Find research datasets worth reusing

opencc-by-4.0Aug 2024View details →

Data accompanying the paper "Regime-dependent turbulence length scale formulation for NWP models based on turbulence kinetic energy, shear and stratification", submitted to Monthly Weather Review

This repository contains the outputs of MicroHH LES (van Heerwaarden et al., 2017) and ALADIN-CZ single-column model simulations of four idealized cases: 1) The continental cumulus case utilizing measurements from the Atmospheric Radiation Measurement (ARM) program, and Cloud and Radiation Testbed (CART) site in Oklahoma (Brown et al. 2002; Lenderink et al. 2004) 2) The trade wind cumulus case from the Barbados Oceanographic and Meteorological Experiment (BOMEX; Siebesma et al. 2003) 3) A drizzling stratocumulus case based on the first research flight data of the second period of the Dynamics and Chemistry of Marine Stratocumulus (DYCOMS-II) campaign (Stevens et al., 2005) 4) A stable planetary boundary layer case based on the Global Energy and Water Cycle Experiment (GEWEX) Atmospheric Boundary Layer Study (GABLS1) data (Beare et al. 2006; Cuxart et al. 2006; Holtslag 2006) The MicroHH LES outputs are taken from Reilley et al. (2022) study and can be also found at https://doi.org/10.5281/zenodo.6372434. Additionally, we provide case study outputs from the ALADIN-CZ 3D NWP model, wherein the fields roughly match those verified/shown in Fig. 9.   The files are organized in the following way: 1) MicroHH LES model configuration files (.ini) and output files (NetCDF format) are stored in the file "LES.zip" within "conf" and "data" folders, respectivelly. Additionally, a sample script to plot LES-derived Turbulence Length Scales (TLS) and those based on NWP formulations (using LES data as input) is provided (plot.py). 2) The vertical profiles of (i) conserved variables and (ii) turbulent fluxes from the ALADIN-CZ single-column model for four idealized cases are provided in the file "single-column_simulations.zip", consisted of individual ASCII files (per case and TLS formulation). A detailed description of its content can be found in the associated README file. 3) Chosen surface and upper-air fields for (i) 23 November 2019 inversion and (ii) 24 June 2022 mesoscale convection system cases are provided in the file "case_studies.zip" and consisted of individual GRIB files per field and prognostic hour.  A detailed description of its content can be found in the associated README file.

opencc-by-4.0Oct 2023View details →

Data for testing the assumption of fractal scaling in canopy surfaces across a diverse range of forest types

This is a collection of scripts and research data for a study on whether canopy surfaces follow fractal scaling laws across a diverse range of forest types. The article citation is: Fischer, F. J., & Jucker, T. (2024). No evidence for fractal scaling in canopy surfaces across a diverse range of forest types. Journal of Ecology, 112, 470–486. <a href="https://doi.org/10.1111/1365-2745.14244">https://doi.org/10.1111/1365-2745.14244</a>. As data, we use canopy height models (CHMs) from 9 Australian research sites belonging to the Terrestrial Ecosystem Research Network (TERN). Their extent is 5 km x 5 km throughout. The underlying data can be found here: https://portal.tern.org.au/metadata/TERN/4ff0b4c9-cfa0-4d09-9520-b5402adc583f. Climatic data are extracted from the CHELSA climatology 1981-2010 (Brun et al. 2022: Global climate-related predictors at kilometer resolution for the past and future. Earth System Science Data, 14(12), 5573–5603. https://doi.org/10.5194/essd-14-5573-2022; Karger et al. 2017: Climatologies at high resolution for the earth's land surface areas. Scientific Data, 4(1), 170122. https://doi.org/10.1038/sdata.2017.122). Each uploaded zip-file corresponds to a folder within a common repository. To reproduce our analysis, unpack into the same folder, upholding naming conventions and overall structure. Please note that some parts of the analysis require external software, e.g., GRASS GIS for the generation of simulated fractal surfaces. Paths need to be reset accordingly.  rscripts.zip:  <ul> <li>the overall R script ("areforestsfractals_v3.R") used to generate fractal surfaces, calculate fractal statistics from CHMs and simulated surfaces, and to carry out the analysis</li> <li>various summary statistics saved both as RData and csv files</li> </ul> TERN.zip: <ul> <li>data within this folder are ordered by site name</li> <li>for each site, we include several CHMs, their corresponding DSMs (digital surface models) and DTMs (digital terrain models), as well as ancillary layers (pulse densities of laser scans)</li> <li>for each site and each CHM/DSM, we also save the fractal scaling properties in separate csv files</li> </ul> TERNtrees.zip: <ul> <li>data within this folder are ordered by site name</li> <li>for each site, we include manual delineations of the largest trees per 1 km x 1 km square (25 in total)</li> <li>for each site, we include subplots of the CHM (200 m x 200 m) centred around the largest tree</li> </ul> climate.zip: <ul> <li>climate layers from CHELSA for precipitation and site water balance</li> </ul> terrain_fractal.zip: <ul> <li>simulated fractal surfaces, based on different generating algorithms</li> <li>fractal scaling properties of simulated fractal surfaces in separate csv files</li> </ul> sites_coordinates.csv <ul> <li>lon/lat coordinates of each site</li> </ul>

Data from: Diversifying large-scale participatory science: The efficacy of engagement through facilitator organizations

Large-scale, scientist-led, participatory science (citizen science) projects often engage primarily participants who are White, wealthy, and well-educated. Calls to diversify contributory projects are increasingly common, but little research has evaluated the efficacy of suggested strategies for diversification. We engaged participants in Crowd the Tap through facilitator organizations like Historically Black Colleges and Universities (HBCUs), predominantly White institutions (PWI), high school science classrooms, and corporate volunteer programs. Crowd the Tap is a contributory project focused on identifying and addressing lead contamination in household drinking water in the United States. We investigated how participant diversity with respect to race, ethnicity, and homeownership (a proxy for income) differed between participation facilitated through a partner organization and in unfacilitated participation in which participants came to the project independently. We were also interested in which facilitators were most effective at increasing participant diversity. White and wealthy participants were overrepresented in unfacilitated participation. Facilitation helped increase engagement of people of color, especially Black households, and lower-income households. High schools were particularly effective at engaging Hispanic or Latino participants and HBCUs were important for engaging Black households. Ultimately, our results suggest that engagement through facilitator organizations may be an effective means of engaging diverse participants in large-scale projects. Our results have important implications for the field of participatory science as we seek to identify evidence-based strategies for diversifying project participants.

opencc-by-4.0Oct 2023View details →

Quantifying the Impact of Vertical Resolution on the Representation of Marine Boundary Layer Physics for Global-Scale Models

Data supporting the findings of DOI: 10.1175/MWR-D-23-0078.1, a 2023 Monthly Weather Review publication with the same title as this dataset.

Data from a flexible framework to assess patterns and drivers of beta diversity across spatial scales

The patterns and underlying ecological (e.g., environmental filtering) and historical (e.g., priority effects) drivers of beta diversity are scale-dependent but generally difficult to distinguish and rarely explored with a sufficiently broad range of spatial scales. We propose a general scale-explicit framework to assess and contrast the patterns and drivers of beta diversity across hierarchical spatial scales ranging from within fine-scale ecoregion-scale to among broad-scale ecoregion-scale. By applying this framework to aquatic macroinvertebrate datasets, we show that beta diversity generally increases with spatial extent. With an increasing spatial extent, beta diversity shifts from being more influenced by environmental filtering to being more influenced by recent historical factors (i.e., past beta diversity). Such recent historical effects may result from past environmental variation rather than priority effects. We also found that the small-scale and large-scale environmental drivers act differently on beta diversity across spatial extents. Our research reveals a complex spatial-scale dependence in beta diversity patterns and their drivers and provides a more holistic understanding of beta diversity dynamics. Our framework represents a flexible way to unravel the internal structure of beta diversity across scales by partitioning of entire beta diversity variation into scale-specific differences and may have broad application in community ecology, landscape planning and biodiversity conservation.

A chromosome-scale assembly of the quinoa genome provides insights into the structure and dynamics of its subgenomes

Quinoa (Chenopodium quinoa Willd.) is an allotetraploid seed crop with the potential to help address global food security concerns. Genomes have been assembled for three accessions of quinoa; however, all assemblies are fragmented and do not reflect known chromosome biology. Here, we used in vitro and in vivo Hi-C data to produce a chromosome-scale assembly of the Chilean quinoa accession PI 614886 (QQ74). The final assembly spanned 1.326 Gb, of which 90.5% was assembled into 18 chromosome-scale scaffolds. The genome was annotated with 54,499 protein-coding genes, 97% of which were located on the 18 largest scaffolds. We also produced an updated genome assembly for the B-genome diploid C. suecicum and used it, together with the A-genome diploid C. pallidicaule, to identify genomic rearrangements within the quinoa genome, including a large pericentromeric inversion representing 71.7% of chromosome Cq3B. Repetitive sequences comprise 65.20%, 48.61%, and 57.91% of the quinoa, C. pallidicaule, and C. suecicum genomes, respectively. Evidence suggests that the B subgenome is more dynamic and has expanded more than the A subgenome. These genomic resources will enable more accurate assessments of genome evolution within the Amaranthaceae and will facilitate future efforts to identify variation in genes underlying important agronomic traits in quinoa.

Gigantic animal cells suggest organellar scaling mechanisms across a 50-fold range in cell volume

Across the tree of life, cell size varies by orders of magnitude, and organelles scale to maintain cell function. Depending on their shape, organelles can scale by increasing volume, length, or number. Scaling may also reflect demands placed on organelles by increased cell size. The 8,653 species of amphibians exhibit diverse cell sizes, providing a powerful system to investigate organellar scaling. Using transmission electron microscopy and stereology, we analyzed three frog and salamander species whose enterocyte cell volumes range from 228 to 10,593 μm3. We show that the nucleus increases in radius while the mitochondria increase in total network length; the endoplasmic reticulum and Golgi apparatus, with their complex shapes, are intermediate. Notably, all four organelles increase in volume proportionate to cell volume. This pattern suggests that protein concentrations are the same across amphibian species that differ 50-fold in cell size, and that organellar building blocks are incorporated into more or larger organelles following the same "rules" across cell sizes, despite variation in metabolic and transport demands. This conclusion contradicts results from experimental cell size increases, which produce severe proteome dilution. We hypothesize that salamanders have evolved the biosynthetic capacity to maintain a functional proteome despite a huge cell volume.

Dissecting muscle power output: Evidence of multi-scale power amplification in skeletal muscle

Many animals use a combination of skeletal muscle and elastic structures to amplify power output for fast motions. Among vertebrates, tendons in series with skeletal muscle are often implicated as the primary power-amplifying spring, but muscles contain elastic structures at all levels of organization, from the muscle tendon to the extracellular matrix to elastic proteins within sarcomeres. The present study used ex vivo muscle preparations in combination with high-speed video to quantify power output, as the product of force and velocity, at several levels of muscle organization to determine where power amplification occurs. Dynamic ramp shortening contractions in isolated frog flexor digitorum superficialis brevis were compared with isotonic power output to identify power amplification within muscle fibers, the muscle belly, free tendon and elements external to the muscle tendon. Energy accounting revealed that artifacts from compliant structures outside of the muscle–tendon unit contributed significant peak instantaneous power. This compliance included deflection of clamped bone that stored and released energy contributing 195.22±33.19 W kg−1 (mean±s.e.m.) to the peak power output. In addition, we found that power detected from within the muscle fascicles for dynamic shortening ramps was 338.78 ±16.03 W kg−1, or nearly twice the maximum isotonic power output of 195.23±8.82 W kg−1. Measurements of muscle belly and muscle–tendon unit also demonstrated significant power amplification. These data suggest that intramuscular tissues, as well as bone, have the capacity to store and release energy to amplify whole-muscle power output.

Finding functionality: Rasch analysis of the Functionality Appreciation Scale in community-dwelling adults in the US

<div class="abstract-content selected"> <div class="abstract-content selected"> Introduction: The Functionality Appreciation Scale (FAS) measures an individual's appreciation for the functions their body can perform, regardless of the individual's physical limitations. Prior studies reported on internal consistency, test-retest reliability, convergent validity, and exploratory or confirmatory factor analyses, but Rasch analysis has not yet been performed to evaluate the structural validity of the FAS. Methods: We recruited community-dwelling adults at the Minnesota State Fair and through contact lists of participants identifying interest in research done in the Brain Body Mind Lab (University of Minnesota). Community-dwelling adults with spinal cord injury (SCI) completed the FAS over Zoom. We analyzed the FAS using Rasch Measurement Theory, which produced the following outputs: item, and person fit, targeting, unidimensionality, person separation reliability (PSR), local item dependence (LID), principal component analysis of residuals (PCAR), and differential item functioning (DIF). Results: We recruited 567 participants (average age 52.15 ± 17.5 years, 63.84% women), among which 14 adults with SCI. After rescoring 3 items and deleting 1 item, the FAS had good person and item fit (except item 4). The PCAR and subsequent paired t-tests (3.53%) confirmed the unidimensionality of the scale. There was no DIF and only one item pair had LID (item 5-6). PSR was 0.75, reflecting a capacity to differentiate groups of people with high or low functionality appreciation levels. However, there was a significant ceiling effect (28.04%) and the person mean location was 3.06 ± 2.07 logits, indicating the FAS is too easy for community-dwelling adults in the US. Discussion: The 6-item Rasch-based FAS demonstrated unidimensionality, good item fit (except item 4) and person fit, but the FAS will require more difficult items to be added to improve the targeting of the scale, and better reliability. </div> </div>

VCF files and regression analyses for: Assessing fine-scale pondscape connectivity with amphibian eyes: an integrative approach using genomic and capture-mark-recapture data

In the face of habitat loss, preserving functional connectivity is essential to maintain genetic diversity and the demographic dynamics required for the viability of biotic communities. This requires knowledge of the dispersal behavior of target species, which can be modeled as kernels, or probability density functions of dispersal distances at increasing geographic distances. We present an integrative approach to investigate the relationships between genetic connectivity and demographic parameters in organisms with low vagility focusing on five syntopic pond-breeding amphibians. We genotyped 1,056 individuals of two anuran and three urodele species (1,732–3,913 SNPs per species) from populations located in a landscape comprising 64 ponds to characterize fine-scale genetic structure in a comparative framework and combined this genetic data with information obtained in a previous two-year capture-mark-recapture (CMR) study. Specifically, we contrasted graphs reconstructed from genomic data with connectivity graphs based on dispersal kernels and demographic information obtained from CMR data from previous studies and assessed the effects of population size, population density, geographical distances, inverse movement probabilities and the presence of habitat patches potentially functioning as stepping stones on genetic differentiation. Our results suggest a significant influence of local population sizes on patterns of genetic connectivity at small spatial scales. In addition, movement records and cluster-derived kernels provide robust inferences on most likely dispersal paths that are consistent with genomic inferences on genetic connectivity. The integration of genetic and CMR data holds great potential for understanding genetic connectivity at spatial scales relevant to individual organisms, with applications for the implementation of management actions at the landscape level.

Accompanying data for "The Response of Tropical Rainfall to Idealized Small-Scale Thermal and Mechanical Forcing", by Martin Velez-Pardo and Timothy W. Cronin

Data accompanying the manuscript "The Response of Tropical Rainfall to Idealized Small-Scale Thermal and Mechanical Forcing", by Martin Velez-Pardo and Timothy W. Cronin.

Proximity-sensors on GPS collars reveal fine-scale predator-prey behavior during a predation event: A case study from Scandinavia

Although the advent of high-resolution GPS tracking technology has helped increase our understanding of individual and multi-species behavior in wildlife systems, detecting and recording direct interactions between free-ranging animals remains difficult. In 2023, we deployed GPS collars equipped with proximity sensors (GPS proximity collars) on brown bears (Ursus arctos) and moose (Alces alces) as part of a multi-species interaction study in central Sweden. On 6 June, 2023, a collar on an adult female moose and a collar on an adult male bear triggered on each other's UHF signal and started collecting fine-scale GPS positioning data. The moose collar collected positions every 2 minutes for 89 minutes and the bear collar collected positions every 1 minute for 41 minutes. On 8 June, field personnel visited the site and found a female neonate moose carcass with clear indications of bear bite marks on the head and neck. During the predation event, the bear remained at the carcass while the moose moved back and forth, moving towards the carcass site about 5 times. The moose was observed via drone with 2 calves on 24 May and with only one remaining calf on 9 June. This case study describes, to the best of our knowledge, the first instance of a predation event between two free-ranging, wild species recorded by GPS proximity collars. Both collars successfully triggered and switched to finer-scaled GPS fix rates when the individuals were in close proximity producing detailed movement data for both predator and prey during and after a predation event. We suggest that, combined with standard field methodology, GPS proximity collars placed on free-ranging animals offer the ability for researchers to observe direct interactions between multiple individuals and species in the wild without the need for direct visual observation.

STAVER: A Standardized Benchmark Dataset-Based Algorithm for Effective Variation Reduction in Large-Scale DIA-MS Data

This project focuses on developing and applying STAVER, an innovative DIA algorithm designed to eliminate non-biological noise and variability from the large-scale DIA-MS study dataset analyses. STAVER is a flexible framework that utilizes prior knowledge regarding peptide separation coordinates (RT) and fragment ion intensities from the standard benchmark datasets, which effectively mitigates non-biological noise potential during library searches, enhancing spectrum identifications and protein quantification accuracy. Furthermore, the robustness and broad applicability of STAVER were validated in multiple large-scale DIA datasets from different platforms and laboratories, demonstrating significantly improved precision and reproducibility of protein quantification. It facilitates the comparative and integrative analysis of DIA datasets across different platforms and laboratories, enhancing the consistency and reliability of findings in clinical research. The project aims to promote the adoption of hybrid library search and improve the sensitivity and quality of DIA proteomics data through the open-source STAVER software package.

opencc-by-4.0Oct 2023View details →

Application of a Comprehensive Hygroscopicity Framework for Simulating Aerosol Water Uptake in a Large-scale Climate Model

This dataset was generated from 18-month simulations of the NCAR Community Atmosphere Model (CAM); the atmospheric component of the Community Earth System Model version 2 (CESM2). The dataset can be used to reproduce the analysis and figures presented in the upcoming JGR publication.

opencc-by-4.0Jun 2023View details →

Dataset to manuscript Excitation's lifetime extracted from electron-photon (EELS-CL) nanosecond-scale temporal coincidences

The datasets provided are raw data after the initial electron-photon temporal lists have been analyzed to determine the electron-photon pairs and their temporal delay. These lists are too long and not very meaningful to be provided in full.The datasets were analyzed with the following Python libraries: Numpy 1.23.5, Matplotlib 3.6.2, Scipy 1.10.0, Hyperspy 1.7.3.The provided jupyter notebooks were used to generate the figures in the manuscript.

Data from: Spatial scale matters for predicting plant invasions along roads

Biological invasions threaten global biodiversity and can have severe economic and social impacts. The complexity of this problem challenges effective management of invasive alien species as the contribution of many factors involved in the invasion processes across different spatial scales is not well understood. Here, we identify the most important determinants associated with the occurrence of two invasive alien plants, the North American goldenrods (Solidago canadensis and S. gigantea), commonly found in agricultural landscapes of Europe. We used Google Street View images to perform a remote, large-scale inventory of goldenrods along 1,347 roadside transects across Poland. Using open access geospatial data and machine learning techniques, we investigated the relative role of nearly 50 variables potentially affecting the distribution of studied species at five spatial scales (from within 0.25 km to 5 km of the studied locations). We found that the occurrence of goldenrods along roadsides was simultaneously associated with multiple drivers among which those related to human impacts, climate, soil properties and landscape structure were the most important, while local characteristics, such as road parameters or the presence of other alien plants were less influential. However, the relative contribution of different variables in predicting goldenrod distribution changed across spatial scales. Synthesis: Mechanisms underlying plant invasions are highly complex and a number of factors can jointly influence the outcomes of this process. However, since different invasion drivers operate at different spatial scales, some important associations may be overlooked when focusing on a single spatial context. Although associations were consistent in direction (positive or negative) across scales, their relative influence on goldenrod occurrence often changed. Socio-economic factors were largely important at local scales, while the effect of landscape factors broadly increased with increasing spatial scale. We highlight that using multi-scale approaches involving a wide range of variables may enable setting priorities for the management of invasive alien plants.

The role of injection method on residual trapping at the pore-scale in continuum-scale samples: raw micro-CT dataset

The experiments in this work explore the role of a variable injection rate on gas saturation and residual trapping. There are 2 experiments in this work H2L (high to low injection rate) and L2H (low to high injection rate). The workflow for processing the micro-CT images to get the segmented images is described in [1]. The following scans are included in this repository NB. all data for this repository is segmented micro-CT data.: <ol><li>Dry scan prior to experiment = <a href="https://zenodo.org/api/records/10145102/draft/files/05_dry_bin2_merged.tif/content">05_dry_bin2_merged.tif</a></li><li>Sample fully saturated with brine = <a href="https://zenodo.org/api/records/10145102/draft/files/07_wet_bin2_merged.tif/content">07_wet_bin2_merged.tif</a></li><li>H2L during high flow  = <a href="https://zenodo.org/api/records/10145102/draft/files/09_h2lh_merged.tif/content">09_h2lh_merged.tif</a></li><li>H2L during low flow  = <a href="https://zenodo.org/api/records/10145102/draft/files/11_h2ll_2_merged.tif/content">11_h2ll_2_merged.tif</a></li><li>H2L at the end of drainage (no flow) = <a href="https://zenodo.org/api/records/10145102/draft/files/16_dra1_pd5_merged.tif/content">16_dra1_pd5_merged.tif</a></li><li>H2L at the end of imbibition (no flow) = <a href="https://zenodo.org/api/records/10145102/draft/files/21_imb1_pi1_merged.tif/content">21_imb1_pi1_merged.tif</a></li><li>Sample fully resaturated with brine = <a href="https://zenodo.org/api/records/10145102/draft/files/28_wet2_bin2_merged.tif/content">28_wet2_bin2_merged.tif</a></li><li>L2H during low flow = <a href="https://zenodo.org/api/records/10145102/draft/files/29_2_l2hl_merged.tif/content">29_2_l2hl_merged.tif</a></li><li>L2H during high flow = <a href="https://zenodo.org/api/records/10145102/draft/files/30_l2hh_merged.tif/content">30_l2hh_merged.tif</a></li><li>L2H at the end of drainage (no flow) =<a href="https://zenodo.org/api/records/10145102/draft/files/31_dra2_pd1_merged.tif/content">31_dra2_pd1_merged.tif</a></li><li>L2H at the end of imbibition (no flow)  =<a href="https://zenodo.org/api/records/10145102/draft/files/33_imb2_pi1_merged.tif/content">33_imb2_pi1_merged.tif</a></li></ol>

National-scale tree species/genera map for Poland from Sentinel-2 time series

Map of 16 dominant tree species/genera in Poland based on classification of time series of Sentinel-2 imagery. This dataset is associated with the article by Grabska-Szwagrzyk et al. (2024): <a href="https://essd.copernicus.org/articles/16/2877/2024/">Map of forest tree species for Poland based on Sentinel-2 data.</a> The map is provided as GeoTiff file. In addition, training and test data is provided in shapefile format. The map can be explored online in a <a href="https://ee-aweaksbarg.projects.earthengine.app/view/speciesmappl">webviewer</a>.

A large-scale longitudinal structured dataset of the dark web cryptomarket Evolution (2014–2015)

Data includes a structured dataset of the forum and marketplace of the dark web cryptomarket Evolution as well as a longitudinal network snapshot dataset of a temporal weighted communication network extracted from the forum data. The datasets were extracted from Dark Net Market archive data while resolving many of the data quality issues inherent to raw data scraped from online sources.Dark web cryptomarkets facilitate the online trade of illicit goods. Evolution was active from January 2014 until March 2015; and formed a combination of  a carding forum and an underground drug market. This dataset includes the vast majority of data that could be obtained from the webpages of the forum and marketplace of Evolution. This includes, for example, information on the number of sales each individual vendor has completed, forum post contents, and product categories.The extracted communication network models users' co-posting in the same forum topics, in essence modelling communication between them.Additionally included is the code used to produce the dataset from the Dark Net Market archive data.

Data from: Associations with landscape and local-scale wetland habitat conditions vary among migratory shorebird species during stopovers

Wetlands provide many ecosystem services and functions, including critical stopover habitat for numberous migratory shorbirds species. We conducted shorebird surveys at >14,000 wetlands and associated observed abundance with wetland variables for 16 species. We found that the scale at which observed abundance was associated with wetland extent varied among speceis, and that for most species abundance was positively associated with higher wetland density, presence of shallow water, more usable area, and limited vegetation. There was considerable variation in the strength and sometimes direction of responses. Our study helps inform optimal habitat requirementes for shorebirds.