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1,079 results for “source data”
Data for Urban Seismic Source Mapping
<p>In this study, we explore the innovative use of existing and ubiquitous urban infrastructure--telecommunication optical fibers--to map urban seismic sources. We integrate seismic interferometry and beamforming algorithms to overcome the proximity limitations of previous urban seismology approaches. <br>Our method models the propagation of seismic surface waves to estimate the spatio-temporal distribution of seismic source power (SSP; average seismic energy per unit of time), enabling the detection and localization of urban seismic sources occurring remotely from optical fibers.</p> <p><code>Put these pickle files into '/urban_das/data/das_data/' and run the scripts at https://github.com/jingxiaoliu/urban_das</code></p> <p>If you use this implementation, please cite our papers:</p> <blockquote> <p>[1] Liu, J., Li, H., Noh, H. Y., Santi, P., Biondi, B., & Ratti, C. (2025). Urban sensing using existing fiber-optic networks. <em>Nature Communications</em>, <em>16</em>(1), 3091.</p> <p>[2] Yuan, S., Liu, J., Noh, H. Y., Clapp, R., & Biondi, B. (2024). Using vehicle‐induced DAS signals for near‐surface characterization with high spatiotemporal resolution. <em>Journal of Geophysical Research: Solid Earth</em>, <em>129</em>(4), e2023JB028033.</p> <p>[3] Liu, J., Yuan, S., Dong, Y., Biondi, B., & Noh, H. Y. (2023). TelecomTM: A fine-grained and ubiquitous traffic monitoring system using pre-existing telecommunication fiber-optic cables as sensors. <em>Proceedings of the ACM on Interactive, Mobile, Wearable and Ubiquitous Technologies</em>, <em>7</em>(2), 1-24.</p> </blockquote>
source data of "Enhanced vegetation drought resistance induced by elephant disturbance in Africa"
Open the record for dataset details and reuse information.
Supplemental Dataset Excel files and Source Data Excel file for "START domains generate paralog-specific regulons from a single network architecture"
<p>Supplemental Dataset Excel files and Source Data Excel file for "START domains generate paralog-specific regulons from a single network architecture" in Nat Comms</p>
Automated Model Discovery for Tensional Homeostasis: Constitutive Machine Learning in Growth and Remodeling (Source code and data)
<p>This dataset contains</p> <ul> <li>the source code</li> <li>the data and examples</li> <li>the material subroutine with examples of uniaxial strain and stress</li> </ul> <p>of the inelastic Constitutive Artificial Neural Network (iCANN) enhanced by the concept of homeostatic surfaces to discover tensional homeostasis.</p> <p>The corresponding publication is:</p> <p>Holthusen, H., Brepols, T., Linka, K., & Kuhl, E..<em> </em></p> <p><em>Automated Model Discovery for Tensional Homeostasis: Constitutive Machine Learning in Growth and Remodeling.</em></p> <p> </p> <p><strong>Standalone_Materialroutine</strong></p> <ul> <li>00_Materialroutine: Contains the material subroutine implemented in FORTRAN</li> <li>01_uniaxial_strain: Example of the material subroutine in a uniaxial strain driven manner</li> <li>02_uniaxial_stress: Example of the material subroutine in a uniaxial stress driven manner</li> </ul> <p> </p> <p><strong>TensorFlow</strong></p> <ul> <li> <p>iCANN:</p> <ul> <li> <p>01_Biax/biax_l1: Keras/TensorFlow implementation of the iCANN. Example of the cross specimen with L1 (Lasso) regularization</p> </li> <li> <p>01_Biax/biax_l2: Keras/TensorFlow implementation of the iCANN. Example of the cross specimen with L2 (ridge) regularization</p> </li> <li> <p>02_Uniax/uniax_l1: Keras/TensorFlow implementation of the iCANN. Example of the stripe specimen with L1 (Lasso) regularization</p> </li> <li>02_Uniax/uniax_l1: Keras/TensorFlow implementation of the iCANN. Example of the stripe specimen with L2 (ridge) regularization</li> </ul> </li> <li> <p>iCANN_ABS_activation: Same four examples as above, however, with the absolute value activation function</p> </li> <li> <p>installed_packages: File containing a list of installed Python modules used to implement the iCANN</p> </li> </ul> <p>The TensorFlow implementations in all 01_Biax/ and 02_Uniax/ sub-directories are the same.</p> <p>The implementation in iCANN_ABS_activation is different with respect to the activation functions of the pseudo potential.</p> <p> </p> <p>The experimental data for the cross and stripe specimen are taken from the literature:</p> <p>Eichinger, J. F., Paukner, D., Szafron, J. M., Aydin, R. C., Humphrey, J. D., & Cyron, C. J. (2020).</p> <p>Computer-controlled biaxial bioreactor for investigating cell-mediated homeostasis in tissue equivalents. <em>Journal of biomechanical engineering</em>, <em>142</em>(7), 071011.</p> <p><a href="https://doi.org/10.1115/1.4046201">https://doi.org/10.1115/1.4046201</a></p>
Figure source data for Riddell-Young et al., 2024 "Abrupt changes in biomass burning during the last glacial period"
<p>These are the source data files for all of the data presented in main text figures 1 through 4 in Riddell-Young et al., 2024: "Abrupt changes in biomass burning during the last glacial period". Each file contains several sheets that correspond to the data presented in each subplot of the figure. Please refer to the manuscript for a detailed description of the data that was collected and analysis that was performed as part of the study. The Data and Code Availability statements discuss where the official dataset and code publications can be found.</p>
Cubic insulin data set collected from multiple lattices on i03 at Diamond Light Source
<p>Dataset collected as part of routine commissioning work, found to have more than one crystal present at the point where data were collected, allowing multiple lattices to be processed. </p> <p> </p> <p>While three lattices are present one is substantially weaker than the other two.</p> <p> </p> <p>Uploading to enable methods development and also to use for tutorials on how to use dials software.</p> <p> </p> <p>Processing data with the usual dials scripts (which will point to this deposition) result in statistics shown below. Tutorial to be uploaded to https://github.com/graeme-winter/dials_tutorials when available.</p> <p> </p> <p><code> -------------Summary of merging statistics-------------- </code></p> <p><code> Suggested Low High Overall</code><br><code>High resolution limit 1.51 4.10 1.51 1.48</code><br><code>Low resolution limit 54.89 54.93 1.54 54.89</code><br><code>Completeness 98.9 100.0 83.7 95.3</code><br><code>Multiplicity 54.7 78.1 4.6 53.5</code><br><code>I/sigma 18.9 89.2 0.3 18.4</code><br><code>Rmerge(I) 0.139 0.060 1.423 0.139</code><br><code>Rmerge(I+/-) 0.138 0.060 1.316 0.138</code><br><code>Rmeas(I) 0.140 0.061 1.590 0.140</code><br><code>Rmeas(I+/-) 0.140 0.060 1.609 0.140</code><br><code>Rpim(I) 0.016 0.007 0.683 0.016</code><br><code>Rpim(I+/-) 0.023 0.009 0.894 0.023</code><br><code>CC half 1.000 1.000 0.271 1.000</code><br><code>Anomalous completeness 97.8 100.0 67.8 92.3</code><br><code>Anomalous multiplicity 28.7 43.6 2.6 28.3</code><br><code>Anomalous correlation 0.038 0.276 -0.050 0.049</code><br><code>Anomalous slope 0.667 </code><br><code>dF/F 0.060 </code><br><code>dI/s(dI) 0.629 </code><br><code>Total observations 669615 52255 2342 670277</code><br><code>Total unique 12231 669 507 12529</code></p>
Data from: Resolving the Northern Hemisphere source region for the long-distance dispersal event that gave rise to the South American endemic dung moss Tetraplodon fuegianus
Premise of the study—American bipolar plant distributions characterize taxa at various taxonomic ranks but are most common in the bryophytes at infraspecific and infrageneric levels. A previous study on the bipolar disjunction in the dung moss genus Tetraplodon found that direct long-distance dispersal from North to South in the Miocene - Pleistocene accounted for the origin of the Southern American endemic Tetraplodon fuegianus, congruent with other molecular studies on bipolar bryophytes. The previous study, however, remained inconclusive regarding a specific Northern Hemisphere source region for the trans-equatorial dispersal event that gave rise to T. fuegianus. Methods—To estimate spatial genetic structure and phylogeographic relationships within the bipolar lineage of Tetraplodon, which includes T. fuegianus, we analyzed thousands of Restriction-site Associated DNA (RADseq) loci and single nucleotide polymorphisms using Bayesian individual assignment and maximum likelihood and coalescent model based phylogenetic approaches. Key results—Northwestern North America is the most likely source of the recent ancestor to T. fuegianus. Conclusions—Tetraplodon fuegianus, which marks the southernmost populations in the bipolar lineage of Tetraplodon, arose following a single long-distance dispersal event involving a T. mnioides lineage that is now rare in the Northern Hemisphere and potentially restricted to the Pacific Northwest region of North America. Furthermore, gene flow between sympatric lineages of Tetraplodon mnioides in the Northern Hemisphere is limited, possibly due to high rates of selfing or reproductive isolation.
Data from: An inexpensive and open-source method to study large terrestrial animal diet and behavior using time-lapse video and GPS
1. The behavior of free-ranging animals is difficult to study, especially on the large spatial and temporal scales relevant to long-lived large species. Animal-borne video and environmental data collection systems (AVEDs) record behavior and other data in real time as animals conduct daily activities. However, few studies have combined systematically collected, long term AVED foraging data with environmental and movement data to test hypotheses on animal foraging. Additionally, AVEDs are often either prohibitively expensive, or require extensive fabrication and programming knowledge. 2. The video and coordinate animal-mounted system (VACAMS) is an animal-mounted data collection system based on a modified GoPro® action camera platform that records short, first "person" perspective videos of animal behavior on an automated time-lapse schedule. As most videos are georeferenced, researchers can return to the locations of specific behaviors and collect accurate, fine-grained data on non-woody vegetation and other habitat characteristics that may influence animal behavior. Moreover, VACAMS are inexpensive and easy to use. 3. This study describes VACAMS preliminary data on cattle foraging and a hypothesis exploring free-ranging cattle browsing habits throughout the rainy season in the tropical dry forest of Sonora, Mexico. I generated a database of vegetation types consumed by cows each month (Annual, Woody, and Leaf litter) and compared actual vegetation type frequencies to a priori assumptions based on seasonal patterns of forage availability. During the monsoons, when palatable vegetation was abundant, frequencies of annual and woody perennial vegetation in cattle diets did not differ from month to month. When the rains ceased and palatable vegetation became scarce, cows switched to leaf litter, dead annual vegetation, twigs, and dried leguminous fruits. 4. Open source software and commercially available hardware make VACAMS financially attainable for many researchers, land managers, students, and other user groups. VACAMS could be used on a range of domestic and semi-domestic free-ranging animals, particularly in dense forests where conventional observations are impossible. With improvements to GPS battery life and durability, the weakest points of the system, VACAMS could also potentially apply to studies of other large terrestrial animals.
PubMed inner references obtained from five freely available bibliographic data sources
<p>This dataset contains PMID-to-PMID citations of PubMed 2020 Baseline extracted from five freely available bibliographic data sources (COCI, Dimensions, MAG, NIH-OCC, and S2ORC).</p> <p>Each line contains one citing PubMed document and its cited references. The citing and cited documents are separated by a tab (\t) and the cited references are separated by a semicolon (;).</p>
Codes and source data files for: Proximity labeling identifies LOTUS domain proteins that promote the formation of perinuclear germ granules in C. elegans
<p>The germ line produces gametes that transmit genetic and epigenetic information to the next generation. Maintenance of germ cells and development of gametes require germ granules—well-conserved membraneless and RNA-rich organelles. The composition of germ granules is elusive owing to their dynamic nature and their exclusive expression in the germ line. Using <i>C. elegans</i> germ granule, called P granule, as a model system, we employed a proximity-based labeling method in combination with mass spectrometry to comprehensively define its protein components. This set of experiments identified over 200 proteins, many of which contain intrinsically disordered regions. An RNAi-based screen identified factors that are essential for P granule assembly, notably EGGD-1 and EGGD-2, two putative LOTUS-domain proteins. Loss of <i>eggd-1</i> and <i>eggd-2</i> results in separation of P granules from the nuclear envelope, germline atrophy and reduced fertility. We show that intrinsically disordered regions of EGGD-1 are required to anchor EGGD-1 to the nuclear periphery while its LOTUS domains are required to promote perinuclear localization of P granules. Together, our work expands the repertoire of P granule constituents and provides new insights into the role of LOTUS-domain proteins in germ granule organization.</p>
Exercise and Sestrin mediate speed and lysosomal activity in Drosophila by partially overlapping mechanisms-source data
<p>Source data, Figures 1-7</p>
Source data for Neutralization of SARS-CoV-2 variants by convalescent and BNT162b2 vaccinated serum
<p>This dataset contains the source data used in the publication: "Neutralization of SARS-CoV-2 variants by convalescent and BNT162b2 vaccinated serum" published in Nature communications on August 26, 2021 (10.1038/s41467-021-25479-6).</p>
Data from: Nitrification is a minor source of nitrous oxide (N2O) in an agricultural landscape and declines with increasing management intensity
<p>The long-term contribution of nitrification to nitrous oxide (N<sub>2</sub>O) emissions from terrestrial ecosystems is poorly known and thus poorly constrained in biogeochemical models. Here, using Bayesian inference to couple 25 years of <i>in situ</i> N<sub>2</sub>O flux measurements with site-specific Michaelis-Menten kinetics of nitrification-derived N<sub>2</sub>O, we test the relative importance of nitrification-derived N<sub>2</sub>O across six cropped and unmanaged ecosystems along a management intensity gradient in the U.S. Midwest. We found that the maximum potential contribution from nitrification to <i>in situ</i> N<sub>2</sub>O fluxes was 13-17% in a conventionally fertilized annual cropping system, 27-42% in a low-input cover-cropped annual cropping system, and 52-63% in perennial systems including a late successional deciduous forest. Actual values are likely to be less than 10% of these values because of low N<sub>2</sub>O yields in cultured nitrifiers (typically 0.04 to 8% of NH<sub>3</sub> oxidized) and competing sinks for available NH<sub>4</sub><sup>+</sup> <i>in situ</i>. Most nitrification-derived N<sub>2</sub>O was produced by ammonia oxidizing bacteria (AOB) rather than archaea (AOA), who appeared responsible for no more than 30% of nitrification-derived N<sub>2</sub>O production in all but one ecosystem. Although the proportion of nitrification-derived N<sub>2</sub>O production was lowest in annual cropping systems, these ecosystems nevertheless produced more nitrification-derived N<sub>2</sub>O (higher V<sub>max</sub>) than perennial and successional ecosystems. We conclude that nitrification is minor relative to other sources of N<sub>2</sub>O in all ecosystems examined.</p>
Data from: Alternative food sources interfere with removal of a fungal amphibian pathogen by zooplankton
<p>1. While the amphibian disease chytridiomycosis is causing ongoing population declines and biodiversity losses around the globe, efficient mitigation strategies are lacking. The free-living zoospores of the causative agents of this disease, the chytrid pathogens <i>Batrachochytrium dendrobatidis</i> (Bd) and <i>Batrachochytrium salamandrivorans</i> (Bsal), are a potential food source for filter-feeding micropredators as part of the aquatic food web. While consumption of zoospores can lower environmental pathogen loads, alternative food sources may interfere with pathogen removal rates.</p> <p>2. We compared the ability of three filter-feeding zooplankton species, i.e. the cladoceran <i>Daphnia magna</i>, the rotifer <i>Brachionus calyciflorus</i> and the ostracod <i>Heterocypris incongruens,</i> to remove Bd zoospores in water and investigated the effect of alternative food sources, i.e. the green algae <i>Pseudokirchneriella subcapitata</i> and <i>Chlorella vulgaris</i>, on zoospore ingestion by <i>D. magna</i>.</p> <p>3.<i> D. magna</i> was the only micropredator candidate that effectively removed Bd zoospores from its environment, with an average removal rate of 1,012 ± 542 GE ind.<sup>-1</sup> h<sup>-1</sup> within our test system. High concentrations (1x10<sup>5</sup> cells/mL) of large and easily ingestible <i>P. subcapitata</i> reduced pathogen removal rates, whereas the small and less edible <i>C. vulgaris</i> did not interfere with pathogen removal.</p> <p>4. <i>Synthesis and applications:</i> We showed that <i>Daphnia spp</i>., which are keystone species in all sorts of aquatic habitats worldwide, are promising target agents for biologically mitigating chytridiomycosis infections and how natural food sources may interfere with this strategy. We also suggest potential management actions for biological disease mitigation, aiming to optimize environmental conditions for these target filter-feeders, thereby reducing pathogen densities and eventually infection pressure in amphibian hosts. Examples of such management actions include, but are not limited to, removal of planktivorous fish, habitat restoration, nutrient control or agrochemical regulation in the vicinity of amphibian breeding ponds. Further studies, including field trials, are needed to confirm the effects of pathogen consumption on infection dynamics in natural situations and investigate the impact of intervention actions.</p>
Source data for "Date of introduction and epidemiologic patterns of SARS-CoV-2 in Mogadishu, Somalia: estimates from transmission modelling of satellite-based excess mortality data in 2020"
<p>Source data for the model fitting code at https://doi.org/10.5281/zenodo.5525349, accompanying the article "<em>Date of introduction and epidemiologic patterns of SARS-CoV-2 in Mogadishu, Somalia: estimates from transmission modelling of satellite-based excess mortality data in 2020</em>"</p>
A Systematic Mapping of the Classification of Open Educational Resources for Computer Science Education in Digital Sources (Data)
<p>Data from a Systematic Mapping of the classification of Open Educational Resources for Computer Science Education.</p> <p>Content:</p> <ul> <li>Studies selected</li> <li>Digital sources used to classify Open Educational Resources for Computer Science Education</li> <li>Computer Science domains explored by Open Educational Resources</li> <li>Approaches for the classification of Open Educational Resources for Computer Science Education</li> </ul>
Source Data for Crowdsourcing Bridge Dynamic Monitoring with Smartphone Vehicle Trips
<p>This data accompanies the study "Crowdsourcing Bridge Dynamic Monitoring with Smartphone Vehicle Trips" published in (Nature) Communications Engineering. This paper focuses on using large and inexpsensive datasets for obtaining information on the dynamics of bridges. In this study, data is collected by smartphones in moving vehicles as the cross over a bridge, in three distinct applications. Smartphone data was collected in controlled field experiments and uncontrolled Uber rides on a long-span suspension bridge in the USA (The Golden Gate Bridge) and an analytical method was developed to accurately recover modal properties. The method was also successfully applied to partially-controlled crowdsourced data collected on a short-span highway bridge in Italy. The results suggest that larve and inexpensive datasets collected by smartphones could play a role in monitoring the health of existing transportation infrastructure.</p> <p>The data provided includes the source data for the figures in the publication as well as the "controlled data" referenced in the study.</p>
Source data
<p>Source data for: Ferromagnetic–antiferromagnetic coexisting ground states and exchange bias effects in MnBi4Te7 and MnBi6Te10</p> <p><a href="https://github.com/Shiqi17Yang/Raw-data-for-main-text/files/9943195/Figure1.xlsx">Figure1.xlsx</a> <a href="https://github.com/Shiqi17Yang/Raw-data-for-main-text/files/9943194/Figure2.xlsx">Figure2.xlsx</a> <a href="https://github.com/Shiqi17Yang/Raw-data-for-main-text/files/9943196/Figure3.xlsx">Figure3.xlsx</a> <a href="https://github.com/Shiqi17Yang/Raw-data-for-main-text/files/9943198/Figure4.xlsx">Figure4.xlsx</a></p>
A STP-HSI index method for urban built-up area extraction based on multi-source remote sensing data
<p>The changes of urban built-up areas can reflect the process of urbanization, and it can reflect the population, economy, and cultural development of the city. Therefore, accurate and timely extraction of urban built-up areas plays an important role in the dynamic management of the city. In the existing research, single-source remote sensing data is used to extract urban built-up areas, and there is a problem that the spectrum of urban areas and non-urban areas is easily confused. Multi-source remote sensing data, including luojia-1 remote sensing data, Landsat 8 OLI remote sensing data, etc., can make up for the spectrum confusing issues.</p> <p>We fuse the time series information of night light remote sensing data, neighborhood information and point of interest (POI) data in spatial dimension, and propose a built-up area extraction method that integrates night light time and space information and POI information.</p>
Data for: Elevational changes in insect herbivory on woody plants in six mountain ranges of temperate Eurasia: Sources of variation
<p>Current theory predicts that the intensity of biotic interactions, and particularly herbivory, decreases with increasing latitude and elevation. However, recent studies have revealed substantial variation in both the latitudinal and elevational patterns of herbivory. This variation is often attributed to differences in study design and type of data collected by different researchers. Here, we used a standardised sampling protocol along elevational gradients in six mountain ranges, located at different latitudes within temperate Eurasia, to uncover the sources of variation in elevational patterns in insect herbivory on woody plant leaves. We discovered the considerable variation in elevational patterns among different mountain ranges; nevertheless, herbivory generally decreased with increasing elevation at both the community-wide and individual plant species levels. This decrease was mostly due to openly living defoliators, whereas no significant association was detected between herbivory and elevation among insects living within plant tissues (i.e. miners and gallers). The elevational decrease in herbivory was significant for deciduous plants but not for evergreen plants, and for low-stature plants but not for tall plants. The community-wide herbivory increased with increases in both specific leaf area and leaf size. The strength of the negative correlation between herbivory and elevation increased from lower to higher latitudes. We conclude that elevational gradients in herbivory demonstrate considerable variation, and that this variation is mostly associated with herbivore feeding habit, some plant traits and latitude of the mountain range.</p>
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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.