Abstract:

BACKGROUND: Genetic predisposition is believed to be responsible for most clinically significant arrhythmias; however, suitable genetic animal models to study disease mechanisms and evaluate new treatment strategies are largely lacking. METHODS AND RESULTS: In search of suitable arrhythmia models, we isolated the zebrafish mutation reggae (reg), which displays clinical features of the malignant human short-QT syndrome such as accelerated cardiac repolarization accompanied by cardiac fibrillation. By positional cloning, we identified the reg mutation that resides within the voltage sensor of the zebrafish ether-à-go-go-related gene (zERG) potassium channel. The mutation causes premature zERG channel activation and defective inactivation, which results in shortened action potential duration and accelerated cardiac repolarization. Genetic and pharmacological inhibition of zERG rescues recessive reg mutant embryos, which confirms the gain-of-function effect of the reg mutation on zERG channel function in vivo. Accordingly, QT intervals in ECGs from heterozygous and homozygous reg mutant adult zebrafish are considerably shorter than in wild-type zebrafish. CONCLUSIONS: With its molecular and pathophysiological concordance to the human arrhythmia syndrome, zebrafish reg represents the first animal model for human short-QT syndrome.

Abstract:

Es wird eine Methode beschrieben, wie medizinische Bilder des Herzens modellbasiert mit EKG-Daten verknüpft werden können, um damit zu einer spezifischen Diagnostik und zu einer besseren Therapieplanung in der Kardiologie zu gelangen. Zunächst wird aus MRT- oder CT-Bildern des Patienten die Geometrie seines Herzens ermittelt. Elektrokardiographische Messungen an der Körperoberfläche (EKG oder Body Surface Potential Mapping) und aus dem Inneren des Herzens (intracardial mapping) werden aufgenommen und die Orte der Messung in den Bilddatensatz eingetragen (registration). Ein elektrophysiologisches Computermodell vom Herzen des Patienten wird mit Hilfe der elektrophysiologischen Messdaten iterativ angepasst. Schließlich entsteht im Computer ein virtuelles Herz des Patienten, welches sowohl die Geometrie als auch die Elektrophysiologie wiedergibt. Ein Modell der Vorhöfe hat beispielsweise das Potenzial, die Ursachen von Vorhofflimmern zu erkennen und die Radiofrequenz-Ablationsstrategie zu optimieren. Ein Modell der Ventrikel des Herzens kann helfen, genetisch bedingte Rhythmusstörungen besser zu verstehen oder auch die Parameter bei der kardialen Resynchronisationstherapie zu optimieren. Die Modellierung des Herzens mit einem Infarktgebiet könnte die elektrophysiologischen Auswirkungen des Infarktes beschreiben und die Risikostratifizierung für gefährliche ventrikuläre Arrhythmien unterstützen oder die Erfolgsrate bei ventrikulären Ablationen erhöhen.

Abstract:

After mathematical modeling of the healthy heart now modeling of diseases comes into the focus of research. Modeling of arrhythmias already shows a large degree of realism. This offers the chance of more detailed diagnosis and computer assisted therapy planning. Options for genetic diseases (channelopathies like Long-QT-syndrome), infarction and infarction-induced ventricular fibrillation, atrial fibrillation (AF) and cardiac resynchronization therapy are demonstrated.

Abstract:

Multi-scale, multi-physical heart models have not yet been able to include a high degree of accuracy and resolution with respect to model detail and spatial resolution due to computational limitations of current systems. We propose a framework to compute large scale cardiac models. Decomposition of anatomical data in segments to be distributed on a parallel computer is carried out by optimal recursive bisection (ORB). The algorithm takes into account a computational load parameter which has to be adjusted according to the cell models used. The diffusion term is realized by the monodomain equations. The anatomical data-set was given by both ventricles of the Visible Female data-set in a 0.2 mm resolution. Heterogeneous anisotropy was included in the computation. Model weights as input for the decomposition and load balancing were set to (a) 1 for tissue and 0 for non-tissue elements; (b) 10 for tissue and 1 for non-tissue elements. Scaling results for 512, 1024, 2048, 4096 and 8192 computational nodes were obtained for 10 ms simulation time. The simulations were carried out on an IBM Blue Gene/L parallel computer. A 1 s simulation was then carried out on 2048 nodes for the optimal model load. Load balances did not differ significantly across computational nodes even if the number of data elements distributed to each node differed greatly. Since the ORB algorithm did not take into account computational load due to communication cycles, the speedup is close to optimal for the computation time but not optimal overall due to the communication overhead. However, the simulation times were reduced form 87 minutes on 512 to 11 minutes on 8192 nodes. This work demonstrates that it is possible to run simulations of the presented detailed cardiac model within hours for the simulation of a heart beat.

Abstract:

Increasing biophysical detail in multi physical, multiscale cardiac model will demand higher levels of parallelism in multi-core approaches to obtain fast simulation times. As an example of such a highly parallel multi-core approaches, we develop a completely distributed bidomain cardiac model implemented on the IBM Blue Gene/L architecture. A tissue block of size 50 times 50 times 100 cubic elements based on ten Tusscher et al. (2004) cell model is distributed on 512 computational nodes. The extracellular potential is calculated by the Gauss-Seidel (GS) iterative method that typically requires high levels of inter-processor communication. Specifically, the GS method requires knowledge of all cellular potentials at each of it iterative step. In the absence of shared memory, the values are communicated with substantial overhead. We attempted to reduce communication overhead by computing the extracellular potential only every 5th time step for the integration of the cell models. We also investigated the effects of reducing inter-processor communication to every 5th, 10th, 50th iteration or no communication within the GS iteration. While technically incorrect, these approximation had little impact on numerical convergence or accuracy for the simulations tested. The results suggest some heuristic approaches may further reduce the inter-processor communication to improve the execution time of large-scale simulations.

Abstract:

Electrophysiological modeling of the heart enable quantitative description of electrical processes during normal and abnormal excitation. Cell models describe e.g. the properties of the cell membrane and the gating process of ionic channels. New measurement data is available for these channels for physiological and some pathological states. These data should be included in the models to enhance their features. In this work we describe a framework adapting ion channel models to measurement data by using a particle swarm optimization (PSO). Models of ion channels can be described by Hogdkin-Huxley equations or by Markovian models. They consider rate constants that are complex functions depending on the transmembrane voltage. Each transition has two rate constants described by several parameters. These parameters need to be varied in order to minimize the difference between measured and simulated ion channel kinetics. Since this minimization procedure is multidimensional and the function can have several local minima, conventional optimization strategies like Powells algorithm and conjugate gradient do not ensure to find the global minimum. To overcome this, a PSO was implemented that inserts several dependent particles randomly into the search space. It is based on the social behavior of swarms. As the particles are independent during each iteration the procedure can be calculated in parallel. The measurement data used for this work were current traces of a voltage-clamp protocol of reggae mutant hERG channels. The same protocol as for the measurement was assigned to the model of Lu et al. describing hERG function with a Markovian model. The value to be minimized was the sum of mean square errors between measured and simulated currents at certain time instances. Both Powell and PSO were started several times with random starting values. In 94% of the cases PSO found the minimum compared to 16% for Powell. On the other hand PSO needed approximately 100 times more function evaluations. The parallelization decreased the overall time needed by the PSO to about the same amount Powell needed. Therefore, the parallel PSO is a fast and reliable approach for adapting ion channel models to measured data.

Abstract:

The sinus node (SN) is the primary pacemaker of the heart. It is a heterogeneous structure in the right atrium composed of two types of cells with different electrophysiological properties. One type is distributed more densely in the periphery the other in the center. Different gap junction types and densities exist leading to a heterogeneity in conduction. It is supposed that this complex interplay of heterogeneities is the basic mechanism that the small SN is able to electrically drive the surrounding atrial muscle. If this interplay is disturbed, the function of the SN can be effected massively. In this simulation study we want to demonstrate the effects of the L532P mutation in hERG called reggae on SN electrophysiology.Mutant hERG channels were expressed in xenopus oocytes and the channel properties were measured with voltage-clamp technique. The data showed mainly a shift of the steady-state inactivation to more positive potentials. This leads to an increase of the ionic current during the depolarized phase. The data was integrated in the heterogeneous rabbit SN model of Zhang et al. by adapting the parameters of the IKr channel with aid of optimization methods using the same stimulation protocol as in the measurements.The most sensitive parameter was the shift voltage of the steady-state inactivation from -19.2 mV in the physiological case to 10.1 mV in the mutant model. When inserting this mutant IKr in the central SN model the ability of the central cells to depolarize spontaneously was eliminated. Peripheral cell still beat but are affected by the mutation. The slope of the pre-potential and the upstroke velocity were not changed. The maximum diastolic potential was increased by 2 mV and the maximum systolic potential decreased by 1.5 mV. The diastolic interval was shortened slightly by 3 ms. The main effect was a reduction of the action potential duration from 108 ms to 84 ms leading to a frequency increase from 6.37 Hz to 7.62 Hz.These effects lead to a changing SN function. The increase of the shift voltage is in good agreement with the measured changes. Especially the loss of auto-rhythmicity in the central zone is expected to change the overall SN activity. Although peripheral SN cells beat faster we expect a bradycardial function of the complete SN because of electrotonic interactions with the silent central SN cells and the low resting membrane voltage of surrounding atrial muscle cells. In a further study this suggestion has to be investigated in an anisotropic and heterogeneous 3D model.

Abstract:

Simulation of cardiac excitation is often a trade-off between accuracy and speed. A promising minimal, time-efficient cell model with four state variables has recently been presented together with parametrizations for ventricular cell behaviour. In this work, we adapt the model parameters to reproduce atrial excitation properties as given by the Courtemanche model. The action potential shape is considered as well as the restitution of action potential duration and conduction velocity. Simulation times in a single cell and a tissue patch are compared between the two models. We further present the simulation of a sinus beat on the atria in a realistic 3D geometry using the fitted minimal model in a monodomain simulation.