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105 results for “entrainment”
Auditory Gamma Entrainment
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Lake Mendota Phosphorus Entrainment at North Temperate Lakes LTER 2005
This dataset contains total (TP) and soluble reactive phosphorus (SRP) data collected in Lake Mendota during the summer of 2005 between 6/28/2005 and 10/14/2005 as well as high-resolution temperature data for that same time period . The phosphorus data were taken at five different locations where buoys were deployed. The buoys were deployed with HOBO temperature data loggers attached at 2 - 4 m intervals. Similarly the phosphorus samples were collected at 2 - 4 m intervals throughout the water column. The position of the five buoys changed a few times during the summer in an effort to monitor circulation patterns due to different wind directions and speeds. Manuscript using this dataset: Kamarainen, A.M., H. Yuan, C. Wu, S.R. Carpenter. 2009. One-dimensional and three-dimensional approaches converge on similar estimates of phosphorus entrainment in Lake Mendota. Limnology and Oceanography Methods 7:553-567 Sampling frequency: Water temperature: generally 1 min; some at 5 min. TP and SRP: approximately at 2 weeks intervals Number of sites: 12
EEG Data for: "Cortical oscillations and entrainment in speech processing during working memory load"
<p>This repository contains EEG and audio data used and described in:</p> <p><strong>Hjortkjær, J, Märcher-Rørsted, J, Fuglsang, SA, Dau, T (2018). Cortical oscillations and entrainment in speech processing during working memory load. European Journal of Neuroscience. </strong><strong>doi</strong><strong>:10.1111/ejn.13855</strong></p> <p>Please cite this article when using the data</p> <p> </p> <p>The MAT-files contain the aligned EEG and audio data for each subject (N=22). The envelopes of the speech audio (without noise) have been extracted as described in the paper. Each file (data_N.mat) contains a Matlab struct in the format of the Fieldtrip toolbox containing the following fields:</p> <p> </p> <p>data.trial: EEG and audio data for all 40 trials [channels x timepoints]</p> <ul> <li>channels 1-64: scalp EEG</li> <li>channel 65: left mastoid electrode</li> <li>channel 66: right mastoid electrode</li> <li>channel 67: horizontal EOG</li> <li>channel 68: vertical EOG for left eye</li> <li>channel 69: vertical EOG for right eye</li> <li>channel 70: audio envelopes</li> </ul> <p>data.trialinfo: Experimental condition in each trial</p> <ul> <li>1 = low noise, 1-back</li> <li>2 = low noise, 2-back</li> <li>3 = high noise, 1-back</li> <li>4 = high noise, 2-back</li> </ul> <p>data.time: Sample indices for each trial in seconds</p> <p>data.label: Name of each channel in data.trial</p> <p>data.fsample: EEG/audio sampling rate in Hz (128)</p>
Interagency Ecological Program San Francisco Estuary Larval Entrainment Study (LES)
Fish entrainment into California's State Water Project (SWP) and Central Valley Project (CVP) has been a source of mortality for native osmerid species, including Delta Smelt (Hypomesus transpacificus) and Longfin Smelt (Spirinchus thaleichthys). While entrained adult and juvenile fishes are collected, identified and enumerated, the facilities design does not allow for a quantifiable estimate of larval fishes being entrained. This knowledge gap makes it difficult for managers to make scientifically informed decisions regarding the endangered Longfin & Delta Smelt. The Larval Entrainment Study (LES) aims to address this gap by providing a high-resolution dataset and insights into the variable abundances of Smelt at risk of entrainment, the community composition surrounding them, and associated water quality data. Our study design utilizes a variety of gear types and maximizes replicates to improve the understanding of larval Smelt abundances within the southern reach of the Sacramento and San Joaquin River Delta, the zone of entrainment for the SWP and CVP. Sampling began in 2022 using 10-minute stepped oblique tows of a Smelt Larval Survey (SLS) sled mounted with a 500 μm net. Tows were conducted in West Canal, outside Clifton Court Forebay (CCF), where the risk of entrainment is highest. Sampling was conducted five days a week in 2022 and three days a week in the following years. . Beginning in mid-January 2023, a 940 μm mesh net with the same dimensions as the SLS net was added, with sampling alternating between the two. This provided an intermediate gear between SLS (500 μm) and 20mm (1600 μm) nets. In 2024 we expanded to sample a transect of sites within the Old and Middle River (OMR) corridor. This provides broader spatial resolution and improves our ability to detect Osmerids within the South Delta. Sampling alternated between a high priority day (with intensive sampling in the lower San Joaquin River, SLS stations 809 & 812) and a longer transect day that ran
Multisensory Gamma Entrainment
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South Bay Salt Pond Restoration Project – Phase-1 (2014-2017) Steelhead Outmigration and Entrainment in the A8 Complex.
The South Bay Salt Pond Restoration Project, the largest wetland restoration project in the western United States, is conducting an adaptive management experiment to restore tidal flows to the tidally muted pond A8 complex. The A8 pond complex is a series of interconnected ponds (A8, A7, and A5) located at the interface of the Guadalupe River with Alviso Marsh in Lower South San Francisco Bay that has had a legacy of mercury contamination from cinnabar open-pit mining in the Guadalupe River watershed. As a result, restoration of salt pond habitats in the Alviso Marsh has taken an adaptive management approach whereby the A8 complex was constructed with operable tide gates to facilitate a stepped approach to opening the pond to tidal action. Fish populations, water and sediment were monitored for mercury contamination before and after opening the tide gates and data was used to inform further restoration actions in the A8 complex. However, Central Coast Steelhead Trout, a threatened species inhabit the streams that enter into the Alviso Marsh and the A8 complex, causing management concern for entrainment of outmigration smolts into the A8 complex. In this study, UC Davis conducted back-pack electrofishing in the streams that enter the Alviso Marsh during the late-fall winter of 2013 and 2014. The primary objective of the electrofishing was to collect Steelhead Trout juveniles prior to outmigration to tag with Passive Integrated Transponder (PIT) tags for detection of outmigration and potential entrainment into the A8 complex. In addition to the capture and tagging of Steelhead Trout, we collected data on water quality and catch of non-target fishes. To detect outmigration Steelhead Trout we installed a RFID stream antennae in the lower reaches of the Guadalupe River and to detect entrainment into the A8 complex we installed RFID antennas on the A8 water control structure. A total of 106 Steelhead Trout were captured during the two years of stream electrofishing, and 1
The effect of pseudofrazil particle entrainment on salinity measurements: Data
<p>This experiment was designed to investigate the effect of entraining frazil ice particles found in supercooled ocean water by mimicking their effect through plastic particles of similar material properties as ice. <br> This was done in order to better control the volume concentration of the particles and avoid damage to sensors by icing which is common in supercooled water.<br> In total six experiments were run in which non-spherical round polyamide-12 seeding particles made by Dantec Dynamics A/S with a mean diameter of 50 micro meters were added to natural saltwater tinged with surfactant whilst recording temperature and conductivity with Sea-Bird Electronics sensors. <br> Surfactant was Ecostore-brand eucalyptus laundry liquid (ingredients can be found here: https://ecostore.com/au/eucalyptus-laundry-liquid-409/, last accessed July 2022).<br> Experiments are H1, H2 and HC performed with saltwater taken from Otago Harbour, Dunedin, New Zealand and M1, M2 and MC performed with saltwater taken from the Munida Transect offshore of Otago Peninsula, Dunedin, New Zealand.<br> HC and MC were run in a walk-in freezer with water temperatures around -1 degrees C, all other experiments were performed at ambient room temperatures.<br> The setup consisted of a 30 litre bucket containing 24 litres of seawater filtered to 1 micro meter. Surfactant was added to the water to aid particle dispersion. <br> Subsequently particles were added in increments to a total mass of particles in the bucket of 100 g.<br> Temperature was recorded with a SBE3plus temperature sensor and conductivity with a SBE4C sensor. <br> These were connected to a SBE pump with standard SBE CT ducting. <br> Data were recorded with a SBE31 deck unit connected to a laptop computer.<br> Data were recorded continuously, times at which particles were added or other operations performed are given in the tables <experimentname>info.xlsx<br> Raw data were converted using the sensors' calibration coefficients and corrected for CT offset and cell thermal mass using the SBE data processing software and standard values for sensors configured as in the SBE911+ setup, which is equivalent to the ducting used by us.<br> A manuscript with results from these experiments is available as Richter, M. E., et al., 2023, The Effect of Pseudofrazil Particle Entrainment on Salinity Measurements, Earth and Space Science, doi:10.1029/2022EA002564</p> <p>. </p>
Field data used in "A field-based estimation of the variability of particle entrainment in coarse-bed rivers"
<p>This file is a companion file to "A field-based estimation of the variability of particle entrainment in coarse-bed rivers ", co-authored by Daniel Vázquez-Tarrío, Estrella Carrero-Carralero, Raúl López, Fanny Ville, Damià Vericat and Ramon J. Batalla .</p> <p>This is a paper published in the <em>Journal of Geophysical Research: Earth Surface</em>, 129 (10) (https://doi.org/10.1029/2024JF007695).</p> <p>This Excel file contains all the raw data used in this research.</p>
Dataset for "Surface-Atmosphere Decoupling Prolongs Cloud Lifetime Under Warm Advection Due To Reduced Entrainment Drying"
<p>Dataset for "Surface-Atmosphere Decoupling Prolongs Cloud Lifetime Under Warm Advection Due To Reduced Entrainment Drying". The LES model used is the System for Atmospheric Modeling (SAM) model (http://rossby.msrc.sunysb.edu/~marat/SAM.html). </p>
Infrared Transmission Spectra and Complex Refractive Indices of Surface Soils from Global Dust Entrainment Regions
<p>Spectral data for the paper “Variations in Infrared Complex Refractive Index Spectra of Surface Soils from Global Dust Entrainment Regions” submitted to the journal of <em>Atmosphere</em> Manuscript ID: atmosphere-2291559.</p> <p>Longwave infrared continuum removed transmission spectra, real (<em>n</em>) and imaginary (<em>k</em>) indices of refraction as well as subtractive Kramers-Kronig (SKK) MATLAB code presented in that paper are included in this Zenodo repository.</p> <p>The continuum removed transmission spectral data are stored in an Excel file format in columns and the first column is the wavelengths (µm). </p> <p>Real (<em>n</em>) and imaginary (<em>k</em>) indices of refraction for each sample are stored in a separate file where the first the column is the wavelengths (µm), and the second and third are <em>k</em> and <em>n</em> respectively.</p> <p> </p> <p>LWIR transmission: LWIR transmission was measured in the wavelength range between ~ 2.5 and 25 µm using a benchtop Nicolet 380 Fourier Transform Infrared (FTIR) spectrometer. First, we made soil-KBr pellets using ~ 0.5 mg of soil and ~ 200 mg of KBr blended using a clean mortar and pestle for 2 to 3 minutes to ensure uniform dispersion of mineral particles in the matrix. Pellet production was performed with the means of an evacuable KBr Die Kit and a CrushIR Digital Hydraulic Press from PIKE Technologies (Madison, WI, USA). The mixture was first transferred to the Die Kit which was then pressed under vacuum for about 4 to 5 minutes at a pressure of ~ 10 t cm<sup>-2</sup>, forming a hard disk 13 mm in diameter. Due to the hygroscopic nature of KBr, we pulled a vacuum on the pellet die for approximately 3 to 4 minutes prior to compression, and we immediately placed the pellets in a desiccant box, and then measured transmission within one or two hours of pellet creation.</p> <p>The pellet was attached to a self-adhesive sampling card and placed into the transmission holder. The resulting transmission spectrum for the sample is recorded with the dust-KBr mixture measurement being ratioed to that for an empty chamber, or blank reference. To avoid contamination of transmission spectra with ambient gases, the instrument was initially purged with dry air for at least 5 minutes, prior to each transmission collection. To increase the quality of the spectra and improve the SNR, the numbers of scans averaged were 200 for the blank reference and 100 for the samples.</p> <p>We ratioed transmission spectra to a blank KBr spectrum and then removed the continuum. The continuum removal (CR) transmission spectrum was employed to derive imaginary index of refraction (<em>k</em>) using Beer-Bouguer-Lambert law and <em>k</em> = <em>β<sub>a</sub></em>λ/4π. Real index of refraction (<em>n</em>) spectrum was consequently derived from the <em>k</em> spectrum with a subtractive Kramers-Kronig (SKK) technique. </p> <p>The spectral range of 4–25 μm was chosen to present the transmission spectra as well as real (<em>n</em>) and imaginary (<em>k</em>) indices of refraction since absorption in the region from 2.5 to 3.5 μm is mainly due to water and is not necessarily diagnostic.</p> <p>Here, we define any acronyms that may be present in the names of uploaded Excel files or their contents.</p> <p>*LWIR = Longwave infrared</p> <p>*T = Transmission</p> <p>*CR = Continuum Removed</p>
Transcriptomic analysis of light-induced genes in Nasonia vitripennis: possible implications for circadian light entrainment pathways
<p class="MDPI17abstract"><span>Circadian entrainment to the environmental day-night cycle is essential for the optimal use of environmental resources. In insects, opsin-based photoreception in the compound eye and ocelli, and CRYPTOCHROME1 (CRY1) in circadian clock neurons are thought to be involved in sensing photic information, but genetic regulation of circadian light entrainment in species without light-sensitive CRY1 remains unclear. To elucidate a possible CRY1-independent light transduction cascade, we analysed light-induced gene expression through RNA-sequencing in <em>Nasonia vitripennis</em>. Entrained wasps were subjected to a light pulse in the subjective night to reset the circadian clock and light-induced changes in gene expression were characterized at four different time points in wasp heads. We used co-expression, functional annotation, and transcription factor binding motif analyses to gain insight into the molecular pathways in response to acute light stimulus and form a hypothesis about the circadian light resetting pathway. Maximal gene induction was found after 2h of light stimulation (1432 genes), including the opsin <em>opblue</em> and the core clock genes <em>cry2</em> and <em>npas2</em>. Pathway and cluster analyses revealed light activation of glutamatergic and GABA-ergic neurotransmission, including CREB and AP-1 transcription pathway signalling. This suggests that circadian photic entrainment in <em>Nasonia</em> may require pathways that are similar to mammals. We propose a model for hymenopteran circadian light resetting that involves opsin-based photoreception, glutamatergic neurotransmission, and gene induction of <em>cry2</em> and <em>npas2</em> to reset the circadian clock.</span></p>
Transcriptomic analysis of light-induced genes in Nasonia vitripennis: possible implications for circadian light entrainment pathways
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Data for: Plastic vasomotion entrainment in eLife
<p>The presence of global synchronization of vasomotion induced by oscillating visual stimuli was identified in the mouse brain. Endogenous autofluorescence was used and the vessel "shadow" was quantified to evaluate the magnitude of the frequency-locked vasomotion. This method allows vasomotion to be easily quantified in non-transgenic wild-type mice using either the wide-field macro-zoom microscopy or the deep-brain fiber photometry methods. Vertical stripes horizontally oscillating at a low temporal frequency (0.25 Hz) were presented to the awake mouse and oscillatory vasomotion locked to the temporal frequency of the visual stimulation was induced not only in the primary visual cortex but across a wide surface area of the cortex and the cerebellum. The visually induced vasomotion adapted to a wide range of stimulation parameters. Repeated trials of the visual stimulus presentations resulted in the entrainment of the amplitude of the vasomotion. Horizontally oscillating visual stimulus is known to induce horizontal optokinetic response (HOKR). The amplitude of the eye movement is known to increase with repeated training sessions and the flocculus region of the cerebellum is known to be essential for this learning to occur. Here, we show a strong correlation between the average HOKR performance gain and the vasomotion entrainment magnitude in the cerebellar flocculus. Therefore, the plasticity of vasomotion and neuronal circuits appeared to occur in parallel. Efficient energy delivery by the entrained vasomotion may contribute to meeting the energy demand for increased coordinated neuronal activity and the subsequent neuronal circuit reorganization.</p>
Raw data for the article: A Cryptochrome adopts distinct moon- and sunlight states and functions as sun- versus moonlight interpreter in monthly oscillator entrainment
<p>The moon's monthly cycle synchronizes reproduction in countless marine organisms. The mass-spawning bristle worm Platynereis dumerilii uses an endogenous monthly oscillator to phase reproduction to specific days. Classical work showed that this oscillator is set by full moon. But how do organisms recognize such a specific moon phase? We uncover that the light receptor L-Cryptochrome (L-Cry) is able to discriminate between different moonlight durations, as well as between sun- and moonlight. Consistent with L-Cry's function as light valence interpreter, its genetic loss leads to a faster re-entrainment under artificially strong nocturnal light. This suggests that L-Cry blocks "wrong" light from impacting on the monthly oscillator. A biochemical characterization of purified L-Cry protein, exposed to naturalistic sun- or moonlight, reveals the formation of distinct sun- and moonlight states characterized by different photoreduction- and recovery kinetics of L-Cry's co-factor Flavin Adenine Dinucleotide. In vivo, L-Cry's sun- versus moonlight states correlate with distinct sub-cellular localizations, indicating different signalling. In contrast, r-Opsin1, the most abundant ocular opsin, is not required for monthly oscillator entrainment. Our work reveals a new concept for correct moonlight interpretation involving a "valence interpreter" that provides entraining photoreceptor(s) with light source and moon phase information. These findings advance our mechanistic understanding of a fundamental biological phenomenon: moon-controlled monthly timing. Such level of understanding is also an essential prerequisite to tackle anthropogenic threats on marine ecology.</p>
Data from: Moist heatwaves intensified by entrainment of dry air that limits deep convection
<p>Moist heatwaves in the tropics and subtropics pose substantial risks to society, yet the dynamics governing their intensity are not fully understood. The onset of deep convection arising from hot, moist near-surface air has been thought to limit the magnitude of moist heatwaves. Here, we use reanalysis data, and output from the Coupled Model Intercomparison Project Phase 6 and model entrainment perturbation experiments, to show that entrainment of unsaturated air in the lower-free troposphere (roughly 1--3 km above the surface) limits deep convection, thereby allowing much higher near-surface moist heat. Regions with large-scale subsidence and a dry lower-free troposphere, such as coastal areas adjacent to hot and arid land, are thus particularly susceptible to moist heat waves. Even in convective regions such as the northern Indian Plain, southeast Asia, and interior South America, the lower-free tropospheric dryness strongly affects the maximum surface wet-bulb temperature. As the climate warms, the dryness (relative to saturation) of the lower-free tropospheric air increases; this allows for a larger increase of extreme moist heat, further elevating the likelihood of moist heatwaves.</p>
X-ray computed tomography reveals that grain protrusion controls entrainment shear stress for entrainment of fluvial gravels: Dataset
<p>This is the dataset that accompanies a paper in Geology:</p> <p>Hodge RA, Voepel H, Leyland J, Sear DA, Ahmed S (2020). X-ray computed tomography reveals that grain protrusion controls entrainment shear stress for entrainment of fluvial gravels. Geology, 48(2), 149-153.</p> <p>The aim of this work was to understand how the properties of a sediment grain in a river bed affect the forces required to entrain that grain. This dataset presents the properties of 1055 sediment grains, which were meaured using CT scanning.</p>
Spectral Measurements of Parent Soils from Globally Important Dust Aerosol Entrainment Regions
<p>Spectral data for the paper “Spectral Characterization of Parent Soils from Globally Important Dust Aerosol Entrainment Regions” submitted to the journal of JGR: Atmospheres article number: 2022JD037666.</p> <p>Visible, short-wave infrared (VSWIR) and longwave infrared (LWIR) reflectance spectra as well as longwave transmission spectra presented in that paper are included in this Zenodo repository.</p> <p>The spectral data are stored in CSV file format in columns and the first columns are the wavelengths.</p> <p><strong>VSWIR reflectance</strong>: VSWIR was measured in the wavelength range between ~ 350 and 2500 nm using Spectral Evolution (SE), model RS-5400 portable spectroradiometer with a spectral resolution of 1.5 to 3.8 nm. Soil samples were placed in an aluminum holder and the reflectance spectra collected using a contact probe, equipped with an internal halogen light source. A reflectance spectrum for a spectralon white reference panel was obtained prior to each soil measurement for calibration. All soil reflectance spectra were automatically ratioed to that of the spectralon calibration target. All spectral measurements were converted to absolute reflectance using the correction for spectralon. To obtain adequate signal to noise ratio (SNR), 60 individual scans were averaged for each final output spectrum.</p> <p><strong>LWIR reflectance: </strong>LWIR reflectance was measured in the wavelength range between ~ 2.5 and 25 µm using a benchtop Nicolet 380 Fourier Transform Infrared (FTIR) spectrometer. We used a diffuse reflectance attachment that holds the sample and reference plate horizontally. Gold was used as a reference reflectance standard, because it is highly reflective at all LWIR wavelengths. Once the reference background is collected, the loaded sample holder is placed into the FTIR device to measure the sample reflectance, which is automatically ratioed to the reflectance of the gold plate. This removes the effects caused by the instrument and by atmospheric gases in the instrument path length so that features in the final spectrum are solely due to the sample. To improve the SNR, we set the numbers of scans averaged for the samples and gold reference to 100 and 200, respectively.</p> <p><strong>LWIR transmission: </strong>LWIR transmission was measured in the wavelength range between ~ 2.5 and 25 µm using a benchtop Nicolet 380 Fourier Transform Infrared (FTIR) spectrometer. First, we made soil-KBr pellets using 0.5 mg of soil and 200 mg of KBr blended using a clean mortar and pestle for 2 to 3 minutes to ensure uniform dispersion of mineral particles in the matrix. Pellet production was performed with the means of an evacuable KBr Die Kit and a CrushIR Digital Hydraulic Press from PIKE Technologies (Madison, WI, USA). The mixture was first transferred to the Die Kit which was then pressed under vacuum for about 4 to 5 minutes at a pressure of ~ 10 t cm<sup>-2</sup>, forming a hard disk 13 mm in diameter. Due to the hygroscopic nature of KBr, we pulled a vacuum on the pellet die for approximately 3 to 4 minutes prior to compression, and we immediately placed the pellets in a desiccant box, and then measured transmission within one or two hours of pellet creation.</p> <p>The pellet was attached to a self-adhesive sampling card and placed into the transmission holder. The resulting transmission spectrum for the sample is recorded with the dust-KBr mixture measurement being ratioed to that for an empty chamber, or blank reference. To avoid contamination of transmission spectra with ambient gases, the instrument was initially purged with dry air for at least 5 minutes, prior to each transmission collection. To increase the quality of the spectra and improve the SNR, the numbers of scans averaged were 200 for the blank reference and 100 for the samples.</p>
Circadian rhythm entrainment of the jewel wasp, Nasonia vitripennis, by antagonistic interactions of multiple spectral inputs
<p>Circadian light entrainment in some insects is regulated by blue-light sensitive cryptochrome (CRY) protein that is expressed in the clock neurons, but this is not the case in hymenopterans. The hymenopteran clock does contain CRY, but it appears to be light-insensitive. Therefore, we investigated the role of retinal photoreceptors in the photic entrainment of the jewel wasp <em>Nasonia</em> <em>vitripennis</em>. Application of monochromatic light stimuli at different light intensities caused phase shifts in the wasp's circadian activity from which an action spectrum with three distinct peaks was derived. Electrophysiological recordings from the compound eyes and ocelli revealed the presence of three photoreceptor classes, with peak sensitivities at 340 nm (ultraviolet), 450 nm (blue), and 530 nm (green). An additional photoreceptor class in the ocelli with sensitivity maximum at 560–580 nm (red) was found. Whereas a simple sum of photoreceptor spectral sensitivities could not explain the action spectrum of the circadian phase shifts, modelling of the action spectrum indicates antagonistic interactions between pairs of spectral photoreceptors, residing in the compound eyes and the ocelli. Our findings imply that the photic entrainment mechanism in <em>N</em>. <em>vitripennis</em> encompasses the neural pathways for measuring the absolute luminance as well as the circuits mediating colour opponency. </p>
Data for: Intracranial entrainment reveals statistical learning across levels of abstraction
<div class="t-landing__text-wall "> <p>The following submission contains the data reported from the manuscript "Intracranial entrainment reveals statistical learning across levels of abstraction". The dataset was obtained from 8 neurosurgical patients who had intracranially implanted electrodes for seizure monitoring. Intracranial EEG (iEEG) data were recorded while the patients viewed a rapid stream of scene images. In the Category-Level Structured condition, patients viewed a series of trial-unique scene images, in which the categories of scenes were paired across repetitions (e.g., images of beach always followed by images of canyons). In the Exemplar-level Structured condition, participants viewed a sequence of 6 repeating scene images (from non-overlapping scene categories), which were paired across repetitions (e.g., image A always followed by image B). In the baseline Random condition, participants again viewed a sequence of 6 repeating scene images, but the images were presented in a random temporal order. Each image was presented for 250 ms, followed by a 250 ms inter-stimulus-interval period.</p> <p>The data presented here contain the raw iEEG data from the 8 patients during these task conditions, as well as information about the anatomical placement of their electrodes.</p> </div>
Entrain_example_brain_dataset
<p>Single-cell RNA sequencing dataset of the developing mouse brain at E10 and E11, produced by [1], and processed by [2]. Data has been subset to E10 and E11 and subsampled to 5% of original cells.</p> <p>RNA Velocity matrix has been run on this dataset, using scvelo [3] workflow.</p> <p>Also attached, for convenience, is the required NicheNet database on intercellular regulation [4].</p> <p>[1] La Manno G, Siletti K, Furlan A, Gyllborg D, Vinsland E, Mossi Albiach A, Mattsson Langseth C, Khven I, Lederer AR, Dratva LM, et al: <strong>Molecular architecture of the developing mouse brain.</strong> <em>Nature </em>2021, <strong>596:</strong>92-96.</p> <p>[2] Abdelaal T, Lelieveldt BPF, Reinders MJT, Mahfouz A: <strong>SIRV: Spatial inference of RNA velocity at the single-cell resolution.</strong> <em>bioRxiv </em>2021<strong>:</strong>2021.2007.2026.453774.</p> <p>[3] Bergen V, Lange M, Peidli S, Wolf FA, Theis FJ: <strong>Generalizing RNA velocity to transient cell states through dynamical modeling.</strong> <em>Nature Biotechnology </em>2020, <strong>38:</strong>1408-1414.</p> <p>[4] Browaeys R, Saelens W, Saeys Y: <strong>NicheNet: modeling intercellular communication by linking ligands to target genes.</strong> <em>Nat Methods </em>2020, <strong>17:</strong>159-162</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.