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Kleinstein SH, Singh JP. Toward quantitative simulation of germinal center dynamics: biological and modeling insights from experimental validation. J Theor Biol 2001; 211:253-75. [PMID: 11444956 DOI: 10.1006/jtbi.2001.2344] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
As models of immune system dynamics are developed, it is important to validate them with specific experimental data in order to understand their shortcomings and guide them toward becoming predictive. In this paper, we examine whether a particular mathematical model of germinal center dynamics, proposed by Oprea and Perelson, can reproduce experimental data from two specific primary responses, namely those directed against the haptens 2-phenyl-5-oxazolone and (4-hydroxy-3-nitrophenyl)acetyl. We develop formulas for estimating response-specific model parameters, as well as constraints for validating the model. In addition, we outline a general methodology for translating a continuous/deterministic model, expressed as a set of ordinary differential equations, into a discrete/stochastic framework. This methodology is used to create a new implementation of the Oprea and Perelson model that enables comparison with data on individual germinal centers. We conclude that while the model can reproduce the average dynamics of splenic germinal centers, it is at best incomplete and does not reproduce the distribution of individual germinal center behaviors. In addition to suggesting possible extensions to the model which can reconcile the dynamics with some aspects of the experimental data, we make a number of specific predictions that can be tested by in vivo experiments to obtain further insights and validation.
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Singh JP, Larson MG, O'Donnell CJ, Levy D. Genetic factors contribute to the variance in frequency domain measures of heart rate variability. Auton Neurosci 2001; 90:122-6. [PMID: 11485278 DOI: 10.1016/s1566-0702(01)00277-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Power spectral analysis of heart rate variability (HRV) provides quantitative phenotypic markers of autonomic nervous system activity. Reported determinants of HRV only partially explain its variability in the population. The purpose of this study was to estimate the contribution of genetic factors to the variance in HRV measures and assess the heritability of HRV. Subjects who underwent Holter recordings at a routine examination were eligible, excluding subjects with congestive heart failure, coronary artery disease, diabetes mellitus and those taking cardioactive medications. We analyzed the low-frequency power (LF), high-frequency power (HF), LF/HF ratio, very low-frequency power (VLF) and total power (TP). Heritability analysis was done by studying correlations between siblings (n = 682, in 291 sibships, 517 pairs) and between spouse pairs (n = 206 pairs). Adjustments were made for sex, age, systolic and diastolic blood pressure, heart rate, coffee and alcohol intake. SAS procedure MIXED was used to estimate and test significance of correlation within sibling pairs and within spouse pairs. Results from separate models were combined to estimate the components of variance of each phenotype, i.e. variance attributable to measured covariates, additive genetic effects (heritability) and household effects. After adjusting for covariates, the correlations were consistently higher among siblings (0.21-0.26) compared to spouses (0.01-0.19). The measured covariates in general accounted for 13-40% of the total phenotypic variance, whereas genes accounted for 13-23% of the variation among HRV measures. Genetic factors contribute towards a substantial proportion of the variance in heart rate and HRV. Recognition of the genetic determinants of HRV may provide additional insight into the pathophysiology of the autonomic nervous system and offer clues toward its modulation.
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Tripathi M, Pandey MB, Jha RN, Pandey VB, Tripathi PN, Singh JP. Cyclopeptide alkaloids from Zizyphus jujuba. Fitoterapia 2001; 72:507-10. [PMID: 11429244 DOI: 10.1016/s0367-326x(01)00278-7] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A new cyclopeptide alkaloid, jubanine-C (1), together with known alkaloids scutianine-C (4) and zizyphine-A (5), have been isolated from the stem bark of Zizyphus jujuba and identified by spectral analysis.
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Zhang H, Yueh FY, Singh JP. Performance evaluation of laser-induced breakdown spectrometry as a multimetal continuous emission monitor. JOURNAL OF THE AIR & WASTE MANAGEMENT ASSOCIATION (1995) 2001; 51:681-687. [PMID: 11355455 DOI: 10.1080/10473289.2001.10464306] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Laser-induced breakdown spectroscopy (LIBS) has been evaluated as a multimetal continuous emissions monitor (CEM) at the U.S. Environmental Protection Agency (EPA) rotary kiln incinerator simulator (RKIS) facility in Raleigh, NC. Two detection systems with a bifurcated optical fiber bundle were used for simultaneously monitoring the concentrations of Be, Cd, Cr, and Hg in the test. Two calibration techniques were evaluated in the laboratory for the field measurements. On-line calibration of relative metal concentration was also performed in the simulated incinerator gas stream. Toxic metal concentrations measured with LIBS have been compared with the EPA reference method (RM) results.
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Wagle A, Singh JP. Fibroblast growth factor protects nitric oxide-induced apoptosis in neuronal SHSY-5Y cells. J Pharmacol Exp Ther 2000; 295:889-95. [PMID: 11082421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023] Open
Abstract
Fibroblast growth factor (FGF) has been shown to protect tissue damage in animal models of cerebral and myocardial ischemia. The cellular and molecular mechanisms of FGF effects have not been fully defined. In the present study, we have investigated the effect of FGF homologs on nitric oxide (NO)-mediated neuronal cell death. Addition of NO donor S-nitroso-N-acetylpenicillamine (SNAP) to cultures of human neuroblastoma SHSY-5Y cells resulted in a concentration-dependent cell death. TdT-mediated dUTP-X nick end labeling and oligonucleosome assays confirmed that NO-mediated cell death occurred through the apoptotic pathway. In the presence of 150 microM SNAP, about 40% of the cells in culture underwent apoptosis. Treatment with FGF-2 resulted in greater than 80% reduction in NO-induced cell death. FGF addition to cell cultures also enhanced cell survival without affecting cell proliferation. FGF-2 effectively inhibited NO-mediated apoptosis even when added 6 h after treatment with SNAP. Examination of other homologs of FGF on NO-mediated cell death showed that in SHSY-5Y cells, FGF-2 and FGF-4, but not other FGF homologs, inhibited NO-mediated apoptosis. These results show that FGF-2 was a potent cell survival factor and protected SHSY-5Y cells from NO-mediated apoptosis. These effects were limited to FGF-2 and FGF-4 homologs.
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Singh JP, Larson MG, O'Donnell CJ, Wilson PF, Tsuji H, Lloyd-Jones DM, Levy D. Association of hyperglycemia with reduced heart rate variability (The Framingham Heart Study). Am J Cardiol 2000; 86:309-12. [PMID: 10922439 DOI: 10.1016/s0002-9149(00)00920-6] [Citation(s) in RCA: 276] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
This study was designed to examine the association of heart rate variability (HRV) with blood glucose levels in a large community-based population. Previous reports have shown HRV to be reduced in diabetics, suggesting the presence of abnormalities in neural regulatory mechanisms. There is scant information about HRV across the spectrum of blood glucose levels in a population-based cohort. One thousand nine hundred nineteen men and women from the Framingham Offspring Study, who underwent ambulatory electrocardiographic recordings at a routine examination, were eligible. HRV variables included the SD of normal RR intervals (SDNN), high-frequency (HF, 0.15 to 0.40 Hz) and low-frequency (LF, 0.04 to 0.15 Hz) power, and LF/HF ratio. Fasting plasma glucose levels were used to classify subjects as normal (<110 mg/dl; n = 1, 779), as having impaired fasting glucose levels (110 to 125 mg/dl; n = 56), and as having diabetes mellitus (DM >/=126 mg/dl or receiving therapy; n = 84). SDNN, LF and HF power, and LF/HF ratio were inversely related to plasma glucose levels (p <0.0001). SDNN and LF and HF powers were reduced in DM subjects (4.28 +/- 0.03, 6.03 +/- 0. 08, and 4.95 +/- 0.09) and in subjects with impaired fasting glucose levels (4.37 +/- 0.04, 6.26 +/- 0.10, and 5.06 +/- 0.11) compared with those with normal fasting glucose (4.51 +/- 0.01, 6.77 +/- 0.02, and 5.55 +/- 0.02, all p <0.005), respectively. After adjusting for covariates (age, sex, heart rate, body mass index, antihypertensive and cardiac medications, systolic and diastolic blood pressures, smoking, and alcohol and coffee consumption), LF power and LF/HF ratio were lower in DM subjects than in those with normal fasting glucose (p <0.005). HRV is inversely associated with plasma glucose levels and is reduced in diabetics as well as in subjects with impaired fasting glucose levels. Additional research is needed to determine if low HRV contributes to the increased cardiovascular morbidity and mortality described in subjects with hyperglycemia.
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Singh JP, Larson MG, O'Donnell CJ, Tsuji H, Evans JC, Levy D. Heritability of heart rate variability: the Framingham Heart Study. Circulation 1999; 99:2251-4. [PMID: 10226089 DOI: 10.1161/01.cir.99.17.2251] [Citation(s) in RCA: 141] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND There is evolving evidence that heart rate (HR) is genetically determined. Heart rate variability (HRV) measured by power spectral analysis provides quantitative phenotypic markers of autonomic nervous system activity. Reported determinants of HR and HRV only partially explain their variability in the population. The purpose of this study was to assess the heritability of HR and HRV and estimate the contribution of genetic factors to their variance. METHODS AND RESULTS Subjects who underwent ambulatory recordings at a routine examination were eligible; subjects with congestive heart failure, coronary artery disease, diabetes mellitus, and those taking cardioactive medications were excluded. We analyzed high-frequency power, low-frequency power, very low-frequency power, total power, low-frequency/high-frequency ratio, and the standard deviation of normal R-R intervals from 2-hour continuous ECG recordings. Heritability analysis was done by studying correlations between siblings (n=682, in 291 sibships, 517 pairs) and between spouse pairs (n=206 pairs) after adjusting for important covariates. Results from separate models were combined to estimate the components of variance attributable to measured covariates, additive genetic effects (heritability), and household effects. After adjusting for covariates, the correlations were consistently higher among siblings (0.21 to 0.26) compared with spouses (0.01 to 0.19). The measured covariates in general accounted for 13% to 40% of the total phenotypic variance, whereas genetic factors accounted for 13% to 23% of the variation among HR and HRV measures. CONCLUSIONS Heritable factors may explain a substantial proportion of the variance in HR and HRV. These results highlight the contribution of genetic versus environmental factors to autonomic nervous system activity.
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Singh JP, Larson MG, Manolio TA, O'Donnell CJ, Lauer M, Evans JC, Levy D. Blood pressure response during treadmill testing as a risk factor for new-onset hypertension. The Framingham heart study. Circulation 1999; 99:1831-6. [PMID: 10199879 DOI: 10.1161/01.cir.99.14.1831] [Citation(s) in RCA: 304] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND Although systolic blood pressure (SBP) response to exercise has been shown to predict subsequent hypertension in small samples of men, this association has not been studied in a large population-based sample of middle-aged men and women. The purpose of this study was to examine, in normotensive subjects, the relations of SBP and diastolic blood pressure (DBP) during the exercise and recovery periods of a graded treadmill test to the risk of developing new-onset hypertension. METHODS AND RESULTS BP data from exercise testing in 1026 men and 1284 women (mean age, 42+/-10 years; range, 20 to 69 years) from the Framingham Offspring Study who were normotensive at baseline were related to the incidence of hypertension 8 years later. New-onset hypertension, defined as an SBP >/=140 mm Hg or DBP >/=90 mm Hg or the initiation of antihypertensive drug treatment, occurred in 228 men (22%) and 207 women (16%). Exaggerated SBP (Ex-SBP 2) and DBP (Ex-DBP 2) response and delayed recovery of SBP (R-SBP 3) and DBP (R-DBP 3) were defined as an age-adjusted BP greater than the 95th percentile during the second stage of exercise and third minute of recovery, respectively. After multivariable adjustment, Ex-DBP 2 was highly predictive of incident hypertension in both men (OR, 4.16; 95% CI, 2.15, 8.05) and women (OR, 2.17; CI, 1.19, 3.96). R-SBP 3 was predictive of hypertension in men in a multivariable model that included exercise duration and peak exercise BP (OR, 1.92; CI, 1.00, 3.69). Baseline resting SBP (chi2, 23.4 in men and 34.7 in women) and DBP (chi2, 11.3 in men and 13.1 in women) had stronger associations with new-onset hypertension than exercise DBP (chi2, 16.4 in men and 6.1 in women) and recovery SBP (chi2, 6.5 in men and 2.1 in women) responses. CONCLUSIONS An exaggerated DBP response to exercise was predictive of risk for new-onset hypertension in normotensive men and women. An elevated recovery SBP was predictive of hypertension in men. These findings may reflect subtle pathophysiological features in the preclinical stage of hypertension.
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Zhang H, Yueh FY, Singh JP. Laser-induced breakdown spectrometry as a multimetal continuous-emission monitor. APPLIED OPTICS 1999; 38:1459-1466. [PMID: 18305767 DOI: 10.1364/ao.38.001459] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Laser-induced breakdown spectrometry (LIBS) has been used to detect atomic and molecular species in various environments. LIBS has the capability to be used as a continuous-emission monitor to monitor toxic-metal concentrations in stack emissions. Recently a mobile LIBS system was calibrated in our laboratory and tested as a multimetal continuous-emission monitor during a joint U.S. Department of Energy-Environmental Protection Agency (EPA) test. LIBS measurements were performed with three sets of metal concentrations at the EPA Rotary Kiln Incinerator Simulator. The LIBS system successfully measured concentrations of Cr, Pb, Cd, and Be in near real time in this test. Real-time LIBS data were averaged and compared with data obtained from an EPA reference method that was conducted concurrently with LIBS. The details of the LIBS calibration and results of these LIBS measurements are described.
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Boudreaux GM, Miller TS, Kunefke AJ, Singh JP, Yueh FY, Monts DL. Development of a photofragmentation laser-induced-fluorescence laser sensor for detection of 2, 4, 6-trinitrotoluene in soil and groundwater. APPLIED OPTICS 1999; 38:1411-1417. [PMID: 18305761 DOI: 10.1364/ao.38.001411] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Laser photofragmentation (PF) and subsequent nitric oxide (NO) laser-induced fluorescence (LIF) have been developed to measure the concentration of energetic materials (EM's), such as 2, 4, 6-trinitrotoluene (TNT), in soil and other media. Gas-phase EM's photodissociate, releasing NO(2), when exposed to laser radiation near 226 nm. Laser-excited NO(2) predissociates to form NO that gives an intense fluorescence when excited near 226 nm. The EM concentration is inferred from the intensity of the NO fluorescence. A PF-LIF laser-based sensor is being developed to be used with the U.S. Army Corps of Engineers' Waterways Experiment Station's cone penetrometer to measure in situ the concentration of subsurface TNT. Several factors that affect the PF-LIF signal waveforms, such as sample temperature, laser power, and heating time, were investigated. Also, effects on the PF-LIF signal of adding water and fertilizer to the TNT mixtures were studied. Decay times were determined by least-squares fitting of the exponential PF-LIF signal waveforms. The use of PF-LIF waveforms promises to enable diagnostics of the sample's characteristics that would otherwise not be possible in situ.
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Zikratov G, Yueh FY, Singh JP, Norton OP, Kumar RA, Cook RL. Spontaneous anti-Stokes Raman probe for gas temperature measurements in industrial furnaces. APPLIED OPTICS 1999; 38:1467-1475. [PMID: 18305768 DOI: 10.1364/ao.38.001467] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
A compact, pulsed Nd:YAG laser-based instrument has been built to measure in situ absolute gas temperatures in large industrial furnaces by use of spontaneous anti-Stokes Raman scattering. The backscattering configuration was used to simplify the optics alignment and increase signal-to-noise ratios. Gated signal detection significantly reduced the background emission that is found in combustion environments. The anti-Stokes instead of the Stokes component was used to eliminate contributions to spectra from cold atmospheric nitrogen. The system was evaluated in a methane/air flame and in a bench-top oven, and the technique was found to be a reliable tool for nonintrusive absolute temperature measurements with relatively clean gas streams. A water-cooled insertion probe was integrated with the Raman system for measurement of the temperature profiles inside an industrial furnace. Gas temperatures near 1500-1800 K at atmospheric pressure in an industrial furnace were inferred by fitting calculated profiles to experimental spectra with a standard deviation of less than 1% for averaging times of approximately 200 s. The temperatures inferred from Raman spectra are in good agreement with data recorded with a thermocouple probe.
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Singh JP, Evans JC, Levy D, Larson MG, Freed LA, Fuller DL, Lehman B, Benjamin EJ. Prevalence and clinical determinants of mitral, tricuspid, and aortic regurgitation (the Framingham Heart Study). Am J Cardiol 1999; 83:897-902. [PMID: 10190406 DOI: 10.1016/s0002-9149(98)01064-9] [Citation(s) in RCA: 797] [Impact Index Per Article: 31.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Abstract
Little information is available on the prevalence and determinants of valvular regurgitation in the general population. This study sought to assess the prevalence and clinical determinants of mitral (MR), tricuspid (TR), and aortic (AR) regurgitation in a population-based cohort. Color Doppler echocardiography was performed in 1,696 men and 1,893 women (aged 54 +/- 10 years) attending a routine examination at the Framingham Study. After excluding technically poor echocardiograms, MR, TR, and AR were qualitatively graded from trace to severe. Multiple logistic regression analysis was used to examine the association of clinical variables with MR and TR (more than or equal to mild severity) and AR (more than or equal to trace severity). MR and TR of more than or equal to mild severity was seen in 19.0% and 14.8% of men and 19.1% and 18.4% of women, respectively, and AR of more than or equal to trace severity in 13.0% of men and 8.5% of women. The clinical determinants of MR were age (odds ratio [OR] 1.3/9.9 years, 95% confidence interval [CI] 1.2 to 1.5), hypertension (OR 1.6; 95% CI 1.2 to 2.0), and body mass index (OR 0.8/4.3 kg/m2; 95% CI 0.7 to 0.9). The determinants of TR were age (OR 1.5/9.9 years; 95% CI 1.3 to 1.7), body mass index (OR 0.7/4.3 kg/m2; 95% CI 0.6 to 0.8), and female gender (OR 1.2; 95% CI 1.0 to 1.6). The determinants of AR were age (OR 2.3/9.9 years; 95% CI 2.0 to 2.7) and male gender (OR 1.6; 95% CI 1.2 to 2.1). A substantial proportion of healthy men and women had detectable valvular regurgitation by color Doppler echocardiography. These data provide population-based estimates for comparison with patients taking anorectic drugs.
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Panda A, Bageshwar LM, Ray M, Singh JP, Kumar A. Deep lamellar keratoplasty versus penetrating keratoplasty for corneal lesions. Cornea 1999; 18:172-5. [PMID: 10090362 DOI: 10.1097/00003226-199903000-00005] [Citation(s) in RCA: 126] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
PURPOSE To compare the effectiveness of deep lamellar keratoplasty (DLK) with that of penetrating keratoplasty (PKP) in cases of corneal lesions not involving the endothelium. METHODS Forty-eight eyes with leukomatous corneal opacity (n = 33), keratoconus with apical scarring (n = 6), granular corneal dystrophy (n = 5), lattice corneal dystrophy (n = 2), and multiple corneal foreign bodies (n = 2) in an age group varying from 16 to 53 years underwent DLK (n = 24) and PKP (n = 24) by utilizing B and (B+ and A) grade M-K preserved donor tissue, respectively. The patients were followed up closely, and the graft clarity, visual achievement, astigmatism and endothelial cell count were evaluated at repeated occasions up to 1 year. RESULTS Astigmatism of <3 diopters (D) and > or = 5D was obtained in 19 eyes and one eye, respectively, after DLK at 6 months, whereas six eyes of the PKP group had astigmatism <3D, and 12 eyes had > or = 5D at the end of 6 months. The same at 1 year was observed in 20 and one eye in the DLK and eight and five eyes of the PKP group. Astigmatism of > or = 5D at the end of 6 months in both the groups showed highly significant changes (p < 0.001). Best corrected visual acuity of 6/18 or more was achieved in 18 and 12 eyes at 6 months after DLK and PKP, respectively, which were statistically highly significant (p < 0.001), whereas at 1 year, it was seen in 17 and 15 eyes of the DLK and PKP groups, respectively, which was nonsignificant. The mean endothelial cell count was 2,233.3+/-64.453 cells/mm2 and 2,219.6+/-102.48 cells/mm2 at 6 months and I year, respectively, after DLK, which was nonsignificant. The mean cell count of the donor eyes used for PKP was 2,191+/-52.164 cells/mm2, 1,902.8+/-70.346 cells/mm2 at 6 months, and 1,579.0+/-80.24 cells/mm2 at 1 year. All the values showed highly significant changes (p < 0.001). Further, the graft clarity of > or = 3+ was achieved in 20 and 18 eyes at 6 months postoperatively in the DLK and PKP groups, whereas the same was observed in 19 and 13 eyes of both the groups, respectively, at 1-year follow-up. CONCLUSION DLK is a promising procedure and should be practiced more frequently for corneal pathology not involving the endothelium.
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Chen CC, Singh JP, Altman RB. Using imperfect secondary structure predictions to improve molecular structure computations. Bioinformatics 1999; 15:53-65. [PMID: 10068692 DOI: 10.1093/bioinformatics/15.1.53] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022] Open
Abstract
MOTIVATION Until ab initio structure prediction methods are perfected, the estimation of structure for protein molecules will depend on combining multiple sources of experimental and theoretical data. Secondary structure predictions are a particularly useful source of structural information, but are currently only approximately 70% correct, on average. Structure computation algorithms which incorporate secondary structure information must therefore have methods for dealing with predictions that are imperfect. EXPERIMENTS PERFORMED: We have modified our algorithm for probabilistic least squares structural computations to accept 'disjunctive' constraints, in which a constraint is provided as a set of possible values, each weighted with a probability. Thus, when a helix is predicted, the distances associated with a helix are given most of the weight, but some weights can be allocated to the other possibilities (strand and coil). We have tested a variety of strategies for this weighting scheme in conjunction with a baseline synthetic set of sparse distance data, and compared it with strategies which do not use disjunctive constraints. RESULTS Naive interpretations in which predictions were taken as 100% correct led to poor-quality structures. Interpretations that allow disjunctive constraints are quite robust, and even relatively poor predictions (58% correct) can significantly increase the quality of computed structures (almost halving the RMS error from the known structure). CONCLUSIONS Secondary structure predictions can be used to improve the quality of three-dimensional structural computations. In fact, when interpreted appropriately, imperfect predictions can provide almost as much improvement as perfect predictions in three-dimensional structure calculations.
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Chen CC, Singh JP, Altman RB. Hierarchical organization of molecular structure computations. J Comput Biol 1998; 5:409-22. [PMID: 9773341 DOI: 10.1089/cmb.1998.5.409] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The task of computing molecular structure from combinations of experimental and theoretical constraints is expensive because of the large number of estimated parameters (the 3D coordinates of each atom) and the rugged landscape of many objective functions. For large molecular ensembles with multiple protein and nucleic acid components, the problem of maintaining tractability in structural computations becomes critical. A well-known strategy for solving difficult problems is divide-and-conquer. For molecular computations, there are two ways in which problems can be divided: (1) using the natural hierarchy within biological macromolecules (taking advantage of primary sequence, secondary structural subunits and tertiary structural motifs, when they are known); and (2) using the hierarchy that results from analyzing the distribution of structural constraints (providing information about which substructures are constrained to one another). In this paper, we show that these two hierarchies can be complementary and can provide information for efficient decomposition of structural computations. We demonstrate five methods for building such hierarchies--two automated heuristics that use both natural and empirical hierarchies, one knowledge-based process using both hierarchies, one method based on the natural hierarchy alone, and for completeness one random hierarchy oblivious to auxiliary information--and apply them to a data set for the procaryotic 30S ribosomal subunit using our probabilistic least squares structure estimation algorithm. We show that the three methods that combine natural hierarchies with empirical hierarchies create decompositions which increase the efficiency of computations by as much as 50-fold. There is only half this gain when using the natural decomposition alone, while the random hierarchy suggests that a speedup of about five can be expected just by virtue of having a decomposition. Although the knowledge-based method performs marginally better, the automatic heuristics are easier to use, scale more reliably to larger problems, and can match the performance of knowledge-based methods if provided with basic structural information.
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Chetty R, Subramoney T, Singh JP. Retinoblastoma and p53 protein expression in sporadic colorectal cancers. Eur J Surg Oncol 1998; 24:436-9. [PMID: 9800976 DOI: 10.1016/s0748-7983(98)92434-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023] Open
Abstract
AIMS To ascertain if a relationship between retinoblastoma (pRb) and p53 proteins exists in sporadic colorectal carcinomas. METHODS Fifty consecutive colectomy specimens for colorectal cancer in patients over the age of 50 and with no family history of cancers in the bowel were examined for immunoexpression of pRb and p53 proteins. These findings were then related to clinicopathological findings. Commercially available monoclonal antibodies to pRb and p53 were used on formalin-fixed, paraffin-embedded tissue. RESULTS The most intense pRb immunoexpression was detected in well-differentiated, low-stage cancers. On the other hand, p53 expression was most intense in poorly differentiated, advanced-stage carcinomas. No statistically significant associations were noted with immunoexpression and age, gender or site of lesion. CONCLUSIONS This study indicates that there is an inverse relationship between pRb and p53 protein expression in a proportion of sporadic colorectal cancers. Twelve tumours which showed low levels of pRb showed high levels of p53 protein. Similarly, seven tumours with high pRb levels displayed low p53 expression. In terms of immunohistochemical profile, p53-high/pRb-low tumours tended to be poorly differentiated and have advanced stage cancer.
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Singh JP, Larson MG, Tsuji H, Evans JC, O'Donnell CJ, Levy D. Reduced heart rate variability and new-onset hypertension: insights into pathogenesis of hypertension: the Framingham Heart Study. Hypertension 1998; 32:293-7. [PMID: 9719057 DOI: 10.1161/01.hyp.32.2.293] [Citation(s) in RCA: 327] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Heart rate variability (HRV) is a useful noninvasive tool to assess cardiac autonomic function. The purpose of this study was to (1) compare measures of HRV between hypertensive and normotensive subjects and (2) examine the role of HRV as a predictor of new-onset hypertension. The first 2 hours of ambulatory ECG recordings obtained from 931 men and 1111 women attending a routine examination at the Framingham Heart Study were processed for HRV. Three time-domain and 5 frequency-domain variables were studied: standard deviation of normal RR intervals (SDNN), percentage of differences between adjacent normal RR intervals exceeding 50 milliseconds, square root of the mean of squared differences between adjacent normal RR intervals, total power (0.01 to 0.40 Hz), high frequency power (HF, 0.15 to 0.40 Hz), low frequency power (LF, 0.04 to 0.15 Hz), very low frequency power (0.01 to 0.04 Hz), and LF/HF ratio. On cross-sectional analysis, HRV was significantly lower in hypertensive men and women. Among 633 men and 801 women who were normotensive at baseline (systolic blood pressure <140 mm Hg and diastolic blood pressure <90 mm Hg and not receiving antihypertensive treatment), 119 men and 125 women were newly hypertensive at follow-up 4 years later. After adjustment for factors associated with hypertension, multiple logistic regression analysis revealed that LF was associated with incident hypertension in men (odds ratio per SD decrement [OR], 1.38; 95% confidence interval [CI], 1.04 to 1.83) but not in women (OR, 1.12; 95% CI, 0.86 to 1.46). SDNN, HF, and LF/HF were not associated with hypertension in either sex. HRV is reduced in men and women with systemic hypertension. Among normotensive men, lower HRV was associated with greater risk for developing hypertension. These findings are consistent with the hypothesis that autonomic dysregulation is present in the early stage of hypertension.
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93
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Singh JP, Musialek P, Sleight P, Davey P, Marinho M, Hart G. Effect of atenolol or metoprolol on waking hour dynamics of the QT interval in myocardial infarction. Am J Cardiol 1998; 81:924-6. [PMID: 9555785 DOI: 10.1016/s0002-9149(98)00022-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
In subjects with a recent acute myocardial infarction, the hour immediately following awakening is associated with an abrupt exaggeration of heart rate-dependent changes and variability of the QT interval. Beta blockers were observed to blunt these waking hour changes.
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94
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Abstract
An increased spatial dispersion of ventricular repolarization duration (QT dispersion) is associated with an increased vulnerability to arrhythmias. This study was designed to examine the effect of exercise on QT dispersion in ischemic heart disease (IHD). QT dispersion, corrected QT dispersion, and percentage change in uncorrected and corrected QT dispersion between rest and peak exercise were examined in 14 members of a control group, 17 patients with IHD, and 14 patients with IHD who were receiving beta-blockers (IHD-B). All subjects had undergone a standard Bruce protocol exercise test, and QT intervals were measured at rest and peak exercise with a digitizing tablet interfaced to a personal computer. QT dispersion at rest was markedly increased in the IHD group compared with that in the control and IHD-B groups, respectively (corrected QT dispersion in milliseconds), 74 +/- 7, 40 +/- 4, 49 +/- 5, p < 0.03). The corrected QT dispersion at peak exercise was greater in the IHD group compared with that in the control group (57 +/- 5 vs 26 +/- 3 msec, p < 0.03). The percentage change in QT dispersion with exercise was significantly higher in the IHD group (52% +/- 5%) compared with that in both the control group (28% +/- 4%, p < 0.002) and the IHD-B group (30% +/- 3%, p < 0.01). A larger mean QT dispersion at peak exercise and an increased percentage change in QT dispersion with exercise may help explain the increased susceptibility of the IHD group for arrhythmias. The cardioprotective action of beta-blockers may be explained by their blunting effect on exercise-related changes in QT dispersion.
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95
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Wood DL, Panda D, Wiernicki TR, Wilson L, Jordan MA, Singh JP. Inhibition of mitosis and microtubule function through direct tubulin binding by a novel antiproliferative naphthopyran LY290181. Mol Pharmacol 1997; 52:437-44. [PMID: 9281606 DOI: 10.1124/mol.52.3.437] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The mechanism of action of a novel antiproliferative compound LY290181 [2-amino-4-(3-pyridyl)-4H-naphtho(1,2-b)pyran-3-carbonitrile] was characterized. LY290181 is a potent inhibitor of cell proliferation, producing 50% inhibition of vascular smooth muscle, endothelial, Chinese hamster ovary, HeLa, and human erythroleukemia cells at concentrations of 8-40 nM. Cell cycle analysis showed that LY290181 caused accumulation of smooth muscle cells at the G2/M phase and induced mitotic arrest in Chinese hamster ovary cells and HeLa cells. At low concentrations (3-30 nM), LY290181 blocked transition of cells from metaphase to anaphase and disrupted mitotic spindle organization. At high concentrations (>/=100 nM), LY290181 produced a concentration-dependent loss of cytoplasmic and spindle microtubules. LY290181 inhibited the polymerization of purified bovine brain microtubule protein into microtubules, and it depolymerized preformed microtubules. Using tubulin-1-anilino-8-naphthalene sulfonate complex fluorescence, we have shown that LY290181 directly interacted with tubulin in a unique manner. These studies show that LY290181 induces cell growth arrest in prometaphase/metaphase, and tubulin appears to be its molecular target.
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96
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Singh JP, Sleight P, Kardos A, Hart G. QT interval dynamics and heart rate variability preceding a case of cardiac arrest. Heart 1997; 77:375-7. [PMID: 9155622 PMCID: PMC484737 DOI: 10.1136/hrt.77.4.375] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
A 71 year old man with hypertensive heart disease and chronic renal failure was wearing a Holter monitor when he had a cardiac arrest. He had ventricular fibrillation (VF) and died despite prompt resuscitation. In the 15 minutes preceding the VF there was a sudden increase in heart rate, followed by a brief period of atrial fibrillation leading to ventricular tachycardia, which in turn rapidly degenerated into VF. The QT interval and heart rate variability were studied half hourly over the seven hours preceding the cardiac arrest, using a computerised Holter system. A further detailed analysis was performed over the final hour before the cardiac arrest. An abrupt increase in the steepness of the QT/RR slope, a prolonged QTc, and a reduction in the heart rate variability were observed in the interval that immediately preceded the onset of the terminal rhythm disturbance.
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97
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Panda D, Singh JP, Wilson L. Suppression of microtubule dynamics by LY290181. A potential mechanism for its antiproliferative action. J Biol Chem 1997; 272:7681-7. [PMID: 9065425 DOI: 10.1074/jbc.272.12.7681] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
LY290181, 2-amino-4-(3-pyridyl)-4H-naphtho(1,2-b)pyran-3-carbonitrile, is a potent antiproliferative compound that blocks cells in the G2/M phase of the cell cycle by an apparent action on microtubules. In the present work we found that LY290181 bound to tubulin with high affinity (1 mol of LY290181 per mol of tubulin dimer; Ka, 3.8 x 10(5) M-1) and that it did not appear to bind at the colchicine or vinblastine-binding sites. LY290181 strongly stabilized microtubule dynamics as determined by video microscopy. It reduced the rate and extent of growing and shortening, reduced the catastrophe frequency and increased the rescue frequency, and increased the percentage of time the microtubules spent in an attenuated state. At the lowest effective LY290181 concentrations (0.1-0.3 microM), suppression of dynamics occurred with little reduction in polymer mass. However, at higher concentrations, LY290181 strongly reduced the polymer mass with half-maximal inhibition at a concentration of 0.75 microM. We suggest that LY290181 may exert its antiproliferative activity by stabilizing spindle microtubule dynamics by binding to tubulin at a novel site.
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98
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Singh JP, Johnston J, Sleight P, Bird R, Ryder K, Hart G. Left ventricular hypertrophy in hypertensive patients is associated with abnormal rate adaptation of QT interval. J Am Coll Cardiol 1997; 29:778-84. [PMID: 9091524 DOI: 10.1016/s0735-1097(96)00576-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
OBJECTIVES This study sought to examine whether the responses of the QT interval to changes in the heart rate were altered in left ventricular hypertrophy (LVH). BACKGROUND The QT interval has been shown to have a delayed adaptation to sudden changes in heart rate in normal subjects. Abnormalities in the adaptation of the QT interval to changes in the RR interval may facilitate the development of ventricular arrhythmias. METHODS Consecutive newly diagnosed hypertensive subjects, not taking any medications, were age and gender matched for LVH (n = 21) versus on LVH (n = 16). QT interval dynamics were analyzed under visual control using a validated algorithm with automatic QT measurements at the end of the T wave. A computerized Holter system was developed to study the QT interval response to changes in the RR interval. The adaptive response of the QT interval was measured as the ratio of the slope from 10% to 90% of the QT change relative to the RR interval change (dQT/dRR10-90). Steady state adaptation was also studied as the percent shortening and lengthening of the QT interval during acceleration and deceleration of heart rate. RESULTS The adaptive response of the QT interval measured as dQT/dRR10-90 was increased in the LVH group compared with that in the control subjects during both acceleration (0.33 +/- 0.06 vs. 0.18 +/- 0.02, p = 0.02) and deceleration phases (0.23 +/- 0.04 vs. 0.16 +/- 0.02, p = 0.03). In the LVH group, the percent lengthening of the QT interval was greater (7.6 +/- 0.7 vs. 5.1 +/- 0.2, p = 0.03), whereas the percent shortening was not significantly different (5.71 +/- 0.5 vs. 4.6 +/- 0.3, p = 0.43), than that in control subjects. CONCLUSIONS The QT interval response to changes in the RR interval is rapid and exaggerated in LVH. These abnormalities of the QT interval response demonstrate that there are altered repolarization dynamics in patients with LVH that may make them vulnerable to serious ventricular arrhythmias.
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Wiernicki TR, Bean JS, Dell C, Williams A, Wood D, Kauffman RF, Singh JP. Inhibition of vascular smooth muscle cell proliferation and arterial intimal thickening by a novel antiproliferative naphthopyran. J Pharmacol Exp Ther 1996; 278:1452-9. [PMID: 8819533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Smooth muscle cell proliferation plays an important role in neointimal thickening after vascular injury and may contribute to restenosis after angioplasty. Development of suitable pharmacological agents modulating smooth muscle cell proliferation is critical for further investigation of vascular hyperplasia and its prevention. In the present study, we report a novel series of compounds that inhibit smooth muscle cell proliferation and arterial intimal thickening after balloon angioplasty. LY290181 (2-amino-4-[3-pyridyl]-4H-naphtho [1, 2-b]pyran-3-carbonitrile) and LY290293 (2-amino-4-[3-pyridyl]-4H-naphtho [1, 2-b]pyran-carbonitrile) produced a dose-dependent inhibition of DNA synthesis and proliferation of vascular smooth muscle cells in culture. Fifty percent inhibition (IC50) of cell proliferation was produced by 20 nM LY290181 or LY290293. Cell growth inhibition was not due to cell death, as demonstrated by the release of intracellular lactate dehydrogenase and by the reversibility of inhibition upon washing. Inhibition of smooth muscle cell proliferation was achieved in cells stimulated by either serum or individual growth factor such as platelet-derived growth factor, fibroblast growth factor or epidermal growth factor. In the rat model of balloon injury to carotid artery, LY290181 and LY290293 produced 61% (P < .005) and 48% (P < .005) inhibition of intimal thickening when administered p.o. at 100 and 120 mg/kg/day, respectively, over a 2-week period. Inhibition of intimal thickening (70%, P < .005) by LY290293 was also demonstrated when the compound was administered s.c. at 10 mg/kg/day. These studies demonstrate that naphthopyrans LY290181 and LY290293 are potent inhibitors of smooth muscle cell proliferation in vitro and that they produce substantial reduction in arterial intimal thickening in a balloon injury model when administered systemically.
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100
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Wu D, Singh JP, Yueh FY, Monts DL. 2,4,6-Trinitrotoluene detection by laser-photofragmentation-laser-induced fluorescence. APPLIED OPTICS 1996; 35:3998-4003. [PMID: 21102802 DOI: 10.1364/ao.35.003998] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Photofragmentation (PF) and subsequent nitric oxide (NO) laser-induced fluorescence (LIF) is being developed to measure the concentration of energetic materials (EM's) in soil and other media. Laser radiation near 226 nm photodissociates gas-phase EM to NO(2), which predissociates into NO that gives an intense luminescence. The EM concentration is inferred from the intensity of the NO fluorescence. We have studied the factors that affect the PF-LIF signal intensity, including the effect of buffer gas on the LIF spectrum of pure NO, the effect of 2,4,6-trinitrotoluene (TNT) pressure on the PF-LIF spectrum, the effect of buffer-gas pressure on the PF-LIF signal intensity of pure TNT, and the effect of temperature on the PF-LIF spectra of pure TNT and of TNT in simulated soil. Heating of the TNT sample above 343 K was found to increase the magnitude of the PF-LIF signal intensity significantly, but also was found to cause physical and chemical changes in the TNT sample. The effects of heating and evacuating on the TNT sample were investigated. TNT concentration calibration curves were obtained for TNT in simulated soil mixtures. The limit of detection of TNT in soil was estimated to be 40 parts in 10(9).
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