Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
465
datasets available to search
ShareScore release 0.9.0
Dataset results
465 results for “energetics”
Data from: Estimation of energetic condition in wild baboons using fecal thyroid hormone determination
Understanding how environmental and social factors affect reproduction through variation in energetic condition remains understudied in wild animals, in large part because accurately and repeatedly measuring energetic condition in the wild is a challenge. Thyroid hormones (THs), such as triiodothyronine (T3) and thyroxine (T4), have a key role in mitigating metabolic responses to energy intake and expenditure, and therefore are considered important biomarkers of an animal's energetic condition. Recent method development has shown that T3 and T4 metabolites can be measured in feces, but studies measuring THs in wild populations remain rare. Here we measured fecal T3 metabolites (mT3) in baboons, and tested whether the conditions of collection and storage used for steroid hormones could also be used for mT3; we focused on mT3 as it is the biologically active form of TH and because fecal T4 metabolites (mT4) were below detection levels in our samples. We also tested if mT3 could be determined in freeze-dried samples stored for long periods of time, and if these concentrations reflected expected biological variations across seasons and reproductive states. Our results show that mT3 can be measured with accuracy and precision in baboon feces. The conditions of collection and storage we use for steroid hormones are appropriate for mT3 determination. In addition, mT3 concentrations can be determined in samples stored at -20 °C for up to 9 years, and are not predicted by the amount of time in storage. As expected, wild female baboons have lower mT3 concentrations during the dry season. Interestingly, mT3 concentrations are lower in pregnant and lactating females, possibly reflecting an energy sparing mechanism. Retroactive determination of mT3 concentration in stored, freeze-dried feces opens the door to novel studies on the role of energetic condition on fitness in wild animals.
Metabolic rate in common shrews is unaffected by seasonal temperature, leading to reduction of energetic costs through size reduction
<p>Small endothermic mammals have high metabolisms, particularly at cold temperatures. In light of this, some species have evolved a seemingly illogical strategy: they reduce the size of the brain and several organs to become even smaller in winter. To test how this morphological strategy affects energy consumption across seasonally shifting ambient temperatures, we measured oxygen consumption and behaviour in the three seasonal phenotypes of the common shrew (<i>Sorex araneus</i>), which differ in size by about 20%. Body mass was the main driver of oxygen consumption, not the reduction of metabolically expensive brain mass. Against our expectations, we found no change in relative oxygen consumption with low ambient temperature. Thus, smaller body size in winter resulted in significant absolute energy savings. This could only partly be explained by a change in activity budgets. Our findings highlight that these shrews manage to avoid one of the most fundamental and intuitive rules of ecology allowing them to subsist with lower resource availability and successfully survive the harsh conditions of winter.</p>
Data from: Context-dependent scaling of kinematics and energetics during contests and feeding in mantis shrimp
Measurements of energy use, and its scaling with size, are critical to understanding how organisms accomplish myriad tasks. For example, energy budgets are central to game theory models of assessment during contests and underlie patterns of feeding behavior. Clear tests connecting energy to behavioral theory require measurements of the energy use of single individuals for particular behaviors. Many species of mantis shrimp (Stomatopoda: Crustacea) use elastic energy storage to power high-speed strikes that they deliver to opponents during territorial contests and to hard-shelled prey while feeding. We compared the scaling of strike kinematics and energetics between feeding and contests in the mantis shrimp Neogonodactylus bredini. We filmed strikes with high-speed video, measured strike velocity, and used a mathematical model to calculate strike energy. During contests, strike velocity did not scale with body size but strike energy scaled positively with size. Conversely, while feeding, strike velocity decreased with increasing size and strike energy did not vary according to body size. Individuals most likely achieved this strike variation through differential compression of their exoskeletal spring prior to the strike. Post-hoc analyses found that N. bredini used greater velocity and energy when striking larger opponents, yet variation in prey size was not accompanied by varying strike velocity or energetics. Our estimates of energetics inform prior tests of contest and feeding behavior in this species. More broadly, our findings elucidate the role behavioral context plays in measurements of animal performance.
Data from: Energetic fitness: field metabolic rates assessed via 3D accelerometry complement conventional fitness metrics
1) Evaluating the fitness of organisms is an essential step towards understanding their responses to environmental change. Connections between energy expenditure and fitness have been postulated for nearly a century. However, testing this premise among wild animals is constrained by difficulties in measuring energy expenditure while simultaneously monitoring conventional fitness metrics such as survival and reproductive output. 2) We addressed this issue by exploring the functional links between field metabolic rate (FMR), body condition, sex, age and reproductive performance in a wild population. 3) We deployed 3D accelerometers on 115 Adélie penguins (Pygoscelis adeliae) during four breeding seasons at one of the largest colonies of this species, Cape Crozier, on Ross Island, Antarctica. The demography of this population has been studied for the past 18 years. From accelerometry recordings, collected for birds of known age and breeding history, we determined the vector of the dynamic body acceleration (VeDBA) and used it as a proxy for FMR. 4) This allowed us to demonstrate relationships between FMR, a breeding quality index (BQI), and body condition. Notably, we found a significant quadratic relationship between mean VeDBA during foraging and BQI for experienced breeders, and individuals in better body condition showed lower rates of energy expenditure. 5) We conclude that using FMR as a fitness component complementary to more conventional fitness metrics will yield greater understanding of evolutionary and conservation physiology.
Data from: Residential development alters behavior, movement, and energetics in an apex predator, the puma
Human development strongly influences large carnivore survival and persistence globally. Behavior changes are often the first measureable responses to human disturbances, and can have ramifications on animal populations and ecological communities. We investigated how a large carnivore responds to anthropogenic disturbances by measuring activity, movement behavior, and energetics in pumas along a housing density gradient. We used log-linear analyses to examine how habitat, time of day, and proximity to housing influenced the activity patterns of both male and female pumas in the Santa Cruz Mountains. We used spatial GPS location data in combination with Overall Dynamic Body Acceleration measurements recorded by onboard accelerometers to quantify how development density affected the average distances traveled and energy expended by pumas. Pumas responded to development differently depending on the time of day; at night, they were generally more active and moved further when they were in developed areas, but these relationships were not consistent during the day. Higher nighttime activity in developed areas increased daily caloric expenditure by 10.1% for females and 11.6% for males, resulting in increases of 3.4 and 4.0 deer prey required annually by females and males respectively. Our results support that pumas have higher energetic costs and resource requirements in human-dominated habitats due to human-induced behavioral change. Increased energetic costs for pumas are likely to have ramifications on prey species and exacerbate human-wildlife conflict, especially as exurban growth continues. Future conservation work should consider the consequences of behavioral shifts on animal energetics, individual fitness, and population viability.
Data from: Protection promotes energetically efficient structures in marine communities
<p>The sustainability of marine communities is critical for supporting many biophysical processes that provide ecosystem services that promote human well-being. It is expected that anthropogenic disturbances such as climate change and human activities will tend to create less energetically-efficient ecosystems that support less biomass per unit energy flow. It is debated, however, whether this expected development should translate into bottom-heavy (with small basal species being the most abundant) or top-heavy communities (where more biomass is supported at higher trophic levels with species having larger body sizes). Here, we combine ecological theory and empirical data to demonstrate that full marine protection promotes shifts towards top-heavy energetically-efficient structures in marine communities. First, we use metabolic scaling theory to show that protected communities are expected to display stronger top-heavy structures than disturbed communities. Similarly, we show theoretically that communities with high energy transfer efficiency display stronger top-heavy structures than communities with low transfer efficiency. Next, we use empirical structures observed within fully protected marine areas compared to disturbed areas that vary in stress from thermal events and adjacent human activity. Using a nonparametric causal-inference analysis, we find a strong, positive, causal effect between full marine protection and stronger top-heavy structures. Our work corroborates ecological theory on community development and provides a quantitative framework to study the potential restorative effects of different candidate strategies on protected areas.</p>
Body-size dependent effects of landscape-level resource energetics on pollinator abundance in woodland remnants
<p><span>Land use change reduces floral resource availability, thereby driving declines in important pollinators. However, the severity of land use impact varies by species, influenced by factors such as dispersal ability and resource specialization, both of which can correlate with body size. Here we test whether floral resource availability in the surrounding landscape (the 'matrix') influences bee species' abundance in isolated remnant woodlands, and whether this effect varies with body size. We sampled quantitative flower-visitation networks within woodland remnants and quantified floral energy resources (calories) available to each bee species both within woodland and the matrix. Bee abundance in woodland increased with floral energy resources in the surrounding matrix, with strongest effects on larger-bodied species. Our findings suggest important but size-dependent effects of declining matrix floral resources on the persistence of bees in remnant woodlands, highlighting the need to incorporate landscape-level floral resources in conservation planning for pollinators in threatened natural habitats. </span></p>
Data from: Quantifying a light-induced energetic change in bacteriorhodopsin by force spectroscopy
<p>Ligand-induced conformational changes are critical to the function of many membrane proteins and arise from numerous intramolecular interactions. In the photocycle of the model membrane protein bacteriorhodopsin (bR), absorption of a photon by retinal triggers a conformational cascade that results in pumping a proton across the cell membrane. While decades of spectroscopy and structural studies have probed this photocycle in intricate detail, changes in intramolecular energetics that underlie protein motions have remained elusive to experimental quantification. Here, we measured these energetics on the millisecond time scale using atomic-force-microscopy–based single-molecule force spectroscopy. Precisely timed light pulses triggered the bR photocycle while we measured the equilibrium unfolding and refolding of the terminal 8-amino-acid region of bR's G-helix. These dynamics changed when the EF-helix pair moved ~9 Å away from this end of the G helix during the "open" portion of bR's photocycle. In ~60% of the data, we observed abrupt light-induced destabilization of 3.4 ± 0.3 kcal/mol, lasting 38 ± 3 ms. The kinetics and pH-dependence of this destabilization were consistent with prior measurements of bR's open phase. The frequency of light-induced destabilization increased with the duration of illumination and was dramatically reduced in the triple mutant (D96G/F171C/F219L) thought to trap bR in its open phase. In the other ~40% of the data, photoexcitation unexpectedly stabilized a longer-lived putative misfolded state. Through this work, we establish a general single-molecule force spectroscopy approach for measuring ligand-induced energetics and lifetimes in membrane proteins.</p>
Data set related to the manuscript "Dynamics and energetics of ion adsorption at the interface between a pure ionic liquid and carbon electrodes"
<p>Text files with data for plotting figures in the quoted manuscript. Example input files for simulations.</p>
SpacePy Cusp Energetic Particle example data
<p>This dataset accompanies the Cusp Energetic Particles tutorial found at <a href="https://github.com/spacepy/examples">https://github.com/spacepy/examples</a></p> <p>It incorporates intermediate products used in the analysis of Niehof et al (2012), <a href="https://doi.org/10.5194/angeo-30-1633-2012">doi:10.5194/angeo-30-1633-2012</a> and a form of the one-minute Dst index from Gannon and Love (2011), <a href="https://doi.org/10.1016/j.jastp.2010.02.013">doi:10.1016/j.jastp.2010.02.013</a> .</p>
The Seasonal Variability in the Semidiurnal Internal Tide; A Comparison between Sea Surface Height and Energetics
<p>This dataset contains data from global HYCOM simulations with realistic atmospheric and tidal forcings. The horizontal resolution is 8 km. Data is stored as netcdf4 classic.</p>
CNN-Based Forecasting of Pitch Angle-Resolved Energetic Electron Flux at MEO Using Solar Wind and Geomagnetic Data
<div> <p> CNN-Based Forecasting of Pitch Angle-Resolved Energetic Electron Flux at MEO Using Solar Wind and Geomagnetic Data. The model and test set data are provided here. Data used for training, validating, and testing the 1.8MeV channel model is also offered as an example.</p> </div> <p><strong>initial_data: </strong>The test set data has been normalized and can be used as model input.</p> <p><strong>norm para: </strong>The normalization parameters used for data processing</p> <p><strong>model_test_dataset_performance.py: </strong>The script to obtain the outputs of the models at different energy levels on the test set. Before running it, unzip “initial_data.rar” and "norm_para.rar"</p> <p><strong>full_dataset_for_rept_ch0: </strong>Data used for training, validating, and testing the 1.8MeV channel model. It's not essential for model_test_dataset_performance.py</p>
A Test of Energetic Particle Precipitation Models Using Simultaneous Incoherent Scatter Radar and Van Allen Probes Observations
<p>BERI modeling reuslts for "A Test of Energetic Particle Precipitation Models Using Simultaneous Incoherent Scatter Radar and Van Allen Probes Observations"</p>
E-scape: consumer-specific landscapes of energetic resources derived from stable isotope analysis and remote sensing
<p>Energetic resources and habitat distribution are inherently linked. Energetic resource availability is a major driver of the distribution of consumers, but estimating how much specific habitats contribute to the energetic resource needs of a consumer can be problematic.</p> <p>We present a new approach that combines remote sensing information and stable isotope ecology to produce maps of energetic resources (<i>E</i>-scapes). <i>E</i>-scapes project species-specific resource use information onto the landscape to classify areas based on energetic importance.</p> <p>Using our <i>E</i>-scapes, we investigated the relationship between energetic resource distribution and white shrimp distribution and how the scale used to generate the <i>E</i>-scape mediated this relationship.</p> <p><i>E</i>-scapes successfully predicted the size, abundance, biomass, and total energy of a consumer in salt marsh habitats in coastal Louisiana, USA at scales relevant to the movement of the consumer.</p> <p>Our <i>E</i>-scape maps can be used alone or in combination with existing models to improve habitat management and restoration practices and have potential to be used to test fundamental movement theory. </p>
Data, code, and metadata for: Daily torpor reduces the energetic consequences of microhabitat selection for a widespread bat
<p>This repository contains all data, code, and metadata required to reproduce the results detailed in "Daily torpor reduces the energetic consequences of microhabitat selection for a widespread bat" by Alston et al.</p>
Data for the article entitled "ENVIRONMENTAL AND SOCIAL CORRELATES, AND ENERGETIC CONSEQUENCES OF FITNESS MAXIMISATION ON DIFFERENT MIGRATORY BEHAVIOURS IN A LONG-LIVED SCAVENGER"
<p>Data used in the statistical analyses of the article entitled "ENVIRONMENTAL AND SOCIAL CORRELATES, AND ENERGETIC CONSEQUENCES OF FITNESS MAXIMISATION ON DIFFERENT MIGRATORY BEHAVIOURS IN A LONG-LIVED SCAVENGER"</p>
Magnetic Field Disorder May Explain Energetic Proton Diffusion through Heliosheath Plasma: Evidence from Voyager 2 Observations
<p>The spreadsheets of monthly data used for Figure 2 in the paper " <strong>Magnetic Field Disorder May Explain Energetic Proton Diffusion through Heliosheath Plasma: Evidence from Voyager 2 Observations</strong>" submitted to Geophysical Research Letters by the authors, and an explanatory text file named "Readme".</p>
Effect of density gradients on the generation of a highly energetic and strongly collimated proton beam from a laser irradiated Gaussian-shaped Hydrogen microsphere
<p>Simulation input files and data sets of "Effect of density gradients on the generation of a highly energetic and strongly collimated proton beam from a laser irradiated Gaussian-shaped Hydrogen microsphere" by A. Bhagawati et al.</p> <p>Simulation code: </p> <p>Picpsi3D, Version 0.1 beta 11<br> (c) Copyright Kartik Patel, L & PTD, BARC<br> </p>
Energetic constraints on body-size niches in a resource-limited marine environment
<p><span>Body size of life on Earth spans many orders of magnitude, and with it scales the energetic requirements of organisms. Thus, changes in environmental energy should impact community body-size distributions in predictable ways by reshaping ecological and niche dynamics. We examine how carbon, oxygen, and temperature, three energetic drivers, impact community size-based assembly in deep-sea bivalves. We demonstrate that body-size distributions are influenced by multiple energetic constraints. Relaxation in these constraints leads to an expansion of body-size niche space through the addition of novel large size classes, increasing the standard deviation and mean of the body-size distribution. With continued Anthropogenic increases in temperature and reductions in carbon availability and oxygen in most ocean basins, our results point to possible radical shifts in invertebrate body size with the potential to impact ecosystem function.</span></p>
Data and plotting code for "Energetic electron scattering by kinetic Alfvén waves at strong magnetic field gradients of dipolarization front"
<p>This publication includes the dataset and plotting code for reproducing results and figures of the manuscript "Energetic electron scattering by kinetic Alfvén waves at strong magnetic field gradients of dipolarization front", which was submitted to Physics of Plasma for potential publication. In this paper, we use test particle simulations to study energetic electron pitch angle and momentum scattering driven by kinetic Alfvén waves, at the magnetic field gradients associated with the dipolarization front, current sheet and plasma sheet fields in the magnetotail. </p> <p>The simulation data contains time history of 1000 test particle trajectories, momentum, energy, and KAW wave phases recorded every 0.001 second. Each simulation for different electron energies and pitch angles has a size of over 1 GB, so here we have only included one example of test particle simulation run associated with Figure 3. Only the final results of pitch angle diffusion coefficients are provided associated with Figure 4. A full set of time history results of all test particle simulation runs for Figure 4 will be available upon reasonable request (yshen@epss.ucla.edu). </p> <p>Detailed descriptions:</p> <p> PoP_figure_1.m --- Matlab plotting code for reproducing magnetic field model and geometry for Figure 1.</p> <p> PoP_figure_2.m --- Matlab plotting code for reproducing resonant energy as a function of wave normal angle, electron pitch angle, and field model parameters in Figure 2.</p> <p> PoP_figure_3.m --- Reading test particle simulation data and plotting code for reproducing Figure 3. Please ensure proper directory setting to read test particle data files. </p> <p> PoP_figure_4_5.m --- Reading saved bounce-averaged diffusion coefficient data and plotting Figure 4 and Figure 5.</p> <p> Daa_Energy_alpha_ad3xp15_e1.csv --- Electron diffusion coefficients driven by KAW scattering as a function of energy and pitch angle obtained from test particle simulations. KAW wave amplitude is set to 1 mV/m. Electrons are initiated from a position of x=150 km within the dipolarization front.</p> <p> Tau_Energy_alpha_xp15.csv --- Electron bounce periods as a function of energy and pitch angle based on numerical test particle simulations without KAW input.</p> <p> pKAW_1000p_dify_E100keV_PA5_Daa_E4_pop.zip --- Data files containing 1000 test particle trajectories, momentum and adiabatic invariant. This one single run is for electrons with an energy of 100 keV and a pitch angle of 5 degree, under influence of KAW wave electric field of 4 mV/m. This dataset is used to plot Figure 3. </p> <p> pKAW_1000p_dify_init_Ppara_mue_E100_PA4_Daa_E4_pop.dat --- initial parallel momentum and first adiabatic invariant of 1000 test particles. Read this file for plotting Figure 3. </p> <p> Bxyz.m --- calculate model magnetic field for given positions in x, y, and z</p> <p> FAC.m --- convert local x, y, z coordinates to field-aligned coordinates</p> <p> gradB.m --- calculate the gradient of magnetic field for given positions in x, y, and z</p> <p> E_to_pnorm_hsr.m --- calculate normalized momentum based on relativistic electron energy</p> <p> mysubplot.m --- plotting function to replace subplot routine of Matlab</p> <p> </p> <p> </p>
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.