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465 results for “energetics”
Energetic mismatch induced by warming decreases leaf litter decomposition by aquatic detritivores
<p>1. The balance of energetic losses and gains is of paramount importance for understanding and predicting the persistence of populations and ecosystem processes in a rapidly changing world. Previous studies suggested that metabolic rate often increases faster with warming than resource ingestion rate, leading to an energetic mismatch at high temperature. However, little is known about the ecological consequences of this energetic mismatch for population demography and ecosystem functions.</p> <p>2. Here, we combined laboratory experiments and modeling to investigate the energetic balance of a stream detritivore (Gammarus fossarum) along a temperature gradient and the consequences for detritivore populations and organic matter decomposition.</p> <p>3. We experimentally measured the energetic losses (metabolic rate) and supplies (ingestion rate) of Gammarus and we modeled the impact of rising temperatures and changes in Gammarus body size induced by warming on population dynamics and benthic organic matter dynamics in freshwater systems.</p> <p>4. Our experimental results indicated an energetic mismatch in a Gammarus population where losses via metabolic rate increase faster than supplies via food ingestion with warming, which translated in a decrease of energetic efficiency with temperature rising from 5 to 20 °C. Moreover, our consumer-resource model predicts a decrease in the biomass of Gammarus population with warming, associated with lower maximum abundances and steeper abundance decreases after biomass annual peaks. These changes resulted in a decrease of leaf litter decomposition rate and thus longer persistence of leaf litter standing stock over years in the simulations. In addition, Gammarus body size reductions led to shorter persistence for both leaf litter and Gammarus biomasses at low temperature and the opposite trend at high temperature, revealing that body size reduction was weakening the effect of temperature on resource and consumer persistence.</p> <p>5. Our model contributes to identifying the mechanisms that explain how thermal effects at the level of individuals may cascade through trophic interactions and influence important ecosystem processes. Considering the balance of physiological processes is crucial to improve our ability to predict the impact of climate change on carbon stocks and ecosystem functions.</p>
Why bears hibernate? Redefining the scaling energetics of hibernation
<p><span>Hibernation is a natural state of suspended animation that many mammals experience and has been interpreted as an adaptive strategy for saving energy. However, the actual amount of savings that hibernation represents, and particularly its dependence on body mass (the "scaling") has not been calculated properly. Here we estimated the scaling of daily energy expenditure of hibernation (DEE<sub>H</sub>), covering a range of five orders of magnitude in mass. We found that DEE<sub>H</sub> scales isometrically with mass, which means that a gram of hibernating bat has a similar metabolism to that of a gram of bear, 20,000 times larger. Given that the metabolic rate of active animals scales allometrically, the point where these scaling curves intersect with DEE<sub>H</sub> represents the mass where energy savings by hibernation are zero. For BMR, these zero savings are attained for a relatively small bear (~100 kg). Calculated on a per-cell basis, the cellular metabolic power of hibernation was estimated to be 1.3x10<sup>-12</sup> ± 2.6x10<sup>-13</sup> W/cell, which is lower than the minimum metabolism of isolated mammalian cells. This supports the idea of the existence of a minimum metabolism that permits cells to survive under a combination of cold and hypoxia.</span></p>
Influence of Titan's Variable Electromagnetic Environment on the Global Distribution of Energetic Neutral Atoms
<p>Data for the manuscript "Influence of Titan's Variable Electromagnetic Environment on the Global Distribution of Energetic Neutral Atoms" by Tippens et al., (2022). See README.txt for a description of the data files included here.</p>
Data from: Individual energetics scale up to community coexistence: Movement, metabolism and biodiversity dynamics in fragmented landscapes
<p>Unraveling the intricate mechanisms that govern community coexistence remains a daunting challenge, particularly amidst ongoing environmental change. To understand the response of individual animals to environmental change, physiology and individual metabolism are often studied. However, this perspective is currently largely lacking in community ecology. We argue that the integration of individual metabolism into community theory can offer new insights into coexistence. We present the first individual-based metabolic community model for a terrestrial mammal community to simulate energy dynamics and home range behavior in different environments. Using this model, we investigate how ecologically similar species coexist and maintain their energy balance under food competition. Only if individuals of different species are able to balance their incoming and outgoing energy over the long-term will they be able to coexist. After thoroughly testing and validating the model against real-world patterns such as of home range dynamics and field metabolic rates, we applied it as a case study to scenarios of habitat fragmentation - a widely discussed topic in biodiversity research. First, comparing single-species simulations with community simulations, we find that the effect of habitat fragmentation on populations is strongly context-dependent. While populations of species living alone in the landscape were mostly positively affected by fragmentation, the diversity of a community of species was highest under medium fragmentation scenarios. Under medium fragmentation, energy balance and reproductive investment were also most similar among species. We therefore suggest that similarity in energy balance among species promotes coexistence. We argue that energetics should be part of community ecology theory, as the relative energetic status and reproductive investment can reveal why and under what environmental conditions coexistence is likely to occur. As a result, landscapes can potentially be protected and designed to maximize coexistence. The metabolic community model presented here can be a promising tool to investigate other scenarios of environmental change or other species communities to further disentangle global change effects and preserve biodiversity.</p>
SERPENTINE catalog of solar energetic particle events observed by Helios
<p>This catalog contains multi-spacecraft solar energetic particle (SEP) events, which were observed by Helios. It has been created within the European Union’s Horizon 2020 project <em>SERPENTINE</em> (Solar energetic particle analysis platform for the inner heliosphere). This catalogue is based on data from the Helios mission provided by the previous European project <a href="https://sepserver.eu/index.php?page=catalogue">SEPServer</a>. In addition, technical reports of the University of Kiel from the time of Helios observation (printed version) were used, but the final judgement was done on the basis of the data from SEPServer.</p> <div> <p>It is not the first time that data from this historical mission are included in a statistical study. In Lario et al., 2006 (<a href="https://doi.org/10.1086/508982">https://doi.org/10.1086/508982</a>) some events observed by two or more spacecraft were analyzed from the point of view of their longitudinal and radial spread. The events where protons with energies above 13 MeV were observed by the Helios spacecraft when they were located at less than ~0.85 AU from the Sun were in the focus of the ESA SOL2UP project (for details see Pacheco, 2019, PhD Thesis, <a href="http://hdl.handle.net/10803/667033">http://hdl.handle.net/10803/667033</a>). The events from our catalogue which overlap with these previous studies are marked by letters L or P, correspondingly. At the same time, the data related to the overlapping events (same as for all other events), either characterizing the solar source, location of the observer (spacecraft) or relating to the properties of the particle fluxes were identified independently for the present catalogue. Nevertheless, we would like to acknowledge the authors of the previous SOL2UP project for providing us with the results of their studies.</p> <p>In the majority of the cases the identification of the location of the solar source was based on the available X-ray data of the related solar flare, published in (<a href="https://www.ngdc.noaa.gov">Solar Geophysical Data</a>). In addition, we used information from a previous study of Helios events (Kallenrode 1997, private communication), marked with the “K” sign. The radial distance of the spacecraft from the Sun, the solar wind speed and the Earth-Sun-spacecraft angle were taken from (<a href="https://cdaweb.gsfc.nasa.gov">CDAweb</a>). If there were no data for the solar wind speed during the time of the event, a standard value of 400 km/s was used (in the list itself and in the calculation of the longitude of the magnetic footpoint of the spacecraft). If there was, e.g., a high speed stream of the solar wind close to the time of the event then the average value of the solar wind stream was used. In both cases we used the “~” sign to denote such uncertainties. The location of the footpoint of the spacecraft of the solar disc was obtained by using a simple ballistic back mapping. The proton onset times are based on the SEPServer data.</p> <p> </p> </div> <p>The csv files provided here are archived versions of the <strong>dynamic catalog available at <a href="https://data.serpentine-h2020.eu/catalogs/sep-helios/">https://data.serpentine-h2020.eu/catalogs/sep-helios/</a></strong></p> <p> </p>
Supplementary Simulation Data for "A contact-based analysis of local energetic frustration dynamics identifies key residues enabling RfaH fold-switch"
<p>Additional simulation data for "A contact-based analysis of local energetic frustration dynamics identifies key residues enabling RfaH fold-switch"</p> <p><strong>Content:</strong></p> <p>'clusters_foldswitch': Contains representative structures in PDB format of the refolding landscape of RfaH using all-atom structure-based models. The QA and QB values indicated in each filename correspond to the fraction of native contacts contain in the representative structure in comparison to the total number of contacts in the structure of the autoinhibited ⍺-folded (A) and active β-folded (B) states of the C-terminal domain of RfaH.</p> <p>'input_one_fs': Contains a trajectory of RfaH refolding from the ⍺-folded to the β-folded state, with each frame contained into a separate PDB file, totalling 400 PDB files. These files can be used with the frustration-based windowing method scripts and Colab notebook made available at https://github.com/pb3lab/RfaH-frustration</p> <p>'input_many_fs': Contains several trajectory of RfaH reversible refolding between the ⍺-folded and β-folded states, with each frame contained into a separate PDB file, totalling 11,999 PDB files. These files can be used with the frustration-based windowing method scripts and Colab notebook made available at https://github.com/pb3lab/RfaH-frustration</p> <p>'output_one_fs': Contains output results from the analysis of local energetic frustration dynamics of the 400 frames contained in 'input_one_fs' using the windowing method available in the Colab notebook at https://github.com/pb3lab/RfaH-frustration.</p> <p>'output_many_fs': Contains output results from the analysis of local energetic frustration dynamics of the 11,999 frames contained in 'input_many_fs' using the windowing method available in the Python script at https://github.com/pb3lab/RfaH-frustration.</p>
Modeling the Emission of Energetic Neutral Atoms in Titan's Dynamic Magnetospheric Environment
<p>Data for the manuscript "Modeling the Emission of Energetic Neutral Atoms in Titan's Dynamic Magnetospheric Environment" by Tippens et al., (2024). See README.txt for a description of the data files included here.</p>
Supplementary data for "Vacancy defect configurations in the metal-organic framework UiO-66: Energetics and electronic structure"
<p>Optimised structures for UiO-66 with various defect configurations in VASP POSCAR format. For naming see the associated paper (DOI:10.1039/c7ta11155j).</p>
Data archive for 'Developmental history, energetic state and choice impulsivity in European starlings, Sturnus vulgaris'
<p>Data and code for Dunn et al. 'Developmental history, energetic state and choice impulsivity in European starlings, Sturnus vulgaris'</p> <p> </p> <p>The r script allows you to carry out all the analyses reported in the paper. Data from the experiment reported in the paper are 'databybird.csv'.</p> <p>In the paper, we also compare the findings of the present experiment with findings from a study of risk preference in the same birds (Andrews et al. 2018), and two earlier studies of impulsivity in different birds (Bateson et al. 2015, Nettle et al. 2015) . For convenience, we have included the relevant data from those earlier studies here too, though those data are all already published in association with the primary paper on those experiments.</p> <p>This version has a revised R script which tweaked some of the analyses in response to peer review.</p>
HEO Energetic Particle and Dosimeter Data
<p>At present, data from two HEO missions is available in this archive:<br>HEO-1 and HEO-3. These data consist of energetic particle<br>measurements, given as proton counts, electron counts, and dose/dose<br>rate. The spacecraft are equipped with a combination of dome dosimeters and<br>particle telescopes. Data from these instruments is available in<br>15-second averages with some magnetic ephemeris in IGRF and<br>Olson-Pfitzer (Quiet) field models. </p>
Correlation between Radiation Enhancements at Aviation Altitudes and Energetic Precipitation Electrons
<p>Figures, data, and code used in my paper describing "Correlation between Radiation Enhancements at Aviation Altitudes and Energetic Precipitation Electrons"</p>
Exploring the Chemistry Induced by Energetic Processing of the H2-bearing, CO-rich Apolar Ice Layer
<p>Interstellar ice mantles on the surfaces of dust grains are thought to have a bilayered structure, with a H2O-rich polar layer, covered by a CO-rich apolar layer that probably harbors H2 and other volatiles such as N2. In this work, we explored the chemistry induced by 2 keV electrons and Lyα photons in H2:CO:15N2 ice analogs of the CO-rich layer when exposed to similar fluences to those expected from the cosmic-ray-induced secondary electrons and UV photons during the typical lifetime of dense clouds. Six products were identified upon 2 keV electron irradiation: CO2, C2O (and other carbon chain oxides), CH4, H2CO, H2C2O, and H15NCO. The total product abundances corresponded to 5%-10% of the initial CO molecules exposed to electron irradiation. Lyα photon irradiation delivered one to two orders of magnitude lower yields with a similar product branching ratio, which may be due to the low UV-photon absorption cross section of the ice sample at this wavelength. Formation of additional N-bearing species, namely C215N2 and 15NH3, was only observed in the absence of H2 and CO molecules, respectively, suggesting that reactants derived from H2 and CO molecules preferentially react with each other instead of with 15N2 and its dissociation products. In summary, ice chemistry induced by energetic processing of the CO-rich apolar ice layer provides alternative formation pathways for several species detected in the interstellar medium, including some related to the complex organic molecule chemistry. </p> <p>Here, we present all the IR spectra and temperature programmed desorption data for the 16 experiments that were used for this publication (Exp. 1-14, A1,A2), along with 7 additional calibration experiments (C1-C7). Please, note that all infrared spectra are taken in reflection-absorption mode, except for those corresponding to Experiments C1-C7, taken in transmittance mode. </p>
Energetic return on investment determines overall soil microbial activity.
<p><strong>Data</strong> and <strong>R codes</strong> used for the manuscript entitled " <strong>Energetic return on investment determines overall soil microbial activity."</strong></p>
The dataset for the submitted paper " Time Series Analysis of Normal Mode Energetics for Rossby Wave Breaking and Saturation using a Simple Barotropic Model".
<p>These files are the data of the result in the submitted paper, titled "Time Series Analysis of Normal Mode Energetics for Rossby Wave Breaking and Saturation using a Simple Barotropic Model".</p> <ul> <li>File Description</li> </ul> <p>pv13.data : Exp. 1<br> pv17.data : Exp. 2</p> <p>The raw potential vorticity (PV) data for the Exp.1 and Exp.2, respectively, used in drawing the Fig.1, 2, and the supplemental movie 1 and 2.<br> These are the grid point value files, 72 levels for the zonal direction, 30 levels for meridional direction. More details are described in the next ctl files.</p> <p> </p> <p>pv13.ctl<br> pv17.ctl</p> <p>Description files for pv13.data and pv17.data. This will be called from grads_pv13.gs and grads_pv17.data, respectively.</p> <p>grads_pv13.gs<br> grads_pv17.gs</p> <p>GrADS script for mapping the PV.</p> <p> </p> <p>energy17.txt : Exp.2</p> <p>The time series table of energy values for exp.2.<br> One raw is identified by combination of the TIME in the experiment and zonal wave number N.</p>
Data for "Transferring Chemical and Energetic Knowledge Between Molecular Systems With Machine Learning"
<p>Data used in the paper "Transferring Chemical and Energetic Knowledge Between Molecular Systems With Machine Learning."</p> <p>The following is a description of each file:</p> <p>- ala_dipep_full.zip contains the JSON files for alanine dipeptide</p> <p>- ala_dipep_full.txt contains the free energy values for alanine dipeptide</p> <p>- trialanine.zip contains the JSON files for trialanine</p> <p>- trialanine.txt contains the free energy values for trialanine</p> <p>- decaalanine.zip contains the JSON files for decaalanine, broken into groups</p> <p> </p> <p>Each JSON file contains the following properties:</p> <p>- atom_types: describing the short strings used for various types of atoms via their mass and radius.</p> <p>- atoms: describing each individual atom, with their type via the short string in atom_types, their partial charge, and coordinates.</p> <p>- angles: describing the angles formed between three atoms, their atom indices, as well as their angular value.</p> <p>- dihedrals: describing the dihedrals formed between four atoms, their atom indices, as well as their dihedral value.</p> <p>- bonds: describing the existence of pairwise bonds between atoms via a binary number.</p> <p>- van_der_waals: describing the van der Waals forces between pairs of atoms.</p> <p>- coulomb: describing the Coulomb forces between pairs of atoms.</p>
Data for "Energetic Particle Fluxes onto Callisto's Atmosphere" by Liuzzo et al., 2022
<p>Data files corresponding to the publication "Energetic Particle Fluxes onto Callisto’s Atmosphere" by Liuzzo et al., 2022.</p>
Size-associated energetic constraints on the seasonal onset of reproduction in a species with indeterminate growth
<p>The seasonal onset of reproduction is constrained in many systems by a need to first accumulate energetic reserves. Consequently, the observation that larger individuals reproduce earlier may be due to a negative relationship between size and mass-specific basal metabolic rate that is shared across diverse taxa. However, an untested prediction of this hypothesis is that individuals should be metabolically efficient enough to escape energetic constraints above a certain size threshold. Seasonally reproducing species, such as temperate fishes, that must recover winter energy losses before reproduction and exhibit indeterminate growth are ideal models to test this prediction. We harness decade-long behavioral data on parental male smallmouth bass, <em>Micropterus dolomieu</em>, to investigate contributions of energetic allometry to differences in reproductive timing. At the population level, peak seasonal reproductive timing (i.e., the median date on which eggs were found in nests each year) was negatively related to degree days–a measure of thermal energy experienced–before reproduction. At the individual level, degree days accumulated by males before reproduction was related to male size and condition in every year, but the impact of temperature on reproductive timing by the largest males was relaxed in most years. Additionally, we used our data to replicate the analyses of two previous studies of <em>M. dolomieu</em> populations and found virtually identical negative associations between male body size and degree days accumulated before reproduction. Our results suggest that in smallmouth bass the onset of seasonal reproduction is constrained by basal metabolic rate–as indicated by total length–and that large individuals can escape size-associated energetic constraints. We reveal a more complicated relationship between size and reproductive timing than earlier studies, which may be relevant for many species. Knowledge of this relationship is critical to understanding how a changing climate will influence population dynamics of economically, ecologically, and recreationally important species like <em>M. dolomieu</em>.</p>
Data for: The energetics of rapid mechanotransduction
<p>Cells throughout the human body detect mechanical forces. While it is known that the rapid (millisecond) detection of mechanical forces is mediated by force-gated ion channels, a detailed quantitative understanding of cells as sensors of mechanical energy is still lacking. Here, we combine atomic force microscopy with patch-clamp electrophysiology to determine the physical limits of cells expressing the force-gated ion channels Piezo1, Piezo2, TREK1, and TRAAK. We find that, depending on the ion channel expressed, cells can function either as proportional or non-linear transducers of mechanical energy, detect mechanical energies as little as ~100 fJ, and with a resolution of up to ~1 fJ. These specific energetic values depend on cell size, channel density, and cytoskeletal architecture. We also make the surprising discovery that cells can transduce forces either nearly instantaneously (<1 ms), or with substantial time delay (~10 ms). Using a chimeric experimental approach and simulations we show how such delays can emerge from channel-intrinsic properties and the slow diffusion of tension in the membrane. Overall, our experiments reveal the capabilities and limits of cellular mechanosensing and provide insights into molecular mechanisms that different cell types may employ to specialize for their distinct physiological roles.</p>
The energetic particle environment of a GJ 436 b-like planet
<p>This data set corresponds to the simulation data presented in the article "The energetic particle environment of a GJ 436b-like planet" (Rodgers-Lee, et al., MNRAS, 2023). Details of the stellar wind and cosmic ray models used for the simulations are available in the article.</p> <p>Each data file consists of the temperature, pressure and heights in the exoplanet atmosphere at a given orbital distance from the star (shown in Fig.3 of Rodgers-Lee et al. 2023). The number density, n(z), of the exoplanet atmosphere can be calculated from the temperature and pressure. Further details relating to the temperature pressure profiles are given in Section 2.3 of Rodgers-Lee et al. (2023). The last two but one columns in the data files are the ionisation rates for molecular hydrogen from Galactic cosmic rays and stellar energetic particles (shown in Fig.4 of Rodgers-Lee et al. 2023). The last column is the assumed planetary effective temperature.</p> <p>The data is given for a number of different orbital distances between 0.01 - 0.2au. File names are formatted as "zenodo_GJ436_manysp_solar_aX_tp.dat" where "X" corresponds to 100 x orbital distance in au (e.g. "a1" corresponds to a=0.01au) considered. The first line describes the data in the file. The second line gives the column headings and units.</p>
Representative structures of the energetic minima of bcl2midG4-ds/TF-PNA1K heterotriplex.
<p>Here, we report the representative structures extracted from the energetic minima retrieved after 500ns of aMD simulations of the heterotriplexes formed by two different peptide nucleic acids (PNA) molecular species, P3 and P4 with double helix DNA of the G-rich tract in the Bcl-2 gene promoter (bcl2midG4-ds). Briefly, due to the lack of experimental structures, the bcl2midG4-ds10/TF-PNA1K heterotriplex systems were manually constructed and submitted to conventional molecular dynamics (cMD) and accelerated molecular dynamics (aMD) simulations to investigate the conformational behaviour. Specifically, two different PNA molecular species, namely P3 and P4, with different numbers and positions of N3-protonated cytosines, were investigated. Three independent cMD simulations of 1 μs each were conducted for a total simulation time of 3 μs for both P3 and P4 systems, followed by 500 ns of aMD simulations to enhance their conformational sampling. Free energy surface (FES) and principal component (PCs) analysis were generated for both P4 and P3 systems to compare the sampled conformational space and identify representative energy minima. Here, we have uploaded the energetic minima structures of P3 and P4. Overall, these findings have implications for the future design of other TF-PNAs targeting G-rich DNA sequences, as they shed light on the importance of protonation patterns, the position of protonation sites, and the influence of PNAs on the DNA structure.</p>
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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.