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Karin Leiderman

Publications and source records attributed to Karin Leiderman.

7 recordsLinked to original sources

Mechanisms of thrombin inhibition by protein S and the TFPIα-fVshort-protein S complex

Protein S (PS) is a notable anticoagulant implicated in both bleeding and thrombotic disorders, making it a promising drug target. Importantly, PS enhances the anticoagulant function of TFPI$α$, likely circulating in the bloodstream together with TFPI$α$ and a truncated form of factor V (fVshort) in the trimolecular complex, TFPI$α$-fVshort-PS, which we call protein S complex (PSC). PSC has been proposed to strongly inhibit thrombin production by enhancing the ability of TFPI$α$ to inhibit clotting factor Xa up to 100-fold and by localizing to platelet membranes, limiting fXa activity shortly after coagulation starts. Yet, exactly how PS functions with TFPI$α$ as an anticoagulant remains poorly understood. To investigate, we extend an experimentally validated mathematical model of blood coagulation to include PSC and free PS (not part of PSC) in the plasma, as well as free PS and TFPI$α$ in platelets. We find that shortly after coagulation initiation, PSC strongly inhibits thrombin production. We find that the (unknown) magnitude of the enhanced affinity of PSC binding to inhibit fXa critically regulates PSC's impact on thrombin production. We find that under flow, PSC can unexpectedly accumulate on platelets to concentrations ~50 times higher than in the plasma. We also find that PSC limits thrombin production by occupying fV-specific binding sites on platelets. Our results show that changes in PSC can dramatically impact severity of pathological bleeding disorders. For the east Texas bleeding disorder, elevated PSC concentrations eliminate thrombin bursts, leading to bleeding. With fV deficiency, reducing PSC rescues thrombin production in severe fV deficiency and returns thrombin production due to mild fV deficiency to normal. Finally, thrombin production in severe hemophilia A can be substantially improved by blocking PSC's anticoagulant function.

q-bio.MN

Sensitivity of ECG QRS Complexes to His-Purkinje Structure in Computational Heart Models

Cardiac digital twins (CDT) are emerging as a potentially transformative tool in cardiology. A critical yet understudied determinant of CDT accuracy is the His-Purkinje system (HPS), which influences ventricular depolarization and shapes the QRS complex of the electrocardiogram (ECG). Here, we quantify how structural variations in the HPS alter QRS morphology and identify which parameters drive this variability. We generated HPS structures using a fractal-tree, rule-based algorithm, systematically varying nine model parameters and assessing their effects on ten QRS-related metrics. We conducted a Sobol sensitivity analysis to quantify direct and interaction-driven contributions of each parameter to observed variability. Our results suggest that most minor changes in HPS structure exert minimal influence on individual QRS features; however, certain parameter combinations can produce abnormal QRS morphologies. Wave durations and peak amplitudes of the QRS complex exhibit low sensitivity to individual HPS parameter variations; however, we found that specific parameter combinations can result in interactions that significantly alter these aspects of QRS morphology. We found that certain HPS structures can cause premature QRS formation, obscuring P-wave formation. QRS timing variability was primarily driven by interactions among branch and fascicle angles and branch repulsivity, though other parameters also showed notable interaction effects. In addition to interactions, individual variations in the number of branches in the HPS also affected QRS timing. While future models should account for these potential sources of variability, this study indicates that minor anatomical differences between a healthy patient's HPS and that of a generic model are unlikely to significantly impact model fidelity or clinical interpretation when both systems are physiologically normal.

q-bio.QM

Evaluating COVID-19 Surveillance Testing Strategies at Colorado School of Mines: A Stochastic Modeling Approach

This study introduces a stochastic model of COVID-19 transmission tailored to the Colorado School of Mines campus and evaluates surveillance testing strategies within a university context. Enhancing the conventional SEIR framework with stochastic transitions, our model accounts for the unique characteristics of disease spread in a residential college, including specific states for testing, quarantine, and isolation. Employing an approximate Bayesian computation (ABC) method for parameter estimation, we navigate the complexities inherent in stochastic models, enabling an accurate fit of the model with the campus case data. We then studied our model under the estimated parameters to evaluate the efficacy of different testing policies that could be implemented on a university campus. This framework not only advances understanding of COVID-19 dynamics on the Mines campus but serves as a blueprint for comparable settings, providing insights for informed strategies against infectious diseases.

stat.AP

clotFoam: An Open-Source Framework to Simulate Blood Clot Formation Under Arterial Flow

Blood clotting involves the coupled processes of platelet aggregation and coagulation. Simulating clotting under flow in complex geometries is challenging due to multiple temporal and spatial scales and high computational cost. clotFoam is an open-source software developed in OpenFOAM that employs a continuum model of platelet advection, diffusion, and aggregation in a dynamic fluid environment and a simplified coagulation model with proteins that advect, diffuse, and react within the fluid and with wall-bound species through reactive boundary conditions. Our framework provides the foundation on which one can build more complex models and perform reliable simulations in almost any computational domain.

physics.flu-dyn

A Mathematical Model of Platelet Aggregation in an Extravascular Injury Under Flow

We present the first mathematical model of flow-mediated primary hemostasis in an extravascular injury, which can track the process from initial deposition to occlusion. The model consists of a system of ordinary differential equations (ODE) that describe platelet aggregation (adhesion and cohesion), soluble-agonist-dependent platelet activation, and the flow of blood through the injury. The formation of platelet aggregates increases resistance to flow through the injury, which is modeled using the Stokes-Brinkman equations. Data from analogous experimental (microfluidic flow) and partial differential equation models informed parameter values used in the ODE model description of platelet adhesion, cohesion, and activation. This model predicts injury occlusion under a range of flow and platelet activation conditions. Simulations testing the effects of shear and activation rates resulted in delayed occlusion and aggregate heterogeneity. These results validate our hypothesis that flow-mediated dilution of activating chemical ADP hinders aggregate development. This novel modeling framework can be extended to include more mechanisms of platelet activation as well as the addition of the biochemical reactions of coagulation, resulting in a computationally efficient high throughput screening tool.

q-bio.CB

A 3-dimensional model of flagellar swimming in a Brinkman fluid

We investigate 3-dimensional flagellar swimming in a fluid with a sparse network of stationary obstacles or fibers. The Brinkman equation is used to model the average fluid flow where a flow-dependent term, including a resistance parameter that is inversely proportional to the permeability, models the resistive effects of the fibers on the fluid. To solve for the local linear and angular velocities that are coupled to the flagellar motion, we extend the method of regularized Brinkmanlets to incorporate a Kirchhoff rod, discretized as point forces and torques along a centerline. Representing a flagellum as a Kirchhoff rod, we investigate emergent waveforms for different preferred strain and twist functions. Since the Kirchhoff rod formulation allows for out-of-plane motion, in addition to studying a preferred planar sine wave configuration, we also study the case with a preferred helical configuration. Our numerical method is validated by comparing results to asymptotic swimming speeds derived for an infinite-length cylinder propagating planar or helical waves. Similar to the asymptotic analysis for both planar and helical bending, we observe that with small amplitude bending, swimming speed is always enhanced relative to the case with no fibers in the fluid (Stokes) as the resistance parameter is increased....

physics.flu-dyn

Swimming Speeds of Waving Cylindrical Tails in Viscous Fluids with Resistance

Many microorganisms swim in a highly heterogeneous environment with obstacles such as fibers or polymers. To better understand how this environment affects microorganism swimming, we study propulsion of a cylinder or filament in a fluid with a sparse, stationary network of obstructions modeled by the Brinkman equation. The mathematical analysis of swimming speeds is investigated by studying an infinite-length cylinder propagating lateral or spiral displacement waves. For fixed bending kinematics, we find that swimming speeds are enhanced due to the added resistance from the fibers. In addition, we examine the work and the torque exerted on the cylinder in relation to the resistance. The solutions for the torque, swimming speed, and work of an infinite-length cylinder in a Stokesian fluid are recovered as the resistance is reduced to zero. Finally, we compare the asymptotic solutions with the numerical results obtained from the Method of Regularized Brinkmanlets. The swimming speed of a finite-length filament decreases as its length decreases and planar bending induces an angular velocity that increases linearly with added resistance. The comparisons between the asymptotic analysis and computation give insight on the effect of the length of the filament, the permeability, and the thickness of the cylinder in terms of the overall performance of planar and helical swimmers

physics.flu-dyn