@article {2967, title = {Use of SPIDER and SPIRE in Image Reconstruction.}, journal = {International Tables for Crystallography}, volume = {F}, year = {2012}, abstract = {SPIDER is a comprehensive command-operated suite of programs for image processing in electron microscopy, with special emphasis on single-particle reconstruction. This chapter provides an outline of the way SPIDER and SPIRE, its interactive graphical user interface, may be used to obtain a three-dimensional reconstruction from projections of many randomly oriented realizations of a biological molecule.}, doi = {10.1107/97809553602060000874}, url = {http://xrpp.iucr.org/cgi-bin/itr?url_ver=Z39.88-2003\&rft_dat=what\%3Dchapter\%26volid\%3DFb\%26chnumo\%3D19o8\%26chvers\%3Dv0001}, author = {Leith, ArDean and Baxter, Bill and Frank, Joachim} } @article {2110, title = {Determination of signal-to-noise ratios and spectral SNRs in cryo-EM low-dose imaging of molecules.}, journal = {J Struct Biol}, volume = {166}, year = {2009}, month = {05/2009}, pages = {126-32}, abstract = {

Attempts to develop efficient classification approaches to the problem of heterogeneity in single-particle reconstruction of macromolecules require phantom data with realistic noise models. We have estimated the signal-to-noise ratios and spectral signal-to-noise ratios for three steps in the electron microscopic image formation from data obtained experimentally. An important result is that structural noise, i.e., the irreproducible component of the object prior to image formation, is substantial, and of the same order of magnitude as the reproducible signal. Based on this result, the noise modeling for testing new classification techniques can be improved.

}, keywords = {Cryoelectron Microscopy, Image Processing, Computer-Assisted}, issn = {1095-8657}, doi = {10.1016/j.jsb.2009.02.012}, url = {http://www.ncbi.nlm.nih.gov/pubmed/19269332}, author = {Baxter, Bill and Grassucci, Robert A and Gao, Haixiao and Frank, Joachim} } @article {2111, title = {Ribosome-induced changes in elongation factor Tu conformation control GTP hydrolysis.}, journal = {Proc Natl Acad Sci U S A}, volume = {106}, year = {2009}, month = {01/2009}, pages = {1063-8}, abstract = {

In translation, elongation factor Tu (EF-Tu) molecules deliver aminoacyl-tRNAs to the mRNA-programmed ribosome. The GTPase activity of EF-Tu is triggered by ribosome-induced conformational changes of the factor that play a pivotal role in the selection of the cognate aminoacyl-tRNAs. We present a 6.7-A cryo-electron microscopy map of the aminoacyl-tRNA x EF-Tu x GDP x kirromycin-bound Escherichia coli ribosome, together with an atomic model of the complex obtained through molecular dynamics flexible fitting. The model reveals the conformational changes in the conserved GTPase switch regions of EF-Tu that trigger hydrolysis of GTP, along with key interactions, including those between the sarcin-ricin loop and the P loop of EF-Tu, and between the effector loop of EF-Tu and a conserved region of the 16S rRNA. Our data suggest that GTP hydrolysis on EF-Tu is controlled through a hydrophobic gate mechanism.

}, keywords = {Cryoelectron Microscopy, Enzyme Activation, Escherichia coli, Escherichia coli Proteins, Guanosine Triphosphate, Histidine, Hydrolysis, Hydrophobic and Hydrophilic Interactions, Models, Molecular, Peptide Elongation Factor Tu, Protein Structure, Secondary, Ribosomal Proteins, Ribosomes, RNA, Transfer, Signal Transduction}, issn = {1091-6490}, doi = {10.1073/pnas.0811370106}, url = {http://www.ncbi.nlm.nih.gov/pubmed/19122150}, author = {Villa, Elizabeth and Sengupta, Jayati and Trabuco, Leonardo G and LeBarron, Jamie and Baxter, Bill and Shaikh, Tanvir R and Grassucci, Robert A and Nissen, Poul and Ehrenberg, M{\r a}ns and Schulten, Klaus and Frank, Joachim} } @article {2114, title = {Exploration of parameters in cryo-EM leading to an improved density map of the E. coli ribosome.}, journal = {J Struct Biol}, volume = {164}, year = {2008}, month = {10/2008}, pages = {24-32}, abstract = {

A number of image processing parameters in the 3D reconstruction of a ribosome complex from a cryo-EM data set were varied to test their effects on the final resolution. The parameters examined were pixel size, window size, and mode of Fourier amplitude enhancement at high spatial frequencies. In addition, the strategy of switching from large to small pixel size during angular refinement was explored. The relationship between resolution (in Fourier space) and the number of particles was observed to follow a lin-log dependence, a relationship that appears to hold for other data, as well. By optimizing the above parameters, and using a lin-log extrapolation to the full data set in the estimation of resolution from half-sets, we obtained a 3D map from 131,599 ribosome particles at 6.7A resolution (FSC=0.5).

}, keywords = {Cryoelectron Microscopy, Escherichia coli, Image Enhancement, Image Processing, Computer-Assisted, Ribosomes}, issn = {1095-8657}, doi = {10.1016/j.jsb.2008.05.007}, url = {http://www.ncbi.nlm.nih.gov/pubmed/18606549}, author = {LeBarron, Jamie and Grassucci, Robert A and Shaikh, Tanvir R and Baxter, Bill and Sengupta, Jayati and Frank, Joachim} } @article {2113, title = {Particle-verification for single-particle, reference-based reconstruction using multivariate data analysis and classification.}, journal = {J Struct Biol}, volume = {164}, year = {2008}, month = {10/2008}, pages = {41-8}, abstract = {

As collection of electron microscopy data for single-particle reconstruction becomes more efficient, due to electronic image capture, one of the principal limiting steps in a reconstruction remains particle-verification, which is especially costly in terms of user input. Recently, some algorithms have been developed to window particles automatically, but the resulting particle sets typically need to be verified manually. Here we describe a procedure to speed up verification of windowed particles using multivariate data analysis and classification. In this procedure, the particle set is subjected to multi-reference alignment before the verification. The aligned particles are first binned according to orientation and are binned further by K-means classification. Rather than selection of particles individually, an entire class of particles can be selected, with an option to remove outliers. Since particles in the same class present the same view, distinction between good and bad images becomes more straightforward. We have also developed a graphical interface, written in Python/Tkinter, to facilitate this implementation of particle-verification. For the demonstration of the particle-verification scheme presented here, electron micrographs of ribosomes are used.

}, keywords = {Algorithms, Artificial Intelligence, Classification, Image Enhancement, Image Processing, Computer-Assisted, Microscopy, Electron, Multivariate Analysis, Ribosomes}, issn = {1095-8657}, doi = {10.1016/j.jsb.2008.06.006}, url = {http://www.ncbi.nlm.nih.gov/pubmed/18619547}, author = {Shaikh, Tanvir R and Trujillo, Ramon and LeBarron, Jamie and Baxter, Bill and Frank, Joachim} } @article {2112, title = {SPIDER image processing for single-particle reconstruction of biological macromolecules from electron micrographs.}, journal = {Nat Protoc}, volume = {3}, year = {2008}, month = {10/2008}, pages = {1941-74}, abstract = {

This protocol describes the reconstruction of biological molecules from the electron micrographs of single particles. Computation here is performed using the image-processing software SPIDER and can be managed using a graphical user interface, termed the SPIDER Reconstruction Engine. Two approaches are described to obtain an initial reconstruction: random-conical tilt and common lines. Once an existing model is available, reference-based alignment can be used, a procedure that can be iterated. Also described is supervised classification, a method to look for homogeneous subsets when multiple known conformations of the molecule may coexist.

}, keywords = {Image Processing, Computer-Assisted, Microscopy, Electron, Models, Molecular, Molecular Structure, Software, User-Computer Interface}, issn = {1750-2799}, doi = {10.1038/nprot.2008.156}, url = {http://www.ncbi.nlm.nih.gov/pubmed/19180078}, author = {Shaikh, Tanvir R and Gao, Haixiao and Baxter, Bill and Asturias, Francisco J and Boisset, Nicolas and Leith, ArDean and Frank, Joachim} } @article {2109, title = {SPIRE: the SPIDER reconstruction engine.}, journal = {J Struct Biol}, volume = {157}, year = {2007}, month = {01/2007}, pages = {56-63}, abstract = {

SPIRE is a Python program written to modernize the user interaction with SPIDER, the image processing system for electron microscopical reconstruction projects. SPIRE provides a graphical user interface (GUI) to SPIDER for executing batch files of SPIDER commands. It also lets users quickly view the status of a project by showing the last batch files that were run, as well as the data files that were generated. SPIRE handles the flexibility of the SPIDER programming environment through configuration files: XML-tagged documents that describe the batch files, directory trees, and presentation of the GUI for a given type of reconstruction project. It also provides the capability to connect to a laboratory database, for downloading parameters required by batch files at the start of a project, and uploading reconstruction results at the end of a project.

}, keywords = {Computational Biology, Image Processing, Computer-Assisted, Software, Software Design}, issn = {1047-8477}, doi = {10.1016/j.jsb.2006.07.019}, url = {http://www.ncbi.nlm.nih.gov/pubmed/17055743}, author = {Baxter, Bill and Leith, ArDean and Frank, Joachim} } @article {2115, title = {Particle picking by segmentation: a comparative study with SPIDER-based manual particle picking.}, journal = {J Struct Biol}, volume = {152}, year = {2005}, month = {12/2005}, pages = {211-20}, abstract = {

Boxing hundreds of thousands of particles in low-dose electron micrographs is one of the major bottle-necks in advancing toward achieving atomic resolution reconstructions of biological macromolecules. We have shown that a combination of pre-processing operations and segmentation can be used as an effective, automatic tool for identifying and boxing single-particle images. This paper provides a brief description of how this method has been applied to a large data set of micrographs of ice-embedded ribosomes, including a comparative analysis of the efficiency of the method. Some results on processing micrographs of tripeptidyl peptidase II particles are also shown. In both cases, we have achieved our goal of selecting at least 80\% of the particles that an expert would select with less than 10\% false positives.

}, keywords = {Algorithms, Aminopeptidases, Cryoelectron Microscopy, Dipeptidyl-Peptidases and Tripeptidyl-Peptidases, Image Processing, Computer-Assisted, Imaging, Three-Dimensional, Internet, Particle Size, Ribosomes, Serine Endopeptidases, Software, Software Validation}, issn = {1047-8477}, doi = {10.1016/j.jsb.2005.09.007}, url = {http://www.ncbi.nlm.nih.gov/pubmed/16330229}, author = {Adiga, Umesh and Baxter, Bill and Hall, Richard J and Rockel, Beate and Rath, Bimal K and Frank, Joachim and Glaeser, Robert M} } @article {2116, title = {A binary segmentation approach for boxing ribosome particles in cryo EM micrographs.}, journal = {J Struct Biol}, volume = {145}, year = {2004}, month = {01/2004}, pages = {142-51}, abstract = {

Three-dimensional reconstruction of ribosome particles from electron micrographs requires selection of many single-particle images. Roughly 100,000 particles are required to achieve approximately 10 A resolution. Manual selection of particles, by visual observation of the micrographs on a\ computer\ screen, is recognized as a bottleneck in automated single-particle reconstruction. This paper describes an efficient approach for automated boxing of ribosome particles in micrographs. Use of a fast, anisotropic non-linear reaction-diffusion method to pre-process micrographs and rank-leveling to enhance the contrast between particles and the background, followed by binary and morphological segmentation constitute the core of this technique. Modifying the shape of the particles to facilitate segmentation of individual particles within clusters and boxing the isolated particles is successfully attempted. Tests on a limited number of micrographs have shown that over 80\% success is achieved in automatic particle picking.

}, keywords = {Algorithms, Anisotropy, Automatic Data Processing, Cryoelectron Microscopy, Image Enhancement, Image Processing, Computer-Assisted, Particle Size, Pattern Recognition, Automated, Ribosomes, Software Design}, issn = {1047-8477}, doi = {10.1016/j.jsb.2003.10.026}, url = {http://www.ncbi.nlm.nih.gov/pubmed/15065681}, author = {Adiga, Umesh and Malladi, Ravi and Baxter, Bill and Glaeser, Robert M} } @article {2968, title = {A scripting language approach to control software for cryo-electron microscopy.}, journal = {Proc IEEE Int. Symp. Biomed. Imag.}, year = {2002}, chapter = {301}, abstract = {Cryo-electron microscopy (Cryo-EM) of single particles has developed into a widely used technique for determining the 3-dimensional structure of large molecules and molecular assemblies. The low signal-to-noise ratio of cryo-EM requires thousands of images of single molecules to be averaged together. The field has matured to the point where realization of high-resolution structures is limited primarily by computational constraints. These constraints are at the algorithmic level, as well as the control level, where dozens of complex procedures and thousands of mathematical operations are applied to the raw data. SPIDER is a highly modular and flexible software package for single particle reconstruction. A typical reconstruction project involves dozens of procedure files, which in turn draw on hundreds of available low-level operations. In the present system, it is virtually impossible to rerun the system from selected branching points in the process flow to determine the effects of various parameters values. A Reconstruction Engine (RE) is being developed as a high-level "shell" for controlling processes in the SPIDER software system. The RE allows backtracking, optimization of parameters, and automation of processing flow. The RE is implemented in a scripting language, Python, which provides an overall management capability at the global level of the project.}, doi = {10.1109/ISBI.2002.1029253}, url = {http://ieeexplore.ieee.org/xpl/freeabs_all.jsp?arnumber=1029253\&abstractAccess=no\&userType=inst}, author = {Baxter, Bill and Leith, ArDean and Frank, Joachim} } @article {2969, title = {Transillumination and optical properties of cardiac tissue.}, journal = {Optical Mapping of Cardiac Excitation and Arrhythmias}, year = {2001}, author = {Baxter, Bill} } @article {2970, title = {Video mapping of spiral waves in the heart.}, journal = {Optical Mapping of Cardiac Excitation and Arrhythmias}, year = {2001}, author = {Baxter, Bill and Davidenko, J M} } @article {2117, title = {Visualizing excitation waves inside cardiac muscle using transillumination.}, journal = {Biophys J}, volume = {80}, year = {2001}, month = {01/2001}, pages = {516-30}, abstract = {

Voltage-sensitive fluorescent dyes have become powerful tools for the visualization of excitation propagation in the\ heart. However, until recently they were used exclusively for surface recordings. Here we demonstrate the possibility of visualizing the electrical activity from inside cardiac muscle via fluorescence measurements in the transillumination mode (in which the light source and photodetector are on opposite sides of the preparation). This mode enables the detection of light escaping from layers deep within the tissue. Experiments were conducted in perfused (8 mm thick) slabs of sheep right ventricular wall stained with the voltage-sensitive dye di-4-ANEPPS. Although the amplitude and signal-to-noise ratio recorded in the transillumination mode were significantly smaller than those recorded in the epi-illumination mode, they were sufficient to reliably determine the activation sequence. Penetration depths (spatial decay constants) derived from measurements of light attenuation in cardiac muscle were 0.8 mm for excitation (520 +/- 30 nm) and 1.3 mm for emission wavelengths (640 +/- 50 nm). Estimates of emitted fluorescence based on these attenuation values in 8-mm-thick tissue suggest that 90\% of the transillumination signal originates from a 4-mm-thick layer near the illuminated surface. A 69\% fraction of the recorded signal originates from \> or =1 mm below the surface. Transillumination recordings may be combined with endocardial and epicardial surface recordings to obtain information about three-dimensional propagation in the thickness of the myocardial wall. We show an example in which transillumination reveals an intramural reentry, undetectable in surface recordings.

}, keywords = {Animals, Biophysical Phenomena, Biophysics, Electrophysiology, Endocardium, Fluorescent Dyes, Heart, Models, Cardiovascular, Myocardium, Optics and Photonics, Perfusion, Pericardium, Pyridinium Compounds, Sheep}, issn = {0006-3495}, doi = {10.1016/S0006-3495(01)76034-1}, url = {http://www.ncbi.nlm.nih.gov/pubmed/11159422}, author = {Baxter, Bill and Mironov, S F and Zaitsev, A V and Jalife, J and Pertsov, A V} } @article {2971, title = {Intramural optical recordings of cardiac electrical activity via transillumination}, year = {1999}, abstract = {PhD Dissertation, October 1999}, author = {Baxter, Bill} } @article {2119, title = {Quantification of effects of global ischemia on dynamics of ventricular fibrillation in isolated rabbit heart.}, journal = {Circulation}, volume = {98}, year = {1998}, month = {10/1998}, pages = {1688-96}, abstract = {

BACKGROUND:\ 

Ventricular fibrillation (VF) leads to global ischemia of the heart. After 1 to 2 minutes of onset, the VF rate decreases and appears more organized. The objectives of this study were to determine the effects of no-flow global ischemia on nonlinear wave dynamics and establish the mechanism of ischemia-induced slowing of the VF rate.

METHODS AND RESULTS:\ 

Activation patterns of VF in the Langendorff-perfused rabbit heart were studied with the use of 2 protocols: (1) 15 minutes of no-flow global ischemia followed by reperfusion (n=7) and (2) decreased excitability induced by perfusion with 5 micromol/L of tetrodotoxin (TTX) followed by washout (n=3). Video imaging ( approximately 7500 pixels per frame; 240 frames per second) with a voltage-sensitive dye, ECG, and signal processing (fast Fourier transform) were used for analysis. The dominant frequency of VF decreased from 13.5+/-1.3 during control to 9.3+/-1.4 Hz at 5 minutes of global ischemia (P\<0.02). The dominant frequency decreased from 13.9+/-1.1 during control to 7.0+/-0.3 Hz at 2 minutes of TTX infusion (P\<0.001). The rotation period of rotors on the epicardial surface (n=27) strongly correlated with the inverse dominant frequency of the corresponding episode of VF (R2=0. 93). The core area, measured for 27 transiently appearing rotors, was 5.3+/-0.7 mm2 during control. A remarkable increase in core area was observed both during global ischemia (13.6+/-1.7 mm2; P\<0.001) and TTX perfusion (16.8+/-3.6 mm2; P\<0.001). Density of wave fronts decreased during both global ischemia (P\<0.002) and TTX perfusion (P\<0.002) compared with control.

CONCLUSIONS:\ 

This study suggests that rotating spiral waves are most likely the underlying mechanism of VF and contribute to its frequency content. Ischemia-induced decrease in the VF rate results from an increase in the rotation period of spiral waves that occurs secondary to an increase in their core area. Remarkably, similar findings in the TTX protocol suggest that reduced excitability during ischemia is an important underlying mechanism for the changes seen.

}, keywords = {Animals, Electrocardiography, Linear Models, Myocardial Ischemia, Rabbits, Rotation, Sodium Channel Blockers, Tetrodotoxin, Ventricular Fibrillation, Video Recording}, issn = {0009-7322}, doi = {10.1161/01.CIR.98.16.1688}, url = {http://www.ncbi.nlm.nih.gov/pubmed/9778336}, author = {Mandapati, R and Asano, Y and Baxter, Bill and Gray, R A and Davidenko, J M and Jalife, J} } @article {2120, title = {Optical mapping of drug-induced polymorphic arrhythmias and torsade de pointes in the isolated rabbit heart.}, journal = {J Am Coll Cardiol}, volume = {29}, year = {1997}, month = {03/1997}, pages = {831-42}, abstract = {

OBJECTIVES:\ 

This study sought to 1) test the hypothesis that in the setting of bradycardia and drug-induced action potential prolongation, multiple foci of early afterdepolarizations (EADs) result in beat to beat changes in the origin and direction of the excitation wave front and are responsible for polymorphic arrhythmias; and 2) determine whether EADs may initiate nonstationary reentry, giving rise to the typical torsade de pointes (TDP) pattern.

BACKGROUND:\ 

In the past, it has been difficult to associate EADs or reentry with the undulating electrocardiographic (ECG) patterns of TDP.

METHODS:\ 

A voltage-sensitive dye was used for high resolution\ videoimaging\ of electrical waves on the\ epicardial\ and endocardial\ surface\ of the Langendorff-perfused\ rabbitheart. ECG and monophasic action potentials from the right septal region were also recorded. Bradycardia was induced by ablation of the atrioventricular node.

RESULTS:\ 

Perfusion of low potassium chloride Tyrode solution plus quinidine led to prolongation of the action potential and the QT interval. Eventually, EADs and triggered activity ensued, giving rise to intermittent episodes of polymorphic arrhythmia. In one experiment, triggered activity was followed by a long episode of vortex-like reentry with an ECG pattern characteristic of TDP. However, in most experiments, focal activity of varying origins and propagation patterns was observed. Triggered responses also showed varying degrees of local block. Similar results were obtained with E-4031. Burst pacing both at control conditions and in the presence of quinidine consistently led to vortex-like reentry whose ECG pattern resembled TDP. However, the cycle length of the arrhythmia with quinidine was longer than that for control ([mean +/- SEM] 194 +/- 12 vs. 132 +/- 8 ms, p \< 0.03).

CONCLUSIONS:\ 

Drug-induced polymorphic ventricular arrhythmias may result from beat to beat changes in wave propagation patterns initiated by EADs or EAD-induced nonstationary reentrant activity. In contrast, burst pacing-induced polymorphic tachycardia in the presence or absence of drugs is the result of nonstationary reentrant activity.

}, keywords = {Action Potentials, Animals, Anti-Arrhythmia Agents, Arrhythmias, Cardiac, Electrocardiography, Heart, Heart Conduction System, Image Processing, Computer-Assisted, Models, Cardiovascular, Organ Culture Techniques, Perfusion, Piperidines, Pyridines, Quinidine, Rabbits, Torsades de Pointes}, issn = {0735-1097}, doi = {10.1016/S0735-1097(96)00588-8}, url = {http://www.ncbi.nlm.nih.gov/pubmed/9091531}, author = {Asano, Y and Davidenko, J M and Baxter, Bill and Gray, R A and Jalife, J} } @article {2118, title = {Technical features of a CCD video camera system to record cardiac fluorescence data.}, journal = {Ann Biomed Eng}, volume = {25}, year = {1997}, month = {07/1997}, pages = {713-25}, abstract = {

A charge-coupled device (CCD) camera was used to acquire movies of transmembrane activity from thin slices of sheep ventricular\ epicardial\ muscle stained with a voltage-sensitive dye. Compared with photodiodes, CCDs have high spatial resolution, but low temporal resolution. Spatial resolution in our system ranged from 0.04 to 0.14 mm/pixel; the acquisition rate was 60, 120, or 240 frames/sec. Propagating waves were readily visualized after subtraction of a background image. The optical signal had an amplitude of 1 to 6 gray levels, with signal-to-noise ratios between 1.5 and 4.4. Because CCD cameras integrate light over the frame interval, moving objects, including propagating waves, are blurred in the resulting movies. A computer model of such an integrating\ imaging\ system was developed to study the effects of blur, noise, filtering, and quantization on the ability to measure conduction velocity and action potential duration (APD). The model indicated that blurring, filtering, and quantization do not affect the ability to localize wave fronts in the optical data (i.e., no systematic error in determining spatial position), but noise does increase the uncertainty of the measurements. The model also showed that the low frame rates of the CCD camera introduced a systematic error in the calculation of APD: for cutoff levels \> 50\%, the APD was erroneously long. Both noise and quantization increased the uncertainty in the APD measurements. The optical measures of conduction velocity were not significantly different from those measured simultaneously with microelectrodes. Optical APDs, however, were longer than the electrically recorded APDs. This APD error could be reduced by using the 50\% cutoff level and the fastest frame rate possible.

}, keywords = {Action Potentials, Algorithms, Animals, Body Surface Potential Mapping, Calibration, Computer Simulation, Electric Conductivity, Fluorescent Dyes, Image Processing, Computer-Assisted, Models, Cardiovascular, Sheep, Ventricular Function, Video Recording}, issn = {0090-6964}, doi = {10.1007/BF02684848}, url = {http://www.ncbi.nlm.nih.gov/pubmed/9236983}, author = {Baxter, Bill and Davidenko, J M and Loew, L M and Wuskell, J P and Jalife, J} } @article {2972, title = {Video imaging of re-entry on the epicardial surface of the isolated rabbit heart.}, journal = {Computational Biology of the Heart}, year = {1997}, chapter = {277}, url = {http://www.researchgate.net/publication/266334442_Video_imaging_of_re-entry_on_the_epicardial_surface_of_the_isolated_rabbit_heart}, author = {Baxter, Bill and Gray, R A and Cabo, C and Davidenko, J M and Pertsov, A V and Jalife, J} } @article {2121, title = {Vortex shedding as a precursor of turbulent electrical activity in cardiac muscle.}, journal = {Biophys J}, volume = {70}, year = {1996}, month = {03/1996}, pages = {1105-11}, abstract = {

In cardiac tissue, during partial blockade of the membrane sodium channels, or at high frequencies of excitation, inexcitable obstacles with sharp edges may destabilize the propagation of electrical excitation waves, causing the formation of self-sustained vortices and turbulent cardiac electrical activity. The formation of such vortices, which visually resembles vortex shedding in hydrodynamic turbulent flows, was observed in sheep epicardial tissue using voltage-sensitive dyes in combination with video-imaging techniques. Vortex shedding is a potential mechanism leading to the spontaneous initiation of uncontrolled high-frequency excitation of the heart.

}, keywords = {Animals, Biophysical Phenomena, Biophysics, Cell Membrane, Computer Simulation, Electric Stimulation, Electrochemistry, Electrophysiology, Heart, Models, Cardiovascular, Myocardial Contraction, Myocardium, Sheep, Sodium Channels}, issn = {0006-3495}, doi = {10.1016/S0006-3495(96)79691-1}, url = {http://www.ncbi.nlm.nih.gov/pubmed/8785270}, author = {Cabo, C and Pertsov, A V and Davidenko, J M and Baxter, Bill and Gray, R A and Jalife, J} } @article {2122, title = {Effects of pacing on stationary reentrant activity. Theoretical and experimental study.}, journal = {Circ Res}, volume = {77}, year = {1995}, month = {12/1995}, pages = {1166-79}, abstract = {

It is well known that electrical pacing may either terminate or change the rate and/or ECG appearance of reentrant ventricular tachycardia. However, the dynamics of interaction of reentrant waves with waves initiated by external pacing are poorly understood. Prevailing concepts are based on simplistic models in which propagation occurs in one-dimensional rings of cardiac tissue. Since reentrant activation in the ventricles occurs in two or three dimensions, such concepts might be insufficient to explain the mechanisms of pacing-induced effects. We used numerical and biological models of cardiac excitation to explore the phenomena, which may take place as a result of electrical pacing during functionally determined reentry. Computer simulations of a two-dimensional array of electrically coupled FitzHugh-Nagumo cells were used to predict the response patterns expected from thin slices of sheep ventricular epicardial muscle, in which self-sustaining reentrant activity in the form of spiral waves was consistently initiated by premature stimulation and monitored by means of video mapping techniques. The results show that depending on their timing and shape, externally induced waves may collide with the self-sustaining spiral and result in one of three possible outcomes: (1) direct annihilation of the spiral, (2) multiplication of the spiral, or (3) shift of the spiral center (ie, core). Multiplication and shift of the spiral core were attended by changes in rate and morphology of the arrhythmia as seen by "pseudo-ECGs." Furthermore, delayed termination (ie, termination of the activity one to three cycles after the stimulus) occurred after both multiplication and shift of the spiral center. Both numerical predictions and experimental results support the hypothesis that whether a pacing stimulus will terminate a reentrant arrhythmia or modify its ECG appearance depends on whether the interactions between the externally induced wave and the spiral wave result in the de novo formation of one or more "wavebreaks." The final outcome depends on the stimulus parameters (ie, position and size of the electrodes and timing of the stimulus) as well as on the position of the newly formed wavebreak(s) in relation to that of the original wave.

}, keywords = {Acceleration, Animals, Cardiac Pacing, Artificial, Computer Simulation, Deceleration, Electrocardiography, Models, Cardiovascular, Sheep, Tachycardia, Ventricular}, issn = {0009-7330}, doi = {10.1161/01.RES.77.6.1166}, url = {http://www.ncbi.nlm.nih.gov/pubmed/7586230}, author = {Davidenko, J M and Salomonsz, R and Pertsov, A V and Baxter, Bill and Jalife, J} } @article {2123, title = {Mechanisms of cardiac fibrillation.}, journal = {Science}, volume = {270}, year = {1995}, month = {11/1995}, pages = {1222-3; author reply 1224-5}, keywords = {Animals, Computer Simulation, Electrocardiography, Heart Ventricles, Models, Cardiovascular, Rabbits, Ventricular Fibrillation}, issn = {0036-8075}, doi = {10.1126/science.270.5239.1222}, url = {http://www.ncbi.nlm.nih.gov/pubmed/7502055}, author = {Gray, R A and Jalife, J and Panfilov, A and Baxter, Bill and Cabo, C and Davidenko, J M and Pertsov, A V} } @article {2124, title = {Nonstationary vortexlike reentrant activity as a mechanism of polymorphic ventricular tachycardia in the isolated rabbit heart.}, journal = {Circulation}, volume = {91}, year = {1995}, month = {05/1995 }, pages = {2454-69}, abstract = {

BACKGROUND:\ 

Ventricular tachycardia may result from vortexlike reentrant excitation of the myocardium. Our general hypothesis is that in the structurally normal heart, these arrhythmias are the result of one or two nonstationary three-dimensional electrical scroll waves activating the heart muscle at very high frequencies.

METHODS AND RESULTS:\ 

We used a combination of high-resolution video imaging, electrocardiography, and image processing in the isolated rabbit heart, together with mathematical modeling. We characterized the dynamics of changes in transmembrane potential patterns on the epicardial surface of the ventricles using optical mapping. Image processing techniques were used to identify the surface manifestation of the reentrant organizing centers, and the location of these centers was used to determine the movement of the reentrant pathway. We also used numerical simulations incorporating Fitzhugh-Nagumo kinetics and realistic heart geometry to study how stationary and nonstationary scroll waves are manifest on the epicardial surface and in the simulated ECG. We present epicardial surface manifestations (reentrant spiral waves) and ECG patterns of nonstationary reentrant activity that are consistent with those generated by scroll waves established at the right and left ventricles. We identified the organizing centers of the reentrant circuits on the epicardial surface during polymorphic tachycardia, and these centers moved during the episodes. In addition, the arrhythmias that showed the greatest movement of the reentrant centers displayed the largest changes in QRS morphology. The numerical simulations showed that stationary scroll waves give rise to monomorphic ECG signals, but nonstationary meandering scroll waves give rise to undulating ECGs characteristic of torsade de pointes.

CONCLUSIONS:\ 

Polymorphic ventricular tachycardia in the healthy, isolated rabbit heart is the result of either a single or paired ("figure-of-eight") nonstationary scroll waves. The extent of the scroll wave movement corresponds to the degree of polymorphism in the ECG. These results are consistent with our numerical simulations that showed monomorphic ECG patterns of activity for stationary scroll waves but polymorphic patterns for scroll waves that were nonstationary.

}, keywords = {Animals, Electrocardiography, Heart, Image Processing, Computer-Assisted, Models, Cardiovascular, Perfusion, Rabbits, Tachycardia, Ventricular}, issn = {0009-7322}, doi = {10.1161/01.CIR.91.9.2454}, url = {http://www.ncbi.nlm.nih.gov/pubmed/7729033}, author = {Gray, R A and Jalife, J and Panfilov, A and Baxter, Bill and Cabo, C and Davidenko, J M and Pertsov, A V} } @article {2125, title = {Wave-front curvature as a cause of slow conduction and block in isolated cardiac muscle.}, journal = {Circ Res}, volume = {75}, year = {1994}, month = {12/1994}, pages = {1014-28}, abstract = {

We have investigated the role of wave-front curvature on propagation by following the wave front that was diffracted through a narrow isthmus created in a two-dimensional ionic model (Luo-Rudy) of ventricular muscle and in a thin (0.5-mm) sheet of sheep ventricular epicardial muscle. The electrical activity in the experimental preparations was imaged by using a high-resolution video camera that monitored the changes in fluorescence of the potentiometric dye di-4-ANEPPS on the surface of the tissue. Isthmuses were created both parallel and perpendicular to the fiber orientation. In both numerical and biological experiments, when a planar wave front reached the isthmus, it was diffracted to an elliptical wave front whose pronounced curvature was very similar to that of a wave front initiated by point stimulation. In addition, the velocity of propagation was reduced in relation to that of the original planar wave. Furthermore, as shown by the numerical results, wave-front curvature changed as a function of the distance from the isthmus. Such changes in local curvature were accompanied by corresponding changes in velocity of propagation. In the model, the critical isthmus width was 200 microns for longitudinal propagation and 600 microns for transverse propagation of a single planar wave initiated proximal to the isthmus. In the experiments, propagation depended on the width of the isthmus for a fixed stimulation frequency. Propagation through an isthmus of fixed width was rate dependent both along and across fibers. Thus, the critical isthmus width for propagation was estimated in both directions for different frequencies of stimulation. In the longitudinal direction, for cycle lengths between 200 and 500 milliseconds, the critical width was \< 1 mm; for 150 milliseconds, it was estimated to be between 1.3 and 2 mm; and for the maximum frequency of stimulation (117 +/- 15 milliseconds), it was \> 2.5 mm. In the transverse direction, critical width was between 1.78 and 2.32 mm for a basic cycle length of 200 milliseconds. It increased to values between 2.46 and 3.53 mm for a basic cycle length of 150 milliseconds. The overall results demonstrate that the curvature of the wave front plays an important role in propagation in two-dimensional cardiac muscle and that changes in curvature may cause slow conduction or block.

}, keywords = {Animals, Computer Simulation, Electric Conductivity, Heart, Heart Block, Heart Conduction System, Humans, Models, Cardiovascular, Motion Pictures as Topic, Sheep, Staining and Labeling}, issn = {0009-7330}, url = {http://www.ncbi.nlm.nih.gov/pubmed/7525101}, author = {Cabo, C and Pertsov, A V and Baxter, Bill and Davidenko, J M and Gray, R A and Jalife, J} } @article {2126, title = {Spiral waves of excitation underlie reentrant activity in isolated cardiac muscle.}, journal = {Circ Res}, volume = {72}, year = {1993}, month = {03/1993 }, pages = {631-50}, abstract = {

The mechanism of reentrant ventricular tachycardia was studied in computer simulations and in thin (approximately 20 x 20 x 0.5-mm) slices of dog and sheep ventricular epicardial muscle. A two-dimensional matrix consisting of 96 x 96 electrically coupled cells modeled by the FitzHugh-Nagumo equations was used to analyze the dynamics of self-sustaining reentrant activity in the form of elliptical spiral waves induced by premature stimulation. In homogeneous anisotropic media, spirals are stationary and may last indefinitely. However, the presence of small parameter gradients may lead to drifting and eventual termination of the spiral at the boundary of the medium. On the other hand, spirals may anchor and rotate around small discontinuities within the matrix. Similar results were obtained experimentally in 10 preparations whose electrical activity was monitored by means of a potentiometric dye and high-resolution optical mapping techniques; premature stimulation triggered reproducible episodes of sustained or nonsustained reentrant tachycardia in the form of spiral waves. As a rule, the spirals were elongated, with the major hemiaxis parallel to the longitudinal axis of the cells. The period of rotation (183 +/- 68 msec [mean +/- SD]) was longer than the refractory period (131 +/- 38 msec) and appeared to be determined by the size of the spiral{\textquoteright}s core, which was measured using a newly devised "frame-stack" plot. Drifting of spiral waves was also observed experimentally. Drift velocity was 9.8\% of the velocity of wave propagation. In some cases, the core became stationary by anchoring to small arteries or other heterogeneities, and the spiral rotated rhythmically for prolonged periods of time. Yet, when drift occurred, spatiotemporal variations in the excitation period were manifested as a result of a Doppler effect, with the excitation period ahead of the core being 20 +/- 6\% shorter than the excitation period behind the core. As a result of these coexisting frequencies, a pseudoelectrocardiogram of the activity in the presence of a drifting spiral wave exhibited "QRS complexes" with an undulating axis, which resembled those observed in patients with torsade de pointes. The overall results show that spiral wave activity is a property of cardiac muscle and suggest that such activity may be the common mechanism of a number of monomorphic and polymorphic tachycardias.

}, keywords = {Animals, Computer Simulation, Disease Models, Animal, Dogs, Electrophysiology, Sheep, Tachycardia, Atrioventricular Nodal Reentry, Torsades de Pointes}, issn = {0009-7330}, doi = {10.1161/01.RES.72.3.631}, url = {http://www.ncbi.nlm.nih.gov/pubmed/8431989}, author = {Pertsov, A V and Davidenko, J M and Salomonsz, R and Baxter, Bill and Jalife, J} } @article {2127, title = {Spatiotemporal irregularities of spiral wave activity in isolated ventricular muscle.}, journal = {J Electrocardiol}, volume = {24 Suppl}, year = {1992}, month = {1992}, pages = {113-22}, abstract = {

Voltage-sensitive dyes and high resolution optical mapping were used to analyze the characteristics of spiral waves of excitation in isolated ventricular myocardium. In addition, analytical techniques, which have been previously used in the study of the characteristics of spiral waves in chemical reactions, were applied to determine the voltage structure of the center of the rotating activity (ie, the core). During stable spiral wave activity local activation occurs in a periodic fashion (ie, 1:1 stimulus: response activation ratio) throughout the preparation, except at the core, which is a small elongated area where the activity is of low voltage and the activation ratio is 1:0. The voltage amplitude increases gradually from the center of the core to the periphery. In some cases, however, regular activation patterns at the periphery may coexist with irregular local activation patterns near the core. Such a spatiotemporal irregularity is attended by variations in the core size and shape and results from changes in the core position. The authors conclude that functionally determined reentrant activity in the heart may be the result of spiral waves of propagation and that local spatiotemporal irregularities in the activation pattern are the result of changes in the core position.

}, keywords = {Animals, Cardiac Pacing, Artificial, Fluorescent Dyes, Heart Conduction System, Membrane Potentials, Optics and Photonics, Pericardium, Signal Processing, Computer-Assisted, Tachycardia, Ventricular Function}, issn = {0022-0736}, doi = {10.1016/s0022-0736(10)80029-9}, url = {http://www.ncbi.nlm.nih.gov/pubmed/1552240}, author = {Davidenko, J M and Pertsov, A V and Salomonsz, R and Baxter, Bill and Jalife, J} } @article {2128, title = {Stationary and drifting spiral waves of excitation in isolated cardiac muscle.}, journal = {Nature}, volume = {355}, year = {1992}, month = {01/1992}, pages = {349-51}, abstract = {

Excitable media can support spiral waves rotating around an organizing centre. Spiral waves have been discovered in different types of autocatalytic chemical reactions and in biological systems. The so-called {\textquoteright}re-entrant excitation{\textquoteright} of myocardial cells, causing the most dangerous cardiac arrhythmias, including ventricular tachycardia and fibrillation, could be the result of spiral waves. Here we use a potentiometric dye in combination with CCD (charge-coupled device) imaging technology to demonstrate spiral waves in the heart muscle. The spirals were elongated and the rotation period, Ts, was about 180 ms (3-5 times faster than normal heart rate). In most episodes, the spiral was anchored to small arteries or bands of connective tissue, and gave rise to stationary rotations. In some cases, the core drifted away from its site of origin and dissipated at a tissue border. Drift was associated with a Doppler shift in the local excitation period, T, with T ahead of the core being about 20\% shorter than T behind the core.

}, keywords = {Animals, Dogs, Heart, Mathematics, Membrane Potentials, Models, Biological, Myocardial Contraction, Sheep}, issn = {0028-0836}, doi = {10.1038/355349a0}, url = {http://www.ncbi.nlm.nih.gov/pubmed/1731248}, author = {Davidenko, J M and Pertsov, A V and Salomonsz, R and Baxter, Bill and Jalife, J} } @article {2129, title = {Horizontal organization of orientation-sensitive cells in primate visual cortex.}, journal = {Biol Cybern}, volume = {61}, year = {1989}, month = {07/1989}, pages = {171-82}, abstract = {

In the visual cortex of the monkey the horizontal organization of the preferred orientations of orientation-selective cells follows two opposing rules: (1) neighbors tend to have similar orientation preferences, and (2) many different orientations are observed in a local region. We have described a classification for orientation maps based on the types of topological singularities and the spacing of these singularities relative to the cytochrome oxidase blobs. Using the orientation drift rate as a measure we have compared simulated orientation maps to published records of horizontal electrode recordings.

}, keywords = {Animals, Electron Transport Complex IV, Form Perception, Models, Neurological, Pattern Recognition, Visual, Visual Cortex}, issn = {0340-1200}, doi = {10.1007/BF00198764}, url = {http://www.ncbi.nlm.nih.gov/pubmed/2548628}, author = {Baxter, Bill and Dow, B M} }