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952 results for “Noise”
Stim Circuits and Data for "Tailoring Dynamical Codes for Biased Noise: The X3Z3 Floquet code"
<p>Example stim circuits used for numerical simulations (for P6, XYZ2, CSS and X3Z3 Floquet codes) and threshold data obtained. See arXiv:2411.04974 for the associated manuscript.</p>
Controlling noise with self-organized resetting
<p>Data used to generate the figures for the manuscript "Controlling noise with self-organized resetting".</p>
Three-dimensional crustal channel flows beneath the southeastern Tibetan Plateau revealed by full-waveform ambient noise tomography
<p>This is a new version of Vp and Vs models for paper titled "Three‐Dimensional Crustal Channel Flows Beneath the Southeastern Tibetan Plateau Revealed by Full‐Waveform Ambient Noise Tomography" published in Geophysical Research Letters.</p> <p>Modification history: new Vs model includes from surface downward to 120 km depth.</p> <p>Please ignore the models in version 1 and 2.</p>
Natural noise affects conspecific signal detection and territorial defense behaviors in songbirds
<p>Recent research suggests that anthropogenic noise can substantially alter animal behavior. Although there are many sources of natural background noise, the relative influence of these sounds on behavior has received much less attention. Using landscape-scale playbacks of rushing rivers and crashing ocean surf, we investigated how habitat appropriate natural noise alters territorial defense behaviors in lazuli buntings (<i>Passerina amoena</i>) occupying riparian areas and spotted towhees (<i>Pipilo maculatus</i>) in riparian and coastal areas when exposed to simulated intruder song. We also incorporated naturally occurring cicada noise as an acoustic source influencing lazuli bunting behavior. Both songbird species possess songs that share substantial spectral overlap with low-frequency, water-generated noise, and lazuli bunting song shares an additional high-frequency overlap with cicada calls. Thus, there is potential for background acoustic conditions to mask conspecific signals. We found that detection and discrimination of conspecific playback occurred more slowly for both species as background sound level increased. Lazuli buntings also exhibited complex flight behavior in noise, suggesting they respond differently depending on the amplitude and type (with versus without cicada calls) of background noise. Our results suggest natural noise can impair territorial defense behaviors in songbirds, highlighting natural soundscapes as an under-appreciated axis of the environment.</p>
Capturing hidden regulation based on noise change of gene expression level from single cell RNA-seq in yeast
<p> </p> <p><strong>Abstract</strong></p> <p><strong>Recent progress in high throughput single cell RNA-seq (scRNA-seq) has activated the development of data-driven inferring methods of gene regulatory networks. Most network estimations assume that perturbations produce downstream effects. However, the effects of gene perturbations are sometimes compensated by a gene with redundant functionality (functional compensation). In order to avoid functional compensation, previous studies constructed double gene deletions, but its vast nature of gene combinations was not suitable for comprehensive network estimation. We hypothesized that functional compensation may emerge as a noise change without mean change (noise-only change) due to varying physical properties and strong compensation effects. Here, we show compensated interactions, which are not detected by mean change, are captured by noise-only change quantified from scRNA-seq. We investigated whether noise-only change genes caused by a single deletion of STP1 and STP2, which have strong functional compensation, are enriched in redundantly regulated genes. As a result, noise-only change genes are enriched in their redundantly regulated genes. Furthermore, novel downstream genes detected from noise change are enriched in “transport”, which is related to known downstream genes. Herein, we suggest the noise difference comparison has the potential to be applied as a new strategy for network estimation that capture even compensated interaction.</strong></p> <p><em><strong>SourceCode</strong></em></p> <p><strong><em>Main.R</em></strong><br> Please execute code along with the guide in this script</p> <p><em><strong>CreateBASiCS.R</strong></em><br> Create BASiCS chain objects, which include mean and noise data, from the raw count matrix. This step takes ~48 hours. Use of HPC is recommended</p> <p><em><strong>DifferenceTestAll.R</strong></em><br> Execute comparison with regard to the mean and noise of expression level quantified from all cells. Test enrichment to the redundantly regulated genes.</p> <p><em><strong>DifferenceTestCluster.R</strong></em><br> Execute comparison with regard to the mean and noise of expression level quantified from cells belonging to the same cluster. Test enrichment to the redundantly regulated genes.</p> <p><em><strong>STP12_detail_analysis.Rmd</strong></em><br> Output results mentioned in the discussion. Code is placed within the chunk.</p> <p><em><strong>CreateSupFig2.R</strong></em><br> Generate supplement figure 2</p> <p><em><strong>CreateFigure4AndS6.R</strong></em><br> Generate figure 4 and supplement figure 6</p> <p><strong>YeastGeneNameList.csv</strong><br> Data that convert ORF id to the common name<br> This data includes 3 columns, Name, ORF, and SGD.<br> - Name: Common name (e.g., TSC3)<br> - ORF: ORF id with Yeastract format (e.g., YBR058C.A)<br> - SGD: ORF id with SGD format (e.g., YBR058C-A)</p> <p><br> <strong>GeneticInteraction(ORF).csv</strong><br> Genetic interaction data downloaded from Yeastract. This data includes two-column, V1 and V2.<br> The interaction is described as two matrices such as V1 output to V2.</p> <p><strong>NoiseChangeGeneList</strong><br> This folder contains data required for generating tables 1 and S2.</p>
NDVI, nocturnal road traffic noise and traffic flow over the canton of Geneva
<p>This dataset relates the spatial distribution of several environmental variables (including NDVI and nocturnal road traffic noise) over the territory of the canton of Geneva (Switzerland) with the aim of studying the potential attenuation effect of vegetation on road traffic noise. Traffic flow measurement points are in this regard also included.</p> <p>The dataset contains two distinct group of files. The first one (hec_grid_ge) contains the hectometric vector grid discretization of the canton of Geneva excluding Lake Geneva. Each cell is characterized by the mean, median and standard deviation of several environmental variables (NDVI, nocturnal road traffic noise, daily road traffic noise and land surface temperature). In addition, BiLISA local Moran's I, p-value and spatial association type for the spatial correlation of median NDVI and spatial lag of median nocturnal road traffic noise are defined for each cell. The second group of files (traffic_ge) contains the traffic flow measurements points which are characterized with "hec_grid_ge" layer variables of the hectometric cell to which they belong to.</p>
Natural and anthropogenic noise increase vigilance and decrease foraging behaviors in song sparrows
<p>Animals glean information about risk from their habitat. The acoustic environment is one such source of information, and is an important, yet understudied ecological axis. Although anthropogenic noise has become recently ubiquitous, risk mitigation behaviors have likely been shaped by natural noise over millennia. Listening animals have been shown to increase vigilance and decrease foraging in both natural and anthropogenic noise. However, direct comparisons could be informative to conservation and understanding evolutionary drivers of behavior in noise. Here, we used 27 song sparrows (Melospiza melodia) and 148 laboratory behavioral trials to assess foraging and vigilance behavior in both anthropogenic and natural noise sources. Using 5 acoustic environments (playbacks of roadway traffic, a white-water river, a white-water river shifted upwards in frequency, a river with the amplitude modulation of roadway traffic, and an ambient control), we attempt to parse out the acoustic characteristics that make a foraging habitat risky. We found that sparrows increased vigilance or decreased foraging in 4 of 6 behaviors when foraging in higher sound levels regardless of the noise source or variation in frequency and amplitude modulation. These responses may help explain previously-reported declines in abundance of song sparrows exposed to playback of intense river noise. Our results imply that natural soundscapes have likely shaped behavior long before anthropogenic noise, and that high sound levels negatively affect the foraging-vigilance trade-off in most intense acoustic environments. Given the ever-increasing footprint of noise pollution, these results imply potential negative consequences for bird populations. </p>
Data from: Coherent mechanical noise cancellation and cooperativity competition in optomechanical arrays
<p>Source data for figures.</p>
Anomalous magnetic noise in an imperfectly flat landscape in the topological magnet Dy_2Ti_2O_7
<p>Noise generated by motion of charge and spin provides a unique window into materials at the atomic scale. From temperature of resistors to electrons breaking into fractional quasiparticles , “listening” to the noise spectrum is a powerful way to decode underlying dynamics. Here, we use ultrasensitive SQUIDS to probe the puzzling noise in a frustrated magnet, the spin-ice compound Dy2Ti2O7 (DTO), revealing cooperative and memory effects. DTO is the first topological magnet in three dimensions–characterised by an emergent magnetostatics and tell-tale fractionalized magnetic monopole quasiparticles–whose real-time dynamical properties have been an enigma from the very beginning. We show that DTO exhibits highly anomalous noise spectra, differing significantly from the expected Brownian noise of monopole random walks, in three qualitatively different regimes: equilibrium spin ice, a ‘frozen’ regime extending to ultra-low temperatures, as well as a high-temperature ‘anomalous’ paramagnet. We present several distinct mechanisms which give rise to varied coloured noise spectra. In addition, we identify the structure of the local spin-flip dynamics as a crucial ingredient for any modelling. Thus, the dynamics of spin ice reflects the interplay of local dynamics with emergent topological degrees of freedom and a frustration-generated imperfectly flat energy landscape, and as such points to intriguing cooperative and memory effects for a broad class of magnetic materials</p>
The cost of noise: Stochastic punishment falls short of sustaining cooperation in social dilemma experiments
<p>Identifying mechanisms able to sustain costly cooperation among self-interested agents is a central problem across social and biological sciences. One possible solution is peer punishment: when agents have an opportunity to sanction defectors, classical behavioral experiments suggest that cooperation can take root. Overlooked from standard experimental designs, however, is the fact that real-world human punishment---the administration of justice---is intrinsically noisy. Here we show that stochastic punishment falls short of sustaining cooperation in the repeated public good game. As punishment noise increases, we find that contributions decrease and punishment efforts intensify, resulting in a 45% drop in gains compared to a noiseless control. Moreover, we observe that uncertainty causes a rise in antisocial punishment, a mutually harmful behavior previously associated with societies with a weak rule of law. Our approach brings to light challenges to cooperation that cannot be explained by economic rationality and strengthens the case for further investigations of the effect of noise---and not just bias---on human behavior.</p>
Associated dataset for "Effects of Additive Noise in Binaural Rendering of Spherical Microphone Array Signals"
<p>The instrumental evaluation utilized the Real-Time Spherical Microphone Renderer (<a href="https://github.com/AppliedAcousticsChalmers/ReTiSAR">ReTiSAR</a>) for binaural reproduction in Python. The employed code state at that time should be used to reproduce the rendering results in this data set exactly. The frozen code state for this data set is available at:<br><a href="https://github.com/AppliedAcousticsChalmers/ReTiSAR/releases/tag/v2021.TASLP">https://github.com/AppliedAcousticsChalmers/ReTiSAR/releases/tag/v2021.TASLP</a></p> <p>Download the rendering pipeline and follow the setup instructions! Use the Conda environment file included here when setting up the Python environment. In this way, you will obtain the exact Python setup as utilized in the instrumental evaluation in the publication:</p> <pre><code>conda env create --file ReTiSAR_environment_freeze.yml</code></pre> <pre><code>source activate ReTiSAR_TASLP_freeze</code></pre> <p>Matlab script "generate_norm_levels.m":</p> <ul> <li>The level contributions used in the publication are contained in "record_CLL_levels.sh", therefore this needs to be executed only in case other level distributions should be generated</li> <li>Generate the string for a ReTiSAR configuration (as used in "record_CLL_levels.sh") to emulate normally contributing EM32 self-noise based on Forum Acusticum publication data</li> <li>Generate the string for aReTiSAR configuration (as used in "record_CLL_levels.sh") to emulate normally contributing GL162 self-noise based on Gaussian normal distribution</li> </ul> <p>Matlab script "prepare_MagLS_HRIRs.m":</p> <ul> <li>Apply Magnitude Least Squares pre-processing to HRIRs (as used in "record_CLL_levels.sh")</li> </ul> <p>Shell script "record_CLL_levels.sh":</p> <ul> <li>Record the output ear signals of the rendering pipeline at multiple head orientations for all investigated configurations (according to Table 1)</li> <li>All captured signals are contained in the respective configuration directory, e.g. "rec_25ch_Fliege_sh4" to "rec_338ch_Gauss_sh12"</li> </ul> <p>Matlab script "calculate_CLL_levels.m":</p> <ul> <li>Read the individual rendering pipeline output recordings for arbitrary configurations</li> <li>Visualize the raw captured signals per configuration</li> <li>Visualize the RMS signal level variations over all head orientations per configuration</li> <li>Visualize the Interaural Level Difference variations over all head orientations per configuration</li> <li>Visualize the Composite Loudness Level variations over all head orientations per configuration (like Figure 2)</li> <li>Gather the above determined RMS, ILD, CLL, etc. metrics in a Matlab dataset per configuration (will be utilized in "plot_gathered_CLL_levels.m")</li> <li>All generated plots and Matlab datasets are contained in the respective configuration directory, e.g. "rec_25ch_Fliege_sh4" to "rec_338ch_Gauss_sh12"</li> </ul> <p>Matlab script "plot_gathered_CLL_levels.m":</p> <ul> <li>Visualize the resulting Composite Loudness Level gradient detections over all head orientations for arbitrary combinations of configurations (like Figure 3 to Figure 14)</li> <li>All generated plots are contained in the "CLL_results" directory</li> </ul>
Vasculature Segmentation Validation Dataset - Part II - Decreasing Contrast-To-Noise Ratio
<p>Dataset to allow exploration of data enhancement, segmentation, and validation for: https://www.biorxiv.org/content/10.1101/2020.07.21.213843v1 and associated future publications</p> <p><strong>Dataset description:</strong></p> <ul> <li><em><strong>LaserForNoise</strong></em>: Example data of the head vasculature of 4dpf of zebrafish. The data were consecutively acquired with 1.2%, 0.8%, and 0.4% laser power (LP), respectively. This allowed us to produce data with decreasing contrast-to-noise ratio, and thus study robustness over a range of signal distributions.</li> </ul> <p><em><strong>Data acquisition</strong></em>:<br> Experiments were performed according to the rules and guidelines of institutional and UK Home Office regulations under the Home Office Project Licence 70/8588 held by TC. Maintenance of adult zebrafish Tg(kdrl: HRAS-mCherry)s916 (Chi et al., 2008) was performed as described in standard husbandry protocols (Westerfield, 1993). Embryos, obtained from controlled mating, were kept in E3 medium buffer with methylene blue and staged as previously described (Kimmel et al., 1995).</p> <p>Embryos were embedded in 2% LMP-agarose with 0.01% Tricaine in E3 (MS-222, Sigma). Data were acquired using a Zeiss Z.1 light sheet microscope, Plan-Apochromat 20x/1.0 Corr nd=1.38 objective, dual-side illumination with online fusion, activated Pivot Scan, image acquisition chamber incubation at 28°C, with a scientific complementary metal-oxide-semiconductor (sCMOS) detection unit. Data properties can be summarised as: 16bit image depth, voxel dimensions in x, y and z of 1920 x 1920 x 400-600, respectively, giving a voxel size of 0.33 x 0.33 x 0.5 µm). </p> <p><strong>Contact</strong>: kugler.elisabeth[at]gmail.com</p> <p><strong>Useful code links</strong>: </p> <ul> <li>https://github.com/ElisabethKugler/ZFVascularQuantification</li> <li>https://github.com/ElisabethKugler/Matlab3D-ImageAnalysis</li> </ul>
Vermilion flycatchers avoid singing during sudden peaks of anthropogenic noise
<p>Data from a playback experiment where we showed that vermilion flycatchers stop singing when experiencing an increase in sudden urban noise, and resume singing showing full vocal recovery after that. This could be an uncommon strategy to enhance information transfer in environments where noise amplitude fluctuates rapidly</p>
Missing eddy feedback may explain weak signal to noise ratios in climate predictions
<p>Python scripts and data files required to reproduce all figures in the publication entitled "Missing eddy feedback may explain weak<br> signal to noise ratios in climate predictions". Please reference the publication if using this code or these data.</p>
Extended Supplement for De-noising distributed acoustic sensing data using an adaptive frequency-wavenumber filter
<p>This electronical extended supplement presents an adaptive frequency-wavenumber filter suppresses the incoherent seismic noise while amplifying the coherent wave field in seismic distributed acoustic sensing (DAS) data. We analyse the response of the filter in time and spectral domain, and we demonstrate its performance on a noisy data set that was recorded in a vertical borehole observatory showing active and passive seismic phase arrivals. In these data we can suppress the noise up to 20 dB. This data publication serves as a repository for data an plotting scripts.</p>
dispersion curvers of southeastern Tibetan Plateau obtained by wave gradiometry and ambient noise cross correlation
<p>azimuth-dependant dispersion curves: bk.gridID.deg.backazimuth.dsp</p> <p>T=5:20s obtained from ambient noise tomography<br> T=21:60s obtained from wave gradiometry<br> grid information: xyloc.txt</p>
Loudness and annoyance ratings of vehicle noise
<p>Loudness and annoyance ratings of the field experiment described in Llorach, Gerard; Oetting, Dirk; Krüger, Melanie; Vormann, Matthias; Fitschen, Christina; Schulte, Michael; Hohmann, Volker; Meis, Markus (2019, September). Vehicle noise: Loudness ratings, loudness models and future experiments with audiovisual immersive simulations. In <em>INTER-NOISE and NOISE-CON Congress and Conference Proceedings</em> (Vol. 259, No. 3, pp. 6752-6759). Institute of Noise Control Engineering. <a href="https://doi.org/10.5281/zenodo.4276090">https://doi.org/10.5281/zenodo.4276090</a>,</p> <p>and of the laboratory experiment in the process of publication.</p> <p>Do not hesitate to contact the main author for more information.</p> <p> </p> <p><strong>Acknowledgments</strong></p> <p>This work received funding from the EU’s H2020 research and innovation program under the MSCA GA 675324 (ENRICH), from the Deutsche Forschungsgemeinschaft (DFG, Cluster of Excellence EXC 1077/1 “Hearing4all”, and SFB1330 Projects B1 and C4).</p>
Impacts of oil well drilling and operating noise on abundance and productivity of grassland songbirds
<p>Anthropogenic noise from natural resource extraction may negatively impact many species, particularly those reliant on acoustic communication. To compare impacts of several types of noise resulting from oil extraction operations on habitat use and productivity of grassland songbirds, we designed and implemented a novel large-scale, spatially and temporally replicated experiment. <br>We recreated soundscapes produced by drilling and operating oil well noise, and compared impacts of noise-producing and quiet playback infrastructure, in twenty-nine 64.7-ha native prairie sites in Alberta, Canada, from 2013–2015. Drilling noise recordings played 24 hours/day for 10 days, twice during each breeding season, while oil well operating noise played continuously, 24 hours/day, throughout each ~90-day breeding season. <br>Despite the much shorter duration of drilling noise playbacks, drilling noise negatively impacted three of our four focal species, and had a much greater impact on habitat use and productivity than did well operating noise. Infrastructure also impacted Vesper Sparrows and Sprague's Pipits, even in the absence of noise. <br>Synthesis and applications: Acute oil drilling noise had a greater negative impact on breeding migratory birds when compared to chronic oil well noise, perhaps because drilling noise is unpredictable. While this study demonstrates that noise alone can negatively impact habitat use, nesting success, and nestling quality, it is also clear that effective mitigation strategies require both noise and above-ground infrastructure management to reduce impacts on wildlife.</p>
Influence of rotation speed on flow field and hydraulic noise in the conduit of a vertical axial-flow pump under low flow rate condition
<p>The complex flow inside the axial-flow pump device will cause the problem of hydraulic noise, in order to explore the influence law of rotation speed on the internal flow characteristics and hydraulic noise of the axial-flow pump conduit, the combination of Computational Fluid Dynamics (CFD) and Computational Acoustics (CA) is used to numerically solve the flow field and internal sound field in the pump device. The results show that the flow in the elbow inlet conduit is smooth at different rotation speeds, and there is no obvious unstable flow. The higher the rotation speed, the more disordered the flow pattern in the left half of the elbow, which intensifies the unstable flow in the straight outlet conduit. The impeller is the main sound source of the internal hydrodynamic noise of the vertical axial-flow pump device, when the sound source propagates upstream and downstream along the conduit, the Total Sound Source Intensity (TSSI) will gradually decay with the increase of distance, the greater the rotation speed is, the faster the Total Sound Source Intensity (TSSI) will decay. When the rotation speed is increased from 1450 r/min to 2200 r/min, the TSSI in the straight outlet conduit is attenuated by 8.9 dB, 13.9 dB and 16.0 dB respectively, and the TSSI in the elbow inlet conduit is attenuated by 11.0 dB, 13.5 dB and 25.9 dB respectively. The vortex structure in the conduit will induce flow noise and delay the attenuation of TSSI in the propagation process, with the increase of rotation speed, this delay will be more obvious.</p>
Dataset, test programs and analysis scripts for the related paper "Effects of reverberation on speech intelligibility in noise for hearing-impaired listeners"
<p>This dataset contains the data, test programs and analyses scripts used for a study submitted as a stage 2 registered report for Royal Society Open Science.</p>
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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.