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837 results for “associational effects”
Environmental context and herbivore traits mediate the strength of associational effects in a meta-analysis of crop diversity
<p>1. Crop diversification offers a promising solution to meet expanding global food demands while maintaining ecosystem services. Diversification strategies that employ mixed planting to reduce pest damage (e.g., intercropping), termed "associational effects" (AE) in the ecological literature, can decrease (associational resistance) or increase (associational susceptibility) herbivore abundance on a focal plant. While application of AE to agroecosystems typically reduces pest abundance, the range of outcomes varies widely.</p> <p>2. We conducted a meta-analysis using 272 estimates of insect herbivore abundance on crops neighbored by a conspecific or heterospecific from 44 studies undertaken on six continents. We focus on four agricultural crops well-represented from sites across the globe to test hypotheses related to understanding how herbivore traits (diet breadth, feeding guild, origin), plant traits (crop type, phylogenetic distance to neighbor), and environmental context (climate, experimental design) contribute to variation in the outcomes of associational effects.</p> <p>3. Overall, bicultures provided a strong reduction of insect abundance on the focal crop. Climate and interactions between herbivore traits, particularly diet breadth and origin, and plant traits or environmental context mediated the strength of associational effects.</p> <p>4. Bicultures provided the strongest reductions in insect abundance at low latitudes and this effect decreased at higher latitudes, but only for insects with certain traits. Abundance of generalist herbivores and globally distributed pests tended to be most strongly negatively affected by bicultures, under certain contexts, whereas specialist herbivores and native pests were less affected by neighbors.</p> <p>5. Synthesis and application. This meta-analysis highlights that variability in AE is determined in part by the interactive effects of herbivore traits and environmental context and provides guidance for incorporating beneficial ecological interactions into integrated pest management strategies.</p>
Summary statistics for: Phenome-wide analyses identify an association between the parent-of-origin effects dependent methylome and the rate of aging in humans
<p>Summary statistics of single POE-CpG based and POE-CpG co-methylation module based phenome-wide association analyses for the manuscript "Phenome-wide analyses identify an association between the parent-of-origin effects dependent methylome and the rate of aging in humans"</p>
Datasets and R code associated with: Acute Health Effects of Wildfire Smoke Exposure During a Compound Event: A Case-Crossover Study of the 2016 Great Smoky Mountain Wildfires
<p>The attached code and csv files accompany the manuscript titled: Acute Health Effects of Wildfire Smoke Exposure During a Compound Event: A Case-Crossover Study of the 2016 Great Smoky Mountain Wildfires by Duncan et al. accepted for publication in the journal GeoHealth in September 2023. </p> <p><a href="https://zenodo.org/api/files/8e030710-b091-48a9-aec4-f9b3de6a0325/Project%20wildfire%20data.csv">Project wildfire data.csv</a> contains a subset wildfire data obtained from:</p> <p>Short, Karen C. 2022. Spatial wildfire occurrence data for the United States, 1992-2020 [FPA_FOD_20221014]. 6th Edition. Fort Collins, CO: Forest Service Research Data Archive. https://doi.org/10.2737/RDS-2013-0009.6</p> <p><a href="https://zenodo.org/api/files/8e030710-b091-48a9-aec4-f9b3de6a0325/Modeled%20PM2.5%20data_clean.csv">Modeled PM2.5 data_clean.csv</a> includes modeled PM<sub>2.5</sub> concentrations used to make Figure 2. Model results can be obtained from <a href="https://www.epa.gov/hesc/rsig-related-downloadable-data-files">EPA's Fused Air Quality Surfaces Using Downscaling Tool</a>. <a href="https://zenodo.org/api/files/8e030710-b091-48a9-aec4-f9b3de6a0325/plot_Modeled.R">plot_Modeled.R</a> contains the R code to generate this figure. </p> <p><a href="https://zenodo.org/api/files/8e030710-b091-48a9-aec4-f9b3de6a0325/ORs%20all%20Counties.csv">ORs all Counties.csv</a> contains the odds ratios, confidence intervals, and p-values used to make Figures 3, 4, and 5.<a href="https://zenodo.org/api/files/8e030710-b091-48a9-aec4-f9b3de6a0325/PM2.5%2035ug-m3%20ORs.csv">PM2.5 35ug-m3 ORs.csv</a> contains the odds ratios, confidence intervals, and p-values used to make Figure S1. <a href="https://zenodo.org/api/files/8e030710-b091-48a9-aec4-f9b3de6a0325/Wildfire_Forest.R">Wildfire_Forest.R</a> contains the R code to generate these figures. </p>
Copy number variations and their effect on the plasma proteome | Associations
<p>Results and supplementary data from a GWAS investigation the relationship of CNVs and blood protein measurements.</p>
A Study to Test if TEV-50717 is Effective in Relieving Tics Associated With Tourette Syndrome (TS)
ClinicalTrials.gov study NCT03571256. IPD Sharing: YES. Countries: 10. Publications: 1.
Data for: The interactive effects of soil fertility and tree mycorrhizal association explain spatial variation of diversity-biomass relationships in a subtropical forest
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Data associated with: Emergence of the physiological effects of elevated CO2 on land-atmosphere exchange of carbon and water
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Individual dietary specialization in a generalist bee varies across populations but has no effect on the richness of associated microbial communities
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Data for: Tolerance of high temperature and associated effects on reproduction in euedaphic Collembola
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Code and datasets associated with: A sex-linked supergene with large effects on sperm traits has little impact on reproductive traits in female zebra finches
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DNA methylation associates with sex-specific effects of experimentally increased yolk testosterone in wild nestlings
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Environmental context and herbivore traits mediate the strength of associational effects in a meta-analysis of crop diversity
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Meta-analytical data on soil organic, particulate organic, and mineral-associated organic carbon under nitrogen fertilization, elevated atmospheric carbon dioxide, atmospheric warming, increased precipitation, drought, and their combined effects
Data were harvested from journal articles found on the Web of Science Core Collection and the ProQuest Agricultural and Environmental Database that studied soil organic matter fraction carbon responses to global changes (nitrogen fertilization, elevated atmospheric carbon dioxide, atmospheric warming, increased and decreased precipitation, and combined effects). Soil organic carbon fractions were designated as particulate organic carbon or mineral-associated organic carbon based on size and density cutoffs. Relevant metadata, including article information (authors, publication year), environmental information (soil type, climate, and land use), and experiment information (rates, methods) were also added to the dataset.
Data from: The effect of root-associated microbes on plant growth and chemical defence traits across two contrasted elevations,
<p>1. Ecotypic differences in plant growth and anti-herbivore defence phenotypes are determined by the complex interactions between the abiotic and the biotic environment.</p> <p>2. Root-associated microbes (RAMs) are pervasive in nature, vary over climatic gradients, and have been shown to influence the expression of multiple plant functional traits related to biomass accumulation and biotic interactions. We addressed how variation in climatic conditions between lowland and sub-alpine habitats in the Alps and RAMs can independently or interactively affect plant growth and anti-herbivore defence trait expression.</p> <p>3. To address the contribution of climate and RAMs on growth and chemical defences of high- and low-elevation Plantago major ecotypes, we performed a full-factorial reciprocal transplant field experiment at two elevations. We coupled it with plant functional trait measurements and metabolomics analyses.</p> <p>4. We found that local growing climatic conditions mostly influenced how the ecotypes grew, but we also found that the high- and low-elevation ecotypes improved biomass accumulation if in the presence of their own-elevation RAMs. Second, we found that while chemical defence expression was affected by climate, they were also more highly expressed when plants were inoculated with low elevation RAMs.</p> <p>5. Synthesis – Our research demonstrated that RAMs from contrasted elevations impact how plants grow or synthesize toxic secondary metabolites. At low elevation, where biotic interactions are stronger, RAMs enhance plant biomass accumulation and the production of toxic secondary metabolites.</p>
The effect of sertraline on depression and associations with persistent depression in survivors of HIV-related cryptococcal meningitis
<p><b>Background</b>: Depression is associated with worse outcomes in persons living with HIV/AIDS and has a prevalence more than three times as high as in the general population. Despite this, there are few randomized studies of antidepressants in HIV-infected Africans.</p> <p><b>Methods: </b>We enrolled 460 HIV-infected Africans with cryptococcal meningitis into a randomized clinical trial of adjunctive sertraline vs placebo (2015-2017). We screened for clinical depression using the Center for Epidemiologic Studies Depression Scale (CES-D) at one and three months after meningitis diagnosis and initiation of treatment. We evaluated the relationship between sertraline and depression, as well as associations with persistent depression, at three months.</p> <p><b>Results: </b>At one- and three-months post meningitis diagnosis, 62% (108/174) and 44% (74/169) of all subjects had depression (CES>15), respectively. At three months, sertraline-treated subjects were non-significantly more likely to be depressed than placebo-treated subjects (64% vs 37%, p=0.09) but were significantly less likely to have severe depression (CES>26) (OR 0.335; 95%CI, 0.130-0.865). Of those with depression at one month, sertraline-treated subjects were less likely than placebo-treated subjects to be depressed at three months (p=0.05). Sertraline was the only factor we found significant in predicting persistent depression at three months among those who had depression at one month.</p> <p><b>Conclusions: </b>Depression is highly prevalent in HIV-infected persons who have survived cryptococcal meningitis. We found that sertraline is associated with a modest reduction in depression in those with depression at baseline and a significant reduction in severe depression.</p>
Data from: Intraspecific DNA contamination distorts subtle population structure in a marine fish: decontamination of herring samples before restriction-site associated (RAD) sequencing and its effects on population genetic statistics
Wild specimens are often collected in challenging field conditions, where samples may be contaminated with the DNA of conspecific individuals. This contamination can result in false genotype calls, which are difficult to detect, but may also cause inaccurate estimates of heterozygosity, allele frequencies, and genetic differentiation. Marine broadcast spawners are especially problematic, because population genetic differentiation is low and samples are often collected in bulk and sometimes from active spawning aggregations. Here, we used contaminated and clean Pacific herring (Clupea pallasi) samples to test (i) the efficacy of bleach decontamination, (ii) the effect of decontamination on RAD genotypes, and (iii) the consequences of contaminated samples on population genetic analyses. We collected fin tissue samples from actively spawning (and thus contaminated) wild herring and non-spawning (uncontaminated) herring. Samples were soaked for 10 minutes in bleach or left untreated, and extracted DNA was used to prepare DNA libraries using a restriction-site associated DNA (RAD) approach. Our results demonstrate that intraspecific DNA contamination affects patterns of individual and population variability, causes an excess of heterozygotes, and biases estimates of population structure. Bleach decontamination was effective at removing intraspecific DNA contamination and compatible with RAD sequencing, producing high-quality sequences, reproducible genotypes, and low levels of missing data. Although sperm contamination may be specific to broadcast spawners, intraspecific contamination of samples may be common and difficult to detect from high-throughput sequencing data, and can impact downstream analyses.
Dataset associated to "Annotation matters: the effect of structural gene annotation on orthology"
<p>Dataset including the input and output files in "Annotation matters: the effect of structural gene annotation on orthology".</p> <ul> <li>Input proteomes for OMA and their corresponding splice files are in the OMAproteomes zipped folder. The OMA results for each annotation method are in the zipped folders with the method name (e.g. Augustus.zip).</li> <li>The fasta files (proteomes) are the same for OrthoFinder input in the cases of UniProt and Augustus (as they only have one isoform per gene). In these cases, the OrthoFinder folders (e.g. OFUniProt.zip), include the OrthoFinder output for that proteomes set. For Ensembl and NCBI, given the different approach each orthology method follows, the specific orthofinder proteomes are also included in the OrthoFinder (OF) zipped folder (e.g. OFtopNCBI.zip), in their corresponding primary_transcripts subfolder. </li> <li>The folder GSTDBenchmarOutput.zip contains the results from the Generalized Species Tree Discordance Benchmark.</li> <li>topNCBI/topEnsembl correspond to the original proteomes downloaded from the databases.</li> <li>priNCBI/primEnsembl correspond to the proteomes sets which include only the genes found on the primary assembly (reference sequences).</li> <li>For the species code to species name correspondance, please check the Code-Species.csv file.</li> </ul>
Data associated to the article "Effects of fluoride salt addition to the physico-chemical properties of the MgCl2-NaCl-KCl heat transfer fluid : a molecular dynamics study"
<p>Contains input file and data used to generate the figures of the article:</p> <p>Effects of fluoride salt addition to the physico-chemical properties of the MgCl<sub>2</sub>-NaCl-KCl heat transfer fluid : a molecular dynamics study</p> <p>Weiguang Zhou, Yanping Zhang, Mathieu Salanne</p> <p>https://chemrxiv.org/engage/chemrxiv/article-details/618e903a2bf8a950c7d98e5d</p> <p>The files <em>data.inpt</em> and <em>runtime.inpt </em>are used to simulate the system using the software MetalWalls</p> <p>The files <em>MgNaKCl.txt, MgNaKClF01.txt, MgNaKClF05.txt, MgNaKClF10.txt, MgNaKClF20.txt</em> contain the computed densities, viscosities and thermal conductivities at various temperatures for several compositions (provided in the header of the files)</p>
Associated dataset for "Effects of Additive Noise in Binaural Rendering of Spherical Microphone Array Signals"
<p>The instrumental evaluation utilized the Real-Time Spherical Microphone Renderer (<a href="https://github.com/AppliedAcousticsChalmers/ReTiSAR">ReTiSAR</a>) for binaural reproduction in Python. The employed code state at that time should be used to reproduce the rendering results in this data set exactly. The frozen code state for this data set is available at:<br><a href="https://github.com/AppliedAcousticsChalmers/ReTiSAR/releases/tag/v2021.TASLP">https://github.com/AppliedAcousticsChalmers/ReTiSAR/releases/tag/v2021.TASLP</a></p> <p>Download the rendering pipeline and follow the setup instructions! Use the Conda environment file included here when setting up the Python environment. In this way, you will obtain the exact Python setup as utilized in the instrumental evaluation in the publication:</p> <pre><code>conda env create --file ReTiSAR_environment_freeze.yml</code></pre> <pre><code>source activate ReTiSAR_TASLP_freeze</code></pre> <p>Matlab script "generate_norm_levels.m":</p> <ul> <li>The level contributions used in the publication are contained in "record_CLL_levels.sh", therefore this needs to be executed only in case other level distributions should be generated</li> <li>Generate the string for a ReTiSAR configuration (as used in "record_CLL_levels.sh") to emulate normally contributing EM32 self-noise based on Forum Acusticum publication data</li> <li>Generate the string for aReTiSAR configuration (as used in "record_CLL_levels.sh") to emulate normally contributing GL162 self-noise based on Gaussian normal distribution</li> </ul> <p>Matlab script "prepare_MagLS_HRIRs.m":</p> <ul> <li>Apply Magnitude Least Squares pre-processing to HRIRs (as used in "record_CLL_levels.sh")</li> </ul> <p>Shell script "record_CLL_levels.sh":</p> <ul> <li>Record the output ear signals of the rendering pipeline at multiple head orientations for all investigated configurations (according to Table 1)</li> <li>All captured signals are contained in the respective configuration directory, e.g. "rec_25ch_Fliege_sh4" to "rec_338ch_Gauss_sh12"</li> </ul> <p>Matlab script "calculate_CLL_levels.m":</p> <ul> <li>Read the individual rendering pipeline output recordings for arbitrary configurations</li> <li>Visualize the raw captured signals per configuration</li> <li>Visualize the RMS signal level variations over all head orientations per configuration</li> <li>Visualize the Interaural Level Difference variations over all head orientations per configuration</li> <li>Visualize the Composite Loudness Level variations over all head orientations per configuration (like Figure 2)</li> <li>Gather the above determined RMS, ILD, CLL, etc. metrics in a Matlab dataset per configuration (will be utilized in "plot_gathered_CLL_levels.m")</li> <li>All generated plots and Matlab datasets are contained in the respective configuration directory, e.g. "rec_25ch_Fliege_sh4" to "rec_338ch_Gauss_sh12"</li> </ul> <p>Matlab script "plot_gathered_CLL_levels.m":</p> <ul> <li>Visualize the resulting Composite Loudness Level gradient detections over all head orientations for arbitrary combinations of configurations (like Figure 3 to Figure 14)</li> <li>All generated plots are contained in the "CLL_results" directory</li> </ul>
Preliminary results: Predicted cooling effect, lives saved and associated economic value from public green spaces in Paris
<p><span>This dataset represents preliminary results predicting the cooling effect from public green spaces in Paris for the 10th, 22nd and 24th July 2019, the lives saved and associated economic valuation.</span></p> <p>The data format is a shapefile with coordinate reference system RGF93 v1 / Lambert-93 (EPSG:2154).</p> <p>Please see the README file for description of the variable names. </p> <p>Full results will be shared in due course, alongside all code and a detailed description of the method. If you would like to know more about the method or would like to be informed when the full results and method are published, please contact Jo Garrett at j.k.garrett@Exeter.ac.uk</p>
ScienceDex guides
Understand access before you commit
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.