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7,228
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7,228 results for “Modules”
Seismicity modulation due to hydrological loading in a stable continental region: a case study from the Jektvik swarm sequence in Northern Norway
<p>This folder contains earthquake catalog used in "Seismicity modulation due to hydrological loading in a stable continental region: a case study from the Jektvik swarm sequence in Northern Norway" by Shiddiqi et al. (2022) submitted to Geophysical Journal International.</p> <p>note: unrelocated earthquakes are marked with 999 in location errors.</p>
Earthquake catalog for "Seismicity modulation due to hydrological loading in a stable continental region: a case study from the Jektvik swarm sequence in Northern Norway"
<p>This folder contains earthquake catalog used in "Seismicity modulation due to hydrological loading in a stable continental region: a case study from the Jektvik swarm sequence in Northern Norway" by Shiddiqi et al. (2022) submitted to Geophysical Journal International.</p>
Experience-driven rate modulation is reinstated during hippocampal replay
<p>Replay, the sequential reactivation within a neuronal ensemble, is a central hippocampal mechanism postulated to drive memory processing. While both rate and place representations are used by hippocampal place cells to encode behavioral episodes, replay has been largely defined by only the latter – based on the fidelity of sequential activity across neighboring place fields. Here, we show that dorsal CA1 place cells in rats can modulate their firing rate between replay events of two different contexts. This experience-dependent phenomenon mirrors the same pattern of rate modulation observed during behavior and can be used independently from place information within replay sequences to discriminate between contexts. Our results reveal the existence of two complementary neural representations available for memory processes.</p>
Autophagosomal/autolysosomal/lysosomal dynamics of FaDu and HGFb cells affected by autophagy modulators (dataset of dual labeling of autophagosomes and labeling lysosomes, confocal microscopy)
<p>In this dataset, the impact of autophagy modulators on the auophagosomes and lysosomes in FaDu and HGF cells was investigated. Experimental details are described in the accompanying paper. This dataset contains total 702 CZI confocal image Z-stacks.</p> <p><strong>Relevant paper</strong>: HANELOVA, Klara, RAUDENSKA, Martina, KRATOCHVILOVA, Monika, NAVRATIL, Jiri, VICAR, Tomas, BUGAJOVA, Maria, GUMULEC, Jaromir, MASARIK, Michal and BALVAN, Jan. Autophagy modulators influence the content of important signalling molecules in PS-positive extracellular vesicles. <em>Cell Communication and Signaling</em>. 24 May 2023. Vol. 21, no. 1, p. 120. DOI <a href="https://doi.org/10.1186/s12964-023-01126-z">10.1186/s12964-023-01126-z</a>.</p> <div> <div> <div> </div> </div> </div> <p><strong>Model cell lines</strong></p> <p> </p> <p>The cell line FaDu (HTB-43TM), derived from a squamous cell carcinoma (SCC) of the hypopharynx, and the human gingival fibroblast cell line HGF (derived from the histologically normal gingival biopsy) were used in this study. The authenticated cell lines were purchased from the American Type Culture Collection (ATCC; Manassas, Virginia, USA) within the last five years. </p> <p><strong>Autophagy modulation</strong></p> <p>For autophagy modulation, FaDu cells were treated for 24 h with 5nM bafilomycin A1 (Sigma-Aldrich, B1793), 50 µM of hydroxychloroquine sulphate (Sigma-Aldrich, H0915), 100 µM of Cpd18 (Calbiochem), 50 nM of autophinib (Sigma, SML2632), 10 µM of EACC (MedChemExpress), 200 nM of rapamycin (Sigma-Aldrich, R0395), 3 nM of Torin-1 (MedChemExpress), or 30 nM of NVP-BEZ235 (MedChemExpress). To induce starvation, cells were cultured in DMEM F12 without glutamine and without FBS (Biosera). Modulation of autophagy did not reduce the viability of FaDu cells.</p> <p><strong>Conditioned media preparation</strong></p> <p>see details in the accompanying paper</p> <p><strong>Fluorescence Microscopy</strong><br>The autophagosomal/autolysosomal/lysosomal dynamics of affected cells were observed using the combination of PremoTM Autophagy Tandem Sensor (P36239, Invitrogen) with the far-red emitting LysoTracker® Deep Red (L12492, Invitrogen) (Ex 647 nm/Em 668 nm). By combining acid-sensitive Emerald GFP (Ex 488 nm/Em 509 nm) with acid-insensitive TagRFP (Ex 555 nm/Em 584 nm) in the PremoTM kit, autophagosomes and autolysosomes labelling (yellow and red, respectively) is possible.<br>Immediately after transduction with 12 µl PremoTM Autophagy Tandem Sensor/2ml cell suspension, cells were seeded at 5 × 10<sup>5</sup> into 35-mm glass-bottomed gelatin-coated dishes (Ibidi, μ-Dish 35 mm, high Glass Bottom) and cultured for 48 h to equilibrate expression levels. Subsequently, cells were exposed to the selected agents for 6, 12, 24 and 48 hours before imaging. LysoTracker® Deep Red staining was performed 1 h before imaging. <br>To monitor the uptake of isolated PS-EVs by fibroblasts, we stained EVs with PKH67 (Sigma, PKH67GL) and then removed the remaining dye using Exosome Spin Columns (MW 3000) (Thermo Scientific, #4484449). The stained EVs were then suspended in 400 ul of cultivation medium and added to HGFB cells growing for 24 h in Ibidi µ-Slide I Luer (Ibidi, 80176). Image acquisition was performed 24 hours after EVs addition. 1 µl of 1 µg/ml of Hoechst 33342 (Enzo) (Ex 350 nm/ Em 461 nm) nuclear stain was added 1 hour before imaging.<br>To determine the viability of the cell population prior to isolation of EVs, cells were left in a culture dish with 1 ml of culture medium to which propidium iodide (Sigma-Aldrich) and Hoechst 33342 were added 45 minutes before capturing. <br>To maximize the possibility of comparison between samples, all samples (from a single cell line) were captured on the same day in a single run using the same microscope settings. For each time and each treatment, 10–12 fields of view were captured from randomized sites of the culture dish. Epifluorescent microscopy images and confocal microscopy images were acquired using Laser scanning confocal microscope Zeiss LSM 880 with AiryscanFast module (Carl Zeiss Inc.) using a C-apochromat 40x/1.20 W and C-Apochromat 63 /1.20 W. LysoTracker® Deep Red was excited HeNe 633 nm solid-state laser and emitted light was detected at 638–759 nm. Emerald GFP was excited 488 nm ArgonRemote laser, and emitted light was detected at 493–576 nm. TagRFP was excited DPSS 561 nm laser, and emitted light was detected at 570–650 nm. Hoechst 33342 was excited with a 405 nm solid-state laser, and emitted light was detected at 410–508 nm. Fluorescence images were acquired by the transmitted light detector. <br>Images were analyzed using ImageJ software and custom MATLAB software developed in our laboratory. The analysis process consists of the segmentation of cells from the background and extraction of the intensity of fluorescence channels (TagRFP, GFP, LysoTracker) inside cells. For segmentation, a thresholding-based method was used, where a manually selected threshold was applied. Segmentation was applied to the image created as the sum of all fluorescence channels to achieve segmentation independent of the intensity of individual channels. To achieve better segmentation without noisy pixels, fluorescence images were preprocessed with median filter (7x7) and Gaussian filter (standard deviation 1); additionally, binary segmentation was post-processed with morphological closing and removal of small binary connected components (<5000px). For intensity extraction, the mean value of segmented cell pixels was used for each field of view. Besides individual fluorescence channels, the mean colocalization of TagRFP and GFP was calculated with a pixel-wise multiplication of TagRFP and GFP channels.</p> <p><strong>File Naming</strong></p> <p>CZI images are organised in folders according to cell line, treatment time, and treatment. Names include magnification, cell line measured, treatment, and time of treatment,</p> <blockquote> <p>40x_FADU_BAF_12h_BF_4.czi</p> </blockquote> <p>The abbreviations used for treatments are as follows: BAF, bafilomycin A1; HCQ, hydroxychloroquine sulphate; Cpd18; APB, autophinib; EACC; RAPA, rapamycin; TOR1, Torin-1; BEZ, NVP-BEZ235; starv, starvation; </p>
Neocortical Localization and Thalamocortical Modulation of Neuronal Hyperexcitability contribute to Fragile X Syndrome: EEG Data
<p>Cleaned 128-channel source electrode data analyzed in manuscript</p>
Seasonality modulates habitat cover effects on avian cross-boundary responses and spillover
Species cross-boundary response is a key mechanism affecting species spillover into agricultural fields. However, temporal changes in edge permeability, which may depend on the seasonal availability of resources in both matrix and native habitats, remain poorly understood. Here we tested how edge crossing behavior and the associated spillover of birds into sun coffee plantations respond to landscape structure and seasonality. We monitored the movement of six insectivorous understory bird species (four forest-specialists and two forest-generalists) using an automated telemetry system along a gradient of forest cover (7-60%) during two seasons (dry vs. wet) at nine sampling sites at the Brazilian Atlantic forest. We monitored 116 individuals and obtained a total of 15,129 bird detections across seasons. Bird resistance to crossing edges was strongly driven by an interaction between seasonality and forest cover in the surrounding landscape, with higher resistance to crossing edges along the dry season and in landscapes with lower amount of forest cover. Furthermore, spillover patterns in plantations were driven by an interaction between forest cover and distance from forest edges, but this was most pronounced for forest-specialist bird species. Forest-specialists moved more intensively and farther from edges in more forested landscapes, whereas forest-generalists showed similar patterns of occupation regardless of forest cover and isolation. Our study contributes to a better understanding of avian cross-boundary responses and spillover in response to landscape structure across seasons and the factors driving bird movement decisions in anthropogenic landscapes. There are a myriad of possible mechanisms governing movement decisions, and these mechanisms may interact in complex ways and remain important foci for research within fields of tropical ecology and evolution in the tropics.
Kangaroo fathers modulate maternal control of offspring sex but not post-partum maternal expenditure
<p>When sons and daughters have different fitness costs and benefits, selection may favor deviations from an even offspring sex ratio. Most theories on sex ratio manipulation focus on maternal strategies and sex-biased maternal allocation. Recent studies report paternal influences on both offspring sex ratio and post-partum sex-biased maternal allocation. We used long-term data on marked kangaroos to investigate if and how paternal mass and skeletal size, both determinants of male reproductive success, influenced (a) offspring sex in interaction with maternal mass, and (b) post-partum sex-biased maternal allocation. When mothers were light, the probability of having a son increased with paternal mass. Heavy mothers showed the opposite trend. A similar result emerged when considering paternal size instead of mass. Post-partum maternal sex-specific allocation was independent of paternal mass or size. Studies of offspring sex manipulation or maternal allocation would benefit from an explicit consideration of paternal traits, as paternal and maternal effects can modulated each other.</p>
Apollo 11 Command Module Exterior
Smithsonian source data on the Interior of the Command Module can be found [here](https://ids.si.edu/ids/media_view?id=3d_package:d8c63e8a-4ebc-11ea-b77f-2e728ce88125) and the Exterior of the Command Module can be found [here](https://ids.si.edu/ids/media_view?id=3d_package:d8c6457e-4ebc-11ea-b77f-2e728ce88125) This media file is in the public domain (free of copyright restrictions). You can copy, modify, and distribute this work without contacting the Smithsonian. For more information and to review the 3D disclaimer, visit the Smithsonian's [Terms of Use](https://www.si.edu/Termsofuse) page. Manufacturer: North American Rockwell Materials: Primary Materials: Aluminum alloy, Stainless steel, Titanium Dimensions: Overall: 8'11" ×12'10", 9130lb. (271.8×391.2cm, 4141.3kg) Other: 1'10" (55.9cm) Support(at base width): 12'10" (391.2cm) Overall capsule on stand height: 10'9" Support(Stand): 2035.7kg (4488lb.) Credit Line: Transferred from the National Aeronautics and Space Administration Source: Objaverse 1.0 / Sketchfab
Lunar Command Module
A basic model of the Lunar Command Module of the NASA Apollo moon misions Source: Objaverse 1.0 / Sketchfab
Modulation Analysis of Whistler Mode Sidebands in VLF Triggered Emissions and Implications for Conditions of Nonlinear Growth
<p>A data set from the Siple experiments (Siple Station Antartica) generated on December 8, 1986. A brief explanation of the data:</p> <p>We investigated one particular 35.5 second record that shows the repeated generation of sidebands. This record, occurring on December 8, 1986 during 14:24:29.30 UT -14:24:64.80 UT was triggered by the transmission of a constant amplitude and constant frequency “key down” tone at 2.7 kHz which, remarkably, was observed as 17 individual ∼2 second packets with sidebands and triggered free running emissions in the conjugate region. </p> <p>To open the data, you will need the files - matGetVariable.m AND matGetHeader.m.</p>
Attention modulates trans-saccadic integration data
<p>Dataset for published paper:</p> <p>Attention Modulates Trans-saccadic Integration (2017), Stewart, EEM & Schütz AC, Vision Research</p> <p>https://doi.org/10.1016/j.visres.2017.11.006</p>
Dataset for model input of WRF model for the paper:Modulation of Extratropical Cyclones by Previous Cyclones via the Sea Surface Temperature Anomaly over the Sea of Japan in Winter
<p>This is the dataset and code for generating the lower boundary condition which used in our study submitted to the JGR-Atmospheres. The meteorological data for the initial condition are available on NCEP-FNL ftp database.</p>
Native mass spectrometry and structural studies reveal modulation of MsbA-nucleotide interactions by lipids
<p>The native MS data for paper <strong>"Native mass spectrometry and structural studies reveal modulation of MsbA-nucleotide interactions by lipids"</strong></p>
Temperature modulates dominance of a superinfecting Arctic virus in its unicellular algal host - Nanopore sequencing reads
<p>Nanopore sequencing reads of two Micromonas polaris viruses, MpoV-45T and MpoV-46T using R9 chemistry.</p>
FunShield4Med e-learning module on Computational Toxicology
<p>This is a two-module presentation about the use of computational methods in toxicology providing the audience with an introduction of molecular modelling techniques applied to toxicology assessment (first module, theoretical part). Taking advantage of selected case studies targeting ochratoxin A, interested persons are learning how in silico methods can be broadly applied to investigate the toxicodynamics and toxicokinetic of mycotoxins (second module, e-learning part), supporting the early stage of risk assessment (i.e. the hazard identification and characterization). The two modules are explaining in depth and step-by-step the procedure used and the underpinning rationale and base of knowledge to make anyone virtually able to reproduce such kind of analysis.</p>
Dataset: Transient subglacial water routing efficiency modulates ice1 velocities prior to surge termination on Sít' Kusá, AK
<p>These files complement the data in <em>Transient subglacial water routing efficiency modulates ice1</em><br><em>velocities prior to surge termination on Sít’ Kusá, AK, </em>submitted to Journal of Glaciology. </p> <p>They contain the following: </p> <ul> <li>SK_runoff.csv: spatially integrated surface runoff modelled from climatic variables with the Energy Balance Firn Model (https://github.com/wardvp/EBFM-glacier). File header gives further detailed information, including location coordinates for which the surface runoff is computed.</li> <li>SK_GHT_3_10Hz.csv: file containing the median tremor time series summed between 3 and 10 Hz, which we associate with glaciohydraulic tremor. </li> <li>SK_lags_GHT.csv: file containing the 3-6 day period lag times between station pairs, when GHT signal coherence is >0.7, computed with wavelet coherence as outlined in the paper. </li> </ul> <p> </p>
From hidden hearing loss to supranormal auditory processing by neurotrophin 3-mediated modulation of inner hair cell synapse density
<p><span><span>Loss of synapses between spiral ganglion neurons and inner hair cells (IHC synaptopathy), leads to an auditory neuropathy called hidden hearing loss (HHL) characterized by normal auditory thresholds but reduced amplitude of sound-evoked auditory potentials. It has been proposed that synaptopathy and HHL result in poor performance in challenging hearing tasks despite a normal audiogram. However, this has only been tested in animals after exposure to noise or ototoxic drugs, which can cause deficits beyond synaptopathy. Furthermore, the impact of supernumerary synapses on auditory processing has not been evaluated. Here, we studied mice in which IHC synapse counts were increased or decreased by altering neurotrophin 3 (Ntf3) expression in IHC-supporting cells. As we previously showed, postnatal Ntf3 knockdown or overexpression reduces or increases, respectively, IHC synapse density and suprathreshold amplitude of sound-evoked auditory potentials without changing cochlear thresholds. We now show that IHC synapse density does not influence the magnitude of the acoustic startle reflex or its prepulse inhibition. In contrast, gap-prepulse inhibition, a behavioral test for auditory temporal processing, is reduced or enhanced according to Ntf3 expression levels. These results indicate that IHC synaptopathy causes temporal processing deficits predicted in HHL. Furthermore, the improvement in temporal acuity achieved by increasing Ntf3 expression and synapse density suggests a therapeutic strategy for improving hearing in noise for individuals with synaptopathy of various etiologies.</span></span></p>
Analysis Data, "Strain dynamics of contaminating bacteria modulate the yield of ethanol biorefineries"
<p>This package contains datasets in `Rdata` format underlying analyses presented in the study "Strain dynamics of contaminating bacteria modulate the yield of ethanol biorefineries", first available as a preprint on February 08, 2021:</p> <p><a href="https://www.biorxiv.org/content/10.1101/2021.02.07.430133v1.article-info">https://www.biorxiv.org/content/10.1101/2021.02.07.430133v1.article-info</a></p>
Dataset associated with "Constraints on the subsecond modulation of striatal dynamics by physiological dopamine signaling"
<p>This repository contains behavioral data, dLight photometry measurements, smoothed spiking data from recorded striatal neurons, and miniscope recordings. Text files with further explanation are provided to assist with replication of the main analyses. Matlab code to perform key analyses can be found in the accompanying GitHub repository (https://github.com/sotmasman/Dopamine-constraints)</p>
Intrinsic and Environmental Modulation of Stereoselective Aldol Organocatalyzed Reactions by Proline-Containing Lipopeptides
<p>Electronic Supplementar Information (ESI) for the "Intrinsic and Environmental Modulation of Stereoselective Aldol Organocatalyzed Reactions by Proline-Containing Lipopeptides" manuscript</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.