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150 results for “data fusion”
Data from: Non-clonal coloniality: genetically chimeric colonies through fusion of sexually produced polyps in the hydrozoan Ectopleura larynx
Hydrozoans typically develop colonies through asexual budding of polyps. Although colonies of Ectopleura are similar to other hydrozoans in that they consist of multiple polyps physically connected through continuous epithelia and shared gastrovascular cavity, Ectopleura larynx does not asexually bud polyps indeterminately. Instead, after an initial phase of limited budding in a young colony, E. larynx achieves its large colony size through the aggregation and fusion of sexually (non-clonally) produced polyps. The apparent chimerism within a physiologically integrated colony presents a potential source of conflict between distinct genetic lineages, which may vary in their ability to access the germline. In order to determine the extent to which the potential for genetic conflict exists, we characterized the types of genetic relationships between polyps within colonies, using a RAD-Seq approach. Our results indicate that E. larynx colonies are indeed comprised of polyps that are clones and sexually reproduced siblings and offspring, consistent with their life history. In addition, we found that colonies also contain polyps that are genetically unrelated, and that estimates of genome-wide relatedness suggests a potential for conflict within a colony. Taken together, our data suggests that there are distinct categories of relationships in colonies of E. larynx, likely achieved though a range of processes including budding, regeneration and fusion of progeny and unrelated polyps, with the possibility for a genetic conflict resolution mechanism. Together these processes contribute to the re-evolution of the ecologically important trait of coloniality in E. larynx.
Data from: Genetic signatures of lineage fusion closely resemble population decline
<p>Accurate interpretation of the genetic signatures of past demographic events is crucial for reconstructing evolutionary history. Lineage fusion (complete merging, resulting in a single panmictic population) is a special case of secondary contact that is seldom considered. Here, the circumstances under which lineage fusion can be distinguished from population size constancy, growth, bottleneck, and decline were investigated. Multi-locus haplotype data were simulated under models of lineage fusion with different divergence versus sampling lag times (D:L ratios). These pseudo-observed datasets also differed in their allocation of a fixed amount of sequencing resources (number of sampled alleles, haplotype length, number of loci). Distinguishability of lineage fusion versus each of 10 untrue non-fusion scenarios was quantified based on six summary statistics (neutrality tests). Some datasets were also analyzed using extended Bayesian skyline plots. Results showed that signatures of lineage fusion very closely resemble those of decline—high distinguishability was generally limited to the most favorable scenario (D:L = 9), using the most sensitive summary statistics (<em>F</em><sub>S</sub> and <em>Z</em><sub>nS</sub>), coupled with the optimal sequencing resource allocation (maximizing number of loci). Also, extended Bayesian skyline plots often erroneously inferred population decline. Awareness of the potential for lineage fusion to carry the hallmarks of population decline is critical.</p>
Terrestrial water storage data based on the generalized three-cornered hat fusion method
<ul> <li>The dataset combines three GRACE Mascon products (CSR, JPL and GSFC) using the generalized three-cornered hat method (GTCH) to generate, referred to as TWS_GTCH. The dataset spans from 2003 to 2022, with a spatial resolution of 0.5 degrees and a temporal resolution of monthly.</li> <li>We deduct 2004-2009 means from the three GRACE terrestrial water storage (TWS) Mascon products to ensure that they have the same reference period. To enhance the reliability of the results and eliminate differences between datasets, we employ the GTCH method to calculate the root mean square error (rmse) of the GRACE TWS data to assess uncertainty. Finally, we utilize the least squares method to fuse the data based on their uncertainties.</li> </ul>
Supplementary data: Bayesian multi-exposure image fusion for robust high dynamic range ptychography
<p>Accompanying supplementary data for the paper. To download this data automatically and use the software, please refer to the details in the README of the linked github repository. </p> <p><strong>Github URL: </strong><a href="https://github.com/microscopic-image-analysis/bayes-mef"><strong>https://github.com/microscopic-image-analysis/bayes-mef</strong></a></p>
Source Data: Visualization of chromosomal reorganization induced by heterologous fusions in the mammalian nucleus
<p>Source data from Visualization of chromosomal reorganization induced by heterologous fusions in the mammalian nucleus</p>
Data for: A zinc-finger fusion protein refines Gal4-defined neural circuits
<p>This is microscopy image data and related information for</p> <p><strong>A zinc-finger fusion protein refines Gal4-defined neural circuits</strong></p> <p>The analysis of behavior requires that the underlying neuronal circuits are identified and genetically isolated. In several major model species—most notably Drosophila, neurogeneticists identify and isolate neural circuits with a binary, heterologous, expression control system: Gal4-UASG. One limitation of Gal4-UASG is that expression patterns are often too broad to map circuits precisely. To help refine the expression of Gal4 lines, we developed an intersectional genetic AND operator. Interoperable with Gal4, the new system’s key component is a fusion protein in which the DNA-binding domain of Gal4 has been replaced with a zinc finger domain with a different DNA-binding specificity. In combination with its cognate binding site (UASZ) the zinc-finger-replaced Gal4 (‘Zal1’) was functional as a standalone transcription factor. Zal1 transgenes also refined Gal4 expression ranges when combined with UASGZ, a hybrid upstream activation sequence. In this way, combining Gal4 and Zal1 drivers captured restricted cell sets compared with single drivers and improved genetic fidelity. This intersectional genetic AND operation presumably derives from the action of a heterodimeric transcription factor: Gal4-Zal1. Configurations of Zal1-UASZ and Zal1-Gal4-UASGZ are versatile tools for defining, refining, and manipulating targeted neural expression patterns with precision.</p>
Multi-Source Precipitation Data Fusion Across Continental United States
<p><strong><span>Dataset Description</span></strong><span>: This dataset supports our research presented in the paper "<em>A deep learning-based framework for multi-source precipitation fusion</em>" by Gavahi et al., (2023) published in <em>Remote Sensing of Environment</em>. The study introduces a novel deep learning architecture for merging and downscaling multiple precipitation products, aiming to enhance quantitative precipitation estimation (QPE) accuracy. The developed model, the Precipitation Data Fusion Network (PDFN), integrates 3D-CNN and ConvLSTM layers to capture the inherent spatiotemporal dependencies of precipitation data. The results indicate significant improvements in error statistics.</span></p> <p><span>The dataset includes merged daily precipitation estimations using the PDFN model. The data cover the Continental United States (CONUS) and are provided at a spatial resolution of 0.05 degrees. Temporal coverage spans from January 1, 2015, to April 30, 2024. The coordinate reference system used is WGS1984.</span></p> <p><strong><span>Note</span></strong><span>: Since the PERSIANN-CDR dataset is only available until the end of 2023, in this dataset, we used PDIR-Now instead to ensure the dataset's continuity and completeness. In the original paper, we used PERSIANN-CDR, but here we used PDIR-Now to extend the dataset to cover the period until April 30, 2024.</span></p> <p><strong><span>Usage Notes</span></strong><span>: This dataset is intended for use in applications such as land surface modeling, flood forecasting, drought monitoring and prediction. Users are requested to cite the associated paper when utilizing the dataset for academic or research purposes. </span></p> <p><strong><span>Related Publications</span></strong><span>: For further details on the methodology and applications of this dataset, refer to the paper "Gavahi, K., E. Foroumandi, and H. Moradkhani (2023), A deep learning-based framework for multi-source precipitation fusion, Remote Sensing of Environment, doi:10.1016/j.rse.2023.113723"</span></p>
Improving Volcanic SO2 Cloud Modeling Through Data Fusion and Trajectory Analysis: A Case Study of 2022 Hunga Tonga Eruption
<p><strong>Dataset Overview</strong>: This dataset comprises approximately 500 clusters of aggregated observational data collected from January 16 to 20 during the ascending (ASC) and descending (DES) periods. We grouped a large number of observation points into these clusters and calculated trajectories from the center of each cluster. The choice of 500 clusters was driven by pragmatic considerations, aiming for a balance between computational feasibility and the level of detail needed for our analysis.</p> <p><strong>Data Unit Description</strong>: The "mass" values in this dataset for each cluster are calculated by multiplying the mass per unit area (<span><span>g/m2</span></span>) of individual data points by the area covered by each point, thus providing the total mass in grams (g). The "heights" are presented in units of kilometers (km), representing the observed top heights of each cluster.</p>
CONUS Riverine Data Fusion TSS Concentration 2000-2023 Dataset
<div> <div> <h1><strong>Overview</strong></h1> <h3><strong>Available here are the datasets producing 1.8M large river sediment concentrations derived from fused (previously MODIS) and non-fused (Landsat-5,7,8,9 & Sentinel-2) image reflectances made over 1,253 CONUS sites, as validated with over 25,000 in situ measurements across these same sites using machine learning. Satellite super-resolution data fusion ‘teaches’ a coarse resolution sensor (500m) what it would have seen if it were a fine resolution satellite (30m). Datasets include:<br></strong></h3> <p><strong>trainingMatchups_2000-2023.csv -</strong> All Fusion and LS2 matchups within +/- 1 day of Water Quality Portal TSS measurements used to train a machine learning model between 2000-2023.</p> <p><strong>fusion_reflectance_raw.csv -</strong> All raw median reflectance, standard deviation, pixel count, date, and siteID data for fusion images generated between 2000-2023.</p> <p><strong>LS2_reflectance_raw.csv -</strong> All raw median reflectance, standard deviation, pixel count, date, and siteID data for LS2 images generated between 2000-2023.</p> <p><strong>fusionSed_all.csv -</strong> All TSS estimates from the RF model including matchup LS2, matchup Fusion, predicted LS2, and predicted Fusion between 2000-2023.</p> </div> </div>
Data from: Efficient summary statistics for detecting lineage fusion from phylogeographic datasets
<p>Aim: Lineage fusion (merging of two or more populations of a species resulting in a single panmictic group) is a special case of secondary contact. It has the potential to counteract diversification and speciation, or to facilitate it through creation of novel genotypes. Understanding the prevalence of lineage fusion in nature requires reliable detection of it, such that efficient summary statistics are needed. Here we report on simulations that characterized the initial intensity and subsequent decay of signatures of past fusion for 17 summary statistics applicable to DNA sequence haplotype data.</p> <p>Location: Global.</p> <p>Taxon: Diploid out-crossing species.</p> <p>Methods: We considered a range of scenarios that could reveal the impacts of different combinations of read length versus number of loci (arrangement of DNA sequence data), and whether or not pre-fusion populations experienced bottlenecks coinciding with their divergence (historical context of fusion). Post-fusion gene pools were sampled along 10 successive time points representing increasing lag times following merging of sister populations, and summary statistic values were recalculated at each.</p> <p>Results: Many summary statistics were able to detect signatures of complete merging of populations after a sampling lag time of 1.5 Ne generations, but the most informative ones included two neutrality tests and four diversity metrics, with ZnS being particularly powerful. Correlation was relatively low among the two neutrality tests and two of the diversity metrics. There were clear benefits of many short (200-bp × 200) loci over a handful of long (4-kb × 10) loci. Also, only the latter genetic dataset type was showed impacts of bottlenecks during divergence upon the number of informative summary statistics.<br> Main conclusions: This work contributes to identifying cases of lineage fusion, and advances phylogeography by enabling more nuanced reconstructions of how individual species, or multiple members of an ecological community, responded to past environmental change.</p>
Electrophysiology Data for "Two functional epithelial sodium channel isoforms are present in rodents despite pronounced evolutionary pseudogenization and exon fusion"
<p>Here we provide the electrophysiology data for the manuscript "Two functional epithelial sodium channel isoforms are present in rodents despite pronounced evolutionary pseudogenization and exon fusion", published in Molecular Biology and Evolution (2021): msab271 (doi: 10.1093/molbev/msab271). Data are reported as current values in Excel format, sorted according to the appearance in Figures and supplemented by explanatory text on the procedures/data presentation.</p>
Research data supporting "Detection of microRNA biomarkers via inhibition of DNA-mediated liposome fusion"
<p>Raw research data supporting Jumeaux, C. et al., Nanoscale (2018), DOI: 10.1039/C8NA00331A .</p>
Data for: Sigma-B responses of Bacillus subtilis exposed to different environmental stressors and containing different single RsbR proteins or hybrid fusions of RsbRs
<p>Bacteria use a variety of systems to sense stress and mount an appropriate response to assure fitness and survival. <em>Bacillus subtilis</em> uses stressosomes—cytoplasmic multiprotein complexes—to sense environmental stressors and enact the general stress response by activating the alternative sigma factor σ<sup>B</sup>. Each stressosome includes 40 RsbR proteins, representing four paralogous (RsbRA, RsbRB, RsbRC, and RsbRD) putative stress sensors. Population-level analyses suggested that the RsbR paralogs are largely redundant, while our prior work using microfluidics-coupled fluorescence microscopy uncovered differences among the RsbR paralogs' σ<sup>B</sup> response profiles with respect to timing and intensity when facing an identical stressor.</p> <p>We used microfluidics and fluorescence microscopy to address the question of whether the σ<sup>B</sup> responses mediated by each paralog differ in the presence of different environmental stressors: can they distinguish among stressors? Wild-type cells (with all four paralogs) and RsbRA-only cells activate σ<sup>B</sup> with characteristic transient response timing irrespective of stressor but show varying response magnitude. However, cells with other individual RsbR paralogs show distinct timing and magnitude in their responses to ethanol, salt, oxidative and acid stress, implying that RsbR proteins can distinguish among stressors. To show this distinct timing, we quantified time-lapse image series of cells with a fluorescent σ<sup>B</sup> transcriptional reporter. Representative videos of time-lapse image series and the results of our quantitation for each RsbR paralog in each stress condition are included in this dataset.</p> <p>We also probed the relative importance of each half of each RsbR paralog. Experiments with hybrid fusion proteins comprising the N-terminal half of one paralog and the C-terminal half of another argued that the N-terminal identity influences response magnitude and that determinants in both halves of RsbRA are important for its stereotypical transient σ<sup>B</sup> response timing. Time-lapse videos for each hybrid fusion protein and the corresponding quantification of these data are also included in the dataset.</p>
Pretrained models and results for "Thunderstorm nowcasting with deep learning: a multi-hazard data fusion model"
<p>This dataset contains the pretrained model weights and precomputed results for the paper "Thunderstorm nowcasting with deep learning: a multi-hazard data fusion model" submitted to <em>Geophysical Research Letters</em>. A preprint of the paper can be found at <a href="https://arxiv.org/abs/2211.01001">https://arxiv.org/abs/2211.01001</a>.</p> <p>The ML code can be found at <a href="https://github.com/MeteoSwiss/c4dl-multi">https://github.com/MeteoSwiss/c4dl-multi</a>. Download all the files here and extract the contents to the following subdirectories in the ML code directory:</p> <ul> <li>Results (<a href="https://zenodo.org/api/files/d4829f50-55fd-4d86-b875-7f2b91dba74f/c4dl-results-lightningdl.zip?versionId=54046830-4c7e-48c6-af42-d6d5606af86b">c4dl-results-lightningdl.zip</a>) -> results/</li> <li>Pretrained models (<a href="https://zenodo.org/api/files/d4829f50-55fd-4d86-b875-7f2b91dba74f/c4dl-models-lightningdl.zip?versionId=364bca7c-e6ad-4ed9-9264-57c759ea0ac6">c4dl-models-lightningdl.zip</a>) -> models/</li> <li>If you want to train models, data (<a href="https://zenodo.org/api/files/0cfc0cf4-755a-4618-8341-39b107a3901c/c4dl-patches-2020-additional.zip">c4dl-patches-2020-additional.zip</a>) -> data/2020/</li> </ul> <p>Additionally, you will need the datasets from <a href="https://zenodo.org/deposit/6802292">this Zenodo archive</a>. Follow the instructions there for downloading.</p>
Data from: A phylogenomic analysis of Lonicera and its bearing on the evolution of organ fusion
<p class="MsoNormal"><strong><span>PREMISE: </span></strong><span>The ~140 species of <em>Lonicera</em> are characterized by variously fused leaves, bracteoles, and ovaries, making it a model system for studying the evolution and development of organ fusion. However, </span><span>previous phylogenetic analyses, based mainly on chloroplast DNA markers, have yielded uncertain and conflicting results. A well-supported phylogeny of <em>Lonicera</em> will allow us to trace the evolutionary history of organ fusion.</span></p> <p class="MsoNormal"><strong><span>METHODS:</span></strong><span> We inferred the phylogeny of <em>Lonicera</em> using Restriction-site Associated DNA Sequencing (RADSeq), sampling all major clades and 18 of the 23 subsections. This provided the basis for inferring the evolution of five fusion-related traits. </span></p> <p class="MsoNormal"><strong><span>RESULTS: </span></strong><span>RADSeq data yielded a well-resolved and well-supported phylogeny. The two traditionally recognized subgenera (<em>Periclymenum</em> and <em>Chamaecerasus</em>), three of the four sections (<em>Isoxylosteum</em>, <em>Coeloxylosteum</em>, and <em>Nintooa</em>), and half of the subsections sampled were recovered as monophyletic. However, the large and heterogeneous section <em>Isika</em> was strongly supported as paraphyletic. <em>Nintooa</em>, a clade of ~22 mostly vine-forming species, including <em>L. japonica</em>, was recovered in a novel position, raising the possibility of cytonuclear discordance. We document the parallel evolution of fused leaves, bracteoles, and ovaries, with rare reversals. Most strikingly, complete cupules, in which four fused bracteoles completely enclose two unfused ovaries, arose at least three times. Surprisingly, these appear to have evolved directly from ancestors with free bracteoles instead of partial cupules. </span></p> <p class="MsoNormal"><strong><span>CONCLUSIONS: </span></strong><span>We provide the most comprehensive and well-supported phylogeny of <em>Lonicera</em> to date. Our inference of multiple evolutionary shifts in organ fusion provides a solid foundation for in-depth developmental and functional analyses.</span></p>
Data from: Fission-fusion dynamics in sheep: The influence of resource distribution and temporal activity patterns
<p><span>Fission-fusion events, i.e. changes to the size and composition of animal social groups, are a mechanism to adjust the social environment in response to short-term changes in the cost-benefit ratio of group living. Furthermore, the time and location of fission-fusion events provide insight into the underlying drivers of these dynamics. Here, we describe a method for identifying group membership over time and for extracting fission-fusion events from animal tracking data. We applied this method to high-resolution GPS data of free-ranging sheep (<em>Ovis aries</em>). Group size was highest during times when sheep typically rest (mid-day and at night), and when anti-predator benefits of grouping are high while costs of competition are low. Consistent with this, fission and fusion frequencies were highest during early morning and late evening, suggesting that social restructuring occurs during periods of high activity. However, fission and fusion events were not more frequent near food patches and water resources when adjusted for overall space use. This suggests a limited role of resource competition. Our results elucidate the dynamics of grouping in response to social and ecological drivers, and we provide a tool for investigating these dynamics in other species.</span></p>
Data from: multiexciton interactions in singlet fission and triplet fusion upconversion dendrimers
<p>Singlet fission (SF) and triplet-triplet annihilation upconversion (TTA-UC) are two multiexciton processes intimately related to the dynamic interaction between one high-lying energy singlet and two low-lying energy triplet excitons. Here, we introduce a series of dendritic macromolecules that serve as a platform to study the effect of interchromophore interactions on the dynamics of multiexciton generation and decay as a function of dendrimer generation. The dendrimers (generations 1-4) consist of trimethylolpropane (TMP) core and 2,2-bis(methylol)propionic acid (bis-MPA) dendrons that provide exponential growth of the branches, leading to a corona decorated with pentacenes for SF or anthracenes for TTA-UC. The findings reveal a trend where a few highly ordered sites emerge as the dendrimer generation grows, dominating the multiexciton dynamics, as deduced from optical spectra, and transient absorption spectroscopy. While the dendritic structures enhance TTA-UC at low annihilator concentrations in the largest dendrimers, the paired chromophore interactions induce a broadened and red-shifted excimer emission. In SF dendrimers of higher generations, the triplet dynamics become increasingly dominated by pairwise sites exhibiting strong coupling (Type II), which can be readily distinguished from sites with weaker coupling (Type I) by their spectral dynamics and decay kinetics.</p>
Data from: Genetic signatures of lineage fusion closely resemble population decline
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Data for: Sigma-B responses of Bacillus subtilis exposed to different environmental stressors and containing different single RsbR proteins or hybrid fusions of RsbRs
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Data from: fission-fusion dynamics in sheep: the influence of resource distribution and temporal activity patterns
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