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Dataset results
376 results for “Causality”
Cross-species identification of DLPFC-specific miR-130a-3p as a causal driver of major depressive disorder implicating microglial neuroimmune suppression
GEO Series GSE316217. Mus musculus. 10 samples. Type: Expression profiling by high throughput sequencing.
Genetic and epigenetic screens in primary human T cells link candidate causal autoimmune variants to T cell networks [MPRA]
GEO Series GSE297471. Homo sapiens. 13 samples. Type: Expression profiling by high throughput sequencing.
ClearCausal: Cross Layer Causal Analysis for Automatic Microservice Performance Debugging
<p>Dataset for the paper: <em>ClearCausal: Cross Layer Causal Analysis for Automatic Microservice Performance Debugging.</em></p>
Towards Better NLI for Spanish: A Multi-Genre Dataset and causal relationships
<p>This project includes the code, dataset and models for the paper: Towards Better NLI for Spanish: A Multi-Genre Dataset and causal<br>relationships.</p> <p>- The params used to extract de data and train the models can be found in the folder params</p> <p>- The dataset can be found in the folder data/base_dataset</p> <p>- The trained models and their metrics can be found in the folder model</p> <p>- The code can be found in the auto_nli folder</p> <p>For execution details read the README file.</p>
Supplementary tables of Causal relationship between gut microbiota, blood metabolites, immune cell traits, inflammatory proteins, and cataract: a two-sample, bidirectional mendelian randomization analysis
<p><span>Table S1: The information of GWAS data for gut microbiota; Table S2: The information of GWAS data for blood metabolites and metabolite ratios; Table S3: The information of GWAS data for immune cell traits; Table S4: The information of GWAS data for circulating inflammatory proteins; Table S5: The results of casual effects and sensitive analysis of identified gut microbiota on cataract; Table S6: The results of casual effects and sensitive analysis of identified blood metabolites and metabolite ratios on cataract; Table S7: The results of casual effects and sensitive analysis of identified immune cell traits on cataract; Table S8: The results of casual effects and sensitive analysis of identified circulating inflammatory proteins on cataract; Table S9: The significant casual effects of two-sample MR analysis in mediation analysis; Table S10: The consistent effect sizes of exposure-outcome, exposure-mediator, and mediator-outcome; Table S11: The results of preliminary MVMR in mediation analysis; Table S12: The results of subsequent MVMR in mediation analysis; Table S13: The results of significant casual effects of cataract on gut microbiota, blood metabolites and metabolite ratios, and circulating inflammatory proteins; Table S14: The genes identified from the causal SNPs using MAGMA; Table S15: The results of functional enrichment analysis of the genes identified from the causal SNPs.</span></p>
Data from: A Socio-technical Perspective on Software Vulnerabilities: A Causal Analysis
<p>This data package contains supplemental material data for the under review TSE submission: A Socio-technical Perspective on Software Vulnerabilities: A Causal Analysis. The restricted access requirement will be lifted upon approval of the manuscript.</p> <p>The comprehensive explanation of this dataset can be found at: https://sailuh.github.io/causal_commit_flow_docs</p> <p>The following briefly describes the contents of the folders. The analysis presented in the manuscript requires the following:</p> <ul> <li>Git Log </li> <li>Mailing List</li> <li>Software Vulnerabilities (NVD Feed)</li> </ul> <p>This data is provided to a mining software repository tool, Kaiaulu. The data specifications and configuration parameters are defined in the OpenSSL project configuration file (.yml), also included in this package. </p> <p>An R notebook in Kaiaulu, taking the dataset above + project configuration file, can then perform the first analysis step:</p> <p>https://github.com/sailuh/kaiaulu/blob/master/vignettes/issue_social_smell_showcase.Rmd</p> <p>The file 1_openssl_social_smells_timeline.csv is generated as an output of this R Notebook, and included in the causal_model folder of this package. The following files in this folder numbered 2 through 16, describe transformation steps using Excel, Python scripts, and Tetrad (also an open source tool). These are described conceptually in the manuscript, but in more detail in the comprehensive explanation of this dataset linked at the start. </p>
Causal association between non-steroidal anti-inflammatory drugs use and the risk of benign prostatic hyperplasia: A univariable and multivariable Mendelian randomization study
<p>Raw data using Mendelian randomization to analyze the association between non-steroidal anti-inflammatory drugs and benign prostatic hyperplasia.</p>
Colocalization of GWAS and molecular QTL signals in human vascular smooth muscle cells predict candidate causal genes for coronary artery disease and vascular disorders
GEO Series GSE198544. Homo sapiens. 10 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Genetic and epigenetic screens in primary human T cells link candidate causal autoimmune variants to T cell networks
GEO Series GSE297472. Homo sapiens. 21 samples. Type: Expression profiling by high throughput sequencing.
Causality of gut bacteria Klebsiella pneumoniae to hypertension development II
GEO Series GSE209720. Mus musculus. 9 samples. Type: Expression profiling by high throughput sequencing.
Data set from the article Bari V, Vaini E, Pistuddi V, Fantinato A, Cairo B, De Maria B, Dalla Vecchia LA, Ranucci M, Porta A. Comparison of Causal and Non-causal Strategies for the Assessment of Baroreflex Sensitivity in Predicting Acute Kidney Dysfunction After Coronary Artery Bypass Grafting. Front Physiol. 2019 Oct 18;10:1319. doi: 10.3389/fphys.2019.01319. PMID: 31681021; PMCID: PMC6813722.
<p>Data set from the article Bari V, Vaini E, Pistuddi V, Fantinato A, Cairo B, De Maria B, Dalla Vecchia LA, Ranucci M, Porta A. Comparison of Causal and Non-causal Strategies for the Assessment of Baroreflex Sensitivity in Predicting Acute Kidney Dysfunction After Coronary Artery Bypass Grafting. Front Physiol. 2019 Oct 18;10:1319. doi: 10.3389/fphys.2019.01319. PMID: 31681021; PMCID: PMC6813722.</p> <p>This is the abstract:</p> <p>Coronary artery bypass graft (CABG) surgery may lead to postoperative complications such as the acute kidney dysfunction (AKD), identified as any post-intervention increase of serum creatinine level. Cardiovascular control reflexes like the baroreflex can play a role in the AKD development. The aim of this study is to test whether baroreflex sensitivity (BRS) estimates derived from non-causal and causal approaches applied to spontaneous systolic arterial pressure (SAP) and heart period (HP) fluctuations can help in identifying subjects at risk of developing AKD after CABG and which BRS estimates provide the best performance. Electrocardiogram and invasive arterial pressure were acquired from 129 subjects (67 ± 10 years, 112 males) before (PRE) and after (POST) general anesthesia induction with propofol and remifentanil. Subjects were divided into AKDs (<em>n</em> = 29) or no AKDs (noAKDs, <em>n</em> = 100) according to the AKD development after CABG. The non-causal approach assesses the transfer function from the HP-SAP cross-spectrum in the low frequency (LF, 0.04-0.15 Hz) band. BRS was estimated according to three strategies: (i) sampling of the transfer function gain at the maximum of the HP-SAP squared coherence in the LF band; (ii) averaging of the transfer function gain in the LF band; (iii) sampling of the transfer function gain at the weighted central frequency of the spectral components of the SAP series dropping in the LF band. The causal approach separated the two arms of cardiovascular control (i.e., from SAP to HP and <em>vice versa</em>) and accounted for the confounding influences of respiration via system identification and modeling techniques. The causal approach provided a direct estimate of the gain from SAP to HP by observing the HP response to a simulated SAP rise from the identified model structure. Results show that BRS was significantly lower in AKDs than noAKDs during POST regardless of the strategy adopted for its computation. Moreover, all the BRS estimates during POST remained associated with AKD even after correction for demographic and clinical factors. Non-causal and causal BRS estimates exhibited similar performances. Baroreflex impairment is associated with post-CABG AKD and both non-causal and causal methods can be exploited to improve risk stratification of AKD after CABG.</p>
Restricted Data of the Reproducibility Package for the paper "Higher-Order Patterns Reveal Causal Timescales of Complex Systems"
<p>Datasets which are not ours, so we do not want to publish them openly. We submitted them here as a backup.</p>
raw data related to article "BEYOND CANVAS: BEHAVIORAL ONSET OF RFC1‑EXPANSION DISEASE IN AN ITALIAN FAMILY—CAUSAL OR CASUAL?"
<p><strong>GENETICS RAW DATA OF A CANVAS FAMILY: RP-PCR, FRAGMENT ANALYSIS</strong></p>
Causal Modeling Using Network Ensemble Simulations Predicts Novel Lipid Metabolism Genes
GEO Series GSE15226. Mus musculus. 120 samples. Type: Expression profiling by array.
Data set from the article Vaini E, Bari V, Fantinato A, Pistuddi V, Cairo B, De Maria B, Ranucci M, Porta A. Causality analysis reveals the link between cerebrovascular control and acute kidney dysfunction after coronary artery bypass grafting. Physiol Meas. 2019 Jul 1;40(6):064006. doi: 10.1088/1361-6579/ab21b1. PMID: 31091519.
<p>Data set from the article Vaini E, Bari V, Fantinato A, et al. Causality analysis reveals the link between cerebrovascular control and acute kidney dysfunction after coronary artery bypass grafting. <em>Physiol Meas</em>. 2019;40(6):064006. Published 2019 Jul 1. doi:10.1088/1361-6579/ab21b1</p> <p>This is the abstract:</p> <p><strong>Background: </strong>Patients undergoing coronary artery bypass graft (CABG) surgery might experience postoperative complications and some of them, such as acute kidney dysfunction (AKD), are the likely consequence of hypoperfusion. We hypothesized that an impaired cerebrovascular control is a hallmark of a vascular damage that might favor AKD after CABG.</p> <p><strong>Objective: </strong>Our aim is to characterize cerebrovascular control in CABG patients through the assessment of the relationship between mean arterial pressure (MAP) and mean cerebral blood flow velocity (MCBFV) and to check whether markers describing MCBFV-MAP dynamical interactions could identify subjects at risk to develop postoperative AKD.</p> <p><strong>Approach: </strong>MAP and MCBFV beat-to-beat series were extracted from invasive arterial pressure and transcranial Doppler recordings acquired simultaneously in 23 patients just before CABG after the induction of propofol general anesthesia. Subjects were divided into AKD group (n = 9, age: 68 ± 9, 8 males) and noAKD group (n = 14, age: 65 ± 8, 12 males) according to whether they developed postoperative AKD or not after CABG. We computed MAP and MCBFV time-domain and spectral markers as well as MCBFV-MAP cross-spectral indexes in very-low-frequency (VLF, 0.02-0.07 Hz), low-frequency (LF, 0.07-0.15 Hz) and high-frequency (HF, 0.15-0.30 Hz) bands. We also calculated model-based transfer entropy (TE) to quantify the degree of MCBFV dependence on MAP and vice versa. The null hypothesis of MCBFV-MAP uncoupling was tested via a surrogate approach associating MAP and MCBFV in different patients.</p> <p><strong>Main results: </strong>Time, spectral and cross-spectral markers had a limited power in separating AKD from noAKD individuals. Conversely, TE from MAP to MCBFV was significantly above the level set by surrogates only in AKD groups and significantly larger than that computed in noAKD.</p> <p><strong>Significance: </strong>The reduced cerebrovascular autoregulation in AKD patients suggest a vascular impairment likely making them more at risk of hypoperfusion during CABG and AKD after CABG.</p>
Examining the Causal Link Between Gut Microbiota and Osteoporosis: A Two-Sample Mendelian Randomization Analysis
<p>Supplementary File(s) for submission in IJOMS</p>
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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.