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Moore SC, Foley Kijewski M, El Fakhri G. Collimator optimization for detection and quantitation tasks: application to gallium-67 imaging. IEEE TRANSACTIONS ON MEDICAL IMAGING 2005; 24:1347-56. [PMID: 16229420 DOI: 10.1109/tmi.2005.857211] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
We describe a new approach to the problem of collimator optimization in nuclear medicine; our methodology is illustrated for the challenging case of gallium-67 imaging. Collimator-design methods based on empirical rules, such as specification of an allowable level of single-septal penetration (SSP) at a fixed energy, are especially inappropriate for radionuclides characterized by an abundance of high-energy contaminant photons that scatter in the patient, collimator, and/or detector before detection within one of a few photopeak energy windows. Lead X-rays produced in the collimator are an additional source of contamination. We designed optimal collimation for 67Ga based on relevant clinical imaging tasks and a realistic simulation of photon transport in a phantom, collimator, and detector. Collimator designs were compared on the basis of performance in lesion detection, as predicted by a three-channel Hotelling observer (CHO), as well as in tumor and background activity estimation (EST), quantified by task-specific signal-to-noise ratios (SNRs). The optimal values of collimator lead content were 22.0 and 23.8 g/cm2, respectively, for CHO and EST, while the optimal geometric resolution values were 1.8 and 1.6 cm full-width at half-maximum (FWHM), respectively, at a distance of 23.5 cm. The resolution of a commercially available medium-energy low-penetration collimator (MELP) is 1.9 cm FWHM at this distance. The optimal values for SSP at 300 keV were 7.3% and 5.8% based on CHO and EST, respectively, compared to 5.2% for the MELP collimator. Compared with the commercial MELP collimator, the 67Ga collimator optimized for tumor detection or activity estimation tasks provided improved geometric spatial resolution with reduced geometric efficiency and, surprisingly, allowed an increased level of single-septal penetration.
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El Fakhri G, Sitek A, Guérin B, Kijewski MF, Di Carli MF, Moore SC. Quantitative dynamic cardiac 82Rb PET using generalized factor and compartment analyses. J Nucl Med 2005; 46:1264-71. [PMID: 16085581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023] Open
Abstract
UNLABELLED We have addressed 2 major challenges of (82)Rb cardiac PET, noninvasive estimation of an accurate input function and absolute quantitation of myocardial perfusion, using a generalized form of least-squares factor analysis of dynamic sequences (GFADS) and a novel compartment analysis approach. METHODS Left and right ventricular (LV + RV) time-activity curves (TACs) were generated from 10 rest/stress studies, and 30 myocardial TACs were modeled to cover a range of clinical values. Two-dimensional PET Monte Carlo simulations of the LV, RV, myocardium, and other organs were generated separately and combined using the above TACs to form 30 realistic dynamic (82)Rb studies. LV and RV TACs were estimated by GFADS and used as input to a 2-compartment kinetic analysis that estimates parametric maps of myocardial tissue extraction (k(1)) and egress (k(2)), as well as LV + RV contributions (f(v), r(v)), by orthogonal voxel grouping. In addition, 13 patients were injected with 2.22 +/- 0.19 GBq (60 +/- 5 mCi) of (82)Rb and imaged dynamically for 6 min at rest and during dipyridamole stress. RESULTS In Monte Carlo simulations, GFADS yielded estimates of the 3 factors and corresponding factor images, with average errors of -4.2% +/- 6.3%, 3.5% +/- 4.3%, and 2.0% +/- 5.5% in the LV, RV, and myocardial factor estimates, respectively. The estimates were significantly more accurate and robust to noise than those obtained using TACs based on manually drawn volumes of interest (P < 0.01). The 2-compartment approach yielded accurate k(1), k(2), f(v), and r(v) parametric maps; the average error of estimates of k(1) was 6.8% +/- 3.6%. In all patient studies, our approach yielded robust estimates of k(1), k(2), f(v), and r(v), which correlated very well with the status of the subject and the catheterization results. CONCLUSION Quantitative dynamic (82)Rb PET using generalized factor analysis of dynamic sequences and compartmental modeling yields estimates of parameters of absolute myocardial perfusion and kinetics with errors of <9%.
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Müller SP, Abbey CK, Rybicki FJ, Moore SC, Kijewski MF. Measures of performance in nonlinear estimation tasks: prediction of estimation performance at low signal-to-noise ratio. Phys Med Biol 2005; 50:3697-715. [PMID: 16077222 DOI: 10.1088/0031-9155/50/16/004] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Maximum-likelihood (ML) estimation is an established paradigm for the assessment of imaging system performance in nonlinear quantitation tasks. At high signal-to-noise ratio (SNR), ML estimates are asymptotically Gaussian-distributed, unbiased and efficient, thereby attaining the Cramer-Rao bound (CRB). Therefore, at high SNR the CRB is useful as a predictor of the variance of ML estimates and, consequently, as a basis for measures of estimation performance. At low SNR, however, the achievable parameter variances are often substantially larger than the CRB and the estimates are no longer Gaussian-distributed. These departures imply that inference about the estimates that is based on the CRB and the assumption of a normal distribution will not be valid. We have found previously that for some tasks these effects arise at noise levels considered clinically acceptable. We have derived the mathematical relationship between a new measure, chi2(pdf-ML), and the expected probability density of the ML estimates, and have justified the use of chi2(pdf-ML)-isocontours in parameter space to describe the ML estimates. We validated this approach by simulation experiments using spherical objects imaged with a Gaussian point spread function. The parameters, activity concentration and size, were estimated simultaneously by ML, and variances and covariances calculated over 1000 replications per condition from 3D image volumes and from 2D tomographic projections of the same object. At low SNR, where the CRB is no longer achievable, chi2(pdf-ML)-isocontours provide a robust prediction of the distribution of the ML estimates. At high SNR, the chi2(pdf-ML)-isocontours asymptotically approach the analogous chi2(pdf-F)-contours derived from the Fisher information matrix. The chi2(pdf-ML) model appears to be suitable for characterization of the influence of the noise level and characteristics, the task, and the object on the shape of the probability density of the ML estimates at low SNR. Furthermore, it provides unique insights into the causes of the variability of estimation performance.
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Park MA, Moore SC, Kijewski MF. Brain SPECT with short focal-length cone-beam collimation. Med Phys 2005; 32:2236-2244. [PMID: 16121578 DOI: 10.1118/1.1929208] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2004] [Revised: 03/22/2005] [Accepted: 04/20/2005] [Indexed: 11/07/2022] Open
Abstract
Single-photon emission-computed tomography (SPECT) imaging of deep brain structures is compromised by loss of photons due to attenuation. We have previously shown that a centrally peaked collimator sensitivity function can compensate for this phenomenon, increasing sensitivity over most of the brain. For dual-head instruments, parallel-hole collimators cannot provide variable sensitivity without simultaneously degrading spatial resolution near the center of the brain; this suggests the use of converging collimators. We have designed collimator pairs for dual-head SPECT systems to increase sensitivity, particularly in the center of the brain, and compared the new collimation approach to existing approaches on the basis of performance in estimating activity concentration of small structures at various locations in the brain. The collimator pairs we evaluated included a cone-beam collimator, for increased sensitivity, and a fan-beam collimator, for data sufficiency. We calculated projections of an ellipsoidal uniform background, with 0.9-cm-radius spherical lesions at several locations in the background. From these, we determined ideal signal-to-noise ratios (SNRCRB) for estimation of activity concentration within the spheres, based on the Cramer-Rao lower bound on variance. We also reconstructed, by an ordered-subset expectation-maximization (OS-EM) procedure, images of this phantom, as well as of the Zubal brain phantom, to allow visual assessment and to ensure that they were free of artifacts. The best of the collimator pairs evaluated comprised a cone-beam collimator with 20 cm focal length, for which the focal point is inside the brain, and a fan-beam collimator with 40 cm focal length. This pair yielded increased SNRCRB, compared to the parallel-parallel pair, throughout the imaging volume. The factor by which SNRCRB increased ranged from 1.1 at the most axially extreme location to 3.5 at the center. The gains in SNRCRB were relatively robust to mismatches between the center of the brain and the center of the imaging volume. Artifact-free reconstructions of simulated data acquired using this pair were obtained. Combining fan-beam and short-focusing cone-beam collimation should greatly improve dual-head brain SPECT imaging, especially for centrally located structures.
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El Fakhri G, Kijewski MF, Albert MS, Johnson KA, Moore SC. Quantitative SPECT leads to improved performance in discrimination tasks related to prodromal Alzheimer's disease. J Nucl Med 2004; 45:2026-31. [PMID: 15585477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2023] Open
Abstract
UNLABELLED We investigated the impact of the quantitation and reconstruction protocol on clinical tasks. The performance of standard clinical reconstruction procedures in discrimination tasks related to the diagnosis of prodromal Alzheimer's disease (AD) was compared with the performance of a quantitative approach incorporating improved corrections for scatter, attenuation, intrinsic spatial resolution, and distance-dependent spatial resolution. METHODS Seventeen normal controls (normal group), 56 subjects who did not have dementia, who did have memory problems, but who did not develop AD within 5 y of follow-up (questionable group), and 27 subjects who did not have dementia, who did have memory problems, and who did develop AD over the follow-up period (converter group) were considered in this study. (99m)Tc-hexamethylpropyleneamine oxime SPECT and MRI studies were performed for each subject at baseline. The standard quantitation protocol (STD), routinely used in our clinic, consisted of Compton window scatter correction followed by filtered backprojection with attenuation correction using a uniform attenuation map. In the improved quantitative approach (QUAN), projections were corrected for scatter by use of a general spectral method and reconstructed by use of ordered-subset(s) expectation maximization, incorporating corrections for collimator response and attenuation using both a uniform attenuation map (QUANunif) and a nonuniform attenuation map (QUANnonunif). Mean SPECT activity concentration and MRI volume were estimated for 7 structures: rostral anterior cingulate gyrus, caudal anterior cingulate gyrus, posterior cingulate gyrus, hippocampus, basal forebrain, amygdala, and the banks of the superior temporal sulcus. Data were analyzed by pairwise discriminant analysis, and performance in binary group discrimination was measured by correlated receiver-operating-characteristic analysis. RESULTS The use of QUANnonunif yielded a small but systematic improvement in discrimination accuracy for normal versus converter groups (accuracy or area under the receiver-operating-characteristic curve [Az], 0.965), normal versus questionable groups (Az, 0.973), and questionable versus converter groups (Az, 0.881) compared with the results obtained with QUANunif (Az, 0.955, 0.962, and 0.866, respectively). Discrimination performance was significantly lower (P < 0.05) with STD than with QUAN in all 3 tasks (Az with STD, 0.906, 0.878, and 0.768, respectively). MRI volume estimation led to a lower overall performance in all 3 tasks than did QUANnonunif (Az with MRI, 0.947, 0.917, and 0.872, respectively). CONCLUSION Improved quantitative image reconstruction with accurate compensation for scatter, attenuation, and variable collimator response led to significantly better performance in discrimination tasks related to the diagnosis of prodromal AD than did standard clinical reconstruction procedures. The use of a nonuniform brain attenuation map yields a small improvement in discrimination accuracy.
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El Fakhri G, Moore SC, Kijewski MF. Optimization of Ga-67 imaging for detection and estimation tasks: dependence of imaging performance on spectral acquisition parameters. Med Phys 2002; 29:1859-66. [PMID: 12201433 DOI: 10.1118/1.1493214] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
UNLABELLED We have compared the use of two (93 and 185 keV) and three (93, 185, and 300 keV) photopeaks for Ga-67 tumor imaging and optimized the placement of each energy window. METHODS The bases for optimization and evaluation were ideal and Bayesian signal-to-noise ratios (SNR) for the detection of spheres embedded in a realistic anthropomorphic digital torso phantom and ideal SNR for the estimation of their size and activity concentration. Seven spheres of radii ranging from 1 to 3 cm, located at several sites in the torso, were simulated using a realistic Monte Carlo program. We also calculated the ideal SNR for the detection from simple phantom acquisitions. RESULTS For detection and estimation tasks, the optimum windows were identical for all sphere sizes and locations. For the 93 keV photopeak, the optimal window was 84-102 keV for the detection and 87-102 keV for estimation; these windows are narrower than the 20% window often used in the clinic (83-101 keV). For the 185 keV photopeak, the optimal window was 170-220 keV for the detection and 170-215 keV for estimation; these are substantially different than the 15% window used in our clinic (171-199 keV). For the 300 keV photopeak, the optimal window for detection was 270-320 keV, and for estimation, 280-320 keV. Using the three optimized, rather than only the two lower-energy, windows yielded a 9% increase in the SNR for the detection of the 3 cm diam sphere (a 12% increase for a 2 cm diam sphere) and a 7% increase in the SNR for estimation of its size. For the acquired phantom data, detection also increased by 9%-12% when using three, rather than two, energy windows.
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Ausió J, Abbott DW, Wang X, Moore SC. Histone variants and histone modifications: a structural perspective. Biochem Cell Biol 2002; 79:693-708. [PMID: 11800010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023] Open
Abstract
In this review, we briefly analyze the current state of knowledge on histone variants and their posttranslational modifications. We place special emphasis on the description of the structural component(s) defining and determining their functional role. The information available indicates that this histone "variability" may operate at different levels: short-range "local" or long-range "global", with different functional implications. Recent work on this topic emphasizes an earlier notion that suggests that, in many instances, the functional response to histone variability is possibly the result of a synergistic structural effect.
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Jason LJ, Moore SC, Ausio J, Lindsey G. Magnesium-dependent association and folding of oligonucleosomes reconstituted with ubiquitinated H2A. J Biol Chem 2001; 276:14597-601. [PMID: 11278847 DOI: 10.1074/jbc.m011153200] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The MgCl2-induced folding of defined 12-mer nucleosomal arrays, in which ubiquitinated histone H2A (uH2A) replaced H2A, was analyzed by quantitative agarose gel electrophoresis and analytical centrifugation. Both types of analysis showed that uH2A arrays attained a degree of compaction similar to that of control arrays in 2 mM MgCl2. These results indicate that attachment of ubiquitin to H2A has little effect on the ability of nucleosomal arrays to form higher order folded structures in the ionic conditions tested. In contrast, uH2A arrays were found to oligomerize at lower MgCl2 concentrations than control nucleosomal arrays, suggesting that histone ubiquitination may play a role in nucleosomal fiber association.
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Wang X, He C, Moore SC, Ausio J. Effects of histone acetylation on the solubility and folding of the chromatin fiber. J Biol Chem 2001; 276:12764-8. [PMID: 11279082 DOI: 10.1074/jbc.m100501200] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The folding ability of chromatin fractions containing approximately identical nucleosome numbers and the same linker histone composition, but with different extents of core histone acetylation, were analyzed by analytical ultracentrifugation. It was found that the acetylated fractions consistently exhibited a relatively small but significantly lower extent of compaction than that of their native nonacetylated counterparts. This was regardless of the extent of the size distribution heterogeneity of the fractions analyzed. Furthermore the acetylated chromatin fibers exhibited an enhanced solubility in both NaCl and MgCl(2), which is neither the result of a differential binding affinity of the linker histones to chromatin nor of an alteration in the relative amounts of the histone H1 variants.
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Moore SC, Kijewski MF, Müller SP, Rybicki F, Zimmerman RE. Evaluation of scatter compensation methods by their effects on parameter estimation from SPECT projections. Med Phys 2001; 28:278-87. [PMID: 11243353 DOI: 10.1118/1.1344201] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Three algorithms for scatter compensation in Tc-99m brain single-photon emission computed tomography (SPECT) were optimized and compared on the basis of the accuracy and precision with which lesion and background activity could be simultaneously estimated. These performance metrics are directly related to the clinically important tasks of activity quantitation and lesion detection, in contrast to measures based solely on the fidelity of image pixel values. The scatter compensation algorithms were (a) the Compton-window (CW) method with a 20% photopeak window, a 92-126 keV scatter window, and an optimized "k-factor," (b) the triple-energy window (TEW) method, with optimized widths of the photopeak window and the abutting scatter window, and (c) a general spectral (GS) method using seventeen 4 keV windows with optimized energy weights. Each method was optimized by minimizing the sum of the mean-squared errors (MSE) of the estimates of lesion and background activity concentrations. The accuracy and precision of activity estimates were then determined for lesions of different size, location, and contrast, as well as for a more complex Bayesian estimation task in which lesion size was also estimated. For the TEW and GS methods, parameters optimized for the estimation task differed significantly from those optimized for global normalized pixel MSE. For optimal estimation, the CW bias of activity estimates was larger and varied more (-2% to 22%) with lesion location and size than that of the other methods. The magnitude of the TEW bias was less than 7% across most conditions, although its precision was worse than that of CW estimates. The GS method performed best, with bias generally less than 4% and the lowest variance; its root-mean square (rms) estimation error was within a few percent of that achievable from primary photons alone. For brain SPECT, estimation performance with an optimized, energy-based, subtractive correction may approach that of an ideal scatter-rejection procedure.
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El Fakhri G, Moore SC, Maksud P, Aurengo A, Kijewski MF. Absolute activity quantitation in simultaneous 123I/99mTc brain SPECT. J Nucl Med 2001; 42:300-8. [PMID: 11216530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023] Open
Abstract
UNLABELLED Dual-isotope imaging can allow simultaneous assessment of brain perfusion using a 99mTc-labeled tracer and neurotransmission using an 123I-labeled tracer. However, the images are affected by scatter, cross talk, attenuation, distance-dependent collimator response (DCR), and partial-volume effect. We determined the accuracy and precision of activity quantitation in simulated normal and pathologic studies of simultaneous 123I/99mTc brain SPECT when compensating for all degrading phenomena. METHODS Monte Carlo simulations were performed using the Zubal brain phantom. Contamination caused by high-energy 123I decay photons was incorporated. Twenty-four 99mTc and 123I activity distributions were simulated on the basis of normal and pathologic patient activity distributions. Cross talk and scatter were corrected using a new method based on a multilayer perceptron artificial neural network (ANN), as well as by the asymmetric window (AW) approach; for comparison, unscattered (U) photons of 99mTc and 123I were recorded. Nonuniform attenuation and DCR were modeled in an iterative ordered-subset expectation maximization (OSEM) algorithm. Mean percentage biases and SDs over the 12 normal and 12 pathologic simulated studies were computed for each structure with respect to the known activity distributions. RESULTS For 123I, AW + OSEM yielded a bias of 7% in the cerebellum, 21% in the frontal cortex, and 36% in the corpus callosum in the simulated normal population. The bias was increased significantly in the striata of simulated pathologic studies (P < 0.05). The bias associated with ANN was significantly lower (<9% in these brain structures, P < 0.05). For 99mTc with AW + OSEM, the bias was 60% in the corpus callosum, 36% in the striata, and 18%-22% in the cortical lobes in the simulated normal population. This bias was <11% in all brain structures with ANN. In the simulated pathologic population, the bias associated with AW increased significantly in the cortical lobes to 55% (P < 0.05), although it did not change significantly with ANN. CONCLUSION The accuracy and variability over simulated normal and pathologic studies of both 99mTc and 123I activity estimates were very close with ANN to those obtained with U + OSEM. ANN + OSEM is a promising approach for absolute activity quantitation in simultaneous 99mTc/123I SPECT.
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Wang X, Moore SC, Laszckzak M, Ausió J. Acetylation increases the alpha-helical content of the histone tails of the nucleosome. J Biol Chem 2000; 275:35013-20. [PMID: 10938086 DOI: 10.1074/jbc.m004998200] [Citation(s) in RCA: 128] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The nature of the structural changes induced by histone acetylation at the different levels of chromatin organization has been very elusive. At the histone level, it has been proposed on several occasions that acetylation may induce an alpha-helical conformation of their acetylated N-terminal domains (tails). In an attempt to provide experimental support for this hypothesis, we have purified and characterized the tail of histone H4 in its native and mono-, di-, tri-, and tetra- acetylated form. The circular dichroism analysis of these peptides shows conclusively that acetylation does increase their alpha-helical content. Furthermore, the same spectroscopic analysis shows that this is also true for both the acetylated nucleosome core particle and the whole histone octamer in solution. In contrast to the native tails in which the alpha-helical organization appears to be dependent upon interaction of these histone regions with DNA, the acetylated tails show an increase in alpha-helical content that does not depend on such an interaction.
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Gagnon D, Laperriere L, Pouliot N, Vries DJD, Moore SC. Monte Carlo analysis of camera-induced spectral contamination for different primary energies. Phys Med Biol 2000. [DOI: 10.1088/0031-9155/37/9/001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Ramirez JJ, Bulsara K, Moore SC, Ruch K, Abrams W. Progressive unilateral damage of the entorhinal cortex enhances synaptic efficacy of the crossed entorhinal afferent to dentate granule cells. J Neurosci 1999; 19:RC42. [PMID: 10559432 PMCID: PMC6782991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/14/2023] Open
Abstract
Progressive injury to the mammalian CNS often reduces the severity of lesion-induced deficits or spares the behavior from deficits altogether. The mechanism(s) underlying this behavioral sparing is not clearly understood, but axonal sprouting is a likely candidate. To test this possibility, unilateral, two-stage (progressive) lesions of the entorhinal cortex, which are known to accelerate sprouting by the crossed temporodentate pathway and spare spatial memory function, were made in rats. We examined the changes in synaptic efficacy (as measured by the amplitude and slope of evoked population EPSPs) of the crossed temporodentate projection after either one-stage or progressive unilateral lesions of the entorhinal area. Whereas the synaptic efficacy of the one-stage group did not differ significantly from the control group at 4, 6, or 8 d after the lesion, the synaptic efficacy of the crossed temporodentate pathway in the progressive lesion group significantly increased above the control values as early as 4 d after the lesion and remained stable thereafter. Axonal sprouting thus may provide a mechanism by which to account for behavioral sparing after progressive brain damage.
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Ausió J, Moore SC. Reconstitution of chromatin complexes from high-performance liquid chromatography-purified histones. Methods 1998; 15:333-42. [PMID: 9740721 DOI: 10.1006/meth.1998.0637] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
We describe a method to reconstitute chromatin complexes from reversed-phase high-performance liquid chromatography (HPLC)-purified histones. The complexes reconstituted in this way exhibit the same structural characteristics as their equivalent native counterparts. Furthermore, this method works independently of the acid- or salt-extracted origin of the histones used for the HPLC fractionation. The potential of this method for the reconstitution of chromatin particles consisting of sequence-defined DNA templates and well-defined histone variants and/or their posttranslationally modified isoforms is discussed.
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Moore SC, Rice P, Iskandar M, Ausió J. Reconstitution of native-like nucleosome core particles from reversed-phase-HPLC-fractionated histones. Biochem J 1997; 328 ( Pt 2):409-14. [PMID: 9371695 PMCID: PMC1218935 DOI: 10.1042/bj3280409] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
We have reconstituted nucleosome core particles from reversed-phase-HPLC-purified chicken erythrocyte core histones and 145 bp random-sequence DNA fragments. Characterization of the resulting nucleoprotein complexes by sedimentation velocity, CD and DNase I footprinting showed that they are structurally indistinguishable from native nucleosome core particles. Furthermore, we have shown that the ability to reproduce these native-like structural features in these reconstituted nucleosome core particles is basically independent of the biological source or the method used (i.e. salt versus acid) for the extraction of histones before their HPLC fractionation. The usefulness and relevance of this approach for the reconstitution of native-like chromatin structures from histone types (histone variants/post-translationally modified histones), which are usually available only in relatively small amounts, is discussed.
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Zimmerman RE, Williams BB, Chan KH, Moore SC, Kijewski MF. Limitations of dual-photopeak window scatter correction for brain imaging. J Nucl Med 1997; 38:1902-6. [PMID: 9430466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
UNLABELLED A method for performing scatter corrections that would directly use the photopeak information and would be straightforward for use in clinical practice would be attractive in SPECT imaging. The dual-photopeak window method may be such a method. It relates the scatter fraction to the ratio of the lower to the total parts of a split-photopeak window. We investigated the use of this scatter correction method on a dedicated brain camera. METHODS Calibration curves for the Ceraspect, a dedicated brain imaging camera, were obtained for four split-window combinations using point sources in air and water. Simulations of the Ceraspect calibration curves at several energy resolution values were obtained using a Monte Carlo simulation of the instrument. RESULTS The calibration curves, experimental and simulated, revealed an ambiguous and unstable relationship between lower-to-total ratio and scatter fraction. CONCLUSION The unsatisfactory calibration curves can be attributed to the limited scatter produced in a brain-sized phantom during the calibration process and inherent stability problems in the calibration process. The dual-photopeak window method is not usable for small-field imaging systems and may even be unstable for larger-field systems.
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Chandry PS, Moore SC, Boyce JD, Davidson BE, Hillier AJ. Analysis of the DNA sequence, gene expression, origin of replication and modular structure of the Lactococcus lactis lytic bacteriophage sk1. Mol Microbiol 1997; 26:49-64. [PMID: 9383189 DOI: 10.1046/j.1365-2958.1997.5491926.x] [Citation(s) in RCA: 103] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Bacteriophage sk1 is a small isometric-headed lytic phage belonging to the 936 species. It infects Lactococcus lactis, a commonly used dairy starter organism. Nucleotide sequence data analysis indicated that the sk1 genome is 28,451 nucleotides long and contains 54 open reading frames (ORFs) of 30 or more codons, interspersed with three large intergenic regions. The nucleotide sequence of several of the sk1 ORFs demonstrated significant levels of identity to genes (many encoding proteins of unknown function) in other lactococcal phages of both small isometric-headed and prolate-headed morphotype. Based on this identity and predicted peptide structures, sk1 genes for the terminase, major structural protein and DNA polymerase have been putatively identified. Genes encoding holin and lysin were also identified, subcloned into an Escherichia coli expression vector, and their function demonstrated in vivo. The sk1 origin of replication was located by identifying sk1 DNA fragments able to support the maintenance in L. lactis of a plasmid lacking a functional Gram-positive ori. The minimal fragment conferring replication origin function contained a number of direct repeats and 179 codons of ORF47. Although no similarity between phage sk1 and coliphage lambda at the nucleotide or amino acid sequence level was observed, an alignment of the sk1 late region ORFs with the lambda structural and packaging genes revealed a striking correspondence in both ORF length and isoelectric point of the ORF product. It is proposed that this correspondence is indicative of a strong conservation in gene order within these otherwise unrelated isometric-headed phages that can be used to predict the functions of the sk1 gene products.
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Moore SC, Ausió J. Major role of the histones H3-H4 in the folding of the chromatin fiber. Biochem Biophys Res Commun 1997; 230:136-9. [PMID: 9020030 DOI: 10.1006/bbrc.1996.5903] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
We have characterized the hydrodynamic behavior of nucleosome arrays in which the N- and C-terminal "tails" of the histone H2A-H2B and H3-H4 domains have been selectively removed by digestion with immobilized trypsin. The sedimentation coefficient of the polynucleosome fibers lacking the histone H2A-H2B tails exhibited a salt dependence close to that of the non-trypsinized nucleosome arrays. In contrast, the salt-dependent behavior of the H3-H4-trypsinized polynucleosome fibers was found to be closer to that observed for the nucleosome arrays on which all the histones were trypsinized. This indicates that the N- and C-terminal domains of histones H3-H4 play a major role in the folding of the chromatin fiber. Magnesium titration of the polynucleosome fibers consisting of these trypsinized histone octamer hybrids at low ionic strength indicates that the histone H3-H4 tails also play an important role in the association of the polynucleosome fibers. These findings suggest that, after linker histones (histones of the H1 family), the tails of the histone H3-H4 domains are the major players in the processes that lead to the intra-association (folding) and inter-association of the chromatin fiber.
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Kijewski MF, Müller SP, Moore SC. Nonuniform collimator sensitivity: improved precision for quantitative SPECT. J Nucl Med 1997; 38:151-6. [PMID: 8998170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
UNLABELLED Attenuation of photons degrades both the accuracy and the precision of SPECT images; attenuation correction algorithms correct the bias but cannot improve precision. Increased noise due to photon attenuation is most pronounced in regions deep in solid body sections, such as the brain and abdomen. We have quantified the degradation in performance in several estimation tasks that can be attributed to photon attenuation and determined the degree to which performance might be improved by a collimator with a nonuniform sensitivity profile. METHODS The analysis used ideal-observer models of performance in tasks involving estimation of the activity and size of a focal lesion. The models were based on the Cramer-Rao lower bound on the variance with which lesion activity and size can be estimated by an unbiased procedure. To quantify the effects of attenuation, values of the Cramer-Rao bound were calculated for each estimation task as a function of location of the lesion in circularly-shaped attenuators of 10- and 20-cm radii, with and without attenuation. Values of the bound were also determined for two nonuniform sensitivity profiles, one of which was designed to equalize (or nearly equalize) task performance throughout the image. RESULTS For 99mTc, photon attenuation increased the variance of the estimates by factors of up to 4.5 for the 10-cm radius attenuator and up to 20.0 for the 20-cm radius attenuator. A collimator with a nonuniform sensitivity function reduced variance by factors of up to 1.8 for the 10-cm radius attenuator and up to 2.8 for the 20-cm radius attenuator. These gains in estimation performance were insensitive to the imaging task and to deviations from the assumed attenuator size and shape. CONCLUSION Performance in estimation tasks using images from SPECT systems with uniform sensitivity collimators is considerably lower than the theoretical optimum. We have derived a sensitivity function, realizable using existing technology, that improves performance substantially.
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Rosenthal MS, Cullom J, Hawkins W, Moore SC, Tsui BM, Yester M. Quantitative SPECT imaging: a review and recommendations by the Focus Committee of the Society of Nuclear Medicine Computer and Instrumentation Council. J Nucl Med 1995; 36:1489-513. [PMID: 7629599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
This article is a review of the physics principles, instrumentation and reconstruction methods behind SPECT imaging. Particular attention is paid to the mechanisms that can significantly affect the accuracy of a SPECT image. We describe instrumentation advances and reconstruction methods used to correct images to improve image quality and produce quantitative images. The clinical importance of improved image quality and quantitation are also reviewed.
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Moore SC, deVries DJ, Nandram B, Kijewski MF, Mueller SP. Collimator optimization for lesion detection incorporating prior information about lesion size. Med Phys 1995; 22:703-13. [PMID: 7565359 DOI: 10.1118/1.597466] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
A Bayesian estimator has been developed as a paradigm for human observer performance in detecting lesions of unknown size in a uniform noisy background. The Bayesian observer used knowledge of the range of possible lesion sizes as a prior; its predictions agreed well with the results of a six-observer perceptual study. The average human response to changes in collimator resolution, as measured by the detectability index, dA, was tracked by the Bayesian detector's signal-to-noise ratio (SNR) somewhat better than by two other estimation models based, respectively, on lesser and greater degrees of lesion size uncertainty. As the range of possible lesion sizes increased, the Bayesian detector's SNR decreased and the optimal collimator resolution shifted towards better resolution. An analytic approximation for the variance of lesion activity estimates (which included the same prior) was shown to predict the variance of the Bayesian estimator over a wide range of collimator resolution values. Because the bias of the Bayesian estimator was small (< 1%), the analytic variance estimate permitted a rapid and convenient prediction of the Bayesian detection SNR. This calculation was then used to optimize the geometric parameters of a two-layer tungsten collimator being constructed from crossed grids for a new imaging detector. A Monte Carlo program was first run to estimate all contributions to the radial point-spread function for collimators of differing tungsten contents and spatial resolution values, imaging 140-keV photons emitted from the center of a 15-cm-diameter, water-filled attenuator. The optimal collimator design for detecting lesions with unknown diameters in the range 2.5-7.5 mm yielded a system resolution of approximately 8.5-mm FWHM, a geometric collimator efficiency of 1.21 x 10(-4), and a single-septum penetration probability of 1%.
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Mundy RR, Moore SC, Corey JB, Mundy GD. Disability syndrome: the effects of early vs delayed rehabilitation intervention. AAOHN JOURNAL : OFFICIAL JOURNAL OF THE AMERICAN ASSOCIATION OF OCCUPATIONAL HEALTH NURSES 1994; 42:379-83. [PMID: 7945588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
1. Disability syndrome occurs when an individual with a work related injury or other disability chooses not to work when it has been medically determined that they are capable of doing so. 2. A possible contributor to the development of disability syndrome includes systems reinforcers or rules that discourage return to work. For example, many attorneys discourage early return to work or modified duty. 3. Early intervention by rehabilitation counselors at the time of injury can facilitate a positive attitude and empower the worker to resist the negative effect of systems reinforcers that discourage early return to work.
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Walsh EG, Minematsu K, Leppo J, Moore SC. Radioactive microsphere validation of a volume localized continuous saturation perfusion measurement. Magn Reson Med 1994; 31:147-53. [PMID: 8133750 DOI: 10.1002/mrm.1910310208] [Citation(s) in RCA: 82] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Detre et al. (Magn. Reson. Med. 23, 37-45 (1992)) and Zhang et al., (Magn. Reson. Med. 25, 362 (1992)) have recently demonstrated a technique for the measurement of regional cerebral blood flow (rCBF) based on the continuous saturation (or inversion) of the arterial blood supply to the brain in rats at 4.7 T. In the work reported here, we combined this technique with volume localized (PRESS) readouts to benefit from recording "perfusion" signals averaged over a larger volume, resulting in rapid acquisition of data with sufficient signal-to-noise ratio for application at 2.0 T. In 10 baseline flow measurements, the mean error between the NMR technique and the microsphere flow measurement was -1.5% with a standard deviation of 15.2%. For five measurements obtained with occlusion of the middle cerebral artery, the mean error was -32.4 +/- 20.2%. Perfusion measurements from a single animal under hypercapnic conditions indicated that the NMR technique could underestimate rCBF at high flow rates. An error analysis of the NMR perfusion model is also presented, along with results for typical parameters encountered at 2.0 T.
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Chandry PS, Moore SC, Davidson BE, Hillier AJ. Analysis of the cos region of the Lactococcus lactis bacteriophage sk1. Gene 1994; 138:123-6. [PMID: 8125289 DOI: 10.1016/0378-1119(94)90793-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The location, structure and nature of the cos site of the Lactococcus lactis bacteriophage sk1 was determined using a Taq DNA polymerase runoff sequencing technique. The cos site contains a single-stranded 3' overhang of 11 nucleotides. The region surrounding cos contains several features which may be involved in the binding and catalytic action of a phage terminase. These include four putative terminase-binding sites which show some homology to lambda R-sites, an 11-bp direct repeat, a 10-bp inverted repeat, a string of eight consecutive C residues and six copies of the pentanucleotide, AATCT. The spacing between adjacent copies of the pentanucleotides would place them on the same side of the DNA helix.
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