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.
1,393
datasets available to search
ShareScore release 0.9.0
Dataset results
1,393 results for “traces”
Figure 6 in Feeding traces attributable to juvenile Tyrannosaurus rex offer insight into ontogenetic dietary trends
Figure 6 Casts of BMR P2002.4.1 maxilla (A) and dentary (B) to illustrate the tooth positions used for spacing measurements. Note the alternating replacement of teeth. Scale bars equal 10 cm. Full-size DOI: 10.7717/peerj.6573/fig-6
Figure 4 in Feeding traces attributable to juvenile Tyrannosaurus rex offer insight into ontogenetic dietary trends
Figure 4 Punctured caudal vertebra of BMR P2007.4.1. BMR P2007.4.1 in anterior (A) posterior (B) and ventral (C), including the two elliptical punctures on the ventral surface of the centrum (D, E). Full-size DOI: 10.7717/peerj.6573/fig-4
Figure 3 in Feeding traces attributable to juvenile Tyrannosaurus rex offer insight into ontogenetic dietary trends
Figure 3 Map of the BMR P2007.4.1 ''Constantine'' Quarry. Dorsal vertebrae (field numbers CON- 2007-010, CON-2007-011, and CON-2007-012) were too weathered for collection, though their relative locations were mapped. Note the relative association of dorsal and caudal vertebrae, and pelvic elements. Full-size DOI: 10.7717/peerj.6573/fig-3
Figure 5 Silicone peel produced from BMR P2007.4.1 in Feeding traces attributable to juvenile Tyrannosaurus rex offer insight into ontogenetic dietary trends
Figure 5 Silicone peel produced from BMR P2007.4.1. Silicone peel produced from the ventral surface of the punctured caudal vertebra of BMR P2007.4.1 in vertical (A), and lateral (B) views. Note the traced outlines demonstrating the shape of the tooth casts. Full-size DOI: 10.7717/peerj.6573/fig-5
Figure 2 in Feeding traces attributable to juvenile Tyrannosaurus rex offer insight into ontogenetic dietary trends
Figure 2 Stratigraphic column of the ''Constantine'' Quarry. Stratigraphy of the BMR P2007.4.1 ''Constantine'' Quarry. Full-size DOI: 10.7717/peerj.6573/fig-2
Figure 1 in Feeding traces attributable to juvenile Tyrannosaurus rex offer insight into ontogenetic dietary trends
Figure 1 Discovery location of BMR P2007.4.1. Locality map showing the geographic location of specimen BMR P2007.4.1 in Carter County, Montana. Full-size DOI: 10.7717/peerj.6573/fig-1
FIG. 2 in Tyrannosaur cannibalism: A case of a tooth-traced tyrannosaurid bone in the Lance Formation (Maastrichtian), Wyoming
FIG. 2.—Tooth traces on SWAU HRS13997. The two sets of Knethichnus paralleum and Linichnus serratus are indicated, with the more prominent pair on the right. Scale bar = 20 mm.
FIG. 5 in Tyrannosaur cannibalism: A case of a tooth-traced tyrannosaurid bone in the Lance Formation (Maastrichtian), Wyoming
FIG. 5.—Comparison between four specimens of tyrannosaurid metatarsals: A) Tyrannosaurus rex metatarsal IV (SWAU HRS13997). B) Tyrannosaurus rex metatarsals II-IV (LACM 23845, with IV sculpted). C) Tyrannosauridae indet. metatarsal IV (IGM 6130; modified from Peecook (2014, fig. 3). D) Tyrannosaurus rex metatarsals II-IV (FMNH PR2081; modified from Brochu (2003, figs. 99, 100, 101). SWAU HRS13997 and IGM 6130 are metatarsal IV. All elements are from the right pes except IGM 6130, which is a left element, although the image has been flipped to make it match the others. Note that FMNH PR2081 is shown in a more medial view than the other metatarsal specimens. Scale bar = 100 mm.
FIGURE 1 in Tracing the roots: clarification on the type locality of Halobates sexualis Distant (Heteroptera: Gerridae)
FIGURE 1. The original type locality of Halobates sexualis is indicated with a yellow star and the assumed type locality with a red circle. Inset shows the map published in 1898 (adapted from RASGBI 1898).
PhD Thesis: Tracing Molecular Patterns of Adaptation in Arctic Brassicaceae
<p>Extreme environments can function as natural laboratories for studying how different organisms adapt to similar selection pressures at the genetic level. This thesis explores how three Arctic plant species independently adapted to some of the coldest biomes on Earth, and how they evolved similar suites of adaptations to extremes in light and temperature. It addresses fundamental questions in plant evolutionary biology, such as the extent to which adaptation follows the same genetic trajectories in different species, and the genetic basis for plant adaptation to extreme environments. The thesis has <u>two main objectives</u> that are addressed through three papers (<b>Papers I-III</b>):<b> </b>1) estimate the degree of adaptive molecular convergence in the three Arctic Brassicaceae <i>Cardamine bellidifolia</i>, <i>Cochlearia groenlandica</i>, and <i>Draba nivalis</i>, and 2) identify putative molecular adaptations to the Arctic environment in the same three species.</p> <p><b>Approach. </b>The first two papers examine the degree of evolutionary repeatability in how <i>C. bellidifolia</i>, <i>C. groenlandica</i>, and <i>D. nivalis</i> adapted to the Arctic environment at the genetic level (<u>objective 1</u>). In <b>Paper I</b>, we estimated molecular convergence at the level of codons, genes, and functional pathways, by comparing genome-wide patterns of positive selection and identifying convergent substitutions in the three species. In <b>Paper II</b>, we conducted a time series experiment to examine the transcriptional responses of the Arctic Brassicaceae to low temperatures, and to identify potential convergent expression patterns in cold response.</p> <p>All three papers identify putative molecular adaptations to extremes in light and temperature (<u>objective 2</u>). In <b>Paper I</b>, we identified candidate genes for adaptation to the Arctic environment by searching for positively selected genes associated with abiotic stresses common in the Arctic. In <b>Paper II</b>, we explored the molecular basis of cold tolerance in Arctic Brassicaceae, and described how their cold-induced transcriptomes differ from that of the temperate model species, <i>Arabidopsis thaliana</i>. In <b>Paper III</b>, we assembled the genome of <i>D. nivalis</i> and explored the genomic characteristics of Arctic plant adaptation, by conducting comparative analyses of chromosomal evolution and functional genomics with other species in the Brassicaceae.</p> <p><b>Main findings and discussion. </b>The findings in <b>Papers I-II</b> suggests that the three Arctic Brassicaceae have adapted to the Arctic environment through independent genetic trajectories (<u>objective 1</u>). In <b>Paper I</b>, we found that positive selection has been acting on different genes, but similar functional pathways in the three species. The positively selected genes sets showed convergent functional profiles associated with abiotic stresses common in the Arctic. However, we found little evidence for convergent substitutions at the same sites, or for positive selection acting on the same genes in the three species. In <b>Paper II</b>, we found that the cold-response of <i>C. bellidifolia</i>, <i>C. groenlandica</i>, and <i>D. nivalis</i> was highly species-specific. Most cold-induced genes were unique for each species, and the number of genes shared by the three Arctic species and the temperate <i>A. thaliana</i> was higher than the number of genes shared by the Arctic species alone. This suggests that the cold response in Arctic Brassicaceae mainly evolved independently, but with some components likely conserved across the family. The low levels of molecular convergence could be explained by the many evolutionary trajectories leading to better performance under temperature and light stress in plants, and/or less repeatable patterns of adaptation in highly polygenic traits such as cold tolerance.</p> <p><b>Papers I-III</b> presents some of the first molecular evidence for putative plant adaptations to the Arctic environment (<u>objective 2</u>). In <b>Paper I</b>, we found multiple candidate genes for Arctic adaptation associated with cold stress, freezing stress, oxidative stress and light stress in all species. Adaptations associated with the plasma membrane seemed to be particularly important in all species, possibly due to its crucial role in freezing tolerance. In <b>Paper II</b>, we found that the Arctic cold response followed similar trends as in the temperate <i>A. thaliana</i>, but a few genes and characteristics were specific for the Arctic species alone. In <b>Paper III</b>, we presented a 302 Mb assembly of <i>D. nivalis</i> that is highly contiguous with 91.6 % assembled into eight chromosomes (the base chromosome of the species). We found that the <i>D. nivalis</i> genome contains expanded suites of genes associated with common Arctic stresses, and the expansion of these gene families appear to partly be driven by the activity of transposable elements.</p> <p><b>Conclusion. </b>The results from this dissertation provide a framework for studies that aim to test the existence of a functional syndrome of Arctic adaptation in Brassicaceae and other flowering plants. The <i>D. nivalis</i> genome assembly may also become an important tool in studies of Arctic plant evolution in general. </p>
Reactome modified for tracing ArangoDB version
<h3>Reactome database download and customization</h3><p>The Reactome database [1,2] was downloaded as a neo4j graph database (<a href="https://reactome.org/download-data">https://reactome.org/download-data</a> version 75), which is covered by the <a href="https://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution 4.0 International (CC BY 4.0)</a> license. A series of database queries was used to generate a database version suitable for graph data science which can be followed in detail in the attached Jupyter notebook (Or at <a href="https://github.com/SBRG/GDS-Public/blob/main/notebooks/reactome/Reactome%20GDS.ipynb">GDS-Public/notebooks/reactome/Reactome GDS.ipynb at main · SBRG/GDS-Public (github.com)</a>). </p><p>Nodes, labels and relationships not required for graph algorithmic analyses were removed. For instance, this included nodes like person, affiliation, and taxa as well as all nodes representing entities of organisms other than <i>Homo sapiens</i>. Subcellular locations (compartments) of biological entities were set as node properties. To allow for improved graph traversal, selected relationships were reversed or added. Because currency metabolites, e.g. ATP, NAD(P)H and H+, can artificially connect metabolic reactions and pathways in network analyses [3,4], we labelled such compounds plus the regulatory protein ubiquitin accordingly and thereby excluded them from all analyses. Finally, the database was transformed into an ArangoDB graph database consisting of 1,703,054 nodes and 3,368,926 edges. </p><h3>References</h3><p>1. Gillespie, M. <i>et al.</i> The reactome pathway knowledgebase 2022. <i>Nucleic Acids Research</i> <strong>50</strong>, D687–D692 (2022).</p><p>2. Fabregat, A. <i>et al.</i> Reactome graph database: Efficient access to complex pathway data. <i>PLoS Computational Biology</i> <strong>14</strong>, (2018).</p><p>3. Ma, H. & Zeng, A.-P. <i>Reconstruction of metabolic networks from genome data and analysis of their global structure for various organisms</i>. <i>BIOINFORMATICS</i> vol. 19 https://academic.oup.com/bioinformatics/article/19/2/270/372721 (2003).</p><p>4. Martínez, V. S. <i>et al.</i> The topology of genome-scale metabolic reconstructions unravels independent modules and high network flexibility. <i>PLoS Computational Biology</i> <strong>18</strong>, (2022).</p><p> </p>
GTT23: A 2023 Dataset of Genuine Tor Traces
<div>The GTT23 dataset contains network metadata of encrypted traffic measured from exit relays in the Tor network over a 13-week measurement period in 2023. The metadata is suitable for analyzing and evaluating website fingerprinting attacks and defenses.</div> <div> </div> <div>Our dataset measurement process was designed to prioritize safety and privacy and was developed through consultation with the <a href="https://research.torproject.org/safetyboard/">Tor Research Safety Board</a> (TRSB, <a href="https://safetyboard.torproject.net/submit/">submission #37</a>). Our TRSB interaction resulted in a “No Objections” score.</div> <div> </div> <div>The measurement process, additional safety and ethical considerations, and a statistical analysis of the dataset is presented in further detail in the article "A Measurement of Genuine Tor Traces for Realistic Website Fingerprinting", arXiv:2404.07892 [cs.CR], <a href="https://doi.org/10.48550/arXiv.2404.07892">https://doi.org/10.48550/arXiv.2404.07892</a>.</div>
The 2023 summer record low Antarctic sea ice traced to synergistic influences of preconditioning, wind-induced transport and the ice albedo feedback
Open the record for dataset details and reuse information.
TRACE-Soils, Dynamics and kinetics of phosphatase activity in European agricultural soils under long-term tillage reduction practices
<p>This dataset contains information of chemical, physical and biological soil parameters including phosphatase activities and kinetics from seven long term agricultural fields throughout Europe under different tillage practices (no-tillage, reduced tillage and standard tillage) at two sampling depths (0 - 10 and 10 - 20 cm). This dataset is linked to the publication Tamara Gómez-Gallego <em>et al. </em>? in Soil Biology and Biochemistry (under review).</p>
Source Tracing of Audio Deepfake Systems: MLAAD Source Tracing Protocol
<p>This data was created as part of the work entitled "Source Tracing of Audio Deepfake Systems", published in Interspeech 2024.</p> <p>In doing our training, development, and testing, Pindrop used WAV files from the Multi-Language Audio Anti-Spoof Dataset (MLAAD) and the M-AILABS Speech Dataset. You can obtain copies of these same WAV files directly from the developers here:<br>MLAAD (version 1): <a href="https://owncloud.fraunhofer.de/index.php/s/tL2Y1FKrWiX4ZtP#editor" target="_blank" rel="noopener">https://owncloud.fraunhofer.de/index.php/s/tL2Y1FKrWiX4ZtP#editor</a><br>M-AILABS: <a href="https://www.caito.de/2019/01/03/the-m-ailabs-speech-dataset/" target="_blank" rel="noopener">https://www.caito.de/2019/01/03/the-m-ailabs-speech-dataset/</a></p>
Fig. 2 in Kinetid in larval cells of Spongillida (Porifera: Demospongiae): tracing the ancestral traits
Fig. 2 Ultrastructure of the kinetid in larval cells of Eunapius fragilis, longitudinal plane. Consecutive sections of three cells (a–d, e–g, i–j) and separate sections of six cells (h, k–o). Scale bars a–l 200 nm, m–o 250 nm. Abbreviations: afb, apical filamentous bundle; axs, axosome; bfb, basal filamentous bundle; bf, basal foot; fb, fibrillar bridge between
DYNAMISM - Postprocessed Execution Traces Of Android Malware and Benign Apps
<p>Protection against malware is particularly relevant on systems running the Android operating system, due to its huge use base and, therefore, its potential for monetization from the attackers.</p> <p>Protection against malware is particularly relevant in systems running the Android operating system, due to its huge users’ base and, therefore, its potential for monetization from the attackers.</p> <p>Dynamic malware detection has been widely adopted by the scientific community but not yet in practical applications.</p> <p>We release <em>DYNAMISM (Dynamic Analysis of Malware)</em>, a dataset containing execution traces of both benign and malicious applications running on Android OS, in order to facilitate further research as well as to facilitate the adoption of dynamic detection in practice. The dataset contains execution traces from 2,386 benign applications and 2,495 malicious applications taken from the Malware Genome Project repository [<a href="http://www.malgenomeproject.org/">http://www.malgenomeproject.org</a>] and from Drebin Dataset [<a href="https://www.sec.cs.tu-bs.de/~danarp/drebin/">https://www.sec.cs.tu-bs.de/~danarp/drebin/</a>]. Execution records were obtained by running the applications, one at a time, on the Android emulator. For each application, a maximum of 2,000 stimuli were applied with a maximum execution time of 10 minutes. For most of the applications, all the stimuli could be applied in this timeframe. In some of the traces none of the two limits is reached due to emulator hiccups. Collected features are related to the memory and CPU usage, network interaction and system calls and their monitoring is performed with a period of two seconds. The Android emulator of the Android Software Development Kit for Android 4.0 (release 20140702) was used. To guarantee that the system was always in a mint condition when a new sample is started, thus avoiding possible interference (e.g., changed settings, running processes, and modifications of the operating system files) from previously run samples, the Android operating system was each time re-initialized before running each application. The application execution process was automated by means of a shell script that made use of Android Debug Bridge (adb) and that was run on a Linux PC. The Monkey application exerciser was used in the script as a generator of the aforementioned stimuli. The Monkey is a command-line tool that can be run on any emulator instance or on a device; it sends a pseudo-random stream of user events (stimuli) into the system, which acts as a stress test on the application software.</p> <p>In this dataset, we provide both per-app CSV files as well as unified files, in which CSV files of single applications have been concatenated. The CSV files contain the features extracted from the raw execution record. The provided files are listed below:</p> <ul> <li> <p>benign-per_app-csv.zip - features obtained by executing benign applications, one CSV per application</p> </li> <li> <p>benign-unified-csv.zip - features obtained by executing benign applications, only one CSV file</p> </li> <li> <p>malicious-per_app-csv.zip - features obtained by executing malicious applications, one CSV per application</p> </li> <li> <p>malicious-unified-csv.zip - features obtained by executing malicious applications, only one CSV file</p> </li> </ul>
FIGURE 13 in Hidden in plain sight: reassessment of the pig-footed bandicoot, Chaeropus ecaudatus (Peramelemorphia, Chaeropodidae), with a description of a new species from central australia, and use of the fossil record to trace its past distribution
FIGURE 13. Principal Component Analysis of cranial a), dental b) and external c) measurements for Chaeropus ecaudatus ecaudatus (squares), C. e. occidentalis (diamonds) and C. yirratji sp. nov. (crosses).
FIGURE 9 in Hidden in plain sight: reassessment of the pig-footed bandicoot, Chaeropus ecaudatus (Peramelemorphia, Chaeropodidae), with a description of a new species from central australia, and use of the fossil record to trace its past distribution
FIGURE 9. Reconstruction of Chaeropus yirratji sp. nov. Artwork by Peter Schouten. Copyright WA Museum.
FIGURE 15 in Hidden in plain sight: reassessment of the pig-footed bandicoot, Chaeropus ecaudatus (Peramelemorphia, Chaeropodidae), with a description of a new species from central australia, and use of the fossil record to trace its past distribution
FIGURE 15. Phylogenetic analyses of Chaeropus taxa using Maximum Likelihood (ML) and Bayesian Inference (BI) approaches for the molecular data.
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.