Find research datasets worth reusing

DATASET From the Reef to the Ocean: Revealing the Acoustic Range of the Biophony of a Coral Reef (Moorea Island, French Polynesia)

Dataset corresponding to the article "From the Reef to the Ocean: Revealing the Acoustic Range of the Biophony of a Coral Reef (Moorea Island, French Polynesia)". 90 sites were recorded from the reef crest to 10 km in the open ocean off Moorea Island (French Polynesia) in 2016. Recordings were realized with drifting antennas made of a floater and an autonomous recorder EA-SDA14 (RTSys®, Caudan, France) connected to a wideband low-noise hydrophone HTI-92 (High Tech Inc., Long Beach, MS, USA) with a sensitivity of −155 ± 3 dB re 1 V µPa−1 and a flat frequency response from 2 Hz to 50 kHz.

ARLCL: Anchor-free Ranging-Likelihood-based Cooperative Localization

This *dataset (68440 files of approx. 30GB unzipped) includes all Bluetooth Low Energy (BLE) Received Signal Strength (RSS) samples used for the evaluation of the Anchor-free Ranging-Likelihood-based Cooperative Localization (ARLCL) method. Each DB file corresponds to an evaluated scenario of a unique combination of nodes/samples (i.e. reflecting different swarm deployments and measurement qualities). The maximal setting is 21 Raspberry Pis and 20 RSS measurement samples. Each DB file contains the true positions of the participating nodes, 100 resampling cases, and one exceptional case (#RSS_0#) where all samples have been used (this case has not been considered in the paper). The specific structure of the DB files is required by our open-sourced Cooperative Localization Optimizer (<a href="https://github.com/CDS-Bern/ARLCL-Optimizer">ARLCL-Optimizer</a>), and also the Mass Spring and Maximum Likelihood - Particle Swarm Optimization implementations that we used in the paper. These are also provided openly in our repo (<a href="https://github.com/CDS-Bern/ARLCL-Optimizer">https://github.com/CDS-Bern/ARLCL-Optimizer</a>). We encourage future cooperative localization solutions to use our provided dataset/software for comparisons or results reproduction. *The files have been compressed using <a href="https://www.7-zip.org/">7-zip</a>.

Raw MS data for "Ligand-specific changes in conformational flexibility mediate long-range allostery in the lac repressor"

These are the raw HDX/MS data for our paper: "Ligand-specific changes in conformational flexibility mediate long-range allostery in the lac repressor."

opencc-by-4.0Feb 2023View details →

Dataset for "Predicting the electrical conductivity of partially saturated frozen porous media, a fractal model for wide ranges of temperatures and salinities"

This dataset supports the research study "Predicting the electrical conductivity of partially saturated frozen porous media, a fractal model for wide ranges of temperatures and salinities" by H. L. Luo, D. Jougnot, A. Jost, J. D. Teng, A. Mendieta, G. Lin, and L. D. Thanh. We provide the experimental data of electrical condutivity and unfrozen water saturation with different initial water saturations and salinities. Meanwhile, we also offer the matlab code for calculating the predicted values of electrical conductivity and apparent formation factor. Each file has its header, describing each column.

opencc-by-4.0Apr 2023View details →

Data of the publication "Transport and entanglement growth in long-range random Clifford circuits"

Conservation laws can constrain entanglement dynamics in isolated quantum systems, manifest in a slowdown of higher Rényi entropies. Here, we explore this phenomenon in a class of long-range random Clifford circuits with U(1) symmetry where transport can be tuned from diffusive to superdiffusive. We unveil that the different hydrodynamic regimes reflect themselves in the asymptotic entanglement growth according to $S(t) \propto t^{1/z}$ where the dynamical transport exponent z depends on the probability $\propto r^{-\alpha}$ of gates spanning a distance r. For sufficiently small $\alpha$, we show that the presence of hydrodynamic modes becomes irrelevant such that S(t) behaves similarly in circuits with and without conservation law. We explain our findings in terms of the inhibited operator spreading in U(1)-symmetric Clifford circuits where the emerging light cones can be understood in the context of classical Lévy flights. Our Letter sheds light on the connections between Clifford circuits and more generic many-body quantum dynamics.

opencc-by-4.0Mar 2023View details →

The $E_2$ page of the 2-primary Adams spectral sequence in a large range

This dataset contains a description of the cohomology of the 2-primary Steenrod algebra in a large range. Broadly, it contains <ul> <li>complete additive data up to stem 256,</li> <li>complete multiplicative and secondary data up to stem 200 (including the Adams $d_2$ differentials).</li> </ul> This data was generated using `<a href="https://github.com/SpectralSequences/sseq/tree/master/ext">ext-rs</a>` running on the Wayne State Grid. The Grid is a high-performance computing cluster operated by Wayne State University Computing & Information Technology. See the accompanying document for a more detailed breakdown of the timeline and the resource usage. This repository is comprised of several files. <ul> <li>`rank.csv`: The rank of the cohomology in each bidegree. This data is complete up to and including stem 256 and homological degree 132. The bidegrees with rank zero are omitted. The columns are as follows: <ul> <li>`stem`: The stem $n$.</li> <li>`Adams_filtration`: The homological degree $s$.</li> <li>`dimension`: The rank of the cohomology at the given stem and homological degree.</li> </ul> </li> </ul> We use `rank.csv` to define a basis for the cohomology. The symbol $x_{n,s,i}$ refers to the $i$th basis element in bidegree $(n,s)$, where $n$ is the stem and $s$ is the homological degree. <ul> <li>`d2.csv`: The Adams $d_2$ differentials. This data is complete up to and including stem 200 and homological degree 128. If the target bidegree is zero-dimensional, the differentials are omitted. The columns are as follows: <ul> <li>`stem`: The stem $n$.</li> <li>`Adams_filtration`: The homological degree $s$.</li> <li>`index`: The index $i$ in the basis of the bidegree $(n,s)$ given by `rank.csv`.</li> <li>`target`: The value of $d_2(x_{n,s,i})$.</li> </ul> </li> <li>`products.csv`: The multiplication table of the product structure with respect to our basis. This data is complete for all pairs of elements whose product is in stem at most 200 and homological degree at most 128. The pairs of elements that multiply to zero are omitted. The columns are as follows: <ul> <li>`stem_1`, `Adams_filtration_1`, `index_1`: The stem $n_1$, homological degree $s_1$, and index $i_1$ of the first element.</li> <li>`stem_2`, `Adams_filtration_2`, `index_2`: The stem $n_2$, homological degree $s_2$, and index $i_2$ of the second element.</li> <li>`product`: The vector representing the product $x_{n_1, s_1, i_1} \cdot x_{n_2, s_2, i_2}$ in bidegree $(n_1 + n_2, s_1 + s_2)$.</li> </ul> </li> <li>`differentials.txt.zst`: The differentials in our minimal resolution, in a human-readable plain text format. The output was generated using <a href="https://github.com/SpectralSequences/sseq/blob/v0.0.4/ext/examples/differentials.rs">this</a> example code. It is compressed using Zstandard for convenience, and decompresses to a 64 GiB file.</li> <li>`change_of_basis.csv`: The correspondence between our basis and the Bruner-Rognes (BR) basis defined in <a href="https://arxiv.org/abs/2109.13117">arXiv:2109.13117</a>. Each row expresses one of our basis elements in terms of the BR basis. The columns are as follows: <ul> <li>`stem`: The stem $n$.</li> <li>`Adams_filtration`: The homological degree $s$.</li> <li>`index`: The index $i$ in the basis given by `rank.csv` in bidegree $(n,s)$.</li> <li>`BR`: The vector in the BR basis corresponding to our element $x_{n,s,i}$.</li> </ul> </li> </ul> All CSV files are in UTF-8 encoded plain text. Unless otherwise noted, the entries are ordered by stem, then homological degree, then index. v1.0.1: We fixed an error in the `products.csv` file. Due to a software error, some products involving elements in bidegrees $(0,9)$, $(9,5)$, $(11,5)$, $(11,6)$, $(20,5)$, $(25,9)$, $(30,9)$, $(31,9)$, and $(33,5)$ were missing. We emphasize that none of the data that was already present in the original file was incorrect. Moreover, we have checked that our multiplication table is compatible with Bruner and Rognes' data (<a href="https://doi.org/10.11582/2022.00015">doi:10.11582/2022.00015</a>), and satisfies the relations described by Lin in (<a href="https://doi.org/10.11582/2022.00015">doi:10.5281/zenodo.7786290</a>).

opencc-by-4.0Jul 2023View details →

Quantum-enhanced sensing on optical transitions via finite-range interactions

This upload contains the data set for the manuscript titled "Quantum-enhanced sensing on optical transitions via finite-range interactions". Notes describing the added data set are uploaded alongside. Please see the Arxiv version https://arxiv.org/abs/2303.10688 for plots.

opencc-by-4.0Jul 2023View details →

Three systems of molecular markers reveal genetic differences between varieties sabina and balkanensis in the Juniperus sabina L. range

Genotypes of 94 Juniperus sabina samples from 14 populations at SNP (Jsabina_SNPs.txt) and SilicoDArT (Jsabina_SilicoDArTs.txt) loci investigated using the DArTseq technology developed by Diversity Array Technology Pty Ltd (DArT, Canberra, ACT, Australia)

opencc-by-4.0Jul 2023View details →

Dataset for paper "A Close-Range Photogrammetric Surface Scanner and its Evaluation"

This dataset is supplementary material to the submission “A low-cost close-range photogrammetric surface scanner”, by Panagiotis Koutlemanis, Xenophon Zabulis, Nikolaos Stivaktakis, Nikolaos Partarakis, Emmanouil Zidianakis, and Ioanna Demeridou. The dataset contains 3D reconstructions that show the results of a close-range photogrammetric approach and its implementation using a low-cost CNC device.

Geographic range size and species morphology determines the organization of sponge host-guest interaction networks across tropical coral reefs (Raw data)

Datasets for the analysis developed in the Article "Geographic range size and species morphology determines the organization of sponge host-guest interaction networks across tropical coral reefs". For more information, please refer to the original publication. Network_Structural_Index_&_SpogeTraits.csv <- Structural Index for the sponge-dwelling fauna network, sponge accumulated area and sponges’ morphology. NWTA_CoralReefs_Sponges_ interactions.csv <- Relationship between host sponges and guest fauna in the Northwester Atlantic coral reefs NWTA_CoralReefs_Sponge_reacords.csv <- Sponge species incidence records in the Northwester Atlantic coral reefs sponges_morphological_description.csv <- Sponge morphological standardization Network.html <- Interactive sponge-dwelling fauna network Enjoy!

opencc-by-4.0Jun 2023View details →

Machine Learning Features from Proton Therapy Treatment Simulations with the Bergen DTC Prototype for Range Verification

Extracted features from the simulation data found at DOI: <a href="https://doi.org/10.5281/zenodo.8192778">10.5281/zenodo.8192778</a> Each simulation constitutes a single data sample. The following features were extracted. Detector features: <ul> <li>Total number of active pixels</li> <li>Total number of clusters (hits)</li> <li>Number of clusters over threshold (5, 20 pixels)</li> <li>Mean and standard deviation of cluster sizes</li> <li>The number of clusters of any given size (1–72)</li> <li>Mean and standard deviation of x- and y-coordinates over each layer (0–42), and the entire detector</li> <li>Number of active pixels in each layer (0–42)</li> <li>Number of clusters (hits) in each layer (0–42)</li> <li>Total energy deposition of the hits in each layer (0–42)</li> </ul> Higher-level detector features, i.e., function fits (linear, cubic, exponential) with their mean squared residuals over the following quantities: <ul> <li>Active pixels over layer</li> <li>Number of clusters over layer</li> <li>Total deposited energy over layer</li> </ul> 201 RSP features extracted from the beam spot, the phantom rotation, and its 3D RSP image. Two datasets are included in two separate archive files: <ul> <li>features.tar.gz: 715-HN phantom by CIRS Inc. (Norfolk, VA, United States), digitized by Giacometti et al. (2017).</li> <li>features-vhf.tar.gz: The Visible Human Female (VHF) Head phantom (Ackermann et al. 1995), courtesy of the U.S. National Library of Medicine, resampled to 1 mm voxels and scaled down to 80% size in the simulation.</li> </ul> After extracting features, some outliers were removed from the datasets: 14 samples for 715-HN and 3 samples for VHF. The rest of the samples were split into train (70%), validation (10%), and test (20%) sets, for both phantoms separately, which can be found in separate CSV files: features_train.csv, features_val.csv, features_test.csv (715-HN) and features-vhf_train.csv, features-vhf_val.csv, features-vhf_test.csv (VHF). The last file (features_shifted_test.csv (715-HN) and features-vhf_shifted_test.csv (VHF)) contains 40 additional samples for each data point in the respective test set, representing a simulated lateral shift between 1 mm and 10 mm in 1 mm intervals in all directions along the x- and y-axis of the beam.

opencc-by-4.0May 2023View details →

Proton Therapy Treatment Simulations with the Bergen DTC Prototype for Range Verification

This dataset contains proton therapy Monte Carlo simulations using GATE (Jan et al. 2004) version 9.2 and Geant4 (Agostinelli et al. 2003; Allison et al. 2006; Allison et al. 2016) version 11.0.0. The treatment targets are the pediatric head phantom 715-HN by CIRS Inc. (Norfolk, VA, United States), digitized by Giacometti et al. (2017), and The Visible Human Female (VHF) head, courtesy of the U.S. National Library of Medicine, resampled to 1 mm voxels and scaled down to 80%. Distal to the phantom, is a simplified geometry of the digital tracking calorimeter designed by the <a href="https://www.uib.no/en/ift/142356/medical-physics-bergen-pct-project">Bergen pCT collaboration</a> for proton computed tomography (Alme et al. 2020). <ul> <li>treatment_simulations.tar.gz: 36258 simulations with the 715-HN phantom</li> <li>treatment_simulations_vhf.tar.gz: 35673 simulations with the VHF phantom</li> </ul> Each simulation is a single pencil beam with $10^7$ primary protons. To determine valid spots to use, probing simulations with $10^5$ primaries were conducted, where the beam position, energy, and phantom rotation were varied: 10 mm interval in the xy-plane for the beam position, 3 mm water range interval for the beam energy, and 30° rotations of the phantom. If no primary was found in the detecter after the probing simulation, it is a valid spot for the dataset. Resulting hit files, containing simulated detector readout, can be found in the archive files for the respective phantom. Each simulation is accompanied by a metafile in JSON format, specifying all parameters used to produce the output. E.g., beam position and energy can be found in "parameters" -> "beam_spot_x", "beam_spot_y", "beam_energy" and the phantom rotation can be found in "parameters" -> "phantom_rotation_angle". Simulation data has been pre-processed with two steps. First, hits for the same track in the same layer are binned together into a single entry by averaging the positions (posX, posY, posZ) and summing the energy depositions (edep). Second, the energy deposition values are discretized into a cluster size and back into MeV, to represent the energy resolution of the ALPIDE chip (Alme et al. 2020). Clusters of size 0 are removed. Additionally, some of the unused GATE output columns are removed and a column specifying the detector layer is created through the formula layer = 2*volumeID[2] + volumeID[3]. Details about the meaning of the other output columns can be found in the <a href="https://opengate.readthedocs.io/en/latest/data_output_management.html">GATE documentation</a>.

opencc-by-4.0Sep 2023View details →

Data of the publication "Hydrodynamics in long-range interacting systems with center-of-mass conservation"

In systems with a conserved density, the additional conservation of the center of mass (dipole moment) has been shown to slow down the associated hydrodynamics. At the same time, long-range interactions generally lead to faster transport and information propagation. Here, we explore the competition of these two effects and develop a hydrodynamic theory for long-range center-of-mass-conserving systems. We demonstrate that these systems can exhibit a rich dynamical phase diagram containing subdiffusive, diffusive, and superdiffusive behaviors, with continuously varying dynamical exponents. We corroborate our theory by studying quantum lattice models whose emergent hydrodynamics exhibit these phenomena.

opencc-by-4.0Sep 2023View details →

Data from: Sex differences in the relationship between maternal and foetal glucocorticoids in a free-ranging large mammal

Description This registration contains the data and scripts used for the analysis in the manuscript "Sex differences in the relationship between maternal and neonate cortisol in a free-ranging large mammal" (https://doi.org/10.1101/2023.05.04.538920). All versions and additional material are posted on the OSF project page: https://osf.io/4ymc8/  Important to note: this is an updated registration from a previous version (www.osf.io/wynke). OSF currently does not allow to change the files that were uploaded previously, which is why we switched to Zenodo. Future updates to the dataset and scripts will take place here.  Changes to previous version Following our review process at PCI Ecology, we made some changes (mostly additions) to the previous version. This includes the addition of more raw data.  Changes to the previous version include:  -    We added the raw faecal data (“Raw_faecal_data.csv) along with a script (“Faecal exploration .R”), which loads the raw faecal datafile and does some minor investigations on it. These include checking whether the sampling time or day matter, and calculating a repeatability estimate. -    In “Faecal exploration.R”, we highlight the outlier that we removed.  -    We have added the t-test reported in the manuscript to the script “Analysis.R”. -    In “Analysis.R”, we now also run the analysis both with as well as without the outlier. We also have adapted our code to plot the outlier in the figure along with the other values.  -    We have updated the README file to include a description of both the data files and the scripts.

dryad44/100

Data from: Seed origin and warming constrain lodgepole pine recruitment, slowing the pace of population range shifts

Open the record for dataset details and reuse information.

publicSep 2021View details →

openCC (other)Mar 2018View details →

Downscaled climate grids at 30m for a variety of bioclimatic variables over the San Joaquin Experimental Range, CA: 2001-2099

Statistically-downscaled grids of bioclimatic variables were produced to study how fine-scale spatio-temporal variation in climate might influence the exposure of tree species to projected climate change in southern California.

openCC (other)Nov 2024View details →

Range size and local abundance data for angiosperm communities across an elevation gradient, Rocky Mountain Biological Lab, 2021-2022

This dataset contains abundance and range size data for angiosperm communities at three sites in Washington Gulch near the Rocky Mountain Biological Laboratory (RMBL, Gothic, Colorado, USA) for 2021 and 2022. RMBL is located in the East River valley of the West Elk mountains, approximately 10 kilometers from Crested Butte, Colorado. Study sites were located at 2815 m (38°53'50"N, 106°58'43"W), 3165 m (38°57'38"N, 107°01'53"W) and 3380 m (38°58'10"N, 107°01'53"W) in elevation, and contained five 1.2 m x 1.2 m plots each. We identified all vascular plants to species level. Each plot was sampled once per year near the peak of the growing season (approximately mid-July, depending on the year and elevation). In each plot, we counted all individuals of every species. To quantify abundance, we averaged local abundance across all five plots at each site and the two data collection years, and then ranked species by averaged abundance within each site (highest to lowest). We calculated range size as Extent of Occurrence (EOO) and Area of Occupancy (AOO). We calculated AOO and EOO with GBIF data using the ‘red’ package. We then ranked species by AOO within each site (largest to smallest).

openCC (other)Jul 2020View details →

Annual Point Count Breeding Bird Survey at Pepperwood Preserve in the California Coast Ranges 2007-2019

The Dwight Center for Conservation Science at Pepperwood is an ecological institute dedicated to educating, engaging, and inspiring our community through habitat preservation, science-based conservation, leading-edge research, and interdisciplinary educational programs. Our mission is to steward the life and landscapes of the 3,200-acre Pepperwood Preserve and to advance science-based conservation of ecosystems throughout our region and beyond. The Pepperwood Breeding Bird Survey was initiated in the spring of 2007 with the goal of establishing a set of baseline bird community data that would be built upon for years to come. Four transects (totaling 38 points) are surveyed annually using standardized five-minute point count protocols outlined by the Point Reyes Bird Observatory (now called Point Blue Conservation Science; Ballard et al. 2003) and the Handbook of Field Methods for Monitoring Landbirds (Ralph et al. 1993). Surveys are conducted by experienced volunteers during the breeding season starting in late April and ending in June, with each transect surveyed a total of three times. The Rogers Creek and Martin Creek transects were established in 2007. The Weimar Flat and Pepperwood Road transects were established in 2008 and 2012, respectively, to ensure comprehensive coverage across the various habitats that occur at the preserve including Douglas-fir forest, mixed hardwood forest, oak woodland/forest, chaparral, and open grasslands. This dataset includes data collected between 2007-2019.

openCC (other)Aug 2020View details →

Post-Tubbs Fire Chaparral Floristic Survey at Pepperwood Preserve in the California Coast Ranges 2018-2019

The Dwight Center for Conservation Science at Pepperwood is an ecological institute dedicated to educating, engaging, and inspiring our community through habitat preservation, science-based conservation, leading-edge research, and interdisciplinary educational programs. Our mission is to steward the life and landscapes of the 3,200-acre Pepperwood Preserve and to advance science-based conservation of ecosystems throughout our region and beyond. Following the October 2017 Tubbs Fire, Pepperwood hired Nomad Ecology, LLC, to implement Nomad Ecology's post-fire research program at Pepperwood. Specifically, Nomad Ecology conducted a two-year study of post-fire plant diversity and succession in chaparral at the preserve. Species richness and ecological dynamics are not well understood in these post-fire areas (especially in northern California) despite high interest from land managers, ecologists, and botanists. Documentation of the post-fire flora and the sensitive species that are part of this fleeting diversity is essential to understanding the full range of natural resources associated with chaparral ecosystems, and thus key to developing conservation goals specific to Pepperwood. This study documented the burn severity and diversity and abundance of the fleeting post-Tubbs Fire flora in spring 2018 and 2019 using species ocular cover estimates across ten 50-meter belt transects in four different soil types: rhyolite, fluvial and lacustrine deposits, andesite, and serpentinite.