Journal Publications
[15] Sebastian R., Zimmerman V., Romero D., Sanchez-Quintana D., Frangi A.F. Characterization and Modeling of the Peripheral Cardiac Conduction System. IEEE Transactions on Medical Imaging. Vol. XX(XX), pp. -, 2013. IF: 3.643 [PDF]
The development of biophysical models of the heart has the potential to get insights in the pathophysiology of the heart, which requires to accurately modeling anatomy and function. The electrical activation sequence of the ventricles depends strongly on the cardiac conduction system (CCS). Its morphology and function cannot be observed in-vivo, and therefore data available come from histological studies. We present a review on data available of the peripheral CCS including new experiments. In order to build a realistic model of the CCS we designed a procedure to extract morphological characteristics of the CCS from stained calf tissue samples. A CCS model personalized with our measurements has been built using L-systems. The effect of key unknown parameters of the model in the electrical activation of the left ventricle has been analyzed. The CCS models generated share the main characteristics of observed stained Purkinje networks. The timing of the simulated electrical activation sequences were in the physiological range for CCS models that included enough density of PMJs. These results show that this approach is a potential methodology for collecting knowledge-domain data and build improved CCS models of the heart automatically.
[14] Sebastian R., Zimmerman V., Romero D., Frangi A.F.. Construction of a Computational Anatomical Model of the Peripheral Cardiac Conduction System. IEEE Transactions on Biomedical Engineering. Vol. 58(12), pp. 3479-82, 2011. IF: 1.792 [PDF]
A methodology is presented here for automatic construction of a ventricular model of the cardiac conduction system (CCS), which is currently a missing block in many multiscale cardiac electromechanic models. It includes the His bundle, left bundle branches, and the peripheral CCS. The algorithm is fundamentally an enhancement of a rule-based method known as the Lindenmayer systems (L-systems). The generative procedure has been divided into three consecutive independent stages, which subsequently build the CCS from proximal to distal sections. Each stage is governed by a set of user parameters together with anatomical and physiological constrains to direct the generation process and adhere to the structural observations derived from histology studies. Several parameters are defined using statistical distributions to introduce stochastic variability in the models. The CCS built with this approach can generate electrical activation sequences with physiological characteristics.
[13] Dux-Santoy L., Sebastian R., Felix-Rodriguez J., Ferrero J.M., Saiz J. Interaction of specialized cardiac conduction system with antiarrhythmic drugs: a simulation study. IEEE Transactions on Biomedical Engineering. Vol. 58(12), pp. 3475-78, 2011. IF: IF: 1.792 [PDF]
The use of antiarrhythmic drugs is common to treat heart rhythm disorders. Computational modeling and simulation are promising tools that could be used to investigate the effects of specific drugs on cardiac electrophysiology. In this paper, we study the multiscale effects of dofetilide, a drug that blocks IKr, from cellular to organ level paying special attention to its effect on heart structures, in particular the specialized cardiac conduction system (CCS). We include a model of the CCS in a patient-specific anatomical ventricular model and study the drug effects in simulations with and without a CCS. Results confirmed the expected effects of dofetilide at cellular level, increasing the action potential duration, and at organ level, prolonging the QT segment. Notable differences are shown between models with and without the CCS on action potential duration distributions. These techniques show the importance of heart heterogeneity and the global effects of the interaction of drugs with cardiac structures.
[12] Pashaei A., Romero D., Sebastian R., Camara O., Frangi, AF. Fast Multiscale Modeling of Cardiac Electrophysiology Including Purkinje System. IEEE Transactions on Biomedical Engineering. Vol. 58(10), pp. 2956-2960 2011. IF: IF: 1.792 [PDF]
In this paper, we present a modeling methodology to couple the cardiac conduction system to cardiac myocytes through a model of Purkinje-ventricular junctions to yield fast and realistic electrical activation of the ventricles. A patient-specific biventricular geometry is obtained from processing computed tomography scan data. A one-manifold implementation of the fast marching method based on Eikonal-type equations is used for modeling heart electrophysiology, which facilitates the multiscale 1-D-3-D coupling at very low computational costs. The method is illustrated in in-silico experiments where we analyze and compare alternative pacing strategies on the same patient-specific anatomy. We also show very good agreement between the results from the proposed approach and more detailed and comprehensive biophysical models for modeling cardiac electrophysiology. The effect of atrioventricular delay on the distribution of activation time in myocardium is studied with two experiments. Given the reasonable computational times and realistic activation sequences provided by our method, it can have an important clinical impact on the selection of optimal implantation sites of pacing leads or placement of ablation catheter's tip in the context of cardiac rhythm management therapies.
[11] Bradley C., Bowery A., Britten R., Budelmann V., Camara O., Christie R., Cookson A., Frangi A., Gamage T.B., Heidlauf T., Krittian S., Ladd D., Little D., Mithraratne K., Nash M., Nickerson D., Nielsen P., Nordbo Y., Omholt S., Pashaei A., Paterson D., Rajagopal V., Reeve A., Röhrle O., Safaei S., Sebastian R., Steghöfer M., Wu T., Yu T., Zhang H., Hunter P. OpenCMISS: A multi-physics and multi-scale computational infrastructure for the VPH/Physiome project. Progress in Biophysics and Molecular Biology. Vol. 107(1), pp. 32-47, 2011. IF: 3.964 [PDF]
The VPH/Physiome Project is developing the model encoding standards CellML (cellml.org) and FieldML (fieldml.org) as well as web-accessible model repositories based on these standards (models.physiome.org). Freely available open source computational modelling software is also being developed to solve the partial differential equations described by the models and to visualise results. The OpenCMISS code (opencmiss.org), described here, has been developed by the authors over the last six years to replace the CMISS code that has supported a number of organ system Physiome projects. OpenCMISS is designed to encompass multiple sets of physical equations and to link subcellular and tissue-level biophysical processes into organ-level processes. In the Heart Physiome project, for example, the large deformation mechanics of the myocardial wall need to be coupled to both ventricular flow and embedded coronary flow, and the reaction-diffusion equations that govern the propagation of electrical waves through myocardial tissue need to be coupled with equations that describe the ion channel currents that flow through the cardiac cell membranes. In this paper we discuss the design principles and distributed memory architecture behind the OpenCMISS code. We also discuss the design of the interfaces that link the sets of physical equations across common boundaries (such as fluid-structure coupling), or between spatial fields over the same domain (such as coupled electromechanics), and the concepts behind CellML and FieldML that are embodied in the OpenCMISS data structures. We show how all of these provide a flexible infrastructure for combining models developed across the VPH/Physiome community.
[10] Camara O., Sermesant M., Lamata P., Wang L., Pop M., Relan J., De Craene M., Delingette H., Liu H., Niederer S., Pashaei A., Plank G., Romero D., Sebastian R., Wong K.C.L., Zhang H., Ayache N., Frangi A.F., Shif P., Smith N., Wright G.A. Inter-Model Consistency and Complementarity: Learning from ex-vivo Imaging and Electrophysiological Data towards an Integrated Understanding of Cardiac Physiology. Progress in Biophysics and Molecular Biology. Vol. 107(1), pp. 122-133, 2011. IF: 3.964 [PDF]
Computational models of the heart at various scales and levels of complexity have been independently developed, parameterised and validated using a wide range of experimental data for over four decades. However, despite remarkable progress, the lack of coordinated efforts to compare and combine these computational models has limited their impact on the numerous open questions in cardiac physiology. To address this issue, a comprehensive dataset has previously been made available to the community that contains the cardiac anatomy and fibre orientations from magnetic resonance imaging as well as epicardial transmembrane potentials from optical mapping measured on a perfused ex-vivo porcine heart. This data was used to develop and customize four models of cardiac electrophysiology with different level of details, including a personalized fast conduction Purkinje system, a maximum a posteriori estimation of the 3D distribution of transmembrane potential, the personalization of a simplified reaction-diffusion model, and a detailed biophysical model with generic conduction parameters. This study proposes the integration of these four models into a single modelling and simulation pipeline, after analyzing their common features and discrepancies. The proposed integrated pipeline demonstrates an increase prediction power of depolarization isochrones in different pacing conditions.
[9] Letinic K, Sebastian R, Barthel, A., Toomre D. Deciphering Sub-Cellular Processes in Live Imaging Data Sets via Dynamic Probabilistic Networks. Bioinformatics. 2010. IF: 4.926 [PDF]
Motivation: Designing mathematical tools that can formally describe the dynamics of complex intracellular processes remains a challenge. Live cell imaging reveals changes in the cellular states, but current simple approaches extract only minimal information of a static snapshot. Results: We implemented a novel approach for analyzing organelle behavior in live cell imaging data based on hidden Markov models (HMMs) and showed that it can determine the number and evolution of distinct cellular states involved in a biological process. We analyzed insulin-mediated exocytosis of single Glut4-vesicles, a process critical for blood glucose homeostasis and impaired in type II diabetes, by using total internal reflection fluorescence microscopy (TIRFM). HMM analyses of movie sequences of living cells reveal that insulin controls spatial and temporal dynamics of exocytosis via the exocyst, a putative tethering protein complex. Our studies have validated the proof-of-principle of HMM for cellular imaging and provided direct evidence for the existence of complex spatial-temporal regulation of exocytosis in non-polarized cells. We independently confirmed insulin-dependent spatial regulation by using static spatial statistics methods. Conclusion: We propose that HMM-based approach can be exploited in a wide avenue of cellular processes, especially those where the changes of cellular states in space and time may be highly complex and non-obvious, such as in cell polarization, signaling and developmental processes.
[8] Romero D., Sebastian, R., Bijnens, B., Zimmerman, V., Boyle, PM., Vigmond, EJ., Frangi, AF. Effects of the Purkinje system and cardiac geometry on biventricular pacing: a model study. Annals of Biomedical Engineering. 2010. IF: 2.605 [PDF]
Heart failure leads to gross cardiac structural changes. While cardiac resynchronization therapy (CRT) is a recognized treatment for restoring synchronous activation, it is not clear how changes in cardiac shape and size affect the electrical pacing therapy. This study used a human heart computer model which incorporated anatomical structures such as myofiber orientation and a Purkinje system (PS) to study how pacing affected failing hearts. The PS was modeled as a tree structure that reproduced its retrograde activation feature. In addition to a normal geometry, two cardiomyopathies were modeled: dilatation and hypertrophy. A biventricular pacing protocol was tested in the context of atrio-ventricular block. The contribution of the PS was examined by removing it, as well as by increasing endocardial conductivity. Results showed that retrograde conduction into the PS was a determining factor for achieving intraventricular synchrony. Omission of the PS led to an overestimate of the degree of electrical dyssynchrony while assessing CRT. The activation patterns for the three geometries showed local changes in the order of activation of the lateral wall in response to the same pacing strategy. These factors should be carefully considered when determining lead placement and optimizing device parameters in clinical practice.
[7] Letinic K, Sebastian R, Toomre D, Rakic P. Exocyst is involved in polarized cell migration and cerebral cortical development. Proc. Nat. Acad. Sci. 106(6). 2009. IF: 9.598. [PDF]
Neuronal migration is essential for proper development of the cerebral cortex. As a first step, a postmitotic cell extends its leading process, presumably by adding new membrane at the growing tip, which would enable directed locomotion. The goal of the present study was to determine if biosynthetic exocytic pathway is polarized in migrating cells and whether polarized exocytosis promotes directed cell migration. A promising candidate for controlling the spatial sites of vesicle tethering and fusion at the plasma membrane is a protein complex called the exocyst. We found that cell migration in a wound assay, as well as cortical neuronal migration during embryonic development was impaired when the exocyst was disturbed. By combining TIRF microscopy and a stochastic model of exocytosis, we found that vesicle exocytosis is preferentially distributed close to the leading edge of polarized cells, that the exocytic process is organized into hotspots, and that the polarized delivery of vesicles and their clustering in hotspots depend on the intact exocyst complex. The exocyst complex seems to achieve this spatial regulation by determining the sites at the membrane where secretory vesicles tether. Thus, our study supports the notion that polarized membrane traffic regulated by the exocyst is an essential component of cell migration and that its deficit may lead to cortical abnormalities involving cortical neuronal malpositioning.
[6] Diaz, E., Sebastian, R. Ayala, G. Díaz, M.E,.Zoncu, R., Toomre, D., Gasman, S. Measuring spatial temporal interaction in bivariate temporal random sets with applications to cell biology. IEEE Transactions on Pattern Analysis and Machine Intelligence. 30(9). 2008. IF:3.579. [PDF]
Analyzing spatiotemporal dependencies between different types of events is highly relevant to many biological phenomena (e.g., signaling and trafficking), especially as advances in probes and microscopy have facilitated the imaging of dynamic processes in living cells. For many types of events, the segmented areas can overlap spatially and temporally, forming random clumps. In this paper, we model the binary image sequences of two different event types as a realization of a bivariate temporal random set and propose a nonparametric approach to quantify spatial and spatiotemporal interrelations using the pair correlation, cross-covariance, and the Ripley IK functions. Based on these summary statistics, we propose a randomization procedure to test independence between event types by applying random toroidal shifts and Monte Carlo tests. A simulation study assessed the performance of the proposed estimators and showed that these statistics capture the spatiotemporal dependencies accurately. The estimation of the spatiotemporal interval of interactions was also obtained. The method was successfully applied to analyze the interdependencies of several endocytic proteins using image sequences of living cells and validated the procedure as a new way to automatically quantify dependencies between proteins in a formal and robust manner.
[5] Zoncu, R. Perera, R.M., Sebastian, R., Chen, H. Ayala, G., Toomre, D., De Camilli, P. Acute depletion of phosphotidylinositol 4,5 biphosphate results in loss of endocytic clathrin coated pits. Proc. Nat. Acad. Sci., 104(10):3793 - 3798. 2007. IF: 9.598. [PDF]
Phosphatidylinositol 4,5-bisphosphate [PI(4,5)P 2], a phosphoinositide concentrated predominantly in the plasma membrane, binds endocytic clathrin adaptors, many of their accessory factors, and a variety of actin-regulatory proteins. Here we have used fluorescent fusion proteins and total internal reflection fluorescence microscopy to investigate the effect of acute PI(4,5)P 2 breakdown on the dynamics of endocytic clathrin-coated pit components and of the actin regulatory complex, Arp2/3. PI(4,5)P 2 breakdown was achieved by the inducible recruitment to the plasma membrane of an inositol 5-phosphatase module through the rapamycin/FRB/FKBP system or by treatment with ionomycin. PI(4,5)P 2 depletion resulted in a dramatic loss of clathrin puncta, which correlated with a massive dissociation of endocytic adaptors from the plasma membrane. Remaining clathrin spots at the cell surface had only weak fluorescence and were static over time. Dynamin and the p20 subunit of the Arp2/3 actin regulatory complex, which were concentrated at late-stage clathrin-coated pits and in lamellipodia, also dissociated from the plasma membrane, and these changes correlated with an arrest of motility at the cell edge. These findings demonstrate the critical importance of PI(4,5)P 2 in clathrin coat dynamics and Arp2/3-dependent actin regulation.
[4] Díaz, M.E., Ayala, G., Sebastian, R., Martinez-costa, L. Granulometric Analysis of Corneal Endothelium specular images by using a germ-grain model. Computers in Biology and Medicine. 37:364-375, 2007. IF: 1.170. [PDF]
Specular microscopy is widely used to study the human corneal endothelium status in vivo. In this paper, the corneal endothelium is represented as a binary image composed of the cell inscribed circles. The granulometric distribution function of the complement of this image is used as a functional descriptor, which provides information about the shape, size and spatial arrangement of cells. Experimental evaluation using bootstrap techniques shows its ability to discriminate between controls and pathological cases. It represents a reliable and graphical alternative to the classical indices (cell density, hexagonality and coefficient of variation of cell areas), which behave poorly when detecting subtle abnormalities.
[3] Sebastian, R., Díaz, E., Ayala, G., M.E. Diaz, Zoncu, R., Toomre, D. Studying Endocytosis in Space and Time by means of Temporal Boolean Models. Pattern Recognition. 39(11):2175-2185, 2006. IF: 2.019. [PDF]
Endocytosis is a process by which cells carry traffic from the extracellular space into various intracellular compartments. Visualization of fluorescently tagged clathrin proteins (mediators of endocytosis) allows us to image endocytosis in real time. When imaging the plasma membrane, areas of fluorescence generated by different endocytic processes overlap spatially and temporally, forming random clumps. Here, a sequence of segmented clathrin spots is considered a realization of a non-isotropic 3D Boolean model. Estimates of the intensity, the mean perimeter and the density function of the durations of endocytic events are obtained.
[2] Ayala, G., Sebastian, R., Díaz, M.E., Diaz, E., Zoncu, R., Toomre, D. Analysis of Spatially and Temporally Overlapping Events with Application to Image Sequences. IEEE Transactions on Pattern Analysis and Machine Intelligence. 28(10):1707-1712, 2006. IF: 3.579. [PDF]
Counting spatially and temporally overlapping events in image sequences and estimating their shape-size and duration features are important issues in some applications. We propose a stochastic model, a particular case of the nonisotropic 3D Boolean model, for performing this analysis: the temporal Boolean model. Some probabilistic properties are derived and a methodology for parameter estimation from time-lapse image sequences is proposed using an explicit treatment of the temporal dimension. We estimate the mean number of germs per unit area and time, the mean grain size and the duration distribution. A wide simulation study in order to assess the proposed estimators showed promising results. The model was applied on biological image sequences of invivo cells in order to estimate new parameters such as the mean number and duration distribution of endocytic events. Our results show that the proposed temporal Boolean model is effective for obtaining information about dynamic processes which exhibit short-lived, but spatially and temporally overlapping events.
[1] Sebastian, R., Díaz, M.E., Ayala, G., Letinic, K., Moncho-Bogani, J, Toomre, D. Spatio-temporal Analysis of Constitutive Exocytosis in Epithelial Cells. IEEE/ACM Transactions on Computational Biology and Bioinformatics. Vol. 3:17-32. 2006. IF: 1.622. [PDF]
Exocytosis is an essential cellular trafficking process integral to the proper distribution and function of a plethora of molecules, including transporters, receptors, and enzymes. Moreover, incorrect protein targeting can lead to pathological conditions. Recently, the application of evanescent wave microscopy has allowed us to image the final steps of exocytosis. However, spatiotemporal analysis of fusion of constitutive vesicular traffic with the plasma membrane has not been systematically performed. Also, the spatial sites and times of vesicle fusion have not yet been analyzed together. In addition, more formal tests are required in testing biological hypotheses, rather than visual inspection combined with statistical descriptives. Ripley K-functions are used to examine the joint and marginal behavior of locations and fusion times. Semiautomatic detection and mapping of constitutive fusion sites reveals spatial and temporal clustering, but no dependency between the locations and times of fusion events. Our novel approach could be translated to other studies of membrane trafficking in health and diseases such as diabetes.
