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Dataset results
19 results for “causal effect”
Causal identification of single-cell experimental perturbation effects with CINEMA-OT
<p>Recent advancements in single-cell technologies allow characterization of experimental perturbations at single-cell resolution. While methods have been developed to analyze such experiments, the application of a strict causal framework has not yet been explored for the inference of treatment effects at the single-cell level. In this work, we present a causal inference-based approach to single-cell perturbation analysis, termed CINEMA-OT (Causal INdependent Effect Module Attribution + Optimal Transport). CINEMA-OT separates confounding sources of variation from perturbation effects to obtain an optimal transport matching that reflects counterfactual cell pairs. These cell pairs represent causal perturbation responses permitting a number of novel analyses, such as individual treatment effect analysis, response clustering, attribution analysis, and synergy analysis. We benchmark CINEMA-OT on an array of treatment effect estimation tasks for several simulated and real datasets and show that it outperforms other single-cell perturbation analysis methods. Finally, we perform CINEMA-OT analysis of two newly-generated datasets: (1) rhinovirus and cigarette smoke-exposed airway organoids, and (2) combinatorial cytokine stimulation of immune cells. In these experiments, CINEMA-OT reveals potential mechanisms by which cigarette smoke exposure dulls the airway antiviral response, as well as the logic that governs chemokine secretion and peripheral immune cell recruitment.</p>
"CausalXtract: a flexible pipeline to extract causal effects from live-cell time-lapse imaging data" datasets
<p>Datasets from the article:</p> <p><strong>CausalXtract: a flexible pipeline to extract causal effects from live-cell time-lapse imaging data </strong></p> <p>by Franck Simon, Maria Colomba Comes, Tiziana Tocci, Louise Dupuis, Vincent Cabeli, Nikita Lagrange, Arianna Mencattini, Maria Carla Parrini, Eugenio Martinelli, Hervé Isambert.</p> <p> </p> <p>The <strong>original videos</strong> are uploaded as: "20161230.zip", "20170105.rar", "Video_2017_0517.zip".</p> <p><strong>Details </strong>for each <strong>experiment </strong>can be found in: "Experiments' details.zip".</p> <p>The <strong>ROIs </strong>(ROI: Region of Interest) are uploaded as .tif files in: "EXTRACTED ROIs.zip".</p> <p>The <strong>MATLAB data</strong> is uploaded in "MATLAB_DATA.rar" and includes: the cancer cells' trajectories (subfolder: "TUMOR TRAJECTORIES"), the immune cells' trajectories (subfolder: "IMMUNE TRAJECTORIES"), the ROIs videos as .mat files for the detection of cells (subfolder: "ROI MAT"), the ROIs further cropped for the extraction of shape descriptors (folder: "ROI_TU MAT"). The ROIs videos .mat files included in the last two subfolders are stopped after their apoptosis has been detected.</p>
Causal identification of single-cell experimental perturbation effects with CINEMA-OT
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Causal effect of familial short stature on three quantitative traits in Taiwan
<p><span><strong>Objectives</strong>: </span><span>With the accumulation of genetic basis for </span><span>familial (genetic) short stature (FSS)</span><span>, the genetic association of FSS with health-related outcomes remains to be elucidated. In this study, we aimed to investigate the FSS genetic architecture and its causal effect on three quantitative traits in Taiwan. </span></p> <p><span><strong>Methods</strong>:</span><span> We </span><span>conducted an FSS genome-wide association study (GWAS) analysis (1,640 FSS cases and 22,372 controls). We performed a GWAS meta-analysis for the Taiwanese meta-height from the Taiwan Biobank (</span><span>TWB)_height (N = 67,452) and the China Medical University Hospital (CMUH)_height GWAS summary statistics (N = 88,854). </span><span>We calculated three polygenic risk scores (PRSs) of SNPs (<em>P</em> < 5 x 10<sup>-8</sup>) for FSS and Taiwanese meta-height with/without FSS, respectively. We explored the associations between three PRSs and the measured height, respectively. We also performed </span><span>Mendelian randomization (MR) analysis</span><span> for the causal effect of FSS and Taiwanese meta-height with/without FSS, on anthropometric, bone mineral density (BMD), and female reproductive traits</span><span>. </span></p> <p><span><strong>Results</strong>: </span><span>FSS GWAS identified 172 SNPs in 4 genomic regions, reported in height </span><span>(<em>P</em> < 5 x 10<sup>-8</sup>)</span><span>. Higher FSS genetic scores correlate with an increased risk of short stature and height reduction tendency </span><span>(</span><em><span>p</span></em> <span><</span><span> 0.001).</span><span> The causal effect showed that a higher risk of FSS was associated with decreased body height, but increased body mass index, and body fat</span> <span>(</span><em><span>p</span></em> <span><</span><span> 0.001)</span><span>. However, higher genetic scores of Taiwanese meta-height with/without FSS correspond with increased body height, body weight, hip circumference, and age at menarche, but decreased BMD_T-score, BMD_Z-score, and stiffness index </span><span>(</span><em><span>p</span></em> <span><</span><span> 0.001)</span><span>. </span></p> <p><span><strong>Conclusion</strong>: </span><span>This study </span><span>contributes to the FSS and height genetic features and their causal effects on three quantitative traits </span><span>in individuals of Han Chinese ancestry in Taiwan. </span></p>
Testing the Causal Effects of a Civic Engagement Intervention on Health and Wellbeing Among Youth (I-ACTED)
ClinicalTrials.gov study NCT04514133. IPD Sharing: NO. Countries: 1. Publications: 3.
Data for: Estimating causal effects with machine learning: A guide for ecologists
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Causal effect of familial short stature on three quantitative traits in Taiwan
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Data from: Direct and indirect causal effects of heterozygosity on fitness-related traits in Alpine ibex
Heterozygosity–fitness correlations (HFCs) are a useful tool to investigate the effects of inbreeding in wild populations, but are not informative in distinguishing between direct and indirect effects of heterozygosity on fitness-related traits. We tested HFCs in male Alpine ibex (Capra ibex) in a free-ranging population (which suffered a severe bottleneck at the end of the eighteenth century) and used confirmatory path analysis to disentangle the causal relationships between heterozygosity and fitness-related traits. We tested HFCs in 149 male individuals born between 1985 and 2009. We found that standardized multi-locus heterozygosity (MLH), calculated from 37 microsatellite loci, was related to body mass and horn growth, which are known to be important fitness-related traits, and to faecal egg counts (FECs) of nematode eggs, a proxy of parasite resistance. Then, using confirmatory path analysis, we were able to show that the effect of MLH on horn growth was not direct but mediated by body mass and FEC. HFCs do not necessarily imply direct genetic effects on fitness-related traits, which instead can be mediated by other traits in complex and unexpected ways.
Non-linear effects of precipitation on river water quality revealed by city-level causal modelling
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Exploring causal components of plasticity in grey seal birthdates: effects of intrinsic traits, demography, and climate
<p>Change in breeding phenology is often a response to environmental forcing, but less is known of the mechanism underlying such changes and their fitness consequences. Here we report on changes in the breeding phenology from a 27-year longitudinal study (1991-2017) of individually marked, known-aged grey seals (Halichoerus grypus) on Sable Island, Nova Scotia, Canada.</p> <p>We used Generalized Linear Mixed Models to test hypotheses about the influence of fixed factors (maternal age, parity, previous reproductive success, pup sex, colony density, AMO, NAO, and SST) and a random factor (female identity) on parturition dates. We also examined the consequences of the shift in birthdates on maternal energy investment in offspring as measured by pup weaning mass. Birthdates were known for 2768 pups of 660 known-age females. For 494 females with ≥ 2 parturition dates, repeatability as measured by the intraclass correlation was high (mean=0.66). 87% of the variation in birthdates was explained by a mixed effects model that included intrinsic and extrinsic fixed effects. Most of the explained variation was associated with the random effect of female identity.</p> <p>Parity was the most important intrinsic fixed effect, with inexperienced mothers giving birth later in the season than multiparous females. Over almost 3 decades, mean birthdates advanced by 15 days. The mixed model with intrinsic effects and population size, the detrended AMO from the previous year and mean NAO in the previous 3 years explained 80 % of the variation with 21 % of variation from the fixed effects. Both primiparous and multiparous individuals responded to the climate forcing, and there was strong evidence for heterogeneity in the response. The shift in birthdates did not impact pup weaning mass. Females exhibited considerable phenotypic plasticity indicating that climate driven changes in breeding phenology may not always have measurable consequences.</p>
Data from: Direct and indirect causal effects of heterozygosity on fitness-related traits in Alpine ibex
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Exploring causal components of plasticity in grey seal birthdates: effects of intrinsic traits, demography, and climate
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Causal Effect of the FEMA CRS Program
<p>Dataset produced and used in the <a href="https://arxiv.org/abs/2312.03843">Cano & Hahn (2023)</a>. The data is produced and used by code in the <a href="https://github.com/changhoonhahn/causalCRS/">causalCRS</a> github repo:</p> <ul> <li><strong> zipcode.fema.fsf.acs.rainfall.v2.FSF_REDACTED.csv</strong>: Dataset compiled from the FEMA Flood Insurance Mitigation <br>Administration NFIP Redacted Claims data with additional information on community characteristics from: the First Street Foundation data set, US Census Bureau American Community Survey, and PRISM climate group data sets. In total, the data set has 74,288 entries from 14,729. See <a href="https://arxiv.org/abs/2312.03843">Cano & Hahn (2023)</a> for details. Note: data from First Street Foundation (FSF) has been redacted (all values set to -999). FSF data was used under license for the study and are not publicly available. Please contact privately for unredacted version. <div> </div> </li> <li><strong>typology_*.npy</strong>: Conditional Average Treatment Effect (CATE) and accompanying measurements for the 27 community typologies defined in the paper. <ul> <li><strong>typology_cate.npy</strong>: Measured CATE for the 27 community typologies</li> <li><strong>typology_sig_cate.npy</strong>: Statistical uncertainty on CATE measurements. </li> <li><strong>typology_y_treat.npy</strong>: Claim per policy in USD (outcome) of the community typologies for treated sample </li> <li><strong>typology_y_control.npy</strong>: Claim per policy in USD (outcome) of the community typologies for control sample</li> <li><strong>typology_covar.npy</strong>: Median covariate values for communities that fall within the typology. This is for reference only. </li> </ul> </li> <li><strong>fema_crs.*.npy</strong>: Compiled dataset for training/validation/testing the q_phi(Y|X) of the treated/control samples used in CausalFlow. </li> <li><strong>qphi_control.tar.gz / qphi_treat.tar.gz</strong>: Compressed tar file that contains all the trained ensemble of flows for the control/treated samples used in CausalFlow. </li> <li><strong>qphi_support.v2.log.control.pt / qphi_support.v2.log.treat.pt</strong>: NDEs estimating the distribution of the covariates for the control/treated samples. </li> <li><strong>fema_cid.almost_only_c300.npy</strong>: An array of communities that participated in the CRS but only executed the c300 activity, which corresponds to the outreach effort. This dataset is used to estimate the overall impact of outreach. </li> </ul>
A Causal Role for Voltage-gated Cav1.2 Calcium Channels in Mediating 5G FR1 Effects on Sleep-associated Brain Health in Humans
ClinicalTrials.gov study NCT06998368. IPD Sharing: NO. Countries: 1. Publications: 0.
The Causal Effects of Old Age Pensions
ClinicalTrials.gov study NCT04029194. IPD Sharing: NO. Countries: 1. Publications: 0.
Causal Effect of Coenzyme Q10 Nutrition and Cognitive Dysfunction in the Metabolic Storm (Hyperglycemia and Sarcopenia) and Brain-derived Neurotrophic Factor
ClinicalTrials.gov study NCT06040905. IPD Sharing: NO. Countries: 1. Publications: 0.
Effective Connectivity in Patients Receiving Spinal Cord Stimulation: an fMRI and EEG Dynamic Causal Modeling Study
ClinicalTrials.gov study NCT03626428. IPD Sharing: Not stated. Countries: 1. Publications: 0.
The Causal Effect of Bariatric Surgery on Cardiovascular Disease and Mortality
ClinicalTrials.gov study NCT06420479. IPD Sharing: NO. Countries: 1. Publications: 0.
Effect of salicylic acid on Fusarium graminearum, the major causal agent of fusarium head blight in wheat
GEO Series GSE24636. Fusarium graminearum. 12 samples. Type: Expression profiling by array.
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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)
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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.