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Biology subjects

Carlson, B. E.

Publications and source records attributed to Carlson, B. E..

3 recordsLinked to original sources

Phenotyping heart failure using model-based analysis and physiology-informed machine learning

To determine the underlying mechanistic differences between diagnoses of Heart Failure (HF) and specifically heart failure with reduced and preserved ejection fraction (HFrEF & HFpEF), a closed loop model of the cardiovascular system coupled with patient specific transthoracic echocardiography (TTE) and right heart catheterization (RHC) measures was used to identify key parameters representing cardiovascular hemodynamics. Thirty-one patient records (10 HFrEF, 21 HFpEF) were obtained from the Cardiovascular Health Improvement Project (CHIP) database at the University of Michigan. Model simulations were tuned to match RHC and TTE pressure, volume and cardiac output measures in each patient with average error between data and model of 4.87 {+/-} 2%. The underlying physiological model parameters were then plotted against model-based norms and compared between the HFrEF and HFpEF group. Our results confirm that the main mechanistic parameter driving HFrEF is reduced left ventricular contractility, while for HFpEF a much wider underlying phenotype is presented. Conducting principal component analysis (PCA), k-means, and hierarchical clustering on the optimized model parameters, but not on clinical measures, shows a distinct group of HFpEF patients sharing characteristics with the HFrEF cohort, a second group that is distinct as HFpEF and a group that exhibits characteristics of both. Significant differences are observed (p-value<.001) in left ventricular active contractility and left ventricular relaxation, when comparing HFpEF patients to those grouped as similar to HFrEF. These results suggest that cardiovascular system modeling of standard clinical data is able to phenotype and group HFpEF as different subdiagnoses, possibly elucidating patient-specific treatment strategies.

physiology↗

Model Annotation and Discovery with the Physiome Model Repository

MotivationMathematics and physics based computational models have the potential to help interpret and encapsulate biological phenomena in a computable and reproducible form. Similarly, comprehensive descriptions of such models encoded in computable form help to ensure that such models are accessible, discoverable, and reusable. To this end, researchers have developed tools and standards to encode mathematical models of biological systems enabling reproducibility and reuse; tools and guidelines to facilitate semantic description of mathematical models; and repositories in which to archive, share, and discover models. Biologists and clinicians can leverage these resources to investigate specific questions and hypotheses.\n\nResultsWe have comprehensively annotated a cohort of models with biological semantics. These annotated models are freely available in the Physiome Model Repository (PMR). To demonstrate the benefits of this approach, we have developed a web-based tool which enables users to discover models relevant to their work, with a particular focus on epithelial transport. In helping a user to discover relevant models this tool will provide users with suggestions for similar or alternative models they may wish to explore or utilize in their model based on the models they would like to use. The semantic annotation and the web tool we have developed is a new contribution enabling scientists to discover relevant models in the PMR as candidates for reuse in their own scientific endeavours. We believe that this approach demonstrates how semantic web technologies and methodologies can contribute to biomedical and clinical research.\n\nAvailability and implementationhttps://github.com/dewancse/model-discovery-tool

bioinformatics↗

Computational Model for Simulating Drug-Induced Arrhythmia Sensitivity of Human iPSC-derived Cardiomyocytes

A mathematical model describing the electrophysiology and ion handling of cardiomyocytes is a complement to experimental analysis predicting drug-induced proarrhythmic potential in humans as proposed by Comprehensive in vitro Proarrhythmia Assay (CiPA). While CiPA endorses the use of the OHara Rudy (ORd) model, which was developed to simulate electrophysiology of human adult ventricular cardiomyocytes (hAVCMs), to predict drug-induced proarrhythmias; the human induced pluripotent stem cell derived-cardiomyocytes (hiPSC-CMs) was proposed for experimental verifications. The hiPSC-CMs, especially cultured in 2D culture dishes, are inherently different from hAVCMs exhibiting different ion channel density and an immature sarcoplasmic reticulum function. To reconcile this mismatch, we have developed a mathematical electrophysiology model of an hiPSC-CM by incorporating differences in gene expressions of ion channels, pumps and receptors in hiPSC-CMs against those found in hAVCMs. This model can be used to model any hiPSC-CM cell line where expression data has been obtained and replaces the background currents for K+ and Na+ in the ORd model with the known ultra-rapid K+ channel and hyperpolarization activated K+/Na+ channel currents. With this new model, three batches each from two different hiPSC-CM cell lines are compared to experimental data of action potential duration. This mathematical model recapitulates a ventricular-like action potential morphology with a Phase 2 plateau lasting a few hundred milliseconds. However, the resting membrane potential is not as depolarized (-65 to -70 mV) as that of hAVCM (-80 mV). The elevated resting membrane potential matches experimental data previously and is thought to keep rapid sodium channels from triggering membrane depolarization instead being replaced by an overexpression of L-Type Ca2+ channel current. This model is a key step in identifying the variability between different hiPSC-CM lines and even batches of the same line, opening the door to realizing analysis of patient specific preparations in the future.

physiology↗