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256
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ShareScore release 0.9.0
Dataset results
256 results for “computational modelling”
Intergenerational Regulation of Mosaic Supernumerary Chromosomes: Evidence for a Developmental Correction Mechanism from Clinical and Computational Models
GEO Series GSE302224. Homo sapiens. 2 samples. Type: Genome variation profiling by SNP array.
Assessment of the Accuracy of Surgical Guide Designed From Digital Impression, Dental Model Scanning Using CBCT and Desktop Scanner in Computer Guided Implantology:
ClinicalTrials.gov study NCT03730506. IPD Sharing: UNDECIDED. Countries: 0. Publications: 0.
Computer Modelling to Plan Surgical Reconstruction
ClinicalTrials.gov study NCT04968704. IPD Sharing: NO. Countries: 0. Publications: 0.
Accuracy of Computer Guided Surgery (vs) Conventional Model Surgery in Treatment of Skeletal Open Bite
ClinicalTrials.gov study NCT03277443. IPD Sharing: UNDECIDED. Countries: 0. Publications: 0.
Connecting Transcriptomics with Computational Modeling to Reveal Developmental Adaptations in Pediatric Human Atrial Tissue
GEO Series GSE276839. Homo sapiens. 117 samples. Type: Expression profiling by array.
Improving Computational Efficiency of Prediction in Model-based Prognostics Using the Unscented Transform
Model-based prognostics captures system knowledge in the form of physics-based models of components, and how they fail, in order to obtain accurate predictions of end of life (EOL). EOL is predicted based on the esti- mated current state distribution of a component and ex- pected profiles of future usage. In general, this requires simulations of the component using the underlying mod- els. In this paper, we develop a simulation-based pre- diction methodology that achieves computational effi- ciency by performing only the minimal number of sim- ulations needed in order to accurately approximate the mean and variance of the complete EOL distribution. This is performed through the use of the unscented trans- form, which predicts the means and covariances of a distribution passed through a nonlinear transformation. In this case, the EOL simulation acts as that nonlinear transformation. In this paper, we review the unscented transform, and describe how this concept is applied to efficient EOL prediction. As a case study, we develop a physics-based model of a solenoid valve, and perform simulation experiments to demonstrate improved com- putational efficiency without sacrificing prediction accu- racy.
The role of structural vs cellular remodeling in arrhythmogenesis: personalized computer models of atrial fibrillation
GEO Series GSE269882. Homo sapiens. 27 samples. Type: Expression profiling by high throughput sequencing.
Measurement dataset for Impedance Standard Substrate Characterization and EM model Definition for Cryogenic and Quantum-Computing Applications
<p>dataset for the data presented in the paper "Impedance Standard Substrate Characterization and EM model definition for Cryogenic and Quantum-Computing Applications"</p> <p>In this contribution, we describe the modeling approaches and the characterization procedures used to develop accurate standard models for cryogenic, probe-level, calibrations substrates.The key electrical and mechanical parameters of the impedance terminations and the lines used in commercially available impedance standard substrates are first characterized versus temperature. After, these component are simulated using 2.5D EM solvers including their mechanical variation when exposed to cryogenic temperatures, to extract their nominal response at 7 Kelvin. The quality of the resulting calibrations at cryogenic is evaluated first using independent CPW lines on the calibration substrates and then by measuring the response of a transformer-based resonator realized on a Si-based technology.Ambient temperature models are used as a comparison, to highlight the accuracy improvement that can be achieved employing optimized Cryo-EM based models.</p>
P in Identification of morphologically cryptic species with computer vision models: wall lizards (Squamata: Lacertidae: Podarcis) as a case study
P. lusitanicus
P in Identification of morphologically cryptic species with computer vision models: wall lizards (Squamata: Lacertidae: Podarcis) as a case study
P. bocagei
Target-agnostic discovery of Rett Syndrome therapeutics by coupling computational network analysis and CRISPR-enabled in vivo disease modeling
GEO Series GSE199049. Xenopus laevis. 13 samples. Type: Expression profiling by array.
Computational modelling of the cellular interplay in Rheumatoid Arthritis. Deciphering the role of innate and adaptive immunity in cartilage destruction and bone erosion
<p>Immune dysregulation was first implicated in the pathogenesis of Rheumatoid Arthritis (RA) by the discovery of anti-immunoglobulin G (IgG) antibodies known as rheumatoid factors. However, concepts of how immune responses contribute to disease have evolved dramatically over the last 50 years. Many cells and their cytokines play critical roles in the development of RA. The synovial compartment is infiltrated by leukocytes and the synovial fluid is inundated with pro-inflammatory mediators that are produced to induce an inflammatory cascade, which is characterized by interactions of fibroblast-like synoviocytes with the cells of the innate immune system, including monocytes, macrophages, mast cells, dendritic cell as well as cells of adaptive immune system such as T cells and B cells. The fulminant stage contains hyperplastic synovium, cartilage damage, bone erosion, and systemic consequence.</p> <p>The objective of my project is to construct a computational model able to decipher the interplay between cells of the innate and adaptive immunity in RA, that eventually leads to bone and cartilage breakdown.</p> <p>To do so, we will start by creating separate maps for T cells, B cells, macrophages, fibroblasts, osteoblasts and osteoclasts. We will use different data mining tools, appropriate data bases such as KEGG (Kanehisa et al, 2000), REACTOME (Fabregat et al, 2018) as well as internal data generated within Sanofi. We will exploit the graph editor CellDesigner (Funahashi et al, 2003) and the platform Minerva (Gawron et al, 2016) for automatic annotation and reference of the cell specific maps. We will benefit greatly from a global, fully annotated RA specific map (Singh et al, 2018, Singh et al, 2020). This map features interactions implicated in RA coming from various cell types, but due to the extensive annotations the user can opt for cell specific interactions and extract the corresponding network. We are also going to use public datasets of expression data (microarrays, RNAseq, RNAseq single cell), data concerning metabolic pathways from MetaCyc and Sanofi’s proprietary datasets to enrich and expand existing pathway resources. These maps will be used to generate cell specific dynamic models using the tool CaSQ (Aghamiri et al, 2020). The next step is the creation of a multicellular model to understand how the different cells interact, contributing to the emergent behavior of the system. We will prioritize signature pathways for each cell type and combine them to build a logical model that will represent the intra- and intercellular relationships.</p> <p> </p>
Design and Computational Fluid Dynamics (CFD) modelling of Biomimetic Voronoi lattice Scaffolds
Open the record for dataset details and reuse information.
Computational Fluid Dynamics Modeling of Proximal Landing Zones for Thoracic Endovascular Aortic Repair in the Bovine Arch Variant.
<p>Dataset from the article Marrocco-Trischitta MM, Romarowski RM, Alaidroos M, Sturla F, Glauber M, Nano G. Computational Fluid Dynamics Modeling of Proximal Landing Zones for Thoracic Endovascular Aortic Repair in the Bovine Arch Variant. Ann Vasc Surg. 2020 Nov;69:413-417. doi: 10.1016/j.avsg.2020.05.024. Epub 2020 May 29. PMID: 32479874.</p> <p><strong>Abstract</strong></p> <p><strong>Background: </strong>To assess the endograft displacement forces (DF), which quantify the forces exerted by the pulsatile blood flow on the vessel wall and transmitted on the terminal fixation site of the endograft after its deployment in proximal landing zones (PLZs) of the bovine aortic arch variant.</p> <p><strong>Methods: </strong>Thirty healthy aortic computed tomographic angiographies of subjects with bovine arch configuration (10 per type of arch, I-III) were selected for the purpose of the study. A 3-dimensional model of the aortic arch lumen was reconstructed. Computational fluid dynamics modeling was then used to compute DF magnitude and orientation (i.e., x, y, and z axes) in PLZs of each case. DF values were normalized to the corresponding aortic wall area to estimate equivalent surface traction (EST).</p> <p><strong>Results: </strong>DF were highest in zone 0, consistently with the greater surface area. DF in zone 3 were much greater than in zone 2 because of a 3-fold greater upward component (z axis) (P < 0.001), being therefore mainly oriented orthogonally to the aortic blood flow and to the vessel longitudinal axis in that zone. EST progressively increased from zone 0 toward more distal PLZs, with EST in zone 3 being much greater than that in zone 2 (P < 0.001). The same pattern was observed after stratification by type of arch.</p> <p><strong>Conclusions: </strong>The bovine arch is associated with a consistent fluid dynamic pattern, which identifies in zone 3 an unfavorable biomechanical environment for endograft deployment.</p>
Dataset related to the article "Prediction of myocardial blood flow under stress conditions by means of a computational model"
<p>This record contains raw data related to the article “Prediction of myocardial blood flow under stress conditions by means<br> of a computational model”</p> <p><strong>Purpose. </strong>Quantification of myocardial blood flow (MBF) and functional assessment of coronary artery disease (CAD) can be achieved through stress myocardial computed tomography perfusion (stress-CTP). This requires an additional scan after the resting coronary computed tomography angiography (cCTA) and administration of an intravenous stressor. This complex protocol has limited reproducibility and non-negligible side effects for the patient. We aim to mitigate these drawbacks by proposing a computational model able to reproduce MBF maps.</p> <p><strong>Methods. </strong>A computational perfusion model was used to reproduce MBF maps. The model parameters were estimated by using information from cCTA and MBF measured from stress-CTP (MBF<sub>CTP</sub>) maps. The relative error between the computational MBF under stress conditions (MBF<sub>COMP</sub>) and MBF<sub>CTP</sub> was evaluated to assess the accuracy of the proposed computational model.</p> <p><strong>Results.</strong> Applying our method to 9 patients (4 control subjects without ischemica vs 5 patients with myocardial ischemia), we found an excellent agreement between the values of MBF<sub>COMP</sub> and MBF<sub>CTP</sub>. In all patients, the relative error was below 8% over all the myocardium, with an average-in-space value below 4%.</p> <p><strong>Conclusion. </strong>The results of this pilot work demonstrate the accuracy and reliability of the proposed computational model in reproducing MBF under stress conditions. This consistency test is a preliminary step in the framework of a more ambitious project which is currently under investigation, i.e. the construction of a computational tool able to predict MBF avoiding the stress protocol and potential side effects while reducing radiation exposure.</p>
Computational models of immunity for pertussis boost (CMI-PB) multiomics datasets used for the first challenge
<p><strong>Systems vaccinology is increasingly generating massive datasets to characterize the immune state of individuals before and after vaccination, which require data science to interpret them. These studies are used to draw conclusions on what drives different individuals to have different vaccine responses. </strong></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.