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Open Access Publications from the University of California

Scholarly Works (34 results)

  • Thesis
  • Peer Reviewed
UCLA Electronic Theses and Dissertations (2013)

Anatomical shape analysis problems are ubiquitous in medical imaging. In brain MRI imaging, the problem arises when comparing cortical features of functional importance, such as gray matter thickness, as well as when performing fine-grained analysis of sub-cortical structures. Two general types of approaches have been developed over the years to perform quantitative shape comparison of anatomy: the first, and more intuitive approach, attempts to bring surface models into dense point-to-point correspondence; the alternative approach avoids the need for dense registration by exploring intrinsic global properties of the shape. Each of these methods has their advantages and disadvantages, and I explore examples from each in applications to brain imaging. The general underlying theme of my work has been spherical parametric shape registration, and other descriptions based on spherical maps. Several times throughout this work I utilize the theory of spherical harmonics, both in their scalar and vector form as a means of parameterizing and describing brain anatomy. Using this theory, I develop several algorithms for rigid and non-rigid shape registration for a variety of brain shapes, which are described in Chapters 1-4.

In Chapter 5, I present an application of the methods developed in previous chapters to developing brain imaging biomarkers of Alzheimer's disease. I show that using the new surface-based features and statistical learning, it is possible to develop biomarkers which outperform all others to date in terms of sensitivity to disease-modifying effects and disease specificity.

A more recent field of application for shape-based analysis comes from human skull models generated from conical CT imaging. The general registration problems are similar in spirit to brain imaging. However, the much lower signal-to-noise ratio and greater topological variability of the shape models require a new set of tools to deal with these shapes in practice. In Chapter 6, I develop an approach to modify the topology of a skull surface while preserving useful features, and again return to the sphere for dense registration and the creation of shape atlases. Due to the noisy nature of the data, a fast non-local non-linear correspondence search is developed for pairs of skull shapes from different subjects. I show that this search is crucial for high-quality registration based on resulting population-based averages and individualized shape analyses.

    Cover page: Shape Analysis Methods for 3D Brain and Skull Imaging
    • Article
    • Peer Reviewed
    UCLA Previously Published Works (2018)
    Although cognitive and behavioral deficits are well known to occur following traumatic brain injury (TBI), motor deficits that occur even after mild trauma are far less known, yet are equally persistent. This study was aimed at making progress toward determining how the brain reorganizes in response to TBI. We used the adult rat controlled cortical impact injury model to study the ipsilesional forelimb map evoked by electrical stimulation of the affected limb, as well as the contralesional forelimb map evoked by stimulation of the unaffected limb, both before injury and at 1, 2, 3, and 4 weeks after using functional magnetic resonance imaging (fMRI). End-point c-FOS immunohistochemistry data following 1 h of constant stimulation of the unaffected limb were acquired in the same rats to avoid any potential confounds due to altered cerebrovascular coupling. Single and paired-pulse sensory evoked potential (SEP) data were recorded from skull electrodes over the contralesional cortex in a parallel series of rats before injury, at 3 days, and at 1, 2, 3, and 4 weeks after injury in order to determine whether alterations in cortical excitability accompanied reorganization of the cortical map. The results show a transient trans-hemispheric shift in the ipsilesional cortical map as indicated by fMRI, remote contralesional increases in cortical excitability that occur in spatially similar regions to altered fMRI activity and greater c-FOS activation, and reduced or absent ipsilesional cortical activity chronically. The contralesional changes also were indicated by reduced SEP latency within 3 days after injury, but not by blood oxygenation level-dependent fMRI until much later. Detailed interrogation of cortical excitability using paired-pulse electrophysiology showed that the contralesional cortex undergoes both an early and a late post-injury period of hyper-excitability in response to injury, interspersed by a period of relatively normal activity. From these data, we postulate a cross-hemispheric mechanism by which remote cortex excitability inhibits ipsilesional activation by rebalanced cortical excitation-inhibition.
      Cover page: Remote Changes in Cortical Excitability after Experimental Traumatic Brain Injury and Functional Reorganization
      • Article
      • Peer Reviewed
      UCLA Previously Published Works (2014)
      The apolipoprotein E epsilon 4 allele (ApoE-ε4) is the strongest known genetic risk factor for late onset Alzheimer's disease. Expansion of the lateral ventricles occurs with normal aging, but dementia accelerates this process. Brain structure and function depend on ApoE genotype not just for Alzheimer's disease patients but also in healthy elderly individuals, and even in asymptomatic young individuals. Therefore, we hypothesized that the ApoE-ε4 allele is associated with altered patterns of longitudinal ventricular expansion, in dementia and normal aging. We tested this hypothesis in a large sample of elderly participants, using a linear discriminant analysis-based approach. Carrying more ApoE-ε4 alleles was associated with faster ventricular expansion bilaterally and with regional patterns of lateral ventricle morphology at 1- and 2-year follow up, after controlling for sex, age, and dementia status. ApoE genotyping is considered critical in clinical trials of Alzheimer's disease. These findings, combined with earlier investigations showing that ApoE is also directly implicated in other conditions, suggest that the selective enrollment of ApoE-ε4 carriers may empower clinical trials of other neurological disorders.
        Cover page: The apolipoprotein E epsilon 4 allele is associated with ventricular expansion rate and surface morphology in dementia and normal aging
        • Article
        • Peer Reviewed
        UCLA Previously Published Works (2015)

        Introduction

        Genetic variants in DAT1, the gene encoding the dopamine transporter (DAT) protein, have been implicated in many brain disorders. In a recent case-control study of Alzheimer's disease (AD), a regulatory polymorphism in DAT1 showed a significant association with the clinical stages of dementia.

        Methods

        We tested whether this variant was associated with increased AD risk, and with measures of cognitive decline and longitudinal ventricular expansion, in a large sample of elderly participants with genetic, neurocognitive, and neuroimaging data from the Alzheimer's Disease Neuroimaging Initiative.

        Results

        The minor allele-previously linked with increased DAT expression in vitro-was more common in AD patients than in both individuals with mild cognitive impairment and healthy elderly controls. The same allele was also associated with poorer cognitive performance and faster ventricular expansion, independently of diagnosis.

        Discussion

        These results may be due to reduced dopaminergic transmission in carriers of the DAT1 mutation.
          Cover page: Carriers of a common variant in the dopamine transporter gene have greater dementia risk, cognitive decline, and faster ventricular expansion
          • Article
          • Peer Reviewed
          UC San Francisco Previously Published Works (2015)
          Dynamic changes in the brain's lateral ventricles on magnetic resonance imaging are powerful biomarkers of disease progression in mild cognitive impairment (MCI) and Alzheimer's disease (AD). Ventricular measures can represent accumulation of diffuse brain atrophy with very high effect sizes. Despite having no direct role in cognition, ventricular expansion co-occurs with volumetric loss in gray and white matter structures. To better understand relationships between ventricular and cortical changes over time, we related ventricular expansion to atrophy in cognitively relevant cortical gray matter surfaces, which are more challenging to segment. In ADNI participants, percent change in ventricular volumes at 1-year (N = 677) and 2-year (N = 536) intervals was significantly associated with baseline cortical thickness and volume in the full sample controlling for age, sex, and diagnosis, and in MCI separately. Ventricular expansion in MCI was associated with thinner gray matter in frontal, temporal, and parietal regions affected by AD. Ventricular expansion reflects cortical atrophy in early AD, offering a useful biomarker for clinical trials of interventions to slow AD progression.
            Cover page: Mapping ventricular expansion onto cortical gray matter in older adults
            • Article
            • Peer Reviewed
            UC San Francisco Previously Published Works (2015)
            In a previous report, we proposed a method for combining multiple markers of atrophy caused by Alzheimer's disease into a single atrophy score that is more powerful than any one feature. We applied the method to expansion rates of the lateral ventricles, achieving the most powerful ventricular atrophy measure to date. Here, we expand our method's application to tensor-based morphometry measures. We also combine the volumetric tensor-based morphometry measures with previously computed ventricular surface measures into a combined atrophy score. We show that our atrophy scores are longitudinally unbiased with the intercept bias estimated at 2 orders of magnitude below the mean atrophy of control subjects at 1 year. Both approaches yield the most powerful biomarker of atrophy not only for ventricular measures but also for all published unbiased imaging measures to date. A 2-year trial using our measures requires only 31 (22, 43) Alzheimer's disease subjects or 56 (44, 64) subjects with mild cognitive impairment to detect 25% slowing in atrophy with 80% power and 95% confidence.
              Cover page: Empowering imaging biomarkers of Alzheimer's disease
              • Article
              • Peer Reviewed
              UCLA Previously Published Works (2016)
              Patients with major depression show reductions in striatal and paleostriatal volumes. The functional integrity and connectivity of these regions are also shown to change with antidepressant response. Electroconvulsive therapy (ECT) is a robust and rapidly acting treatment for severe depression. However, whether morphological changes in the dorsal and ventral striatum/pallidum relate to or predict therapeutic response to ECT is unknown. Using structural MRI, we assessed cross-sectional effects of diagnosis and longitudinal effects of ECT for volume and surface-based shape metrics of the caudate, putamen, pallidum, and nucleus accumbens in 53 depressed patients (mean age: 44.1 years, 13.8 SD; 52% female) and 33 healthy controls (mean age: 39.3 years, 12.4 SD; 57% female). Patients were assessed before ECT, after their second ECT, and after completing an ECT treatment index. Controls were evaluated at two time points. Support vector machines determined whether morphometric measures at baseline predicted ECT-related clinical response. Patients showed smaller baseline accumbens and pallidal volumes than controls (P<0.05). Increases in left putamen volume (P<0.03) occurred with ECT. Global increases in accumbens volume and local changes in pallidum and caudate volume occurred in patients defined as treatment responders. Morphometric changes were absent across time in controls. Baseline volume and shape metrics predicted overall response to ECT with up to 89% accuracy. Results support that ECT elicits structural plasticity in the dorsal and ventral striatum/pallidum. The morphometry of these structures, forming key components of limbic-cortical-striatal-pallidal-thalamic circuitry involved in mood and emotional regulation, may determine patients likely to benefit from treatment.
                Cover page: Effect of Electroconvulsive Therapy on Striatal Morphometry in Major Depressive Disorder
                • Article
                • Peer Reviewed
                UC San Francisco Previously Published Works (2013)
                A recent genome-wide association meta-analysis showed a suggestive association between alcohol intake in humans and a common single nucleotide polymorphism in the ras-specific guanine nucleotide releasing factor 2 gene. Here, we tested whether this variant - associated with lower alcohol consumption - showed associations with brain structure and longitudinal ventricular expansion over time, across two independent elderly cohorts, totaling 1,032 subjects. We first examined a large sample of 738 elderly participants with neuroimaging and genetic data from the Alzheimer's Disease Neuroimaging Initiative (ADNI1). Then, we assessed the generalizability of the findings by testing this polymorphism in a replication sample of 294 elderly subjects from a continuation of the first ADNI project (ADNI2) to minimize the risk of reporting false positive results. The minor allele - previously linked with lower alcohol intake - was associated with larger volumes in various cortical regions, notably the medial prefrontal cortex and cingulate gyrus in both cohorts. Intriguingly, the same allele also predicted faster ventricular expansion rates in the ADNI1 cohort at 1- and 2-year follow up. Despite a lack of alcohol consumption data in this study cohort, these findings, combined with earlier functional imaging investigations of the same gene, suggest the existence of reciprocal interactions between genes, brain, and drinking behavior.
                  Cover page: A single nucleotide polymorphism associated with reduced alcohol intake in the RASGRF2 gene predicts larger cortical volumes but faster longitudinal ventricular expansion in the elderly
                  • Article
                  • Peer Reviewed
                  UC Irvine Previously Published Works (2015)
                  Mild Cognitive Impairment (MCI) is a transitional stage between normal aging and dementia and people with MCI are at high risk of progression to dementia. MCI is attracting increasing attention, as it offers an opportunity to target the disease process during an early symptomatic stage. Structural magnetic resonance imaging (MRI) measures have been the mainstay of Alzheimer's disease (AD) imaging research, however, ventricular morphometry analysis remains challenging because of its complicated topological structure. Here we describe a novel ventricular morphometry system based on the hyperbolic Ricci flow method and tensor-based morphometry (TBM) statistics. Unlike prior ventricular surface parameterization methods, hyperbolic conformal parameterization is angle-preserving and does not have any singularities. Our system generates a one-to-one diffeomorphic mapping between ventricular surfaces with consistent boundary matching conditions. The TBM statistics encode a great deal of surface deformation information that could be inaccessible or overlooked by other methods. We applied our system to the baseline MRI scans of a set of MCI subjects from the Alzheimer's Disease Neuroimaging Initiative (ADNI: 71 MCI converters vs. 62 MCI stable). Although the combined ventricular area and volume features did not differ between the two groups, our fine-grained surface analysis revealed significant differences in the ventricular regions close to the temporal lobe and posterior cingulate, structures that are affected early in AD. Significant correlations were also detected between ventricular morphometry, neuropsychological measures, and a previously described imaging index based on fluorodeoxyglucose positron emission tomography (FDG-PET) scans. This novel ventricular morphometry method may offer a new and more sensitive approach to study preclinical and early symptomatic stage AD.
                    Cover page: Studying ventricular abnormalities in mild cognitive impairment with hyperbolic Ricci flow and tensor-based morphometry
                    • Article
                    • Peer Reviewed
                    UCLA Previously Published Works (2014)
                    Alterations in gray matter (GM) density/volume and cortical thickness (CT) have been demonstrated in small and heterogeneous samples of subjects with differing chronic pain syndromes, including irritable bowel syndrome (IBS). Aggregating across 7 structural neuroimaging studies conducted at University of California, Los Angeles, Los Angeles, CA, USA, between August 2006 and April 2011, we examined group differences in regional GM volume in 201 predominantly premenopausal female subjects (82 IBS, mean age: 32±10 SD, 119 healthy controls [HCs], 30±10 SD). Applying graph theoretical methods and controlling for total brain volume, global and regional properties of large-scale structural brain networks were compared between the group with IBS and the HC group. Relative to HCs, the IBS group had lower volumes in the bilateral superior frontal gyrus, bilateral insula, bilateral amygdala, bilateral hippocampus, bilateral middle orbital frontal gyrus, left cingulate, left gyrus rectus, brainstem, and left putamen. Higher volume was found in the left postcentral gyrus. Group differences were no longer significant for most regions when controlling for the Early Trauma Inventory global score, with the exception of the right amygdala and the left postcentral gyrus. No group differences were found for measures of global and local network organization. Compared to HCs, in patients with IBS, the right cingulate gyrus and right thalamus were identified as being significantly more critical for information flow. Regions involved in endogenous pain modulation and central sensory amplification were identified as network hubs in IBS. Overall, evidence for central alterations in patients with IBS was found in the form of regional GM volume differences and altered global and regional properties of brain volumetric networks.
                      Cover page: Irritable bowel syndrome in female patients is associated with alterations in structural brain networks
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