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1,454 results for “large scale”
SPREAD: A Large-scale, High-fidelity Synthetic Dataset for Multiple Forest Vision Tasks (Part II)
<p><strong>This page only provides the </strong><strong>drone-view image</strong><strong> dataset. </strong></p> <ul> <li><strong>For the ground-level image dataset, please visit <a href="https://zenodo.org/records/13570934" target="_blank" rel="noopener"><em>SPREAD: A Large-scale, High-fidelity Synthetic Dataset for Multiple Forest Vision Tasks (Part I)</em></a>.</strong></li> <li><strong>For the point clouds, please visit <em><a href="https://zenodo.org/records/14228467" target="_blank" rel="noopener">SPREAD: A Large-scale, High-fidelity Synthetic Dataset for Multiple Forest Vision Tasks (Part III)</a>.</em></strong></li> </ul> <p>The dataset contains drone-view RGB images, depth maps and instance segmentation labels collected from different scenes. Data from each scene is stored in a separate .7z file, along with a <code>color_palette.xlsx</code> file, which contains the RGB_id and corresponding RGB values.</p> <p>All files follow the naming convention: <code>{central_tree_id}_{timestamp}</code>, where <code>{central_tree_id}</code> represents the ID of the tree centered in the image, which is typically in a prominent position, and <code>timestamp</code> indicates the time when the data was collected.</p> <p>Specifically, each 7z file includes the following folders:</p> <ul> <li> <p><strong>rgb</strong>: This folder contains the RGB images (PNG) of the scenes and their metadata (TXT). The metadata describes the weather conditions and the world time when the image was captured. An example metadata entry is: <code>Weather:Snow_Blizzard,Hour:10,Minute:56,Second:36</code>.</p> </li> <li> <p><strong>depth_pfm</strong>: This folder contains absolute depth information of the scenes, which can be used to reconstruct the point cloud of the scene through reprojection.</p> </li> <li> <p><strong>instance_segmentation</strong>: This folder stores instance segmentation labels (PNG) for each tree in the scene, along with metadata (TXT) that maps <code>tree_id</code> to <code>RGB_id</code>. The <code>tree_id</code> can be used to look up detailed information about each tree in <code>obj_info_final.xlsx</code>, while the <code>RGB_id</code> can be matched to the corresponding RGB values in <code>color_palette.xlsx</code>. This mapping allows for identifying which tree corresponds to a specific color in the segmentation image.</p> </li> <li> <p><strong>obj_info_final.xlsx</strong>: This file contains detailed information about each tree in the scene, such as position, scale, species, and various parameters, including trunk diameter (in cm), tree height (in cm), and canopy diameter (in cm).</p> </li> <li> <p><strong>landscape_info.txt</strong>: This file contains the ground location information within the scene, sampled every 0.5 meters.</p> </li> </ul> <p>For birch_forest, broadleaf_forest, redwood_forest and rainforest, we also provided COCO-format annotation files (.json). Two such files can be found in these datasets:</p> <ul> <li><strong>{name}_coco.json</strong>: This file contains the annotation of each tree in the scene.</li> <li><strong>{name}_filtered.json</strong>: This file is derived from the previous one, but filtering is applied to rule out overlapping instances.</li> </ul> <p>⚠️: 7z files that begin with "<strong>!</strong>" indicate that the RGB values in the images within the <code>instance_segmentation</code> folder cannot be found in <code>color_palette.xlsx</code>. Consequently, this prevents matching the trees in the segmentation images to their corresponding tree information, which may hinder the application of the dataset to certain tasks. This issue is related to a bug in Colossium/AirSim, which has been reported in <a href="https://github.com/microsoft/AirSim/issues/3423" target="_blank" rel="noopener">link1</a> and <a href="https://github.com/microsoft/AirSim/issues/1852" target="_blank" rel="noopener">link2</a>.</p>
Data for: Concordant phylogeographic responses to large-scale coastal disturbance in intertidal macroalgae and their epibiota
<p>Major ecological disturbance events can provide opportunities to assess multispecies responses to upheaval. In particular, catastrophic disturbances that regionally extirpate habitat-forming species can potentially influence the genetic diversity of large numbers of co-distributed taxa. However, due to the rarity of such disturbance events over ecological timeframes, the genetic dynamics of multispecies recolonization processes have remained little understood. Here we use single nucleotide polymorphism (SNP) data from multiple coastal species to track the dynamics of co-colonization events in response to ancient earthquake disturbance in southern New Zealand. Specifically, we use a comparative phylogeographic approach to understand the extent to which epifauna (with varying ecological associations with their macroalgal hosts) share comparable spatial and temporal recolonization patterns. Our study reveals concordant disturbance-related phylogeographic breaks in two intertidal macroalgal species along with two associated epibiotic species (a chiton and an isopod). By contrast, two co-distributed species, one of which is an epibiotic amphipod and the other a subtidal macroalga, show few if any genetic effects of palaeoseismic coastal uplift. Phylogeographic model selection reveals similar post-uplift recolonization routes for the epibiotic chiton and isopod and their macroalgal hosts. Additionally, co-demographic analyses support synchronous population expansions of these four phylogeographically similar taxa. Our findings indicate that coastal paleoseismic activity has driven concordant impacts on multiple codistributed species, with concerted recolonization events likely facilitated by macroalgal rafting. These results highlight that high-resolution comparative genomic data can help reconstruct concerted multispecies responses to recent ecological disturbance.</p>
Impacts of growth form and phylogenetic relatedness on seed germination: a large-scale analysis of a subtropical regional flora
<p>Plant regeneration strategy plays a critical role in species survival and can be used as a proxy for the evolutionary response of species to climate change. However, information on the effects of key plant traits and phylogenetic relatedness on seed germination is limited at large regional scales that vary in climate. To test the hypotheses that phylogenetic niche conservatism plays a critical force in shaping seed ecophysiological traits across species, and also drives their response to climatic fluctuation, we conducted a controlled experiment on seed germination and determined the percentage and rate of germination for 249 species in subtropical China under two temperature regimes (i.e., daily 25ºC; daily alternating 25/15ºC for each 12 h). Germination was low with a skewed distribution (mean = 38.9% at 25ºC, and 43.3% at 25/15ºC). One fifth of the species had low (<10%) and slow (4–30d) germination, and only a few (8%) species had a high (>80%) and rapid (1.2–6.6d) germination. All studied plant traits (including germination responses) showed a significant phylogenetic signal, with an exception of seed germination percentage under the alternating temperature scenario. Generalized linear models (GLMs) and phylogenetic generalized estimation equations (GEEs) demonstrated that growth form and seed dispersal mode were strong drivers of germination. Our experimental study highlights that integrating plant key traits and phylogeny is critical to predicting seed germination response to future climate change.</p>
A Framework for Automated Construction of Heterogeneous Large-Scale Biomedical Knowledge Graphs (Recorded Talk)
<p>This entry contains the recording of the presentation that was presented at the 2020 Intelligent Systems for Molecular Biology as part of the Bio-Ontologies COSI (https://www.iscb.org/ismb2020).</p>
Data related to "Near-bed sediment transport during offshore bar migration in large-scale experiments"
<p>Abstract: </p> <p>This paper presents novel insights into hydrodynamics and sediment fluxes in large-scale laboratory experiments with bi-chromatic wave groups on a relatively steep initial slope (1:15). An Acoustic Concentration and Velocity Profiler provided detailed information of velocity and sand concentration near the bed from shoaling up to the outer breaking zone including suspended sediment and sheet flow transport. The morphological evolution was characterized by offshore migration of the outer breaker bar. Decomposition of the total net transport revealed a balance of onshore-directed, short wave-related and offshore-directed, current-related net transport. The short wave-related transport mainly occurred as bedload over small vertical extents. It was linked to characteristic intrawave sheet flow layer expansions during short wave crests. The current-related transport rate featured lower maximum flux magnitudes but occurred over larger vertical extents. As a result, it was larger than the short wave-related transport rate in all but one cross-shore position, driving the bar's offshore migration. Net flux magnitudes of the infragravity component were comparatively low but played a non-negligible role for total net transport rate in certain cross-shore positions. Net infragravity flux profiles sometimes featured opposing directions over the vertical. The fluxes were linked to a standing infragravity wave pattern and to the correlation of the short wave envelope, controlling suspension, with the infragravity wave velocity.</p> <p>About the data:</p> <p>The data on beach profile (from mechanical profiler), velocity (from ACVP and ADV), sand concentration (from ACVP and OBS) and water surface elevation (from RWG, AWG and PT) measurements is given in .mat (MATLAB) files.</p> <p>The folder “Beach Profiles” contains the measurements from the mechanical profiler before and after each test. To save time, only the morphologically active section of the profiles was measured. Additionally, the folder contains the initial profiles at the start of a sequence (after application of the benchmark waves). Here the full profile was measured.</p> <p>The structure “MobFrame” contains the absolute cross-shore position of the mobile frame (from which detailed measurements were taken) in the considered tests.</p> <p>The folder “ACVP” contains structures with ensemble-averaged velocity and concentration measurements in vertical reference to the undisturbed bed level or a few bins below it (zeta0-coordinate system) sampled at 50.5051Hz. For better interpretation of the measurements, it also features the ensemble-averaged intrawave instantaneous erosion depth (bed elevation) and the upper limit of the sheet flow layer.</p> <p>The folder “ADV” contains structures with the ensemble-averaged ADV data of each test sampled at 100Hz. Apart from the velocity components of each ADV it contains the vertical elevation of each ADV with respect to the ACVP transceiver. The ADV measurements were not subject to the same vertical referencing procedure that was described in the paper for the near-bed ACVP measurements and a more or less constant distance to the bed was assumed.</p> <p>The folder “OBS” contains structures with the ensemble-averaged OBS data of each test sampled at 40Hz. Apart from the concentration measurements it contains the vertical elevation of the OBSs with respect to the ACVP transceiver.</p> <p>The folder “ETA” contains structures with the ensemble-averaged water surface elevation measurements in many different absolute cross-shore locations in the flume sampled at 40Hz.</p> <p>For visualizing the near-bed concentration data, which may not be as trivial as visualizing the rest of the data, an example of MATLAB code is given:</p> <p>%S=ACVP_xx; %to choose which ACVP file you want to look into<br> con=S.c;<br> con(con<1)=1; %to cater for the cells where the logarithm is not defined<br> xphase=linspace(0,1,length(S.solbed)).*ones(size(S.c,2),size(S.c,1));<br> figure; hold on; box on; <br> [C,h]=contourf(xphase,S.z,log10(transpose(con)),[0:0.1:3]); <br> cbh=colorbar; caxis([0 3]); <br> set(h,'edgecolor','none'); <br> tt=get(cbh,'Title'); set(tt,'String','$^{10}log(c)$ $[kg/m^3]$','Interpreter','Latex');<br> plot(xphase(1,:),S.solbed,'k','Linewidth',1.5);<br> plot(xphase(1,:),S.solflo,'r','Linewidth',1.5);<br> xlabel('$t/T_r$','Interpreter','Latex')<br> ylabel('$\zeta_0$ $[m]$','Interpreter','Latex')<br> set(gca,'Fontsize',18)</p> <p> </p> <p> </p>
Large-scale homogenization of soil bacterial communities in response to agricultural practices in paddy fields, China
<div>This dataset contains data from 257 sites in four typical rice-growing regions across a 4,000-km transect in China, including geographic location data and environment factors data.</div> <div> <br> The study was conducted across a 4,000-km transect of China's rice-growing areas, from Heilong Jiang province to Yunnan province (100°55′ E to 134°08′° E, 22°46′ N to 48°02′ N, Table S1). Four typical rice-growing regions were selected along this transect: Sanjiang Plain (modern mechanical farming), Taihu Plain (mechanical plus minor manual farming), Lianghu Plain (manual plus minor mechanical farming), and Hani Terrace (traditional manual farming).</div> <div> <br> Field sampling was conducted during July and August in 2014 and 2015. Soil samples were collected from 178 flooded paddy fields and 79 surrounding non-paddy areas across four typical rice-growing regions of China. At each site, one homogenized sample was obtained, which was then separated into two parts. One part, which was obtained for DNA extraction, was placed into a sterile plastic tube then immediately placed in liquid nitrogen for short-term transportation. After shipping to the laboratory, these tubes were stored at −80 °C. The second part of the soil sample was placed into a plastic bag and stored at 4.0 °C for determining the soil physicochemical properties.</div> <div> <br> Main results of the experiments are that: (1) Distance–decay patterns of bacterial communities in paddy fields revealed reduced β-diversity compared to surrounding natural habitats. (2) Modern rice farming practices (plowing with machines) caused stronger homogenization of soil bacterial communities than traditional farming (plowing by hand). Among the four paddy regions, plowing by hand retained the highest soil bacterial β-diversity. (3) Moreover, a significant inverse correlation was observed between bacterial β-diversity and the agricultural mechanization level. (4) Among multiple environmental factors, dramatic spatial homogenization of soil physicochemical properties, particularly soil nutrient contents, and reduced dispersal limitation caused by modern farming activities both strongly predict a reduction of bacterial β-diversity in modern paddy fields.</div>
Large-scale Three-dimensional Hydraulic Tomography Analyses of Long-term Municipal Wellfield Operations
<p>This file includes all the datasets utilized to accomplish the above study. Basically, it includes the information of grid for groundwater modeling, the distribution of wells, as well as water-level variations for model calibration and validation.</p>
Harnessing large-scale herbarium image datasets through representation learning (application images)
<p>Herbarium specimen images used in the manuscript <a href="https://www.frontiersin.org/articles/10.3389/fpls.2021.806407/full"><em>Harnessing large-scale herbarium image datasets through representation learning</em></a> for application tasks 2 and 3. These tasks were formulated to test the applicability of representations learned by three different neural networks trained on <a href="https://www.kaggle.com/c/herbarium-2021-fgvc8">the Half-Earth Challenge dataset</a>.</p> <p>All images are for specimens held by Royal Botanic Gardens, Kew. The images from Kew's HerbCat service, using URLs collated by <a href="https://www.idigbio.org/portal/search">iDigBio</a>. We first search iDigBio for the specimens we wanted, then downloaded the associated occurrence and image metadata files. We then used the URLs in the image metadata files to download the specimen images. The code used to download these images can be found in the <a href="https://doi.org/10.5281/zenodo.5776894">GitHub repository for the paper</a>.</p> <p>We searched iDigBio using these parameters:</p> <pre><code>[x] Must have media Genus: Dendrobium Institution Code: K Basis of Record: PreservedSpecimen</code></pre> <p> </p> <p>©<em> All images copyright of the Board of Trustees of the Royal Botanic Gardens, Kew.</em></p>
Supporting Information: Environmental benefits of large-scale second-generation bioethanol production in the EU: An integrated supply chain network optimization and Life Cycle Assessment approache
<p>This supporting information provides all input data of the model, the assumptions made and the literature and database references for the publication<em> Environmental benefits of large-scale second-generation bioethanol production in the EU: An integrated supply chain network optimization and Life Cycle Assessment approache</em>. The environmental data is based on life cycle assessments, with full information on the life cycle inventory and the results of the life cycle impact assessment based on the ReCiPe method. It also includes detailed results for all objective functions in all scenarios (optimization of 18 midpoints, 3 endpoints, and economic optimization in 5 tax scenarios and 2 feedstock scenarios), and detailed results of the sensitivity analysis and Pareto optimization.</p>
A method for identifying environmental stimuli and genes responsible for genotype-by-environment interactions from a large-scale multi-environment data set
<p>It has not been fully understood in real fields what environment stimuli cause the genotype-by-environment (G × E) interactions, when they occur, and what genes react to them. Large-scale multi-environment data sets are attractive data sources for these purposes because they potentially experienced various environmental conditions. In this study, we developed a data-driven approach termed <u>E</u>nvironmental <u>C</u>ovariate Search Affecting <u>G</u>enetic <u>C</u>orrelations (ECGC) to identify environmental stimuli and genes responsible for the G × E interactions from large-scale multi-environment data sets. ECGC was applied to a soybean (<i>Glycine max</i>) data set that consisted of 25,158 records collected at 52 environments. ECGC illustrated what meteorological factors shaped the G × E interactions in six traits including yield, flowering time, and protein content and when they were involved. For example, it illustrated the relevance of precipitation around sowing dates and hours of sunshine just before maturity to the interactions observed for yield. Moreover, genome-wide association mapping on the sensitivities to the identified stimuli discovered candidate and known genes responsible for the G × E interactions. Our results demonstrate the capability of data-driven approaches to bring novel insights on the G × E interactions observed in fields. This dataset provides the data used in this study and supplementary tables cited in the manuscript.</p>
Elucidating gene expression patterns across multiple biological contexts through a large-scale investigation of transcriptomic datasets
<p>This contains data for described in detail in our paper, "Elucidating gene expression patterns across multiple biological contexts through a large-scale investigation of transcriptomic datasets" (Figueiredo <em>et al.</em>, 2022) which aims at revealing common and specific biological processes and mechanisms across contexts by identifying transcriptional patterns that are unique to various cell types, tissues, and cell lines, as well as patterns which are consistent across them.</p>
Data and code from: A large-scale experiment demonstrates line marking reduces power line collision mortality for large terrestrial birds, but not bustards, in the Karoo, South Africa
<p>Line markers are widely used to mitigate bird collisions with power lines, but few studies have robustly tested their efficacy. Power line collisions are an escalating problem for several threatened bird species endemic to southern Africa, so it is critical to know whether or not marking works to adequately manage this problem. Over 8 years, a large-scale experiment was set up on 72 of 117 km of monitored transmission power lines in the eastern Karoo, South Africa, to assess whether line markers reduce bird collision mortality, particularly for Blue Cranes <i>Grus paradisea</i> and Ludwig's Bustards <i>Neotis ludwigii</i>. We tested the two marking devices commonly used in South Africa: bird flappers and static bird flight diverters. Using a before-after-control-impact design, we show that line marking reduced collision rates for Blue Cranes by 92% (95% CI 77-97%) and all large birds by 51% (95% CI 23-68%), but had no effect on bustards. Both marker types appeared similarly effective. Given that monitoring at this site also confirmed high levels of mortality of a range of species of conservation concern, we recommend that marking be widely installed on new power lines. However, other options need to be explored urgently to reduce collision mortality of bustards. Five bustard species were in the top ten list of most frequently found carcasses, and high collision rates of Ludwig's Bustards (0.68 birds·km<sup>-1</sup>·year<sup>-1</sup> uncorrected for survey biases) add to wider concerns about population level effects for this range-restricted and Endangered species. </p> <p>This dataset includes the data and R code for this journal paper.</p>
Supporting Information for "First Observations of Large Scale Traveling Ionospheric Disturbances Using Automated Amateur Radio Receiving Networks"
<p><strong>Introduction</strong></p> <p>The supporting information for this paper consists of a movie version of Figure 2 in the main paper, comparing the high frequency (HF) amateur radio observations to differential Global Navigation Satellite System (GNSS) Total Electron Content (TEC) measurements. In this revised version of the repository, the TEC data has been reprocessed such that all GNSS data with elevation angles down to 10 degrees were kept when applying the Savitzky–Golay (SG) filter. After the SG filter was applied, data with elevation angles below 30 degrees were discarded. This was done to remove artifacts observed in the original movies.</p> <p> </p> <p><strong>Movie S1 (20171103 Ham and TEC LSTID.mp4)</strong></p> <p>(Top Panel) Time series showing the TX-RX distance for 14 MHz amateur radio spots in 2 min by 25 km bins from 1200 UT 3 Nov 2017 - 0000 UT 4 Nov 2017. (Bottom Panel) differential Global Navigation Satellite System (GNSS) Total Electron Content (TEC) measurements over the Continental United States corresponding to the times indicated by the moving white vertical line in the top panel.</p> <p> </p> <p><strong>Movie S2 (20171103 Ham and TEC LSTID – With Arrow.mp4)</strong></p> <p>Same as movie S1, but with a fiducial black arrow indicating an estimated LSTID horizontal wavelength of 1681 km and propagation azimuth of 163°.</p>
Additional 1000 notebooks for the paper "A Large-Scale Comparison of Python Code in Jupyter Notebooks and Scripts"
<p>Additional 1000 notebooks for the review of the paper "A Large-Scale Comparison of Python Code in Jupyter Notebooks and Scripts".</p> <p>The notebooks can be processed using Matroskin tool from the supplementary materials. To do that, place:</p> <p>- the folder "1k_notebooks_dataset" into the folder ".../databases/datasets"</p> <p>- the file "mapping_of_1k_notebooks.json" into the folder ".../databases/mappings"</p>
Multiple drivers of large‐scale lichen decline in boreal forest canopies
<p>Thin, hair-like lichens (<em>Alectoria, Bryoria, Usnea</em>) form conspicuous epiphyte communities across the boreal biome. These poikilohydric organisms provide important ecosystem functions and are useful indicators of global change. We analyse how environmental drivers influence changes in occurrence and length of these lichens on Norway spruce (<em>Picea abies</em>) over 10 years in managed forests in Sweden using data from >6000 trees. <em>Alectoria</em> and <em>Usnea</em> showed strong declines in southern-central regions, whereas Bryoria declined in northern regions. Overall, relative loss rates across the country ranged from 1.7% per year in <em>Alectoria </em>to 0.5% in <em>Bryoria</em>. These losses contrasted with increased length of <em>Bryoria </em>and <em>Usnea </em>in some regions. Occurrence trajectories (extinction, colonization, presence, absence) on remeasured trees correlated best with temperature, rain, nitrogen deposition, and stand age in multinomial logistic regression models. Our analysis strongly suggests that industrial forestry, in combination with nitrogen, is the main driver of lichen declines. Logging of forests with long continuity of tree cover, short rotation cycles, substrate limitation and low light in dense forests are harmful for lichens. Nitrogen deposition has decreased but is apparently still sufficiently high to prevent recovery. Warming correlated with occurrence trajectories of <em>Alectoria</em> and <em>Bryoria</em>, likely by altering hydration regimes and increasing respiration during autumn/winter. The large-scale lichen decline on an important host has cascading effects on biodiversity and function of boreal forest canopies. Forest management must apply a broad spectrum of methods, including uneven-aged continuous cover forestry and retention of large patches, to secure the ecosystem functions of these important canopy components under future climates. Our findings highlight interactions among drivers of lichen decline (forestry, nitrogen, climate), functional traits (dispersal, lichen colour, sensitivity to nitrogen, water storage), and population processes (extinction/colonization).</p>
Data from: Large-scale evolution of body temperatures in land vertebrates
<p>Body temperature is a crucial variable in animals that affects nearly every aspect of their lives. Here we analyze for the first time large-scale patterns in the evolution of body temperatures across terrestrial vertebrates (tetrapods, including amphibians, mammals, birds and other reptiles). Despite the traditional view that endotherms (birds and mammals) have higher body temperatures than ectotherms, we find they are not significantly different. However, rates of body-temperature evolution are significantly different, with lower rates in endotherms than ectotherms, and the highest rates in amphibians. We find that body temperatures show strong phylogenetic signal over 350 million years of evolutionary history in tetrapods, and some lineages appear to have retained similar body temperatures over time for hundreds of millions of years. Although body temperatures are often unrelated to climate in tetrapods, we find that body temperatures are significantly related to day-night activity patterns. Specifically, body temperatures are generally higher in diurnal species than nocturnal species, both across ectotherms and, surprisingly, across endotherms also. Overall, our results suggest that body temperatures are significantly linked to phylogeny and diel-activity patterns within and among tetrapod groups, rather than just climate and the endotherm-ectotherm divide.</p>
Diet analysis of bats killed at wind turbines suggest large-scale losses of trophic interactions
<p>Agricultural practice has led to landscape simplification and biodiversity decline, yet recently, energy producing infrastructures, such as wind turbines, have been added to these simplified agroecosystems, turning them into multi-functional energy-agroecosystems. Here, we studied the trophic interactions of bats killed at wind turbines using a DNA metabarcoding approach to shed light on how turbine-related bat fatalities may possibly feedback on local habitats. Specifically, we identified insect DNA in the stomachs of common noctule bats (<em>Nyctalus noctula</em>) killed by wind turbines in Germany to infer in which habitats these bats hunted. Common noctule bats consumed a wide variety of insects from different habitats, ranging from aquatic to terrestrial ecosystems (e.g. wetlands, farmland, forests, and grasslands). Agricultural and silvicultural pest insects made up about 20% of insect species consumed by the studied bats. Our study suggests that the potential damage of wind energy production goes beyond the loss of bats and the decline of bat populations. Bat fatalities at wind turbines may lead to the loss of trophic interactions and ecosystem services provided by bats, which may add to the functional simplification and impaired crop production, respectively, in multi-functional ecosystems.</p>
Data related to "Near-bed sediment transport processes during onshore bar migration in large-scale experiments. Comparison with offshore bar migration."
<p>Abstract:</p> <p>This paper presents novel insights into nearshore sediment transport processes during bar migration on the basis of large-scale laboratory experiments with bichromatic wave groups on a relatively steep initial beach slope (1:15). Insights are based on detailed measurements of velocity and sand concentration near the bed from shoaling up to the outer breaking zone including suspended sediment and sheet flow transport. The analysis focuses on onshore migration under an accretive wave condition but comparison to an erosive condition highlights important differences. Decomposition shows that total net transport mainly results from a balance of short wave-related, bedload net onshore transport and current-related, suspended net offshore transport. When comparing the accretive to the more energetic erosive condition, the balance shifts towards net onshore transport, and onshore migration, because the short wave-related transport does not decrease as much as the current-related transport. This is related to the effects of skewness and asymmetry combined with larger sediment entrainment and undertow magnitude under the erosive condition. Net transports from streaming in the wave boundary layer and from infragravity waves are noticeable but only play a subordinate role. Identified priorities for numerical model development include parametrization of wave nonlinearity effects and better description of wave breaking and its influences on sediment suspension. The present data, unique in their combination of high measurement detail with fully-evolving accretive beach profiles, help to improve numerical modeling of long-term morphological evolution.</p> <p>About the data:</p> <p>The folder “Beach Profiles” contains the measurements from the mechanical profiler before and after each test. To save time, only the morphologically active section of the profiles was measured. Additionally, the folder contains the initial profiles at the start of each sequence (after application of the benchmark waves). Here the full profile was measured.</p> <p>The structure “MobFrame” contains the absolute cross-shore position of the mobile frame (from which detailed measurements were taken) in the considered tests.</p> <p>The folder “ACVP” contains structures with ensemble-averaged velocity and concentration measurements in vertical reference to the undisturbed bed level or a few bins below it (zeta<sub>0</sub>-coordinate system as described in the paper). For better interpretation of the measurements, it also features the ensemble-averaged intrawave instantaneous bed elevation (erosion depth) and the upper limit of the sheet flow layer.</p> <p>The folder “ADV” contains structures with the ensemble-averaged ADV data of each test. Apart from the velocity components of each ADV they contain the vertical elevation of each ADV with respect to the ACVP transceiver. The ADV measurements were not subject to the same vertical referencing procedure that was described in the paper for the near-bed ACVP measurements.</p> <p>The folder “OBS” contains structures with the ensemble-averaged OBS data of each test. Apart from the concentration measurements in each OBS sensor they contain the vertical elevation of each OBS with respect to the ACVP transceiver.</p> <p>The folder “ETA” contains structures with the ensemble-averaged surface elevation data of each test (from different instruments as described in the paper). The location of each instrument is given in absolute cross-shore coordinates x.</p> <p> </p> <p>For visualizing the near-bed concentration data, which may not be as trivial as visualizing the rest of the data, an example of MATLAB code is given:</p> <p>%S=ACVP_xx; %to choose which ACVP file you want to look into</p> <p>con=S.c;</p> <p>con(con<1)=1; %to cater for the cells where the logarithm is not defined</p> <p>xphase=linspace(0,1,length(S.solbed)).*ones(size(S.c,2),size(S.c,1));</p> <p>figure; hold on; box on;</p> <p>[C,h]=contourf(xphase,S.z,log10(transpose(con)),[0:0.1:3]);</p> <p>cbh=colorbar; caxis([0 3]);</p> <p>set(h,'edgecolor','none');</p> <p>tt=get(cbh,'Title'); set(tt,'String','$log_{10}(c)$ $[kg/m^3]$','Interpreter','Latex');</p> <p>plot(xphase(1,:),S.solbed,'k','Linewidth',1.5);</p> <p>plot(xphase(1,:),S.solflo,'r','Linewidth',1.5);</p> <p>xlabel('$t/T_r$','Interpreter','Latex')</p> <p>ylabel('$\zeta_0$ $[m]$','Interpreter','Latex')</p> <p>set(gca,'Fontsize',18)</p>
FIGURES – 0. Cocconeis sp. (cf. capensis (Cholnoky) Witkowski). SEM (New Caledonia, Melanesia). External views. Biseriate SV striae (16, 18, twin arrows), narrow and straight SV sternum, marginal large area with one row of beads (16–18), SV marginal area with tiny pores (17), SV crater-like areolae with oblong in a zigzag lumen (19), SV areolae with sort of expansions (20). Scale bars: 4 µm (16), 3 µm (18), 700 nm (17), 400 nm (19–20). in Marine Achnanthales (Bacillariophyceae) from New Caledonia (Melanesia): assemblage specificities, ultramafic environment
FIGURES – 0. Cocconeis sp. (cf. capensis (Cholnoky) Witkowski). SEM (New Caledonia, Melanesia). External views. Biseriate SV striae (16, 18, twin arrows), narrow and straight SV sternum, marginal large area with one row of beads (16–18), SV marginal area with tiny pores (17), SV crater-like areolae with oblong in a zigzag lumen (19), SV areolae with sort of expansions (20). Scale bars: 4 µm (16), 3 µm (18), 700 nm (17), 400 nm (19–20).
FIGURES –. Cocconeis sp. (cf. C. bilicis F.Meister). SEM (New Caledonia, Melanesia). Different specimens with SV sectors separated (or not) by a crista marginalis (21, 24), SV striae uniseriae near the sternum and biseriate thereafter (21, 24), SV areolae lumen with circular ornamentation (23, arrow), crista marginalis (22), SVVC in advalvar view with digit fimbriae (25, arrowhead), large RV axial concave area (26). Scale bars = 6 µm (24), 5 µm (26), 4 µm (21), 3 µm (25), 1 µm (22–23). in Marine Achnanthales (Bacillariophyceae) from New Caledonia (Melanesia): assemblage specificities, ultramafic environment
FIGURES –. Cocconeis sp. (cf. C. bilicis F.Meister). SEM (New Caledonia, Melanesia). Different specimens with SV sectors separated (or not) by a crista marginalis (21, 24), SV striae uniseriae near the sternum and biseriate thereafter (21, 24), SV areolae lumen with circular ornamentation (23, arrow), crista marginalis (22), SVVC in advalvar view with digit fimbriae (25, arrowhead), large RV axial concave area (26). Scale bars = 6 µm (24), 5 µm (26), 4 µm (21), 3 µm (25), 1 µm (22–23).
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.