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FIG. 6 in Évolution de la diversité des Brissopsis (Echinoida, Spatangoida) en Méditerranée depuis la « crise messinienne »: application paléoécologique aux B. lyrifera intragypses de Sorbas (SE Espagne)
FIG. 6. — Diagramme montrant les variations du rapport des longueurs entre les pétales antérieurs et les pétales postérieurs (LA/LP) en fonction de la taille (L) chez B. gr. atlantica et B. gr. lyrifera. Même légende qu'en Fig. 4.
Fig. 5 in Use of stereophotography in insect science - methods and applications
Fig. 5: Electron-microscopic 3D images of the spermatophore (a) and single spermatozoa (b) Australian field cricket (image widths: a: 0.5 mm; b: 0.05 mm).
Fig. 3 in Use of stereophotography in insect science - methods and applications
Fig. 3: Microsccopic 3D image of the opened abdomen of the ffemale Australiaan field cricket (image width: 5 mm).
Fig. 4 in Use of stereophotography in insect science - methods and applications
Fig. 4: Light-microscopic 3D images of the terminal sections of the female accessory glands in the Mediterranean field cricket (a) and Australian field cricket (b) (image widths: 2 mm).
Fig. 2 in Use of stereophotography in insect science - methods and applications
Fig. 2: Stereoscopic macro-photographs (red-green anaglyphs) of different insects: (a) Australian field cricket; (b) hoverfly. All images have to be watched by using red-green glasses.
Fig. 1 in Use of stereophotography in insect science - methods and applications
Fig. 1: Methodds for the generation of stereo-ppairs in microsccopy (STURM 20016a, STURM 20016b): (a) procedure wwith slight rotatioon of the object by an angle α; ((b) displacementt of the focus plaane by the value d andd resulting produuction of an imagge stack.
Fig. 4 in Preliminary study on the application of radio-telemetry techniques to evaluate movements of fish in the Lateral canal at Itaipu Dam, Brazil
Fig. 4. Movements of Prochilodus lineatus (fish no 1 and 4) and Pseudoplatystoma fasciatum (fish no 9, 10 and 13) in the lateral channel located near Itaipu Dam (detections in the fixed stations, in number of hours post-release, are shown in the white circles).
Fig. 3 in Preliminary study on the application of radio-telemetry techniques to evaluate movements of fish in the Lateral canal at Itaipu Dam, Brazil
Fig. 3. Radio-telemetry fixed station at "Lago das Grevilhas", in the lateral channel near Itaipu Dam.
Fig. 1 in Preliminary study on the application of radio-telemetry techniques to evaluate movements of fish in the Lateral canal at Itaipu Dam, Brazil
Fig. 1. Locations of the fixed-station receivers (numbers inside the white circles) during the pilot study conducted in the lateral channel located near Itaipu Dam.
Fig. 2 in Preliminary study on the application of radio-telemetry techniques to evaluate movements of fish in the Lateral canal at Itaipu Dam, Brazil
Fig. 2. Surgical implantation of a radiotransmitter in Pseudoplatystoma fasciatum, captured in the lateral channel located near Itaipu Dam.
Control Accuracy Measurement of a Mixed Reality Application for Digital Twin based Crane Operation
<p>The dataset corresponds the measurement that was implemented on the control accuracy of a mixed reality application for a digital twin based crane. </p> <p>The dataset contains two CSV files, one "Target" ", which is the selected target positions, and one "Measurement results", which is the actual crane position after moving to the target position. </p>
IISWC 2021 Characterizing and Mitigating the I/O Scalability Challenges for Serverless Applications (Dataset and Scripts)
<p>As serverless computing paradigm becomes widespread, it is important to understand the I/O performance characteristics on serverless computing platforms. To the best of our knowledge, we provide the first study that analyzes the observed I/O performance characteristics -- some expected and some unexpected findings that reveal the hidden, complex interactions between the application I/O characteristics, the serverless computing platform, and the storage engines. The goal of this analysis is to provide data-driven guidelines to serverless programmers and system designers about the performance trade-offs and pitfalls of serverless I/O.</p>
Low-resolution infrared thermal dataset and potential privacy-preserving applications
<p>A low-resolution infrared thermal dataset of people and thermal objects, such as a working laptop, in indoor environments. The dataset was collected by a far infrared thermal camera (32 by 24 pixels), which can capture the position and shape information of thermal objects without privacy issues that enable trustworthy computer vision applications. The dataset consists of 1770 thermal images with high-quality annotation collected from an indoor room with around 15 degrees.</p>
A Collection of Industry-Developed Blockchain-based Applications
<p>A set of blockchain-based applications (DApps) consists of 400 public, private, and hybrid DApps. They are manually selected between September 2019 and February 2020 from nine blockchain platforms: Blockstack, Corda, Ethereum, EOS, Hive, Hyperledger Fabric, Klaytn, POA, and Steem.</p>
Late-time spectral line formation in Type IIb supernovae, with application to SN 1993J, SN 2008ax, and SN 2011dh
<p>Spectral models for stripped cores of M_ZAMS=12, 13, 17 Msun progenitors, 100-500d. Distance 7.8 Mpc assumed.</p>
Research Compendium for Harrington et al. (2021): "An Open-Source Bayesian Atmospheric Radiative Transfer (BART) Code: I. Design, Tests, and Application to Exoplanet HD 189733 b"
<p>This archive is the Reproducible Research Compendium for<br> <br> An Open-Source Bayesian Atmospheric Radiative Transfer (BART) Code: I. Design, Tests, and Application to Exoplanet HD 189733 b<br> <br> by Harrington et al. (2021), published in The Planetary Science Journal.<br> <br> BART is an atmospheric parameter retrieval code. It infers the properties of planetary atmospheres from spectroscopic observations. The compendium includes all the software, documentation, configuration files, plots, and data published in the paper. The compendium is under the Reproducible Research Software License; see LICENSE file. The README provides additional information and describes the contents of each compressed .tar.gz file.</p>
Application of hyperbolic geometry of multiplex networks under layer link-based attacks
<p>As real multilayer networks, we consider four networks. The multilayer networks are converted to multiplex networks by assuming that all layers have the same number of nodes (the maximum number of nodes of all layers). Explanation of these networks is as follow:</p> <ol> <li><em>CS-Aarhus_multiplex [1]</em> : The first network used in this study is a 5-layer multiplex network, named CS-Aarhus_multiplex, which has 61 nodes and 620 edges. The multiplex social network consists of five kinds of online and offline relationships (Facebook, Leisure, Work, Co-authorship, Lunch) between the employees of the Computer Science department at Aarhus.</li> <li><em>Data_malaria_PLOSCompBiology_2013 [2]</em>: The second network is a 9-layer multiplex network, which consists of 307 nodes and 35306 edges. Networks of recombinant antigen genes from the human malaria parasite P. falciparum. Each of the 9 networks shares the same set of vertices but has different edges, corresponding to the 9 highly variable regions (HVRs) in the DBLa domain of the var protein. Nodes are var genes, and two genes are connected if they share a substring whose length is statistically significant.</li> <li>VICKERS CHAN 7th-GRADERS [3] : The third network is a 3-layer multiplex network, called VICKERS CHAN 7th-GRADERS, which includes 29 nodes and 740 edges. The data were collected by Vickers from 29 seventh-grade students in a school in Victoria, Australia. Students were asked to nominate their classmates on several relations including the three layers.</li> </ol> <p> 4. FAO MULTIPLEX TRADE NETWORK [4]: The fourth network is a 364-layer multiplex network, which contains 214 nodes and 318346 edges. We consider different types of trade relationships among countries, obtained from FAO (Food and Agriculture Organization of the United Nations)</p>
Data from: Fertiliser application modulates the impact of interannual climate fluctuations and plant-to-plant interactions on the dynamics of annual species in a Mediterranean grassland
<p><span><strong><span>Background:</span></strong><span> Climate and land-use changes, which include the application of various types of organic and inorganic fertilisers, have been reducing the species diversity of Mediterranean grasslands and threatening their conservation. Annual plants are one of the most diverse functional groups of species in these grasslands, despite suffering competitive pressure from perennial herbaceous and woody species, and they are essential for ecosystem functioning and stability. </span></span></p> <p><span><strong><span>Aims:</span></strong><span> To quantify how fertilisation modulates the impact of plant-to-plant interactions and climate fluctuations on the dynamics of annuals in Mediterranean grasslands. We hypothesised that the application of sewage sludge would increase competition between functional groups, reducing the abundance of annuals in the long-term, but would buffer the negative impacts of drought on the year-to-year fluctuation of the diversity of annuals.</span></span></p> <p><span><strong><span>Methods:</span></strong><span> In a semi-natural species-rich Mediterranean grassland in northern Spain, we analysed the changes in the taxonomical and functional composition and diversity of annuals over 14 years in response to variations in the abundance of perennial herbaceous and woody species, climate fluctuations, and fertilisation with sewage sludge. We quantified separately the patterns of year-to-year fluctuations and long-term trends. </span></span></p> <p><span><strong><span>Results:</span></strong><span> The frequency and diversity of annuals decreased with a higher abundance of perennial herbaceous species, drought in June, and cold winters. The addition of sewage sludge decreased the abundance of annuals in the long-term, seemed to promote competition between annuals and other functional groups at an interannual scale, and mitigated the negative effects of drought and cold.</span></span></p> <p><span><span><strong>Conclusions:</strong> Fertilisation influences differently the temporal response of annuals to climate fluctuations and plant-to-plant interactions.</span></span></p>
Numerical methodology for design and evaluation of natural circulation systems for MSR applications - Dataset
<p>Dataset associated to the 2022 ANS Annual meeting conference paper "Numerical methodology for design and evaluation of natural circulation systems for MSR applications".</p>
The adapted Activity-By-Contact model for enhancer-gene assignment and its application to single-cell data
<p>In our work, we implemented the ABC-model and could show that one assay for measuring the openness of enhancers is sufficient. Further, we propose a generalised calculation of the ABC-score, which describes enhancer activity in a gene-specific manner, and which includes all TSS, without requiring any additional data. We combined our implementation of the ABC-score with an approach to quantify TF binding affinity into STARE: a framework to derive TF affinities to genes. STARE was also designed for potential application on single-cell data. You can find the code in our <a href="https://github.com/schulzlab/stare">GitHub repository</a> and more details in our <a href="https://doi.org/10.1093%2Fbioinformatics%2Fbtad062">publication</a>.</p> <p>We provide the data for the validation of our ABC-implementation on two CRISPR-screens. We also provide the results of our analysis of single-cell data of the human heart with STARE. All data is in hg19.</p> <p>Content:</p> <ul> <li>CRISPRi_screens: One file for each CRISPRi-screen with interactions that were used to plot precision-recall curves, containing columns for different ABC scoring versions.</li> <li>Enformer: Similar to the CRISPRi_screens, but containing columns for different calculations for Enformer's predicted expression change upon in silico mutagenesis of the enhancer region.</li> <li>K562_CandidateEnhancer: K562 enhancer with the 4th column for enhancer activity, one file for each activity representation that was measured.</li> <li>K562_ABC_Predictions: Regular ABC-scores and generalised ABC-scores for each activity measurement. The files contain all scored interactions for a 10MB window, without any cut-off. We also included the results of the implementation of the ABC-score of Fulco et al. (2019).</li> <li>STARE_Hocker_*: Whole STARE output for human heart single-cell data, one for regular ABC, generalised ABC, generalised ABC with average Hi-C matrix and one based on co-accessibility analysis. All approaches were run with a 5 MB window (except for GeneralisedABC500kb), the ABC-based runs with a score cut-off of 0.02. Each folder contains two subdirectories, one for the ABC-scoring and one for the Gene-TF affinity matrices. The 'ABC_output' also contains a GeneInfo file for each cell type, summarising different attributes per gene.</li> <li>INVOKE_Hocker_*: Folder with the input and output of INVOKE (see https://github.com/schulzlab/tepic), based on the STARE runs. CS genes stands for cell type-specific genes, defined as genes with a z-score across cell types of ≥ 2 and TPM ≥ 0.5. The INVOKE commands were as follows: <ul> <li>Rscript INVOKE.R --dataDir=<TF-Gene matrix> --outDir=<out_path> --response=Expression --regularization=E --performance=TRUE --outerCV=10 --seed=1234</li> </ul> </li> </ul> <p>Importantly, the results are based on data from the following publications:</p> <ul> <li>CRISPRi-screens: <ul> <li>Gasperini, Molly, Andrew J. Hill, José L. McFaline-Figueroa, Beth Martin, Seungsoo Kim, Melissa D. Zhang, Dana Jackson, et al. “A Genome-Wide Framework for Mapping Gene Regulation via Cellular Genetic Screens.” <em>Cell</em> 176, no. 1–2 (January 2019): 377-390.e19. https://doi.org/10.1016/j.cell.2018.11.029.</li> <li> <p>Schraivogel, Daniel, Andreas R. Gschwind, Jennifer H. Milbank, Daniel R. Leonce, Petra Jakob, Lukas Mathur, Jan O. Korbel, Christoph A. Merten, Lars Velten, and Lars M. Steinmetz. “Targeted Perturb-Seq Enables Genome-Scale Genetic Screens in Single Cells.” <em>Nature Methods</em> 17, no. 6 (June 2020): 629–35. https://doi.org/10.1038/s41592-020-0837-5.</p> </li> <li> <p>Fulco, Charles P., Joseph Nasser, Thouis R. Jones, Glen Munson, Drew T. Bergman, Vidya Subramanian, Sharon R. Grossman, et al. “Activity-by-Contact Model of Enhancer–Promoter Regulation from Thousands of CRISPR Perturbations.” <em>Nature Genetics</em> 51, no. 12 (December 2019): 1664–69. https://doi.org/10.1038/s41588-019-0538-0.</p> </li> </ul> </li> <li>Enformer model: Avsec, Žiga, Vikram Agarwal, Daniel Visentin, Joseph R. Ledsam, Agnieszka Grabska-Barwinska, Kyle R. Taylor, Yannis Assael, John Jumper, Pushmeet Kohli, and David R. Kelley. “Effective Gene Expression Prediction from Sequence by Integrating Long-Range Interactions.” <em>Nature Methods</em> 18, no. 10 (October 2021): 1196–1203. https://doi.org/10.1038/s41592-021-01252-x.</li> <li>K562 predictions and average Hi-C matrix: Fulco, Charles P., Joseph Nasser, Thouis R. Jones, Glen Munson, Drew T. Bergman, Vidya Subramanian, Sharon R. Grossman, et al. “Activity-by-Contact Model of Enhancer–Promoter Regulation from Thousands of CRISPR Perturbations.” <em>Nature Genetics</em> 51, no. 12 (December 2019): 1664–69. https://doi.org/10.1038/s41588-019-0538-0.</li> <li>Hi-C matrix for K562 predictions: Rao, S. et al. (2014). A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping. Cell, 159(7), 1665–1680</li> <li>STARE and INVOKE runs: Hocker, J. D. et al. (2021). Cardiac cell type–specific gene regulatory programs and disease risk association. Science Advances, 7(20), eabf1444</li> <li>H3K27ac HiChIP for STARE runs: Anene-Nzelu, C. G. et al. (2020). Assigning Distal Genomic Enhancers to Cardiac Disease–Causing Genes. Circulation, 142(9), 910–912</li> <li>INVOKE software: Combining transcription factor binding affinities with open-chromatin data for accurate gene expression prediction Schmidt et al., Nucleic Acids Research 2016; doi: 10.1093/nar/gkw1061</li> </ul> <p> </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.