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1,037 results for “large-scale”
Forecasting of the Geomagnetic Activity for the Next 3 Days Utilizing Neural Networks Based on Parameters Related to Large-scale Structures of the Solar Corona
<p>These are supplementary data for the paper "Forecasting of the Geomagnetic Activity for the Next 3 Days Utilizing Neural Networks Based on Parameters Related to Large-scale Structures of the Solar Corona". They are:</p> <ul> <li>Python code to forecast Kp index</li> <li><span>Code to construct a nerual network model</span></li> </ul>
Large-scale eDNA metabarcoding survey reveals marine biogeographic break and transitions over tropical north-western Australia
<p><b>Aim:</b> Environmental DNA (eDNA) metabarcoding has demonstrated its applicability as a highly sensitive biomonitoring tool across small spatial and temporal scales in marine ecosystems. However, it has rarely been tested across large spatial scales, or biogeographical barriers. Here, we scale up marine eDNA metabarcoding, test its ability to detect a major marine biogeographic break, and evaluate its use as a regional biomonitoring tool in Australia.</p> <p><b>Location:</b> North-western Australia (NWA)</p> <p><b>Methods:</b> We applied metabarcoding assays targeting the mitochondrial 16S rRNA and CO1 genes to 284 surface seawater eDNA samples collected from 71 mid-shelf, inshore, coastal and nearshore estuarine sites over 700 km of the NWA coastline.</p> <p><b>Results:</b> Metabarcoding detected a wide range of bony fish (404 taxa), elasmobranchs (44) and aquatic reptiles (5). We detected bioregional and depth differentiation within inshore bony fish communities. These findings support the presence of a marine biogeographic break, which is purported to occur in the vicinity of Cape Leveque, demarcating the border between the Kimberley and Canning bioregions. Inshore bony fish and elasmobranch communities, as well as coastal bony assemblages, were additionally found to differ between the South and North Kimberley regions <span><span>suggesting</span></span> previously unrecognised subregional differentiation among these taxa. The overall compositional data has been used to update distribution information for a number of endangered, elusive and data-deficient taxa, including sawfish (family: Pristidae), northern river shark (<i>Glyphis garricki</i>) and wedgefish (genus: <i>Rhynchobatus</i>).</p> <p><b>Main conclusions</b>: eDNA metabarcoding demonstrated a high level of sensitivity that was able to discern fine-scale patterns across the large-scale, remote and oceanographically complex region of North-western Australia. Importantly, this study highlights the potential of integrating broad-scale eDNA metabarcoding alongside other baseline surveys and long-term monitoring approaches, which are crucial for the sustainable management and conservation of marine biodiversity in this unique marine region.</p>
Specimens from Brand et al. 2021, "Large-scale phylogenomics of the genus Macrostomum (Platyhelminthes) reveals cryptic diversity and novel sexual traits"
<p>The deposited folders contain image and video material of free-living flatworm specimens that were documented in vivo. These data support the following publication:</p> <p>Jeremias N. Brand, Gudrun Viktorin, R. Axel W. Wiberg, Christian Beisel, Lukas Schärer.<br> Large-scale phylogenomics of the genus<em> Macrostomum</em> (Platyhelminthes) reveals cryptic diversity and novel sexual traits.<br> Molecular Phylogenetics and Evolution. Volume 166. 2022. <a href="https://doi.org/10.1016/j.ympev.2021.107296">https://doi.org/10.1016/j.ympev.2021.107296</a></p> <p>For more information about these specimens see also http://macrostomorpha.info.</p>
EnGRaiN : A Supervised Ensemble Learning Method for Recovery of Large-scale Gene Regulatory Networks
<p>EnGRaiN is a supervised machine learning method to construct ensemble networks. To benefit from the typical accuracy advantages of supervised learning methods while taking into account the impossibility of knowing true networks for training, we devised a method that uses small training datasets of true positives and true negatives among gene pairs.</p> <p>The datasets used to evaluate the performance of EnGaiN include (i) simulated datasets generated from Yeast networks and (ii) A. thaliana gene expression datasets.</p>
Large-scale conformational changes of FhaC provide insights into the two-partner secretion mechanism
<p>This dataset contains raw and processed data and analyses related to the manuscript "Large-scale conformational changes of FhaC provide insights into the two-partner secretion mechanism" by the authors. A preprint of this manuscript is available on bioRxiv (https://doi.org/10.1101/2021.11.09.467682).</p>
Large-scale temporal graph datasets
<p>Large scale datasets used for evaluation in the article: `Optimizing the Interval-centric Distributed<br> Computing Model for Temporal Graph Algorithms` to appear in `EuroSys 2022`.</p>
Example data and scripts for the paper: Team maturity and reorganization during a very large-scale agile transformation in the automotive industry
<p>Example data and scripts for the paper: Team maturity and reorganization during a very large-scale agile transformation in the automotive industry. </p>
Large-scale dataset for the analysis of outdoor-to-indoor propagation for 5G mid-band operational networks
<p>We present a comprehensive dataset of channel measurements, performed to analyze outdoor-to-indoor propagation characteristics in the mid-band spectrum identified for the operation of 5th Generation (5G) cellular systems. The dataset includes measurements of channel power delay profiles from two 5G networks operating in Band n78, i.e., 3.3--3.8 GHz. Such measurements were collected at multiple locations in a large office building in the city of Rome, Italy, by using the Rohde & Schwarz (R&S) network scanner TSMA6 for several weeks in 2020 and 2021. A primary goal of the dataset is to provide an opportunity for researchers to investigate a large set of 5G channel measurements, aiming at analyzing the corresponding propagation characteristics towards the definition and refinement of empirical channel propagation models.</p>
Large-scale fungal strain sequencing unravels the molecular diversity in mating loci maintained by long-term balancing selection
<p><span>Balancing selection, an evolutionary force that retains genetic diversity, has been detected in multiple genes and organisms, such as the sexual mating loci in fungi. However, to quantify the strength of balancing selection and define the mating-related genes require a large number of strains. In tetrapolar basidiomycete fungi, sexual type is determined by two unlinked loci, <em>MATA </em>and <em>MATB</em>. Genes in both loci define mating type identity, control successful mating and completion of the life cycle. These loci are usually highly diverse. Previous studies have speculated, based on culture crosses, that species of the non-model genus <em>Trichaptum </em>(Hymenochaetales, Basidiomycota) possess a tetrapolar mating system, with multiple alleles. Here, we sequenced a hundred and eighty strains of three <em>Trichaptum </em>species. We characterized the chromosomal location of <em>MATA </em>and <em>MATB</em>, the molecular structure of <em>MAT </em>regions and their allelic richness. The sequencing effort was sufficient to molecularly characterize multiple <em>MAT </em>alleles segregating before the speciation event of <em>Trichaptum </em>species. Analyses suggested that long-term balancing selection has generated trans-species polymorphisms. Mating sequences were classified in different allelic classes based on an amino acid identity (AAI) threshold supported by phylogenetics. 17,550 mating types were predicted based on the allelic classes. <em>In vitro </em>crosses allowed us to support the degree of allelic divergence needed for successful mating. Even with the high amount of divergence, key amino acids in functional domains are conserved. We conclude that the genetic diversity of mating loci in <em>Trichaptum </em>is due to long-term balancing selection, with limited recombination and duplication activity. The large number of sequenced strains highlighted the importance of sequencing multiple individuals from different species to detect the mating-related genes, the mechanisms generating diversity and the evolutionary forces maintaining them.</span></p>
A large-scale assessment of ant diversity across the Brazilian Amazon Basin: integrating geographic, ecological, and morphological drivers of sampling bias
<p>Tropical ecosystems are often biodiversity hotspots, and invertebrates represent the main underrepresented component of diversity in large-scale analyses. This problem is partly related to the scarcity of data widely available to conduct these studies and the lack of systematic organization of knowledge about invertebrates' distributions in biodiversity hotspots. Here, we introduce and analyze a comprehensive data compilation of Amazonian ant diversity. Using records from 1817 to 2020 from both published and unpublished sources, we describe the diversity and distribution of ant species in the Brazilian Amazon Basin. Further, using high-definition images and data from taxonomic publications, we build a comprehensive database of morphological traits for the ant species that occur in the region. In total, we recorded 1,067 nominal species in the Brazilian Amazon Basin, with sampling locations strongly biased by access routes, urban centers, research institutions, and major infrastructure projects. Large areas where ant sampling is non-existent represent about 52% of the basin and are concentrated mainly in the North, Southeastern, and Western Brazilian Amazon. We found that distance to roads is the main driver of ant sampling in the Amazon. Contrary to our expectations, morphological traits had lower predictive power in predicting sample bias than purely geographic variables. However, when geographic predictors were controlled, habitat stratum and traits contribute to explain the remaining variance. More species were recorded in better-sampled areas, but species richness estimation models suggest that areas in South Amazonian edge forests are associated with especially high species richness. Our results represent the first trait-based, large-scale study for insects in Amazonian forests and a starting point for macroecological studies focusing on insect diversity in the Amazon Basin.</p>
Bed topography of the large-scale meandering rivers at dynamic equilibrium state
<p>The simulation results for the bed topography of the 42 large-scale testbed rivers at dynamic equilibrium (along with instantaneous bed shear stress distributions) are presented.</p>
Mean bed shear stress of large-scale meandering rivers
<p>The source files (in Tecplot, and readable by ParaView) are the mean bed shear stress distribution of the 42 testbed rivers.</p>
First large-scale quantification study of DNA preservation in insects from natural history collections using genome-wide sequencing
<p>Insect declines are a global issue with significant ecological and economic ramifications. Yet we have a poor understanding of the genomic impact these losses can have. Genome-wide data from historical specimens has the potential to provide baselines of population genetic measures to study population change, with natural history collections representing large repositories of such specimens. However, an initial challenge in conducting historical DNA data analyses, is to understand how molecular preservation varies between specimens. Here, we highlight how Next Generation Sequencing methods developed for studying archaeological samples can be applied to determine DNA preservation from only a single leg taken from entomological museum specimens, some of which are more than a century old. An analysis of genome-wide data from a set of 113 red-tailed bumblebee (Bombus lapidarius) specimens, from five British museum collections, was used to quantify DNA preservation over time. Additionally, to improve our analysis and further enable future research we generated a novel assembly of the red-tailed bumblebee genome. Our approach shows that museum entomological specimens are comprised of short DNA fragments with mean lengths below 100 base pairs (BP), suggesting a rapid and large-scale post-mortem reduction in DNA fragment size. After this initial decline, however, we find a relatively consistent rate of DNA decay in our dataset, and estimate a mean reduction in fragment length of 1.9bp per decade. The proportion of quality filtered reads mapping our assembled reference genome was around 50 %, and decreased by 1.1 % per decade. We demonstrate that historical insects have significant potential to act as sources of DNA to create valuable genetic baselines. The relatively consistent rate of DNA degradation, both across collections and through time, mean that population level analyses - for example for conservation or evolutionary studies - are entirely feasible, as long as the degraded nature of DNA is accounted for. </p>
Supplementary data - "Learning Reduced Models for Large-Scale Agent-Based Systems"
<p>This repository contains supplementary data on my PhD thesis "Learning Reduced Models for Large-Scale Agent-Based Systems". Chapters 1-3, 7 and A do not have supplementary data.</p> <p><strong>Chapter 4</strong></p> <ul> <li><em>Large_deviation_example.zip</em> contains the trajectory for Figure 4.8.</li> <li><em>mean_exit_time*</em> contains the raw data to compute the mean exit time and standard deviation for the ABM process (JP) and SDE process (CLE). It contains additionally a precomputed mean and standard deviation as well as the corresponding numbers of agents.</li> <li><em>transition_matrix*</em> contain the computed box discretizations as MATLAB and Numpy files as used for Figures 4.2-4.4, 4.6 and Tables 4.1 and 4.2.</li> </ul> <p><strong>Chapter 5</strong></p> <ul> <li><em>CVM_2021-07-09-15-53_training_data.npz</em> contains the training data for Figure 5.7 a and b.</li> <li><em>CVM_2021-09-29-07-13_distribution.npz </em>contains the raw data for Figure 5.7 c.</li> <li>The remaining data for Chapter 5 can be found in the related dataset <a href="https://doi.org/10.5281/zenodo.4522119">doi.org/10.5281/zenodo.4522119</a>.</li> </ul> <p><strong>Chapter 6</strong></p> <ul> <li><em>CVM_pareto_estimate</em> contains trajectory data required for Figure 6.6 b to estimate points in the Pareto Front using the civil violence model. </li> <li><em>CVM_training_data</em> contains the training data to construct the surrogate model. Each data set consists of <em>CVM_*_cops_train.npz</em> as training set, <em>CVM_*_cops_trajectory.npz</em> as sample trajectory and <em>CVM_*_cops.pkl</em> to compute the training data.</li> <li><em>CVM_covering_iterations_8.mat</em> Pareto set covering after 8 iterations for the civil violence model. Required for Figure 6.6 a.</li> <li><em>CVM_pareto_set+front.npz</em> is required for Figure 6.6 b. </li> <li><em>CVM_surrogate_model.mat</em> contains the surrogate model for the civil violence model</li> <li><em>Expl_iterations_*</em> contains Pareto set coverings after 8 and 12 iterations for Example 6.1.4 and Figure 6.1.</li> <li><em>VM_covering_iterations_12.mat</em> contains the Pareto set covering depicted in Figure 6.4 a.</li> <li><em>VM_ODE_covering_iterations_12_subset_front.mat</em> contains the Pareto set covering depicted in Figure 6.5 and 6.5 c.</li> <li><em>VM_ODE_covering_iterations_12_subset.mat</em> contains the Pareto set covering depicted in Figure 6.5 and 6.5 d.</li> <li><em>VM_ODE_covering_iterations_12.mat</em> contains the Pareto set covering depicted in Figure 6.4 b.</li> <li><em>VM_surrogate_model.mat</em> contains the surrogate model for the extended voter model.</li> <li><em>VM_test_points_non_pareto.npz</em> contains Non-Pareto points in Figure 6.5 and 6.5 d.</li> <li><em>VM_test_points_pareto.npz</em> contains Pareto points in Figure 6.5 and 6.5 c.</li> </ul>
Transmission and Distribution Substation Energy Management Considering Large-Scale Energy Storage, Demand Side Management and Security-Constrained Unit Commitment
<p>Data used in "Transmission and Distribution Substation Energy Management Considering Large-Scale Energy Storage, Demand Side Management and Security-Constrained Unit Commitment".</p>
ReSPack: A Large-Scale Rectilinear Steiner Tree Packing Benchmark for Wire Routing
<p>Combinatorial optimization (CO) has been studied as a useful tool for modeling industrial problems, but it still remains a challenge in complex domains because of the NP-hardness. With recent advances in machine learning, the field of CO is shifting to the study of neural combinatorial optimization using a large amount of data, showing promising results in some CO problems. Rectilinear Steiner Tree Packing Problem (RSTPP) is a well-known CO problem and is widely used in modeling wiring problem among components in a printed circuit board and an integrated circuit design. Despite the importance for a design automation, the lack of availab le data has restricted to fully leverage machine learning approaches. In this paper, we present ReSPack, a large-scale synthetic RSTPP dataset and a benchmark for wire routing. ReSPack includes a source code for generating RSTPP problems of various types with different sizes, data instances generated for the benchmark testing, and implementations of several baseline algorithms. We believe that ReSPack can contribute to solving circuit design problems as well as the development of CO with machine learning.</p>
Assessing Vaccine-Related Content for Journalistic Quality: A large-scale dataset and article repository
<p>This dataset was produced through a collaboration with the NSF-funded <a href="https://artt.cs.washington.edu/">ARTT project</a> (led by Hacks/Hackers) and <a href="https://overtone.ai/">Overtone</a>. It consists of 1,000 vaccine-related articles, pulled from a wide variety of news media sources, with associated scores based on their journalistic quality. The scores were provided through Overtone’s algorithm, and range from one (low-quality or low informational value add) to five (high-quality or high informational value add). Articles were sourced from traditional journalism outlets (news and news-leaning websites), as well as non-journalistic sources of vaccine information, such as governmental websites, healthcare and NGO websites, and medical journals. Given the algorithm’s focus on editorial content, as opposed to other metrics such as author, outlet, or engagement, analyzing a diverse set of article types allowed the research team to examine how different styles of vaccine-related content measured against traditional journalistic quality standards.<strong> </strong>Therefore, this dataset provides a unique insight into the spectrum of vaccine reporting, and serves as a contribution to the field of automated quality assessment. </p> <p><strong>About ARTT:</strong> The Analysis and Response Toolkit for Trust (ARTT) project is focused on helping people engage in trust-building ways when discussing vaccine efficacy and other topics online. </p> <p><strong>About Overtone:</strong> Overtone has built a Natural Language Processing algorithm that finds and sorts online content by its intrinsic qualities, rather than clicks or shares. Their AI assesses texts for journalistic signals that demonstrate human effort.</p> <p>For any questions about this dataset, please contact artt@hackshackers.com.</p>
Large-scale reforestation can increase water yield and reduce drought risk for water-insecure regions in the Asia-Pacific
<p>Large-scale reforestation can potentially bring both benefits and risks to the water cycle, which needs to be better quantified under future climates to inform reforestation decisions. We identified 477 water-insecure basins worldwide accounting for 44.6% (380.2 Mha) of the global reforestation potential. As many of these basins are in the Asia-Pacific, we used regional coupled land-climate modelling for the period 2041–2070 to reveal that reforestation increases evapotranspiration and precipitation for most water-insecure regions over the Asia-Pacific. This resulted in a statistically significant increase in water yield (p < 0.05) for the Loess Plateau-North China Plain, Yangtze Plain, Southeast China and Irrawaddy regions. Precipitation feedback was influenced by the degree of initial moisture limitation affecting soil moisture response and thus evapotranspiration, as well as precipitation advection from other reforested regions and moisture transport away from the local region. Reforestation also reduces the probability of extremely dry months in most of the water-insecure regions. However, some regions experience non-significant declines in net water yield due to heightened evapotranspiration outstripping increases in precipitation, or declines in soil moisture and advected precipitation.</p>
Large-scale grid computing for content-based image retrieval
<p>The author presents an approach in which a large distributed processing Grid has been used to apply a range of content-based image retrieval methods to a substantial number of images. By massively distributing the required computational task across thousands of Grid nodes, we have achieved very high throughput at relatively low overheads.</p> <p> </p>
Do large-scale associations in birds imply biotic interactions or environmental filtering?
<p><strong>Aim</strong>: There has been a wide interest in the effect of biotic interactions on species' occurrences and abundances at large spatial scales, coupled with a vast development of the statistical methods to study them. Still, the evidence whether the effects of within-trophic level biotic interactions (e.g. competition and heterospecific attraction) are discernible beyond local scales remains inconsistent. Here, we present a novel hypothesis-testing framework based on joint dynamic species distribution models (JDSDMs) and functional trait similarity to dissect between environmental filtering and biotic interactions. </p> <p><strong>Location</strong>: France and Finland. </p> <p><strong>Taxon</strong>: Birds. </p> <p><strong>Methods</strong>: We estimated species-to-species associations within a trophic level, independent of the main environmental variables (mean temperature and total precipitation) for common species at large spatial scale with joint dynamic species distribution models (VAST). We created hypotheses based on species' functionality (morphological and/or diet dissimilarity) and habitat preferences about the sign and strength of the pairwise spatio-temporal associations to estimate the extent to which they result from biotic interactions (competition, heterospecific attraction) and/or environmental filtering. </p> <p><strong>Results</strong>: Spatio-temporal associations were mostly positive (80%), followed by random (15%), and only 5% were negative. Negative spatio-temporal associations in different communities were due to a few species when they existed. The relationship between spatio-temporal association and functional dissimilarity among species was negative, which fulfills the predictions of both environmental filtering and heterospecific attraction. </p> <p><strong>Main conclusions: </strong>We showed that processes leading to species aggregation (mixture between environmental filtering and heterospecific attraction) seem to dominate assembly rules, and we did not find evidence for competition. Altogether, hypothesis-testing framework based on joint dynamic species distribution models and functional trait similarity is beneficial in ecological interpretation of species-to-species associations from the long-term large-scale data. </p>
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.