Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
1,880
datasets available to search
ShareScore release 0.9.0
Dataset results
1,880 results for “Dimensionality”
Data from: The dimensionality of stability depends on disturbance type
Ecosystems respond in various ways to disturbances. Quantifying ecological stability therefore requires inspecting multiple stability properties, such as resistance, recovery, persistence, and invariability. Correlations among these properties can reduce the dimensionality of stability, simplifying the study of environmental effects on ecosystems. A key question is how the kind of disturbance affects these correlations. We here investigated the effect of three disturbance types (random, species-specific, local) applied at four intensity levels, on the dimensionality of stability at the population and community level. We used previously parameterized models that represent five natural communities, varying in species richness and the number of trophic levels. We found that disturbance type but not intensity affected the dimensionality of stability and only at the population level. The dimensionality of stability also varied greatly among species and communities. Therefore, studying stability cannot be simplified to using a single metric and multi-dimensional assessments are still to be recommended.
Data from: Ultrasonic cavitation induces necrosis and impairs growth in three-dimensional models of pancreatic ductal adenocarcinoma
Introduction: Pancreatic ductal adenocarcinoma (PDAC) is a rapidly increasing cause of mortality whose dismal prognosis is mainly due to overwhelming chemoresistance. New therapeutic approaches include physical agents such as ultrasonic cavitation, but clinical applications require further insights in the mechanisms of cytotoxicity. Three dimensional in vitro culture models such as spheroids exploit realistic spatial, biochemical and cellular heterogeneity that may bridge some of the experimental gap between conventional in vitro and in vivo experiments. Purpose: to assess the feasibility and efficiency of inertial cavitation associated or not with chemotherapy, in a spheroid model of PDAC. Methods: we used DT66066 cells ,derived from a genetically-engineered murine PDAC, isolated from KPC-transgenic mice (LSL-KrasG12D/+; LSL-Trp53R172H/+; Pdx-1- Cre). Spheroids were obtained by either a standard centrifugation-based method, or by using a magnetic nano-shuttle method allowing the formation of spheroids within 24 hours and facilitating their handling. The spheroids were exposed to ultrasonic inertial cavitation in a specially designed setup. Four conditions were studied: control, gemcitabine alone , US cavitation alone , US cavitation + gemcitabine. Five US inertial cavitation indexes, corresponding to increased US intensities, were evaluated . The effectiveness of treatment was assessed after 24 hours with the following criteria: spheroid size (growth), ratio of phase S cells (proliferation), proportion of cells in apoptosis or necrosis (cellular mortality). These parameters were assessed by quantitative immunofluorescence techniques. Results: The 3D culture model presented excellent reproducibility. Eight or nine spheroids were analyzed for each condition. Cavitation induced a significant decrease in the size of spheroids , an effect significantly correlated to an increasing cavitation index (p < 0.0001). The treatment induced cell death whose predominant mechanism was necrosis (p < 0.0001). There was a tendency to a synergistic effect of US cavitation and gemcitabine at 5μM concentration, however significant in only one of the cavitation indexes used (p = 0. 013). Conclusion: Ultrasonic inertial cavitation induced a significant reduction of tumor growth in a spheroid model of PDAC., with necrosis rather than apoptosis as a Cell dominant mechanism of cell death. More investigations are needed to understand the potential role of inertial cavitation in overcoming chemoresistance.
Data from: Three-dimensional camouflage: exploiting photons to conceal form
Many animals have a gradation of body color, termed "countershading," where the areas that are typically exposed to more light are darker. One hypothesis is that this patterning enhances visual camouflage by making the retinal image of the animal match that of the background, a fundamentally two-dimensional theory. More controversially, countershading may also obliterate cues to three-dimensional (3D) shape delivered by shading. Despite relying on distinct cognitive mechanisms, these two potential functions hitherto have been amalgamated in the literature. It has previously not been possible to validate either hypothesis empirically, because there has been no general theory of optimal countershading that allows quantitative predictions to be made about the many environmental parameters involved. Here we unpack the logical distinction between using countershading for background matching and using it to obliterate 3D shape. We use computational modeling to determine the optimal coloration for the camouflage of 3D shape. Our model of 3D concealment is derived from the physics of light and informed by perceptual psychology: we simulate a 3D world that incorporates naturalistic lighting environments. The model allows us to predict countershading coloration for terrestrial environments, for any body shape and a wide range of ecologically relevant parameters. The approach can be generalized to any light distribution, including those underwater.
Data from: Three-dimensional morphological variability of recent rhynchonellide brachiopod crura
Crura, the calcareous support structures of the lophophore in rhynchonellide brachiopods, have historically been used to justify higher-level rhynchonellide classification and reveal major evolutionary lineages within rhynchonellides. Seventeen crural types have been described and categorized into four groups based on variation in overall structure and cross-sectional shape, but not evaluated in a quantitative or comprehensive manner. Heterochrony has been hypothesized to play a role in the evolutionary transitions among some types, but the structural, developmental, and phylogenetic context for testing these hypotheses has not yet been established. In this study, we use three-dimensional geometric morphometric techniques to quantify morphological disparity among all six crural morphs in Recent adult rhynchonellides, with the goal of delineating more objective criteria for identifying and comparing crural morphs, ultimately to test hypotheses explaining morphological transformations in ontogeny and phylogeny. We imaged the crura of seven Recent rhynchonellide species, using X-ray computed microtomography. We used landmarks and semi-landmarks to define the dimensions and curvature of the crura and the surrounding hinge area. Procrustes-standardized landmark coordinates were analyzed using a principal component analysis to test the discreteness of the individual crural morphs and named groups of morphs, and to identify features that vary most among the crural configurations. Our results demonstrate that microCT imaging techniques provide novel ways to investigate the morphology of small features that may be otherwise impossible to quantify using more conventional imaging techniques. Although we predicted overlap among crural morphs in the 3-D shape space, the principal component analyses suggest that five of the six crural morphs differ distinctly from one another. Some but not all previously designated crural groups appear to exhibit morphological cohesion. This study establishes a quantitative morphological foundation necessary to begin an investigation of the phylogenetic significance of ontogenetic changes in crura, which will allow hypotheses of heterochrony to be tested.
Data from: ZeitZeiger: supervised learning for high-dimensional data from an oscillatory system
Numerous biological systems oscillate over time or space. Despite these oscillators' importance, data from an oscillatory system is problematic for existing methods of regularized supervised learning. We present ZeitZeiger, a method to predict a periodic variable (e.g. time of day) from a high-dimensional observation. ZeitZeiger learns a sparse representation of the variation associated with the periodic variable in the training observations, then uses maximum-likelihood to make a prediction for a test observation. We applied ZeitZeiger to a comprehensive dataset of genome-wide gene expression from the mammalian circadian oscillator. Using the expression of 13 genes, ZeitZeiger predicted circadian time (internal time of day) in each of 12 mouse organs to within ∼1 h, resulting in a multi-organ predictor of circadian time. Compared to the state-of-the-art approach, ZeitZeiger was faster, more accurate and used fewer genes. We then validated the multi-organ predictor on 20 additional datasets comprising nearly 800 samples. Our results suggest that ZeitZeiger not only makes accurate predictions, but also gives insight into the behavior and structure of the oscillator from which the data originated. As our ability to collect high-dimensional data from various biological oscillators increases, ZeitZeiger should enhance efforts to convert these data to knowledge.
Data quality definitions systematic search; data and coding (2008-2024 april, version edit Dimensional-definitions worksheet)
Open the record for dataset details and reuse information.
Three-Dimensional Geostatistical Inverse Analyses of Transient Head and Temperature Data from a Long-Term Heat Tracer Test
<p>The spreadsheet contains datasets utilized to accomplish the study. </p>
Active learning molecular dynamics-assisted insights into ultralow thermal conductivity of two-dimensional covalent organic frameworks
<p>This is a training sets for monolayer COF-5, which could be used for NEP trainging.</p>
FIGURE 1 in Ex vivo three-dimensional reconstruction of Acutiramus: a giant pterygotid sea scorpion
FIGURE 1. The traditional reconstruction of Pterygotus from Clarke and Ruedemann (1912: pls. 67, 68): A. dorsal reconstruction; B. ventral reconstruction.
FIGURE 2 in Ex vivo three-dimensional reconstruction of Acutiramus: a giant pterygotid sea scorpion
FIGURE 2. Acutiramus and Erettopterus specimens showing the general morphology and arrangement of appendages and ventral structures. A, B. Acutiramus cummingsi from the Silurian (Pridoli), Bertie Group, Williamsville Formation, Bennett Quarry (= Buffalo Cement Company), Buffalo, NY (N 42.942, W 78.825). A. USNM PAL 60053 (Clarke and Ruedemann, 1912: pl. 72, fig. 1). B. NYSM 10193 (Clarke and Ruedemann, 1912: pl. 78, fig. 3). C. Acutiramus macrophthalmus (Hall, 1859) from the Silurian (Pridoli), Bertie Group, Fiddlers Green dolomite. No locality data. NYSM E3584. D. Erettopterus bilobus (Salter, 1856) from the Silurian (latest Llandovery and Wenlock) Patrick or Kip Burn formation, Scotland. NHMUK PI In 59342. A–C. Photographed under water. B, C. Photographs by Lisa Amati.
Dataset for "Linear theory analysis and one-dimensional hybrid simulations of high-frequency EMIC waves in a dipole magnetic field"
<p>Processed dataset to produce the figures in the manuscript</p>
Three-dimensional simulation results of Perkins instability in the midlatitude F-region ionosphere
<p>The simulated results for Perkins instability</p>
Data from "Three-dimensional wave breaking"
Open the record for dataset details and reuse information.
Two-dimensional arsenene/HfNBr van der Waals Heterojunction as water splitting photocatalyst: first-principles predictions
<p>Please see ref:</p> <p> </p> <p>(under review)</p>
Simulation Data and postprocessing code for "Two-Dimensional Nonlocal Eshelby's Inclusion Theory: Eigenstress-Driven Formulation and Applications"
Open the record for dataset details and reuse information.
Prevalence of two-dimensional photonic topology
<p>A dataset of two-dimensional photonic crystals and their attendant topological properties.</p>
lcUMAPtSNE: Use of non-linear dimensionality reduction techniques with genotype likelihoods
<p>This repository contains genotype likelihood estimations derived from open-access whole-genome re-sequencing datasets of the scimitar-horned oryx (SO). The dataset was downsampled to exhibit varying coverage levels, including 6x, 2x, and 0.5x. Genotype likelihoods were estimated, followed by the calculation of principal components and subsequent application of UMAP and t-SNE with varying parameter settings, as detailed in Uzel et al. (2025). All intermediate and input files generated from these datasets are available here. Genotype likelihood estimations are provided in the formats '.beagle.gz' and '.mafs.gz'. Additionally, the repository contains the input covariance matrix ('.cov') for each dataset and the population information file for each group, which were employed in the non-linear dimensionality reduction steps described in Uzel et al. (2025).</p> <h3>Raw data resources</h3> <p>All raw sequencing data we used in this study were downloaded from public databases, and no new data were generated.</p> <p>The scimitar-horned oryx data were acquired from NCBI BioProject PRJEB37295 (Humble et al. 2023)</p> <h3>Code/Software</h3> <p>All bioinformatic codes used for generating the results and guidelines presented in Çilingir et al. (2024) are available at <strong><a href="https://github.com/fgcilingir/lcUMAPtSNE">https://github.com/fgcilingir/lcUMAPtSNE</a>.</strong></p> <h3>Literature Cited</h3> <p>Humble, E., Stoffel, M. A., Dicks, K., Ball, A. D., Gooley, R. M., Chuven, J., Pusey, R., Remeithi, M. A., Koepfli, K.-P., Pukazhenthi, B., Senn, H., & Ogden, R. (2023). Conservation management strategy impacts inbreeding and mutation load in scimitar-horned oryx. <em>Proceedings of the National Academy of Sciences of the United States of America</em>, <em>120</em>(18), e2210756120.<br><br>Uzel, K., Grossen, C., Çilingir, F.G. (2025) lcUMAPtSNE: Use of non-linear dimensionality reduction techniques with genotype likelihoods. <em>bioRxiv,</em> https://doi.org/10.1101/2024.04.01.587545.</p>
Strain Mapping of Two-Dimensional Heterostructures with Subpicometer Precision
<p>The sample is a WS<sub>2</sub>-WSe<sub>2</sub> lateral heterojunction with an in-plane epitaxial interface. The datasets were collected by electron microscope pixel array detector (EMPAD) under the condition described in this paper (Han, et al. Nano Letters, 18, 3746-3751 (2018)). The rotation angle between the real space and diffraction space in these datasets is 15 degrees. The data have also been analyzed in our recent paper (arXiv:2111.06496) and a conference proceeding (Shi, et al. Microsc. Microanal. 27 Suppl 1, 2021). </p>
Ciliary beating patterns map onto a low-dimensional behavioural space
<p>Biological systems are robust to perturbations at both the genetic and environmental levels, although these same perturbations can elicit variation in behaviour. The interplay between functional robustness and behavioural variability is exemplified at the organellar level by the beating of cilia and flagella. Cilia are motile despite wide genetic diversity between and within species, differences in intracellular concentrations of ATP and calcium, and considerable environment fluctuations in temperature and viscosity. At the same time, these perturbations result in a variety of spatio-temporal patterns that span a rich behavioural space. To investigate this behavioural space we analysed the dynamics of isolated cilia from the unicellular algae Chlamydomonas reinhardtii under many different environmental and genetic conditions. We found that, despite large changes in beat frequency and amplitude, the space of waveform shapes is low-dimensional in the sense that two features account for 80% of the observed variation. The geometry of this behavioural space accords with the predictions of a simple mechanochemical model in the low-viscosity regime. This allowed us to associate waveform shape variability with changes in only the curvature response coefficients of the dynein motors.</p>
A4. Lista de propuestas que conforman las dimensiones
<p>A4. Lista de propuestas que conforman las dimensiones</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.