Find research datasets worth reusing

Meaning maps and saliency models based on deep convolutional neural networks are insensitive to image meaning when predicting human fixations - data

Data from the paper: Meaning maps and saliency models based on deep convolutional neural networks are insensitive to image meaning when predicting human fixations. Preprint: https://www.biorxiv.org/content/10.1101/840256v1 Marek A. Pedziwiatr marek.pedziwi@gmail.com September 2020

opencc-by-4.0Mar 2018View details →

Vanadium nitrogenase - anomalous maps for resting and turnover states

The data set contains anomalous difference electron density maps (in CCP4 format) for two published crystal structures of Azotobacter vinelandii vanadium-dependent nitrogenase. These are: 1. VFe protein - resting state. PDB-ID 5N6Y.    Sippel et al. (2017) Nature Chem. Biol. 13, 956-960. DOI: 10.1038/Nchembio.2428 2. VFe protein - turnover state. PDB-ID 6FEA.  Sippel et al. (2018) Science 359, 1484-1489. DOI: 10.1126/science.aar2765 For each deposition, the maps provided are calculated with anomalous differences as Fourier coefficients, to 1.9 Å or 2.0 Å resoution, respectively. Depending on energies of data collection, these maps were used to visualize: 12398 eV - anomalous contirbution of iron ions 7000 eV - anomalous contribution of sulfur atoms (with strong contribution of V) 6200 eV - improved signal for S/Fe and S/V, respectively (not shown in publications).

Dataset used to map a stump tail sperm defect of Swiss Large White boars

This dataset contains genotypes for 106 Swiss Large White boars that were used to map a stump tail sperm defect and a VCF file that contains genotypes of candiate variants for 87 boars. The subdirectories contain plink binaries, corresponding phased haplotypes (in MaCH format), the results of a haplotype-based GWAS, and a VCF file that contains genotypes at candidate causal variants. The affection status (case=2, control=1) of 106 boars is indicated in the file "pheno". The R script "haplo_linear.R" performs the haplotype-based association study. The README file provides instructions on how to run the GWAS as well as on how to create the Manhattan plot.

opencc-zeroDec 2018View details →

Data from: Mapping of cetacean and seabird populations in the North-East Atlantic

1. Distribution maps of cetaceans and seabirds at basin and monthly scales are needed for conservation and marine management. These are usually created from standardised and systematic aerial and vessel surveys, with recorded animal densities interpolated across study areas. However, as individual surveys have restricted spatial and temporal coverage, distribution maps at basin and monthly scales have previously not been possible. 2. This study develops an alternative approach consisting of: (1) collating diverse survey data to maximise spatial and temporal coverage, (2) using detection functions to estimate variation in the surface area covered (km2) among these surveys, standardising measurements of effort and animal densities, (3) developing species distribution models (SDM) that overcome issues with heterogeneous and uneven coverage. 3. 2.68 million km of survey data in the North-East Atlantic between 1980 and 2018 were collated and standardised. SDM using Generalized Linear Models (GLM) and General Estimating Equations (GEE) in a hurdle-model were developed. Distribution maps were then created for 12 cetacean and 12 seabird species at 10 km and monthly resolution. Qualitative and quantitative assessment indicated good model performance. 4. Applications and synthesis: This study provides the largest ever collation and standardisation of diverse survey data for cetaceans and seabirds, and the most comprehensive distribution maps of these taxa in the North-East Atlantic. These distribution maps have numerous applications including the identification of important areas needing protection, and the quantification of overlap between vulnerable species and anthropogenic activities. This study demonstrates how the analysis of existing and diverse survey data can meet conservation and marine management needs.

opencc-zeroOct 2020View details →

Spatial mapping of root systems reveals diverse strategies of soil exploration and resource contest in grassland plants

1. When foraging and competing for belowground resources, plants have to coordinate the behaviour of thousands of root tips in a manner similar to that of eusocial animal colonies. While well described in animals, we know little about the spatial behaviour of plants, particularly at the level of individual roots. 2. Here, we employed statistical methods previously used to describe animal ranging behaviour to examine root system overlap and the efficiency of root positioning in eight grassland species grown in monocultures and mixtures along a gradient of neighbour densities. 3. Species varied widely in their ability to distribute roots efficiently, with the majority of species showing significant root aggregation at very fine spatial scales. Extensive root system overlap was observed in species mixtures, indicating a lack of territoriality at the level of whole root systems. However, with increasing density of competitors, several species withdrew roots from the periphery of foraging ranges and increased intraplant root aggregation in the remaining area, which may indicate consolidation of foraging areas under competitive pressure. 4. Several species exhibited responses consistent with resource contest in species mixtures where encounters with competitors' roots triggered increased root aggregation at the expense of foraging efficiency. Such responses only occurred in mixtures of species with comparable competitive abilities but were absent in asymmetric species combinations. 5. Synthesis. Combining fine-scale measurement of plant root distributions with spatial statistics yields new insights into plant behavioural strategies with significant potential to impact resource foraging efficiency and productivity.

L4D - Probability map of giant trees occurrence (> 70 m) in the Brazilian Amazon

The probability of giant trees occurrence (> 70m) based on environmental conditions. The observations higher than 70 m were filtered out and used to adjust an envelope model based on maximum entropy. In its optimization routine, the algorithm tracked how much the model gain was improved when small changes were made to each coefficient value associated with a particular variable. The resulting map of predicted occurrence of the tallest trees in the Amazon from the MaxEnt model shows that the probability of maximum tree height occurrence is highest in the northeastern Amazon (Fig. 6), more specifically in the Roraima and Guianan Lowlands. We considered 18 environmental variables: (1) fraction of absorbed photosynthetically active radiation (FAPAR; in %); (2) elevation above sea level (Elevation; in m);  (3) the component of the horizontal wind towards east, i.e. zonal velocity (u-speed ; in m s-1); (4) the component of the horizontal wind towards north, i.e. meridional velocity (v-speed ; in m s-1); (5) the number of days not affected by cloud cover (clear days; in days yr-1); (6) the number of days with precipitation above 20 mm (days > 20mm; in days yr-1 ); (7) the number of months with precipitation below 100 mm (months < 100mm; in months yr-1 ) ; (8) lightning frequency (flashes rate); (9) annual precipitation (in mm); (10) potential evapotranspiration (in mm); (11) coefficient of variation of precipitation (precipitation seasonality; in %); (12) amount of precipitation on the wettest month (precip. wettest; in mm); (13) amount of precipitation on the driest month (precip. driest; in mm); (14) mean annual temperature (in °C); (15)  standard deviation of temperature (temp. seasonality; in °C); (16) annual maximum temperature (in °C); (17) soil clay content (in %); and (18) soil water content (in %).

L4B - Maximum tree height map for the Brazilian Amazon

Maximum tree height distribution estimated by the Random Forest model based on the environmental variables. To explore the influence and importance of the environmental variables for development in tree height, we employed Random Forest modeling, which consists of generating a large number of regression trees, each constructed considering a random data subset. The regression trees are used to identify the best sequence to split the solution space to estimate the output. Were considered 18 environmental variables: (1) fraction of absorbed photosynthetically active radiation (FAPAR; in %); (2) elevation above sea level (Elevation; in m);  (3) the component of the horizontal wind towards east, i.e. zonal velocity (u-speed ; in m s-1); (4) the component of the horizontal wind towards north, i.e. meridional velocity (v-speed ; in m s-1); (5) the number of days not affected by cloud cover (clear days; in days yr-1); (6) the number of days with precipitation above 20 mm (days > 20mm; in days yr-1 ); (7) the number of months with precipitation below 100 mm (months < 100mm; in months yr-1 ) ; (8) lightning frequency (flashes rate); (9) annual precipitation (in mm); (10) potential evapotranspiration (in mm); (11) coefficient of variation of precipitation (precipitation seasonality; in %); (12) amount of precipitation on the wettest month (precip. wettest; in mm); (13) amount of precipitation on the driest month (precip. driest; in mm); (14) mean annual temperature (in °C); (15)  standard deviation of temperature (temp. seasonality; in °C); (16) annual maximum temperature (in °C); (17) soil clay content (in %); and (18) soil water content (in %).

opencc-by-4.0Jul 2016View details →

Prototyping Modes of Interactive Mapping

3rd Project Presentation

opencc-by-4.0Aug 2020View details →

Augmented emission maps: 1968 cc 55 Kw Euro 6 diesel engine: update 2

In order to enable the sharing of data the emission data for vehicles is standardized. The data exchange format contains all data that is applicable for a specific engine taxonomy code. This specific data set refers to the 1968 cc 55 kW Euro 6 diesel engine that has been applied in the Volkswagen Caddy. The standardized emission map has a “.map.txt” extension and is also human readable. The files starts with metadata which contains information about: <ul> <li>the engine taxonomy code,</li> <li>total driven kilometers over which the data was gathered,</li> <li>total time in hours over which the data was gathered,</li> <li>the number of vehicles which were tested to create the emission map,</li> <li>the DOI (Digital Object Identifier) reference,</li> <li>Which emission maps are available in the file.</li> </ul> The DOI  <a href="http://doi.org/10.5281/zenodo.4268034">http://doi.org/10.5281/zenodo.4268034</a> refers to a updated meta-data document that provides the full description of the standardized emission map.

opencc-by-4.0Aug 2020View details →

Augmented emission maps: 1199 cc 55 kW Euro 5a diesel engine: update 2

In order to enable the sharing of data the emission data for vehicles is standardized. The data exchange format contains all data that is applicable for a specific engine taxonomy code. This specific data set refers to the 1199 cc 55 kW Euro 5a diesel engine that has been applied in the Volkswagen Polo, Seat Ibiza, Skoda Fabia and Skoda Roomster. The standardized emission map has a “.map.txt” extension and is also human readable. The files  starts with metadata which contains information about: <ul> <li>the engine taxonomy code,</li> <li>total driven kilometers over which the data was gathered,</li> <li>total time in hours over which the data was gathered,</li> <li>the number of vehicles which were tested to create the emission map,</li> <li>the DOI (Digital Object Identifier) reference,</li> <li>Which emission maps are available in the file.</li> </ul> The DOI  <a href="http://doi.org/10.5281/zenodo.4268034">http://doi.org/10.5281/zenodo.4268034</a> refers to a updated meta-data document that provides the full description of the standardized emission map.

opencc-by-4.0Nov 2020View details →

Co-seismic and post-seismic differential Interferograms and displacement maps for the 2020 M6.5 Monte Cristo Range, Nevada earthquake

Differential interferograms for the Mw 6.5 Monte Cristo, Nevada earthquake, processed with SNAP and CNR-IREA P-SBAS in the <a href="https://geohazards-tep.eu">Geohazards Exploitation Platform</a>. USGS event page for the Monte Cristo earthquake: <a href="https://earthquake.usgs.gov/earthquakes/eventpage/nn00725272/">https://earthquake.usgs.gov/earthquakes/eventpage/nn00725272/</a> Co-seismic and post-seismic (May 16 - May 23) interferograms are included. For each interferometric pair, three products are included: coherence, phase interferogram and unwrapped interferogram (LOS displacement). Decomposition.zip files includes the processed East-West and Vertical deformation maps from combining ascending and descending interferograms.

opencc-by-4.0Oct 2020View details →

Snapshots, frequency contact maps analysis, Poisson Boltzmann calculations, and data scripts for characterization of structural and energetic differences between conformations of the SARS-CoV-2 spike protein

Molecular dynamics simulation trajectories, which have been performed using the Amber ff14SB force field running with the Amber18 package at the NSF-funded (OAC-1826915, OAC-1828163) ELSA high performance computing cluster at The College of New Jersey. Simulation methodology and further details are described in [1] and [2]. For further details on the trajectories, please contact Joseph Baker (bakerj@tcnj.edu). The Poisson Boltzmann energy calculations have been achieved by using the input_files.tar.xz found here and solving the Poisson Boltzmann equation with pygbe. A more detailed example and tutorial can be found at [4]. For further details contact Horacio V Guzman. The dataset contains <ul> <li>A total of 30 snapshots of the three trajectories (10 snapshots each system = two per replica x 5 replicas/system):</li> </ul> <ol> <li>SARS-CoV-2002 spike protein with three RBD in the down positions: "COV2-DDD/PDB/" .</li> <li>SARS-CoV-2002 spike protein with one RBD in the up and two RBD in the down positions: "COV2-UDD/PDB/".</li> <li>SARS-CoV-2002 spike protein with two RBD in the up and one RBD in the down positions: "COV2-DUU/PDB/".</li> </ol> <ul> <li>Input files for Poisson-Boltzmann analysis:</li> </ul> <ol> <li>PoissonBoltzmann/input_files.tar.xz</li> </ol> <ul> <li>Data for the frequency contact map and processing scripts:</li> </ul> <ol> <li>cov2-ddd.pdb, cov2-udd.pdb, cov2-duu.pdb reference PDB files.</li> <li>Contact maps [3] at  "COV2-DDD/CONTACT_MAP/",  "COV2-UDD/CONTACT_MAP/",  "COV2-DUU/CONTACT_MAP/".</li> <li>frequency.lua: get frequency of contacts from a set of contacts map files.</li> <li>diff_frequency.lua: get differential frequency of contacts from a set of frequency files.</li> <li>Frequency of contacts listed in frequency.data files at "COV2-DDD/", "COV2-UDD/" and "COV2-DUU/" directories.</li> </ol> Read the "INFO" files for further informations. This dataset and the code is part of a collaboration between: <ul> <li>The Institute of Fundamental Technological Research, Polish Academy of Sciences, Warsaw, Poland (supported by the National Science Centre, Poland, under grant No. 2017/26/D/NZ1/0046)</li> <li>Department of Chemistry, The College of New Jersey, New Jersey, United States (supported by National Science Foundation under grant numbers OAC-1826915 and OAC-1828163).</li> <li>Jozef Stefan Institute, Ljubljana, Slovenia (supported by the Slovenian Research Agency (Funding No. P1-0055)).</li> <li>School of engineering in bioinformatics, University of Talca, Talca, Chile.</li> </ul> [1] Rodrigo A. Moreira, Mateusz Chwastyk, Joseph L. Baker, Horacio V Guzman, & Adolfo B. Poma. (2020). All-atom simulations snapshots and contact maps analysis scripts for SARS-CoV-2002 and SARS-CoV-2 spike proteins with and without ACE2 enzyme (Version 0.1) [Data set]. Zenodo. http://doi.org/10.5281/zenodo.3817447 [2] Chad W. Hopkins, Scott Le Grand, Ross C. Walker, and Adrian E. Roitberg. Long-Time-Step Molecular Dynamics through Hydrogen Mass Repartitioning. Journal of Chemical Theory and Computation 2015 11 (4), 1864-1874. http://doi.org/10.1021/ct5010406 [3] Rodrigo A. Moreira, Mateusz Chwastyk, Joseph L. Baker, Horacio V Guzman, & Adolfo B. Poma. Quantitative determination of mechanical stability in the novel coronavirus spike protein. Nanoscale, 2020,12, 16409-16413. <a href="https://doi.org/10.1039/D0NR03969A">https://doi.org/10.1039/D0NR03969A</a> [4] https://github.com/pyF4all

Tropical North Atlantic phases: A Self-Organizing Maps (SOM) approach.

Data from SOM analysis

Homozygosity mapping reveals population history and trait architecture in self- incompatible pear (Pyrus spp.)

Homozygosity mapping reveals population history and trait architecture in self- incompatible pear (Pyrus spp.)

Runs of homozygosity (ROH) are successive homozygous segments of the genome where the two haplotypes inherited from the parents are identical-by-descent. A key focus of this project is to investigate ROH distribution patterns in the genomes of outbred fruit crops using pear as a study caseRuns of homozygosity (ROH) are successive homozygous segments of the genome where the two haplotypes inherited from the parents are identical-by-descent. A key focus of this project is to investigate ROH distribution patterns in the genomes of outbred fruit crops using pear as a study case

Homozygosity mapping reveals population history and trait architecture in self- incompatible pear (Pyrus spp.)

opencc-zeroDec 2019View details →

Fitness maps to a large-effect locus in introduced stickleback populations

Mutations of small effect underlie most adaptation to new environments, but beneficial variants with large fitness effects are expected to contribute under certain conditions. Genes and genomic regions having large effects on phenotypic differences between populations are known from numerous taxa, but fitness effect sizes have rarely been estimated. We mapped fitness over a generation in an F2 intercross between a marine and a lake stickleback population introduced to a freshwater pond. A QTL map of the number of surviving offspring per F2 female detected a single, large-effect locus near Ectodysplasin (Eda), a gene having an ancient freshwater allele causing reduced bony armor and other changes. F2 females homozygous for the freshwater allele had twice the number of surviving offspring as homozygotes for the marine allele, producing a large selection coefficient, s = 0.50 ± 0.09 SE. Correspondingly, the frequency of the freshwater allele increased from 0.50 in F2 mothers to 0.58 in surviving offspring. We compare these results to observed allele frequency changes at the Eda gene in an Alaskan lake population colonized by marine stickleback in the 1980's. The frequency of the freshwater Eda allele rose steadily over multiple generations and reached 95% within 20 years, yielding a similar estimate of selection, s = 0.49 ± 0.05. These findings are consistent with other studies suggesting strong selection on this gene (and/or linked genes) in fresh water. Selection on ancient genetic variants carried by colonizing ancestors is likely to increase the prevalence of large-effect fitness variants in adaptive evolution.

opencc-zeroDec 2020View details →

The genetic basis of coordinated plasticity across functional units in a Lake Malawi cichlid mapping population

Adaptive radiations are often stereotypical, as populations repeatedly specialize along conserved environmental axes. Phenotypic plasticity may be similarly stereotypical, as individuals respond to environmental cues. These parallel patterns of variation, which are often consistent across traits, have led researchers to propose that plasticity can facilitate predictable patterns of evolution along environmental gradients. This "flexible stem" model of evolution raises questions about the genetic nature of plasticity, including: How complex is the genetic basis for plasticity? Is plasticity across traits mediated by many distinct loci, or few "global" regulators? To address these questions, we reared a hybrid cichlid mapping population on alternate diet regimes mimicking an important environmental axis. We show that plasticity across an array of ecologically relevant traits is generally morphologically integrated, such that traits respond in a coordinated manner, especially those with overlapping function. Our genetic data are more ambiguous. While our mapping experiment provides little evidence for global genetic regulators of plasticity, these data do contain a genetic signal for the integration of plasticity across traits. Overall, our data suggest a compromise between genetic modularity, whereby plasticity may evolve independently across traits, and low-level but widespread genetic integration, establishing the potential for plasticity to experience coordinated evolution.

Buildings indicating the multicultural character of Balat on the Pervitich Maps

Buildings indicating the multicultural character of Balat on the Pervitich Maps includes: (i) geo-referenced tiff images of the base maps (Pervititch Maps), tiff images of the 1946-aerial photos, a shapefile data on monuments and attributes, and a readme.txt file which explains the attributes.