluation of neuron developmental morphology <em>in vitro</em> using the change-point test" by AS Liao, W Cui, VS Webster-Wood, and YJ Zhang (submitted to Neuroinformatics 2022).</p>
Dataset: Multi-level network dataset of social-ecological interdependencies in ten Swiss wetlands based on qualitative interviews and quantitative surveys
<p>The dataset originated from quantitative online surveys and qualitative expert interviews with organizational actors relevant to the governance of ten Swiss wetlands from 2019 till 2021. Multi-level networks represent the wetlands governance for each of the ten cases. The collaboration networks of actors form the first level of the multi-level networks and are connected to multiple other network levels that account for the social and ecological systems those actors are active in. 521 actors relevant to the management of the ten wetlands are included in the collaboration networks; quantitative survey data exists for 71% of them. A unique feature of the collaboration networks is that it differentiates between positive and negative forms of collaboration specified based on actors' activity areas. Therefore, the data describes not only if actors collaborate but also how and where actors collaborate. Further additional two-mode networks (actor participation in forums and involvement in other regions outside the case area) are elicited in the survey and connected to the collaboration network. Finally, the dataset also contains data on ecological system interdependencies in the form of conceptual maps derived from 34 expert interviews (3-4 experts per case).</p>
UK Biobank release and systematic evaluation of optimised polygenic risk scores for 53 diseases and quantitative traits
<p>Summary-level GWAS data for 53 traits generated by <a href="https://www.genomicsplc.com/">Genomics plc</a> as presented in:</p> <p>Thompson D. et al. UK Biobank release and systematic evaluation of optimised polygenic risk scores for 53 diseases and quantitative traits (<a href="https://doi.org/10.1101/2022.06.16.22276246">https://doi.org/10.1101/2022.06.16.22276246</a>)</p> <p>If you have any questions or comments regarding these files, please contact Genomics plc at <a href="mailto:research@genomicsplc.com">research@genomicsplc.com</a></p> <p><strong>NOTES</strong></p> <p>These analyses were carried out using the full UK Biobank (UKB) imputation data release (v3b). After removal of exclusions and withdrawals, a subset of 337,151 UKB individuals, the White British Unrelated (WBU) subgroup, was defined as the intersection of two sample groups created by Bycroft et al 2018 (Nature 562, 203-209): the ‘White British ancestry’ group (UKB Data Field 22006) and the ‘used in genetic principal components’ group (UKB Data Field 22020), the latter being high quality samples that were filtered to avoid closely related individuals. All GWAS analyses were performed on the WBU subgroup.</p> <p>Phenotypes were defined as described in Supplementary Table 1 ‘Phenotype definitions’ using a combination of Hospital Episode Statistics, Cancer Registry reports (where applicable) and self-report responses, with the exception of coronary artery disease (CAD). GWAS data was generated for both a “narrow” and a “broad” definition of CAD. The former was used as part of the training data for the Enhanced CAD PRS, the latter was used as part of the training data for the Enhanced CVD PRS. The phenotype definitions for “narrow” and a “broad” CAD are as follows:</p> <table> <tbody> <tr> <td>Narrow CAD<br> (includes angina)</td> <td>ICD10 codes (where .X indicates all subcodes) from both hospital and death records: I21, I22, I23, I24.1, I25.2, I20.X. ICD9 codes: 410-412, 42979, 413.X. OPCS-4 codes (K40.1–40.4, K41.1–41.4, K45.1–45.5,K49.1–49.2, K49.8–49.9, K50.2, K75.1–75.4, K75.8–75.9), self-reported heart attack (UKB codes 1075 in field 20002; code 1 in field 6150), self-reported coronary angioplasty (ptca) or coronary artery bypass graft (UKB codes 1070 and 1095 in field 20004), self-reported angina.</td> </tr> <tr> <td>Broad CAD<br> (includes angina and all ischaemic heart disease)</td> <td>As for Narrow CAD, plus ICD10 codes I24.X, I25X, and ICD9 codes 414.X (where .X indicates all subcodes).</td> </tr> </tbody> </table> <p>Note that there is no GWAS for cardiovascular disease (CVD) per se. This is because the UKB training data for the Enhanced CVD PRS consisted of separate GWASs for “narrow” CAD and ischaemic stroke.</p> <p>All analyses included Age at assessment, sex (for non-sex specific traits), genotyping chip, and 10 principal components as covariates.</p> <p>GWAS summary statistics for each trait were generated by applying PLINK 2.0 to the WBU subgroup, using a logistic regression for disease traits, and a linear regression model for quantitative traits. For chromosome X variants males were treated as having 0 or 2 alternative alleles.</p> <p>The results are not adjusted for genomic control.</p> <p><strong>DATA FILE CONTENT DESCRIPTION (DISEASE TRAITS)</strong></p> <table> <tbody> <tr> <td>cpra</td> <td>Variant ID in ‘CPRA’ format. Position reflects position in b37</td> </tr> <tr> <td>chrom</td> <td>Chromosome</td> </tr> <tr> <td>pos</td> <td>Position in base pairs (b37, 1-based)</td> </tr> <tr> <td>alt</td> <td>Alternative allele (effect allele)</td> </tr> <tr> <td>beta</td> <td>Effect size (log odds ratio)</td> </tr> <tr> <td>standard_error</td> <td>Standard error of beta</td> </tr> <tr> <td>minus_log10_p</td> <td>Minus log(base 10) of P-value</td> </tr> <tr> <td>ref</td> <td>Reference allele (non-effect allele)</td> </tr> <tr> <td>ncase</td> <td>Number of cases</td> </tr> <tr> <td>ncontrol</td> <td>Number of controls</td> </tr> </tbody> </table> <p><strong>DATA FILE CONTENT DESCRIPTION (QUANTITATIVE TRAITS)</strong></p> <table> <tbody> <tr> <td>cpra</td> <td>Variant ID in ‘CPRA’ format. Position reflects position in b37</td> </tr> <tr> <td>chrom</td> <td>Chromosome</td> </tr> <tr> <td>pos</td> <td>Position in base pairs (b37, 1-based)</td> </tr> <tr> <td>alt</td> <td>Alternative allele (effect allele)</td> </tr> <tr> <td>beta</td> <td>Effect size</td> </tr> <tr> <td>standard_error</td> <td>Standard error of beta</td> </tr> <tr> <td>minus_log10_p</td> <td>Minus log(base 10) of P-value</td> </tr> <tr> <td>ref</td> <td>Reference allele (non-effect allele)</td> </tr> <tr> <td>ntotal</td> <td>Total sample size</td> </tr> </tbody> </table> <p><strong>FILE NAMES</strong></p> <p>The following is a list of traits and their corresponding file names.</p> <p><em><strong>DISEASE TRAITS</strong></em></p> <table> <tbody> <tr> <td>Age-related macular degeneration</td> <td>amd_strict_UKB_WBU.csv.gz</td> </tr> <tr> <td>Alzheimer's disease</td> <td>alzheimers_disease_UKB_WBU.csv.gz</td> </tr> <tr> <td>Asthma</td> <td>asthma_UKB_WBU.csv.gz</td> </tr> <tr> <td>Atrial fibrillation</td> <td>atrial_fibrillation_UKB_WBU.csv.gz</td> </tr> <tr> <td>Bipolar disorder</td> <td>bipolar_disorder_UKB_WBU.csv.gz</td> </tr> <tr> <td>Bowel cancer</td> <td>CRC_UKB_WBU.csv.gz</td> </tr> <tr> <td>Breast cancer</td> <td>BC_UKB_WBU_women.csv.gz</td> </tr> <tr> <td>Coeliac disease</td> <td>celiac_disease_UKB_WBU.csv.gz</td> </tr> <tr> <td>Narrow coronary artery disease</td> <td>NARROW_CAD_UKB_WBU.csv.gz</td> </tr> <tr> <td>Broad coronary artery disease</td> <td>BROAD_CAD_UKB_WBU.csv.gz</td> </tr> <tr> <td>Crohn's disease</td> <td>crohns_disease_UKB_WBU.csv.gz</td> </tr> <tr> <td>Epithelial ovarian cancer</td> <td>OC_UKB_WBU.csv.gz</td> </tr> <tr> <td>Hypertension</td> <td>HT_UKB_WBU.csv.gz</td> </tr> <tr> <td>Ischaemic stroke</td> <td>IS_stroke_UKB_WBU.csv.gz</td> </tr> <tr> <td>Melanoma</td> <td>melanoma_UKB_WBU.csv.gz</td> </tr> <tr> <td>Multiple sclerosis</td> <td>multiple_sclerosis_UKB_WBU.csv.gz</td> </tr> <tr> <td>Osteoporosis</td> <td>OP_WBU_training.csv.gz</td> </tr> <tr> <td>Prostate cancer</td> <td>PC_UKB_WBU.csv.gz</td> </tr> <tr> <td>Parkinson's disease</td> <td>parkinsons_disease_UKB_WBU.csv.gz</td> </tr> <tr> <td>Primary open angle glaucoma</td> <td>POAG_WBU_training.csv.gz</td> </tr> <tr> <td>Psoriasis</td> <td>psoriasis_UKB_WBU.csv.gz</td> </tr> <tr> <td>Rheumatoid arthritis</td> <td>rheumatoid_arthritis_UKB_WBU.csv.gz</td> </tr> <tr> <td>Schizophrenia</td> <td>schizophrenia_UKB_WBU.csv.gz</td> </tr> <tr> <td>Systemic lupus erythematosus</td> <td>lupus_UKB_WBU.csv.gz</td> </tr> <tr> <td>Type 1 diabetes</td> <td>t1d_UKB_WBU.csv.gz</td> </tr> <tr> <td>Type 2 diabetes</td> <td>T2D_UKB_WBU.csv.gz</td> </tr> <tr> <td>Ulcerative colitis</td> <td>ulcerative_colitis_UKB_WBU.csv.gz</td> </tr> <tr> <td>Venous thromboembolic disease</td> <td>VTE_UKB_WBU.csv.gz</td> </tr> </tbody> </table> <p><em><strong>QUANTITATIVE TRAITS</strong></em></p> <table> <tbody> <tr> <td>Age at menopause</td> <td>age_at_menopause_UKB_WBU.csv.gz</td> </tr> <tr> <td>Apolipoprotein A1</td> <td>apolipoprotein_a1_UKB_WBU.csv.gz</td> </tr> <tr> <td>Apolipoprotein B</td> <td>apolipoprotein_b_UKB_WBU.csv.gz</td> </tr> <tr> <td>Body mass index</td> <td>bmi_UKB_WBU.csv.gz</td> </tr> <tr> <td>Calcium</td> <td>calcium_UKB_WBU.csv.gz</td> </tr> <tr> <td>Docosahexaenoic acid</td> <td>docosahexaenoic_acid_UKB_WBU.csv.gz</td> </tr> <tr> <td>Estimated bone mineral density T-score</td> <td>BMD_WBU_training.csv.gz</td> </tr> <tr> <td>Estimated glomerular filtration rate (creatinine based)</td> <td>egfr_UKB_WBU.csv.gz</td> </tr> <tr> <td>Estimated glomerular filtration rate (cystatin based)</td> <td>egfr_cys_UKB_WBU.csv.gz</td> </tr> <tr> <td>Glycated haemoglobin</td> <td>hba1c_UKB_WBU_nodiabetes.csv.gz</td> </tr> <tr> <td>High density lipoprotein cholesterol</td> <td>hdl_cholesterol_UKB_WBU.csv.gz</td> </tr> <tr> <td>Height</td> <td>height_UKB_WBU.csv.gz</td> </tr> <tr> <td>Intraocular pressure</td> <td>iop_WBU_training.csv.gz</td> </tr> <tr> <td>Low density lipoprotein cholesterol</td> <td>ldl_UKB_WBU_nostatins.csv.gz</td> </tr> <tr> <td>Omega-6 fatty acids</td> <td>omega_6_fatty_acids_UKB_WBU.csv.gz</td> </tr> <tr> <td>Omega-3 fatty acids</td> <td>omega_3_fatty_acids_UKB_WBU.csv.gz</td> </tr> <tr> <td>Phosphatidylcholines</td> <td>phosphatidylcholines_UKB_WBU.csv.gz</td> </tr> <tr> <td>Phosphoglycerides</td> <td>phosphoglycerides_UKB_WBU.csv.gz</td> </tr> <tr> <td>Polyunsaturated fatty acids</td> <td>polyunsaturated_fatty_acids_UKB_WBU.csv.gz</td> </tr> <tr> <td>Resting heart rate</td> <td>resting_heart_rate_UKB_WBU.csv.gz</td> </tr> <tr> <td>Remnant cholesterol (Non-HDL, Non-LDL cholesterol)</td> <td>remnant_cholesterol__UKB_WBU.csv.gz</td> </tr> <tr> <td>Sphingomyelins</td> <td>sphingomyelins_UKB_WBU.csv.gz</td> </tr> <tr> <td>Total cholesterol</td> <td>total_cholesterol_UKB_WBU.csv.gz</td> </tr> <tr> <td>Total fatty acids</td> <td>total_fatty_acids_UKB_WBU.csv.gz</td> </tr> <tr> <td>Total triglycerides</td> <td>total_triglycerides_UKB_WBU.csv.gz</td> </tr> </tbody> </table>
Phenotypic variation and quantitative trait loci for resistance to southern anthracnose and clover rot in red clover
<p>Red clover (<em>Trifolium pratense</em> L.) is an important forage legume of temperate regions, particularly valued for its high yield potential and its high forage quality. Despite substantial breeding progress during the last decades, continuous improvement of cultivars is crucial to ensure yield stability in view of newly emerging diseases or changing climatic conditions. The high amount of genetic diversity present in red clover ecotypes, landraces and cultivars provides an invaluable, but often unexploited resource for the improvement of key traits such as yield, quality, and resistance to biotic and abiotic stresses.</p> <p>A collection of 397 red clover accessions was genotyped using a pooled genotyping-by-sequencing approach with 200 plants per accession. Resistance to the two most pertinent diseases in red clover production, southern anthracnose caused by <em>Colletotrichum trifolii</em>, and clover rot caused by <em>Sclerotinia trifoliorum, </em>was assessed using spray inoculation. The mean survival rate for southern anthracnose was 22.9% and the mean resistance index for clover rot was 34.0%. Genome-wide association analysis revealed several loci significantly associated with resistance to southern anthracnose and clover rot. Most of these loci are in coding regions. One quantitative trait locus (QTL) on chromosome 1 explained 16.8% of the variation in resistance to southern anthracnose. For clover rot resistance we found eight QTL, explaining together 80.2% of the total phenotypic variation. The SNPs associated with these QTL provide, once validated, a promising resource for marker-assisted selection in existing breeding programs, facilitating the development of novel cultivars with increased resistance against two devastating fungal diseases of red clover.</p>
Numerical refractive index correction for the stitching procedure in tomographic quantitative phase imaging – dataset
<p>Raw volumetric data used in the work "Numerical refractive index correction for the stitching procedure in tomographic quantitative phase imaging" (<a href="http://doi.org/10.1364/BOE.466403">doi.org/10.1364/BOE.466403</a>). The data is packaged using the FIJI BigStitcher into HDF5 file. The file is split into 89 parts in ZIP format. Additionally we provide XML file needed for opening the data with BigStitcher and the TXT file with the nominal locations of the volumes based on the readings from the X-Y translation stage. The volumes inside the HDF5 file are already registered for stitching using the BigStitcher pairwise registration and global optimization procedure. Using the BigStitcher option "Resave to TIFF" one can access the raw data that we processed in the work. The processing code which operates on TIFF files is available here: <a href="https://github.com/biopto/QPI-stitching-2D-3D">https://github.com/biopto/QPI-stitching-2D-3D</a>.</p>
Data and code accompanying: A quantitative synthesis of and predictive framework for studying winter warming effects in reptiles
<p>This data and code were used to generate the publication "A quantitative synthesis of and predictive framework for studying winter warming effects in reptiles", doi: 10.1007/s00442-022-05251-3</p> <p>Please direct any queries or requests to use these datasets/code to: k.macleod@bangor.ac.uk</p> <p>Two datasets are presented in separate excel files: one contains meta-analytical data from experimental studies on winter warming effects on reptiles, and the other contains the same type of data from observational studies on the same.</p> <p>R code for analysis is in an R file; this should be openable in any text editing application.</p> <p>Manuscript abstract below:</p> <p><em>Increases in temperature related to global warming have important implications for organismal fitness. For ectotherms inhabiting temperate regions, ‘winter warming’ is likely to be a key source of the thermal variation experienced in future years. Studies focusing on the active season predict largely positive responses to warming in the reptiles; however, overlooking potentially deleterious consequences of warming during the inactive season could lead to biased assessments of climate change vulnerability. Here, we review the overwinter ecology of reptiles, and test specific predictions about the effects of warming winters, by performing a meta-analysis of all studies testing winter warming effects on reptile traits to date. We collated information from observational studies measuring responses to natural variation in temperature in more than one winter season, and experimental studies which manipulated ambient temperature during the winter season. Available evidence supports that most reptiles will advance phenologies with rising winter temperatures, which could positively affect fitness by prolonging the active season although effects of these shifts are poorly understood. Conversely, evidence for shifts in survivorship and body condition in response to warming winters was equivocal, with disruptions to biological rhythms potentially leading to unforeseen fitness ramifications. Our results suggest that the effects of warming winters on reptile species are likely to be important but highlight the need for more data and greater integration of experimental and observational approaches. To improve future understanding, we recap major knowledge gaps in the published literature of winter warming effects in reptiles and outline a framework for future research.</em></p>
Quantitative Representativeness and Constituency of the Long-Term Agroecosystem Research Network
<p><strong>Data Description</strong>:</p> <p>The USDA Long-Term Agroecosystem Research (LTAR) Network coordinates agricultural research across 18 research sites in the conterminous United States (CONUS). However, it is unclear how well these sites represent the totality of agricultural working lands within the CONUS. Therefore, we performed a quantitative analysis of the 18 sites, based on 15 climatic and edaphic characteristics, to produce maps of representativeness and constituency across the CONUS. Representativeness shows how well the combination of environmental drivers at each CONUS location was represented by the LTAR sites’ environments, while constituency shows which LTAR site was the closest match for each location.</p> <p>Files in collection (22):</p> <p>Collection contains 11 geospatial rasters and 11 PNGs visualizing them.</p> <p>TIF files:</p> <p>├── conus_ltar_constituency_workinglands.tif [Constituency of LTAR network]<br> ├── conus_ltar_representativeness_workinglands.tif [Representativeness of LTAR network]<br> ├── conus_ltar_v5.pc1.tif [Principal Component 1]<br> ├── conus_ltar_v5.pc2.tif [Principal Component 2]<br> ├── conus_ltar_v5.pc3.tif [Principal Component 3]<br> ├── conus_ltar_v5.pc4.tif [Principal Component 4]<br> ├── conus_ltar_v5.pc5.tif [Principal Component 5]<br> ├── conus_ltar_v5.pc6.tif [Principal Component 6]<br> ├── conus_ltar_v5.pc7.tif [Principal Component 7]<br> ├── LTAR_NEON_LTER_bestnetwork_workinglands.tif [Raster identifying best network, among LTAR, NEON, LTER, representing the location]<br> └── LTAR_NEON_LTER_representativeness_workinglands.tif [Representativeness of combined LTAR + NEON + LTER networks]</p> <p>PNG files:</p> <p>├── conus_ltar_constituency_workinglands.png [Constituency of LTAR network]<br> ├── conus_ltar_representativeness_workinglands.png [Representativeness of LTAR network]<br> ├── conus_ltar_v5.pc1.png [Principal Component 1]<br> ├── conus_ltar_v5.pc2.png [Principal Component 2]<br> ├── conus_ltar_v5.pc3.png [Principal Component 3]<br> ├── conus_ltar_v5.pc4.png [Principal Component 4]<br> ├── conus_ltar_v5.pc5.png [Principal Component 5]<br> ├── conus_ltar_v5.pc6.png [Principal Component 6]<br> ├── conus_ltar_v5.pc7.png [Principal Component 7]<br> ├── LTAR_NEON_LTER_bestnetwork_workinglands.png [Raster identifying best network, among LTAR, NEON, LTER, representing the location]<br> └── LTAR_NEON_LTER_representativeness_workinglands.png [Representativeness of combined LTAR + NEON + LTER networks]</p> <p><strong>Data format</strong>:</p> <p>Geospatial files are provided in Geotiff format in Lat/Lon WGS84 EPSG: 4326 projection at 30 arc second resolution, while the geospatial visualizations are provided in PNG format.</p> <p><strong>Geospatial projection</strong>: </p> <pre><code class="language-bash">GEOGCS["GCS_WGS_1984", DATUM["D_WGS_1984", SPHEROID["WGS_1984",6378137,298.257223563]], PRIMEM["Greenwich",0], UNIT["Degree",0.017453292519943295]] (base) [jbk@theseus ltar_regionalization]$ g.proj -w GEOGCS["wgs84", DATUM["WGS_1984", SPHEROID["WGS_1984",6378137,298.257223563]], PRIMEM["Greenwich",0], UNIT["degree",0.0174532925199433]] </code></pre> <p><strong>Category labels for Constituency data</strong>:</p> <table> <caption> </caption> <thead> <tr> <th scope="col">Cat</th> <th scope="col">LTAR Siite</th> </tr> </thead> <tbody> <tr> <td>1</td> <td>Archbold-University of Florida</td> </tr> <tr> <td>2</td> <td>Central Mississippi River Basin</td> </tr> <tr> <td>3</td> <td>Central Plains Experimental Range</td> </tr> <tr> <td>4</td> <td>Eastern Corn Belt</td> </tr> <tr> <td>5</td> <td>Great Basin</td> </tr> <tr> <td>6</td> <td>Gulf Atlantic Coastal Plain</td> </tr> <tr> <td>7</td> <td>Jornada Experimental Range</td> </tr> <tr> <td>8</td> <td>Kellogg Biological Station</td> </tr> <tr> <td>9</td> <td>Lower Chesapeake Bay</td> </tr> <tr> <td>10</td> <td>Lower Mississippi River Basin</td> </tr> <tr> <td>11</td> <td>Northern Plains</td> </tr> <tr> <td>12</td> <td>Platte River High Plains Aquifer</td> </tr> <tr> <td>13</td> <td>R.J. Cook Agronomy Farm</td> </tr> <tr> <td>14</td> <td>Southern Plains</td> </tr> <tr> <td>15</td> <td>Texas Gulf</td> </tr> <tr> <td>16</td> <td>Upper Chesapeake Bay</td> </tr> <tr> <td>17</td> <td>Upper Mississippi River Basin</td> </tr> <tr> <td>18</td> <td>Walnut Gulch Experimental Watershed</td> </tr> </tbody> </table> <p><strong>Paper describing data and methods</strong>:</p> <p>Kumar, J., Coffin, A. W., Baffaut, C., Ponce-Campos, G. E., Witthaus, L., & Hargrove, W. W. (2023). Quantitative Representativeness and Constituency of the Long-Term Agroecosystem Research Network and Analysis of Complementarity with Existing Ecological Networks. In Environmental Management. Springer Science and Business Media LLC. https://doi.org/10.1007/s00267-023-01834-9</p> <p> </p>
Three-dimensional Reconstructions and Quantitative Indicators for colloidal particles in Dry and Liquid Conditions in Scanning Transmission Electron Microscope (STEM)
<p>This dataset accompanies the research presented in the paper:</p> <div>Esteban, D.A., Wang, D., Kadu, A., Olluyn, N., Iglesias, A.S., Perez, A.G., Casablanca, J.G., Nicolopoulos, S., Liz-Marzán, L.M. and Bals, S., 2023. Liquid phase fast electron tomography unravels the true 3D structure of colloidal assemblies. <em>arXiv preprint arXiv:2311.05309</em>. [<a href="https://arxiv.org/pdf/2311.05309" target="_blank" rel="noopener">link</a>]</div> <p>It provides a comprehensive collection of three-dimensional reconstructions and quantitative descriptors for small colloidal particles. These gold nanoparticles are arranged in tetrahedral and other intricate geometries under both dry and liquid conditions. The dataset contains 3D reconstructions and quantitative indicators such as centroids, volumes, surface areas, solidity measures, and principal axis lengths for assemblies with 4, 5, and 6 particles. </p> <p>The dataset includes: <code>N4_dry_dart.rec</code> and <code>N4_liquid_dart.rec</code> for the 3D reconstructions of an assembly with 4 particles in dry and liquid conditions respectively; <code>N4_quant_descriptors_dry.mat</code> and <code>N4_quant_descriptors_liquid.mat</code> providing quantitative descriptors for these conditions. Similar files are provided for assemblies with 5 and 6 particles, such as <code>N5_dry_dart.rec</code>, <code>N5_liquid_dart.rec</code>, <code>N5_quant_descriptors_dry.mat</code>, <code>N5_quant_descriptors_liquid.mat</code>, and the corresponding files for N6. </p> <p>This dataset can be used to study the structural dynamics of nanoparticle assemblies and studies in colloidal chemistry, materials science, and nanotechnology. The <code>.rec</code> files can be visualized using volume rendering software (e.g. Amira or Avizo), while the <code>.mat</code> files contain structured data for analysis in MATLAB. The supporting code and scripts for this dataset are available on the GitHub repository: <a href="https://github.com/ajinkyakadu/LiquidET_NatComm2024" target="_new" rel="noreferrer">https://github.com/ajinkyakadu/LiquidET_NatComm2024</a>. </p>
A Quantitative Tomotectonic Plate Reconstruction of Western North America and the Eastern Pacific Basin
<p>The two plate model archives in this directory are linked to the paper (<em>Geochemistry, Geophysics, Geosystems</em>, in press):</p> <p>A Quantitative Tomotectonic Plate Reconstruction of Western North America and the Eastern Pacific Basin by Edward J. Clennett1, Karin Sigloch1, Mitchell G. Mihalynuk2, Maria Seton3, Martha A. Henderson2, Kasra Hosseini1,4, Afsaneh Mohammadzaheri1, Stephen T. Johnston5, and R. Dietmar Muller3</p> <p>1. Department of Earth Sciences, University of Oxford, South Parks Road, Oxford OX1 3AN, UK</p> <p>2. British Columbia Geological Survey, P.O. Box Stn Prov Govt, Victoria, BC, V8W 9N3, Canada</p> <p>3. EarthByte Group, School of Geosciences, The University of Sydney, NSW 2006, Australia</p> <p>4. The Alan Turing Institute, British Library, 96 Euston Road, London NW1 2DB, UK</p> <p>5. Department of Earth and Atmospheric Sciences, University of Alberta, Edmonton, AB T6G 2E3, Canada</p> <p>The zipped archive contains two plate models: <strong>Clennett_etal_2020_M2019.zip</strong> and <strong>Clennett_etal_2020_S2013.zip</strong>. The former is our model in the Müller et al. (2019) reference frame, and the latter is our model implemented into the Shephard et al. (2013) plate reconstruction. Both of these folders contain the same types of files: coastlines, plate boundaries, plate topologies, a rotation file and terrane shapefiles.</p> <p>To view the models, open GPlates (downloadable at: <a href="https://www.gplates.org">www.gplates.org</a>), click 'File' > 'Open Project', navigate to the folder containing the desired model, and then click on the file <strong>Clennett_etal_2020_G3_XXXX.gproj</strong>. This will simultaneously open all the files that comprise the model. A layers panel will appear, with the option to turn on/off certain files. The view can be changed by clicking on the globe, and the model can be run by clicking the play button in the animation bar, starting from 170Ma. Features can be inspected by clicking the 'choose feature' tab, selecting a feature, and clicking 'query feature'.</p> <p>The files that comprise the model are described below:</p> <p>1. <strong>Clennett_etal_2020_Coastlines.gpml</strong>: Coastlines used in the reconstruction. The coastlines of western North America and Mexico were edited from the global model to account for later terrane accretions. </p> <p>2. <strong>Clennett_etal_2020_NAm_bounds.gpml</strong>: File containing the new plate boundaries digitised in this study.</p> <p>3. <strong>Clennett_etal_2020_Plates.gpml</strong>: File containing the edited plate boundaries of the global model, as well as our new continuously-closing plate topologies.</p> <p>4. <strong>Clennett_etal_2020_Rotations.rot</strong>: This is the rotation file that contains the relative motions between plates, terranes and plate boundaries for western North America and the eastern Pacific basin. The first column specifies the plate ID, the second column the timestep, the third, fourth and fifth columns are the latitude, longitude and angle of the stage rotations, and the sixth column is the plate that the feature moves relative to. Most lines are accompanied with a comment describing the rotation.</p> <p>5. <strong>Clennett_etal_2020_Terranes.gpml</strong>: This file contains all the terranes shown in the model. We further divided these into superterranes, so that each can be coloured accordingly for better visualisation purposes: a. Angayucham.gpml b. Farallon.gpml c. Guerrero.gpml d. Insular.gpml e. Intermontane.gpml f. Kula.gpml g. North_America.gpml h. Western_Jurassic.gpml</p> <p>6. <strong>Movie</strong> <strong>S1</strong>. Movie showing plate evolution at 1 million-year intervals, embedded within the Muller et al. (2019) global model. Blue boundaries are subduction zones, red boundaries are mid-ocean ridges, green boundaries are transform faults, and pink boundaries are other unspecified boundaries. Plates are not labelled but can be identified from figures 5-10.</p> <p>7. <strong>Movie S2</strong>. Movie showing plate evolution at 1 million-year intervals, embedded within the Shephard et al. (2013) global model. Blue boundaries are subduction zones, red boundaries are mid-ocean ridges, green boundaries are transform faults, and pink boundaries are other unspecified boundaries. Plates are not labelled but can be identified from figures 5-10.</p> <p> </p> <p>The agegrids and spreading rate grids associated with this model can be accessed at: <a href="https://repo.gplates.org/webdav/PlateModel_Age_SR_Grids/Clennett_etal_2020_G3/" target="_blank" rel="noopener">https://repo.gplates.org/webdav/PlateModel_Age_SR_Grids/Clennett_etal_2020_G3/</a></p>
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.