Biomedical subjects

J C Rajapakse

Publications and source records attributed to J C Rajapakse.

At least 19 recordsLinked to original sources

PubMed2005

Two-stage multi-class support vector machines to protein secondary structure prediction.

Bioinformatics techniques to protein secondary structure (PSS) prediction are mostly single-stage approaches in the sense that they predict secondary structures of proteins by taking into account only the contextual information in amino acid sequences. In this paper, we propose two-stage Multi-class Support Vector Machine (MSVM) approach where a MSVM predictor is introduced to the output of the first stage MSVM to capture the sequential relationship among secondary structure elements for the prediction. By using position specific scoring matrices, generated by PSI-BLAST, the two-stage MSVM approach achieves Q3 accuracies of 78.0% and 76.3% on the RS126 dataset of 126 nonhomologous globular proteins and the CB396 dataset of 396 nonhomologous proteins, respectively, which are better than the highest scores published on both datasets to date.

Computational Biology↗

PubMed2001

Proton spectroscopic imaging shows abnormalities in glial and neuronal cell pools in frontal lobe epilepsy.

PURPOSE: Proton magnetic resonance spectroscopic imaging (1H MRSI) can lateralize the epileptogenic frontal lobe by detecting metabolic ratio abnormalities in frontal lobe epilepsy (FLE). We used 1H MRS to lateralize and localize the epileptogenic focus, and we also sought to characterize further the metabolic abnormality in FLE. METHODS: We measured signals from N-acetyl aspartate (NAA), choline-containing compounds (Cho), and creatine + phosphocreatine (Cr) in the supraventricular brain of 14 patients with frontal or frontoparietal epilepsy and their matched controls. The supratentorial brain also was segmented into gray matter, white matter, and cerebrospinal fluid classes. Regional metabolite alterations were compared with localizing and lateralizing results from other examination modalities and with histology from three patients. RESULTS: Spectroscopy lateralized the epileptogenic focus in 10 patients in agreement with video-EEG and functional imaging. In four patients, spectroscopy showed bilateral, focal metabolic abnormality, whereas video-EEG suggested unilateral or midline abnormality. In the epileptogenic focus, Cho and Cr were increased by 23% and 14%, respectively, and NAA was decreased by 11%, suggesting metabolic disturbances both in the glial and in the neuronal cell pools. Two Taylor dysplasia lesions confirmed by histology and one with radiologic diagnosis showed high Cho and low or normal NAA, whereas two dysembryoplastic neurogenic tumors had normal Cho and low NAA. Contralateral hemisphere NAA/(Cho + Cr) was decreased in FLE, indicating diffusely altered brain metabolism. Segmentation of brain tissue did not reveal atrophic changes in FLE. CONCLUSIONS: Spectroscopy is useful in lateralizing frontoparietal epilepsy and shows promise as a "noninvasive biopsy" in epileptogenic lesions.

Adolescent↗

PubMed2001

Bayesian approach to segmentation of statistical parametric maps.

A contextual segmentation technique to detect brain activation from functional brain images is presented in the Bayesian framework. Unlike earlier similar approaches [Holmes and Ford (1993) and Descombes et al. (1998)], a Markov random field (MRF) is used to represent configurations of activated brain voxels, and likelihoods given by statistical parametric maps (SPM's) are directly used to find the maximum a posteriori (MAP) estimation of segmentation. The iterative segmentation algorithm, which is based on a simulated annealing scheme, is fully data-driven and capable of analyzing experiments involving multiple-input stimuli. Simulation results and comparisons with the simple thresholding and the statistical parametric mapping (SPM) approaches are presented with synthetic images, and functional MR images acquired in memory retrieval and event-related working memory tasks. The experiments show that an MRF is a valid representation of the activation patterns obtained in functional brain images, and the present technique renders a superior segmentation scheme to the context-free approach and the SPM approach.

Algorithms↗

PubMed2000

Random-grid stereologic volumetry of MR head scans.

Point count stereology is a useful tool in obtaining volumetric measures of objects in three-dimensional (3D) images when the segmentation of objects is not feasible. Presently, fixed-grid 3D stereology is being used where a 3D parallelepiped grid is randomly placed for sampling the image space in order to generate test points. Although this is a popular technique, the use of a fixed grid introduces errors in the final estimate in practice and makes the technique inefficient. Random-grid 3D stereology is introduced to improve the efficiency of the volume estimates in stereology. In this manuscript, we prove random-grid stereology as a more consistent technique than fixed-grid stereology and use it for volumetry of the brain and ventricles in magnetic resonance (MR) head scans. We demonstrate superior efficiency and accuracy of random-grid stereology with experiments. Also, the effects of grid sizes, the optimal directions of sectioning the object for volume estimates of the brain and ventricles, and the reliability of the technique are investigated. J. Magn. Reson. Imaging 2000;12:833-841.

Brain↗

PubMed2000

Efficient sampling in 3-D stereologic volumetry.

Present 3-D stereology techniques use fixed grid sampling where the sampling grid of test points is randomly placed in 3-D. In order to increase randomness of sampling, in this paper we propose random grid sampling scheme where grid sections are placed randomly over 2-D cross-sections. A random grid sampler has superior efficiency and accuracy compared with fixed grid sampling. Using MR head scans we demonstrate the use of random grid sampling in volumetry of structures in 3-D biomedical images.

Cerebral Ventricles↗

PubMed2000

Probabilitic fusion of hemodynamic parameter maps.

Hemodynamic parameter maps (HPMs) depict values of parameters of hemodynamic response, namely, gain, lag, and dispersion, in response to neuronal activation. Large intensity values of any of the HPMs indicate greater likelihoods of brain activation. We apply the probabilistic data fusion equation to combine three HPMs. The statistical map of the fused probability map derived from HPMs is compared with statistical parameter mapping (SPM) in a visual experiment. The statistical hemodynamic parameter map (SHPM) gives better contrast to distinguish activated voxels from nonactivated voxels.

Brain Mapping↗

PubMed1999

Development of the human corpus callosum during childhood and adolescence: a longitudinal MRI study.

1. Interest in the morphologic development of the corpus callosum (CC) during childhood and adolescence stems from adolescent changes in cognitive functions subserved by the CC, reports of CC anomalies for a wide variety of childhood neuropsychiatric illnesses, and controversy regarding sexual dimorphism. 2. Characterization of the normal developmental pattern of the CC is hindered by enormous variability of its size. This is especially problematic for cross-sectional studies seeking to assess possible non-linear developmental curves. 3. To more accurately characterize developmental changes, a longitudinal brain magnetic resonance imaging study with subjects rescanned at approximately 2 year intervals was conducted resulting in 251 scans from 139 healthy children and adolescents. 4. Midsagittal area of the CC, especially the posterior regions, increased robustly from ages 5 to 18 years. 5. Although the genu of the CC was significantly larger in males there were no sex differences in mean area after adjustment for total cerebral volume and the growth patterns did not differ between sexes. 6. Analysis revealed a non-linear increase in the splenium, the most posterior region, with increases greatest in the younger years. 7. The results of this longitudinal study, in addition to confirming and extending previous cross-sectional reports, provide an increasingly accurate yardstick from which to assess pathological development.

Adolescent↗

PubMed1998

Modeling hemodynamic response for analysis of functional MRI time-series.

The standard Gaussian function is proposed for the hemodynamic modulation function (HDMF) of functional magnetic resonance imaging (fMRI) time-series. Unlike previously proposed parametric models, the Gaussian model accounts independently for the delay and dispersion of the hemodynamic responses and provides a more flexible and mathematically convenient model. A suboptimal noniterative scheme to estimate the hemodynamic parameters is presented. The ability of the Gaussian function to represent the HDMF of brain activation is compared with Poisson and Gamma models. The proposed model seems valid because the lag and dispersion values of hemodynamic responses rendered by the Gaussian model are in the ranges of their previously reported values in recent optical and fMR imaging studies. An extension of multiple regression analysis to incorporate the HDMF is presented. The detected activity patterns exhibit improvements with hemodynamic correction. The proposed model and efficient parameter estimation scheme facilitated the investigation of variability of hemodynamic parameters of human brain activation. The hemodynamic parameters estimated over different brain regions and across different stimuli showed significant differences. Measurement of hemodynamic parameters over the brain during sensory or cognitive stimulation may reveal vital information on physiological events accompanying neuronal activation and functional variability of the human brain, and should lead to the investigation of more accurate and complex models.

Brain↗

PubMed1998

Regional glucose metabolic abnormalities are not the result of atrophy in Alzheimer's disease.

OBJECTIVE: To determine whether the hypometabolism observed in PET images of patients with Alzheimer's disease (AD) is due entirely to brain atrophy. BACKGROUND: Reduced brain glucose metabolism in AD patients measured using PET has been reported by numerous authors. Actual glucose metabolic values in AD may be reduced artificially because of brain atrophy, which accentuates the partial volume effect (PVE) on data collected by PET. METHODS: Using segmented MR images, we corrected regional cerebral metabolic rates for glucose for PVEs to evaluate the effect of atrophy on uncorrected values for brain metabolism in AD patients and healthy control subjects. RESULTS: Global glucose metabolism was reduced significantly before and after correction in AD patients compared with controls. Before PVE correction, glucose metabolic values in patients were lower than in control subjects in the inferior parietal, frontal, and lateral temporal cortex; in the posterior cingulate; and in the precuneus. These reductions remained significantly lower after PVE correction, although in the posterior cingulate the difference in metabolism between AD patients and control subjects lessened. Regional glucose metabolism of these areas with PVE correction was lower in moderately-severely demented patients than in mildly demented patients. CONCLUSION: Reduced glucose metabolism measured by PET in AD is not simply an artifact due to an increase in CSF space induced by atrophy, but reflects a true metabolic reduction per gram of tissue.

Aged↗

PubMed1997

Quantitative magnetic resonance imaging of the corpus callosum in childhood onset schizophrenia.

Corpus callosum size has been found to be abnormal in adult schizophrenia, and other studies have implicated abnormal interhemispheric communication in this disorder. To assess continuity with brain abnormalities in the later onset disorder and to further localize brain maldevelopment, this structure was examined in a unique sample of childhood onset schizophrenics. Anatomic brain magnetic resonance imaging scans were acquired for 25 patients (mean age 13.9 +/- 2.1) who had onset of schizophrenia by age 12 (mean age at onset 9.9 +/- 1.9) and 55 normal children. The midsagittal area of the corpus callosum was divided into seven sections. With no adjustment for brain volume, no diagnostic differences were observed. After adjustment for the smaller cerebral volume of the schizophrenics, larger total, anterior and posterior corpus callosum areas emerged for the schizophrenics. These findings provide further evidence for continuity between childhood onset and later onset schizophrenia and support other studies showing white matter sparing in the context of decreased cortical volume.

Adolescent↗

PubMed1997

Sexual dimorphism of the developing human brain.

1. Sexual dimorphism of human brain anatomy has not been well-studied between 4 and 18 years of age, a time of emerging sex differences in behavior and the sexually specific hormonal changes of adrenarche (the predominantly androgenic augmentation of adrenal cortex function occurring at approximately age 8) and puberty. 2. To assess sex differences in brain structures during this developmental period volumes of the cerebrum, lateral ventricles, caudate, putamen, globus pallidus temporal lobe, amygdala, and hippocampus, and midsagittal area measurements of the corpus callosum were quantified from brain magnetic resonance images of 121 healthy children and adolescent and examined in relation to age and sex. 3. Males had a 9% larger cerebral volume. When adjusted for cerebral volume by ANCOVA only the basal ganglia demonstrated sex differences in mean volume with the caudate being relatively larger in females and the globus pallidus being relatively larger in males. The lateral ventricles demonstrated a prominent sex difference in brain maturation with robust increases in size in males only. A piecewise-linear model revealed a significant change in the linear regression slope of lateral ventricular volume in males after age 11 that was not shared by females at that or other ages. 4. Amygdala and hippocampal volume increased for both sexes but with the amygdala increasing significantly more in males than females and hippocampal volume increasing more in females. 5. These sexually dimorphic patterns of brain development may be related to the observed sex differences in age of onset, prevalence, and symptomatology seen in nearly all neuropsychiatric disorders of childhood.

Adolescent↗

PubMed1997

Statistical approach to segmentation of single-channel cerebral MR images.

A statistical model is presented that represents the distributions of major tissue classes in single-channel magnetic resonance (MR) cerebral images. Using the model, cerebral images are segmented into gray matter, white matter, and cerebrospinal fluid (CSF). The model accounts for random noise, magnetic field inhomogeneities, and biological variations of the tissues. Intensity measurements are modeled by a finite Gaussian mixture. Smoothness and piecewise contiguous nature of the tissue regions are modeled by a three-dimensional (3-D) Markov random field (MRF). A segmentation algorithm, based on the statistical model, approximately finds the maximum a posteriori (MAP) estimation of the segmentation and estimates the model parameters from the image data. The proposed scheme for segmentation is based on the iterative conditional modes (ICM) algorithm in which measurement model parameters are estimated using local information at each site, and the prior model parameters are estimated using the segmentation after each cycle of iterations. Application of the algorithm to a sample of clinical MR brain scans, comparisons of the algorithm with other statistical methods, and a validation study with a phantom are presented. The algorithm constitutes a significant step toward a complete data driven unsupervised approach to segmentation of MR images in the presence of the random noise and intensity inhomogeneities.

Adolescent↗

PubMed1996

Quantitative MRI of the temporal lobe, amygdala, and hippocampus in normal human development: ages 4-18 years.

The volume of the temporal lobe, superior temporal gyrus, amygdala, and hippocampus was quantified from magnetic images of the brains of 99 healthy children and adolescents aged 4-18 years. Variability in volume was high for all structures examined. When adjusted for a 9% larger total cerebral volume in males, there were no significant volume differences between sexes. However, sex-specific maturational changes were noted in the volumes of medial temporal structures, with the left amygdala increasing significantly only in males and with the right hippocampus increasing significantly only in females. Right-greater-than-left laterality effects were found for temporal lobe, superior temporal gyrus, amygdala, and hippocampal volumes. These results are consistent with previous preclinical and human studies that have indicated hormonal responsivity of these structures and extend quantitative morphologic findings from the adult literature. In addition to highlighting the need for large samples and sex-matched controls in pediatric neuroimaging studies, the information from this understudied age group may be of use in evaluating developmental hypotheses of neuropsychiatric disorders.

Adolescent↗

PubMed1996

A quantitative MRI study of the corpus callosum in children and adolescents.

Total midsagittal area and seven subdivisions of the corpus callosum were measured on magnetic resonance images of 114 healthy boys and girls, aged 4 to 18. Striking variability of size was noted for all measures. Total midsagittal corpus callosum area increased in a robust and linear fashion from ages 4 to 18 (slope = 13.1 mm2/year, P = 0.0001 and slope = 11.1 mm2/year, P = 0.0001 for females and males, respectively). Posterior and mid regions demonstrated greater age-related changes than anterior regions with the rostrum and genu (anterior regions) having reached adult sizes in the youngest of our subjects. There were no significant effects of sex for any measures. These findings support anatomical studies indicating ongoing myelination of higher association areas throughout adolescence, but raise intriguing questions about anterior-posterior gradients of interhemispheric myelination.

Adolescent↗

PubMed1996

Quantitative brain magnetic resonance imaging in attention-deficit hyperactivity disorder.

BACKGROUND: Anatomic magnetic resonance imaging (MRI) studies of attention-deficit hyperactivity disorder (ADHD) have been limited by small samples or measurement of single brain regions. Since the neuropsychological deficits in ADHD implicate a network linking basal ganglia and frontal regions, 12 subcortical and cortical regions and their symmetries were measured to determine if these structures best distinguished ADHD. METHODS: Anatomic brain MRIs for 57 boys with ADHD and 55 healthy matched controls, aged 5 to 18 years, were obtained using a 1.5-T scanner with contiguous 2-mm sections. Volumetric measures of the cerebrum, caudate nucleus, putamen, globus pallidus, amygdala, hippocampus, temporal lobe, cerebellum; a measure of prefrontal cortex; and related right-left asymmetries were examined along with midsagittal area measures of the cerebellum and corpus callosum. Interrater reliabilities were .82 or greater for all MRI measures. RESULTS: Subjects with ADHD had a 4.7% smaller total cerebral volume (P = .02). Analysis of covariance for total cerebral volume demonstrated a significant loss of normal right > left asymmetry in the caudate (P = .006), smaller right globus pallidus (P = .005), smaller right anterior frontal region (P = .02), smaller cerebellum (P = .05), and reversal of normal lateral ventricular asymmetry (P = .03) in the ADHD group. The normal age-related decrease in caudate volume was not seen, and increases in lateral ventricular volumes were significantly diminished in ADHD. CONCLUSION: This first comprehensive morphometric analysis is consistent with hypothesized dysfunction of right-sided prefrontal-striatal systems in ADHD.

Adolescent↗

PubMed1996

Brain anatomic magnetic resonance imaging in childhood-onset schizophrenia.

BACKGROUND: Early-onset schizophrenia (first psychotic symptoms by age 12 years) has been the subject of a small number of studies, and its biological continuity with later-onset disorder has not been established. In this study quantitative anatomic brain magnetic resonance images of children and adolescents with early-onset schizophrenia were compared with those of matched controls. Brain abnormalities in childhood-onset schizophrenia were examined in relation to those reported for later-onset schizophrenics. METHODS: Anatomic brain magnetic resonance imaging scans were obtained for 21 patients (mean +/- SD age, 14.6 +/- 2.1 years; range, 10 to 18 years) with childhood-onset schizophrenia (13 males, eight females) and 33 age-, sex-, height-, and weight-matched normal controls. Quantitative measurements were obtained for the cerebrum, anterior frontal region, lateral ventricles, thalamus, caudate, putamen, and globus pallidus. RESULTS: Total cerebral volume and midsagittal thalamic area were smaller in the patients (analysis of variance, P = .002, and analysis of covariance, P = .03, respectively); the caudate, putamen, and globus pallidus were larger in the patients (analysis of covariance, P = .05, P = .007, and P < .001, respectively); and the lateral ventricles tended to be larger in the patients (analysis of covariance, P = .06). Globus pallidus enlargement correlated with neuroleptic exposure and with age of onset of psychosis. The magnitude of abnormalities compared with controls was similar to that reported in adult studies, although there was a trend toward relatively smaller cerebral volumes for the childhood-onset group compared with controls. CONCLUSION: Brain anatomic abnormalities in childhood-onset schizophrenia are similar to those reported for adult populations, indicating overall continuity between these rare childhood cases and the adult schizophrenia populations.

Adolescent↗

PubMed1996

A technique for single-channel MR brain tissue segmentation: application to a pediatric sample.

A segmentation method is presented for gray matter, white matter, and cerebrospinal fluid (CSF) in thin-sliced single-channel brain magnetic resonance (MR) scans. The method is based on probabilistic modeling of intensity distributions and on a region growing technique. Interrater and intrarater reliabilities for the method were high, and comparison with phantom studies and hand-traced results from an experienced rater indicated good validity. The method was designed to account for spatially dependent image intensity inhomogeneities. Segmentation of MR brain scans of 105 (56 male and 49 female) healthy children and adolescents showed that although the total brain volume was stable over age 4-18, white matter increased and gray matter decreased significantly. There were no sex differences in total gray and white matter growth after correction for total brain volume. White matter volume increased the most in superior and posterior regions and laterality effects were seen in hemisphere tissue volumes. These findings are consistent with other reports, and further validate the segmentation technique.

Adolescent↗

PubMed1996

Temporal lobe morphology in childhood-onset schizophrenia.

OBJECTIVE: Neurodevelopmental models of schizophrenia imply that a more severe early brain lesion may produce earlier onset of psychotic symptoms. The medial temporal lobes have been proposed as possible locations for such a lesion. The authors tested this hypothesis in a group of children and adolescents with childhood-onset schizophrenia who had severe, chronic symptoms and who were refractory to treatment with typical neuroleptics. METHOD: Anatomic brain magnetic resonance imaging scans were acquired with a 1.5-T scanner for 21 patients (mean age=14.6 years, SD=2.1) who had onset of schizophrenia by age 12 (mean age at onset=10.2, SD=1.5) and 41 normal children. Volumes of the temporal lobe, superior temporal gyrus, amygdala, and hippocampus were measured by manually outlining these structures on contiguous 2-mm thick coronal slices. RESULTS: Patients with childhood-onset schizophrenia had significantly smaller cerebral volumes. With no adjustment for brain volume, no diagnostic differences were observed for any temporal lobe structure. Unexpectedly, with adjustment for total cerebral volume, larger volumes of the superior temporal gyrus and its posterior segment and a trend toward larger temporal lobe volume emerged for the patients with schizophrenia. These patients lacked the normal (right-greater-than-left) hippocampal asymmetry. CONCLUSIONS: These findings do not indicate a more severe medial temporal lobe lesion as the basis of very early onset schizophrenia.

Adolescent↗