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11,506 results for “Dynamics”
Data for Simulating strong-field electron-hole dynamics in solids probed by attosecond transient absorption spectroscopy
<p>These are the source data for <em>Simulating strong-field electron-hole dynamics in solids probed by </em><em>attosecond transient absorption spectroscopy</em>. A preprint is available at: https://arxiv.org/abs/2409.01033. A readme.txt file is included with the data.</p>
Rawdata for publication: An Efficient and Stable Polarizing Agent for In-Cell Magic-Angle Spinning Dynamic Nuclear Polarization NMR Spectroscopy
<p>This is the raw dataset for the publication: An Efficient and Stable Polarizing Agent for In-Cell Magic-Angle Spinning Dynamic Nuclear Polarization NMR Spectroscopy. It contains the EPR and NMR data used in this publication. DOI of this pubcliation: 10.1021/acs.jpclett.4c02709</p>
Data for: A snapshot of sediment dynamics on an inshore coral reef
Open the record for dataset details and reuse information.
Molecular Dynamics Trajectories for GPR6 without Ligand (ApoNoLig)
<p>Molecular Dynamics Data for 10.1126/scisignal.ado8741 for publication at Science Signalling</p> <p>Barekatain M., Johansson L.C., Lam J.H. et al Structural Insights into the High Basal Activity and Inverse Agonism of the Orphan Receptor GPR6 Implicated in Parkinson's Disease, Sci Signal. 2024 Dec 3;17(865):eado8741. doi: 10.1126/scisignal.ado8741. Epub 2024 Dec 3.</p> <p>This folder contains the PDB format file ("Topology") and the XTC format file (Trajectories). The timestep in this strided trajectory is 0.1 ns per frame. Periodic boundary condition (pbc) can be restored using VMD's standard pbc commands.</p> <p>Please cite us if you find this data useful!</p>
Molecular Dynamics Trajectories for GPR6 with Ligand OLA
<p>Molecular Dynamics Data for 10.1126/scisignal.ado8741 for publication at Science Signalling</p> <p>Barekatain M., Johansson L.C., Lam J.H. et al Structural Insights into the High Basal Activity and Inverse Agonism of the Orphan Receptor GPR6 Implicated in Parkinson's Disease, Sci Signal. 2024 Dec 3;17(865):eado8741. doi: 10.1126/scisignal.ado8741. Epub 2024 Dec 3.</p> <p>This folder contains the PDB format file ("Topology") and the XTC format file (Trajectories). The timestep in this strided trajectory is 0.1 ns per frame. Periodic boundary condition (pbc) can be restored using VMD's standard pbc commands.</p> <p>Please cite us if you find this data useful!</p>
Molecular Dynamics Trajectories for GPR6 without Ligand (IagNoLig)
<p>Molecular Dynamics Data for 10.1126/scisignal.ado8741 for publication at Science Signalling</p> <p>Barekatain M., Johansson L.C., Lam J.H. et al Structural Insights into the High Basal Activity and Inverse Agonism of the Orphan Receptor GPR6 Implicated in Parkinson's Disease, Sci Signal. 2024 Dec 3;17(865):eado8741. doi: 10.1126/scisignal.ado8741. Epub 2024 Dec 3.</p> <p>This folder contains the PDB format file ("Topology") and the XTC format file (Trajectories). The timestep in this strided trajectory is 0.1 ns per frame. Periodic boundary condition (pbc) can be restored using VMD's standard pbc commands.</p> <p>Please cite us if you find this data useful!</p>
Replication files for: Integrative modeling of the spread of serious infectious diseases and corresponding wastewater dynamics
<p>This repository contains the inputs used and outputs produced by the urban water management modelling software ++SYSTEMS for the paper Integrative Modeling of the Spread of Serious Infectious Diseases and Corresponding Wastewater Dynamics. It includes the following files:</p> <ol> <li>simulation_output.zip:</li> <ol> <li>In the subfolder infection_model, .csv and .txt files containing the agent-based model outputs for 250 simulations with homogeneous infection initialisation (2024_09_17) or localised infection initialisation (2024_10_15). These files were used as inputs for ++SYSTEMS.</li> <li>In the subfolder wastewater_model, .txt files containing the flow rates by pipe and the viral concentrations by sampling location for each combination of ABM simulation and rain/decay scenario. These files were the outputs of ++SYSTEMS.</li> </ol> <li>S1_INSIDe_Demonstrator_AreaList.txt: .txt file defining the area types and number of inhabitants for each surface area within the synthetic neighbourhood used in the paper. This file was also used as an input for ++SYSTEMS.<span> </span></li> <li>S2_systems_model_files.zip: .csv files defining the characteristics of the sewage system for the synthetic neighbourhood as well as the rain scenarios used in the paper. These file were also used as inputs for ++SYSTEMS.<span> </span></li> </ol>
Project files provided as supporting information to the manuscript "How Communication Pathways Bridge Local and Global Conformations in an IgG4 Antibody: a Molecular Dynamics Study"
<p>June 23, 2021</p> <p>Thomas Tarenzi, Marta Rigoli and Raffaello Potestio</p> <p>==================================</p> <p>The dataset contains the following folders:</p> <p>- contact_area_binding_site: files with the computed surface area, used for the calculation of the contact area between PD-1 and the antibody Fab (Fig. S41).</p> <p>- hbonds_ab-pd1: number of hydrogen bonds between the antigen and the antibody, for each holo cluster (Fig. S41).</p> <p>- mutual_information: matrices with the computed mutual information, for each pair of residues (Fig. S34, S35, S46). The folder contains also the generalized correlation coefficients (Fig. S43) and the correlation scores (Fig. 4, S44, S45), computed from the mutual informations.</p> <p>- networks: communities - for each cluster, each residue is assigned to a community within the interaction network (Fig. S32, S33). betweenness - the values of edge betweenness for each cluster (S30, S31).</p> <p>- output_clustering: each frame of the apo and holo simulations is assigned a cluster index, on the basis of the structural similarity (Fig. S4).</p> <p>- PAD: per-residue values of PAD parameter, for apo and holo systems (Fig. 3, S39).</p> <p>- PCA: principal component analysis for each conformational cluster (Section S2.1).</p> <p>- representative_structures: representative structures for each conformational cluster (Fig. 2).</p> <p>- r_gyr_antibody: radii of gyration of the antibody, for each cluster (Fig. 2).</p> <p>- r_gyr_hinge: radii of gyration of the sole hinge segment, for each cluster (Fig. S36).</p> <p>- RMSD_antibody: distributions of the root-mean-square deviation of the antibody, for each cluster (Fig. S5). </p> <p>- RMSD_antigen: root-mean-square deviation of the antigen PD-1, for each cluster (Fig. S42).</p> <p>- RMSD_binding_site: distributions of the root-mean-square deviation of the residues belonging to the paratope, for each cluster (Fig. S40, S47).</p> <p>- RMSD_matrix: root-mean-square deviation between structures belonging to different pairs of clusters (Fig. S9).</p> <p>- rmsf_antigen: root-mean-square fluctuation of the antigen PD-1, for each cluster (Fig. S42).</p> <p>- rmsf_hinge: difference between the total root-mean-square fluctuations of the two hinge segments, for each cluster (Fig. S38).</p> <p>- salt_bridge: distribution of distances between residues R979 and D1377 (Fig. 4).</p> <p>- sasa_domains: contact area between Fab and Fc antibody domains, for each cluster (Fig. S8).</p> <p>- sasa_hinge: solvent accessible surface area of each hinge segment, for each cluster (Fig. S37).</p>
Data from: Dynamic measurements of black oystercatcher (Haematopus bachmani) predation on mussels (Mytilus californianus)
Intertidal zone mussels can face threats from a variety of predatory species during high and low tides, and they must balance the threat of predation against other needs such as feeding and aerobic respiration. Black oystercatchers (Haematopus bachmani) on the Pacific coast of North America can depend on the mussel Mytilus californianus for a substantial portion of their diet. Observations suggest that oystercatchers tend to focus on mussels beginning to gape their valves during rising tides, following periods of aerial emersion. We present detailed, autonomous field measurements of the dynamics of three such predation events in the rocky intertidal zone. We measured accelerations of up to 4 g imposed on mussels, with handling times of 115 to 290 s required to open the shell and remove the majority of tissue. In each case a single oystercatcher attacked a mussel that had gaped the shell valves slightly wider than its neighbors as the rising tide began to splash the mussel bed, but no other obvious characteristic of the mussels, such as body temperature or orientation, could be linked to the oystercatcher's individual prey choice.
Data from: Linking social and spatial networks to viral community phylogenetics reveals subtype-specific transmission dynamics in African lions
1.Heterogeneity within pathogen species can have important consequences for how pathogens transmit across landscapes; however, discerning different transmission routes is challenging. 2.Here we apply both phylodynamic and phylogenetic community ecology techniques to examine the consequences of pathogen heterogeneity on transmission by assessing subtype specific transmission pathways in a social carnivore. 3.We use comprehensive social and spatial network data to examine transmission pathways for three subtypes of feline immunodeficiency virus (FIVPle) in African lions (Panthera leo) at multiple scales in the Serengeti National Park, Tanzania. We used FIVPle molecular data to examine the role of social organization and lion density in shaping transmission pathways and tested to what extent vertical (i.e., father and/or mother offspring relationships) or horizontal (between unrelated individuals) transmission underpinned these patterns for each subtype. Using the same data, we constructed subtype specific FIVPle co-occurrence networks and assessed what combination of social networks, spatial networks, or co-infection best structured the FIVPle network. 4.While social organization (i.e., pride) was an important component of FIVPle transmission pathways at all scales, we find that FIVPle subtypes exhibited different transmission pathways at within- and between-pride scales. A combination of social and spatial networks, coupled with consideration of subtype co-infection, was likely to be important for FIVPle transmission for the two major subtypes, but the relative contribution of each factor was strongly subtype specific. 5.Our study provides evidence that pathogen heterogeneity is important in understanding pathogen transmission, which could have consequences for how endemic pathogens are managed. Furthermore, we demonstrate that community phylogenetic ecology coupled with phylodynamic techniques can reveal insights into the differential evolutionary pressures acting on virus subtypes, which can manifest into landscape-level effects.
Data from: Complex dynamics underlie the evolution of imperfect wing pattern convergence in butterflies
Adaptive radiation is characterized by rapid diversification that is strongly associated with ecological specialization. However, understanding the evolutionary mechanisms fueling adaptive diversification requires a detailed knowledge of how natural selection acts at multiple life-history stages. Butterflies within the genus Adelpha represent one of the largest and most diverse butterfly lineages in the Neotropics. Although Adelpha species feed on an extraordinary diversity of larval hosts, convergent evolution is widespread in this group suggesting that selection for mimicry may contribute to adaptive divergence among species. To investigate this hypothesis, we conducted predation studies in Costa Rica using artificial butterfly facsimiles. Specifically, we predicted that non-toxic, palatable Adelpha species that do not feed on host plants in the family Rubiaceae would benefit from sharing a locally convergent wing pattern with the presumably toxic Rubiaceae-feeding species via reduced predation. Contrary to expectations, we found that the presumed mimic was attacked significantly more than its locally convergent model, at a frequency paralleling attack rates on both novel and palatable prey. Although these data reveal the first evidence for protection from avian predators by the supposed toxic, Rubiaceae-feeding Adelpha species, we conclude that imprecise mimetic patterns have high costs for Batesian mimics in the tropics.
Data from: Linking beaver dam affected flow dynamics to upstream passage of Arctic grayling
Beaver reintroductions and beaver dam structures are an increasingly utilized ecological tool for rehabilitating degraded streams, yet beaver dams can potentially impact upstream fish migrations. We collected two years of data on Arctic grayling movement through a series of beaver dams in a low gradient mountain stream, utilizing radio-telemetry techniques, to determine how hydrology, dam characteristics, and fish attributes impeded passage and movement rates of spawning grayling. We compared fish movement between a "normal" flow year and a "low" flow year, determined grayling passage probabilities over dams in relation to a suite of factors, and predicted daily movement rates in relation to the number of dams each fish passed and distance between dams during upstream migration to spawning areas. We found that the average passage probability over unbreached beaver dams was 88%, though we found that it fell below 50% at specific dams. Upstream passage of grayling was affected by three main characteristics: 1) temperature 2) breach status and 3) hydrologic linkages that connect sections of stream above and below the dam. Other variables influence passage, but to a lesser degree. Cumulative passage varied with distance upstream and total number of dams passed in low versus normal flow years, while movement rates upstream slowed as fish swam closer to dams. Our findings demonstrate that upstream passage of fish over beaver dams is strongly correlated with hydrologic conditions with moderate controls by dam- and fish-level characteristics. Our results provide a framework that can be applied to reduce barrier effects when and where beaver dams pose a significant threat to the upstream migration of fish populations while maintaining the diverse ecological benefits of beaver activity when dams are not a threat to fish passage.
Data from: Watershed versus within-lake drivers of nitrogen: phosphorus dynamics in shallow lakes
Research on lake eutrophication often identifies variables affecting amounts of phosphorus (P) and nitrogen (N) in lakes, but understanding factors influencing N:P ratios is important given its influence on species composition and toxin production by cyanobacteria. We sampled 80 shallow lakes in Minnesota (USA) for three years to assess effects of watershed size, proportion of watershed as both row crop and natural area, fish biomass, and lake alternative state (turbid versus clear) on total N: total P (TN:TP), ammonium, total dissolved phosphorus (TDP), and seston stoichiometry. We also examined N:P stoichiometry in 20 additional lakes that shifted states during the study. Lastly, we assessed importance of denitrification by measuring denitrification rates in sediment cores from a subset of 34 lakes, and by measuring seston δ15N in four additional experimental lakes before and after they were experimentally manipulated from turbid to clear states. Results showed alternative state had the largest influence on overall N:P stoichiometry in these systems, as it had the strongest relationship with TN:TP, seston C:N:P, ammonium, and TDP. Turbid lakes had higher N at given levels of P than clear lakes, with TN and ammonium two-fold and 1.4-fold higher in turbid lakes, respectively. In lakes that shifted states, TN was three-fold higher in turbid lakes, while TP was only two-fold higher, supporting the notion N is more responsive to state shifts than is P. Seston δ15N increased after lakes shifted to clear states, suggesting higher denitrification rates may be important for reducing N levels in clear states, and potential denitrification rates in sediment cores were among the highest recorded in the literature. Overall, our results indicate lake state was a primary driver of N:P dynamics in shallow lakes, and lakes in clear states had much lower N at a given level of P relative to turbid lakes, likely due to higher denitrification rates. Shallow lakes are often managed for the clear-water state due to increased value as wildlife habitat. However, our results indicate lake state also influences N biogeochemistry, such that managing shallow lakes for the clear-water state may also mitigate excess N levels at a landscape scale.
Data from: Diversity, dynamics and effects of long terminal repeat retrotransposons in the model grass Brachypodium distachyon
<ul> <li><span>Transposable elements (TEs) are the main reason for the high plasticity of plant genomes, where they occur as communities of diverse evolutionary lineages. Because research has typically focused on single abundant families or summarized TEs at a coarse taxonomic level, our knowledge about how these lineages differ in their effects on genome evolution is still rudimentary. </span></li> <li><span>Here we investigate the community composition and dynamics of 32 long terminal repeat retrotransposon (LTR-RT) families in the 272 Mb genome of the Mediterranean grass <i>Brachypodium distachyon. </i></span></li> <li><span>We find that much of the recent transpositional activity in the <i>B. distachyon </i>genome is due to centromeric <i>Gypsy </i>families and <i>Copia </i>elements belonging to the Angela lineage. With a half-life as low as 66 ky, the latter are the most dynamic part of the genome and an important source of within-species polymorphisms. Second, GC-rich <i>Gypsy </i>elements of the Retand lineage are the most abundant TEs in the genome. Their presence explains more than 20 percent of the genome-wide variation in GC content and is associated with higher methylation levels. </span></li> <li><span>Our study shows how individual TE lineages change the genetic and epigenetic constitution of the host beyond simple changes in genome size. </span></li> </ul>
Dynamic changes in DNA methylation during postnatal development in zebra finches (Taeniopygia guttata) exposed to different temperatures
<p>Epigenetic changes associated with early life conditions are known to play a significant role in shaping the adult phenotype. Studies of DNA methylation in wild animals are lacking, yet are important for understanding the fitness consequences of environmentally induced epigenetic change. In our study, we quantified variation in DNA methylation in wild, post-hatch zebra finches Taeniopygia guttata developing at seasonally variable temperatures in the Australian desert. We also compared variation in DNA methylation among captive zebra finch siblings raised in temperature controlled 'hot' or 'cool' rooms. We detected an increase in genome-wide levels of DNA methylation between day 3 and day 11 of post hatch development in wild zebra finches. In the wild, ambient temperatures were also found to affect genome-wide levels of DNA methylation and plasticity in the methylation state of individual loci. Family effects had a significant influence on DNA methylation throughout our study, and while we did not detect an effect of temperature on DNA methylation levels in non-related captive birds, our sibling pair analyses revealed that within families, elevated temperatures were associated with higher levels of DNA methylation. Our findings suggest a wide window in early development during which climatically induced variation in DNA methylation could occur. Further work is necessary to understand the potential for such variation to promote ecologically relevant variation in wild birds.</p>
Molecular Dynamics Simulation of MC-congeners in complex with PPP1 - Replicate 3
<p>This data sets contains Molecular Dynamics (MD) Simulation files and analysis. Microcystin (MC) congeners were simulated in solvent (water) and in complex with protein phosphatase 1 (PPP1). MD Simulation was repeated for three times. This data is replicate 3 and related data sets are available.</p> <p>Please cite the original publication when using all or part of the data:</p> <p>S. Jaeger-Honz, J. Nitschke, S. Altaner, K. Klein, D. R. Dietrich, F. Schreiber:<a href="https://doi.org/10.1016/j.cbi.2021.109766"> Investigation of microcystin conformation and binding towards PPP1 by molecular dynamics simulation</a>. <em>Chemico-Biological Interactions</em>, 2021</p>
Molecular Dynamics Simulation of MC-congeners in complex with PPP1 - Replicate 2
<p>This data sets contains Molecular Dynamics (MD) Simulation files and analysis. Microcystin (MC) congeners were simulated in solvent (water) and in complex with protein phosphatase 1 (PPP1). MD Simulation was repeated for three times. This data is replicate 2 and related data sets are available.</p> <p>Please cite the original publication when using all or part of the data:</p> <p>S. Jaeger-Honz, J. Nitschke, S. Altaner, K. Klein, D. R. Dietrich, F. Schreiber:<a href="https://doi.org/10.1016/j.cbi.2021.109766"> Investigation of microcystin conformation and binding towards PPP1 by molecular dynamics simulation</a>. <em>Chemico-Biological Interactions</em>, 2021</p>
Molecular Dynamics Simulation of MC-congeners in complex with PPP1 - Replicate 1
<p>This data sets contains Molecular Dynamics (MD) Simulation files and analysis. Microcystin (MC) congeners were simulated in solvent (water) and in complex with protein phosphatase 1 (PPP1). MD Simulation was repeated for three times. This data is replicate 1 and related data sets are available.</p> <p>Please cite the original publication when using all or part of the data:</p> <p>S. Jaeger-Honz, J. Nitschke, S. Altaner, K. Klein, D. R. Dietrich, F. Schreiber:<a href="https://doi.org/10.1016/j.cbi.2021.109766"> Investigation of microcystin conformation and binding towards PPP1 by molecular dynamics simulation</a>. <em>Chemico-Biological Interactions</em>, 2021</p>
Dataset - Dynamic persistence of intracellular bacterial communities of uropathogenic Escherichia coli in a human bladder-chip model of urinary tract infections
<p>Dataset for manuscript posted at biorxiv: https://doi.org/10.1101/2021.01.03.42483 and in revision for eLife. Data corresponding to each main figure and its associated figure supplements are in seperate .zip folders.</p>
Data from: Computational fluid dynamics confirms drag reduction associated with trilobite queuing behaviour
<p>Queuing behaviour has been documented in marine arthropods from Cambrian to modern oceans. One possible explanation of this behaviour is drag reduction, with trilobites in the following positions hypothesized to produce less drag than those leading. In this study, we evaluate the hydrodynamics of queuing behaviour in the Devonian trilobite Trimerocephalus chopini using computational fluid mechanics. Our results show that the drag forces of the trilobites following in the queue were substantially lower than those produced by the leader (75.1% lower at 2 cm s-1). Drag reduction is positively correlated with the movement speed of the trilobites, but decreases with increasing distance from the leader. Our results support the hypothesis that the queuing behaviour of trilobites was an adaptation for reducing hydrodynamic drag. This drag reduction effect compensated for the energy cost of movement, which would have been particularly advantageous during migration.</p>
ScienceDex guides
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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.