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3,264 results for “FAST”
Fibertools: fast and accurate m6A calling using single-molecule long-read sequencing (ML data)
<p>Fibertools is a convolutional neural network that permits the fast and accurate identification of endogenous and exogenous N6-methyladenine (m6A)-marked bases using single-molecule long-read sequencing.<strong> </strong>This dataset (ML data) provides training and validation data for training fibertools supervised and semi-supervised CNN models for three long-read chemistries.</p>
Parvalbumin interneuron activity drives fast inhibition-induced vasoconstriction followed by slow substance P-mediated vasodilation
<p>Here, we investigated the hemodynamic responses elicited by optogenetic stimulation of parvalbumin (PV) neurons, the largest population of GABAergic interneurons in the neocortex. This dataset corresponds to the following publication: Thanh Tan Vo, Geun Ho Im, Kayoung Han, Minah Suh, Patrick J. Drew, and SG Kim. Parvalbumin interneuron activity drives fast inhibition-induced vasoconstriction followed by slow substance P-mediated vasodilation. Proceedings of the National Academy of Sciences of the United States of America 2023; Accepted.</p>
Data from: Fast visual adaptation to dim light in a cavity-nesting bird
<p class="MsoNormal"><span>Many birds move fast into dark nest cavities forcing the visual system to adapt to low light intensities. Their visual system takes between 15 and 60 minutes for complete dark adaptation, but little is known about the visual performance of birds during the first seconds in low light intensities. </span></p> <p class="MsoNormal"><span>In a forced two-choice behavioural experiment we studied how well budgerigars can discriminate stimuli of different luminance directly after entering a darker environment. The birds made their choices within about one second and did not wait to adapt their visual system to the low light intensities. When moving from a bright facility into an environment with 0.5 log unit lower illuminance, the budgerigars detected targets with a luminance of 0.825 cd/m<sup>2</sup> on a black background. When moving into an environment with 1.7 or 3.5 log units lower illuminance, they detected targets with luminances between 0.106 and 0.136 cd/m<sup>2</sup>. In tests with two simultaneously displayed targets, the birds discriminated similar luminance differences between the targets (Weber fraction of 0.41-0.54) in all light levels. Our results support the notion that partial adaptation of bird eyes to the lower illumination occurring within one second allows them to safely detect and feed their chicks. </span></p>
ION-FAST 2022-2023 dataset
<p>IONFAST_V_PNG_AUG2022.zip - archive of vertical sounding ionograms in PNG format, registered with ION-FAST during test operation at the Vasilsursk test site in August 2022.</p> <p>IONFAST_V_NPZ_AUG2022.zip - Archive of vertical sounding ionograms in NPZ format (Numpy python zip archive), registered with ION-FAST during test operation at the Vasilsursk test site in August 2022. Each NPZ file contains three variables: "f_axe" - frequency axis (one-dimensional array); "h_axe" - height axis; "ion" - ionogram (two-dimensional array).</p> <p>ION-FAST_FW_V_TX_BPSK.bit - Red Pitaya SDRlab 122-16 firmware that implements the ION-FAST's (vertical ionosonde) TX part with BPSK manipulation.</p> <p>ION-FAST_FW_V_RX.bit - Red Pitaya SDRlab 122-16 firmware that implements the ION-FAST's (vertical ionosonde) RX part.</p> <p>ION-FAST_FW_V_RX.c - the source code of the program that writes the stream of samples from the FPGA to the memory card of the SDRlab 122-16 board.</p> <p>ion-fast-sw.zip - archive with source code, executable file (for the arm6 architecture of the SDRlab 122-16 board) and example input data for the program for calculating the averaged ionogram from a stream of IQ samples.</p> <p>ION-FAST_Chirp_Cyprus_tests.zip - archive containing: 1) files with IQ samples of ION-FAST (chirp ionosonde mode) recordings made on 04/15/2023 11:05:20 UT, 11:20:20 UT and 11:35:20 UT ("bin" extension); 2) files with IQ samples of records made at the same time by a commercial ionosonde ("wav" extension); 3) jupyter notebook file containing the script that calculates and plots ION-FAST's oblique sounding ionograms.</p> <p> </p> <p> </p>
Review data for: SnowQM 1.0: A fast R Package for bias-correcting spatial fields of snow water equivalent using quantile mapping
<p>Climatology of snow water equivalent of Switzerland between winters 1962 and 2021. Obtained using quartile mapping between a model using data assimilation since 1998 and a model without data assimilation. This version of the dataset corresponds to the publication revision time. The publication has been submitted to GMD Copernicus journal as: <em>SnowQM 1.0: A fast R Package for bias-correcting spatial fields of snow water equivalent using quantile mapping</em></p>
Investigating the fast spectral diffusion of a quantum emitter in hBN using resonant excitation and photon correlations
<p>Data from the article "Investigating the fast spectral diffusion of a quantum emitter in hBN using resonant excitation and photon correlations" (<a href="https://journals.aps.org/prb/abstract/10.1103/PhysRevB.107.195304">Phys. Rev. B <strong>107</strong>, 195304 (2023)</a> – [<a href="https://arxiv.org/abs/2303.05315">arXiv</a>])</p>
Drought intensity alters productivity, carbon allocation, and plant nitrogen uptake in fast versus slow grassland communities
<p><span>Grasslands face more frequent and extreme droughts, yet their responses to increasing drought intensity are poorly understood. Increasing drought intensity likely triggers abrupt shifts (thresholds) in grassland ecosystem functioning which can implicate recovery trajectories. </span></p> <p><span>Here, we determined how drought intensity affects plant productivity, and plant-soil carbon (C) and nitrogen (N) cycling. We exposed model grassland plant communities with contrasting resource acquisition strategies (a fast- vs a slow-strategy plant community), to a gradient of drought intensity. The drought gradient ranged from well-watered to severely water-limited conditions. We identified thresholds of plant community productivity (above-ground biomass) at peak drought and two months after re-wetting, and measured net ecosystem exchange and ecosystem respiration of carbon throughout the drought and recovery phases. At peak drought and one week after re-wetting, we traced recently acquired C from plants to the soil and into microbial biomass and fatty acids using <sup>13</sup>C pulse labelling, and measured plant and soil N. </span></p> <p><span>At peak drought, slow-strategy plant communities were more drought resistant than fast-strategy communities, as the threshold in plant productivity occurred at a higher drought intensity for the slow- than the fast-strategy community. Shortly after re-wetting, microbial uptake of recent plant-assimilated C increased with increasing past drought intensity, coinciding with an increase in soil N availability and leaf N. Threshold responses to drought intensity at peak drought translated into non-linear recovery responses, with greater compensatory growth in the fast-strategy community. At peak drought, increasing drought intensity reduced C uptake and increased relative C partitioning to leaves and microbial biomass. Upon re-wetting, plant community strategy mediated drought intensity effects on plant and soil C and N dynamics and plant recovery trajectories. The fast strategy community recovered quickly, with higher leaf N than the slow community, while the slow community increased C allocation to microbial biomass. </span></p> <p><strong><span>Synthesis:</span></strong><span> Our findings highlight that C and N dynamics in the plant-soil system display non-linear responses to increasing drought intensity both during and after drought, which has implications for trajectories of plant community recovery. </span></p>
Dataset - Fast mechanical and biochemical cell wall dynamics underlie plant nutation
<p>Dataset and codes (Python and Matlab) used to produce the figures in the article "Fast mechanical and biochemical cell wall dynamics underlie plant nutation".</p>
Supplemental data for: Visualization of rank-citation curves for fast detection of possible manipulations with the h-index of the university
<p>This dataset consists of papers of universities in the top 30 Scopus Ranking of Ukrainian Universities (May 2023). The data was obtained from Scopus using the search query "AF-ID (“university name”) AND PUBYEAR < 2023 AND PUBYEAR > 2002". Rank-citation curves were also generated for the publications of each university. In this analysis, the rank of publications was plotted along the horizontal axis, while the corresponding citation counts were depicted on the left axis. All types of documents were included in the dataset.</p>
Data from: Reliable and fast genotyping protocol for galactosylceramidase (GALC) in the Twitcher (Twi) mouse
<p><span>The Twitcher (Twi) mouse is a neurological Krabbe disease (KD, or globoid cell leukodystrophy) spontaneous mutant line. The genome of the Twi mouse presents a single nucleotide polymorphism (SNP), leading to an enzymatically inactive galactosylceramidase (GALC) protein and causing KD. In this context, mouse Twi genotyping is an essential step in KD research. To date,</span><span> the genotyping method used is labor-intensive and often drives ambiguous results</span><span>.</span><span> </span><span>Here, we evaluate a novel protocol for the genotype determination of GALC mutation status in Twi mice based on the allele-discrimination real-time polymerase chain reaction (PCR).</span><br><br><span>DNA is extracted from Twi mice (n = 20, pilot study; n = 120, verification study) and control group (n = 10, pilot study; n = 30 verification study) and assessed by allele-discrimination real-time PCR to detect SNP c.355G>A.</span><br><br><span>Using the allele-discrimination PCR, all the samples are identified correctly with the genotype GG (wild-type, WT), GA (heterozygote, HET), or AA (homozygote, HOM) by the first analysis and no animals were not genotyped.</span><br><br><span>We demonstrated that this novel method can be used to distinguish timely, accurately and without </span><span>ambiguity among </span><span>HOM, WT, and HET animals. This protocol represents a great opportunity to increase accuracy and speed in KD research.</span></p>
Data from: Form function relationships support fast ecological shift in a lizard
<p>Macroevolutionary changes such as variation in habitat use or diet are often associated with convergent, adaptive changes in morphology. However, it is still unclear how small-scale morphological variation at the population level can drive shifts in ecology as observed at a macroevolutionary scale. Here, we address this question by investigating how variation in cranial form and feeding mechanics relate to rapid changes in diet in an insular lizard (<em>Podarcis siculus</em>) after experimental introduction into a new environment. We first quantified differences in the skull and jaw muscle architecture between the source and introduced population using 3D geometric morphometrics and dissections. Next, we tested the impact of the observed variation in morphology on the mechanical performance of the masticatory system using computer-based biomechanical simulation techniques. Our results show that the small differences in shape, combined with variation in muscle architecture, can result in significant differences in performance allowing access to novel trophic resources. The confrontation of these data with the already described macroevolutionary relationships between cranial form and function in these insular lizards provides insights into how selection can, over relatively short time scales, drive major changes in ecology through its impact on mechanical performance.</p>
Data from: Fast drug rotation reduces bacterial resistance evolution in a microcosm experiment
<p><span>Drug rotation (cycling), in which multiple drugs are administrated alternatively, has the potential for limiting resistance evolution in pathogens. The frequency of drug alternation could be a major factor to determine the effectiveness of drug rotation. Drug rotation practices often have low frequency of drug alternation, with an expectation of resistance reversion. Here we, based on evolutionary rescue and compensatory evolution theories, suggest that fast drug rotation can limit resistance evolution in the first place. This is because fast drug rotation would give little time for the evolutionarily rescued populations to recover in population size and genetic diversity, and thus decrease the chance of future evolutionary rescue under alternate environmental stresses. We experimentally tested this hypothesis using the bacterium <em>Pseudomonas</em> <em>fluorescens</em> and two antibiotics (chloramphenicol and rifampin). Increasing drug rotation frequency reduced the chance of evolutionary rescue, and most of the final surviving bacterial populations are resistant to both drugs. Drug resistance incurred significant fitness costs, which did not differ among the drug treatment histories. A link between population sizes during the early stages of drug treatment and the end-point fates of populations (extinction versus survival) suggested that population size recovery and compensatory evolution before drug shift increase the chance of population survival. Our results therefore advocate fast drug rotation as a promising approach to reduce bacterial resistance evolution, which in particular could be a substitute for drug mixing when the latter has safety risks.</span></p>
Data from: Individual life histories: Neither slow nor fast, just diverse
<p><span>The slow-fast continuum is known to structure variation in life-history strategies across species. Within populations, it is also assumed to structure individual life histories, yet evidence of its existence remains unclear. We formally assessed the presence of a slow-fast continuum of life histories both within populations and across species using detailed individual-based data for 17 bird and mammal species with contrasting life histories. We estimated adult lifespan, age at first reproduction, breeding frequency and fecundity, and identified the main axes of variation using Principal Component Analyses. The slow-fast continuum was the main axis of life-history variation across species, but within populations individual variation did not follow the slow-fast continuum in any species. This suggests that individual life histories are neither slow nor fast, but rather follow an idiosyncratic pattern across species because of relative differences in the importance of processes such as stochasticity, density dependence, and variation in individual performance.</span></p>
Memory kernel extraction and mean first-passage time for fast-folding proteins (Q - trajectories)
<p>Fraction of native contacts reaction coordinate (Q) trajectories for the 8 proteins that appear in the Dalton et. al. PNAS 2023. For the original all-atom data from which the Q(t) were calculated, contact the group of David E. Shaw at Shaw Research (see the paper - K. Lindorff-Larsen, S. Piana, R. O. Dror, D. E. Shaw, How fast-folding proteins fold. Science 334, 517–520 (2011))</p> <p>Data contains:<br> - Q(t) trajectories for 8 proteins <br> - Corresponding free energy profiles<br> <br> Example analysis codes (written in C++) are included for:<br> - Free energy calculation<br> - Mean first-passage times<br> - Velocity-velocity correlation function and position-force correlation function calculations, needed for memory kernel extraction<br> - Memory kernel extraction (see Ayaz et. al. PNAS 2021)</p>
Dataset for the paper titled "The Fast X-ray Transient XRT 210423 and its Host Galaxy"
<p>This package is the dataset for the paper titled "The Fast X-ray Transient XRT 210423 and its Host Galaxy".<br> <br> Instructions for analysis and to reproduce the figures:</p> <p>Note: These are minimalistic instructions. Please get in touch with me (deepakeappachen5@gmail.com) for more details. </p> <p><br> 1a) We used ESO reflex, la cosmic and IRAF for cleaning, cosmic ray removal, astrometric correction and stacking - the wcs corrected, cosmic ray removed FORS images for XRT 210423 are given as xrt210423_astrometrycorrec.fits.</p> <p><br> 1b) We used the HiPERCAM pipeline to reduce the images. We used the la cosmic and IRAF for astrometric corrections, cosmic removal and stacking. The ugriz fits files are attached.</p> <p>2) We found the zero point by comparing it with the PanSTARRS Catalogue (zp.py is the script used, for FORS R band, we converted the PanSTARRS mags to R band using the transformation_eqn_to_R_band.py)</p> <p>3) For the artificial star experiment and PSF photometry, we used IRAF/Pyraf (python version 2.7). We modelled the PSF from the FORS and HiPERCAM images. (phot_pyraf_new.py was used for the artificial star experiment)<br> - the PSF images: <br> R: Rfors.fits.psf.1.fits<br> u: u.fits.psf.1.fits<br> g: g.fits.psf.1.fits<br> r: r.fits.psf.1.fits<br> i: i.fits.psf.1.fits<br> z: z.fits.psf.1.fits</p> <p> </p> <p>5) For the photometry, we used the SExtractor. </p> <p>6) For spectroscopy, we use XSHOOTER pipeline to obtain the cleaned 2D spectrum.<br> TOO_hard-hostXRT210423_SCI_SLIT_FLUX_MERGE2D_NIR.fits<br> TOO_hard-hostXRT210423_SCI_SLIT_FLUX_MERGE2D_VIS.fits</p> <p>7) For SED fitting we used BAGPIPES. <br> The code used for SED fiiting: photz_bagpipes_n.py</p> <p> Note: We used the stantard filter profiles from http://svo2.cab.inta-csic.es/svo/theory/fps3/index.php?mode=browse&gname=GTC&gname2=HIPERCAM&asttype=astro</p> <p>The codes and the necessary files required for reproducing the Figures are given.</p> <p>Figure 1:</p> <p> plot_abell.py<br> plot_n.py</p> <p><br> Figure 2:<br> XRT_210423.ipynb<br> XRT_210423_pow.txt<br> XRT_210423_HR.txt<br> XRT_210423_model.txt<br> <br> Figure 3:</p> <p> 2dspec_plot_O3.py</p> <p>Figure 4:</p> <p> Obtained by running the BAGPIPES code.</p> <p>Figure 5:</p> <p> offset.py<br> usING: comparison_offset_data.txt<br> fong+22_deepak.txt</p> <p> and </p> <p> sfr_mass.py<br> usING: SNII.dat<br> SNIc.dat<br> SNIb.dat<br> SGRBs_host_properties_fong.txt<br> Schulze_host_properties.txt</p> <p><br> Figure 6:<br> OL_lightcurves.py<br> using: kilonova.csv<br> SGRB_AG.dat<br> SN_2008D.dat</p>
Per- and Polyfluoroalkyl Substances in Canadian Fast Food Packaging
<p>Supporting information (open data) from Per- and Polyfluoroalkyl Substances in Canadian Fast Food Packaging</p>
Schroedinger Bridge Refinement Fast and Full Sim Data
<p>Electron showers in a 10x10 calorimeter simulated with fast simulation methods (GFlash) and full simulation (Geant4). These showers were used for the Schroedinger Bridge Refinement project.<br> 4 different electron energy settings are available:<br> - randomly sampled between 10 and 100 GeV (split into a training and eval set)<br> - 20 GeV<br> - 50 GeV<br> - 80 GeV</p> <p>Each set contains 100k showers. Each shower is a 201-dimensional object, where the first 100 dimensions correspond to the deposited energies in the 10x10 calorimeter cells, the next 100 dimensions. describe the total number of depositions in the cells (not used in the refinement project) and the final dimension gives the incident electron energy. The energy depositions are in units of [GeV], the incident particle energy in units of [MeV]</p>
Data for: Dietary nucleotides can prevent glucocorticoid-induced telomere attrition in a fast-growing wild vertebrate
<p><span>T<span>elomeres are chromosome protectors that shorten during eukaryotic cell replication and in stressful conditions. Developing individuals are </span>susceptible <span>to telomere erosion when their growth is fast and resources are limited. This is critical because the rate of telomere attrition in early life is linked to health and life span of adults. The metabolic telomere attrition hypothesis (MeTA) suggests that telomere dynamics can respond to biochemical signals conveying information about the organism's energetic state. Among these signals are glucocorticoids, hormones that promote catabolic processes, potentially impairing costly telomere maintenance, and nucleotides, which activate anabolic pathways through the cellular enzyme target of rapamycin (TOR), thus preventing telomere attrition. During the energetically demanding growth phase, the regulation of telomeres in response to two contrasting signals—one promoting telomere maintenance and the other attrition—provides an ideal experimental setting to test the MeTa. We studied nestlings of a rapidly developing free-living passerine, the great tit (<em>Parus</em> <em>major</em>), that either received glucocorticoids (Cort-chicks), nucleotides (Nuc-chicks), or a combination of both (NucCort-chicks), comparing these with controls (Cnt-chicks). As expected, Cort-chicks showed telomere attrition, while NucCort- and Nuc-chicks did not. NucCort-chicks was the only group showing increased expression of a proxy for TOR activation (the gene telo2), of mitochondrial enzymes linked to ATP production (cytochrome oxidase and ATP-synthase) and a higher efficiency in aerobically producing ATP. NucCort-chicks had also a higher expression of telomere maintenance genes (shelterin protein TERF2 and telomerase TERT) and of enzymatic antioxidant genes (glutathione peroxidase and superoxide dismutase). The findings show </span>that nucleotide availability is crucial for preventing telomere erosion during fast growth in stressful environments. </span></p>
Dataset_Multiscale Fast Fourier Transform homogenization of additively manufactured fiber reinforced composites from component-wise description of morphology
<p>Original micro-CT imaging data and output of processing via the OpenFiberSeg software of additively manufactured carbon fiber reinforced composites. </p> <p>This dataset accompanies the publication in Composite Science and Technology available at https://doi.org/10.1016/j.compscitech.2023.110261</p> <p> </p>
Dataset for E. Grohs et al., Neutrino fast flavor instability in three dimensions for a neutron star merger, Physics Letters B, https://doi.org/10.1016/j.physletb.2023.138210
<p>.tgz file with hdf5 files for simulation data of a neutron star merger with neutrino flavor transformation. .h5 files are same information in plots 2 and 4 of https://doi.org/10.1016/j.physletb.2023.138210</p>
ScienceDex guides
Understand access before you commit
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.