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1,045 results for “Generated Data”
Generating an expression matrix for droplet single-cell RNA-seq (dscRNA-seq) data
<p>This tutorial is adapted from the 'Generating an expression matrix' training session at the EBI (https://www.ebi.ac.uk/training/events/2019/single-cell-rna-seq-analysis-questions-clusters).</p>
Dataset used for "Somatic hypermutation analysis for improved identification of B cell clonal families from next-generation sequencing data"
<p>Each simulated dataset was generated using the AbSim R package (version 0.2.6) in a B cell single-lineage fashion. Each B cell clone simulation begins with a random selection from sets of IGHV, IGHD, and IGHJ germline sequences to produce a unique V(D)J recombination event. Then, clones are made by introducing mutations using a local nucleotide context-dependent model (S5F model) along a phylogenetic tree in which branching events occur stochastically. </p>
MarTREC Data Set for Report: Developing and Applying an Analysis Methodology to Identify Flow Generation Influences between Vessel and Truck Shipments
<p>Truck activity is logically connected to vessel activity at a port. In turn, vessel activity is also influenced by truck shipments. Although one might expect a direct and straightforward relation between these two types of shipments, that is rarely the case. For instance, many maritime containers carry consolidated cargos that have multiple and different final destinations. Also, different truck capacities, customs clearance and regulations play a critical role in determining the actual relation between these two types of shipments. This project aims at shedding light on the nuances of maritime and roadway flow relations by quantitatively analyzing the linkages between these two types of shipments.</p> <p>The study performed a statistical analysis to determine the probability distributions of vessel and truck activity, and then explore the correlation of each activity with the other. The analysis yielded coefficients that function as explanatory values for specific truck flows.</p> <p>The ultimate purpose of this study is to provide a clearer and quantitative understanding of the relationship between maritime and truck shipments, and by doing so, to provide tools to develop a system for managing trucks that maximizes efficiency for industry, while minimizing industry’s negative impacts on a region.</p> <p>For this purpose, the study selected the Port Freeport as a case study.</p>
A genomic data set of single‐nucleotide polymorphisms (SNPs) generated by ddRAD tag sequencing in Q. petraea (Matt.) Liebl. populations from Central-Eastern Europe and Balkan Peninsula
<p>This genomic dataset provides highly variable single-nucleotide polymorphism (SNP) markers from georeferenced natural <em>Quercus petraea</em> (Matt.) Liebl. populations collected in Bulgaria, Hungary, Romania, Serbia, Bosnia and Herzegovina, Kosovo and Albania. These SNP loci can be used to assess genetic diversity, differentiation, population structure, and can also be used to detect signatures of selection and local adaptation.</p>
The data generated or compiled in the study of "Diverse polygonal patterned grounds in the northern Eridania basin, Mars: Possible origins and implications"
<p>The data that we generated or compiled, that is used to make a figure (e.g. geologic maps (Figure 2), mapped ridges (included in Figure 2), tables of measurements underlying the histograms (Figures 10 and 18), crater counts (Figure 12)), are placed in a public data repository outside of the JGR paywall. They have been introduced in the following publication, where more details can be found:</p> <p> </p> <p>Y. Dang, F. Zhang, J. Zhao, J. Wang, Y. Xu, T. Huang, and L. Xiao</p> <p>Diverse Polygonal Patterned Grounds in the Northern Eridania Basin, Mars: Possible Origins and Implications.</p> <p>Journal of Geophysical Research: Planets, 2020,125, e2020JE006647. https://<br> doi.org/10.1029/2020JE006647</p> <p> </p> <p>The file format is "Shp" processed in the software ArcGIS 10.6. The detailed description and information can be found in the title of each file below, and also their corresponding figure caption in the paper after it is formally published.</p>
Generating Physically Sound Training Data for Image Recognition of Additively Manufactured Parts Data and Scripts
<p>The repository contains the data corresponding to the Paper "Generating Physically Sound Training Data for Image Recognition of Additively Manufactured Parts".</p> <p>Random30, Random50, Random100, Similiar10, Similar30 and Similar50.zip contain the data sets (obj Files).</p> <p>R30_physical_images.zip and sim50_physical_images.zip contain the photos made from the physical components which are used for the evaluation.</p>
Dataset accompanying paper submission for "Toward data-driven generation and evaluation of model structure for integrated representations of human behavior in water resources systems"
<p>This data set accompanies code archived at DOI: <a href="https://doi.org/10.5281/zenodo.3833186">10.5281/zenodo.3833186</a>, which was used in the experiments for the paper submission "Toward data-driven generation and evaluation of model structure for integrated representations of human behavior in water resources systems"</p>
Data from: Mycorrhizal feedbacks generate positive frequency dependence accelerating grassland succession
1. Plant mutualists including arbuscular mycorrhizal (AM) fungi have been postulated as being important drivers of plant community diversity and succession. Late successional plants have been shown to be more responsive to AM fungi and more sensitive to AM fungal species identity, which could generate positive feedback and potentially accelerate succession. 2. We test the effect of AM fungi on plant diversity and on frequency dependence predicted by positive plant‐AM fungi feedback across a successional gradient. We created prairie mesocosms comprised of a majority early‐successional, equal abundance and a majority late successional plant species. We inoculated these mesocosms and a field restoration experiment with 14 different communities of AM fungi from late successional prairies that varied in levels of species richness. 3. Overall, we found that AM fungi increased plant diversity and this was driven by the response of late successional plant species to mycorrhizae. Our results indicate that AM fungal composition is more important than AM fungal diversity per se. We found that the effect of inoculation with a single species or groups of AM fungi depended on whether those fungi benefited late successional plant species. Early successional plants consistently exhibited negative frequency dependent growth regardless of fungal composition, while late successional plants demonstrated positive frequency dependent growth in our mesocosms—but only in the presence of beneficial AM fungal species. These results are consistent with positive plant‐mycorrhizal feedbacks accelerating plant community successional trajectories once late successional plants establish. Mesocosm results were mirrored with field inoculation assays where we found that beneficial AM fungi facilitated late successional plant establishment. 4. Synthesis. Our results provide support for beneficial AM fungi being a primary mechanism for positive plant‐soil feedback driving plant community succession, as late successional seedlings grew faster and larger when their neighbors were also late successional plant species when they were associated with beneficial AM fungi. We found that this positive feedback thereby accelerated succession in mesocosms and in the field.
Data from: Explosion-generated infrasound recorded on ground and airborne microbarometers at regional distances
Recent work in deploying infrasound (low frequency sound) sensors on aerostats and free flying balloons has shown them to be viable alternatives to ground stations. However, no study to date has compared the performance of surface and free floating infrasound microbarometers with respect to acoustic events at regional (100s of kilometers) range. The prospect of enhanced detection of aerial explosions at similar ranges, such as those from bolides, has not been investigated either. We examined infrasound signals from three 1 ton TNT equivalent explosions using microbarometers on two separate balloons at ranges of 280 to 400 km and ground stations at ranges of 6.3 to 350 km. Signal celerities were consistent with acoustic waves traveling in the stratospheric duct. However, significant differences were noted between the observed arrival patterns and those predicted by an acoustic propagation model. Very low background noise levels on the balloons were consistent with previous studies that suggest wind interference is minimal on freely drifting sensors. Simulated propagation patterns and observed noise levels also confirm that balloon-borne microbarometers should be very effective at detecting explosions in the middle and upper atmosphere as well as those on the surface.
Data from: Multi-generational genetic consequences of reinforcement in a bird metapopulation
<p>Translocation of conspecific individuals to reduce extinction risk of small, isolated populations and prevent genetic depletion is a powerful tool in conservation biology. An important question is how the translocated individuals influence the long-term genetic composition of the recipient population. Here, we experimentally reinforced a house sparrow (<i>Passer domesticus</i>) population, and examined the impact of this translocation on allele frequencies, levels of heterozygosity and genetic differentiation over six cohorts. We found no permanent increase in the mean number of alleles across loci or levels of observed heterozygosity, but a few alleles private to the translocated individuals remained in the population and we found a short-term increase in heterozygosity. Consequently, genetic differentiation of the recipient population compared to the genetic composition prior to reinforcement was small. The limited genetic impact was due to combined effects of a small probability of establishment and low mating success for the translocated individuals, together with increased genetic drift in the recipient population. Our findings emphasize the importance of selection and genetic drift as forces that may decrease the genetic contribution of reinforcement, especially in small populations. Conservation managers should aim to improve habitat quality in the recipient population to reduce genetic drift following translocation and thereby avoid the need for continued reinforcement. Furthermore, by facilitating establishment success and selecting individuals expected to have high mating success, possibly indicated by sexually selected traits, genetic contribution of released individuals is increased which in turn will decrease reproductive skew and genetic drift.</p>
Data from: Propagule pressure and genetic diversity enhance colonization by a ruderal species: a multi-generation field experiment
Colonization is a critical filter, setting the stage for short-term and long-term population success. Increased propagule pressure (e.g., more founding individuals) usually enhances colonization; however, this pattern may be driven by purely numeric effects, population genetic diversity effects, or both. To determine the independent and interactive effects of propagule pressure and genetic diversity, we conducted a seed addition experiment in the field using the ruderal annual Arabidopsis thaliana. Propagule pressure treatments spanned five levels, from 32 to 960 seeds per 0.25-m2 plot. Founder populations were composed of one, four or eight genotypes and exposed to ambient or reduced levels of interspecific competition. Genotype monocultures were included to quantify additive versus non-additive effects. Populations were followed for three generations, with abundance, population persistence and genotype retention (the proportion of introduced genotypes persisting over time) as the major response variables. Increased propagule pressure enhanced abundance immediately following introduction, particularly where nutrient availability was high and competition reduced. Greater propagule pressure also increased the likelihood of population persistence and genotype retention through three generations. However, most populations experienced rapid abundance declines over time, yielding no relationship between propagule pressure and third-generation abundance across persisting populations. Under reduced competition, increased genetic diversity led to a marginal increase in persistence through the third generation that was more pronounced, and statistically significant, in low nutrient conditions. Genetic diversity did not affect persistence through the first generation, thus indicating that genetic diversity effects strengthened over time. Nevertheless, genotypic mixture populations fell short of expectations based on performance in monocultures (negative non-additive effects). Increased genetic diversity was also associated with abundance declines, largely due to one particularly high-performing genotype in the lowest diversity treatments (i.e, genotypic identity effects). Overall, our results indicate that increases in both propagule pressure and genetic diversity can enhance colonization success but are highly context-dependent. They also highlight novel ways in which both factors can impact the retention of introduced genetic diversity over time. Our findings pinpoint the determinants of a fundamental population process and have key implications for applications where enhanced or suppressed colonization is desired, including ecological restoration and invasive species management.
Data from: Upper atmosphere heating from ocean-generated acoustic wave energy
Colliding sea surface waves generate the ocean microbarom, an acoustic signal that may transmit significant energy to the upper atmosphere. Previous estimates of acoustic energy flux from the ocean microbarom and mountain/wind interactions are on the order of 0.01 to 1 mW/m2, heating the thermosphere by tens of degrees Kelvin per day. We captured up going ocean microbarom waves with a balloon borne infrasound microphone; the maximum acoustic energy flux was approximately 0.05 mW/m2. This is about half the average value reported in previous ground-based microbarom observations spanning eight years. The acoustic flux from the microbarom episode described here may have heated the thermosphere by several degrees Kelvin per day while the source persisted. We suggest that ocean wave models could be used to parameterize acoustically-generated heating of the upper atmosphere based on sea state.
Data from: Priority effects can persist across floral generations in nectar microbial metacommunities
The order of species arrival can influence how species interact with one another and, consequently, which species may coexist in local communities. This phenomenon, called priority effects, has been observed in various types of communities, but it remains unclear whether priority effects persist over the long term spanning multiple generations of local communities in metacommunities. Focusing on bacteria and yeasts that colonize floral nectar of the sticky monkey flower, Mimulus aurantiacus, via hummingbirds and other flower-visiting animals, we experimentally manipulated initial microbial dominance on plants (regarded as metacommunities) to examine whether its effects persisted across multiple generations of flowers (regarded as local microbial habitats). The experimental introduction of Neokomagataea (= Gluconobacter) bacteria and Metschnikowia yeasts into wild flowers showed that the effects of initial dominance were observable across multiple floral generations. Three weeks after introduction, corresponding approximately to three floral generations, Neokomagataea introduction led to exclusion of yeasts, whereas Metschnikowia introduction did not result in the exclusion of Neokomagataea. Our results suggest that, even when local habitats are ephemeral, priority effects may influence multiple generations of local communities within metacommunities.
Data from: Vertical differentiation in tropical forest butterflies: a novel mechanism generating insect diversity?
Many tropical fruit-feeding nymphalid butterflies are associated with either the forest canopy or the understory, however, the exceptions offer insights into the origins of tropical diversity. As it occurs in both habitats of tropical forests in Ecuador and Peru, Archaeoprepona demophon is one such exception. We compared patterns of occurrence of A. demophon in the canopy and understory and population genomic variation for evidence of ecological and genetic differentiation between habitats. We found that butterfly occurrences in the canopy were largely uncorrelated with occurrences in the understory at both localities, indicating independent demographic patterns in the two habitats. We also documented modest, significant genome-level differentiation at both localities. Genetic differentiation between habitat types (approximately 20m in elevation) were comparable to levels of differentiation between sampling locations (approximately 1500km). We conclude that canopy and understory populations of A. demophon represent incipient independent evolutionary units. These findings support the hypothesis that divergence between canopy and understory-associated populations might be a mechanism generating insect diversity in the tropics.
Generative AI in University Communication - Survey Data (June 2023)
<p>Der Datensatz mit dem Titel "Generative KI in der Hochschulkommunikation - Umfragedaten (Juni 2023)" erfasst Informationen zur Einführung und Nutzung von generativer künstlicher Intelligenz (KI) im Kontext der Hochschulkommunikation. Die Umfrage, die im Juni 2023 unter 318 deutschen Hochschulen durchgeführt wurde, von denen 101 geantwortet haben, untersucht verschiedene Aspekte, darunter Bekanntheit und Wissen über verschiedene KI-Tools (z.B. ChatGPT), Diskussionen in Gremien, das Vorhandensein von Richtlinien für die Nutzung, das Vorhandensein von Arbeitsgruppen für generative KI, strategische Ziele und Initiativen, Schulungsangebote für generative KI-Tools und die wahrgenommene Bedeutung von generativen KI-Tools in der Hochschulkommunikation. Ziel des Datensatzes ist es, Einblicke in die aktuelle Landschaft und Praxis der Integration generativer KI im universitären Umfeld zu geben.</p><p>The dataset, titled "Generative AI in University Communication - Survey Data (June 2023)," captures information related to the adoption and utilization of generative artificial intelligence (AI) in the context of university communication. This survey, conducted in June 2023 among 318 German universities of which 101 responded, explores various aspects, including awarenes and knowledge of various AI tools (e.g. ChatGPT), discussions in committees, the existence of guidelines for usage, the presence of working groups for generative AI, strategic goals and initiatives, training offerings for generative AI tools, and the perceived importance of generative AI tools in university communication. The dataset aims to provide insights into the current landscape and practices regarding the integration of generative AI within university settings.</p><p> </p><p>More information here: <a href="https://www.hof.uni-halle.de/projekte/hochki/">https://www.hof.uni-halle.de/projekte/hochki/</a></p>
DNA Data Visualizations Generated with DDV Software
<p>A ZIP file containing the DNA Data Visualization interfaces generated with DDV software. These interfaces are available live at: at: http://www.photomedia.ca/DDV/dnadata/ </p> <p>The corresponding source code for this project is at: https://github.com/photomedia/DDV</p> <p> </p>
Interferogram generated with DORIS and TerraSAR-X data
Interferogram generated with DORIS and <b>TerraSAR-X</b> data
Non-random network connectivity comes in pairs: Code & generated data to reproduce results and figures of the article
<p>Complete research code and generated data for the article to reproduce the figures and computations referenced.</p> <p>Please visit https://non-random-connectivity-comes-in-pairs.github.io/ for documentation of the code.</p>
Supplementary material 17: Generating Interactive Dashboard Charts Based on Plazi Treatment Data from: Integrating and visualizing primary data from prospective and legacy taxonomic literature - Biodiversity Data Journal 3: e5063 (12 May 2015) https://doi.org/10.3897/BDJ.3.e5063
A brief explanation of how to create and customize interactive charts using data on Plazi.
Data: Muon Tomography sites for Colombia volcanoes for generate muon flux trought volcanic structures (arXiv:1705.09884v1)
<p><strong>Data: Muon Tomography sites for Colombia volcanoes (arXiv:1705.09884v1)</strong><br> <strong>The MuTe Collaboration</strong><br> <em>Data for generating figure 6<br> Muon Tomography sites for Colombia volcanoes (arXiv:1705.09884v1)</em></p> <p>The files in this record contain data from Extensive Atmospheric Shower simulations made by CORSIKA and Magnetocosmic codes, in a muography of Machin Volcano (Colombia) [https://volcano.si.edu/volcano.cfm?vn=351040] for a particular observation point. The objective was to count muons crossing the volcanic structure for a fixed observation point. Muon transport through the volcanic edifice is calculated by using an algorithm taken Corsika-Magnetocosmic output and taking into account the energy losses with the muon stopping power tables given by Particle Data Group (PDG).</p> <p>This dataset contains:</p> <ul> <li>Six (6) Corsika output files of 4 hours of simulation each using a flat detector (equivalent to 12 hours of simulated cosmic rays).</li> <li>One (1) Corsika output file of 12 hours of simulation using flat detector (equivalent to 6 hours of simulated cosmic rays).</li> <li>One (1) Corsika output file of 48 hours of simulation using flat detector (equivalent to 24 hours of simulated cosmic rays).</li> <li>Two (2) Corsika output files of 24 hours of simulation each using volumetric detector (equivalent to 48 hours of simulated cosmic rays).</li> <li>Everything makes a total simulated time of 3.75 days.</li> </ul> <p>The output files necessary for the determination of the muon flux through the volcanic structure are obtained through the following process:</p> <ul> <li>From the .shw.bz2 files it is possible to obtain an output file with the momentum information of the particle in the x, y, and z directions, and also the total momentum of the muons, essentially a formatted file (px, py, pz, p). This file can be built by typing in a terminal shell (bash code):</li> </ul> <p><em><strong>> </strong></em><strong>bzcat *.shw.bz2 | awk '{if($1==0006 ||$1==0005){j=sqrt(($2*$2)+($3*$3)+($4*$4));printf "%s %s %s %.s\n",$2, $3, $4, j }}' | sort -n > salida.out</strong></p> <ul> <li>Metadata in the showers file is as this type (for example):</li> </ul> <p># # # shw</p> <p># # CURVED mode is ENABLED and observation level is 2750 m a.s.l.</p> <p># # This is the Secondaries file - CrkTools v3r0</p> <p># # 12 column format is:</p> <p># # CorsikaId px py pz x y z shower_id prm_id prm_energy prm_theta prm_phi</p> <p>0001 +1.42146e-04 -3.96008e-05 +1.60247e-04 -1.31716e+03 -6.10051e+01 +2.44986e+03 00000001 0703 +1.25065e+02 +43.016 +021.768</p> <p>0003 +1.80713e-04 +1.89560e-03 +4.49373e-03 -1.32279e+03 -5.62869e+01 +2.44986e+03 00000001 0703 +1.25065e+02 +43.016 +021.768</p> <p>0003 +9.41713e-03 +2.38845e-03 +1.10020e-02 -1.32098e+03 -5.68323e+01 +2.44986e+03 00000001 0703 +1.25065e+02 +43.016 +021.768</p> <ul> <li>Concatenate all output files.</li> <li>Then, the muon flux trought rock can be calculated from two python codes, available in https://github.com/AstroparticulasBucaramanga/Propagacion-Muones-en-Roca. This step generates the final files to be graphed with any plotter, in our case, also using python.</li> </ul>
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.