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.
5,371
datasets available to search
ShareScore release 0.9.0
Dataset results
5,371 results for “Flow”
Combining StarDist and TrackMate example 3 - Flow chamber dataset
<p><strong>Description</strong>: Contains a StarDist example training dataset, a test dataset, and the StarDist model generated using ZeroCostDL4Mic (see https://github.com/HenriquesLab/ZeroCostDL4Mic/wiki/Stardist)</p> <p><strong>Training dataset</strong>: Paired microscopy images (brightfield) and corresponding masks</p> <p><strong>Microscopy data type</strong>: brightfield microscopy and masks obtained via manual segmentation (see <a href="https://github.com/HenriquesLab/ZeroCostDL4Mic/wiki/Stardist">https://github.com/HenriquesLab/ZeroCostDL4Mic/wiki/Stardist</a> for details about the segmentation)</p> <p><strong>Microscope</strong>: Images were acquired with a brightfield microscope (Zeiss Laser-TIRF 3 Imaging System, Carl Zeiss) and a 10X objective.</p> <p><strong>File format</strong>: .tif (8-bit for brightfield images and 8 and 16-bit for the masks)</p> <p><strong>Image size</strong>: 1024x1024 (Pixel size: 650 nm)</p>
NUMERICAL INVESTIGATION OF CONDENSING FLOWS IN A SUPERSONIC SEPARATOR- 0,25bar
<p>As a contribution to overcoming the challenges of numerical simulation involving the phenomenon of condensation, this work aims to investigate the nucleation of simple molecules, through the classical nucleation theory (CNT) associated with the Hill’s Moments (MoM) models . The main objective of this simulations was to investigate the numerical precision of the CFD open source code - Stanford University Unstructured(SU2) - to correctly capture the occurrence of a condensation wave, and to analyze thenucleation of liquid droplets through the moments of order zero to three</p>
Neural Reverse Engineering of Stripped Binaries using Augmented Control Flow Graphs
<p>This dataset and pre-trained models are released as a companion to our OOPSLA '20 publication: "Neural Reverse Engineering of Stripped Binaries using Augmented Control Flow Graphs":</p> <ol> <li>The dataset file (<a href="https://zenodo.org/api/files/0e98c909-50b4-43e3-8ab2-bb9673eed786/nero_dataset_binaries.tar.gz?versionId=b943752a-e89e-43c1-b32f-19d4a7420e00">nero_dataset_binaries.tar.gz</a>) is composed from packages of binary executables created by compiling several GNU source-code packages. We used these executables to evaluate our approach as implemented in our prototype "Nero" and compare it to other approaches. All executables contain debug information which serves as the ground truth for the procedure name predictions. The packages are split into three sets: training, validation and test. <ol> <li>The executable file name structure is: "<compiler>-<compiler version>__O<Optimization level(u for default)>__<Package name>[-<optional package version>]__<Executable name>". For example "gcc-5__Ou__cssc__sccs".</li> </ol> </li> <li>The procedure representation file (<a href="https://zenodo.org/api/files/0e98c909-50b4-43e3-8ab2-bb9673eed786/procedure_representations.tar.gz?versionId=fef2380c-c869-4a3f-8e32-bc4972dbb219">procedure_representations.tar.gz</a>) contains: <ol> <li>The raw representations for all the binary procedures in the above dataset. Each procedure is represented by one line in the relevant file for each set (training.json, validation.json and test.json) </li> <li>The above representations preprocessed for training.</li> </ol> </li> <li>The pre-trained model file (<a href="https://zenodo.org/api/files/0e98c909-50b4-43e3-8ab2-bb9673eed786/nero_gnn_model.tar.gz">nero_gnn_model.tar.gz</a>) was created using the above preprocessed dataset and contains: <ol> <li>Pre-trained model.</li> <li>Training log.</li> <li>Prediction results log.</li> </ol> </li> </ol> <p>For the code of the "Nero" prototype, and more information about the above artifacts see <a href="https://github.com/tech-srl/Nero">our Github repo</a></p>
The asymmetric diurnal latent heat flux in Chi-Lan montane cloud-fog forest: CLM simulations and sap flow observations
<p>Chilan_30min_sap_flow_V_2020JJA.csv recorded the data of sap flow velocity during JJA 2020.</p> <p>CL_CTR.*.nc is the analyzed CTR simulations which consider fog interception as a source of canopy water.</p> <p>CL_EXP.*.nc is the analyzed EXP simulations that do not allow the canopy to hold the water.</p>
Global flow of earth science scientific articles based on several databases
<p>Global flow of earth science scientific articles based on several databases contains the summary of our findings from our search of earth science articles in ten databases:</p> <ol> <li>Google Scholar</li> <li>Lens</li> <li>Dimensions</li> <li>Korean Citation Index</li> <li>Russian Scientific Citation Index</li> <li>Garuda Ristekbrin</li> <li>HAL</li> <li>Scielo</li> <li>Scopus</li> <li>Web of Science</li> </ol> <p>The data are visualized using Datawrapper in the following links. All graphs contain links to the data sources (click "Get the data" under each graph):</p> <ol> <li><a href="https://www.datawrapper.de/_/YxTc9/">https://www.datawrapper.de/_/YxTc9/ (Scielo)</a></li> <li><a href="https://www.datawrapper.de/_/blOXM/">https://www.datawrapper.de/_/blOXM/ (Dimensions)</a></li> <li><a href="https://www.datawrapper.de/_/0fyDw/">https://www.datawrapper.de/_/0fyDw/ (Lens)</a></li> <li><a href="https://www.datawrapper.de/_/ad6c8/">https://www.datawrapper.de/_/ad6c8/ (Scopus)</a></li> <li><a href="https://www.datawrapper.de/_/NyypS/">https://www.datawrapper.de/_/NyypS/ (Maximum score for documents in rank promotion regulation of Indonesia)</a></li> <li><a href="https://www.datawrapper.de/_/s1KMD/">https://www.datawrapper.de/_/s1KMD/ (Percentage of OA earth sciences documents in several databases)</a></li> <li><a href="https://www.datawrapper.de/_/2nBnP/">https://www.datawrapper.de/_/2nBnP/ (Sum of earth sciences documents in several databases)</a></li> <li><a href="https://www.datawrapper.de/_/CgpLO/">https://www.datawrapper.de/_/CgpLO/ (Distribution of earth sciences documents by year in log scale)</a></li> </ol>
Renormalisation of the energy-momentum tensor in three-dimensional scalar SU(N) theories using the Wilson flow -- data release
<p>This repository contains the lattice two-point function measurements required to reproduce the results of the paper "Renormalisation of the energy-momentum tensor in three-dimensional scalar SU(N) theories using the Wilson flow" (<a href="https://arxiv.org/abs/2009.14767">https://arxiv.org/abs/2009.14767</a>).</p> <p>The code required to perform the data analysis can be found in <a href="https://github.com/josephleekl/scalar_emt_analysis">https://github.com/josephleekl/scalar_emt_analysis</a>.</p> <p>For any questions please get in touch: joseph.lee@ed.ac.uk </p>
Dataset: COVID-19 implications on maritime trade flows
<p>This dataset can be used to reproduce the results as described in Verschuur et al. (2020), "The implications of large-scale containments policies on global maritime trade during the COVID-19 pandemic", under review. </p> <p> </p> <p>The dataset includes the port-level estimated maritime trade flows (imports and exports) on a daily time scale from January 2019 till August 2020. The data is disaggregated into a 22 sector classification system, which can be aggregated to a 11 sector classification system given the conversion table included. Moreover, the data can be easily aggregated to a country-level using the iso3 code provided. </p>
Debris flow inventory and data for regionally modelling runout in the upper Maipo river basin, Chile
<p>This dataset contains mapped debris flow source points, runout track polygons and elevation data for the upper Maipo river basin, Chile</p>
Analysing landscape effects on dispersal networks and gene flow with genetic graphs
<p>Graph-theoretic approaches have relevant applications in landscape genetic analyses. When species form populations in discrete habitat patches, genetic graphs can be used i) to identify direct dispersal paths followed by propagules or ii) to quantify landscape effects on multigenerational gene flow. However, the influence of their construction parameters remains to be explored. Using a simulation approach, we constructed genetic graphs using several pruning methods (geographical distance thresholds, topological constraints, statistical inference) and genetic distances to weight graph links (F<sub>ST</sub>, D<sub>PS</sub>, Euclidean genetic distances). We then compared the capacity of these different graphs to i) identify the precise topology of the dispersal network and ii) to infer landscape resistance to gene flow from the relationship between cost-distances and genetic distances. Although not always clear-cut, our results showed that methods based on geographical distance thresholds seem to better identify dispersal networks in most cases. More interestingly, our study demonstrates that a subselection of pairwise distances through graph pruning (thereby reducing the number of data points) can counter-intuitively lead to improved inferences of landscape effects on dispersal. Finally, we showed that genetic distances such as the D<sub>PS</sub> or Euclidean genetic distances should be preferred over the F<sub>ST</sub> for landscape effect inference as they respond faster to landscape changes.</p>
Pressure and Inertial sensing drifter data for glacial hydrology flow path.
<p>Raw data for paper titled 'Topology and pressure distribution reconstruction of an englacial channel'</p> <p>The dataset consists of field measurements conducted on Austre Brøggerbreen, Ny-Ålesund, Svalbard. The dataset consists of:</p> <p>(1)Raw englacial data (6 deployments), 2019; (2) Raw supraglacial data (11 deployments), 2019; (3) Average GNSS drifter path along the supraglacial channel, 2019; (4) GNSS drifter path along the englacial channel, 2020; (5) Englacial river mapped from a satellite image.</p> <p>The experimental work was conducted between 30.06.2019 and 05.07.2019, during the period of the main spring snow melt. All drifters were recovered by hand from the river.</p>
Data from: Genomic signatures of sympatric speciation with historical and contemporary gene flow in a tropical anthozoan (Hexacorallia: Actiniaria)
Sympatric diversification is increasingly thought to have played an important role in the evolution of biodiversity around the globe. However, an in situ sympatric origin for co-distributed taxa is difficult to demonstrate empirically because different evolutionary processes can lead to similar biogeographic outcomes- especially in ecosystems that can readily facilitate secondary contact due to a lack of hard barriers to dispersal. Here we use a genomic (ddRADseq), model-based approach to delimit a species complex of tropical sea anemones that are co-distributed on coral reefs throughout the Tropical Western Atlantic. We use coalescent simulations in fastsimcoal2 to test competing diversification scenarios that span the allopatric-sympatric continuum. We recover support that the corkscrew sea anemone Bartholomea annulata (Le Sueur, 1817) is a cryptic species complex, co-distributed throughout its range. Simulation and model selection analyses suggest these lineages arose in the face of historical and contemporary gene flow, supporting a sympatric origin, but an alternative secondary contact model also receives appreciable model support. Leveraging the genome of Exaiptasia diaphana we identify five loci under divergent selection between cryptic B. annulata lineages that fall within mRNA transcripts or CDS regions. Our study provides a rare empirical, genomic example of sympatric speciation in a tropical anthozoan. Finally, these data represent the first range-wide molecular study of any tropical sea anemone, underscoring that anemone diversity is under described in the tropics, and highlighting the need for additional systematic studies into these ecologically and economically important species.
Data from: Anthropogenic land-use change intensifies the effect of low flows on stream fishes
1. As ecosystems experience simultaneous disturbances, it is critical to understand how multiple stressors interact to affect ecological change. Land-use change (LUC) and extreme flow events are two important stressors that could interact to affect fish populations. 2. We evaluated the individual and interactive effects of discharge and LUC associated with oil and natural gas development (ONGD) on populations of two stream fishes over a seven-year period. We used repeated-state (i.e., abundance trends) and rate (i.e., colonization and persistence) responses to advance our understanding of flow-ecology relationships in a multiple-stressor framework. 3. Overall, fish abundance, colonization, and persistence declined in association with discharge. The effect of LUC associated with ONGD differed between species, with the abundance of Mottled Sculpin declining and Mountain Sucker increasing. We found both synergistic and antagonistic interactions between discharge and LUC. LUC intensified the effect of low flows for one species and lead to greater variability in responses to flows for the other species. These differences between species' responses are likely due to differences in their physiological tolerances and behavioral adaptations to disturbance. 4. Synthesis and applications. Our research provides empirical evidence for the complex interactions that can arise between discharge and anthropogenic LUC. Management efforts (e.g., silt fences, vegetation replanting, and in-stream restoration) to mitigate the effects of anthropogenic alterations and promote high-quality refuge habitats could help mitigate the effect of hydrologic extremes. Further development of flow-ecology relationships in a multiple-stressor framework will help guide management of stream fishes, and provide a better understanding of the mechanisms underlying flow-ecology relationships for different species.06-Sep-2019
Data from: Does gene flow aggravate or alleviate maladaptation to environmental stress in small populations?
Environmental change can expose populations to unfamiliar stressors, and maladaptive responses to those stressors may result in population declines or extirpation. Although gene flow is classically viewed as a cause of maladaptation, small and isolated populations experiencing high levels of drift and little gene flow may be constrained in their evolutionary response to environmental change. We provide a case study using the model Trinidadian guppy system that illustrates the importance of considering non-adaptive forces (i.e., gene flow and genetic drift) when predicting (mal)adaptive response to acute stress. We compared population genomic patterns and acute stress responses of inbred guppy populations from headwater streams either with or without a recent history of gene flow from a more diverse mainstem population. Compared to 'no-gene flow' analogues, we found that populations with recent gene flow showed higher genomic variation and increased stress tolerance – but only when exposed to a stress familiar to the mainstem population (heat shock). All headwater populations showed similar responses to a familiar stress in headwater environments (starvation) regardless of gene flow history, whereas exposure to an entirely unfamiliar stress (copper sulphate) showed population-level variation unrelated to environment or recent evolutionary history. Our results suggest that (mal)adaptive responses to acutely stressful environments are determined in part by recent evolutionary history and in part by previous exposure. In some cases, gene flow may provide the variation needed to persist, and eventually adapt, in the face of novel stress.
Data from: The relevance of gene flow with wild relatives in understanding the domestication process
<p><span><span><span>The widespread use of genomic tools has allowed for a deeper understanding of the genetics and the evolutionary dynamics of domestication. Recent studies have suggested that multiple domestications and introgression are more common than previously thought. However, the ability to correctly infer the domestication process depends on having an adequate representation of wild relatives. Cultivated maize (<i>Zea mays</i> spp. <i>mays</i>) is one of the most important crops in the world, with a long and a relatively well documented history of domestication. The current consensus points towards a single domestication event from teosinte <i>Zea mays</i> spp. <i>parviglumis</i> from the Balsas Basin in Southwest central Mexico. However, the underlying diversity of teosintes from lowlands <i>Z. mays</i> spp<i>. parviglumis</i> and highlands <i>Zea mays</i> spp. <i>mexicana</i>) was not taken into account in early studies. We used 32,739 SNPs obtained from 29 teosinte populations and 43 maize landraces to explore the relationship between wild and cultivated members of <i>Zea.</i> We then inferred levels of gene flow among teosinte populations and maize, the degree of population structure of <i>Zea mays</i> subspecies, and potential domestication location of maize. We confirmed a strong geographic structure within <i>Z. mays </i>spp. <i>parviglumis</i> and documented multiple gene flow events with other members of the genus, including an event between <i>Z. mays</i> spp. <i>mexicana </i>and maize. Our results suggest that the likely ancestor of maize may have been domesticated not in the Balsas Basin as previously thought, but in Jalisco or in the Pacific coast, and that different populations of the teosinte subspecies have contributed to modern maize's gene pool. Our results points towards a long period of domestication marked by gene flow with wild relatives, making domestication a long and ongoing process. </span></span></span></p>
Quantification of uncertainties introduced by data-processing procedures of sap flow measurements using the cut-tree method on a large mature tree
<p>Motivation: Sap flow sensors are crucial instruments to understand whole-tree water use. The lack of direct calibration of the available methods on large trees and the application of several data-processing procedures may jeopardize our understanding of water uptake dynamics by increasing the uncertainties around sensor-based estimates. We directly compared the heat ratio method (HRM) sap flow measurements to water uptake measured gravimetrically using the cut-tree method on a large mature aspen tree to quantify those uncertainties for ten consecutive days.</p> <p>Dataset: In this dataset, we provide sap flux density (ten-minutes intervals; g.cm-2.hr-1; corrected for wounding and sapwood thermal diffusivity) obtained from four HRM sap flow sensors installed at 2.5 m high on the focus tree (20 m tall, 60 years old trembling aspen in the boreal mixedwood region of Alberta) between July 18th and August 22nd 2017. We present the code and data (weather data from neighboring weather station) used to calculate whole-tree sap flux (L.hr-1) from each of the individual sensors using different methods of radial integration of sap flux density across the sapwood area estimated via different calculations, as well as different zero-flow corrections used. The cut-tree procedure was applied to the focus tree, and gravimetric measurements of water uptake (ten-minutes intervals) were made using a recording scale. We directly compared the different estimates of hourly, daily and cumulative sap flows obtained with gravimetric measurement of water uptake. We present the code providing the statistical analysis and results reported in the associated publication (Merlin, M., Solarik, K.A., Landhäusser, S.M. Quantification of uncertainties introduced by data-processing procedures of sap flow measurements using the cut-tree method on a large mature tree. 2020. Agricultural and Forest Meteorology, http://dx.doi.org/10.1016/j.agrformet.2020.107926)</p>
Data from: Spatio-temporal dynamics of impulse responses to figure motion in optic flow neurons
White noise techniques have been used widely to investigate sensory systems in both vertebrates and invertebrates. White noise stimuli are powerful in their ability to rapidly generate data that help the experimenter decipher the spatio-temporal dynamics of neural and behavioral responses. One type of white noise stimuli, maximal length shift register sequences (m-sequences), have recently become particularly popular for extracting response kernels in insect motion vision. We here use such m-sequences to extract the impulse responses to figure motion in hoverfly lobula plate tangential cells (LPTCs). Figure motion is behaviorally important and many visually guided animals orient towards salient features in the surround. We show that LPTCs respond robustly to figure motion in the receptive field. The impulse response is scaled down in amplitude when the figure size is reduced, but its time course remains unaltered. However, a low contrast stimulus generates a slower response with a significantly longer time-to-peak and half-width. Impulse responses in females have a slower time-to-peak than males, but are otherwise similar. Finally we show that the shapes of the impulse response to a figure and a widefield stimulus are very similar, suggesting that the figure response could be coded by the same input as the widefield response.
Something old, something new: evolution of Colombian weedy rice (Oryza spp.) through de novo de-domestication, exotic gene flow, and hybridization
<p>Weedy rice (<i>Oryza</i> spp.) is a worldwide weed of domesticated rice (<i>O. sativa</i>), considered particularly problematic due to its strong competition with the crop, which leads to reduction of yields and harvest quality. Several studies have established multiple independent origins for weedy rice populations in the U.S. and various parts of Asia; however, the origins of weedy rice in South America have not been examined in a global context. We evaluated the genetic variation of weedy rice populations in Colombia, as well as the contributions of local wild<i> Oryza </i>species, local cultivated varieties, and exotic <i>Oryza</i> groups to the weed, using polymorphism generated by genotyping by sequencing (GBS). We found no evidence for genomic contributions from local wild <i>Oryza </i>species<i> </i>(<i>O. glumaepatula</i>, <i>O. grandiglumis</i>, <i>O. latifolia </i>and <i>O. alta</i>) to Colombian weedy rice. Instead, Colombian weedy rice has evolved from local <i>indica</i> cultivars, and has also likely been inadvertently imported as an exotic pest from the US. Additionally, weeds comprising <i>de novo</i> admixture between these distinct weedy populations now represent a large proportion of genomic backgrounds in Colombian weedy rice. Our results underscore the impressive ability of weedy rice to evolve through multiple evolutionary pathways, including in situ de-domestication, range expansion, and hybridization.</p>
Using a coalescent approach to assess gene flow and effective population size of Acrocomia aculeata (Jacq.) Lodd. Ex Mart. in the Brazilian Atlantic Forest
<p><i>Acrocomia aculeata</i> is a tropical palm tree native to Central and South America that has significant economic, social, and environmental potential. However, land encroachment due to the expansion of agribusiness, and other factors such as urban sprawl, have resulted in the fragmentation and destruction of its habitat, leading to the loss of genes and genotypes in <i>A. aculeata</i> populations. In this context, the objective of this study was to characterize the genetic variability of <i>A. aculeata</i> populations by estimating gene flow and effective population size using an approach based on coalescent theory. Four populations located in the municipalities of Teodoro Sampaio (TSI and TSII), Rosana (RA), and Amparo (AP) in São Paulo State, Brazil, were genotyped with nine microsatellite markers. Gene flow and effective population size were estimated using a coalescent-based Bayesian inference implemented in the MIGRATE-N software. The effective population size (<i>N<sub>e</sub></i>) was obtained considering an assumed mutation rate of <a name="_Hlk6565387">5x10<sup>-5</sup>. </a>Gene flow (<i>Nm</i>) for pairwise populations ranged from 0.28 to 1.17, with higher levels of migration between the three geographically proximal locations (TSI, TSII, and RA). The estimates of effective population size (<i>N<sub>e</sub></i>) were 444, 835, 838, and 874 for AP, TSII, RA, and TSI, respectively, showing that the effects caused by genetic drift may be more pronounced when <i>N<sub>e</sub></i> is smaller. The coalescent-based results add to our understanding of <i>A. aculeata</i> population genetics and suggest that some traditional assessment methods may be ineffective in characterizing historical evolutionary processes.</p>
Bridging the flux gap: sap flow measurements reveal species-specific patterns of water-use in a tallgrass prairie
<p>Predicting the hydrological consequences following changes in grassland vegetation type (i.e., woody encroachment) requires an understanding of water flux dynamics at high spatiotemporal resolution for predominant species within grassland communities. However, grassland fluxes are typically measured at the leaf or landscape scale, which inhibits our ability to predict how individual species contribute to changing ecosystem fluxes. We used external heat balance sap flow sensors and a hierarchical Bayesian state-space modeling approach to bridge this "flux-gap" and estimate continuous species-level water flux in common tallgrass prairie species. Specifically, we asked: 1) How do diurnal and nocturnal water fluxes differ among woody and herbaceous plants? (2) How sensitive are woody and herbaceous species to environmental drivers of diurnal and nocturnal water flux? We highlight three results: (1) <i>Cornus drummondii</i>, the primary woody encroacher in this grassland, exhibited the greatest canopy-level water loss, (2) nocturnal transpiration was a large component of the water lost in this ecosystem and was driven primarily by C<sub>4</sub> grasses and <i>C. drummondii</i>, and (3) the sensitivity of canopy transpiration to environmental drivers varies among plant functional types and throughout a 24-hour period. Our data reveal important insights regarding the water-use strategies of woody versus herbaceous species in tallgrass prairies, and about the potential hydrological consequences of ongoing woody encroachment. We suggest that the high, static flux rates observed in woody species will likely deplete deep water stores over time, potentially creating hydrological deficits in grasslands experiencing woody encroachment and concomitantly increasing the vulnerability of these ecosystems to drought.</p>
Riccati-Based Feedback Stabilized Navier-Stokes Flow
Closed-loop simulation of Navier-Stokes flow within "von Kármán vortex street". The vertical component of the velocity field is illustrated. The top video shows the velocity field without any feedback. The middle video shows the influence of the initial feedback, compute via a Bernoulli equation. The bottom video shows the stabilizing influence of the Riccati-based feedback for $\lambda=2$.
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.