Find research datasets worth reusing

opencc-by-4.0Mar 2022View details →

Decoding Physical and Cognitive Impacts of Particulate Matter Concentrations at Ultra-fine Scales

Data, plots, and software to accompany (unpublished) paper: Decoding Physical and Cognitive Impacts of Particulate Matter Concentrations at Ultra-fine Scales. This work uses an ultra-fine, holistic environmental and biometric sensing paradigm to generate empirical particulate matter models estimated by biometric variables. GitHub repository: <a href="https://github.com/mi3nts/DUEDARE">https://github.com/mi3nts/DUEDARE</a>

opencc-by-4.0Nov 2021View details →

MODYS-video: 2D Human pose estimation data and Dyskinesia Impairment Scale scores from children and young adults with dyskinetic cerebral palsy

The dataset contains the 2D coordinates in pixels of body landmarks (wrists, ankles, shoulders, hips, knees and ankles) extracted from 188 videos of 34 children with dyskinetic cerebral palsy using DeepLabCut [1] and appertaining clinical scores of the Dyskinesia Impairment Scale (DIS) [2]. The videos were collected during the item “lying in rest” and “sitting in rest” of the DIS at three time points during a clinical trial on the effect of intrathecal baclofen [3]. Children had a mean age of 14y2m (SD 4.0), 26 were male. Their gross motor function classification system level ranged from IV-V and their manual ability classification system level from III-V. Original videos have length of 4-35 seconds with a resolution of 720x575 pixels and are sampled with 25 Hz. We added stick figures to complement the data for context and ease of understanding. They were created from the 2D coordinates that were extracted with a likelihood >0.8. Clinical scoring was performed by three trained experts (according to the DIS) on the original videos. Within the items “lying in rest” and “sitting in rest” the amplitude and duration of dystonia and choreoathetosis of the trunk, proximal right arm, proximal left arm, proximal right leg and proximal left leg are scored on a 0-4 ordinal scale and calculated towards a percentage score between 0-1. The dataset can be used in a machine learning approach to automatically assess dystonia and choreoathetosis of children with dyskinetic cerebral palsy using 2D coordinates of body points extracted from videos.   References: 1. Mathis, A., et al., DeepLabCut: markerless pose estimation of user-defined body parts with deep learning. Nat Neurosci, 2018. 21(9): p. 1281-1289. 2. Monbaliu, E., et al., The dyskinesia Impairment Scale: a new instrument to measure dystonia and choreoathetosis in dyskinetic cerebral palsy. Dev Med Child Neurol, 2012. 54: p. 278-283. 3. Bonouvrie, L.A., et al., The Effect of Intrathecal Baclofen in Dyskinetic Cerebral Palsy: The IDYS Trial. Ann Neurol, 2019. 86: p. 79-90.

opencc-by-4.0Sep 2021View details →

Simulation files to accompany the manuscript "Two-dimensional basin-scale seismic site effects in the Kitimat Valley, British Columbia, Canada: A practical example of using a fast hybrid FE/BE method"

Simulation files to accompany the two-dimensional basin-scale seismic site effects investigation in the Kitimat valley, located in the northern coastal region of British Columbia, Canada.

opencc-by-4.0Sep 2021View details →

Data used in JAMES paper "Sensitivity of the Horizontal Scale of Convective Self‐Aggregation to Sea Surface Temperature in Radiative Convective Equilibrium Experiments Using a Global Nonhydrostatic Model"

Data used in JAMES paper "Sensitivity of the Horizontal Scale of Convective Self‐Aggregation to Sea Surface Temperature in Radiative Convective Equilibrium Experiments Using a Global Nonhydrostatic Model" by Shuhei Matsugishi and Masaki Satoh  doi: 10.1029/2021MS002636

opencc-by-4.0Dec 2021View details →

The scale of a Martian hydrothermal system explored using combined neutron and X-ray tomography

Neutron and X-ray tomography data of MIL 03346,230 and MIL 03346,231   Neutron data was acquired at the Institut Laue-Langevin, https://doi.ill.fr/10.5291/ILL-DATA.UGA-480 79  X-ray data was acquired at the 4D Imaging Lab at Lund University, Sweden

opencc-zeroMar 2022View details →

Ignoring species availability biases occupancy estimates in single-scale occupancy models

1. Most applications of single-scale occupancy models do not differentiate between availability and detectability, even though species availability is rarely equal to one. Species availability can be estimated using multi-scale occupancy models, and the availability process includes elements of species movement, behavior, and phenology. However, for the practical application of multi-scale occupancy models, it can be unclear what a robust sampling design looks like and what the statistical properties of the multi-scale and single-scale occupancy models are when availability is less than one. 2. Using simulations, we explore the following common questions asked by ecologists during the design phase of a field study: (Q1) what is a robust sampling design for the multi-scale occupancy model when there are a priori expectations of parameter estimates?, (Q2) what is a robust sampling design when we have no expectations of parameter estimates?, and (Q3) can a single-scale occupancy model with a random effects term adequately absorb the extra heterogeneity produced when availability is less than one and provide reliable estimates of occupancy probability?. 3. Our results show that there is a tradeoff between the number of sites and surveys needed to achieve a specified level of acceptable error for occupancy estimates using the multi-scale occupancy model. We also document that when species availability is low (< 0.40 on the probability scale), then single-scale occupancy models underestimate occupancy by as much as 0.40 on the probability scale, produce overly precise estimates, and provide poor parameter coverage. This pattern was observed when a random effects term was and was not included in the single-scale occupancy model, suggesting that adding a random-effects term does not adequately absorb the extra heterogeneity produced by the availability process. In contrast, when species availability was high (> 0.60), single-scale occupancy models performed similarly to the multi-scale occupancy model. 4. As a companion, we provide an RShiny app that allows users to further explore our results and sampling designs across a number of different scenarios <a href="https://gdirenzo.shinyapps.io/multi-scale-occ/">https://gdirenzo.shinyapps.io/multi-scale-occ/</a>. Our results suggest that unaccounted for availability can lead to underestimating species distributions when using single-scale occupancy models, which can have large implications on ecological inference and predictions for practitioners, such as those working at the front lines of invasion ecology, disease emergence, and species conservation.

opencc-by-4.0Mar 2022View details →

Datasets for Yue et al. (2022), Atmospheric Measurement Techniques: "Evaluating the Consistency and Continuity of Pixel-Scale Cloud Property Data Records From Aqua and SNPP"

Pixel scaled collocated AIRS, Aqua MODIS, SNPP CrIS, and SNPP VIIRS cloud retrieval products. These datasets are used to generate analyses and results presented in Yue et al. (2022, AMT): "Evaluating the Consistency and Continuity of Pixel-Scale Cloud  Property Data Records From Aqua and SNPP"

opencc-zeroMar 2022View details →

Large-scale fungal strain sequencing unravels the molecular diversity in mating loci maintained by long-term balancing selection

Balancing selection, an evolutionary force that retains genetic diversity, has been detected in multiple genes and organisms, such as the sexual mating loci in fungi. However, to quantify the strength of balancing selection and define the mating-related genes require a large number of strains. In tetrapolar basidiomycete fungi, sexual type is determined by two unlinked loci, MATA and MATB. Genes in both loci define mating type identity, control successful mating and completion of the life cycle. These loci are usually highly diverse. Previous studies have speculated, based on culture crosses, that species of the non-model genus Trichaptum (Hymenochaetales, Basidiomycota) possess a tetrapolar mating system, with multiple alleles. Here, we sequenced a hundred and eighty strains of three Trichaptum species. We characterized the chromosomal location of MATA and MATB, the molecular structure of MAT regions and their allelic richness. The sequencing effort was sufficient to molecularly characterize multiple MAT alleles segregating before the speciation event of Trichaptum species. Analyses suggested that long-term balancing selection has generated trans-species polymorphisms. Mating sequences were classified in different allelic classes based on an amino acid identity (AAI) threshold supported by phylogenetics. 17,550 mating types were predicted based on the allelic classes. In vitro crosses allowed us to support the degree of allelic divergence needed for successful mating. Even with the high amount of divergence, key amino acids in functional domains are conserved. We conclude that the genetic diversity of mating loci in Trichaptum is due to long-term balancing selection, with limited recombination and duplication activity. The large number of sequenced strains highlighted the importance of sequencing multiple individuals from different species to detect the mating-related genes, the mechanisms generating diversity and the evolutionary forces maintaining them.

opencc-by-4.0Mar 2022View details →

Data from: Net plant interactions are highly variable and weakly dependent on climate at the global scale

Data were collected from the literature. The dataset is a compilation of published studies. An ISI Web of Science search covering the time period from 1900 onwards was conducted to identify the publications on plant interactions. Each publication was individually reviewed, and the reference list was inspected to identify additional relevant publications. We collected a total 1,220 publications for data compilation. We built a global dataset of 10,502 pairs of plant interaction data.

Variations of Subgrid-scale Turbulent Fluxes in the Convective Boundary Layer at Gray Zone Resolutions

This dataset contains the data used in the submitted manuscript of Liu and Zhou 2022 JAS. Please refer to the manuscript for the detailed description of the dataset.

Afterslip Model Database RC2022 (Afterslip Moment Scaling and Variability from a Global Compilation of Estimates)

Churchill2022AfterslipDatabase.xlsx is a detailed database of aseismic afterslip models and corresponding mainshock information compiled by Robert Churchill (under the supervision of Maximilian Werner, Juliet Biggs and Åke Fagereng). The database contains afterslip models of mainshocks since 1979, with a publication cut-off at the end of 2018. The database is near complete, but not exhaustive. Descriptions of each column can be found as comments in the header field, as well as in the accompanying paper. Not all fields are not complete, some are also approximate or inferred values. This accompanies the paper: Churchill, R.M., Werner, M.J., Biggs, J. and Fagereng, Å., 2022. Afterslip Moment Scaling and Variability from a Global Compilation of Estimates. Journal of Geophysical Research: Solid Earth, p.e2021JB023897. <a href="https://doi.org/10.1029/2021JB023897">https://doi.org/10.1029/2021JB023897</a>. We hope the database serves as a useful resource to the afterslip community. Please reference our associated paper when using this database, as well as the database itself. References for individual afterslip papers can be found on the second sheet of the database, and references for additional data used in our study can be found in the third sheet. In the future, the database may be updated to include additional (missed) studies, however, this first version accompanies our study. *Headers for columns U and V are mislabelled Afterslip Upper Depth Limit (km) and Afterslip Lower Depth Limit (km), when these should be Coseismic Slip Upper Depth Limit (km) and Coseismic Slip Lower Depth Limit (km). The data in these columns is otherwise correct.

Data from: Scaling and relations of morphology with locomotor kinematics in the sidewinder rattlesnake Crotalus cerastes

The movement of limbless terrestrial animals differs fundamentally from that of limbed animals, yet few scaling studies of their locomotor kinematics and morphology are available. We examined scaling and relations of morphology and locomotion in sidewinder rattlesnakes (Crotalus cerastes). During sidewinding locomotion, a snake lifts sections of its body up and forward while other sections maintain static ground contact. We used high-speed video to quantify whole-animal speed and acceleration; the height to which body sections are lifted; and the frequency, wavelength, amplitude, and skew angle (degree of tilting) of the body wave. Kinematic variables were not sexually dimorphic, and most did not deviate from isometry, except wave amplitude. Larger sidewinders were not faster, contrary to many results from limbed terrestrial animals. Free from the need to maintain dynamic similarity (because their locomotion is dominated by friction rather than inertia), limbless species may have greater freedom to modulate speed independently of body size. Path analysis supported: (1) a hypothesized relationship between body width and wavelength, indicating that stouter sidewinders form looser curves; (2) a strong relationship between cycle frequency and whole-animal speed; and (3) weaker effects of wavelength (positive) and amplitude (negative) on speed. We suggest that sidewinding snakes may face a limit on stride length (to which amplitude and wavelength both contribute), beyond which they sacrifice stability. Thus, increasing frequency may be the best way to increase speed. Finally, frequency and skew angle were correlated, a result that deserves future study from the standpoint of both kinematics and physiology.

opencc-by-4.0Jun 2021View details →

Large Scale Volcanism and the heat-death of terrestrial worlds

The files herein are used to generate the main and SI figures in the GRL paper: Title: Large Scale Volcanism and the heat-death of terrestrial worlds Authors: M.J. Way, Richard E. Ernst, Jeffrey D. Scargle The data are derived from an Excel formatted table: WAY2021-TableS1.xlsx

Data from: Do metal mines and their runoff affect plumage color? A regional scale study of streak-backed orioles in south-central Mexico

Metal mining causes serious ecological disturbance, due partly to heavy metal (HM) pollution that can accumulate at mining sites themselves and be dispersed downstream as runoff. Plumage coloration is important in birds' social and ecological interactions and sensitive to environmental stressors, and several local-scale studies have found decreased carotenoid-based plumage and/or increased melanin-based plumage in wild birds exposed to HM pollution. We investigated regional-scale effects of proximity to mines and their downstream rivers as a proxy of exposure to HM-contaminated mining waste on plumage coloration in streak-backed orioles (Icterus pustulatus) in south-central Mexico. We measured the plumage color of museum skins using reflectance spectrometry and digital photography, then used geographic information systems to estimate each specimen's distance from the nearest mining concession and river and determine whether that river's watershed contained mines. Proximity to mines and their downstream rivers was related to ventral (but not dorsal) carotenoid-based coloration; birds collected farther from mines had more vivid yellow-orange breast plumage, and belly plumage was more vivid and redder with increasing distance from rivers with upstream mines. Breast background reflectance unexpectedly decreased with mine distance and was higher among birds whose nearest river had mines upstream. The area (but not reflectance) of melanin-based plumage was also related to mines. The area of dark back streaks decreased with mine distance, while the bib patch was smaller among birds presumably more exposed to mining waste. While some of these results are consistent with predicted effects of HM pollution on plumage, most were not straightforward, and effects differed among plumage patches and variables. Further investigation is needed to understand the direct (e.g., toxicity, oxidative stress) and/or indirect (e.g., decreased availability of carotenoid-rich food) mechanisms responsible and their individual, population, and community-level implications.

Modeled data related to the article "Diffusive Wave Models for Operational Forecasting of Channel Routing at Continental Scale"

The data holder contains modeled data on water level and discharge from some test cases.

Trends in functional composition of small mammal communities across millennial time scales

Rich fossil deposits of the late Quaternary help us understand responses of biodiversity to global change and thus predict the future of ecosystems. Studies from the late Quaternary, however, are often limited taxonomically, geographically (often one site), and by their use of largely taxon-based metrics that do not inform about ecosystem-level consequences of biodiversity change. Here, we compare change in functional composition of small mammal communities at El Mirón Cave (Spain) and Samwell Cave (California, USA) across the last 22,000 years, and examine their relationships with climate and vegetation. We find opposing temporal trends between the two locations. European small mammal communities occupied increasingly greater trait space, driven by increases in arboreal granivory and frugivory as ground-dwelling herbivory declined toward the late Holocene. North American communities occupied smaller trait space as ground-level foraging and insectivory increased and arboreal herbivory and mean body mass declined. Our results point to the importance of the interaction between climate change and vegetation shifts for explaining changes in small mammal functional diversity, through their synergistic impacts on individual traits. Specifically, increasing temperature across both continents likely led to increases in nocturnal activity and declines in assemblage mean body mass, while transition to mixed forest (El Mirón) or open woodland (Samwell) resulted in increasing structural complexity of vegetation that potentially supported more diverse community-level dietary characteristics. These results demonstrate the ability of a trait-based approach to identify how environmental variables correlate with changes in community functional composition through time and gain insight into the potential consequences of environmental change for ecosystem functioning.

Improving landscape-scale productivity estimates by integrating trait-based models and remotely-sensed foliar-trait and canopy-structural data

Assessing the impacts of anthropogenic degradation and climate change on global carbon cycling is hindered by a lack of clear, flexible, and easy-to-use productivity models along with scarce trait and productivity data for parameterizing and testing those models. We provide a simple solution: a mechanistic framework (RS-CFM) that combines remotely-sensed foliar-trait and canopy-structural data with trait-based metabolic theory to efficiently map productivity at large spatial scales. We test this framework by quantifying net primary productivity (NPP) at high-resolution (0.01-ha) in hyper-diverse Peruvian tropical forests (30,040 hectares) along a 3,322-m elevation gradient. Our analysis captures hotspots and elevational shifts in productivity more accurately and in greater detail than alternative empirical- and process-based models that use plant functional types. This result exposes how high-resolution, location-specific variation in traits and light competition drive variability in productivity, opening up possibilities to fully harness remote sensing data and reliably scale up from traits to map global productivity in a more direct, efficient, and cost-effective manner.

Case study data of the paper: A methodological guide to observe local-scale geodiversity for biodiversity research and management

Current global environmental change calls for comprehensive and complementing approaches for biodiversity conservation. According to recent research, consideration of the diversity of Earth's abiotic features (i.e., geodiversity) could provide new insights and applications into the investigation and management of biodiversity. However, methods to map and quantify geodiversity at local scale have not been developed although this scale is important for conservation planning. Here, we introduce a field methodology for observing plot-scale geodiversity, pilot the method in an Arctic-alpine tundra environment, provide empirical evidence on the plot-scale biodiversity-geodiversity relationship and give guidance for practitioners on the implementation of the method. The field method is based on observation of geofeatures, i.e., elements of geology, geomorphology, and hydrology, from a given area surrounding a location of species observations. As a result, the method provides novel information on the variation of abiotic nature for biodiversity research and management. The method was piloted in northern Norway and Finland by observing geofeatures from 76 sites at three scales (5, 10 and 25 m radii). To explore the relationship between measures of biodiversity and geodiversity, the occurrence of vascular plant species was recorded from 2 m x 2 m plots at the same sites. According to the results, vascular plant species richness was positively correlated with the richness of geofeatures (Rs = 0.18–0.59). The connection was strongest in habitats characterized by deciduous shrubs. The method has a high potential for observing geofeatures without extensive geological or geomorphological training or field survey experience and could be applied by conservation practitioners. Consideration of geodiversity in understanding, analysing and conserving biodiversity could facilitate environmental management and ensure the long-term sustainability of ecosystem functions. With the developed method, it is possible to cost-efficiently observe the elements of geodiversity that are useful in ecology and biodiversity conservation. Our approach can be adapted in different ecosystems and biodiversity investigations. The method can be adjusted depending on the abiotic conditions, expertise of the observer(s), and the equipment available.

Urban Stream Environmental and Sequencing Datasets for Exploring the Impacts of Full-Scale Distribution System Orthophosphate Corrosion Control Implementation on the Microbial Ecology of Hydrologically Connected Urban Streams

The dataset of environmental parameters and sequence fastqs used to create figures and do analysis in the paper Exploring the Impacts of Full-Scale Distribution System Orthophosphate Corrosion Control Implementation on the Microbial Ecology of Hydrologically Connected Urban Streams submitted to Applied and Environmental Microbiology.

Data from: Repeatability of adaptive radiation depends on spatial scale: regional versus global replicates of stickleback in lake versus stream habitats

The repeatability of adaptive radiation is expected to be scale dependent, with determinism decreasing as greater spatial separation among "replicates" leads to their increased genetic and ecological independence. Threespine stickleback (Gasterosteus aculeatus) provide an opportunity to test whether this expectation holds for the early stages of adaptive radiation -their diversification in freshwater ecosystems has been replicated many times. To better understand the repeatability of that adaptive radiation, we examined the influence of geographic scale on levels of parallel evolution by quantifying phenotypic and genetic divergence between lake and stream stickleback pairs sampled at regional (Vancouver Island) and global (North America and Europe) scales. We measured phenotypes known to show lake-stream divergence and used reduced representation genome-wide sequencing to estimate genetic divergence. We assessed the scale-dependence of parallel evolution by comparing effect sizes from multivariate models and also the direction and magnitude of lake-stream divergence vectors. At the phenotypic level, parallelism was greater at the regional than the global scale. At the genetic level, putative selected loci showed greater lake-stream parallelism at the regional than the global scale. Generally, the level of parallel evolution was low at both scales, except for some key univariate traits. Divergence vectors were often orthogonal, highlighting possible ecological and genetic constraints on parallel evolution at both scales. Overall, our results confirm that the repeatability of adaptive radiation decreases at increasing spatial scales. We suggest that greater environmental heterogeneity at larger scales imposes different selection regimes, thus generating lower repeatability of adaptive radiation at larger spatial scales.