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1,067 results for “perturbation”
Understanding muscle function during perturbed in vivo locomotion using a muscle avatar approach
<p>To investigate in vivo mechanics of the guinea fowl lateral gastrocnemius (LG) muscle during obstacle negotiation while running on a treadmill, we used mouse extensor digitorum longus (EDL) muscles in ex vivo experiments with in vivo strain inputs from perturbed and steady strides obtained in a previous study. In vivo strain trajectories from a stride down from obstacle to treadmill, two strides up from treadmill to obstacle, and a level stride with no obstacle, as well as a sinusoidal strain trajectory at the same amplitude and frequency, were used as inputs in work loop experiments. With five strain trajectories and three activation patterns, each muscle was used in a total of 15 work loop experiments. EDL forces produced using in vivo strain trajectories were more similar to in vivo LG forces (<em>R<sup>2</sup></em> = 0.58 – 0.94) than to forces produced using the sinusoidal trajectory (average <em>R<sup>2</sup></em> = 0.045). Given the same activation, in vivo strain trajectories produced consistent work loops that showed a shift in muscle function from more positive work during strides up from treadmill to obstacle to less positive work in strides down from obstacle to treadmill. Activation, strain trajectory, and activation*strain trajectory interaction had significant effects on all work loop variables, with the interaction having the largest effect on peak force and work per cycle. These results support the hypothesis that muscle is an active material whose viscoelastic properties are tuned by activation, and which produces forces in response to deformations of length associated with time-varying loads.</p>
European badger (Meles meles) responses to low-intensity, selective culling: using mark recapture and relatedness data to assess social perturbation
<p>Culling the main wildlife host of bovine tuberculosis in Great Britain (GB) and Ireland, the European badger (Meles meles) to reduce infections in cattle, has been employed in both territories. In GB, this has been controversial, with results suggesting that culling induces disturbance to badger social structure, facilitating wider disease dissemination. Previous analyses hypothesized that even very low-level, selective culling may cause similar deleterious effects by increasing ranging of individuals and greater mixing between social-groups. To assess this hypothesis, a novel, prospective, landscape-scale 'before-and-after' Test and vaccinate or remove (TVR) study was implemented. Test-positive badgers were culled and test-negative badgers were BCG vaccinated and released. Mark-recapture metrics of badger ranging and genetic metrics of social group relatedness did not change significantly over the study period. However, selective culling was associated with a localised reduction in social-group relatedness in culled groups. Synthesis and application: Ecological context is important; extrapolation across territories and other disease epidemiological-systems (epi-systems) is likely to be challenging. However, we demonstrate that small-scale, selective removal of test-positive badgers was not associated with metrics of increased ranging but was associated with localised changes in social-group relatedness. This adds to the evidence base on badger control options for policy makers.</p>
Dataset from: An intuitive form of the energy functional for resistive plasma perturbations
<p>The energy functional of ideal magnetohydrodynamics (MHD) is extended to the regime of finite resistivity and transformed to an intuitive form, which separates pressure-gradient, current-density drive and stabilizing phenomena, analogously to the ideal version of the functional derived by Johnson and Greene. The resulting resistive energy functional is not in the form of a solvable eigenvalue problem but is intended to analyze the energetic composition of eigenfunctions which were calculated in advance by solving the MHD equations. The new resistive energy functional provides information on the different energetic drives and stabilizing phenomena of an eigenfunction. The new energy functional has been implemented in the CASTOR3D code in general 3D curvilinear coordinates and successfully validated across three different coordinate systems for a numerical test case.</p>
Gait behavioral and neuromuscular characterization in response to increasing working memory load while walking under optic flow perturbations in young adults
<p>The precise role of cognitive control on optic flow processing during locomotion has rarely been investigated. Therefore, this study aimed to determine whether coping with unreliable visual inputs during walking requires attentional resources. Twenty-four healthy young adults walked on an instrumented treadmill in a virtual environment under two optic flow conditions: normal (NOF) and perturbed (POF, continuous mediolateral pseudo-random oscillations). Each condition was performed under single-task and dual-task conditions of increasing difficulty (1-, 2-, 3-back). In all conditions, subjective mental workload was estimated (raw NASA-TLX). For kinematic variables, mean, standard deviation, statistical persistence and step-to-step error correction were computed from gait time series in mediolateral and anteroposterior directions. For EMG variables of soleus and gluteus medius, the full width at half maximum and the variance ratio were calculated. Performance on N-back tasks was assessed using mean reaction time and d-prime. Cognitive performance was not affected by simultaneous walking in any optic flow condition. Gait variability was altered under POF compared to NOF, so that young adults sought to counteract those perturbations by adopting an effortful gait control strategy, independently of concurrent working memory (WM) load. Increasing WM load led changes first at the neuromuscular level, then at the behavioral level, with a prioritization of gait control in the mediolateral direction. Interestingly, dual-tasking lowered the effects of POF but in the anteroposterior direction only. These findings and their theoretical implications provide valuable insight into the complex interaction effects of cognitive and visual constraints on gait control during treadmill walking.</p>
Thallium(I) exposure perturbs the gut microbiota and metabolic profile as well as the regional immune function of C57BL/6 J mice
<p><span>Intestinal microbes</span><span> regulate the development of diseases induced by environmental exposure. Thallium (Tl) is a highly toxic heavy metal</span><span>, </span><span>and its toxicity is rarely discussed in relation to gut microbes. Herein, we showed that Tl(I) exposure (10 ppm for two weeks) affected the alpha diversity of bacteria in </span><span>the ileum, colon, and </span><span>feces, but had little effect on the beta diversity of bacteria through 16S rRNA sequencing. LEfSe analysis revealed that Tl(I) exposure changed the abundance of intestinal microbiota along the digestive tract. Cecum metabolomic detection and analysis showed that Tl(I) exposure altered the abundance and composition of metabolites. In addition, the Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed that Tl(I) exposure impaired amino acid, lipid, purine metabolism, and G protein-coupled receptor signalling pathways. A consistency test revealed a strong correlation, and a Pearson's correlation analysis showed an extensive interaction, between microorganisms and metabolites. Analysis of the intestinal immunity revealed that Tl(I) exposure suppressed the immune responses, which also had regional differences. These results identify the perturbation of the intestinal microenvironment by Tl exposure and provide a new explanation for Tl toxicity.</span></p>
Carbohydrate complexity limits microbial growth and reduces the sensitivity of synthetic human gut communities to perturbations
<p>Illumina sequencing data for "Carbohydrate complexity limits microbial growth and reduces the sensitivity of synthetic human gut communities to perturbations". Nature Ecology and Evolution, 2022</p>
Dataset used in "Steady state visual evoked potential (SSVEP) based brain-computer interface (BCI) performance under different perturbations" 2018, PLOS ONE
<p>This file contains the segmented EEG data in offline and online conditions. Please read the readme.doc file for the detailed explanation.</p>
Data for "Structure, short-range order, and phase stability of the Al$_x$CrFeCoNi high-entropy alloy: Insights from a perturbative, DFT-based analysis"
<p>Data associated with "Structure, short-range order, and phase stability of the AlxCrFeCoNi high-entropy alloy: Insights from a perturbative, DFT-based analysis", published in npj Comput. Mater. <strong>10</strong>, 271 (2024).</p>
Stochastic Ocean Energy Backscatter via Pressure and Momentum Perturbation
<p>Our research aims to enhance the representation of mesoscale eddies in ocean models, particularly for eddy-permitting resolutions, by incorporating a dynamic backscatter parameterization and additional stochastic perturbations. This study addresses several key modeling issues, including enhancing the representation of missing variability through stochastic forcing, the need for incorporating stochastic terms alongside dynamic backscatter, the propagation of energy across scales and regimes, and distinguishing between different stochastic approaches.</p> <div> <div> <div> <div> <div> </div> </div> </div> </div> </div> <div> <div> <div> <div> <div> <div> <p>The output data from the FESOM2 model (<a href="https://fesom.de/" target="_new" rel="noreferrer">https://fesom.de/</a>) is available here. The file names include information about the corresponding plot in the paper, the simulation name, and the relevant diagnostic variable. Additionally, the uploaded data includes the high-resolution array used to produce stochastic perturbation.</p> </div> </div> </div> </div> </div> </div>
Different behavior of density perturbations between dayside and nightside in the Martian thermosphere and the ionosphere associated with atmospheric gravity waves
<div>---------------------</div> <div>GENERAL INFORMATION</div> <div>---------------------</div> <div> </div> <div>1. Title of Dataset: Different behavior of density perturbations between dayside and nightside in the Martian thermosphere and the ionosphere associated with atmospheric gravity waves</div> <div> </div> <div>2. Authors: Nakagawa, England, et al.</div> <div> </div> <div>3. Contact information: hiromu.nakagawa.c1@tohoku.ac.jp</div> <div> </div> <div>4. Date of data collection: April 2024</div> <div> </div> <div> </div> <div>---------------------</div> <div>DATA & FILE OVERVIEW</div> <div>---------------------</div> <div> </div> <div>1. Original MAVEN data access:</div> <div> </div> <div>The MAVEN/NGIMS (level-2, version-8, revision-1) are publicly available in ASCII format on the NASA Planetary Data System (PDS) at https://atmos.nmsu.edu/data_and_services/atmospheres_data/MAVEN/ngims.html.</div> <div> </div> <div>As for references in Figures 2-4, the MAVEN/MAG Calibrated data are publicly available in ASCII format on the NASA Planetary Data System (PDS) at https://pds-ppi.igpp.ucla.edu/search/view/?id=pds://PPI/maven.mag.calibrated.</div> <div> </div> <div> </div> <div>2. File List:</div> <div> </div> <div>[1] correlate_coefficients.txt</div> <div>[2] rmse_170-190_coupling_case.txt</div> <div>[3] rmse_190-210_coupling_case.txt</div> <div>[4] rmse_170-190_ion_specific_case.txt</div> <div>[5] rmse_190_210_ion_specific_case.txt</div> <div> </div> <div>---------------------</div> <div>DATA-SPECIFIC INFORMATION</div> <div>---------------------</div> <div> </div> <div>[1] correlate_coefficients.txt</div> <div>This includes the geometric information and the calculated correlate coefficient between neutrals and ions in all profiles applied in this study. The first header provides the information in the file: Orbit, Year, Month, Day, Hour, Minute, Unix time, SZA(deg), Lon(deg), Lat(deg), LST(hr), CC(CO2-N2), CC(CO2-CO2+). The geometric information corresponds to those at altitude around 190 km. The last two columns represents the correlate coefficients between CO2 and N2 and between CO2 and CO2+. </div> <div> </div> <div>[2] rmse_170-190_coupling_case.txt</div> <div>This includes RMSE (the unit is percentage) between the observed perturbations and the model fit. The first header provides the information in the file: unix_time, orbit number, sza, lon, lat, lst, rmse_neu_gw_%, rmse_neu_aw_%, rmse_ion_gw_%, rmse_ion_aw_%. The geometric information corresponds to those at altitude around 190 km. The last four RMSEs represents those with the model to fit with the gravity waves (gw) parameters and with the acoustic waves (aw) for the neutral (neu) perturbations (N2) and for the ion (ion) perturbations (CO2+) at altitude range between 170 km and 190 km for the case of ion-neutral coupling case. </div> <div> </div> <div>[3] rmse_190-210_coupling_case.txt</div> <div>This includes RMSE (the unit is percentage) between the observed perturbations and the model fit. The first header provides the information in the file: unix_time, orbit number, sza, lon, lat, lst, rmse_neu_gw_%, rmse_neu_aw_%, rmse_ion_gw_%, rmse_ion_aw_%. The geometric information corresponds to those at altitude around 190 km. The last four RMSEs represents those with the model to fit with the gravity waves (gw) parameters and with the acoustic waves (aw) for the neutral (neu) perturbations (N2) and for the ion (ion) perturbations (CO2+) at altitude range between 190 km and 210 km for the case of ion-neutral coupling case. </div> <div> </div> <div>[4] rmse_170-190_ion_specific_case.txt</div> <div>This includes RMSE (the unit is percentage) between the observed perturbations and the model fit. The first header provides the information in the file: unix_time, orbit number, sza, lon, lat, lst, rmse_neu_gw_%, rmse_neu_aw_%, rmse_ion_gw_%, rmse_ion_aw_%. The geometric information corresponds to those at altitude around 190 km. The last four RMSEs represents those with the model to fit with the gravity waves (gw) parameters and with the acoustic waves (aw) for the neutral (neu) perturbations (N2) and for the ion (ion) perturbations (CO2+) at altitude range between 170 km and 190 km for the case of ion-specific case. </div> <div> </div> <div>[5] rmse_190_210_ion_specific_case.txt</div> <div>This includes RMSE (the unit is percentage) between the observed perturbations and the model fit. The first header provides the information in the file: unix_time, orbit number, sza, lon, lat, lst, rmse_neu_gw_%, rmse_neu_aw_%, rmse_ion_gw_%, rmse_ion_aw_%. The geometric information corresponds to those at altitude around 190 km. The last four RMSEs represents those with the model to fit with the gravity waves (gw) parameters and with the acoustic waves (aw) for the neutral (neu) perturbations (N2) and for the ion (ion) perturbations (CO2+) at altitude range between 190 km and 210 km for the case of ion-specific case. </div> <div> </div> <div>---------------------</div> <div>METHODOLOGICAL INFORMATION</div> <div>---------------------</div> <div> </div> <div>Period to analysis: from March 2015 to August 2020 (orbit number from 713 to 11881)</div> <div> </div> <div>Number of files (CO2): 8,911</div> <div> </div> <div>Number of files (N2): 8,913</div> <div> </div> <div>Number of files (CO2+): 7,053(?)</div> <div> </div> <div>Data selection:</div> <div> </div> <div>1. Neutral species with inbound valid (IV)</div> <div> </div> <div>2. Ion species with SCP (quality flag=0)</div> <div> </div> <div>3. Simultaneous observations of CO2, N2, and CO2+ at altitudes 170-210 km</div> <div> </div> <div>4. All three species CO2, N2, and CO2+ are valid with data sample >10 points in a single orbit.</div> <div> </div> <div>Total number of files after data selection = 3,018</div> <div> </div> <div>Fitting:</div> <div> </div> <div>4th-order polynomial fit to extract the perturbation components of density in the range between 160 and 220 km.</div> <div> </div> <div> </div> <div>Correlation coefficient:</div> <div> </div> <div>The correlation coefficients between perturbations are calculated in the range between 170 and 210 km.</div> <div> </div> <div>Ion-neutral coupling cases whose correlation coefficient between CO2 and CO2+ larger than 0.7: Total number = 839</div> <div> </div> <div>Ion-specific case whose correlation coefficient between CO2 and CO2+ smaller than 0.2: Total number = 823</div> <div> </div> <div>#We also define CME cases based on Lee et al. (2017): Total number = 31 cases</div> <div> </div>
Mechanical energetic contributions of the rectus femoris during perturbed walking
<p>Biomechanical data (kinematics, kinetics, leg EMG) and rectus femoris dynamics of 7 healthy, young participants walking on a treadmill with rapid transient belt accelerations delivered in early or late stance.</p>
Machine Learning Guided AQFEP: A Fast & Efficient Absolute Free Energy Perturbation Solution for Virtual Screening
<p>Data to reproduce primary figures in the manuscript titled: Machine Learning Guided AQFEP: A Fast & Efficient Absolute Free Energy Perturbation Solution for Virtual Screening.</p> <p>URL: https://chemrxiv.org/engage/chemrxiv/article-details/6583785e66c1381729ac86f5</p>
Chemical perturbations impacting histone acetylation regulate colorectal cancer differentiation
<p>M60.count.Rdata: Rdata that includes the raw count, scaled CPM value and meta data of each sample. (Fig. 1 & 4)</p> <p>DAP.merged.Log2FC.csv: integrated DiffBind results that shows the log2FC and P-value/FDR of peaks. (Fig. 1 & 4)</p> <p>rawdata_scRNA-seq.zip: raw count data of scRNA-seq data from cellranger (labels: A: DMSO, B: MRK60, D: MRK60 + JQAD1). (Fig. 5)</p>
Polluting white dwarfs with perturbed exo-comets
<p>MESA inlists associated with <a href="https://ui.adsabs.harvard.edu/#abs/2017MNRAS.469.2750C/abstract">Caiazzo et al. (2017)</a>. MESA version 5456.</p> <p>Publication DOI: <a href="https://doi.org/10.1093/mnras/stx1036">10.1093/mnras/stx1036</a></p>
Atmospheric and sea ice model fields from the perturbed parameter ensemble E3SMv0-HILAT used to examine emergent relationships among climate variables in the Arctic
<p>These files contain time series of several sea ice ad atmospheric fields produced in an ensemble of perturbed parameter simulations using the E3SMv0-HiLAT model. The time series are used to produced seasonal means, which are used to examine emerging relationships in the ensemble discussed in our manuscript, as of September 2019, in review at JGR</p>
Analysis of single-cell CRISPR perturbations indicates that enhancers predominantly act multiplicatively
<p>This repository contains simulated data generated with GLiMMIRS-sim that was analyzed and presented in Zhou & Guyuvayurappan et al, as well as data pertaining to the <em>NMU</em> RT-qPCR experiment described in the manuscript. </p> <p> </p> <ul> <li><span>sim_base_data.tar.gz: directory containing simulated data for baseline model </span></li> <li> <p><span>sim_data_interactions_pos.tar.gz: directory containing simulated data for interactions model with positive interaction effects </span></p> </li> <li> <p><span>sim_data_interactions_neg.tar.gz: directory containing simulated data for interactions model with negative interaction effects </span></p> </li> <li><span>NMU.xlsx: spreadsheet containing data from the <em>NMU</em> RT-qPCR experiment </span></li> </ul>
Data and scripts for: "Exceptional point and hysteresis in perturbations of Kerr black holes" and "Massive scalar perturbations in Kerr Black Holes: near extremal analysis"
<p>Datasets associated with the article <strong>Exceptional point and hysteresis in perturbations of Kerr black holes </strong>- arXiv:2407.20850 [gr-qc] and <strong>Massive scalar perturbations in Kerr Black Holes: near extremal analysis</strong> - 2408.13964 [gr-qc]. The file Isomonodromy.zip contains three subfolders and the file CFM.zip contains two subfolders. Each subfolder includes a readme file that provides a description of the folder contents. A brief description of each subfolder is given below:</p> <p><strong>1) Isomonodromy.zip</strong></p> <p>1.1) Folder "Data" contains data obtained through the isomonodromic method. Data consists of radial eigenvalues (quasinormal frequencies) and angular eigenvalues as a function of the mass of the scalar field and the spin of the Kerr black hole. </p> <p>1.2) Folder "Notebook - Mathematica" contains a Mathematica notebook to compute the angular eigenvalue expansion and the asymptotic expression for the frequency in the extremal limit. </p> <p>1.3) Folder "Script - Julia" constains a script that implements the isomonodromic method to compute quasinormal modes of massive scalar perturbations in Kerr black holes.</p> <p>Note: This script has been tested with Julia 1.10.7 LTS and ArbNumerics 1.5.3. It is currently NOT compatible with Julia 1.11.X, likely due to changes in memory allocation breaking compatibility with libArb.</p> <p><strong>2) CFM.zip</strong></p> <p>1.1) Folder "Data" contains data obtained through the continued fraction method. Data consists of radial eigenvalues (quasinormal frequencies) and angular eigenvalues as a function of the mass of the scalar field and the spin of the Kerr black hole. </p> <p>1.2) Folder "Notebook - Mathematica" implements the continued fraction method to compute quasinormal modes of massive scalar perturbations in Kerr black holes.</p>
Gene Expression Transcriptomics Data for benchmarking Perturbation Models - Part 2
Open the record for dataset details and reuse information.
SPH modelling of companion-perturbed AGB outflows including a new morphology classification scheme
<p><strong>ABSTRACT</strong></p> <p><em>Context.</em> Asymptotic giant branch (AGB) stars are known to lose a significant amount of mass by a stellar wind, which controls the remainder of their stellar lifetime. High angular-resolution observations show that the winds of these cool stars typically exhibit mid- to small-scale density perturbations such as spirals and arcs, believed to be caused by the gravitational interaction with a (sub-)stellar companion.<br> <em>Aims.</em> We aim to explore the effects of the wind-companion interaction on the 3D density and velocity distribution of the wind, as a function of three key parameters: wind velocity, binary separation and companion mass. For the first time, we compare the impact on the outflow of a planetary companion to that of a stellar companion. We intend to devise a morphology classification scheme based on a singular parameter.<br> <em>Methods.</em> We ran a small grid of high-resolution polytropic models with the smoothed particle hydrodynamics (SPH) numerical code Phantom to examine the 3D density structure of the AGB outflow in the orbital and meridional plane and around the poles. By constructing a basic toy model of the gravitational acceleration due to the companion, we analysed the terminal velocity reached by the outflow in the simulations.<br> <em>Results.</em> We find that models with a stellar companion, large binary separation and high wind speed obtain a wind morphology in the orbital plane consisting of a single spiral structure, of which the two edges diverge due to a velocity dispersion caused by the gravitational slingshot mechanism. In the meridional plane the spiral manifests itself as concentric arcs, reaching all latitudes. When lowering the wind velocity and/or the binary separation, the morphology becomes more complex: in the orbital plane a double spiral arises, which is irregular for the closest systems, and the wind material gets focussed towards the orbital plane, with the formation of an equatorial density enhancement (EDE) as a consequence. Lowering the companion mass from a stellar to a planetary mass, reduces<br> the formation of density perturbations significantly.<br> <em>Conclusions.</em> With this grid of models we cover the prominent morphology changes in a companion-perturbed AGB outflow: slow winds with a close, massive binary companion show a more complex morphology. Additionally, we prove that massive planets are able to significantly impact the density structure of an AGB wind. We find that the interaction with a companion affects the terminal velocity of the wind, which can be explained by the gravitational slingshot mechanism. We distinguish between two types of wind focussing to the orbital plane resulting from distinct mechanisms: global flattening of the outflow as a result of the AGB star’s orbital motion and the formation of an EDE as a consequence of the companion’s gravitational pull. We investigate different morphology classification schemes and uncover that the ratio of the gravitational potential energy density of the companion to the kinetic energy density of the AGB outflow yields a robust classification parameter for the models presented in this paper.</p>
OpenIFS experiment data for "How do stratospheric perturbations influence North American weather regime predictions?"
<p>Primary processed experiment data output from 20 OpenIFS experiments used in "<em>How do stratospheric perturbations influence North American weather regime predictions?</em>" (Lee et al., submitted to J. Climate).</p> <p>Date in file string corresponds to initialisation date.</p> <p>Each netCDF file contains:</p> <ul> <li>Valid time</li> <li>500 hPa geopotential heights and anomalies for both control run & polar stratosphere relaxed runs</li> <li>North American principal component loadings for control & relaxed runs</li> <li>Daily North American regime attribution for control & relaxed ensembles, and regime of ensemble mean (0 = ArH, 1 = ArL, 2 = AkR, 3 = PT)</li> <li>100 hPa 60N zonal-mean zonal winds in control & relaxed ensembles</li> </ul> <p>Ensembles contain 21 members, where member 0 is the unperturbed member.<br> <br> </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.