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579 results for “Stratification”
STRATIFICATION EFFECTS ON FLOW HYDRODYNAMICS AND MIXING AT A CONFLUENCE WITH A HIGHLY DISCORDANT BED AND A RELATIVELY LOW VELOCITY RATIO
<p>The effects of temperature induced stratification on flow hydrodynamics, thermal mixing and the capacity of the flow to entrain sediment at a medium-size stream confluence with a highly discordant bed are investigated. To isolate the effects due to differences in the temperature/density of the incoming streams, two simulations were conducted with identical flow conditions (mean velocity ratio VR=2.44, temperature difference between the two streams ΔT=4.7<sup>0 </sup>C). In the first case the Richardson number was Ri=0 (no coupling between the temperature and the momentum equations via the Boussinesq approximation), while in the second simulation Ri=0.67. Even in the Ri=0 case the structure of the mixing interface (MI) was different from the one expected for concordant bed confluences with a similar confluence angle and VR. The MI contained only co-rotating eddies shed in the shear layer forming on the fast speed side of the confluence apex. In the Ri = 0.67 case no wake region was present but a large recirculation eddy formed not far from the confluence apex. In both cases, the flow near the upstream part of the MI was found to be highly 3D and to allow the passage of particles from one side of the confluence to the other. While in the Ri = 0 case mixing was driven by the MI eddies, in the Ri = 0.67 case mixing was controlled by large near-bed intrusions of heavier fluid from the tributary containing colder water and also by the fluid advected in and out of the recirculation eddy.</p>
Figures 1–2 in Vertical stratification of Sphingidae moths (Lepidoptera: Bombycoidea: Sphingidae) in the Tapajós National Forest, Pará, Brazil
Figures 1–2. Map of the location of the sampling unit (red circle): (1) Tapajós National Forest, western Pará (Google Earth satellite image); (2) LBA platform tower located at Forest National Tapajós. Photo: Genilson Rego, 2009.
Figure 6 in Vertical stratification of Sphingidae moths (Lepidoptera: Bombycoidea: Sphingidae) in the Tapajós National Forest, Pará, Brazil
Figure 6. Rarefaction curves of the observed species richness of Sphingidae based on the number of specimens, collected with light traps, in the three strata canopy (C), midstory (M) and understory (U), in the Forest National Tapajós, Pará, Brazil, from May 2019 to February 2020.
Figure 5 in Vertical stratification of Sphingidae moths (Lepidoptera: Bombycoidea: Sphingidae) in the Tapajós National Forest, Pará, Brazil
Figure 5. Species diversity profiles in the Rényi series samples in the three strata canopy, midstor and understory, in the Forest National Tapajós, Pará, Brazil, from May 2019 to February 2020.
Figures 3–4 in Vertical stratification of Sphingidae moths (Lepidoptera: Bombycoidea: Sphingidae) in the Tapajós National Forest, Pará, Brazil
Figures 3–4. Faunal composition of Sphingidae from canopy (C), midstory (M) and understory (U) samples of the Forest National Tapajós, Pará, Brazil, from May 2019 to February 2020. Analyzes were based on (3) abundance and (4) richness.
Figure 7 in Vertical stratification of Sphingidae moths (Lepidoptera: Bombycoidea: Sphingidae) in the Tapajós National Forest, Pará, Brazil
Figure 7. Non-metric Multidimensional Scaling analysis (NMDS) based on the Bray-Curtis index for Sphingidae species collected with a light trap in Forest National Tapajós, Pará, Brazil, from May 2019 to February 2020. Canopy (green dots), midstory (orange dots) and understory (blue dots).
Depth-dependent anisotropy in the Earth's inner core linked to chemical stratification
Open the record for dataset details and reuse information.
Dataset for "Influence of thermal stratification on the structure and1evolution of the Martian core"
<p>Dataset from Monte-Carlo simulations produced in "Influence of thermal stratification on the structure and1evolution of the Martian core"</p>
Dataset: Impact of salinization on lake stratification and spring mixing v1.0 L&O Letters
<p>Scripts, model configurations and outputs to process the data and recreate the figures from Ladwig, R., Rock, L.A, Dugan, H.A. (-): Impact of salinization on lake stratification and spring mixing. This repository includes the setup and output from the lake model ensemble (GLM, GOTM, Simstrat) ran on the lakes Mendota and Monona. Scripts to run the models are located under /numerical and the scripts to process the results for the discussion of the paper are in the top main repository. The scripts to derive the theoretical solution are located under /analytical. Buoy monitoring data are located under /fieldmonitoring. The final figures are located under /figs_HD.</p>
Data for: Stratification and recovery time jointly shape ant functional re-assembly in a Neotropical forest
<p>Microhabitat differentiation of species communities such as vertical stratification in tropical forests contributes to species coexistence and thus biodiversity. However, little is known about how the extent of stratification changes during forest recovery and influences community reassembly. Environmental filtering determines community reassembly in time (succession) and in space (stratification), hence functional and phylogenetic composition of species communities are highly dynamic. It is poorly understood if and how these two concurrent filters – forest recovery and stratification – interact.</p> <p>In a tropical forest chronosequence in Ecuador spanning 34 years of natural recovery, we investigated the recovery trajectory of ant communities in three overlapping strata (ground, leaf litter, lower tree trunk) by quantifying 13 traits, as well as the functional and phylogenetic diversity of the ants. We expected that functional and phylogenetic diversity increase with recovery time and that each ant community within each stratum shows a distinct functional reassembly. We predicted that traits related to ant diet show divergent trajectories reflecting an increase in niche differentiation with recovery time. On the other hand, traits related to the abiotic environment were predicted to show convergent trajectories due to a more similar microclimate across strata with increasing recovery age.</p> <p>Most of the functional traits and the phylogenetic diversity of the ants were clearly stratified, confirming previous findings. However, neither functional nor phylogenetic diversity increased with recovery time. Community-weighted trait means had complex relationships to recovery time and the majority were shaped by a statistical interaction between recovery time and stratum, confirming our expectations. However, most trait trajectories converged among strata with increasing recovery time regardless of whether they were related to ant diet or environmental conditions.</p> <p>We confirm the hypothesized interaction among environmental filters during the functional reassembly in tropical forests. Communities in individual strata respond differently to recovery, and possible filter mechanisms likely arise from both abiotic (e.g., microclimate) and biotic (e.g., diet) conditions. Since vertical stratification is prevalent across animal and plant taxa, our results highlight the importance of stratum-specific analysis in dynamic ecosystems and may generalize beyond ants.</p>
Edge effects and vertical stratification of aerial insectivorous bats across the interface of primary-secondary Amazonian rainforest
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Data from: Urbanization strengthens vertical stratification of ant nutrient preferences in a temperate forest ecosystem
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Data for: Stratification and recovery time jointly shape ant functional re-assembly in a Neotropical forest
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Thermal stratification and fish thermal preference explain vertical eDNA distributions in lakes
<p>Significant advances have been made towards surveying animal and plant communities using DNA isolated from environmental samples. Despite rapid progress, we lack a comprehensive understanding of the "ecology" of environmental DNA (eDNA), particularly its temporal and spatial distribution and how this is shaped by abiotic and biotic processes. Here, we tested how seasonal variation in thermal stratification and animal habitat preferences influence the distribution of eDNA in lakes. We sampled eDNA depth profiles of five dimictic lakes during both summer stratification and autumn turnover, each containing warm- and cool-water fishes as well as the cold-water stenotherm, lake trout (<i>Salvelinus namaycush</i>). Habitat use by <i>S. namaycush</i> was validated by acoustic telemetry and was significantly related to eDNA distribution during stratification. Fish eDNA became "stratified" into layers during summer months, reflecting lake stratification and the thermal niches of the species. During summer months, <i>S. namaycush</i>, which rarely ventured into shallow waters, could only be detected at the deepest layers of the lakes, whereas the eDNA of warm-water fishes was much more abundant above the thermocline. By contrast, during autumn lake turnover, the fish species assemblage as detected by eDNA was homogenous throughout the water column. These findings contribute to our overall understanding of the "ecology" of eDNA within lake ecosystems, illustrating how the strong interaction between seasonal thermal structure in lakes and thermal niches of species on very localised spatial scales influences our ability to detect species.</p>
Genome-wide association results from: Transcriptomic stratification of late-onset Alzheimer's cases reveals novel genetic modifiers of disease pathology
<p>Late-Onset Alzheimer's disease (LOAD) is a common, complex genetic disorder well-known for its heterogeneous pathology. The genetic heterogeneity underlying common, complex diseases poses a major challenge for targeted therapies and the identification of novel disease-associated variants. Case-control approaches are often limited to examining a specific outcome in a group of heterogenous patients with different clinical characteristics. Here, we developed a novel approach to define relevant transcriptomic endophenotypes and stratify decedents based on molecular profiles in three independent human LOAD cohorts. By integrating post-mortem brain gene co-expression data from 2114 human samples with LOAD, we developed a novel quantitative, composite phenotype that can better account for the heterogeneity in genetic architecture underlying the disease. We used iterative weighted gene co-expression network analysis (WGCNA) to reduce data dimensionality and to isolate gene sets that are highly co-expressed within disease subtypes and represent specific molecular pathways. We then performed single variant association testing using whole genome-sequencing data for the novel composite phenotype in order to identify genetic loci that contribute to disease heterogeneity. Distinct LOAD subtypes were identified for all three study cohorts (two in ROSMAP, three in Mayo Clinic, and two in Mount Sinai Brain Bank). Single variant association analysis identified a genome-wide significant variant in <i>TMEM106B</i> (p-value < 5´10<sup>-8</sup>, rs1990620<sup><span><span>G</span></span></sup>) in the ROSMAP cohort that confers protection from the inflammatory LOAD subtype. Taken together,<b> </b>our novel approach can be used to stratify LOAD into distinct molecular subtypes based on affected disease pathways.</p>
Vertical Stratification of Peat Pore Water Dissolved Organic Matter composition in a peat bog in Northern Minnesota
<p>Currently peatlands represent a sink for carbon dioxide and source of atmospheric methane. It is unclear the impact that climate change will have on these systems. As such, a large-scale ecosystem manipulation (Spruce and Peatland Responses under Climatic and Environmental Change, SPRUCE) has been implemented at a peat bog (S1 bog) at the Marcel Experimental Forest (MEF), Minnesota, USA, to determine the effects of climatic forcing on ecosystem processes in northern peatlands. In this study, we aimed to: (i) identify peat pore water dissolved organic matter (DOM) composition as a function of depth before the initiation of the manipulation experiment and (ii) contribute to the knowledge of DOM chemistry and decomposition processes at the S1 bog. We found strong vertical resolution in DOM molecular composition and optical properties within the peat column at the S1 bog. Surface samples were dominated by inputs from surface vegetation. The mid-depth, 30-75cm was an area of high reactivity and increased microbial activity with diagenetic formation of many unique compounds such as polycyclic aromatic compounds (PAC) that contain both nitrogen and sulfur heteroatoms. These compounds were previously observed in coal-derived products and were assumed to be responsible for coal’s biological activity. Biological processes taking place at the intermediate depth zone of the peat profile at the S1 bog are assumed to be responsible for the formation of these heteroatomic PAC in our system. Conversely, these compounds might stem from black carbon and nitrogen from potential fires that occurred at the site in the past. Surface and deep DOM exhibited more similar characteristics suggesting the possibility of lateral and vertical advection of pore water from the surface to the deeper horizons. Our results highlight the importance of understanding processes that control DOM production and transformation with depth.</p> <p>Included: FTICR MS data and optical properties data</p>
Data accompanying the paper "Regime-dependent turbulence length scale formulation for NWP models based on turbulence kinetic energy, shear and stratification", submitted to Monthly Weather Review
<p>This repository contains the outputs of MicroHH LES (van Heerwaarden et al., 2017) and ALADIN-CZ single-column model simulations of four idealized cases:</p> <p>1) The continental cumulus case utilizing measurements from the Atmospheric Radiation Measurement (ARM) program, and Cloud and Radiation Testbed (CART) site in Oklahoma (Brown et al. 2002; Lenderink et al. 2004)</p> <p>2) The trade wind cumulus case from the Barbados Oceanographic and Meteorological Experiment (BOMEX; Siebesma et al. 2003)</p> <p>3) A drizzling stratocumulus case based on the first research flight data of the second period of the Dynamics and Chemistry of Marine Stratocumulus (DYCOMS-II) campaign (Stevens et al., 2005)</p> <p>4) A stable planetary boundary layer case based on the Global Energy and Water Cycle Experiment (GEWEX) Atmospheric Boundary Layer Study (GABLS1) data (Beare et al. 2006; Cuxart et al. 2006; Holtslag 2006)</p> <p>The MicroHH LES outputs are taken from Reilley et al. (2022) study and can be also found at https://doi.org/10.5281/zenodo.6372434. Additionally, we provide case study outputs from the ALADIN-CZ 3D NWP model, wherein the fields roughly match those verified/shown in Fig. 9.</p> <p> </p> <p>The files are organized in the following way:</p> <p>1) MicroHH LES model configuration files (.ini) and output files (NetCDF format) are stored in the file "LES.zip" within "conf" and "data" folders, respectivelly. Additionally, a sample script to plot LES-derived Turbulence Length Scales (TLS) and those based on NWP formulations (using LES data as input) is provided (plot.py).</p> <p>2) The vertical profiles of (i) conserved variables and (ii) turbulent fluxes from the ALADIN-CZ single-column model for four idealized cases are provided in the file "single-column_simulations.zip", consisted of individual ASCII files (per case and TLS formulation). A detailed description of its content can be found in the associated README file.</p> <p>3) Chosen surface and upper-air fields for (i) 23 November 2019 inversion and (ii) 24 June 2022 mesoscale convection system cases are provided in the file "case_studies.zip" and consisted of individual GRIB files per field and prognostic hour. A detailed description of its content can be found in the associated README file.</p> <p> </p> <p> </p>
A potential patient stratification biomarker for Parkinson´s disease based on LRRK2 kinase-mediated centrosomal alterations in peripheral blood-derived cells
<p>Annotated WES VCF file and phenotype file used in Gene burden analysis of Naaldijk et al., "A potential patient stratification biomarker for Parkinson´s disease based on LRRK2 kinase-mediated centrosomal alterations in peripheral blood-derived cells", 2023. </p><p> </p>
Vertical stratification of leaf physical traits exerts bottom-up pressures on insect herbivory in a sugar maple temperate forest
<p>Do vertical gradients in temperate forest structure insect herbivore communities? We tested the hypothesis that the increase in light intensity from understory to forest canopy level drives differences in leaf physical traits and budburst phenology that impact insect herbivores and thus play a role in structuring both herbivore communities and the leaf damages they cause. Twelve sugar maple <em>(Acer saccharum)</em> sites were monitored in southern Quebec, examining insect herbivore patterns from understory to the shaded and sun canopy over the summers of 2020, 2021, and 2022. Additionally, we recorded leaf physical traits, temperature, humidity, and sun exposure. Our findings revealed that leaf thickness increased along the vertical gradient in 2021, making leaves less favorable to herbivores in the canopy level. Accordingly, we recorded a consistent decrease in insect herbivory damage rates from the understory to the shaded canopy and sun canopy in 2020 and 2021, driven by leaf cutters, skeletonizers, stipplers, and leaf miners. These results support our hypothesis that variation in plant physical traits due to sun exposure contributes to the vertical stratification of insect damage. In 2022, the gradient of insect herbivore abundance corroborated the observed damage trends from the previous years. Moreover, we calculated an average annual herbivory rate of 9.1% of the leaf surface in our study site, suggesting limited evidence supporting a significant contribution of background herbivory to the decline of sugar maple forests. Overall, our study highlights the importance of vertical gradients in structuring insect herbivore communities and emphasizes the role of leaf traits in mediating these interactions.</p>
Splicing-Aware Patient Stratification Using Different Biclustering Methods
<div> <div> <div> <p>Patient stratification refers to the process of categorizing patients into specific groups based on whether they exhibit certain characteristics of a disease. In this research, we investigated the feasibility of splicing-aware measurements for patient stratification in complex diseases like breast cancer and dilated cardiomyopathy.</p> <p>Splicing-aware patient stratification integrates the intricate dynamics of RNA splicing with the stratification of patients in clinical settings. The significance of this approach lies in its potential to revolutionize personalized medicine by offering more precise and effective treatment strategies. To execute our research, we collected datasets at three levels: genomic, transcrip- tomic, and isoform-specific expressions for both breast cancer and dilated cardiomyopathy. We applied network-constrained (BiCoN) and unconstrained (MoSBi) biclustering algorithms to classify individuals into subtypes. Here, we show that working not just with transcripts but with dominant isoforms of transcripts and different measurements can unveil new information. We took the dominant isoform of transcripts by a median of expression into account to examine the splicing effect. Despite various factors, we included in our research, both BiCoN and MoSBi appeared more efficient on the gene level. We observed that different biclustering methods or approaches work differently in both diseases and also on different levels in each disease.</p> <p>With our results, we aim to shed light on the potential applications of alternative splicing analysis for disease subtyping.</p> </div> </div> </div>
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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.