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Open Access Publications from the University of California

Scholarly Works (17 results)

  • Thesis
  • Peer Reviewed
UC San Diego Electronic Theses and Dissertations (2010)
Buildings and environmental monitoring systems sense their surrounding conditions using various types of sensors. They process information and react to their environments in real time. The integrated cyberinfrastructure (CI) for the real-time data acquisition, real-time data processing and decision making is proposed, analyzed, implemented, and tested in this thesis. The open architecture solution is presented and implemented with open source software packages. Then, the CI is applied in two settings, the simulation and the real world. The smart building application uses the simulation environment, and the coral reef monitoring system uses the sensors deployed in the Pacific Ocean. This research is based on studies performed in Moorea. The use case scenarios and the configuration for detecting and responding to such scenarios are described for both applications
    Cover page: An integrated cyberinfrastructure for real-time data acquisition and decision making in smart buildings and coral reef monitoring
    • Thesis
    • Peer Reviewed
    UC San Francisco Electronic Theses and Dissertations (2014)

    One major challenge in cancer biology is to monitor cancer metabolism in vivo with the goal of improved diagnosis. NMR detection of 13C isotope has the potential to provide the necessary information, but traditional methods have been hampered by the low concentration of the crucial metabolites. Newly emerging hyperpolarization techniques give dramatically increased MR signals, thereby enabling real-time investigation of injected 13C substrates and their downstream metabolic products. The transient nature of the hyperpolarized signal, however, introduces a number of challenges, necessitating the development of accelerated data acquisition schemes.

    This dissertation first discusses the application of hyperpolarized 13C metabolic imaging for monitoring the tumor progression and regression in murine cancer models. Then, a number of new methods are presented that improve the research and future clinical value of this molecular imaging technique. In particular, novel data encoding and image reconstruction algorithms were developed based on state of the art techniques such as parallel imaging, compressed sensing, and low-rank matrix completion. The presented framework was applied to in vivo [1-13C]pyruvate metabolic imaging to accelerate data acquisition speed and improve the spatial and temporal resolution for the acquired metabolic data.

      Cover page: Accelerated Hyperpolarized 13C MR Metabolic Imaging
      • Thesis
      • Peer Reviewed
      UC Berkeley Electronic Theses and Dissertations (2023)

      Bits torn from words examines the mental health condition of generalized anxiety disorder – how the dread of even the most inconsequential circumstances feels gargantuanly out of proportion to its relative impact. In expanded song form, voices traverse through wavering pitches, surrendered exclamations, and quivering breaths, all conveying the vivid manifestations of anxiety in the body and psyche. The title comes from the opening pages of Dictee (1982) by the pioneering Korean American conceptual artist Theresa Hak Kyung Cha (1951-82). Through intricate diagrams and vivid prose, Cha illustrates the visceral phenomenology of vocalization, and the yearning to say and be heard.In the first movement, Reach across oceans (intro), a soloist desperately wails into the expanse in an attempt to reach another. Evoking p’ansori, this Korean vocal tradition nearly requires damage to the vocal cords in such a way to produce a uniquely raw and soul-wrenching intensity. In the second movement, I’m terrible at making decisions (refrain), the mental fatigue of facing infinite options is expressed through a repetitive torrent of utterances. The third movement, Notice how your body spreads like water (post-refrain), comes from Yoga nidra, a guided meditation practice for the purposes of sleep and relieving stress which often helps me to find a place allowing the ability to rest. The fourth movement, GaNaDaRaMaBaSa AJaChaKaTaPaHa (bridge), concentrates on the 14 consonants of the Korean alphabet, the very roots and building blocks of the language through aspirated articulations layered in chained suspensions. From here, the beginning of the piece returns in this fifth movement, embracing our coexistence with the natural ebb and flow of anxiety in our consciousness. Finally, the last movement poses the question: “If __________ did happen, how bad would it be?” Taken from a worksheet from my therapist on disputing irrational anxieties, the question serves as a space for introspection and mindfulness, to be more compassionate with ourselves, to comfort and to nourish. If it doesn’t go perfectly, if it doesn’t pan out, and so on and so forth… how bad would it be?

        Cover page: Bits torn from words
        • Article
        • Peer Reviewed
        Western Journal of Emergency Medicine: Integrating Emergency Care with Population Health, Volume 9, Issue 2 (2008)

        Objectives: With regard to sedative agents used in procedural sedation and analgesia (PSA), such as etomidate, the focus has been on variables usually related to side effect profile and the success rates of various procedures, with both variables specifically taking place during the patients’ stay in the emergency department (ED). There have been no extensive data on the functional status of patients after they leave the ED following PSA.

        Methods: Prospective questionnaire evaluating functional status among consecutive adult patients discharged from the ED after undergoing etomidate PSA for orthopedic procedures.

        Results: The study sample consisted of 26 cases using only etomidate for closed orthopedic reductions. The mean age was 50.1 years (SD: 20.5), mean weight 86.3 kg (SD: 17.2), and 61.5% were males. The average dose of etomidate given was 0.14 mg/kg with 26.9% requiring a second dose of 0.11 mg/kg. The average dose of analgesic given was 0.11mg/kg in morphine equianalgesic units. The median time between procedural sedation and return to normal sleep was 36 hours, while return to operating a motor vehicle or return to work was 72 hours. Overall, 80% to 100% of respondents felt that any temporary dysfunction was secondary to the orthopedic problems and not to the procedural sedation.

        Conclusion: In this small follow-up study, adult patients undergoing PSA with etomidate for orthopedic closed reduction attribute post-discharge functional disability to the injury sustained and not to the PSA itself.

          Cover page: Patient Satisfaction and Return to Daily Activities Using Etomidate Procedural Sedation for Orthopedic Injuries
          • Article
          • Peer Reviewed
          UC San Francisco Previously Published Works (2014)

          Purpose

          A calibrationless parallel imaging reconstruction method, termed simultaneous autocalibrating and k-space estimation (SAKE), is presented. It is a data-driven, coil-by-coil reconstruction method that does not require a separate calibration step for estimating coil sensitivity information.

          Methods

          In SAKE, an undersampled, multichannel dataset is structured into a single data matrix. The reconstruction is then formulated as a structured low-rank matrix completion problem. An iterative solution that implements a projection-onto-sets algorithm with singular value thresholding is described.

          Results

          Reconstruction results are demonstrated for retrospectively and prospectively undersampled, multichannel Cartesian data having no calibration signals. Additionally, non-Cartesian data reconstruction is presented. Finally, improved image quality is demonstrated by combining SAKE with wavelet-based compressed sensing.

          Conclusion

          Because estimation of coil sensitivity information is not needed, the proposed method could potentially benefit MR applications where acquiring accurate calibration data is limiting or not possible at all.
            Cover page: Calibrationless parallel imaging reconstruction based on structured low‐rank matrix completion
            • Article
            • Peer Reviewed
            UC San Francisco Previously Published Works (2018)
            Acceleration of dynamic 2D (T2 Mapping) and 3D hyperpolarized 13C MRI acquisitions using the balanced steady-state free precession sequence was achieved with a specialized reconstruction method, based on the combination of low rank plus sparse and local low rank reconstructions. Methods were validated using both retrospectively and prospectively undersampled in vivo data from normal rats and tumor-bearing mice. Four-fold acceleration of 1-2 mm isotropic 3D dynamic acquisitions with 2-5 s temporal resolution and two-fold acceleration of 0.25-1 mm2 2D dynamic acquisitions was achieved. This enabled visualization of the biodistribution of [2-13C]pyruvate, [1-13C]lactate, [13C, 15N2]urea, and HP001 within heart, kidneys, vasculature, and tumor, as well as calculation of high resolution T2 maps.
              Cover page: Using a local low rank plus sparse reconstruction to accelerate dynamic hyperpolarized 13C imaging using the bSSFP sequence
              • Article
              • Peer Reviewed
              UC San Francisco Previously Published Works (2018)
              With the translation of metabolic MRI with hyperpolarized 13C agents into the clinic, imaging approaches will require large volumetric FOVs to support clinical applications. Parallel imaging techniques will be crucial to increasing volumetric scan coverage while minimizing RF requirements and temporal resolution. Calibrationless parallel imaging approaches are well-suited for this application because they eliminate the need to acquire coil profile maps or auto-calibration data. In this work, we explored the utility of a calibrationless parallel imaging method (SAKE) and corresponding sampling strategies to accelerate and undersample hyperpolarized 13C data using 3D blipped EPI acquisitions and multichannel receive coils, and demonstrated its application in a human study of [1-13C]pyruvate metabolism.
                Cover page: 3D hyperpolarized C-13 EPI with calibrationless parallel imaging
                • Article
                • Peer Reviewed
                UC San Francisco Previously Published Works (2017)
                The purpose of this work was to study the anatomic and metabolic changes that occur with tumor progression, regression and recurrence in a switchable MYC-driven murine breast cancer model. Serial 1H MRI and hyperpolarized [1-13C]pyruvate metabolic imaging were used to investigate the changes in tumor volume and glycolytic metabolism over time during the multistage tumorigenesis. We show that acute de-induction of MYC expression in established tumors results in rapid tumor regression and significantly reduced glycolytic metabolism as measured by pyruvate-to-lactate conversion. Moreover, cancer recurrences occurring at the tumor sites independently of MYC expression were observed to accompany markedly increased lactate production.
                  Cover page: Cancer recurrence monitoring using hyperpolarized [1-13C]pyruvate metabolic imaging in murine breast cancer model
                  • Article
                  • Peer Reviewed
                  UC Berkeley Previously Published Works (2016)
                  Magnetic resonance imaging is an inherently signal-to-noise-starved technique that limits the spatial resolution, diagnostic image quality and results in typically long acquisition times that are prone to motion artefacts. This limitation is exacerbated when receive coils have poor fit due to lack of flexibility or need for padding for patient comfort. Here, we report a new approach that uses printing for fabricating receive coils. Our approach enables highly flexible, extremely lightweight conforming devices. We show that these devices exhibit similar to higher signal-to-noise ratio than conventional ones, in clinical scenarios when coils could be displaced more than 18 mm away from the body. In addition, we provide detailed material properties and components performance analysis. Prototype arrays are incorporated within infant blankets for in vivo studies. This work presents the first fully functional, printed coils for 1.5- and 3-T clinical scanners.
                    Cover page: Screen-printed flexible MRI receive coilsCreative Commons 'BY' version 4.0 license
                    • Article
                    • Peer Reviewed
                    UC San Francisco Previously Published Works (2013)

                    Purpose

                    To implement and evaluate combined parallel magnetic resonance imaging (MRI) and partial Fourier acquisition and reconstruction for rapid hyperpolarized carbon-13 ((13) C) spectroscopic imaging. Short acquisition times mitigate hyperpolarized signal losses that occur due to T1 decay, metabolism, and radiofrequency (RF) saturation. Human applications additionally require rapid imaging to permit breath-holding and to minimize the effects of physiologic motion.

                    Materials and methods

                    Numerical simulations were employed to validate and characterize the reconstruction. In vivo MR spectroscopic images were obtained from a rat following injection of hyperpolarized (13) C pyruvate using an 8-channel array of carbon-tuned receive elements.

                    Results

                    For small spectroscopic matrix sizes, combined parallel imaging and partial Fourier undersampling resulted primarily in decreased spatial resolution, with relatively less visible spatial aliasing. Parallel reconstruction qualitatively restored lost image detail, although some pixel spectra had persistent numerical error. With this technique, a 30 × 10 × 16 matrix of 4800 3D MR spectroscopy imaging voxels from a whole rat with isotropic 8 mm(3) resolution was acquired within 11 seconds.

                    Conclusion

                    Parallel MRI and partial Fourier acquisitions can provide the shorter imaging times and wider spatial coverage that will be necessary as hyperpolarized (13) C techniques move toward human clinical applications.
                      Cover page: Combined parallel and partial fourier MR reconstruction for accelerated 8‐channel hyperpolarized carbon‐13 in vivo magnetic resonance Spectroscopic imaging (MRSI)
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