00876nas a2200133 4500008004100000245005300041210005200094490000600146520041000152100001800562700001700580700001900597856012600616 2012 eng d00aUse of SPIDER and SPIRE in Image Reconstruction.0 aUse of SPIDER and SPIRE in Image Reconstruction0 vF3 aSPIDER 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.1 aLeith, ArDean1 aBaxter, Bill1 aFrank, Joachim uhttp://xrpp.iucr.org/cgi-bin/itr?url_ver=Z39.88-2003&rft_dat=what%3Dchapter%26volid%3DFb%26chnumo%3D19o8%26chvers%3Dv000101443nas a2200205 4500008004100000022001400041245010400055210006900159260001200228300001100240490000800251520078400259653002801043653004001071100001701111700002501128700001701153700001901170856004801189 2009 eng d a1095-865700aDetermination of signal-to-noise ratios and spectral SNRs in cryo-EM low-dose imaging of molecules.0 aDetermination of signaltonoise ratios and spectral SNRs in cryoE c05/2009 a126-320 v1663 a

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.

10aCryoelectron Microscopy10aImage Processing, Computer-Assisted1 aBaxter, Bill1 aGrassucci, Robert, A1 aGao, Haixiao1 aFrank, Joachim uhttp://www.ncbi.nlm.nih.gov/pubmed/1926933202370nas a2200445 4500008004100000022001400041245009000055210006900145260001200214300001100226490000800237520103400245653002801279653002201307653002101329653003001350653002701380653001401407653001501421653004501436653002201481653003301503653003301536653002301569653001401592653001801606653002401624100002101648700002101669700002501690700002001715700001701735700002201752700002501774700001701799700002101816700002001837700001901857856004801876 2009 eng d a1091-649000aRibosome-induced changes in elongation factor Tu conformation control GTP hydrolysis.0 aRibosomeinduced changes in elongation factor Tu conformation con c01/2009 a1063-80 v1063 a

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.

10aCryoelectron Microscopy10aEnzyme Activation10aEscherichia coli10aEscherichia coli Proteins10aGuanosine Triphosphate10aHistidine10aHydrolysis10aHydrophobic and Hydrophilic Interactions10aModels, Molecular10aPeptide Elongation Factor Tu10aProtein Structure, Secondary10aRibosomal Proteins10aRibosomes10aRNA, Transfer10aSignal Transduction1 aVilla, Elizabeth1 aSengupta, Jayati1 aTrabuco, Leonardo, G1 aLeBarron, Jamie1 aBaxter, Bill1 aShaikh, Tanvir, R1 aGrassucci, Robert, A1 aNissen, Poul1 aEhrenberg, Måns1 aSchulten, Klaus1 aFrank, Joachim uhttp://www.ncbi.nlm.nih.gov/pubmed/1912215001752nas a2200265 4500008004100000022001400041245010100055210006900156260001200225300001000237490000800247520093400255653002801189653002101217653002201238653004001260653001401300100002001314700002501334700002201359700001701381700002101398700001901419856004801438 2008 eng d a1095-865700aExploration of parameters in cryo-EM leading to an improved density map of the E. coli ribosome.0 aExploration of parameters in cryoEM leading to an improved densi c10/2008 a24-320 v1643 a

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).

10aCryoelectron Microscopy10aEscherichia coli10aImage Enhancement10aImage Processing, Computer-Assisted10aRibosomes1 aLeBarron, Jamie1 aGrassucci, Robert, A1 aShaikh, Tanvir, R1 aBaxter, Bill1 aSengupta, Jayati1 aFrank, Joachim uhttp://www.ncbi.nlm.nih.gov/pubmed/1860654902306nas a2200289 4500008004100000022001400041245013100055210006900186260001200255300000900267490000800276520139700284653001501681653002801696653001901724653002201743653004001765653002501805653002601830653001401856100002201870700002001892700002001912700001701932700001901949856004801968 2008 eng d a1095-865700aParticle-verification for single-particle, reference-based reconstruction using multivariate data analysis and classification.0 aParticleverification for singleparticle referencebased reconstru c10/2008 a41-80 v1643 a

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.

10aAlgorithms10aArtificial Intelligence10aClassification10aImage Enhancement10aImage Processing, Computer-Assisted10aMicroscopy, Electron10aMultivariate Analysis10aRibosomes1 aShaikh, Tanvir, R1 aTrujillo, Ramon1 aLeBarron, Jamie1 aBaxter, Bill1 aFrank, Joachim uhttp://www.ncbi.nlm.nih.gov/pubmed/1861954701670nas a2200289 4500008004100000022001400041245011900055210006900174260001200243300001200255490000600267520076600273653004001039653002501079653002201104653002401126653001301150653002801163100002201191700001701213700001701230700002701247700002101274700001801295700001901313856004801332 2008 eng d a1750-279900aSPIDER image processing for single-particle reconstruction of biological macromolecules from electron micrographs.0 aSPIDER image processing for singleparticle reconstruction of bio c10/2008 a1941-740 v33 a

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.

10aImage Processing, Computer-Assisted10aMicroscopy, Electron10aModels, Molecular10aMolecular Structure10aSoftware10aUser-Computer Interface1 aShaikh, Tanvir, R1 aGao, Haixiao1 aBaxter, Bill1 aAsturias, Francisco, J1 aBoisset, Nicolas1 aLeith, ArDean1 aFrank, Joachim uhttp://www.ncbi.nlm.nih.gov/pubmed/1918007801572nas a2200217 4500008004100000022001400041245004500055210004300100260001200143300001000155490000800165520098000173653002601153653004001179653001301219653002001232100001701252700001801269700001901287856004801306 2007 eng d a1047-847700aSPIRE: the SPIDER reconstruction engine.0 aSPIRE the SPIDER reconstruction engine c01/2007 a56-630 v1573 a

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.

10aComputational Biology10aImage Processing, Computer-Assisted10aSoftware10aSoftware Design1 aBaxter, Bill1 aLeith, ArDean1 aFrank, Joachim uhttp://www.ncbi.nlm.nih.gov/pubmed/1705574302034nas a2200361 4500008004100000022001400041245010100055210006900156260001200225300001100237490000800248520093900256653001501195653002001210653002801230653005301258653004001311653003101351653001301382653001801395653001401413653002601427653001301453653002401466100001701490700001701507700002101524700001801545700001901563700001901582700002301601856004801624 2005 eng d a1047-847700aParticle picking by segmentation: a comparative study with SPIDER-based manual particle picking.0 aParticle picking by segmentation a comparative study with SPIDER c12/2005 a211-200 v1523 a

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.

10aAlgorithms10aAminopeptidases10aCryoelectron Microscopy10aDipeptidyl-Peptidases and Tripeptidyl-Peptidases10aImage Processing, Computer-Assisted10aImaging, Three-Dimensional10aInternet10aParticle Size10aRibosomes10aSerine Endopeptidases10aSoftware10aSoftware Validation1 aAdiga, Umesh1 aBaxter, Bill1 aHall, Richard, J1 aRockel, Beate1 aRath, Bimal, K1 aFrank, Joachim1 aGlaeser, Robert, M uhttp://www.ncbi.nlm.nih.gov/pubmed/1633022902292nas a2200301 4500008004100000022001400041245008900055210006900144260001200213300001100225490000800236520138600244653001501630653001501645653003001660653002801690653002201718653004001740653001801780653003501798653001401833653002001847100001701867700001801884700001701902700002301919856004801942 2004 eng d a1047-847700aA binary segmentation approach for boxing ribosome particles in cryo EM micrographs.0 abinary segmentation approach for boxing ribosome particles in cr c01/2004 a142-510 v1453 a

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.

10aAlgorithms10aAnisotropy10aAutomatic Data Processing10aCryoelectron Microscopy10aImage Enhancement10aImage Processing, Computer-Assisted10aParticle Size10aPattern Recognition, Automated10aRibosomes10aSoftware Design1 aAdiga, Umesh1 aMalladi, Ravi1 aBaxter, Bill1 aGlaeser, Robert, M uhttp://www.ncbi.nlm.nih.gov/pubmed/1506568101856nas a2200121 4500008004100000245008400041210006900125520138600194100001701580700001801597700001901615856010001634 2002 eng d00aA scripting language approach to control software for cryo-electron microscopy.0 ascripting language approach to control software for cryoelectron3 aCryo-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.1 aBaxter, Bill1 aLeith, ArDean1 aFrank, Joachim uhttp://ieeexplore.ieee.org/xpl/freeabs_all.jsp?arnumber=1029253&abstractAccess=no&userType=inst00372nas a2200085 4500008004100000245006400041210006300105100001700168856010100185 2001 eng d00aTransillumination and optical properties of cardiac tissue.0 aTransillumination and optical properties of cardiac tissue1 aBaxter, Bill uhttps://neurotechcenter.org/publications/transillumination-and-optical-properties-cardiac-tissue00348nas a2200097 4500008004100000245004800041210004700089100001700136700001900153856007800172 2001 eng d00aVideo mapping of spiral waves in the heart.0 aVideo mapping of spiral waves in the heart1 aBaxter, Bill1 aDavidenko, J M uhttps://neurotechcenter.org/publications/video-mapping-spiral-waves-heart03049nas a2200361 4500008004100000022001400041245008000055210006900135260001200204300001100216490000700227520206900234653001202303653002602315653001502341653002202356653001602378653002102394653001002415653002702425653001502452653002502467653001402492653001602506653002502522653001002547100001702557700001702574700001702591700001402608700001702622856004802639 2001 eng d a0006-349500aVisualizing excitation waves inside cardiac muscle using transillumination.0 aVisualizing excitation waves inside cardiac muscle using transil c01/2001 a516-300 v803 a

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.

10aAnimals10aBiophysical Phenomena10aBiophysics10aElectrophysiology10aEndocardium10aFluorescent Dyes10aHeart10aModels, Cardiovascular10aMyocardium10aOptics and Photonics10aPerfusion10aPericardium10aPyridinium Compounds10aSheep1 aBaxter, Bill1 aMironov, S F1 aZaitsev, A V1 aJalife, J1 aPertsov, A V uhttp://www.ncbi.nlm.nih.gov/pubmed/1115942200450nas a2200097 4500008004100000245008700041210006900128520003500197100001700232856010300249 1999 eng d00aIntramural optical recordings of cardiac electrical activity via transillumination0 aIntramural optical recordings of cardiac electrical activity via3 aPhD Dissertation, October 19991 aBaxter, Bill uhttps://neurotechcenter.org/publications/intramural-optical-recordings-cardiac-electrical-activity03960nas a2200325 4500008004100000022001400041245011500055210006900170260001200239300001200251490000700263520302600270653001203296653002403308653001803332653002403350653001203374653001303386653002803399653001703427653002903444653002003473100001703493700001303510700001703523700001403540700001903554700001403573856004703587 1998 eng d a0009-732200aQuantification of effects of global ischemia on dynamics of ventricular fibrillation in isolated rabbit heart.0 aQuantification of effects of global ischemia on dynamics of vent c10/1998 a1688-960 v983 a

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.

10aAnimals10aElectrocardiography10aLinear Models10aMyocardial Ischemia10aRabbits10aRotation10aSodium Channel Blockers10aTetrodotoxin10aVentricular Fibrillation10aVideo Recording1 aMandapati, R1 aAsano, Y1 aBaxter, Bill1 aGray, R A1 aDavidenko, J M1 aJalife, J uhttp://www.ncbi.nlm.nih.gov/pubmed/977833605025nas a2200385 4500008004100000022001400041245011300055210006900168260001200237300001100249490000700260520391000267653002204177653001204199653002704211653002504238653002404263653001004287653002804297653004004325653002704365653002904392653001404421653001604435653001404451653001404465653001204479653002404491100001304515700001904528700001704547700001404564700001404578856004704592 1997 eng d a0735-109700aOptical mapping of drug-induced polymorphic arrhythmias and torsade de pointes in the isolated rabbit heart.0 aOptical mapping of druginduced polymorphic arrhythmias and torsa c03/1997 a831-420 v293 a

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 video imaging of electrical waves on the epicardial and endocardial surface of the Langendorff-perfused rabbit heart. 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.

10aAction Potentials10aAnimals10aAnti-Arrhythmia Agents10aArrhythmias, Cardiac10aElectrocardiography10aHeart10aHeart Conduction System10aImage Processing, Computer-Assisted10aModels, Cardiovascular10aOrgan Culture Techniques10aPerfusion10aPiperidines10aPyridines10aQuinidine10aRabbits10aTorsades de Pointes1 aAsano, Y1 aDavidenko, J M1 aBaxter, Bill1 aGray, R A1 aJalife, J uhttp://www.ncbi.nlm.nih.gov/pubmed/909153103382nas a2200349 4500008004100000022001400041245008900055210006900144260001200213300001100225490000700236520236800243653002202611653001502633653001202648653003502660653001602695653002402711653002602735653002102761653004002782653002702822653001002849653002502859653002002884100001702904700001902921700001402940700001702954700001402971856004702985 1997 eng d a0090-696400aTechnical features of a CCD video camera system to record cardiac fluorescence data.0 aTechnical features of a CCD video camera system to record cardia c07/1997 a713-250 v253 a

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.

10aAction Potentials10aAlgorithms10aAnimals10aBody Surface Potential Mapping10aCalibration10aComputer Simulation10aElectric Conductivity10aFluorescent Dyes10aImage Processing, Computer-Assisted10aModels, Cardiovascular10aSheep10aVentricular Function10aVideo Recording1 aBaxter, Bill1 aDavidenko, J M1 aLoew, L M1 aWuskell, J P1 aJalife, J uhttp://www.ncbi.nlm.nih.gov/pubmed/923698300570nas a2200145 4500008004100000245008600041210006900127100001700196700001400213700001200227700001900239700001700258700001400275856013500289 1997 eng d00aVideo imaging of re-entry on the epicardial surface of the isolated rabbit heart.0 aVideo imaging of reentry on the epicardial surface of the isolat1 aBaxter, Bill1 aGray, R A1 aCabo, C1 aDavidenko, J M1 aPertsov, A V1 aJalife, J uhttp://www.researchgate.net/publication/266334442_Video_imaging_of_re-entry_on_the_epicardial_surface_of_the_isolated_rabbit_heart01811nas a2200373 4500008004100000022001400041245008700055210006900142260001200211300001200223490000700235520078300242653001201025653002601037653001501063653001801078653002401096653002501120653002101145653002201166653001001188653002701198653002701225653001501252653001001267653002001277100001201297700001701309700001901326700001701345700001401362700001401376856004701390 1996 eng d a0006-349500aVortex shedding as a precursor of turbulent electrical activity in cardiac muscle.0 aVortex shedding as a precursor of turbulent electrical activity  c03/1996 a1105-110 v703 a

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.

10aAnimals10aBiophysical Phenomena10aBiophysics10aCell Membrane10aComputer Simulation10aElectric Stimulation10aElectrochemistry10aElectrophysiology10aHeart10aModels, Cardiovascular10aMyocardial Contraction10aMyocardium10aSheep10aSodium Channels1 aCabo, C1 aPertsov, A V1 aDavidenko, J M1 aBaxter, Bill1 aGray, R A1 aJalife, J uhttp://www.ncbi.nlm.nih.gov/pubmed/878527003253nas a2200301 4500008004100000022001400041245009200055210006900147260001200216300001200228490000700240520238200247653001702629653001202646653003102658653002402689653001702713653002402730653002702754653001002781653002902791100001902820700001702839700001702856700001702873700001402890856004702904 1995 eng d a0009-733000aEffects of pacing on stationary reentrant activity. Theoretical and experimental study.0 aEffects of pacing on stationary reentrant activity Theoretical a c12/1995 a1166-790 v773 a

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.

10aAcceleration10aAnimals10aCardiac Pacing, Artificial10aComputer Simulation10aDeceleration10aElectrocardiography10aModels, Cardiovascular10aSheep10aTachycardia, Ventricular1 aDavidenko, J M1 aSalomonsz, R1 aPertsov, A V1 aBaxter, Bill1 aJalife, J uhttp://www.ncbi.nlm.nih.gov/pubmed/758623000781nas a2200289 4500008004100000022001400041245004000055210003900095260001200134300003200146490000800178653001200186653002400198653002400222653002100246653002700267653001200294653002900306100001400335700001400349700001600363700001700379700001200396700001900408700001700427856004700444 1995 eng d a0036-807500aMechanisms of cardiac fibrillation.0 aMechanisms of cardiac fibrillation c11/1995 a1222-3; author reply 1224-50 v27010aAnimals10aComputer Simulation10aElectrocardiography10aHeart Ventricles10aModels, Cardiovascular10aRabbits10aVentricular Fibrillation1 aGray, R A1 aJalife, J1 aPanfilov, A1 aBaxter, Bill1 aCabo, C1 aDavidenko, J M1 aPertsov, A V uhttp://www.ncbi.nlm.nih.gov/pubmed/750205504137nas a2200313 4500008004100000022001400041245013200055210006900187260001300256300001200269490000700281520321100288653001203499653002403511653001003535653004003545653002703585653001403612653001203626653002903638100001403667700001403681700001603695700001703711700001203728700001903740700001703759856004703776 1995 eng d a0009-732200aNonstationary vortexlike reentrant activity as a mechanism of polymorphic ventricular tachycardia in the isolated rabbit heart.0 aNonstationary vortexlike reentrant activity as a mechanism of po c05/1995  a2454-690 v913 a

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.

10aAnimals10aElectrocardiography10aHeart10aImage Processing, Computer-Assisted10aModels, Cardiovascular10aPerfusion10aRabbits10aTachycardia, Ventricular1 aGray, R A1 aJalife, J1 aPanfilov, A1 aBaxter, Bill1 aCabo, C1 aDavidenko, J M1 aPertsov, A V uhttp://www.ncbi.nlm.nih.gov/pubmed/772903303423nas a2200337 4500008004100000022001400041245009300055210006900148260001200217300001200229490000700241520247800248653001202726653002402738653002602762653001002788653001602798653002802814653001102842653002702853653002902880653001002909653002602919100001202945700001702957700001702974700001902991700001403010700001403024856004703038 1994 eng d a0009-733000aWave-front curvature as a cause of slow conduction and block in isolated cardiac muscle.0 aWavefront curvature as a cause of slow conduction and block in i c12/1994 a1014-280 v753 a

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.

10aAnimals10aComputer Simulation10aElectric Conductivity10aHeart10aHeart Block10aHeart Conduction System10aHumans10aModels, Cardiovascular10aMotion Pictures as Topic10aSheep10aStaining and Labeling1 aCabo, C1 aPertsov, A V1 aBaxter, Bill1 aDavidenko, J M1 aGray, R A1 aJalife, J uhttp://www.ncbi.nlm.nih.gov/pubmed/752510103364nas a2200289 4500008004100000022001400041245008700055210006900142260001300211300001100224490000700235520252500242653001202767653002402779653002702803653000902830653002202839653001002861653004802871653002402919100001702943700001902960700001702979700001702996700001403013856004703027 1993 eng d a0009-733000aSpiral waves of excitation underlie reentrant activity in isolated cardiac muscle.0 aSpiral waves of excitation underlie reentrant activity in isolat c03/1993  a631-500 v723 a

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'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.

10aAnimals10aComputer Simulation10aDisease Models, Animal10aDogs10aElectrophysiology10aSheep10aTachycardia, Atrioventricular Nodal Reentry10aTorsades de Pointes1 aPertsov, A V1 aDavidenko, J M1 aSalomonsz, R1 aBaxter, Bill1 aJalife, J uhttp://www.ncbi.nlm.nih.gov/pubmed/843198902348nas a2200313 4500008004100000022001400041245009000055210006900145260000900214300001100223490001300234520141700247653001201664653003101676653002101707653002801728653002401756653002501780653001601805653004101821653001601862653002501878100001901903700001701922700001701939700001701956700001401973856004701987 1992 eng d a0022-073600aSpatiotemporal irregularities of spiral wave activity in isolated ventricular muscle.0 aSpatiotemporal irregularities of spiral wave activity in isolate c1992 a113-220 v24 Suppl3 a

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.

10aAnimals10aCardiac Pacing, Artificial10aFluorescent Dyes10aHeart Conduction System10aMembrane Potentials10aOptics and Photonics10aPericardium10aSignal Processing, Computer-Assisted10aTachycardia10aVentricular Function1 aDavidenko, J M1 aPertsov, A V1 aSalomonsz, R1 aBaxter, Bill1 aJalife, J uhttp://www.ncbi.nlm.nih.gov/pubmed/155224001940nas a2200289 4500008004100000022001400041245008300055210006900138260001200207300001100219490000800230520115000238653001201388653000901400653001001409653001601419653002401435653002301459653002701482653001001509100001901519700001701538700001701555700001701572700001401589856004701603 1992 eng d a0028-083600aStationary and drifting spiral waves of excitation in isolated cardiac muscle.0 aStationary and drifting spiral waves of excitation in isolated c c01/1992 a349-510 v3553 a

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 're-entrant excitation' 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.

10aAnimals10aDogs10aHeart10aMathematics10aMembrane Potentials10aModels, Biological10aMyocardial Contraction10aSheep1 aDavidenko, J M1 aPertsov, A V1 aSalomonsz, R1 aBaxter, Bill1 aJalife, J uhttp://www.ncbi.nlm.nih.gov/pubmed/173124801417nas a2200229 4500008004100000022001400041245008500055210006900140260001200209300001100221490000700232520073000239653001200969653003400981653002001015653002501035653003201060653001801092100001701110700001301127856004701140 1989 eng d a0340-120000aHorizontal organization of orientation-sensitive cells in primate visual cortex.0 aHorizontal organization of orientationsensitive cells in primate c07/1989 a171-820 v613 a

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.

10aAnimals10aElectron Transport Complex IV10aForm Perception10aModels, Neurological10aPattern Recognition, Visual10aVisual Cortex1 aBaxter, Bill1 aDow, B M uhttp://www.ncbi.nlm.nih.gov/pubmed/2548628