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Dataset for paper "Flow Resistance for a Varying Density of Obstacles on Smooth and Rough Beds"
<p>This dataset contains the experimental data that supports the paper:</p> <p>Guillén-Ludeña, S., Lopez, D., Mignot, E., & Riviere, N. (2019). Flow Resistance for a Varying Density of Obstacles on Smooth and Rough Beds. <em>Journal of Hydraulic Engineering</em>, <em>146</em>(2), 04019059.</p> <p>The file Readme.txt contains al explanations regarding the data organization.</p>
ICECAP-2 consortium bed elevation model for Princess Elizabeth Land, East Antarctica
<p>We present a new topographic digital elevation model (DEM) for Princess Elizabeth Land (PEL) – the last remaining region in Antarctica to be surveyed. The DEM covers an area of 899,730 km2 and was established from new aero geophysical data collected by the ICECAP-2 consortium, led by the Polar Research Institute of China, from four different surveys since 2015. Two products are available; (1) 500 m bed elevation model; and (2) 500 m ice thickness model. The mass conservation (MC) method is used to infer ice thickness DEM across faster-flowing (>30 m yr-1) regions of the ice sheet, and streamline diffusion at slower-flowing areas. The ice thickness DEM is then integrated with the ice surface DEM from the Reference Elevation Model of Antarctica (Howat, et al., 2019) to generate the bed elevation model. Together with BedMachine Antarctica, and Bedmap2, this new bed DEM for PEL completes the first-order measurement of subglacial Antarctica – an international mission that began 70 years ago. </p>
Flow through a submerged canopy partially covering the bed: spatial flow pattern, multi-dimensional vortices and junction momentum exchange
<p>The dataset (including videos) are uploaded to support the research study <strong>Flow through a submerged canopy partially covering the bed: spatial flow pattern, multi-dimensional vortices and junction momentum exchange (submitted to Water Resources Research) </strong></p>
FIGURE 5. Decapods from the Moeshima Silt Bed. A in Fossil decapods from the Upper Quaternary in Shinjima Island in Kagoshima Kyushu, Japan, and description of a new species of ghost shrimp (Axiidea Eucalliacidae)
FIGURE 5. Decapods from the Moeshima Silt Bed. A, Munida sp., MFM145609, dorsal view of carapace. B, C, Tymolus un-
FIGURE 6. Decapods from the Moeshima Shell Bed. A–J in Fossil decapods from the Upper Quaternary in Shinjima Island in Kagoshima Kyushu, Japan, and description of a new species of ghost shrimp (Axiidea Eucalliacidae)
FIGURE 6. Decapods from the Moeshima Shell Bed. A–J, Laticallichirus grandis (Karasawa & Goda, 1996); A, 145597, lateral view of left major cheliped; B, MFM145598, lateral view of right major cheliped; C, MFM145599, lateral view of right carpus; D, MFM145600, lateral view of left minor cheliped; E, MFM145601, lateral view of right dactylus; F, MFM145602, lateral view of right dactylus; G, MFM145603, lateral view of right dactylus; H, MFM145604, lateral view of left dactylus; I, MFM145605, lateral view of right merus; J, MFM145606, lateral view of left merus. K, Paguridae gen. et sp. indet., MFM145607, lateral view of fragment of the fixed finger. L, Pagurus cf. megalops (Stimpson, 1858b), MFM 145608, lateral view of left cheliped. M, Ebalia tuberculosa (A. Milne-Edwards, 1873), MFM145612, dorsal view of carapace. N, Myra sp., MFM145613, lateral view of fragment of the merus. O, Philyra cf. syndactyla Ortmann, 1892, MFM145614, lateral view of right cheliped. P, Majidae gen. et sp. indet., MFM145615, dorsal view of fragment of the carapace. Q, Leptomithrax sp., MFM 145616, lateral view of left cheliped. R, Romaleon sp., MFM 145617, lateral view of fragment of the dactylus. S, Charibdis sp. MFM145619, lateral view of fragment of the fixed finger. Scale bars of A–H, K, M, O, Q and S indicate 5.0 mm, and I, J, L, N, P and R indicate 1.0 mm.
Data from: A 454 survey reveals the community composition and core microbiome of the common bed bug (Cimex lectularius) across an urban landscape
Elucidating the spatial dynamic and core constituents of the microbial communities found in association with arthropod hosts is of crucial importance for insects that may vector human or agricultural pathogens. The hematophagous Cimex lectularius (Hemiptera: Cimicidae), known as the human bed bug, has made a recent resurgence in North America, as well as worldwide, potentially owing to increased travel, climate change and resistance to insecticides. A comprehensive survey of the bed bug microbiome has not been performed to date, nor has an assessment of the spatial dynamics of its microbiome. Here we present a survey of internal and external bed bug microbial communities by amplifying the V4–V6 hypervariable region of the 16S rDNA gene region followed by 454 Titanium sequencing using 31 individuals from eight distinct collection locations obtained from residences in Cincinnati, OH. Across all samples, 97% of the microbial community is made up of two dominant OTUs, previously identified as the α-proteobacterium Wolbachia and an unnamed γ-proteobacterium from the Enterobacteriaceae. Microbial communities varied among host locations for measures of community diversity and exhibited structure according to collection location. This broad survey represents the most in-depth assessment, to date, of the microbes that associate with bed bugs.
Data from: North Atlantic Gateway: test bed of deep-sea macroecological patterns
Aim: The deep waters around Iceland, known as the North Atlantic Gateway, constitute an ideal location to investigate deep-sea ecological hypotheses. Using ostracods, we constructed a comprehensive deep-sea macroecological dataset of the North Atlantic Gateway region and investigated the controlling factors of large-scale, deep-sea species diversity patterns. Location: Sub-polar North Atlantic Ocean Time period: Modern Major taxa studied: Ostracoda (Crustacea) Methods: We investigated deep-sea biodiversity patterns and applied ecological modeling (multiple regression and model averaging) to test whether these patterns are governed by environmental factors such as temperature, surface primary productivity, and seasonality. Beta diversity analyses were applied to evaluate the effect of a geographical barrier (Greenland-Iceland-Faeroe Ridge) on deep-sea benthic faunal distributions. Results: We constructed a deep-sea macroecological dataset with 32 stations, 5676 specimens, and 122 species. We confirmed a linear latitudinal diversity gradient with higher diversity in the North Atlantic proper than in the Nordic Seas. We report a unimodal depth diversity gradient south of the ridge, but a linear diversity-decline with depth north of the ridge. The turnover component of beta diversity increased toward the ridge. Main conclusions: We found both temperature and surface primary production are important for deep-sea biodiversity. For the first time, we report a significant diversity-temperature relationship in both macroecological (spatial; this study) and existing paleoecological (time-series) data for the same taxa. In addition to temperature and surface primary production, bathymetric features such as a shallow ridge acting as a barrier, are an important factor for deep-sea biodiversity distribution. The low diversity of the Nordic Seas is likely due to a combination of low temperatures and bathymetric barriers. These results substantially expand our understanding of the well-known yet poorly understood Greenland-Iceland-Faeroe Ridge faunal transition with possible insight to its cause.
Data from: Local coastal configuration rather than latitudinal gradient shape clonal diversity and genetic structure of Phymatolithon calcareum maerl beds in North European Atlantic
Maerl beds are one of the world's key coastal ecosystems and are threatened by human activities and global change. In this study, the genetic diversity and structure of one of the major European maerl-forming species, Phymatolithon calcareum, was studied using eight microsatellite markers. Two sampling scales (global: North East Atlantic and regional: Galicia) were investigated and fifteen maerl beds from Atlantic Europe were sampled. At the regional-scale the location of sites outside and within four estuaries allowed to test for the influence of coastal configuration on population connectivity and genetic diversity. Results suggested that clonal reproduction plays an important role in the population dynamics of P. calcareum maerl beds. Clonality was variable among populations, even within the same region. At the European scale, these differences in clonality cannot be explained by the geographic or latitudinal distribution of the populations studied. A significant genetic differentiation was found among almost all population pairs and a positive correlation between geographic and genetic distances showed the limited dispersal capacity of P. calcareum. Moreover, a very clear pattern of genetic structure was revealed at the regional scale between populations located within and at the mouth of the estuaries. Genetic differentiation among estuaries was less marked for the sites located in outer-zones compared to those located in the inner-zones. In addition, variation in level of clonality linked to seascape was also observed: populations situated in the outer-zones of the estuaries were less clonal than those in the inner-zones. Finally, populations from the same estuary generally shared one or several mutilocus genotypes.
Data from: Evidence for stratigraphy in molluscan death assemblages preserved in seagrass beds: St. Croix, U.S. Virgin Islands
Death assemblages that occupy the upper tens of centimeters of sediment in shallow-marine settings are often subject to extensive mixing, thereby limiting their usefulness in assessing environmentally mediated compositional changes through time in the local biota. Here, we provide evidence that dense, Thalassia-rich seagrass beds preserve a stratigraphic record of biotic variation because their dense root–rhizome mats inhibit mixing. We sampled benthic mollusk assemblages at seven localities in Thalassia-rich beds around St. Croix, USVI, collecting three separate sediment intervals of ~13 cm each to a total depth of ~40 cm below the sediment–water interface, and found evidence that sedimentary intervals preserved compositional stratigraphy. Further, some localities displayed systematic, directional changes down-core. An examination of interval-to-interval changes in composition revealed that compositional variation was unique from locality to locality rather than reflecting coordinated, island-wide transitions. In general, however, relative abundances of epifaunal gastropods and small lucinid bivalves tended to decrease with depth below the sediment–water interface. Quantitative comparisons of life-to-death assemblages from each successive sedimentary interval demonstrated that the shallowest death assemblages were typically more similar to the life assemblages than were deeper assemblages, suggesting that deeper intervals provide records of earlier community states.
Bed morphology adjustment under the impact of a near-bank emergent model vegetation patch: implications for urban channel restoration
<p>The dataset (including videos) are uploaded to support the research study <strong>Bed morphology adjustment under the impact of a near-bank emergent model vegetation patch: implications for urban channel restoration</strong> </p>
Data from: Spatial scaling of environmental variables improves species-habitat models of fishes in a small, sand-bed lowland river
Habitat suitability and the distinct mobility of species depict fundamental keys for explaining and understanding the distribution of river fishes. In recent years, comprehensive data on river hydromorphology has been mapped at spatial scales down to 100 m, potentially serving high resolution species-habitat models, e.g., for fish. However, the relative importance of specific hydromorphological and in-stream habitat variables and their spatial scales of influence is poorly understood. Applying boosted regression trees, we developed species-habitat models for 13 fish species in a sand-bed lowland river based on river morphological and in-stream habitat data. First, we calculated mean values for the predictor variables in five distance classes (from the sampling site up to 4000 m up- and downstream) to identify the spatial scale that best predicts the presence of fish species. Second, we compared the suitability of measured variables and assessment scores related to natural reference conditions. Third, we identified variables which best explained the presence of fish species. The mean model quality (AUC = 0.78, area under the receiver operating characteristic curve) significantly increased when information on the habitat conditions up- and downstream of a sampling site (maximum AUC at 2500 m distance class, +0.049) and topological variables (e.g., stream order) were included (AUC = +0.014). Both measured and assessed variables were similarly well suited to predict species' presence. Stream order variables and measured cross section features (e.g., width, depth, velocity) were best-suited predictors. In addition, measured channel-bed characteristics (e.g., substrate types) and assessed longitudinal channel features (e.g., naturalness of river planform) were also good predictors. These findings demonstrate (i) the applicability of high resolution river morphological and instream-habitat data (measured and assessed variables) to predict fish presence, (ii) the importance of considering habitat at spatial scales larger than the sampling site, and (iii) that the importance of (river morphological) habitat characteristics differs depending on the spatial scale.
Data from: Biodiversity-ecosystem functioning relationships in long-term time series and palaeoecological records: deep sea as a test bed
The link between biodiversity and ecosystem functioning (BEF) over long temporal scales is poorly understood. Here, we investigate biological monitoring and palaeoecological records on decadal, centennial and millennial time scales from a BEF framework, by using deep-sea, soft-sediment environments as a test bed. Results generally show positive BEF relationships, in agreement with BEF studies based on present-day spatial analyses and short-term manipulative experiments. However, the deep-sea BEF relationship is much noisier across longer time scales compared with modern observational studies. We also demonstrate with palaeoecological time-series data that a larger species pool does not enhance ecosystem stability through time, whereas abundance, as an indicator of higher ecosystem functioning, may enhance ecosystem stability. These results suggest that BEF relationships are potentially timescale-dependent. Environmental impacts on biodiversity and ecosystem functioning may be much stronger than biodiversity impacts on ecosystem functioning at long, decadal–millennial, time scales. Longer time-scale perspectives, including palaeoecological and ecosystem monitoring data, are critical for predicting future BEF relationships on a rapidly changing planet.
Data from: Paleocommunity analysis of the Burgess Shale Tulip Beds, Mount Stephen, British Columbia: comparison with the Walcott Quarry and implications for community variation in the Burgess Shale
The Tulip Beds locality on Mount Stephen (Yoho National Park, British Columbia) yields one of the most abundant and diverse (~10,000 specimens in 110 taxa) Burgess Shale fossil assemblages in the Canadian Rockies. Detailed semi quantitative and quantitative analyses of this assemblage suggest strong similarities with the Walcott Quarry on Fossil Ridge. Both assemblages are dominated by epibenthic, sessile, and suspension feeding taxa, mostly represented by arthropods and sponges and have comparable diversity patterns, despite sharing only about half the genera. However, the Tulip Beds has a higher relative abundance of suspension feeders and taxa of unknown affinity compared to the Walcott Quarry. These biotic variations are probably largely attributable to ecological and evolutionary differences between the two temporally distinct communities that adapted to similar, but not identical, environmental settings. For instance, the Tulip Beds is farther away from the Cathedral Escarpment than the Walcott Quarry. The Tulip Beds and Walcott Quarry assemblages are more similar to each other than either one is to the assemblages of the Chengjiang biota, although the relative diversity of major taxonomic groups and ecological patterns are similar in all assemblages. The conserved diversity patterns and ecological structures among sites suggest that the ecological composition of Cambrian Burgess Shale-type communities was relatively stable across wide geographic and temporal scales.
Data from: Macrobenthic assemblage structure in a cool-temperate intertidal dwarf-eelgrass bed in comparison to those in lower latitudes.
The evolution and ecology of latitudinal patterns in marine macrofaunal biodiversity and assemblage structure are contentious. With the aim of investigating the occurrence of such patterns in intertidal dwarf-eelgrass beds (Nanozostera spp.), those at cool-temperate Scolt Head Island, UK (latitude 52°N), were examined and compared to equivalent systems in warm-temperate Knysna, South Africa (34°S), and subtropical Moreton Bay, Australia (27°S); systems that had earlier been examined using identical methodology. The Scolt Head bed supported the highest faunal density (mean 6,568 0.1m-2), lowest observed and estimated species richness (32 and 33 spp respectively), lowest species diversity (Simpson's Index 0.34), highest mean Constancy Index (23.0), lowest proportion of total numbers contributed by singletons or doubletons (0.06%), largest Berger-Parker Dominance (0.81), and least degree of variability between component samples. The beds at Knysna were intermediate between those at Scolt Head and Moreton Bay in all those respects, as well as in nature and composition of the fauna. Similar dwarf-eelgrass beds at Arcachon, France, likewise appear intermediate between those of Scolt Head and Knysna. Community variance in all three regions was greatest at the smallest spatial scale of ≤1 m, at which scale two of the three also displayed randomly organized faunal assemblages, although this changed to non-random at larger spatial scales. Assemblages were deterministically structured at all spatial scales at Knysna. A consistent series of changes in structural characteristics of macrofaunal dwarf-eelgrass assemblages therefore occurred along the latitudinal sequence of Scolt Head (530): Arcachon (450): Knysna (340): Moreton Bay (270). Community assembly patterns did not change with latitude, however, but did so with spatial scale in two of the three regions.
Data from: Modeling effects of climate change and phase shifts on detrital production of a kelp bed
The exchange of energy and nutrients between ecosystems (i.e., resource subsidies) plays a central role in ecological dynamics over a range of spatial and temporal scales. Little attention has been paid to the role of anthropogenic impacts on natural systems in altering the magnitude, timing, and quality of resource subsidies. Kelp ecosystems are highly productive on a local scale and export over 80% of kelp primary production as detritus, subsidizing consumers across broad spatial scales. Here, we generate a model of detrital production from a kelp bed in Nova Scotia to hindcast trends in detrital production based on temperature and wave height recorded in the study region from 1976 to 2009, and to project changes in detrital production that may result from future climate change. Historical and projected increases in temperature and wave height led to higher rates of detrital production through increased blade breakage and kelp dislodgment from the substratum, but this reduced kelp biomass and led to a decline in detrital production in the long term. We also used the model to demonstrate that the phase shift from a highly productive kelp bed to a low-productivity barrens, driven by the grazing activity of sea urchins, reduces kelp detrital production by several orders of magnitude, an effect that would be exacerbated by projected increases in temperature and wave action. These results indicate that climate-mediated changes in ecological dynamics operating on local scales may alter the magnitude of resource subsidies to adjacent ecosystems, affecting ecological dynamics on regional scales.
Data from: An unusual new neosauropod dinosaur from the lower Cretaceous Hastings Beds Group of East Sussex, England
Xenoposeidon proneneukos gen. et sp. nov. is a neosauropod represented by BMNH R2095, a well-preserved partial mid-to-posterior dorsal vertebra from the Berriasian–Valanginian Hastings Beds Group of Ecclesbourne Glen, East Sussex, England. It was briefly described by Lydekker in 1893, but it has subsequently been overlooked. This specimen's concave cotyle, large lateral pneumatic fossae, complex system of bony laminae and camerate internal structure show that it represents a neosauropod dinosaur. However, it differs from all other sauropods in the form of its neural arch, which is taller than the centrum, covers the entire dorsal surface of the centrum, has its posterior margin continuous with that of the cotyle, and slopes forward at 35 degrees relative to the vertical. Also unique is a broad, flat area of featureless bone on the lateral face of the arch; the accessory infraparapophyseal and postzygapophyseal laminae which meet in a V; and the asymmetric neural canal, small and round posteriorly but large and teardrop-shaped anteriorly, bounded by arched supporting laminae. The specimen cannot be referred to any known sauropod genus, and clearly represents a new genus and possibly a new 'family'. Other sauropod remains from the Hastings Beds Group represent basal Titanosauriformes, Titanosauria and Diplodocidae; X. proneneukos may bring to four the number of sauropod 'families' represented in this unit. Sauropods may in general have been much less morphologically conservative than is usually assumed. Since neurocentral fusion is complete in R2095, it is probably from a mature or nearly mature animal. Nevertheless, size comparisons of R2095 with corresponding vertebrae in the Brachiosaurus brancai holotype HMN SII and Diplodocus carnegii holotype CM 84 suggest a rather small sauropod: perhaps 15 m long and 7600 kg in mass if built like a brachiosaurid, or 20 m and 2800 kg if built like a diplodocid.
Data from: Hurricane-mediated defoliation of kelp beds and pulsed delivery of kelp detritus to offshore sedimentary habitats
Severe storm events are important agents of disturbance that can transport large quantities of algal detritus from highly productive kelp beds (or forests) in shallow water to deeper, more food-limited areas. We measured canopy cover in shallow kelp beds (5 to 15 m depth) and the cover of detrital kelp in sedimentary habitats directly offshore of these beds (20 to 45 m) before and after Hurricane Earl, which struck the Atlantic coast of Nova Scotia in September 2010. The storm resulted in large losses of kelp canopy cover (from 71.0 to 38.7%, averaged across sites) and significantly increased the cover of detrital kelp deposits below the kelp beds (from 1.5 to 3.4%). Detrital deposits were more commonly found in a semi-protected bay than off an exposed headland and persisted in the bay for at least 6 wk. Sea urchins Strongylocentrotus droebachiensis were associated with detrital kelp deposits in offshore habitats. At sites with the greatest amount of detrital kelp, we estimated that sea urchins could consume this material within 2 mo, indicating that storm-generated detrital pulses may be an important form of trophic connectivity between adjacent ecosystems off this coast.
Data from: Detrital production in Nova Scotian kelp beds: patterns and processes
Connectivity via the transport of detrital material from areas of high to low productivity may be an important determinant of secondary productivity and biodiversity in receiving communities. On the Atlantic coast of Nova Scotia, detritus exported from subtidal kelp beds contributes to food webs in communities inhabiting deeper waters offshore. To estimate the amount of energy available via this pathway, we measured rates of detrital production via erosion of kelp blades in kelp beds at 5 sites varying in wave exposure. Specifically, we measured productivity and erosion of the 2 dominant species of kelp, Laminaria digitata and Saccharina longicruris, over 16 mo. We also examined the effect of environmental and biological factors on erosion rates, including temperature, wave exposure, grazing by snails and cover by the invasive bryozoan Membranipora membranacea. We observed clear seasonal and spatial patterns in productivity, with the highest production in spring. Erosion rate was highly variable across sites and seasons, and was strongly related to the cover of M. membranacea and the intensity of snail grazing at the distal end of kelp blades. Both factors cause tissue degradation, abrasions and perforations that weaken blades. Erosion rate was also positively related to water temperature and site exposure. Annual detrital production from the erosion of kelp blades increased linearly with kelp bed biomass, and ranged from 0.5 to 1.71 kg dry weight m–2 (150–513 g C m–2) across sites. These rates equal or exceed annual phytoplankton production off the Atlantic coast of Nova Scotia and estimates of detrital production in seagrass beds in North America.
Data from: Spatial and temporal variation in grazing damage by the gastropod Lacuna vincta in Nova Scotian kelp beds
Population increases of the gastropod Lacuna vincta have been associated with significant damage to kelp blades and decreases in kelp biomass in subtidal kelp beds off Nova Scotia, Canada. We measured the total level and along-blade distribution of grazing damage by Lacuna vincta on the dominant kelp species at 5 sites in Nova Scotia, Canada, over a 15 mo period. Grazing was typically low or absent in the basal regions of blades, consistent with seasonal fluctuations in growth and physical properties of blade tissues. Grazing was largely concentrated in middle and distal sections, although this distribution varied with site exposure and over time. The cover of the invasive bryozoan Membranipora membranacea on the surface of kelp blades did not have a strong effect on grazing by L. vincta. The total level of grazing damage (max. 1% of blade area for Saccharina longicruris and 1.5% for Laminaria digitata) varied seasonally, with peaks in September at some sites. Spatial variation was driven in part by a negative relationship with site exposure. In a field experiment, simulated grazing damage that exceeded a threshold value of 0.5 to 1.0% of blade area caused a significant increase in blade loss during a period of heavy wave action due to a passing hurricane. Our results show that direct reductions in kelp biomass through grazing by L. vincta are relatively small, but can indirectly lead to significant losses of kelp biomass during large wave events.
Painted Bed Headboard
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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.