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October 2019 700 kHz multibeam echo sounder data used for Seasonal Change of Multifrequency Backscatter in three Baltic Sea Habitats
<p>The raw data used for the study</p> <p>Seasonal Change of Multifrequency Backscatter in three Baltic Sea Habitats</p> <p>by Schulze et al.; currently under review at Frontiers in Remote Sensing. </p> <p> </p> <p>Files are stored in the s7k-Format, and sorted by date of acquisition and frequency. 200 and 400 kHz data were manufacturer-calibrated. Correct absorption values have been applied duirng the export. Refer to the paper for further dataset information.</p> <p> </p> <p>This upload stores the 700 kHz data recorded in October 2019.</p>
Data, scripts and supplementary information for analysis of the functioning of a three-species microcosm under cadmium pressure
<p>Data files of different experiments conducted with a three-species microcosm + Rscript for infering paremeters from a mechanistic EDO based model describing the functioning of the microcosm and the effect of cadmium + JAGS script of the model + supplementary information</p>
Neuroanatomical shifts mirror patterns of ecological divergence in three diverse clades of mimetic butterflies
<p class="MsoNormal"><span>Microhabitat partitioning in heterogenous environments can support more diverse communities but may expose partitioned species to distinct perceptual challenges. Divergence across microhabitats could therefore lead to local adaptation to contrasting sensory conditions across small spatial scales, but this aspect of community structuring is rarely explored. Diverse communities of ithomiine butterflies provide an example where closely related species partition tropical forests, where shifts in mimetic colouration are tightly associated with shifts in habitat preference. </span><span>We test the hypothesis </span><span>that these mimetic and ecological shifts are associated with distinct patterns of sensory neural investment by comparing brain structure across 164 individuals of 16 species from three ithomiine clades. We find distinct brain morphologies between Oleriina<em> </em>and <em>Hypothyris</em>, which are mimetically homogenous and occupy a single microhabitat. Oleriina, which occur in low-light micro-habitats, invests less in visual brain regions than <em>Hypothyris</em>, with one notable exception, <em>Hyposcada anchiala, </em>the only Oleriina<em> </em>sampled to have converged on mimicry rings found in <em>Hypothyris</em>. We also find that <em>Napeogenes</em>, which has diversified into a range of mimicry rings, shows intermediate patterns of sensory investment. We identify flight height as a critical factor shaping neuroanatomical diversity, with species that fly higher in the canopy investing more in visual structures. Our work suggests that the sensory ecology of species may be impacted by, and interact with, the ways in which communities of closely related organisms are adaptively assembled.</span></p>
Fig. 15 in The genus Milnesium (Eutardigrada, Apochela, Milnesiidae) in Argentina: description of three new species and key to the species of South America
Fig. 15. Semi-schematic drawing of pseudoplate configuration in Milnesium irenae sp. nov.
FishShapes v1: functionally relevant measurements of teleost shape and size on three dimensions
<p>Teleost fishes account for 96% of all fish species and exhibit a spectacular variety of body forms. Teleost lineages range from deep-bodied to elongate (e.g. eels, needlefish), laterally compressed (e.g. ribbonfish) to globular (e.g. pufferfish) and include uniquely shaped lineages such as seahorses, flatfishes and ocean sunfishes. Adaptive body shape convergence within fishes has long been hypothesized but the nature of the relationships between fish form and ecological and environmental variables remain largely unknown at the macroevolutionary scale. To facilitate the investigation of the interacting factors influencing teleost body shape evolution we measured 8 functionally relevant linear traits on adult-sized specimens along with specimen mass. Linear measurements of standard length, maximum body depth, maximum fish width, lower jaw length, mouth width, head depth, minimum caudal peduncle depth and minimum caudal peduncle width were taken in millimeters with calipers, or tape measures for oversized specimens. We measured these traits on a total of 16523 specimens (1-3 specimens per species) at the Smithsonian National Museum of Natural History and took approximately 7000 person hours of data collection to complete. The data went through a three-step error-checking process to clean and validate the data and then species averages were calculated. We present the complete specimen dataset, which encompasses approximately one fifth of extant teleost species diversity, spanning ~90% of teleost families and ~96% of orders. The species and family names are compatible with the FishBase taxonomy (Pauly & Froese, 2019) and the order information with the phylogenetically informed taxonomy of Betancur-R et al. (2014). This dataset is licensed under a Creative Commons Attribution - Non-Commercial 4.0 International License (CC BY-NC), please cite this paper when using the data or a subset of it.</p>
Accounting for the three-dimensional nature of mountain waves: parametrizing partial critical level filtering
<p>This data is used in the production of figures and results presented in the paper 'Accounting for the three-dimensional nature of mountain waves: parametrizing partial critical level filtering', submitted to the Quarterly Journal of the Royal Meteorological Society.</p> <p> </p> <p>See README file for details.</p> <p> </p> <p> </p>
Three-dimensional stratification pattern in an old-growth lowland forest: how does height in canopy and season influence temperate bat activity?
<p class="PaperLauftext">The study of animal-habitat interactions is of primary importance for the formulation of conservation recommendations. Flying, gliding and climbing animals have the ability to exploit their habitat in a three-dimensional way and the vertical canopy structure in forests plays an essential role for habitat suitability. Forest bats as flying mammals may seasonally shift their microhabitat use due to differing energy demands or changing prey availability, but the patterns are not well understood.</p> <p>We investigated three-dimensional and seasonal habitat use by insectivorous bats in a temperate lowland old-growth forest, the <i>Belovezhskaya Pushcha</i> in Belarus. We acoustically sampled broadleaved and mixed coniferous plots in the forest interior and in gaps in three heights during two reproductive periods (pregnancy/lactation versus post-lactation). In canopy gaps, vertical stratification in bat activity was less pronounced than in the forest interior. Vertical activity patterns differed among species. The upper canopy levels were important foraging habitats for the open-space forager guild and for some edge-space foragers like the Barbastelle bat <i>Barbastella barbastellus</i> and the soprano pipistrelle <i>Pipistrellus pygmaeus</i>. <i>Myotis</i> species had highest activity levels near the ground in forest gaps. Moreover, we found species-dependent seasonal microhabitat shifts. Generally, all species and species groups considered except <i>Myotis</i> species showed higher activity levels during post-lactation. <i>Myotis</i> species tended towards higher activity in the forest interior during post-lactation. <i>P. pygmaeus</i> switched from high activity levels in the upper canopy during pregnancy and lactation to high activity levels near the ground during post-lactation. We conclude that a full comprehension of forest bat habitat use is only possible when height in canopy and seasonal patterns are considered.</p>
Marine biodiversity patterns in coastal Australian waters revealed by a three-year environmental DNA survey
<p><strong>Aim</strong></p> <p>To test the capacity of eDNA to characterise the spatial and seasonal patterns found within a range of zooplankton communities, and investigate links with concurrent abiotic data collected as part of Australia's Integrated Marine Observing System (IMOS) programme.</p> <p><strong>Location</strong></p> <p>Samples were sourced seasonally for three years from nine Pan-Australian marine sites (n=90).</p> <p><strong>Methods</strong></p> <p>Here we apply a multi-assay metabarcoding approach to environmental DNA extracted from a rare long-term collection of bulk plankton samples. Six assays (targeting both the 16SrRNA and COI genes) were used to amplify and sequence the zooplankton diversity found within each sample. The data generated from each assay was filtered and clustered into OTUs prior to analysis. Abiotic IMOS data collected alongside the plankton collection enabled us to explore the physical and chemical drivers of community composition.</p> <p><strong>Results</strong></p> <p>The eDNA metabarcoding generated over 25 million sequences, identified in excess of 500 distinct taxa and detected clear spatial differences in marine metazoan communities. We found that site and sea surface temperature are the most consistent predictors of differences between zooplankton communities. We detected endangered and invasive species such as the bryozoan Membranipora membranace and the mollusc Maoricolpus roseus, and seasonal occurrences of species such as humpback whales (Megaptera novaeangliae). We also estimated the number of samples required to ensure robust marine eDNA metabarcoding biomonitoring programs into the future.</p> <p><strong>Main Conclusion</strong></p> <p>Our results demonstrate the ability of eDNA to capture and map zooplankton community changes in response to seasonal and spatial stressors and provide vital evidence to environmental stakeholders. We confirm that eDNA offers a practical opportunity for an ecosystem-wide approach to the long-term biomonitoring and understanding marine biomes where a morphological approach is not feasible.</p>
EXAMPLE: Lattice-based equation of state tables with three conserved charges (BSQ)
<p>These table is intended to provide an example format of the equation of state expected for the CCAKE hydrodynamic code which propagates conserved charge densities for baryon number <span class="math-tex">\(B\)</span>, net strangeness <span class="math-tex">\(S\)</span>, and electric charge <span class="math-tex">\(Q\)</span>. They are included primarily for demonstration purposes and no claim is made as to the accuracy of their contents.</p>
Training and validation data for artificial neural networks using three-dimensional partial convolutions to fill gaps in satellite image time series
<p>This dataset contains training and validation data for artificial neural networks using three-dimensional partial convolutions to fill gaps in satellite image time series. The data have been derived from Sentinel-5P total column carbon monoxide observations, using the offline processing stream.</p> <p><strong>Preprocessing</strong></p> <p>The following operations have been applied on the original S5P imagery:</p> <ol> <li>Images have been resampled to 0.1 by 0.1 degree spatial resolution</li> <li>Pixels with quality assessment value less than or equal to 0.5 have been set to NA</li> <li>Images have been aggregated by day of observation</li> <li>Images have been cropped to -60 to 60 degrees latitude</li> <li>Images have been devided into spatiotemporal blocks of size 128 x 128 pixels and 16 days</li> </ol> <p>Imagery has been recorded between 2021-01-01 and 2021-11-25. Notice that both the training and the validation blocks have been randomly sampled from all available blocks.</p> <p><br> <strong>Data Format and Naming Conventions</strong></p> <p>Input and output data blocks are stored as GeoTIFF files, where bands represent time. Notice the following file naming conventions:</p> <ul> <li>Files starting with <em>X</em> represent input measurements for training, where artificial gaps have been added.</li> <li>Files starting with <em>Y</em> represent true measurements without artificially added gaps (but still containing gaps in many cases).</li> <li>Binary masks of input data where all pixels with valid measurements are 1 and others 0 are stored in files whose name starts with <em>MASK</em></li> <li>Files starting with <em>VALMASK</em> contain a binary mask where only pixels that are available in Y but not in X are 1. The latter is used for validation on artificially removed pixels only.</li> </ul> <p>Numbers in filenames encode spatial and temporal block indexes.</p> <p>In addition, the dataset contains prediction of the validation blocks from different models in the `predictions` directory. The subfolders contain output from different models:</p> <ul> <li>mean refers to simple block-wise mean predictions.</li> <li>timeseries refers to simple linear time series interpolation.</li> <li>gapfill refers to the method proposed in [1].</li> <li>stmra refers to the method proposed in [2].</li> <li>STpconv refers to predictions passed on an artificial neural netowork with three-dimensional partial convolutions.</li> </ul> <p><strong>References</strong></p> <p>[1] Gerber, F., de Jong, R., Schaepman, M. E., Schaepman-Strub, G., & Furrer, R. (2018). Predicting missing values in spatio-temporal remote sensing data. IEEE Transactions on Geoscience and Remote Sensing, 56(5), 2841-2853.</p> <p>[2] Appel, M., & Pebesma, E. (2020). Spatiotemporal multi-resolution approximations for analyzing global environmental data. Spatial Statistics, 38, 100465.</p>
THREE-DIMENSIONAL VOLUMETRIC EVALUATION OF ROOT RESORPTION IN MAXILLARY ANTERIORS FOLLOWING EN-MASSE RETRACTION WITH VARYING FORCE VECTORS - A RANDOMIZED CONTROL TRIAL
<p>To assess the severity of root resorption (RR) during retraction of maxillary anteriors with and without skeletal anchorage (three different force systems); and analyze it comprehensively using cone-beam computed tomography (CBCT) superimpositions.</p>
Three-dimensional mapping of carbon, nitrogen, and phosphorus in soil microbial biomass and their stoichiometry at the global scale
<p>R code, raw datasets, and predicted global maps of soil microbial biomass C, N, and P and their stoichiometric ratios at 0-30 cm depth.</p> <p>When using any of these layers, please cite: Gao et al., Three-dimensional mapping of carbon, nitrogen, and phosphorus in soil microbial biomass and their stoichiometry at the global scale (2022). Global Change Biology. DOI: 10.1111/gcb.16374</p>
Data for: Forecasting shifts in habitat suitability of three marine predators suggests a rapid decline in inter-specific overlap under future climate change
<p><strong><span>Aim:</span></strong><span> To estimate spatiotemporal changes in habitat suitability and inter-specific overlap among three marine predators: Baltic grey seals (<em>Halichoerus grypus grypus</em>), harbour seals (<em>Phoca vitulina</em>), and harbour porpoises (<em>Phocoena phocoena</em>) under contemporary and future conditions.</span></p> <p><strong><span>Location: </span></strong><span>The southwestern region of the Baltic Sea, including the Danish Straits and the Kattegat, one of the fastest-warming semi-enclosed seas in the world.</span></p> <p><strong><span>Methods: </span></strong><span>Location data (>200 tagged individuals) were analysed within the </span><span>maximum entropy (MaxEnt) </span><span>algorithm to estimate changes in total area size and overlap of species-specific habitat suitability between 1997-2020 and 2091-2100. A total of eleven candidate predictor variables were considered </span><span>representing anthropogenic activity, environmental, and climate sensitive oceanographic conditions in the area. Sea surface temperature and salinity</span><span> data were taken from </span><span>representative concentration pathways [RCPs] scenarios 6.0 and 8.5</span><span> to forecast potential </span><span>climate change effects</span><span>.</span></p> <p><strong><span>Results:</span></strong><span> Model output suggests that habitat suitability of Baltic grey seals will decline drastically over space and time, largely driven by changes in sea surface salinity and a loss of currently available haulout sites following sea level rise in the future. A similar though weaker response was observed for harbour seals, while suitability of habitat for harbour porpoises was predicted to remain fairly stable over space and time. Inter-specific overlap in highly suitable habitat was predicted to increase slightly under RCP scenario 6.0 when compared to contemporary conditions but to largely disappear under RCP scenario 8.5.</span></p> <p><strong><span>Main conclusions:</span></strong><strong> </strong><span>Marine predators in the southwestern Baltic Sea and adjacent waters may respond differently to future climatic conditions, leading to divergent shifts in habitat suitability that are likely to decrease inter-specific overlap.<strong> </strong>We, therefore, conclude that climate change can lead to a marked redistribution of area use by marine predators in the region, which may influence local food-web dynamics and ecosystem functioning.</span></p>
Three-dimensional surface scans of tooth surfaces of Japanese wild boars.
<p>Three-dimensional surface scans of tooth surfaces of Japanese wild boars are saved in .sur format and surface analyses files in .mnt format, which are analyzed in:</p> <p>Miyamoto, K., Kubo, M. O. and Yokohata, Y. "Dental microwear texture of wild boars from Japan reflects inter- and intra-populational feeding preferences" submitted to Frontiers in Ecology and Evolution.</p> <p>Please see information in the paper for details.</p>
Data on three-year flowering intensity monitoring in an apple orchard
<p>The present dataset contains UAV images during the full blooming period of an apple orchard for three consecutive years, 2018, 2019, and 2020. It is directly linked to a research article entitled “Feasibility assessment of tree-level flower intensity quantification from UAV RGB imagery: A triennial study in an apple orchard”. The data collection site was an apple orchard located at Randwijk, Overbetuwe, The Netherlands (51.938, 5.7068 in WGS84 UTM 31U). This dataset aims to support researchers focussing on remote sensing, machine vision, deep learning, and image classification, and the stakeholders interested in precision horticulture and orchard management. It can be used for flowering intensity estimation and prediction, and spatial and temporal flowering variability mapping by using digital photogrammetry and 3D reconstruction.</p>
The effects of temperature extremes on survival in two semi-arid Australian bird communities over three decades, with predictions to 2104
<p>Aim: Organisms in arid and semi-arid regions are frequently exposed to climatic extremes and accordingly among the most vulnerable to climate change. Studies of seasonal differences in vital rates, which mediate effects of climate on viability, are rare in arid species limiting ability to project population trends. We quantified survival patterns for two bird communities as a function of expo-sure to temperature extremes in winter and summer, then project survival patterns to 2104.</p> <p>Location: semi-arid eastern Australia</p> <p>Time period: 1986-2016; 1986-2104</p> <p>Major taxa studied: Birds</p> <p>Methods: Using mark recapture time-dependent Cormack-Jolly-Seber models and data for 37 species from two 30-year ringing programs, we tested for effects on 6-monthly survival of expo-sure to temperatures >38oC and <0oC. We then predicted future survival for different emission scenarios, testing whether changes in survival associated with warming winters would be suffi-cient to offset the effects of rising summer temperatures. Results: Survival probability declined strongly with increasing exposure to days >38oC and to a lesser extent to days <0oC, with temperature extremes explaining 43% and 13% of temporal varia-tion in survival among years, respectively. Summer survival patterns were similar across avian guilds but only survival of nectarivores declined in winter. Our models predict that gains in winter survival will not offset reductions in summer survival.</p> <p>Annual survival is predicted to decline sub-stantially by the end of the century: from 0.63 in 1986 to 0.43 in 2104 under an optimistic emis-sion scenario and to 0.11 under a pessimistic scenario. Main conclusions: We highlight the significance of temperature extremes for species' persistence in arid and semi-arid regions, comprising 70% of Australia's land mass, and 40% globally. Our demography-based results are consistent with physiological-based projections evaluating avian survival in arid and semi-arid regions globally and suggest rising summer temperatures pose a risk to population persistence in these regions. </p>
Fig. 6 in Australian Cleotychini planthoppers: review of the genus Cleotyche Emeljanov, 1997 with three new species (Hemiptera: Fulgoromorpha: Dictyopharidae)
Fig. 6. The distribution of described species of Cleotychini in Australia.
Variations of the urban PM2.5 chemical components and corresponding light extinction for three heating seasons in the Guanzhong Plain, China
<p>The basic data of the thesis “Variations of the urban PM2.5 chemical components and corresponding light extinction for three heating seasons in the Guanzhong Plain, China”.</p>
Transient Nuclear Criticality Excursion Analysis of Highly Dispersed Particulate Three-Phase Fluidised Systems
<p>The aim of this study was to perform sensitivity analysis, investigating how different fluidisation and sedimentation characteristics of three-phase, wetted UO2 powder beds, may affect a transient nuclear criticality excursion initiated through the addition of water into a fissile powder bed. This type of postulated nuclear criticality accident scenario may occur in nuclear fuel fabrication facilities when a fire is fought through the use of water, supplied via an automatic or manual fire-suppression system. A similar scenario may also develop as a result of water leaks or flooding of the process area housing UO2 powder. The article introduces a model for gas-bubble induced fluidisation of a UO2 powder bed and examines how this phenomenon may affect the neutron kinetic response of a three-phase fluidised fissile powder system. Empirical analysis has shown that fissile suspensions form agglomerated structures when suspended in water, at agglomerate sizes that range from 18 µm to 40 µm. Simulation results indicate that both the critical gas velocity and rate of fluidisation may significantly affect transient nuclear criticality excursion dynamics. The re-distribution of fissile mass into a highly dispersed suspension generally reduces the reactivity of the system, however, depending on the H/U ratio, a positive reactivity may be added to the system. Low Péclet numbers in the suspension suggest that gas-bubble induced motion of the suspension causes a highly dispersive flow field. An oscillatory power response is predicted for low critical gas velocities where the reactivity of the system is predominantly governed by the re-distribution of fissile mass within the system. The frequency of these oscillations is greater for a higher hindered settling rate of powder particles. At higher critical gas velocity, the transient nuclear criticality excursion is governed by the voidage reactivity feedback, making the response quite independent of fluidisation. In all cases, large volumes of UO2 powder may leave the domain due to overflowing of the suspension. Transient nuclear criticality excursions in UO2 powder beds with a low critical gas velocity are terminated once the bed becomes fully saturated.</p>
Grassland bird population declines at three Breeding Bird Survey spatial scales in contrast to a large native prairie
<p>Grassland biomes in North America are threatened by agricultural intensification with implications for grassland associated bird populations via habitat loss, alteration, pesticide use and declining landscape heterogeneity. Despite decades of conservation concern, steep declines of North American grassland bird populations continue. Key to optimizing conservation effort is understanding how land-use practices, such as agriculture, across the annual cycle affects population status. Determining the relative influence of impacts on grassland bird declines is difficult given that the most robust estimates of population trends, the North American Breeding Bird Survey (BBS), are from surveys throughout agriculturally dominated regions. Our goal was to explore whether agriculture during the breeding season is a major driver of grassland bird declines. We derived trends for 16 grassland bird species spanning 23 years (1994-2016) at a large (459 km2), native prairie site, Suffield National Wildlife Area (SNWA) in Alberta, Canada. We compared those trends to the BBS across three spatial scales, a regional monitoring scheme with higher than average native grass cover (GBM), BCR 11 - Canada (Canada) and all of BCR 11 (BCR 11). Trends measured as annual percent change and credible interval varied greatly among species and survey strata. Across all species, declines were greatest for Canada (-1.3%, CI: -2.8, 0.0) and BCR 11 (-1.9%, CI: -3.2, -0.6). This contrasts with positive mean trends for GBM routes (1.0%, CI: -0.4, 2.3) and the SNWA data (1.7%, CI: 0.3, 3.3). Six of 16 species at SNWA were increasing with one decreasing. Five species increased at GBM and four declined. Canada had 10 species declines and three increases and BCR 11 had 10 declines and no increases. None of six grassland obligate species declined at SNWA, two declined at GBM, and all six declined over the two larger BBS strata. Our results showing fewer negative population trends at a large native grassland site compared to BBS at three spatial scales across the North American prairies support the prediction that agricultural intensification on breeding grounds is a major driver of declining populations and protection of remaining native grasslands should remain a key component of grassland bird conservation efforts.</p>
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.