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579 results for “stratification”
Modeling the effects of lake morphology on chloride retention and salt-driven stratification in two urban lakes in St. Paul, MN
Road salt inputs have caused widespread salinization of urban lakes in northern temperate regions. Watershed characteristics are known to be important drivers of lake chloride concentrations, but there has been less focus on how lake morphometry influences seasonal and interannual dynamics in lake chloride, and how these chloride levels may alter mixing in the water column. We analyzed chloride retention for two urban lakes (Como Lake and Lake McCarrons) in Saint Paul, Minnesota, that are in adjacent watersheds and have similar surface areas, but differ in depth and water residence time. Summer chloride concentrations were negatively related to total summer precipitation for Como Lake (maximum depth 2.2 m), but the relationship was less strong for Lake McCarrons (maximum depth 7.6 m). We used a zero-dimensional model to simulate chloride dynamics in both lakes and tracked the fate of chloride over time. In Como Lake, the mass of chloride in the lake turns over within three years, whereas chloride inputs are retained for >10 years in Lake McCarrons. We then used a one-dimensional hydrodynamic lake model (GLM-AED) to examine how lake depth affects how current chloride loading rates alter lake mixing. Salt inputs significantly extended the duration of summer stratification for simulated lakes with depths of 8 m or more, and salt inputs increased the number of days of hypoxia and anoxia across all depths. These results underscore the importance of considering lake morphometry in understanding the effects of salt inputs on lake ecosystems.
Modelling of Stably Stratified Atmospheric Boundary Layers with Varying Stratifications
<p>This repository contains data that was used for publishing article called <a href="https://link.springer.com/article/10.1007%2Fs10546-020-00527-8"><em>Modelling of Stably Stratified Atmospheric Boundary Layers with Varying Stratifications</em></a>. The repository compliments the publication in the sense that it provides qualitative insight for comparison and exploration.</p> <p><strong>Keywords</strong>: GABLS1, Open data, Stably-stratified turbulence, Turbulence parametrization</p> <p>The data is stored inside sixteen files. The file names are split into a part that describes variables and part that describes simulation. Here's an example of a file name:</p> <p>budgets.cr0375.csv</p> <p>The first part <em>budgets</em> refers to variables inside the file and the second part <em>cr0375</em> refers to forcing conditions (in this example cooling rate of 0.375 Kelvin per hour) used in the simulation.</p> <p><strong>Variables</strong>:</p> <ul> <li>mean wind speed and mean potential temperature (<em>first_order_stat</em>)</li> <li>variance and covariance variables that describe turbulence properties (<em>second_order_stat)</em></li> <li>variables in the turbulent kinetic energy and half the temperature variance equations <em>(budgets</em>)</li> <li>contain values for model coefficients that can be used for calculating second order statistics <em>(lambda_beta_coeffs)</em></li> </ul> <p><strong>Simulations</strong>:</p> <ul> <li>cooling rate at the surface 0.25 Kelvin per hour <em>(cr025)</em></li> <li>cooling rate at the surface 0.375 Kelvin per hour <em>(cr0375)</em></li> <li>cooling rate at the surface 0.5 Kelvin per hour (<em>cr05)</em></li> <li>cooling rate at the surface 1.0 Kelvin per hour <em>(cr1)</em></li> </ul> <p><strong>Note</strong>: The results presented in the repository are taken after the ninth hour of the simulation while the results in the published paper is averaged between the eight and ninth hour. This difference should be negligible.</p>
Ultrasensitive ctDNA detection for preoperative disease stratification in early-stage lung adenocarcinoma
<p>Code and data for the MS <strong>"Ultrasensitive ctDNA detection for preoperative disease stratification in early-stage lung adenocarcinoma"</strong></p>
DATASET Invertebrate sounds from photic to mesophotic coral reefs reveal vertical stratification and diel diversity
<p>This dataset contains 17 wave folders. The original files were used for the study published by Raick et al. (2024) in Oecologia (10.1007/s00442-024-05572-5), while subsampled versions of these files were used for the studies published by Raick et al. (2023) in Coral Reefs (10.1007/s00338-022-02343-7) and Raick et al. (2023) in Scientia Marina (10.3989/scimar.05395.078).</p>
High-wind events on the Southern New England continental shelf (2015-2022), their impact on shelf stratification, and corresponding high-wind event category: Dataset and Code
<p>Dataset of identified high-wind events on the Southern New England continental shelf (2015-2022), their impact on shelf stratification, and corresponding high-wind event category, as well as the associated code to reproduce the figures of accompanying publication. The data have been recorded by the Ocean Observatories Initiative (OOI) Coastal Pioneer New England Shelf Array. </p><p><i>Accompanying publication:</i> Taenzer, L.L., Gawarkiewicz, G., and Plueddemann, A. (2023). Categorization of High-Wind Events and Their Contribution to the Seasonal Breakdown of Stratification on the Southern New England Shelf. Journal of Geophysical Research: Oceans, 128, e2022JC019625. https://doi.org/10.1029/2022JC019625</p><p><i>Contact:</i> Lukas Taenzer (lukas.taenzer@whoi.edu)</p><p><strong>Structure of provided code:</strong></p><ul><li>PART A: Local high-wind ocean impact analysis</li><li>PART B: Analysis of seasonal high-wind impacts on stratification</li><li>PART C: High-wind event categorization and the impact of different categories</li></ul><p>Code has been written in MATLAB R2023a.</p><p><strong>Output:</strong></p><ul><li>Processed data of all locally detected high-wind events incl. scalar forcing and shelf impact estimates as well as their corresponding high-wind event category:<ul><li>'OOIcp_HighWindEvents_ScalarMetrics.nc' (see userflag 'save_peak_ooi')</li><li>See README_HighWindEvents_ScalarMetrics for further details and license.</li></ul></li><li>Figures 2, 3, 4, 5, 6, 7, 8, and 9 of accompanying publication<ul><li>saved as .png file (always)</li><li>saves as .eps file (see userflag 'save_fig_eps')</li></ul></li></ul><p><strong>Input for Analysis:</strong></p><ul><li>Gridded Hydrography and Bulk Air-Sea interactions time series observed by the Ocean Observatories Initiative (OOI) Coastal Pioneer New England Shelf Mooring Array (2015-2022) (Taenzer et al., 2023). The required fields to reproduce the results of the accompanying publication are provided:<ul><li>Input/OOIcp_Met_Combined.nc</li><li>Input/OOIcp_CTD_ISSM_stat.nc</li><li>Input/OOIcp_CTD_PMUI_prof.nc</li></ul></li><li>High-wind event categorization based on their spatio-temporal sea level pressure and temporal surface wind stress signatures around/at the OOI Coastal Pioneer Array location:<ul><li>Input/storm_type_2015-2021_v5.mat</li></ul></li></ul><p><strong>Additional input for reproducing figures:</strong></p><ul><li>Manually determined cyclone tracks for cyclones that occur during the fall destratification seasons 2015-2021:<ul><li>Input/stormtracks_cyclones_20152021_save.mat</li></ul></li><li>ERA5 sea level pressure data (Hersbach et al., 2018) on a 6-hour temporal and a 1°x1° spatial resolution for the time period 2015-01-01 to 2022-06-30 and across the Eastern US, Canada, and the Northwest Atlantic with the OOI Coastal Pioneer Array in the center<ul><li>Input/ERA5_6h_2015-2022_region_1x1.mat</li></ul></li></ul>
Lung ultrasonography features and risk stratification in 80 patients with COVID-19: a prospective observational cohort study
<p><strong>Background</strong></p> <p>Point-of-care lung ultrasound (LUS) is a promising and pragmatic risk stratification tool in COVID-19. This study describes and compares early LUS characteristics across of range of clinical outcomes.</p> <p><strong>Method</strong></p> <p>Prospective observational study of PCR-confirmed COVID-19 patients in the emergency department (ED) of Lausanne University Hospital. A trained physician recorded LUS images using a standardized protocol. Two experts retrospectively reviewed images blinded to patient outcome. We describe and compare early LUS findings (acquired within 24hours of presentation at the ED) between patient groups based on their outcome at 7-days after inclusion: 1) self-resolving outpatients, 2) hospitalised and 3) intubated/death. The LUS score was used to discriminate between groups.</p> <p><strong>Findings</strong></p> <p>Between March 6 and April 3 2020, we included 80 patients (18 outpatients, 41 hospitalized and 21 intubated/dead). 73 patients (91%) had abnormal LUS (72% outpatients, 95% hospitalised and 100% intubated/death; p=0.004). The proportion of involved zones was lower in outpatients compared with other groups (median 30% [IQR 0-40%], 44% [33-70%] and 70% [50-88%], p<0.001). Predominant abnormal patterns were bilateral and multifocal spread thickening of the pleura with pleural line irregularities (77%), confluent B lines (66%) and pathologic B lines (55%). Posterior inferior zones were more often affected. Median LUS score had a good level of discrimination between outpatients and others with area under the ROC of 0.80 (95% CI 0.66-0.95).</p> <p><strong>Interpretation</strong></p> <p>Systematic LUS is a reliable, cheap and easy-to-use triage tool for the early stratification of risk in COVID-19 patients presenting at emergency departments.</p> <p><strong>Funding</strong></p> <p>Leenaards Foundation</p>
phenology data of lake mixing, and stratification based on the CESM2-LE output
<p>The phenology data of lake mixing, and stratification calculated from the daily output of CESM2 large ensemble. For more information about this dataset, please refer to the manuscript entitled 'Projected changes in the phenology of stratification and overturning in ice-covered lakes of the Northern Hemisphere (Lei Huang et al)'. For more information about CESM2 large ensemble, please refer to https://www.cesm.ucar.edu/community-projects/lens2. </p>
Fig. 9 Morphometric relationship between a in Eurythenes atacamensis sp. nov. (Crustacea: Amphipoda) exhibits ontogenetic vertical stratification across abyssal and hadal depths in the Atacama Trench, eastern South Pacific Ocean
Fig. 9 Morphometric relationship between a total body length and weight and b coxa 4 diagonal length and total body length. Bathymetric relationship of total body length for c juvenile and d female Eurythenes atacamensis sp. nov. Grey areas in b and c represent 95% confidence intervals of the model mean
Fig. 7 in Eurythenes atacamensis sp. nov. (Crustacea: Amphipoda) exhibits ontogenetic vertical stratification across abyssal and hadal depths in the Atacama Trench, eastern South Pacific Ocean
Fig. 7 Bayesian phylogenies showing the relationship of Eurythenes atacamensis sp. nov. within Eurythenes based on a 16S rRNA and b COI. Specimens added by this study are in bold, with E. atacamensis sp. nov. in blue. An asterisk next to the name denotes holotype. References for comparative sequences are in Table 2. Branch nodes have Bayesian posterior probabilities and maximum likelihood bootstrap support values. Values less than 0.7 or 70 are not stated or depicted by an asterisk. Species delimitation inferences by the bPTP and/or GYMC analyses are shown on the right side of each phylogeny.
Fig. 8 in Eurythenes atacamensis sp. nov. (Crustacea: Amphipoda) exhibits ontogenetic vertical stratification across abyssal and hadal depths in the Atacama Trench, eastern South Pacific Ocean
Fig. 8 The relative proportion of females, males, juveniles, and intersex of Eurythenes atacamensis sp. nov. by depth (m) at the Atacama Trench
Fig. 6 a in Eurythenes atacamensis sp. nov. (Crustacea: Amphipoda) exhibits ontogenetic vertical stratification across abyssal and hadal depths in the Atacama Trench, eastern South Pacific Ocean
Fig. 6 a Eurythenes atacamensis sp. nov. feeding on bait and b two colour morphs prior to ethanol preservation. Still image and specimens are from 8074 m in the Atacama Trench during the 2010 RV Sonne SO209 Expedition (see Eustace et al. (2016) for site location details)
Fig. 5 in Eurythenes atacamensis sp. nov. (Crustacea: Amphipoda) exhibits ontogenetic vertical stratification across abyssal and hadal depths in the Atacama Trench, eastern South Pacific Ocean
Fig. 5 Eurythenes atacamensis sp. nov. holotype (MNHNCL AMP-15816). a left pereopod 5; b left pereopod 6; c left pereopod 7; d epimeron and epimeron 3 insert with arrow denoting small tooth on the posteroventral corner; e left uropod 1; f left uropod 2; g left uropod 3 with the arrow showing plumose setae; h telson; i telson distal margin insert
Fig. 3 in Eurythenes atacamensis sp. nov. (Crustacea: Amphipoda) exhibits ontogenetic vertical stratification across abyssal and hadal depths in the Atacama Trench, eastern South Pacific Ocean
Fig. 3 Eurythenes atacamensis sp. nov. holotype (MNHNCL AMP-15816). a left antenna 1; b left antenna 2; c left mandible with an arrow to highlight the broad palp; d head with arrows to highlight the anterior lobe and ventral corner of the eye; e left maxilla 1 outer plate and palp not flattened; f left maxilla 1 inner plate; g left maxilla 1 palp insert; h left maxilla 1 outer plate face; i left maxilla 2; j left and right maxillipeds with inner plates removed; k left maxilliped dactylus insert; l left maxilliped inner plate (medio-facial spines not shown)
Fig. 4 in Eurythenes atacamensis sp. nov. (Crustacea: Amphipoda) exhibits ontogenetic vertical stratification across abyssal and hadal depths in the Atacama Trench, eastern South Pacific Ocean
Fig. 4 Eurythenes atacamensis sp. nov. holotype (MNHNCL AMP-15816). a left gnathopod 1; b chela of left gnathopod 1; c left gnathopod 2; d chela of left gnathopod 2; e left pereopod 3; f left pereopod 4
Fig. 2 a in Eurythenes atacamensis sp. nov. (Crustacea: Amphipoda) exhibits ontogenetic vertical stratification across abyssal and hadal depths in the Atacama Trench, eastern South Pacific Ocean
Fig. 2 a Eurythenes atacamensis sp. nov.: female holotype from 8052 m (h; MNHNCL AMP-15816), juvenile paratype from 6714 m (pj; MNHNCL AMP-15818), intersex paratype from 7834m (pi; MNHNCL AMP-15820), male paratype from 7204 m (pm; MNHNCL AMP-15817); b Eurythenes atacamensis sp. nov., mature female, holotype, MNHNCL AMP-15816
Fig. 1 a in Eurythenes atacamensis sp. nov. (Crustacea: Amphipoda) exhibits ontogenetic vertical stratification across abyssal and hadal depths in the Atacama Trench, eastern South Pacific Ocean
Fig. 1 a Map of the Peru-Chile Trench defined by depths>4900 m (red). Historical collection records of this species (circle), and the historical abyssal sampling with the absence of Eurythenes atacamensis sp. nov. (triangle). The extent of map (b) is indicated by the blue box. b The eleven deployments where E. atacamensis sp. nov. was recovered in the Atacama Trench during the Atacamex Expedition (square) and the RV Sonne SO216 Expedition (circle). Isobaths are shown every 1000 m between 3000- and 7000-m-depth contours.
Gulf Stream Daily Temperature, Salinity and Mixed Layer Depth fields from Ocean Stratification network (OSnet).
<p>The OSnet Gulf Stream product consists of 4D daily Temperature, Salinity and Mixed Layer Depth, available on a 1/4 degree regular grid and on 51 depth levels from the surface down to 1000m, in the Gulf Stream region from 01-01-1993 to 31-12-2019.<br> We introduce OSnet (Ocean Stratification network) in the Gulf Stream region, a new ocean reconstruction system aimed at providing a physically consistent analysis of the upper ocean stratification. The interpolation scheme is a bootstrapped multilayer perceptron trained to predict simultaneously temperature and salinity (T-S) profiles down to 1000m and the Mixed Layer Depth (MLD) from satellite data covering 1993 to 2019. The inputs are sea surface temperature and sea level anomaly, complemented with mean dynamic topography, bathymetry, longitude, latitude and the day of the year. The in-situ profiles are from the CORA database and include Argo floats and ship-based profiles. The prediction of the MLD is used to adjust a posteriori the vertical gradients of predicted T-S profiles, thus increasing the accuracy of the solution and removing vertical density inversions. The prediction is generalized on a 1/4 degree daily grid, producing four-dimensional fields of temperature, salinity and mixed layer depth, with their associated confidence interval issued from the bootstrap.</p> <p>The full dataset is downloadable with the <a href="https://github.com/dvolgyes/zenodo_get">zenodo_get</a> tool and the command :<code> zenodo_get 6011144</code></p>
Dataset Methods for stratification and validation cohorts: a scoping review
<p>We searched PubMed, EMBASE and the Cochrane Library for reviews that described the tools and methods applied to define cohorts used for patient stratification or validation of patient clustering. We focused on cancer, stroke, and Alzheimer’s disease (AD) and limited the searches to reports in English, French, German, Italian and Spanish, published from 2005 to April 2020. Two authors screened the records, and one extracted the key information from each included review. The result of the screening process was reported through a PRISMA flowchart.</p>
Edge effects and vertical stratification of aerial insectivorous bats across the interface of primary-secondary Amazonian rainforest
<p><span>Edge effects - abiotic and biotic changes associated with habitat boundaries - are key drivers of community change in fragmented landscapes. Their influence is heavily modulated by matrix composition. With over half of the world's tropical forests predicted to become forest edge by the end of the </span><span>century, it is paramount that conservationists gain a better understanding of how tropical biota is impacted by edge gradients. Bats comprise a large fraction of tropical mammalian fauna and are demonstrably sensitive to habitat modification. Yet, </span><span>knowledge about how bat assemblages are affected by edge effects remains scarce</span><span>. Capitalizing on a whole-ecosystem manipulation in the Central Amazon, the aims of this study were to i) assess the consequences of edge effects for twelve aerial insectivorous bat species across the interface of primary and secondary forest and ii) investigate if the activity levels of these species differed between the understory and canopy and if they were modulated by distance from the edge</span><span>. Acoustic surveys were conducted along four 2-km transects each traversing equal parts of primary and ca. 30-year-old secondary forest. Five models were used to assess the changes in the relative activity of forest specialists (three species), flexible forest foragers (three species), and edge foragers (six species). Modelling results revealed no evidence of edge effects, except for forest specialists in the understory. No significant differences in activity were found between the secondary or primary forest but most species exhibited pronounced vertical stratification. Our study highlights that forest specialist bats are more edge-sensitive than both flexible forest and edge foraging bats and suggests that the influence of edge effects on aerial insectivorous bats may exceed 2 km. The absence of pronounced edge effects and the comparable activity levels between primary and old secondary forests indicates that old secondary forest can help ameliorate the consequences of fragmentation on tropical aerial insectivorous bats. </span></p>
Correcting for population stratification reduces false positive and false negative results in joint analyses of host and pathogen genomes [G2G-Simulator: Simulated dataset]
<p>Data associated with the paper 'Correcting for population stratification reduces false positive and false negative results in joint analyses of host and pathogen genomes'.</p> <p>It contains the raw simulated data from the 'G2G-Simulator' program. </p> <p>Those data need to be loaded in a R environment .</p> <p>You can reproduce plots present in the paper by parsing the R object using the script 'parse_paper_data.R' present in the G2G-Simulator GitHub repository (https://github.com/onaret/G2G-Simulator/paper/parse_paper_dataset.R). </p>
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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.