Cardiovascular diseases are major causes of morbidity and mortality in Western-style populations. Atherosclerosis and Abdominal Aortic Aneurysms (AAAs) are two prevalent vascular diseases that may progress without symptoms and contribute to acute cardiovascular events such as stroke and AAA rupture, which are consistently among the leading causes of death worldwide. The imaging methods used in the diagnosis of these diseases, have been reported to present several limitations. Given that both are associated with mechanical changes in the arterial wall, imaging of the arterial mechanical properties may improve early disease detection and patient care. Pulse wave velocity (PWV) refers to the velocity at which arterial waves generated by ventricular ejection travel along the arterial tree. PWV is a surrogate marker of arterial stiffness linked to cardiovascular mortality. The foot-to-foot method that is typically used to calculate PWV suffers from errors of distance measurements and time-delay measurements. Additionally, a single PWV estimate is provided over a relatively long distance, thus inherently lacking the capability to provide regional arterial stiffness measurements. Pulse Wave Imaging (PWI) is a noninvasive, ultrasound-based technique for imaging the propagation of pulse waves along the wall of major arteries and providing a regional PWV value for the imaged artery. The aim of this work was to enable PWI to provide more localized PWV and stiffness measurements within the imaged arterial segment and to further extend it into a 2-D and 3-D technique for the detection and monitoring of focal vascular disease at high temporal and spatial resolution. The improved modality was integrated with blood flow imaging modalities aiming to render PWI a comprehensive methodology for the study of arterial biomechanics in vivo. Spatial information was increased with the introduction of piecewise PWI. This novel technique was used to measure PWV within small sub-regions of the imaged vessel in murine aneurysmal (n = 8) and atherosclerotic aortas (n = 11) in vivo. It provided PWV and stiffness maps while capturing the progressive arterial stiffening caused by atherosclerosis. PWI was further augmented with a sophisticated adaptive algorithm, enabling it to optimally partition the imaged artery into relatively homogeneous segments, automatically isolating arterial stiffness inhomogeneities. Adaptive PWI was validated in silicone phantoms consisting of segments of varying stiffness and then tested in murine aortas in vivo. Subsequently, the conventional tradeoff between spatial and temporal resolution was addressed with a plane wave compounding implementation of PWI, allowing the acquisition of full field of view frames at over 2000 Hz. A GPU-accelerated PWI post-processing framework was developed for the processing of the big bulk of generated data. The parameters of coherent compounding were optimized in vivo. The optimized sequences were then used in the clinic to assess the mechanical properties of atherosclerotic carotids (n=10) and carotids of patients after endarterectomy (n=7), a procedure to remove the plaque and restore blood flow to the brain. In the case of atherosclerotic patients undergoing carotid endarterectomy, the results were compared against the histology of the excised plaques. Investigation of the mechanical properties of plaques was also conducted for the first time with a high-frequency transducer (18.5 MHz). Additionally, 4-D PWI was introduced, utilizing high frame rate 3-D plane wave acquisitions with a 2-D matrix array transducer (16x16 elements, 2.5 MHz). A novel methodology for PWV estimation along the direction of pulse wave propagation was implemented and validated in silicone phantoms. 4-D PWI provided comprehensive views of the pulse wave propagation in a plaque phantom and the results were compared against conventional PWI. Finally, its feasibility was tested in the carotid arteries of healthy human subjects (n=6). PWVs derived in 3-D were within the physiological range and showed good agreement with the results of conventional PWI. Finally, PWI was integrated with flow imaging modalities (Color and Vector Doppler). Thus, full field-of-view, high frame-rate, simultaneous and co-localized imaging of the arterial wall dynamics and color flow as well as 2-D vector flow was implemented. The feasibility of both techniques was tested in healthy subjects (n=6) in vivo. The relationship between the timings of the flow and wall velocities was investigated at multiple locations of the imaged artery. Vector flow velocities were found to be aligned with the vessel’s centerline during peak systole in the common carotid artery and interesting flow patterns were revealed in the case of the carotid bifurcation Consequently, with the aforementioned improvements and the inclusion of 3-D imaging, PWI is expected to provide comprehensive information on the mechanical properties of pathological arteries, providing clinicians with a powerful tool for the early detection of vascular abnormalities undetectable on the B-mode, while also enabling the monitoring of fully developed vascular pathology and of the recovery of post-operated vessels.

The phosphatidylinositol-3-kinase/AKT (Protein Kinase B)/mammalian target of rapamycin (PI3K/AKT/mTOR) signalling pathway, downstream of tyrosine kinase receptors, is upregulated in human cancers including breast and colon cancers. Glycogen synthase kinase 3 (GSK 3) is a serine/threonine protein kinase plays important role in various cellular processes including glycogen synthesis mediated by insulin signalling pathway. Moreover, 5' adenosine monophosphate activated protein kinase (AMPK), a crucial cellular energy sensor, has regulatory role in cell growth and proliferation through mTOR pathway. Phosphatidylcholine (PtdCho) is the major phospholipid in the mammalian cell membranes and is mainly synthesized by the CDP-choline pathway. Malignant transformation has been reported to be associated with altered choline metabolism. Hyperactivation of the PI3K/AKT signalling pathway upregulates the key enzymes of phospholipid metabolism. The first line antidiabetic drug, metformin, modulates glucose and concomitant lipid metabolism through AMPK activation. Studies suggest phosphatidylcholine biosynthesis and breakdown through CDP-choline pathway are modulated by glucose metabolism and de novo fatty acid synthesis. Cancer cell growth inhibitory effect of PI3K/AKT/mTOR/GSK3 pathway inhibitors and metformin were investigated by cytotoxic assay, western blot and cell cycle analysis in breast and colon cancer cells. IC50 values of anticancer drugs and combination indices between drug combinations were determined. 31P-NMR was carried out on cell extracts after drug treatments. [14C (U)] glucose and [3H] choline incorporation into lipids were also determined. All inhibitors targeting PI3K/AKT/mTOR signaling pathway, GSK3 and metformin have cancer cell growth inhibition. By 31P-NMR, PI3K/AKT/mTOR pathway inhibition induced agent-specific changes in PCho intensity. Increased UDP-sugars observed in breast and colon cancer cell extracts treated with LY294002 and AZD8055, an effect abrogated by inclusion of a GSK3 inhibitor. A link between glycolytic intermediates and phosphatidylcholine biosynthesis was investigated by metformin and GSK3 inhibitor in breast and colon cancer cells.

Optical coherence tomography (OCT) has been emerging as a promising imaging technique, with a strong capability of non-invasive, in vivo, high resolution, depth-resolved imaging. There is a great potential to use OCT to guide the treatment of arrhythmias, to prevent preterm birth, and to detect breast cancer. To facilitate the clinical applications, this thesis presents three image analytic tools to characterize biological tissue: 1) automated fiber direction analysis; 2) automated volumetric stitching; 3) automated tissue classification. The fiber direction analysis consists of a particle-filter-based 3D tractography scheme and a pixel-wise fiber analysis scheme. The stitching algorithm enlarges the field of view of current OCT system from millimeter to centimeter level by volumetric stitching using scale-invariant feature transform. Based on relevance vector machine, a region-based classification scheme and a grid-based classification scheme are developed to automatically identify tissue composition in human cardiac tissue and human breast tissue. These tools are collaboratively used to study OCT images from cardiac, cervical, and breast tissue. In cardiac tissue, we apply the fiber orientation analysis to reconstruct 3D cardiac myofibers tractography and perform pixel-wise fiber analysis on the collagen region within human heart. In addition, we apply the region-based algorithm to segment and classify tissue compositions, such as collagen, adipose tissue, fibrotic myocardium, and normal myocardium, over a single or a stitched OCT volume. Using our algorithm, we observe fiber directionality change over depths and find that the fiber orientation changes more dramatically in atria than in ventricle. We also observe different dispersion patterns within collagen layer. In cervical tissue, our stitching algorithm enables a paramount 3D view of entire axial slices. Together with pixel-wise fiber orientation scheme, we analyze the difference of dispersion property within inner/outer regions of four quadrants. We observe two dispersion patterns in pregnant and non-pregnant cervical tissue at the location close to upper cervix. In addition, we discover that an increasing trend of dispersion and an increasing trend of penetration depth from internal orifice (os) to external os. In breast tissue, we visualize various features in both benign and malignant tissues such as invasive ductal carcinoma (IDC), ductal carcinoma in situ, cyst, and terminal duct lobule unit in stitched OCT images. Focusing on the automated detection of IDC, we propose a hierarchy framework of classification model and apply our classifier in two OCT systems and achieve both reasonable sensitivity and specificity in identifying cancerous region.

It is a major challenge to understand functional neuronal circuits across the whole brain. Existing methods for observing neuronal activity represent a major bottleneck in addressing biological problems. In our lab, we developed Swept Confocally Aligned Planar Excitation (SCAPE) microscopy, which offers the ability to image a large 3D volume (e.g. 1000x800x250um) at speeds exceeding 10 volumes per second. Used with different genetically encoded fluorescent indicators, SCAPE enables us to observe neuronal activity across the whole brain of different small animal models, or a much larger volume of intact cortex/tissue compared to traditional approaches. The unique single objective design and flexible system layout of SCAPE makes it simple to image different samples without complex sample preparation and restraint. During this thesis work, I collaborated with biology and neuroscience labs to develop and optimize a range of novel in-vivo/in-vitro neuroimaging applications using SCAPE microscopy. In particular, my research has focused on using SCAPE to image freely crawling Drosophila Melanogaster larvae, intact mouse olfactory epithelium, head fixed behaving adult Drosophila, larval zebrafish brain and beating heart, and the neuronal system of behaving C. elegans, all in collaboration with experts in these models from Columbia University and other research institutions. I also developed and optimized different sample preparations and experimental procedures to take full advantage of the high-speed 3D imaging capabilities and flexibility of SCAPE microscopy. Finally, I optimized computational and image analysis techniques for large scale 5D SCAPE imaging datasets, including 3D cell tracking, large scale 3D data motion correction/registration, and cellular level neuronal activity extraction with different dimensionality reduction methods. The experiments I have performed in different animal models have enriched the long-term development of SCAPE by providing valuable feedback for system improvement and dissemination, and pushing the SCAPE design towards a more interchangeable platform with diverse capabilities suitable for routine uses by our collaborators and the wider neuroscience community.

Computer vision approximates human vision using computers. Two subsets are explored in this work: image segmentation and visual tracking. Segmentation involves partitioning an image into logical parts, and tracking analyzes objects as they change over time. The presented research explores a key hypothesis: localizing analysis of visual information can improve the accuracy of segmentation and tracking results. Accordingly, a new class of segmentation techniques based on localized analysis is developed and explored. Next, these techniques are applied to two challenging problems: neuron bundle segmentation in diffusion tensor imagery (DTI) and plaque detection in computed tomography angiography (CTA) imagery. Experiments demonstrate that local analysis is well suited for these medical imaging tasks. Finally, a visual tracking algorithm is shown that uses temporal localization to track objects that change drastically over time.

Computer vision encompasses a host of computational techniques to process visual information. Medical imagery is one particular area of application where data comes in various forms: X-rays, ultrasound probes, MRI volumes, EEG recordings, NMR spectroscopy, etc. This dissertation is concerned with techniques for accurate reconstruction of neural pathways from diffusion magnetic resonance imagery (dMRI). This dissertation describes a filtered approach to neural tractography. Existing methods independently estimate the diffusion model at each voxel so there is no running knowledge of confidence in the estimation process. We propose using tractography to drive estimation of the local diffusion model. Toward this end, we formulate fiber tracking as recursive estimation: at each step of tracing the fiber, the current estimate is guided by those previous. We argue that this approach is more accurate than conventional techniques. Experiments demonstrate that this filtered approach significantly improves the angular resolution at crossings and branchings. Further, we confirm its ability to trace through regions known to contain such crossing and branching while providing inherent path regularization. We also argue that this approach is flexible. Experiments demonstrate using various models in the estimation process, specifically combinations of Watson directional functions and rank-2 tensors. Further, this dissertation includes an extension of the technique to weighted mixtures using a constrained filter.

A complete scientific understanding of human nature requires delineation of the neurobiological characteristics underlying the unique features of the human mind. This effort can be facilitated by comparing the human brain with the brains of other living primate species. Humans are more susceptible to neurodegenerative diseases than other primate species, including our closest living primate relatives, the chimpanzees. Comparing age-related changes in brain structure between humans and non-human primates could, therefore, potentially shed light on the neurological basis of this human vulnerability. Further, human brains are lateralized with specialized cognitive and behavioral functions. Comparing the magnitude of hemispheric asymmetries in brain structure between humans and non-human primates can probe insights into this human specific capability and learn more about human evolution. Diffusion weighted MRI protocols were developed for different species, taking into account their neuroanatomical differences. For Chimpanzees, a multi-shot DWI sequence was developed and compared with a single-shot DWI sequence to determine which provided a better quality diffusion data free of acquisition related artifacts. Different simulation techniques were used to evaluate the effect of segmentation-related motion artifact (ghosting) on the multi-shot DTI data. Although both protocols generated high-resolution diffusion MRI data with correctable susceptibility-induced distortions, the single-shot protocol enables the acquisition of the high-resolution diffusion MRI data freed of ghosting and with twice the signal-to-noise ratio (SNR), for the same scan duration. The acquired chimpanzee and macaque diffusion data were used to compare the magnitude of microstructural asymmetries and age-related decline of brain white matter with those in humans. Hemispheric asymmetry results show a pattern of strong leftward asymmetry in human DTI indices that differs markedly from the chimpanzee (multi-shot data) and the rhesus macaque patterns involving both rightward and leftward asymmetries. The magnitude of leftward asymmetry increased for chimpanzees scanned with single-shot DTI sequence. Region of interest analyses within the corpus callosum revealed a significant age-related increase in fractional anisotropy (FA) in the genu for chimpanzees (multi-shot data) and no significant change in any region for macaques. Additionally, voxel-wise analysis using Tract Based Spatial Statistics (TBSS) revealed widespread age-related FA increases for chimpanzees (multi-shot data) and weak age-related decreases in FA for macaques across most white matter tracts. Overall, results from these multi-shot data analyses suggest that rhesus monkeys show age-related decreases in white matter integrity that parallel changes found in humans, whereas chimpanzees show age-related increases in white matter integrity. On the contrary, the single-shot data results for chimpanzees revealed no significant relationship between age and the different DTI indices. These noteworthy species differences may help to explain the unique features of the human mind and why humans are more susceptible to neurodegenerative diseases. Furthermore, these studies demonstrate the need for complementary histological studies of white matter microstructure in humans, chimpanzees and macaques to clarify the cellular and molecular basis of these findings.

Thesis (Ph. D.)--University of Missouri-Columbia, 2003. / Typescript. Vita. Includes bibliographical references (leaves 103-108). Also available on the Internet.

Thesis (Ph. D.)--University of Missouri-Columbia, 2003. / Typescript. Vita. Includes bibliographical references (leaves 103-108). Also available on the Internet.

Thesis (M. Phil.)--Hong Kong University of Science and Technology, 2003. / Includes bibliographical references (leaves 66-69). Also available in electronic version. Access restricted to campus users.