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1,026 results for “Linked data”
Data from: Steatotic liver disease induced by TCPOBOP-activated hepatic constitutive androstane receptor: Primary and secondary gene responses with links to disease progression
<p>Constitutive Androstane Receptor (CAR, <em>Nr1i3</em>), a liver nuclear receptor and xenobiotic sensor, induces drug, steroid and lipid metabolizing enzymes, stimulates liver hypertrophy and hyperplasia, and ultimately, hepatocellular carcinogenesis. The mechanisms linking early CAR responses to later disease development are poorly understood. Here we show that exposure of CD-1 mice to TCPOBOP, a halogenated xenochemical and selective CAR agonist ligand, induces pericentral steatosis marked by hepatic accumulation of cholesterol and neutral lipid, and elevated circulating alanine aminotransferase, indicating hepatocyte damage. TCPOBOP-induced steatosis was weaker in the pericentral region but stronger in the periportal region in females compared to males. Early (1-day) TCPOBOP transcriptional responses were enriched for CAR-bound primary response genes, and for lipogenesis and xenobiotic metabolism and oxidative stress protection pathways; late (2-wk) TCPOBOP responses included many CAR binding-independent secondary response genes, with enrichment for macrophage activation, immune response and cytokine and reactive oxygen species production. Late upstream regulators specific to TCPOBOP-exposed male liver were linked to pro-inflammatory responses and hepatocellular carcinoma progression. TCPOBOP administered weekly to male mice using a high corn oil vehicle activated carbohydrate-responsive transcription factor (MLXIPL)-regulated target genes, dysregulated mitochondrial respiratory and translation regulatory pathways, and induced more advanced liver pathology. Overall, TCPOBOP exposure recapitulates histological and gene expression changes characteristic of emerging steatotic liver disease, including secondary gene responses in liver non-parenchymal cells indicative of transition to a more advanced disease state. Upstream regulators of both the early and late TCPOBOP response genes include novel biomarkers for foreign chemical-induced metabolic dysfunction-associated steatotic liver disease.</p>
Data from: Linking in vivo muscle dynamics to in situ force-length and force-velocity reveals that guinea fowl lateral gastrocnemius operates at shorter than optimal lengths
<p>Force-length (F-L) and force-velocity (F-V) properties characterize skeletal muscle's intrinsic properties under controlled conditions, and it is thought that these properties can inform and predict <em>in vivo</em> muscle function. Here, we map dynamic <em>in vivo</em> operating range and mechanical function during walking and running, to the measured <em>in situ</em> F-L and F-V characteristics of guinea fowl (<em>Numida meleagris</em>) lateral gastrocnemius (LG), a primary ankle extensor. We use <em>in vivo</em> patterns of muscle (tendon) force, fascicle length, and activation to test the hypothesis that muscle fascicles operate at optimal lengths and velocities to maximize force or power production during walking and running. Our findings only partly support our hypothesis: <em>in vivo</em> LG velocities are consistent with optimizing power during work production, and economy of force at higher loads. However, LG does not operate at lengths on the force plateau (±5% Fmax) during force production. LG length was near L<sub>0</sub> at the time of EMG onset but shortened rapidly such that force development during stance occurred almost entirely on the ascending limb of the F-L curve, at shorter than optimal lengths. These data suggest that muscle fascicles shorten across optimal lengths in late swing, to optimize the potential for rapid force development near the swing-stance transition. This may provide resistance against unexpected perturbations that require rapid force development at foot contact. We also found evidence of passive force rise (in absence of EMG activity) in late swing, at lengths where passive force is zero <em>in situ</em>, suggesting that history dependent and viscoelastic effects may contribute to <em>in vivo</em> force development. Direct comparison of<em> in vivo </em>work loops and physiological operating ranges to traditional measures of F-L and F-V properties suggests the need for new approaches to characterize dynamic muscle properties in controlled conditions that more closely resemble <em>in vivo </em>dynamics.</p>
MS data linked to manuscript: https://doi.org/10.1111/1751-7915.14215
Open the record for dataset details and reuse information.
Link Discovery on AIS and Contextual data sets
<p>This data set contains the links discovered between AIS synopses provided in https://zenodo.org/record/2576152 and contextual data sets available at https://zenodo.org/record/2576584 . Specifically, the detected relations and the contextual data sets used are:</p> <p>a) C1 ports of Brittany, World Port Index and SeaDataNet fishing ports for proximity relation "nearto", stored in AIS_nearto_ports.ttl.7z</p> <p>b) C4 fishing areas (European Commission) for "within" relation stored in AIS_within_fishingAreas.ttl.7z</p> <p>c) C5 fishing interdiction for "within" relation stored in AIS_within_FishingConstraints.ttl.7z</p> <p>d) C5 Natura2000 for "within" relation stored in AIS_within_natura2000.ttl.7z</p> <p>Please notice that the attached data sets contain only the detected links. Description of the resources is provided in the corresponding TTL files.</p>
Data Analysis for Context- and sex-dependent links between sire sexual success and offspring pathogen resistance
<p>Data Analysis for "Context- and sex-dependent links between sire sexual success and offspring pathogen resistance"</p> <p>By Aijuan Liao and Tadeusz J. Kawecki</p>
Linked multipoint cotranscriptional RNA chemical probing data for the E. coli SRP RNA, C. beijerinckii pfl ZTP riboswitch, and B. cereus crcB fluoride riboswitch
<p>Cotranscriptional RNA chemical probing data for the <em>E. coli</em> signal recognition particle (SRP) RNA, <em>Clostridium beijerinckii pfl</em> ZTP riboswitch, and <em>Bacillus cereus crcB </em>fluoride riboswitch. Data were generated using the linked multipoint Transcription Elongation Complex RNA structure probing (TECprobe-LM) and variable length Transcription Elongation Complex RNA structure probing (TECprobe-VL) procedures.</p>
Model results and data associated with "Antecedent effect models as an exploratory tool to link climate drivers to herbaceous perennial population dynamics data"
<p>Model results and data (including Bayesian posteriors) associated with "Antecedent effect models as an exploratory tool to link climate drivers to 3 herbaceous perennial population dynamics data".</p> <p>This is a repository created to store the posteriors of the models fit within this project. Because these occupy so much space, it makes sense to store them in a separate repository.</p> <p>There are two directories:</p> <ul> <li><em>model_results/</em> contains all of the posteriors (files with character pattern <em>main_posterior_#.csv</em>). The three types of files contained in this directory are described in <em>metadata_model_results.xlsx</em>. The number # corresponds to column "index" in file <em>raw_data/design_insample.csv</em>.</li> <li><em>raw_data/</em> is mostly not essential: it contains the raw data to fit models, and it replicates folder <em>data/</em> in repository https://dx.doi.org/10.5281/zenodo.13909628.</li> </ul>
PollyXT and COSMO-MUSCAT data for "Investigating the link between mineral dust hematite content and intensive optical properties by means of lidar measurements and aerosol modelling"
<p>The dataset contains 4 different files: </p> <ul> <li>For the single case example on the 24 August 2021 between 2:45 to 5:27 UTC in Mndelo, Cabo Verde: <ul> <li>-Mindelo-PollyXT_CPV-20210824_0245-0527-77smooth-info.txt : contains the information of the vertically retrieved optical properties from PollyXT lidar measurements. The information contained refers to the chosen retrieval times, vertical smoothing, and reference heights</li> <li>-Mindelo-PollyXT_CPV-20210824_0245-0527-77smooth.txt : vertically retrieved optical properties per height.</li> <li>-Mindelo-model_24aug.csv : COSMO-MUSCAT vertical results of dust and mineral mass concentrations per height. The columns that end with "int mass" correspond to the integrated mass per dust layer and columns that end with numbers correspond to different size bins. For reference to the size bins see Table 1 in Gómez Maqueo Anaya et al., 2024</li> </ul> </li> <li>Mutiple case studies: <ul> <li>-Mindelo-lidar-uvvisdiff_model.csv : Twenty-two case studies with the following order: first, the mean values of the lidar-derived optical properties, along with their corresponding retrieval times and heights that define the dust plume. This is followed by the POLIPHON (Mamouri and Ansmann, 2014, 2017) data. The mean values from dust and mineral mass concentrations from the model start with the model heights where the dust plumes were calculated. At the end of the dataset rows, the times from which the modeled mean values are calculated can be found.</li> </ul> </li> </ul>
Data from: Linking social and spatial networks to viral community phylogenetics reveals subtype-specific transmission dynamics in African lions
1.Heterogeneity within pathogen species can have important consequences for how pathogens transmit across landscapes; however, discerning different transmission routes is challenging. 2.Here we apply both phylodynamic and phylogenetic community ecology techniques to examine the consequences of pathogen heterogeneity on transmission by assessing subtype specific transmission pathways in a social carnivore. 3.We use comprehensive social and spatial network data to examine transmission pathways for three subtypes of feline immunodeficiency virus (FIVPle) in African lions (Panthera leo) at multiple scales in the Serengeti National Park, Tanzania. We used FIVPle molecular data to examine the role of social organization and lion density in shaping transmission pathways and tested to what extent vertical (i.e., father and/or mother offspring relationships) or horizontal (between unrelated individuals) transmission underpinned these patterns for each subtype. Using the same data, we constructed subtype specific FIVPle co-occurrence networks and assessed what combination of social networks, spatial networks, or co-infection best structured the FIVPle network. 4.While social organization (i.e., pride) was an important component of FIVPle transmission pathways at all scales, we find that FIVPle subtypes exhibited different transmission pathways at within- and between-pride scales. A combination of social and spatial networks, coupled with consideration of subtype co-infection, was likely to be important for FIVPle transmission for the two major subtypes, but the relative contribution of each factor was strongly subtype specific. 5.Our study provides evidence that pathogen heterogeneity is important in understanding pathogen transmission, which could have consequences for how endemic pathogens are managed. Furthermore, we demonstrate that community phylogenetic ecology coupled with phylodynamic techniques can reveal insights into the differential evolutionary pressures acting on virus subtypes, which can manifest into landscape-level effects.
Data from: Split between two worlds: automated sensing reveals links between above- and belowground social networks in a free-living mammal
Many animals socialize in two or more major ecological contexts. In nature, these contexts often involve one situation in which space is more constrained (e.g. shared refuges, sleeping cliffs, nests, dens or burrows) and another situation in which animal movements are relatively free (e.g. in open spaces lacking architectural constraints). Although it is widely recognized that an individual's characteristics may shape its social life, the extent to which architecture constrains social decisions within and between habitats remains poorly understood. Here we developed a novel, automated-monitoring system to study the effects of personality, life-history stage and sex on the social network structure of a facultatively social mammal, the California ground squirrel (Otospermophilus beecheyi) in two distinct contexts: aboveground where space is relatively open and belowground where it is relatively constrained by burrow architecture. Aboveground networks reflected affiliative social interactions whereas belowground networks reflected burrow associations. Network structure in one context (belowground), along with preferential juvenile–adult associations, predicted structure in a second context (aboveground). Network positions of individuals were generally consistent across years (within contexts) and between ecological contexts (within years), suggesting that individual personalities and behavioural syndromes, respectively, contribute to the social network structure of these free-living mammals. Direct ties (strength) tended to be stronger in belowground networks whereas more indirect paths (betweenness centrality) flowed through individuals in aboveground networks. Belowground, females fostered significantly more indirect paths than did males. Our findings have important potential implications for disease and information transmission, offering new insights into the multiple factors contributing to social structures across ecological contexts.
Data from: Linking beaver dam affected flow dynamics to upstream passage of Arctic grayling
Beaver reintroductions and beaver dam structures are an increasingly utilized ecological tool for rehabilitating degraded streams, yet beaver dams can potentially impact upstream fish migrations. We collected two years of data on Arctic grayling movement through a series of beaver dams in a low gradient mountain stream, utilizing radio-telemetry techniques, to determine how hydrology, dam characteristics, and fish attributes impeded passage and movement rates of spawning grayling. We compared fish movement between a "normal" flow year and a "low" flow year, determined grayling passage probabilities over dams in relation to a suite of factors, and predicted daily movement rates in relation to the number of dams each fish passed and distance between dams during upstream migration to spawning areas. We found that the average passage probability over unbreached beaver dams was 88%, though we found that it fell below 50% at specific dams. Upstream passage of grayling was affected by three main characteristics: 1) temperature 2) breach status and 3) hydrologic linkages that connect sections of stream above and below the dam. Other variables influence passage, but to a lesser degree. Cumulative passage varied with distance upstream and total number of dams passed in low versus normal flow years, while movement rates upstream slowed as fish swam closer to dams. Our findings demonstrate that upstream passage of fish over beaver dams is strongly correlated with hydrologic conditions with moderate controls by dam- and fish-level characteristics. Our results provide a framework that can be applied to reduce barrier effects when and where beaver dams pose a significant threat to the upstream migration of fish populations while maintaining the diverse ecological benefits of beaver activity when dams are not a threat to fish passage.
Data for: Linking behavioural type with cannibalism in Eurasian perch
<p>Behavioural data and prey selection data</p> <p>V3 includes corrected Fulton's K and date of behavioural trials </p>
Demonstaration of the use of Zenodo website to upload data and link it to the PersonalizeAF project
<p>This video demonstarates the use of Zenodo website to upload data and link it to the PersonalizeAF project</p>
TCTracer: Establishing Test-to-Code Traceability Links Using Dynamic and Static Techniques - Evaluation Data - Empirical Software Engineering 2021
<p>This repository provides the data artefacts for the experiments conducted using our tool TCTracer for the journal paper "TCTracer: Establishing Test-to-Code Traceability links Using Dynamic and Static Techniques" as submitted to the Empirical Software Engineering journal in 2021.</p>
Linked Data Workshops papers (LDOW)
<p>We analyzed the published articles of the Linked Data on the web (LDOW) workshop series and performed a scientometric analysis on them. This dataset includes the metadata of published papers in the LDOW workshops (between 2008 and 2018).</p>
Data and code for the manuscript Retrieving Water Vapor From an E-band Microwave Link With an Empirical Model Not Requiring In-situ Calibration
<p>Data and code for the manuscript <em>Retrieving Water Vapor From an E-band Microwave Link With an Empirical Model Not Requiring In-situ Calibration</em> accepted for publication to<em> </em> <em>Earth and Space Science</em> in October 2021.</p> <p>The dataset contains 7 month of total losses (transmitted - received power levels) and retrieved water vapor density from a 4.87 km long full-duplex E-band commercial microwave link (CML) operating at 73.5 and 83.5 GHz in Prague, CZ. The CML was operated as a part of a mobile phone backhaul. Furthermore, observations of air temperature, and air relative humidity from sites close to the CML end nodes are provided. Finally, theoretical gaseous attenuation calculated from the air temperature and relative humidity is included as a part of the dataset.</p> <p>Data are stored in semicolon-delimited csv files. Time stamps are in UTC time in the format yyyy-mm-dd HH:MM:SS. All time series are regular and have 5-min temporal resolution. Metadata are stored in text files.</p> <p>The code is in a form of R Markdown files and html notebooks. Results presented in the manuscript Retrieving Water Vapor From an E-band Microwave Link With an Empirical Model Not Requiring In-situ Calibration and in its Supporting information are fully reproducible using this dataset.</p>
IPBES Global Assessment in Linked Open Data format
<p>This dataset contains the Thematic Assessment Report on Invasive Alien Species and their Control of the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services in linked open data format.</p> <p>The structure of the file follows the IPBES ontology version 06: <a href="https://github.com/IPBES-Data/IPBES_Ontology">https://github.com/IPBES-Data/IPBES_Ontology</a></p> <p>The report is published in 2019 and consists of 6 chapters and a Summary for Policy Makers. For more information about the report, see: <a href="https://www.ipbes.net/global-assessment">https://www.ipbes.net/global-assessment</a></p> <p>For any questions and enquiries, please contact the IPBES Data and Knowledge Unit <a href="mailto:aidin.niamir@senckenberg.de">aidin.niamir@senckenberg.de</a></p>
CPSV-AP 2.0 based public service descriptions of the Region of Epirus (Greece) as linked data
<p>It comprises a set of 45 CPSV-AP 2.0 based public service descriptions as linked data. The fields of the included public service descriptions were adapted from a regional public service catalogue, namely "The Citizen's Guide of the Region of Epirus", in order to comply with CPSV-AP 2.0 data model. The public service descriptions that are included in the linked dataset are not updated as the intended usage of the linked dataset is for research or educational activities and not for providing valid information to citizens.</p>
Geochemical, timescales data in orthopyroxenes from Kizimen 2010 eruption and database of studies linking diffusion timescales with monitoring signals.
<p>This dataset comprises the geochemical data on whole rock analysis, melt inclusions, residual glasses, magnetites and orthopyroxenes in samples from the 2010 eruption of Kizimen volcano (Kamchatka), as well as the timescales modelled in the orthopyroxenes and a database of studies linking diffusion timescales with monitoring signals, associated with the publication: Ostorero, L., Balcone-Boissard, H., Boudon, G. <em>et al.</em> Correlated petrology and seismicity indicate rapid magma accumulation prior to eruption of Kizimen volcano, Kamchatka. <em>Commun Earth Environ</em> <strong>3</strong>, 290 (2022). https://doi.org/10.1038/s43247-022-00622-3</p> <p> </p>
Data for: Fitness costs of female competition linked to resource defence and relatedness of competitors
<p>Female reproductive success is often limited by access to resources and this can lead to social competition both within and between kin groups. Theory predicts that both resource availability and relatedness should influence the fitness consequences of social competition. However, testing key predictions requires differentiating the effects of these two factors. <span>Here we achieve this experimentally by manipulating the social environment of house mice, a facultative communal breeding species with known kin discrimination ability. </span>Our results support the hypothesis that resource defence can be costly for females, potentially trading off against maternal investment. When competition for nest sites was more intense, subjects: 1) were more active during resting phases, 2) responded more strongly to simulated territory intrusions via competitive signalling, and 3) produced smaller weaned offspring. However, we found no evidence that the propensity for kin to cooperate was influenced by relatedness of rivals. Communal breeding between sisters occurred independently of the relatedness of competitors, and costs of competition with non-kin were not mitigated by greater inclusive fitness benefits. Rather, communally breeding sisters weaned fewer offspring when competing with unrelated females, indicating that competition with non-kin is more costly overall. Our findings thus demonstrate that social competition has fitness costs and that associating with kin is beneficial to avoid negative fitness consequences of competing with non-kin, in addition to more widely recognised kin-selected benefits.</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.