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85 results for “Functional Enrichment”
Mammary single-cell RNA-seq analysis and prostate cancer survival as a function of H2AFJ expression for the paper entitled: The histone variant H2A.J is enriched in luminal epithelial cells
<p>H2A.J is a poorly studied mammalian-specific variant of histone H2A. We used immunohistochemistry to study its localization in various human and mouse tissues. H2A.J showed cell-type specific expression with a striking enrichment in luminal epithelial cells of multiple glands including those of breast, prostate, pancreas, thyroid, stomach, and salivary glands. H2A.J was also highly expressed in many carcinoma cell lines and in particular, those derived from luminal breast and prostate cancer. H2A.J thus appears to be a novel marker for luminal epithelial cancers. Knocking-out the H2AFJ gene in T47D luminal breast cancer cells reduced the expression of several estrogen-responsive genes which may explain its putative tumorigenic role in luminal-B breast cancer.</p>
Example Datasets for Functional Enrichment Analysis
<p>This dataset contains a set of example data for a functional enrichment tutorial.</p>
Data and code from: Species interactions amplify functional group responses to elevated CO2 and N enrichment in a 24-year grassland experiment
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Plant and soil organic matter responses to ten years of nutrient enrichment in the Nutrient Network:Nutrient Network. A cross-site investigation of bottom-up control over herbaceous plant community dynamics and ecosystem function
This experiment is one implementation of a globally distributed experiment, known as the Nutrient Network. At Cedar Creek, as in over 70 other sites in grasslands around the world, the experiment aims to describe impacts of increased nutrients (nitrogen, phosphorus, potassium, sulfur and other metals) and decreased herbivory (removal of mammals by fencing). Two overarching questions are being explored with these manipulations: 1. To what extent are plant production and diversity co-limited by multiple nutrients in herbaceous-dominated communities? 2. Under what conditions do grazers or fertilization control plant biomass, diversity, and composition? By utilizing identical protocols at diverse grassland sites around the world, NutNet aims to uncover both the generalities in ecosystem functioning, and the contingencies or differences which can obscure those common mechanisms. In addition to the standard NutNet protocol, e247 includes an additional low Nitrogen gradient (1 gram Nitrogen per meter squared per year and 5 grams Nitrogen per meter squared per year in addition to the standard 10 grams Nitrogen per meter squared per year).
Probabilistic inference of the genetic architecture of functional enrichment of complex traits
<p>We develop a Bayesian model (BayesRR-RC) that provides robust SNP-heritability estimation, an alternative to marker discovery, and accurate genomic prediction, taking 22 seconds per iteration to estimate 8.4 million SNP-effects and 78 SNP-heritability parameters in the UK Biobank. We find that only $\leq$ 10\% of the genetic variation captured for height, body mass index, cardiovascular disease, and type 2 diabetes is attributable to proximal regulatory regions within 10kb upstream of genes, while 12-25% is attributed to coding regions, 32-44% to introns, and 22-28% to distal 10-500kb upstream regions. Up to 24% of all cis and coding regions of each chromosome are associated with each trait, with over 3,100 independent exonic and intronic regions and over 5,400 independent regulatory regions having >95% probability of contributing >0.001% to the genetic variance of these four traits. Our open-source software (GMRM) provides a scalable alternative to current approaches for biobank data.</p>
Functional traits explain the consistent resistance of biodiversity to plant invasion under nitrogen enrichment
<p>Elton's biotic resistance hypothesis, which posits that diverse communities should be more resistant to biological invasions, has received considerable experimental support. However, it remains unclear whether such a negative diversity–invasibility relationship would persist under anthropogenic environmental change. By using the common ragweed (Ambrosia artemisiifolia) as a model invader, our four-year grassland experiment demonstrated consistently negative relationships between resident species diversity and community invasibility, irrespective of nitrogen addition, a result further supported by a meta-analysis. Importantly, our experiment showed that plant diversity consistently resisted invasion simultaneously through increased resident biomass, increased trait dissimilarity among residents, and increased community weighted means of resource-conservative traits that strongly resist invasion, pointing to the importance of both trait complementarity and sampling effects for invasion resistance even under resource enrichment. Our study provides unique evidence that considering species functional traits can help further our understanding of biotic resistance to biological invasions in a changing environment.</p>
Data from: Nitrogen enrichment alters multiple dimensions of grassland functional stability via changing compositional stability
<p>Anthropogenic nutrient enrichment is known to alter the composition and functioning of plant communities. However, how nutrient enrichment influences multiple dimensions of community- and ecosystem-level stability remains poorly understood. Using data from a nitrogen (N) and phosphorus (P) addition experiment in a temperate semi-arid grassland that experienced a natural drought, we show that N enrichment, not P enrichment, decreased grassland functional and compositional temporal stability, resistance, and recovery, but increased functional and compositional resilience. Compositional stability and species asynchrony, rather than species diversity, were identified as key determinants of all dimensions of grassland functional stability, except for recovery. Whereas grassland functional recovery was decoupled from compositional recovery, N enrichment altered other dimensions of functional stability primarily through changing their corresponding compositional stability dimensions. Our findings highlight the need to examine ecological stability at the community level for a more mechanistic understanding of ecosystem dynamics in the face of environmental change.</p>
Extremely Metal-Poor Stars used in "A Modified Initial Mass Function of the First Stars with Explodability Theory under Different Enrichment Scenarios"
<p>This is the Extremely Metal-Poor stars used in the paper "A Modified Initial Mass Function of the First Stars with Explodability Theory under Different Enrichment Scenarios" by Jiang, Zhao, Li and Xing 2024. Table "EMPs_list.csv" contains the number of available abundance elements, metallicity and reference. References are also listed as related works in this record, by DOI. </p> <p>If you have any questions about this data, please contact jiangrz@bao.ac.cn for further information. </p>
Data from: Nitrogen enrichment alters multiple dimensions of grassland functional stability via changing compositional stability
Open the record for dataset details and reuse information.
Functional traits explain the consistent resistance of biodiversity to plant invasion under nitrogen enrichment
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Nitrogen and phosphorus enrichment differentially affect grassland ecosystem functioning via multi-trophic pathways
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Probabilistic inference of the genetic architecture of functional enrichment of complex traits
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Data from: Warming reduces the effects of enrichment on stability and functioning across levels of organization in an aquatic microbial ecosystem
Warming and nutrient enrichment are major environmental factors shaping ecological dynamics. However, cross-scale investigation of their combined effects by linking theory and experiments is lacking. We collected data from aquatic microbial ecosystems investigating the interactive effects of warming (constant and rising temperatures) and enrichment across levels of organization and contrasted them with community models based on metabolic theory. We found high agreement between our observations and theoretical predictions: we observed in many cases the predicted antagonistic effects of high temperature and high enrichment across levels of organization. Temporal stability of total biomass decreased with warming but did not differ across enrichment levels. Constant and rising temperature treatments with identical mean temperature did not show qualitative differences. Overall, we conclude that model and empirical results are in broad agreement due to robustness of the effects of temperature and enrichment, that the mitigating effects of temperature on effects of enrichment may be common, and that models based on metabolic theory provide qualitatively robust predictions of the combined ecological effects of enrichment and temperature.
The influence of nutrient enrichment on riverine food web function and stability
<p>Nutrient enrichment of rivers and lakes has been increasing rapidly over the past few decades, primarily because of agricultural intensification. Although nutrient enrichment is known to drive excessive algal and microbial growth, which can directly and indirectly change the ecological community composition, the resulting changes in food web emergent properties are poorly understood. We used ecological network analysis (ENA) to examine the emergent properties of 12 riverine food webs across a nutrient enrichment gradient in the Manawatu, New Zealand. We also derive Keystone Sensitivity Indices to explore whether nutrients change the trophic importance of species in a way that alters the resilience of the communities to further nutrient enrichment or floods. Nutrient enrichment resulted in communities composed of energy inefficient species with high community (excluding microbes) respiration. Community respiration was several times greater in enriched communities and this may drive hypoxic conditions even without concomitant changes in microbial respiration. Enriched communities exhibited weaker trophic cascades, which may yield greater robustness to energy flow loss. Interestingly, enriched communities were also more structurally and functionally affected by species sensitive to flow disturbance making these communities more vulnerable to floods. </p>
Trajectories and thresholds of multi-diversities and multi-functions in response to nitrogen enrichment
<p><span>An ecosystem is composed by multiple biota across several trophic levels, which interactively perform multiple ecosystem functions. </span><span>Anthropogenic reactive nitrogen</span><span> is expected to alter these ecosystem attributes including biota diversities and ecosystem functions. </span><span>Here, </span><span>we find that five biota diversities differ substantially in response trajectory and threshold with increasing nitrogen amount, and so do the four examined functions. </span><span>Our study provides a vivid picture of how multi-biota diversities and multiple functions concurrently respond to nitrogen enrichment and suggests that the attribute-specific response trajectories and thresholds should be taken into account in models predicting ecosystem feedbacks to nitrogen deposition.</span></p>
Example Datasets for Functional Enrichment Analysis
<p>This dataset contains a set of example data for a functional enrichment tutorial.</p>
Beetroot Enriched Bread, Blood Pressure and Vascular Function
ClinicalTrials.gov study NCT01706718. IPD Sharing: Not stated. Countries: 1. Publications: 2.
Impact of Pulse-enriched Foods on Cognitive Function and Cardiometabolic Health in Obese Adults
ClinicalTrials.gov study NCT01495832. IPD Sharing: Not stated. Countries: 2. Publications: 41.
Erinacine A-enriched Hericium Erinaceus Mycelia for Improvement of Recognition, Vision, and Functional MRI Alterations
ClinicalTrials.gov study NCT04065061. IPD Sharing: NO. Countries: 1. Publications: 1.
Probiotic-enriched Artichoke in Functional Constipation
ClinicalTrials.gov study NCT01212146. IPD Sharing: Not stated. Countries: 1. Publications: 4.
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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.