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10,478 results for “variation”
Evaluation of background ionizing radiation dose variation in Ploiesti city area, 2022
<p>Measurements of background ionizing radiation dose rate, done in Ploiesti city area in 2022 (Romania), by the student Tripac Flavius Gabriel under supervision of Prof. Dr. Adrian Iftime as part of a diploma thesis project (C.Davila University of Medicine and Pharmacy). </p> <p>A graphical overview of the values is included (ploiesti_values_2022.png). <br> </p>
Evaluation of background ionizing radiation dose variation in Bucharest city area, 2022
<p>Measurements of background ionizing radiation dose rate, done in Bucharest city area in 2022, by the student Damalan Daria Liana under supervision of prof. Adrian Iftime as part of a diploma thesis project.</p> <p>A graphical overview of the values is included (bucharest_values_2022.png).</p>
WACCM-X simulation output in support of publication "Impact of upward propagating migrating diurnal and semidiurnal tides on the ionosphere-thermosphere seasonal variation"
<p>This dataset contains simulation output from the Whole Atmosphere Community Climate Model with thermosphere-ionosphere eXtension (WACCM-X) in support of the publication "Impact of upward propagating migrating diurnal and semidiurnal tides on the ionosphere-thermosphere seasonal variation". Data files include the simulation results for a five-member ensemble of free-running simulations, simulations without the upward propagating diurnal migrating tide (DW1), and simulations without the upward propagating semidiurnal migrating tide (SW2). </p>
Data for 'Genetic variation in trophic avoidance shows fruit flies are generally attracted to bacterial pathogens'
<p>Raw data dn R code for the analysis of data dn generation of all figures in the above referenced paper. Descriptions of each data file are included wihtin the R script. </p>
Data set: Variations in water economy traits in two Sphagnum species across their distribution boundaries
<p><em>Sphagnum</em> trait data collected (2016-2017) across a climatic gradient in Sweden. Trait data for both shoot and canopy traits. Data for <em>Sphagnum cuspidatum</em> and <em>Sphagnum lindbergii</em>. Also contains data on species occurrence records in Sweden and output from speceis distribution modelling. See published paper for more information.</p> <p>Files contain (i) processed data ("calculated_trait_data...cvs"), (ii) raw data ("Campbell_etal_clim_traits_...cvs"), (iii) their readme files, and (iv) R-scripts to run the analyses. Note that you need the files in the zip-file to run the analyses in the R-script. The zip-file contains all raw data (climate, traits, species occurences), MaxEnt output, and raster files from photogrammetry.</p> <p>More info in paper: <a href="https://doi.org/10.1002/ajb2.16347" target="_blank" rel="noopener">https://doi.org/10.1002/ajb2.16347</a></p>
A map of canine sequence variation relative to a Greenland wolf outgroup
<p><span>For over 15 years, canine genetics research relied on a reference assembly from a Boxer breed dog named Tasha (i.e., canFam3.1). Recent advances in long-read sequencing and genome assembly have led to the development of numerous high-quality assemblies from diverse canines. These assemblies represent notable improvements in completeness, contiguity, and the representation of gene promoters and gene models. Although genome graph and pan-genome approaches have promise, most genetic analyses in canines rely upon the mapping of Illumina sequencing reads to a single reference. The Dog10K consortium, and others, have generated deep catalogs of genetic variation through an alignment of Illumina sequencing reads to a reference genome obtained from a German Shepherd Dog named Mischka (i.e, canFam4, UU_Cfam_GSD_1.0). However, alignment to a breed-derived genome may introduce bias in genotype calling across samples. Since the use of an outgroup reference genome may remove this effect, we have reprocessed 1,929 samples analyzed by the Dog10K consortium using a Greenland wolf (mCanLor1.2) as the reference. We efficiently performed remapping and variant calling using a GPU-implementation of common analysis tools. The resulting call set removes the variability in genetic differences seen across samples while maintaining general patterns of breed relationships. Using this sequence data, we inferred the history of population sizes and found that village dog populations experienced a 9-13 fold reduction in historic effective population size relative to wolves. </span></p>
Assessing Quality Variations in Early Career Researchers' Data Management Plans: Quantitative Data of the Content Analysis
<p>The data includes the numerical results of the ranking of the data management plans created during the Basics of Research Data Management (BRDM) courses worth 3 ECTS credits in the years 2020 - 2022. The ranking was made using the Finnish DMP Evaluation Guidance (https://doi.org/10.5281/zenodo.4729831). Additionally, the data contains the results of the analysis of the best RDM practices included in the DMPs.</p> <p>Note 1: The comma-separated coded CSV version 1 (5.2.2024) may not open correctly on MacOS. You can use the comma-delimited CSV file version 2 or 3 (31.5.2024).</p> <p>Note 2: Versions 1 (Quality_variations_in_ECRs_DMPs_data) and 3 (Quality_variations_in_ECRs_DMPs_data_ver_3) contain evaluations of DMPs, best practices for data management, as well as methods for data sharing, storage, and preservation. In version 2 (Quality_variations_in_ECRs_DMPs_data_ver_2), the methods for data sharing, storage, and preservation are missing.</p> <p>Data is related to the research article https://doi.org/10.2218/ijdc.v18i1.873.</p>
Replication data for Global variation in the preferred temperature for recreational outdoor activity
<p><strong>Description</strong></p> <p>This dataset contains the processed data used for the statistical analysis in Linsenmeier, M. (2024): <a href="https://doi.org/10.1016/j.jeem.2024.103032">Global variation in the preferred temperature for recreational outdoor activity</a>, published in the Journal of Environmental Economics and Management.</p> <p>The main data on temperature and rainfall are from ERA5 reanalysis (Hersbach et al. 2018). Data on mobile phone activity are from the Google Mobility Reports. Data on GDP per capita are from the World Bank.</p> <p><strong>Acknowledgements</strong></p> <p>The data contain modified Copernicus Climate Change Service information 2020. Neither the European Commission nor ECMWF is responsible for any use that may be made of the Copernicus information or data it contains.</p> <p><strong>Bibliography</strong></p> <ul> <li>Hersbach, H., Bell, B., Berrisford, P., Biavati, G., Horányi, A., Muñoz Sabater, J., Nicolas, J., Peubey, C., Radu, R., Rozum, I., Schepers, D., Simmons, A., Soci, C., Dee, D., Thépaut, J-N. (2018): ERA5 hourly data on single levels from 1959 to present. Copernicus Climate Change Service (C3S) Climate Data Store (CDS). 10.24381/cds.adbb2d47</li> </ul>
Supplementary material for "Dynamics of a goshawk population across half a century is driven by the variation of first-year survival"
<p><strong><span>Abstract</span></strong></p> <p><span>Population dynamics are driven by stochastic and density-dependent processes acting on demographic rates. Individuals differ demographically, and to capture these differences, models of population dynamics are usually structured by age and stage, rarely by sex. An effect of sex on population dynamics is expected if the dynamics of males and females differ, requiring an unequal sex ratio at birth and/or sex-specific survival probabilities. Goshawks (<em>Accipiter gentilis</em>) show large sexual size dimorphism and differential survival, but it is unknown whether males and females contribute differently to population dynamics. We studied a goshawk population in northern Germany over 47 years using brood monitoring data, collected feathers and nestling ringing data. We jointly analyzed the data using a two-sex integrated population model and performed retrospective and prospective population analyses to understand whether the demographic drivers of population change differ between the sexes. The population showed large fluctuations, during which the number of breeding pairs doubled, but the long-term trend of the population was slightly negative. Female survival exceeded male survival during the first year of life. Females started to reproduce at a younger age than males, productivity increased with female age, the sex ratio of nestlings was male biased and there was moderate male immigration. Despite these differences, temporal variation in sex ratio did not contribute to population dynamics and the contribution of temporal variation in survival was similar for both sexes. Variation in first-year survival was the strongest driver in this population, regulated by a weak density-dependent feedback acting through female first-year survival. Overall, the contributions of the two sexes to population dynamics were similar in this monogamous species with strong sexual size dimorphism.</span></p> <p><strong><span>Read me</span></strong></p> <p><span>Data files and code for carrying out all analyses and generating all figures presented in the paper. The six data files are provided in csv format. There are five code files written for R, but some of the main analyses require the NIMBLE software. The main code (IPM_Code.txt) contains a description of the data, code for loading and managing the data, and for fitting the integrated population models. The other files contain custom written functions (Functions.txt), code for performing posterior predictive tests (PPT_Code.txt), code for reporting results and performing various other analyses (Output_analyses_Code.txt), and code for generating figures (Figures_Code.txt).</span></p>
Estimation of the variation in specific discharge over large depth using Distributed Temperature Sensing (DTS) measurements of the heat pulse response
<p>The data contains measurements and derived values that are used for the manuscript "Estimation of the variation in specific discharge over large depth using Distributed Temperature Sensing (DTS) measurements of the heat pulse response, [Paper # 2018WR024171]" Currently under review at the Water Resources Research journal.</p> <p>The data is stored in netCDF files with xarray (Python), and should be readable with any other netCDF reader. </p> <ul> <li>TEMP is the measured temperature in degrees Celsius relative to the background temperature</li> <li>tempinfty is one of the calibration parameters. Represents the steady state temperature increase</li> <li>A is one of the calibration parameters. Represents the timescale in days</li> <li>b is one of the calibration parameters. Represents the scaled distance to the heat source</li> <li>err_alpha is one of the calibration parameters. Represents the autoregressive parameter</li> <li>TEMPmodel is the best fit temperature response in degrees Celsius relative to the background temperature</li> <li>Innovation is termed the noise in the article, in degrees Celsius.</li> <li>q is the estimated specific discharge in meters per day</li> <li>q_MC_XX are the confidence intervals of the estimated specific discharge calculated with Monte Carlo as presented in the article</li> <li>q_lmfit_XX are the confidence intervals of the estimated specific discharge calculated with LMFIT. Is a rough estimate for q_MC_XX calculated by lmfit (Python package).</li> </ul> <p>Time is measured in days with respect to when the heating cable is turned on.</p> <p>Additionally, a Jupyter notebook is supplemented to the article. It demonstrates the calibration routine and the calculation of the confidence interval for the temperature response at a single depth.</p>
The SPARC water vapour assessment II: Comparison of annual, semi-annual and quasi-biennial variations in stratospheric and lower mesospheric water vapour observed from satellites
<p>Here we provide a NetCDF data set that contains the amplitudes and phases for the annual, semi-annual and quasi-biennial variations in stratospheric and lower mesospheric water vapour as observed by 30 satellite data sets. In addition, we combine the results from all data sets to provide average amplitudes and the corresponding standard deviations, among other.</p> <p>The content description of the NetCDF file looks as follows:</p> <p>netcdf results.amt-10-1111-2017 {<br> dimensions:<br> dataset = 30 ;<br> string_length = 60 ;<br> latitude = 37 ;<br> bands = 2 ;<br> altitude = 59 ;<br> variables:<br> char dataset_short(string_length, dataset) ;<br> dataset_short:standard_name = "data set" ;<br> dataset_short:long_name = "data set name" ;<br> dataset_short:description = "short label of data set" ;<br> char dataset_long(string_length, dataset) ;<br> dataset_long:standard_name = "data set" ;<br> dataset_long:long_name = "data set name" ;<br> dataset_long:description = "long label of data set" ;<br> double latitude(latitude) ;<br> latitude:standard_name = "latitude" ;<br> latitude:units = "degree_north" ;<br> latitude:minimum_value = "-90" ;<br> latitude:maximum_value = "90" ;<br> latitude:axis = "Y" ;<br> latitude:_CoordinateAxisType = "Lat" ;<br> double latitude_bands(bands, latitude) ;<br> latitude_bands:units = "degree_north" ;<br> double altitude(altitude) ;<br> altitude:standard_name = "altitude" ;<br> altitude:long_name = "pressure levels" ;<br> altitude:units = "hPa" ;<br> altitude:axis = "Z" ;<br> altitude:_CoordinateAxisType = "Alt" ;<br> double tropopause(latitude) ;<br> tropopause:standard_name = "tropopause" ;<br> tropopause:long_name = "tropopause pressure" ;<br> tropopause:description = "climatological tropopause pressure based on MERRA reanalysis data 2000 - 2014" ;<br> tropopause:units = "hPa" ;</p> <p>// global attributes:<br> :summary = "this file contains the results published in Lossow et al. (2017)" ;<br> :url = "https://www.atmos-meas-tech.net/10/1111/2017/amt-10-1111-2017.html" ;<br> :project = "second SPARC water vapour assessment (WAVAS-II)" ;<br> :creator_name = "Stefan Lossow & Farahnaz Khosrawi" ;<br> :creator_email = "stefan.lossow@kit.edu & farahnaz.khosrawi@kit.edu" ;<br> :creator_email_supplemental = "stefan.lossow@yahoo.se & f.khosrawi@gmail.com" ;<br> :value_for_nodata = "NaN" ;<br> :date_created = "20190105T112425Z" ;</p> <p>group: AO {<br> dimensions:<br> latitude = 37 ;<br> altitude = 59 ;<br> dataset = 30 ;<br> variables:<br> double amplitude(dataset, altitude, latitude) ;<br> amplitude:standard_name = "amplitude" ;<br> amplitude:long_name = "amplitude of the AO variation" ;<br> amplitude:description = "regression model is given by Eq. (1) in the manuscript; amplitude calculation based on Eq. (2)" ;<br> amplitude:units = "ppmv" ;<br> double phase(dataset, altitude, latitude) ;<br> phase:standard_name = "phase" ;<br> phase:long_name = "phase of the AO variation" ;<br> phase:description = "regression model is given by Eq. (1) in the manuscript; phase calculation based on Eq. (3)" ;<br> phase:units = "month" ;<br> double offset(dataset, altitude, latitude) ;<br> offset:standard_name = "offset" ;<br> offset:long_name = "offset component of the regression model" ;<br> offset:description = "regression model is given by Eq. (1) in the manuscript; meant for calculation of relative amplitudes" ;<br> offset:units = "ppmv" ;<br> double screening(dataset, altitude, latitude) ;<br> screening:standard_name = "screening" ;<br> screening:long_name = "screening for the amplitude and phase data" ;<br> screening:description = "screening matrix for the amplitude and phase data to calculate the standard deviations described in Sect. 3.3; 1 means screening; 0 means no screening" ;<br> screening:units = "" ;<br> double phase_difference(dataset, altitude, latitude) ;<br> phase_difference:standard_name = "phase difference" ;<br> phase_difference:long_name = "phase difference with respect to the reference data set" ;<br> phase_difference:reference_data_set_short = "MLS" ;<br> phase_difference:reference_data_set_long = "Aura/MLS v4.2" ;<br> phase_difference:description = "phase difference has been adapted so that it not exceeds the [-6,6] months interval by adding +/- 12 months; has been calculated after the screening" ;<br> phase_difference:units = "month" ;<br> double amplitude_standard_deviation(altitude, latitude) ;<br> amplitude_standard_deviation:standard_name = "standard deviation of amplitude" ;<br> amplitude_standard_deviation:long_name = "standard deviation of amplitude over all data sets" ;<br> amplitude_standard_deviation:description = "standard deviation calculation based on Eq. (6)" ;<br> amplitude_standard_deviation:units = "ppmv" ;<br> double amplitude_mean(altitude, latitude) ;<br> amplitude_mean:standard_name = "mean amplitude" ;<br> amplitude_mean:long_name = "mean amplitude over all data sets" ;<br> amplitude_mean:description = "mean calculation based on Eq. (6)" ;<br> amplitude_mean:units = "ppmv" ;<br> double amplitude_relative_standard_deviation(altitude, latitude) ;<br> amplitude_relative_standard_deviation:standard_name = "relative standard deviation of amplitude" ;<br> amplitude_relative_standard_deviation:long_name = "relatuve standard deviation of amplitude " ;<br> amplitude_relative_standard_deviation:description = "relavtive standard deviation calculation based on Eq. (6); uses \"amplitude_mean\" as reference" ;<br> amplitude_relative_standard_deviation:units = "ppmv" ;<br> double phase_difference_standard_deviation(altitude, latitude) ;<br> phase_difference_standard_deviation:standard_name = "standard deviation of phase difference" ;<br> phase_difference_standard_deviation:long_name = "standard deviation of phase difference over all data sets" ;<br> phase_difference_standard_deviation:description = "standard deviation calculation based on Eq. (7)" ;<br> phase_difference_standard_deviation:units = "month" ;<br> double phase_difference_mean(altitude, latitude) ;<br> phase_difference_mean:standard_name = "mean of phase difference" ;<br> phase_difference_mean:long_name = "mean of phase difference over all data sets" ;<br> phase_difference_mean:description = "mean calculation based on Eq. (7)" ;<br> phase_difference_mean:units = "month" ;<br> } // group AO</p> <p>group: SAO {<br> dimensions:<br> latitude = 37 ;<br> altitude = 59 ;<br> dataset = 30 ;<br> variables:<br> double amplitude(dataset, altitude, latitude) ;<br> amplitude:standard_name = "amplitude" ;<br> amplitude:long_name = "amplitude of the SAO variation" ;<br> amplitude:description = "regression model is given by Eq. (4) in the manuscript; amplitude calculation based on Eq. (2)" ;<br> amplitude:units = "ppmv" ;<br> double phase(dataset, altitude, latitude) ;<br> phase:standard_name = "phase" ;<br> phase:long_name = "phase of the SAO variation" ;<br> phase:description = "regression model is given by Eq. (4) in the manuscript; phase calculation based on Eq. (3)" ;<br> phase:units = "month" ;<br> double offset(dataset, altitude, latitude) ;<br> offset:standard_name = "offset" ;<br> offset:long_name = "offset component of the regression model" ;<br> offset:description = "regression model is given by Eq. (4) in the manuscript; meant for calculation of relative amplitudes" ;<br> offset:units = "ppmv" ;<br> double screening(dataset, altitude, latitude) ;<br> screening:standard_name = "screening" ;<br> screening:long_name = "screening for the amplitude and phase data" ;<br> screening:description = "screening matrix for the amplitude and phase data to calculate the standard deviations described in Sect. 3.3; 1 means screening; 0 means no screening" ;<br> screening:units = "" ;<br> double phase_difference(dataset, altitude, latitude) ;<br> phase_difference:standard_name = "phase difference" ;<br> phase_difference:long_name = "phase difference with respect to the reference data set" ;<br> phase_difference:reference_data_set_short = "MLS" ;<br> phase_difference:reference_data_set_long = "Aura/MLS v4.2" ;<br> phase_difference:description = "phase difference has been adapted so that it not exceeds the [-3,3] months interval by adding +/- 6 months; has been calculated after the screening" ;<br> phase_difference:units = "month" ;<br> double amplitude_standard_deviation(altitude, latitude) ;<br> amplitude_standard_deviation:standard_name = "standard deviation of amplitude" ;<br> amplitude_standard_deviation:long_name = "standard deviation of amplitude over all data sets" ;<br> amplitude_standard_deviation:description = "standard deviation calculation based on Eq. (6)" ;<br> amplitude_standard_deviation:units = "ppmv" ;<br> double amplitude_mean(altitude, latitude) ;<br> amplitude_mean:standard_name = "mean amplitude" ;<br> amplitude_mean:long_name = "mean amplitude over all data sets" ;<br> amplitude_mean:description = "mean calculation based on Eq. (6)" ;<br> amplitude_mean:units = "ppmv" ;<br> double amplitude_relative_standard_deviation(altitude, latitude) ;<br> amplitude_relative_standard_deviation:standard_name = "relative standard deviation of amplitude" ;<br> amplitude_relative_standard_deviation:long_name = "relatuve standard deviation of amplitude " ;<br> amplitude_relative_standard_deviation:description = "relavtive standard deviation calculation based on Eq. (6); uses \"amplitude_mean\" as reference" ;<br> amplitude_relative_standard_deviation:units = "ppmv" ;<br> double phase_difference_standard_deviation(altitude, latitude) ;<br> phase_difference_standard_deviation:standard_name = "standard deviation of phase difference" ;<br> phase_difference_standard_deviation:long_name = "standard deviation of phase difference over all data sets" ;<br> phase_difference_standard_deviation:description = "standard deviation calculation based on Eq. (7)" ;<br> phase_difference_standard_deviation:units = "month" ;<br> double phase_difference_mean(altitude, latitude) ;<br> phase_difference_mean:standard_name = "mean of phase difference" ;<br> phase_difference_mean:long_name = "mean of phase difference over all data sets" ;<br> phase_difference_mean:description = "mean calculation based on Eq. (7)" ;<br> phase_difference_mean:units = "month" ;<br> } // group SAO</p> <p>group: QBO {<br> dimensions:<br> latitude = 37 ;<br> altitude = 59 ;<br> dataset = 30 ;<br> variables:<br> double amplitude(dataset, altitude, latitude) ;<br> amplitude:standard_name = "amplitude" ;<br> amplitude:long_name = "amplitude of the QBO variation" ;<br> amplitude:description = "regression model is given by Eq. (5) in the manuscript; amplitude calculation based on Eq. (2)" ;<br> amplitude:units = "ppmv" ;<br> double phase(dataset, altitude, latitude) ;<br> phase:standard_name = "phase" ;<br> phase:long_name = "phase of the QBO variation" ;<br> phase:description = "regression model is given by Eq. (5) in the manuscript; phase is derived as the shift of the QBO regression fit for which the correlation with the Singapore (1N, 104E) winds at 50 hPa maximises" ;<br> phase:units = "month" ;<br> double offset(dataset, altitude, latitude) ;<br> offset:standard_name = "offset" ;<br> offset:long_name = "offset component of the regression model" ;<br> offset:description = "regression model is given by Eq. (5) in the manuscript; meant for calculation of relative amplitudes" ;<br> offset:units = "ppmv" ;<br> double screening(dataset, altitude, latitude) ;<br> screening:standard_name = "screening" ;<br> screening:long_name = "screening for the amplitude and phase data" ;<br> screening:description = "screening matrix for the amplitude and phase data to calculate the standard deviations described in Sect. 3.3; 1 means screening; 0 means no screening" ;<br> screening:units = "" ;<br> double phase_difference(dataset, altitude, latitude) ;<br> phase_difference:standard_name = "phase difference" ;<br> phase_difference:long_name = "phase difference with respect to the reference data set" ;<br> phase_difference:reference_data_set_short = "MLS" ;<br> phase_difference:reference_data_set_long = "Aura/MLS v4.2" ;<br> phase_difference:description = "phase difference has been adapted so that it not exceeds the [-14,14] months interval by adding +/- 28 months; has been calculated after the screening" ;<br> phase_difference:units = "month" ;<br> double amplitude_standard_deviation(altitude, latitude) ;<br> amplitude_standard_deviation:standard_name = "standard deviation of amplitude" ;<br> amplitude_standard_deviation:long_name = "standard deviation of amplitude over all data sets" ;<br> amplitude_standard_deviation:description = "standard deviation calculation based on Eq. (6)" ;<br> amplitude_standard_deviation:units = "ppmv" ;<br> double amplitude_mean(altitude, latitude) ;<br> amplitude_mean:standard_name = "mean amplitude" ;<br> amplitude_mean:long_name = "mean amplitude over all data sets" ;<br> amplitude_mean:description = "mean calculation based on Eq. (6)" ;<br> amplitude_mean:units = "ppmv" ;<br> double amplitude_relative_standard_deviation(altitude, latitude) ;<br> amplitude_relative_standard_deviation:standard_name = "relative standard deviation of amplitude" ;<br> amplitude_relative_standard_deviation:long_name = "relatuve standard deviation of amplitude " ;<br> amplitude_relative_standard_deviation:description = "relavtive standard deviation calculation based on Eq. (6); uses \"amplitude_mean\" as reference" ;<br> amplitude_relative_standard_deviation:units = "ppmv" ;<br> double phase_difference_standard_deviation(altitude, latitude) ;<br> phase_difference_standard_deviation:standard_name = "standard deviation of phase difference" ;<br> phase_difference_standard_deviation:long_name = "standard deviation of phase difference over all data sets" ;<br> phase_difference_standard_deviation:description = "standard deviation calculation based on Eq. (7)" ;<br> phase_difference_standard_deviation:units = "month" ;<br> double phase_difference_mean(altitude, latitude) ;<br> phase_difference_mean:standard_name = "mean of phase difference" ;<br> phase_difference_mean:long_name = "mean of phase difference over all data sets" ;<br> phase_difference_mean:description = "mean calculation based on Eq. (7)" ;<br> phase_difference_mean:units = "month" ;<br> } // group QBO<br> }</p> <p> </p>
Retrotransposon-based genetic variation of Poa annua populations from contrasting climate conditions
<p>Raw photographs of agarose electrophoresis. Material: six Poa annua populations. Method: inter-Primer Binding Site (iPBS) markers This is the documentation of studies described in the manuscript entitled "Retrotransposon-based genetic variation of Poa annua populations from contrasting climate conditions" accepted for publication in PeerJ journal (decision received on 02.04.2019)</p>
Geographic variation of tree height of Pinus pinea L. gathered from common gardens in Europe
<p>This dataset collects individual georeferenced tree height data from <em>Pinus pinea </em>L. planted in common gardens in France and Spain, between years 1993 and 1997. The experimental design varies depending on the common garden, from a randomized complete to incomplete block design, RCB or RIB, respectively. The final dimensions of this database is 56,624 individual tree height measurements <em> </em>with 9 common gardens and 55 different provenances. The data can be used to assess genetic variation and phenotypic plasticity with further applications in biogeography and forest management. </p>
Geographic variation of tree height of Pinus nigra Arn. gathered from common gardens in Europe
<p>This dataset collects individual georeferenced tree height data from <em>Pinus nigra</em> Arn. planted in common gardens in France, Germany and Spain, between years 1968 and 2009. The experimental design varies depending on the common garden, from a randomized complete to incomplete block design, RCB or RIB, respectively. The final dimension of the dataset is 194,642 individual tree height data measurements <em> </em>with 15 common gardens and 78 different provenances. The data can be used to assess genetic variation and phenotypic plasticity with further applications in biogeography and forest management. </p> <p> </p>
Geographic variation of tree height of Pinus pinaster Aiton gathered from common gardens in Europe and North-Africa
<p>This dataset collects individual georeferenced tree height data from <em>Pinus pinaster</em> Aiton planted in common gardens in France, Morocco and Spain, between years 1966 and 1992. The experimental design varies depending on the common garden, from a randomized complete to incomplete block design, RCB or RIB, respectively. The final dimension of the dataset is 123,801 individual tree height data measurements <em> </em>with 14 common gardens and 182 different genetic units. The data can be used to assess genetic variation and phenotypic plasticity with further applications in biogeography and forest management. </p>
Variations in Solar Activity Across the Sporer Minimum Based on Radiocarbon in Danish Oak (dataset)
<p>This dataset (AARAMS_Radiocarbon_1432_1578_ver2) provides radiocarbon ages of LW tree rings from Danish oak from the period AD 1432 to 1578. The measurements were conducted at the Aarhus AMS Centre (AARAMS) at Aarhus University, Denmark. Ring widths of the two wood samples (SchB and Gr02) used for the measurements are found in the two files: TableS1_SchB_Ringwidths and TableS2_Gr02_Ringwidths. These data are presented in a paper submitted to Geophysical Research Letters with the title: Variations in Solar Activity Across the Sporer Minimum Based on Radiocarbon in Danish Oak.</p>
Bone metabolism gene variation and response to bisphosphonate treatment in women with postmenopausal osteoporosis
<p>This repository contains the raw and source data for the manuscript "Bone metabolism gene polymorphism and response to bisphosphonate treatment in women with postmenopausal osteoporosis" submitted to PLOS ONE.</p> <p><strong>Abstract: </strong></p> <p><em>Introduction:</em> Long-term treatment is used in patients with osteoporosis, and bisphosphonates (BPs) are the most commonly prescribed medications. However, in some patients this therapy is not effective, cause different side effects and complications. Unfortunately, at least one year is needed to identify and confirm an ineffectiveness of BPs therapy on bone mineral density (BMD). Among other factors, a response to BPs therapy may also be explained by genetic factors. The aim of this study was to analyze the influence of <em>SOST, PTH, FGF2, FDPS, GGPS1, </em>and<em> LRP5</em> gene polymorphisms on the response to treatment with BPs.</p> <p><em>Materials and methods: </em>Women with postmenopausal osteoporosis were included to this study if they used bisphosphonates for at least 12 months. Exclusion criteria were: persistence on BPs therapy less than 80%, bone metabolic diseases, diseases deemed to affect bone metabolism, malignant tumours, using of any medications influencing BMD. The study protocol was approved by the local ethics committee. The BMD at the lumbar spine and femoral neck were measured using dual x-ray absorptiometry (GE Lunar) before and at least 12 months after treatment with BPs. According to BMD change, patients were divided in two groups – responders and non-responders to BPs terapy. Polymorphic variants in <em>SOST, PTH, FGF2, FDPS, GGPS1, </em>and<em> LRP5</em> genes were determined using PCR analysis with TaqMan probes (Thermo Scientific).</p> <p><em>Results:</em> In total, 201 women with BPs therapy were included in the study. No statistically significant differences were observed in age, age at menopause, weight, height, BMI and baseline BMD levels between responders (122 subjects) and non-responders (79 subjects).</p> <p>As single markers, the <em>SOST </em>rs1234612 T/T (OR=2.3; P=0.02), <em>PTH</em> rs7125774 T/T (OR=2.8, P=0.0009), <em>FDPS</em> rs2297480 G/G (OR=29.3, P=2.2×10<sup>-7</sup>), and <em>GGPS1</em> rs10925503 C/C+C/T (OR=2.9; P=0.003) gene variants were over-represented in non-responders group. No significant association between <em>FGF2</em> rs6854081 and <em>LRP5</em> rs3736228 gene variants and response to BPs treatment was observed. The carriers of T-T-G-C allelic combination (constructed from rs1234612, rs7125774, rs2297480, and rs10925503) were predisposed to negative response to BPs treatment (OR = 4.9, 95% CI 1.7–14.6, P=0.005). The C-C-T-C combination was significantly over-represented in responders (OR = 0.1, 95% CI 0.1–0.5, P=0.006).</p> <p><em>Conclusions:</em> Our findings highlight the importance of identified single gene variants and their allelic combinations for pharmacogenetics of BPs therapy of osteoporosis. Complex screening of these genetic markers could be used as a new strategy for personalized antiresorptive therapy.</p>
Sample data for analysis of sequence variation in HIV
<p>These are downsampled interleaved paired fastq datasets from Jair et. 2019 (<a href="https://doi.org/10.1371/journal.pone.0214820">https://doi.org/10.1371/journal.pone.0214820</a>). The datasets were prepared by:</p> <ol> <li>Downloading original data from NCBI SRA (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA517147)</li> <li>Trimming contaminating Nextera adapters using trim-galore</li> <li>Mapping reads against nxb2 reference of HIV genome (K03455.1) with BWA MEM</li> <li>Restricting mapped reads to <em>pol</em> gene vicinity (K03455.1:2000-5100)</li> <li>Downsampling mapped data to ~10% of the original with Picard's DownsampleSam</li> <li>Converting BAM to Interleaved Fastq with Picard's SamToFastq</li> <li>Gzipping resultant interleaved paired fastq files</li> </ol>
Recombination and aneuploidy data for: Insights about variation in meiosis from 31,228 human sperm genomes
<p>This repository holds crossover and aneuploidy data for 31,228 human sperm genomes sequenced with Sperm-seq. Data are described in the preprint/paper "Insights about variation in meiosis from 31,228 human sperm genomes." Several levels of data are available, e.g., each crossover (allcrossovers_hg38.txt.gz) and the numbers of crossovers detected per sperm cell (numbercrossoverspercell.txt.gz). Each data file is described in its own readme, so README_allgainsdivisionoforigin.txt explains the data present in allgainsdivisionoforigin.txt. All files are either text files or text files compressed via gzip. All data was generated as described in the preprint/paper, using scripts available in the companion repository (most recent version DOI: 10.5281/zenodo.3561080).</p> <p>This new version has updated sex chromosome ploidies after identifying a minor coding error affecting ~24 cells (sexchromosomeploidy.txt.gz) and includes more detail about possible crossover error modes (README_allcrossovers_hg38.txt.gz).</p>
Database for GWAS SVatalog: a visualization tool to aid fine-mapping of GWAS loci with structural variations.
<p>GWAS SVatalog is a novel visualization tool and database for structural variants (SV) found in a predominantly European population of 101 individuals with Cystic Fibrosis (CF). Aside from the CF-causing variants on chromosome 7 and the LD block in which they lie, the remainder of the genome is comparable to a the 1000 Genomes healthy European population. This data is a collection of SV calls and their linkage disequilibrium (LD) statistics with GWAS-significant SNPs reported in the GWAS Catalog.</p> <p> </p> <p>The goal of this project is to provide a resource to aid fine mapping of GWAS loci using SVs. GWAS loci are generally identified by SNPs which account for an incomplete proportion of genetic variation and phenotypic heritability. Their relevance to the phenotype might be limited, tagging other polymorphisms, such as SVs, that could be the cause of the association signal. To leverage this data to its full potential, visit the <a href="https://svatalog.research.sickkids.ca/" target="_blank" rel="noopener">GWAS SVatalog</a> web tool. Here, interactive visualizations can illustrate SVs identified in high LD with GWAS-significant SNPs, suggesting putative causal variation that could guide additional functional investigation.</p> <p> </p> <p>For more information on how to use GWAS SVatalog, visit the<a href="https://gwas-svatalog-docs.readthedocs.io/en/latest/index.html" target="_blank" rel="noopener noreferrer"> documentation</a>.</p> <p> </p> <p>This project was accomplished in collaboration with the <a href="https://lab.research.sickkids.ca/strug/" target="_blank" rel="noopener">Strug Lab</a> at <a href="https://www.sickkids.ca/en/" target="_blank" rel="noopener">The Hospital for Sick Children (SickKids)</a>, <a href="https://www.tcag.ca/" target="_blank" rel="noopener">The Center for Applied Genomics (TCAG)</a>, and <a href="https://www.utoronto.ca/" target="_blank" rel="noopener">University of Toronto</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.