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11,506 results for “Dynamics”
Data from: In situ 15N-N2O site preference and O2 concentration dynamics disclose the complexity of N2O production processes in agricultural soil
<p class="MsoNormal"><span>Arable soil continues to be the dominant anthropogenic source of nitrous oxide (N<sub>2</sub>O) emissions owing to application of nitrogen (N) fertilizers </span><span>and manures across the world. Using</span><span> laboratory </span><span>and </span><em><span>in-situ</span></em><span> studies to elucidate the key factors controlling soil N<sub>2</sub>O emissions remains challenging due to the potential importance of multiple complex processes. We<em> </em>examined soil surface N<sub>2</sub>O fluxes in an arable soil, combined with<em> in-situ</em> high</span><span>-</span><span>frequency measurements of soil matrix oxygen (O<sub>2</sub>) and N<sub>2</sub>O concentrations, </span><em><span>in situ</span></em><span> <sup>15</sup>N labeling, and</span><span> N<sub>2</sub>O <sup>15</sup>N site preference (SP). The </span><em><span>in situ</span></em><span> O<sub>2</sub> concentration and further microcosm visualized spatiotemporal distribution of O<sub>2</sub> both suggested that O<sub>2</sub> dynamics were the proximal determining factor to matrix N<sub>2</sub>O concentration and fluxes due to quick O<sub>2</sub> depletion after N fertilization. Further SP analysis<em> </em>and<em> in situ</em> <sup>15</sup>N labeling experiment revealed </span><span>that the main source for N<sub>2</sub>O emissions was bacterial denitrification during the hot-wet summer with lower soil </span><span>O<sub>2</sub></span><span> concentration, while nitrification or fungal denitrification contributed about 50<span>.0</span>% to total emissions during the cold-dry winter with higher soil </span><span>O<sub>2</sub></span><span> concentration. </span><span>The robust positive correlation between O<sub>2</sub> concentration and SP values underpinned that the O<sub>2</sub> dynamics were the key factor to differentiate the composite processes of N<sub>2</sub>O production in <em>in situ</em> structured soil. Our findings deciphered the complexity of N<sub>2</sub>O production processes in real field conditions, and suggest that O<sub>2</sub> dynamics rather than stimulation of functional gene abundances play a key role in controlling soil N<sub>2</sub>O production processes in undisturbed structure soils. </span><span>Our results help to develop targeted N<sub>2</sub>O mitigation measures and to improve process models for constraining global N<sub>2</sub>O budget.</span></p>
GNSS time series from "Subdaily slow fault slip dynamics captured by low-frequency earthquakes" (Mouchon et al., 2023)
<p>GNSS raw time series from "Subdaily slow fault slip dynamics captured by low-frequency earthquakes" (Mouchon et al., 2023)</p> <p>The raw GNSS time series are available for each three GNSS stations we focus on in this study (COYU, IGUA and MECZ), as well as the three distant stations use to correct from common mode (INEG, TAMP and UXAL), at both 24-hour and 6-hour sampling rates.<br> Each file contains the date, East, North and Vertical displacement and associated errors in meters (format: Decimal year, E (m), N (m), U (m), dE (m), dN (m), dU (m)).</p>
Species, hybrid and genotype effects on leaf litter curling, and their extended consequences for spiders and soil moisture dynamics
<p>This archive contains datasets from a group of studies testing the hypotheses that leaf litter curling is influenced by plant species, hybridization and genotype, and has extended consequences for associated organisms and soil processes. A novel litter curling index (LCI) was used to characterize the curling of newly senesced leaves. There are four distinct datasets represented here. 1) A dataset of LCI from 11 plant species (tall annual forb = <em>Helianthus annuus</em> L.; evergreen shrubs = <em>Arctostaphylos pungens</em> Kunth, <em>Quercus turbinella</em> Greene, <em>Rhus ovata</em> S. Watson; deciduous shrubs = <em>Rhus trilobata</em> Nutt., <em>Ribes cereum</em> Douglas, <em>Acer glabrum</em> Torr.; deciduous trees = <em>Elaeagnus angustifolia</em> L., <em>Quercus gambelii</em> Nutt., <em>Populus tremuloides</em> Michx., <em>Populus fremontii</em> S. Watson) mostly growing in natural habitats of Northern Arizona, USA. 2) A dataset containing LCI from two <em>Populus</em> species (<em>P.</em> <em>fremontii</em> James, <em>P. angustifolia</em> S. Watson) and their F1 hyrbids in a common garden in Ogden, UT, USA (including replicated genotypes of <em>P. angustifolia</em> but not the other tree types). 3) The third dataset examined the relationship between average LCI for a tree and the abundance of agilenid webs under <em>Populus</em> trees growing in a common garden; the LCI values are averages per tree from data collected for dataset 2, and previously published spider web data. 4) The last dataset contains litter and soil moisture values from a litter/soil drying experiment that tested the effect of litter curling on soil moisture dynamics. See the README file for more details on the different datasets.</p>
A bovine GWAS reveals determinants of mobilization rate and dynamics of endogenous retroviruses
<p>We develop a novel method to measure the rate of ERVK[2-1-LTR] mobilization in the male germline, and show that this rate averages 1 per 150 sperm cells, yet varies more than ten-fold between animals. We perform a genome wide association study with 430 bulls and identify eight loci that affect ERVK[2-1-LTR] mobilization rate. We provide strong evidence that ERVK[2-1-LTR] elements in four of these, cause the association. We generate an exhaustive catalogue of ERVK[2-1-LTR] elements for the bovine, and show that is composed for 15% of 10 Kb <em>C</em>-type autonomous elements encoding GAG, PRO, POL and ENV genes, and 85% of 6.8 Kb <em>D</em>-type non-autonomous elements devoid of functional genes. We show that >25% of the variance of ERVK[2-1-LTR] mobilization rate is determined by the number of <em>C</em>-type elements in the genome, yet that <em>de novo</em> ERVK[2-1-LTR] insertions are dominated by <em>D</em>-type elements. </p>
Universal Dynamic Fitting of Magnetic Resonance Spectroscopy - Data
<p>Original data for the in vivo experiments included in the article Universal Dynamic Fitting of Magnetic Resonance Spectroscopy by William T Clarke, Clémence Ligneul, Michiel Cottaar, Betina Ip and Saad Jbabdi (Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, UK).</p> <p>This data accompanies the online <a href="https://git.fmrib.ox.ac.uk/wclarke/fsl-mrs-dynamic-fitting">code repository</a>. Note that this repository contains preprocessed versions of this data already.</p> <p>Two files are included:</p> <ol> <li>fmrs_invivo_unprocessed_data.zip - NIfTI-MRS formatted data relating to the fMRS in vivo example in this work. Data is originally from <a href="https://doi.org/10.1016/j.neuroimage.2017.04.030">10.1016/j.neuroimage.2017.04.030</a>.</li> <li>dwmrs_invivo_original_data.zip = matlab .mat data relating tot he dwMRS in vivo example in this work. Data is originally from <a href="https://doi.org/10.1016/j.neuroimage.2019.02.046">10.1016/j.neuroimage.2019.02.046</a>.</li> </ol> <p>If you use this data in your work please cite this work (Universal Dynamic Fitting of Magnetic Resonance Spectroscopy) once available and the originating publications.</p>
Dataset for "Charge transfer dynamics in Ar+ + CO"
<p>Dataset for "Charge transfer dynamics in Ar+ + CO"</p>
IL-17 signalling is critical for controlling subcutaneous adipose tissue dynamics and parasite burden during chronic Trypanosoma brucei infection
<p>In the skin, <em>Trypanosoma brucei </em>colonises the subcutaneous white adipose tissue (WAT) and harbours a pool of parasites competent for forward transmission. The interaction between parasites, adipose tissue, and the local immune system is likely to drive adipose tissue wasting and weight loss observed in cattle and humans infected with <em>T. brucei</em>. However, mechanistically, this process is not fully understood. Here, using several complementary approaches including mass cytometry by time of flight, bulk and single cell transcriptomics, we found that <em>T. brucei</em> infection drives a local expansion of several IL-17A-producing cells in the murine WAT, including T<sub>H</sub>17 and Vg6<sup>+</sup> T cells. We also found that global IL-17 deficiency, or mice lacking IL-17 receptor expression specifically on adipocytes, were protected from infection-induced WAT wasting and weight loss. Unexpectedly, we found that abrogation of IL-17 signalling on adipocytes results in higher burden of extravascular parasites in the WAT. Taken together, our study highlights the central role of IL-17 signalling on adipocytes in controlling WAT responses to infection, suggesting that adipocytes are a critical coordinator of the tissue immune response to <em>T. brucei</em> infection. </p>
Revealing the nonadiabatic tunneling dynamics in solid-state high harmonic generation
<p>Dataset of the publication “Revealing the nonadiabatic tunneling dynamics in solid-state high harmonic generation“, by Ruixin Zuo, Xiaohong Song, Shuai Ben, Torsten Meier, and Weifeng Yang, published in PHYSICAL REVIEW RESEARCH 5, L022040 (2023) ( <a href="https://doi.org/10.1103/PhysRevResearch.5.L022040">https://doi.org/10.1103/PhysRevResearch.5.L022040</a> )<br> The zip file includes the data on which the plots 2 – 9 are based.</p>
MD trajectories for "Kinetic barrier to enzyme inhibition is manipulated by dynamical local interactions in E. coli DHFR"
<p>Dihydrofolate reductase (DHFR) is an important drug target and a highly studied model<br> protein for understanding enzyme dynamics. DHFR’s crucial role in folate synthesis renders it<br> an ideal candidate to understand protein function and protein evolution mechanisms. In this<br> study, to understand how a newly proposed DHFR inhibitor, 4’-deoxy methyl trimethoprim<br> (4’-DTMP), alters evolutionary trajectories, we studied interactions that lead to its superior<br> performance over trimethoprim (TMP). To elucidate the inhibition mechanism of 4’-DTMP,<br> we first confirmed, both computationally and experimentally, that the relative binding free<br> energy cost for the mutation of TMP and 4’-DTMP are the same, pointing to the origin of the<br> characteristic differences to be kinetic rather than thermodynamic. We then employed an<br> interaction-based analysis by focusing first on the active site, then on the whole enzyme. We<br> confirmed that the polar modification in 4’-DTMP induces additional local interactions with<br> the enzyme, particularly the M20 loop. These changes are propagated to the whole enzyme as<br> shifts in the hydrogen bond networks. To shed light on the allosteric interactions, we support<br> our analysis with network-based community analysis and show that segmentation of the loop<br> domain of the inhibitor-bound DHFR must be avoided by a successful inhibitor.</p>
Data for: Spatial heterogeneity and infection patterns on epidemic transmission disclosed by a combined contact-dependent dynamics and compartmental model
<p>Epidemics, such as COVID-19, have caused significant harm to human society worldwide. A better understanding of epidemic transmission dynamics can contribute to more efficient prevention and control measures. Compartmental models, which assume homogeneous mixing of the population, have been widely used in the study of epidemic transmission dynamics, while agent-based models rely on a network definition for individuals. In this study, we developed a real-scale contact-dependent dynamic (CDD) model and combined it with the traditional susceptible-exposed-infectious-recovered (SEIR) compartment model. </p>
Source data for paper "Operando electron microscopy investigation of polar domain dynamics in twisted van der Waals homobilayers"
<p>Source data for paper "Operando electron microscopy investigation of polar domain dynamics in twisted van der Waals homobilayers"</p>
Input files for Húsavík-Flatey Fault Zone dynamic simulations
<p>This repository contains the input files needed to reproduce the simulations shown in the paper "<a href="https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2022JB025886">Dynamic rupture models, fault interaction and ground motion simulations for the segmented Húsavík‐Flatey Fault Zone, Northern Iceland</a>"</p>
Data associated with Cell Reports publication: Dura-Bernal et al. 2023, "Multiscale model of primary motor cortex circuits predicts in vivo cell type-specific, behavioral state-dependent dynamics"
<p>This dataset includes experimental data used to constrain and validate the model, and model simulation output data. The source code for the associated M1 model and data analysis can be found here: https://github.com/suny-downstate-medical-center/M1_NetPyNE_CellReports_2023</p> <p>Please download the data_v2.zip file, which contains the most updated and complete version of the data.</p> <p>For more information please contact: salvador.dura-bernal@downstate.edu </p>
Control of the electron dynamics in solid-state high harmonic generation on ultrafast time scales by a polarization-skewed laser pulse
<p>Dataset of the publication “Control of the electron dynamics in solid-state high harmonic generation on ultrafast time scales by a polarization-skewed laser pulse”, by X. Song, S. Yang, G. Wang, J. Lin, L. Wang, T. Meier, and W. Yang, published in Optics Express 31, 18862 (2023) , <a href="https://doi.org/10.1364/OE.491418">https://doi.org/10.1364/OE.491418</a> .<br> The zip file includes a brief description, the data on which the plot of figures 1 – 3 are based, and matlab figure files.</p>
Data used by Calenge et al. in "Assessing the dynamics of Mycobacterium bovis infection in three French badger populations"
<p>The zip file contains the raw dataset used by Calenge et al. in their model of the <em>Mycobacterium bovis</em> infection in three French badger populations. The README file explains the content of this dataset.</p>
Data supporting 'Modeling Antarctic ice shelf basal melt patterns using the one-Layer Antarctic model for Dynamical Downscaling of Ice--ocean Exchanges (LADDIE v1.0)'
<p>This data set contains the data produced for the paper 'Modeling Antarctic ice shelf basal melt patterns using the one-Layer Antarctic model for Dynamical Downscaling of Ice--ocean Exchanges (LADDIE v1.0)'</p> <p>The data set contains output from LADDIE simulations, including basal melt rates.</p> <p>The main simulations used in the man text are:</p> <p>- Crosson-Dotson: <a href="https://zenodo.org/api/files/0640a922-97a9-4ced-ad3d-dab66f05c696/CrossDots_0.5_tanh_Tdeep0.4_ztcl-500_050.nc">CrossDots_0.5_tanh_Tdeep0.4_ztcl-500_050.nc </a><br> - Filchner-Ronne: <a href="https://zenodo.org/api/files/0640a922-97a9-4ced-ad3d-dab66f05c696/FRIS_1.0_linear_S134.8_T1-2.3_720.nc">FRIS_1.0_linear_S134.8_T1-2.3_720.nc </a><br> </p> <p>The additional simulations included in the Appendix are:</p> <p>- 3D forcing of Crosson-Dotson: <a href="https://zenodo.org/api/files/0640a922-97a9-4ced-ad3d-dab66f05c696/CrossDots_0.5_mitgcm_2003_2008_100.nc">CrossDots_0.5_mitgcm_2003_2008_100.nc </a><br> - Tuning of Crosson-Dotson: XX_YY_ZZ.nc, where XX is the resolution in km, YY is the value for Cd,top, and ZZ is the value for Dmin<br> - Pine Island Ice Shelf: <a href="https://zenodo.org/api/files/0640a922-97a9-4ced-ad3d-dab66f05c696/PIG.nc">PIG.nc </a><br> </p>
Code for manuscript "Analysis of dynamic susceptibility contrast perfusion MRI using physics-informed deep learning"
<p>This is the processing code and in vivo statistics for the manuscript "Analysis of dynamic susceptibility contrast perfusion MRI using physics-informed deep learning".</p>
Data for Dynamic Nuclear Polarisation of 1H in Gd-Doped In(OH)3
<p>Supporting data for Dynamic Nuclear Polarisation of 1H in Gd-Doped In(OH)3</p> <p>Raw and processed 1H, 17O and 115In NMR and DNP-enhanced NMR, EPR, and XRD data for In(OH)3 and Gd-doped In(OH)3. </p> <p>This data is described in the associated publication www.doi.org/10.1016/j.jmr.2023.107509</p>
Dynamic gravity and topography modeling: the Venus case
<p>This archive contains codes and data files supporting the study "The Mantle Viscosity Structure of Venus" by Julia Maia, Mark Wieczorek and Ana-Catalina Plesa submitted to Geophysical Research Letters.</p> <p>The dynamic loading code is based on the model by Hager and Clayton (1989).</p>
Chikungunya intra-vector infection dynamics in a French Aedes albopictus population reveals low vector barrier intensity and supports an explosive epidemic potential
<p>Arbovirus emergence and epidemic potential, as approximated by the vectorial capacity formula, depends on host and vector parameters, including the vector’s intrinsic ability to replicate then transmit the pathogen known as vector competence. Vector competence is a complex, time-dependent, quantitative phenotype influenced by biotic and abiotic factors. A combination of experimental and modelling approaches is required to assess arbovirus intra-vector dynamics and estimate its epidemic potential. In this study, we measured infection, dissemination, and transmission dynamics of chikungunya virus (CHIKV) in a field-derived <em>Aedes albopictus</em> population (Lyon metropolis, France) after oral exposure to a range of virus doses spanning human viraemia. Statistical modelling indicates rapid and efficient CHIKV progression in the vector mainly due to an absence of a dissemination barrier, with 100% of the infected mosquitoes ultimately exhibiting a disseminated infection, regardless of the virus dose. Transmission rate data revealed a time-dependent, but overall weak, transmission barrier, with individuals transmitting as soon as 2 days post-exposure (dpe) and >50% infectious mosquitoes at 6 dpe for the highest dose. Based on these experimental intra-vector dynamics data, epidemiological simulations conducted with an agent-based model showed that even at low mosquito biting rates, CHIKV could trigger explosive outbreaks. Together, this reveals the high epidemic potential of CHIKV upon transmission by <em>Aedes albopictus</em> in mainland France.</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.