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Open Access Publications from the University of California

Scholarly Works (18 results)

  • Thesis
  • Peer Reviewed
UC Irvine Electronic Theses and Dissertations (2019)

Spectral analysis in high-energy astrophysics typically requires sampling from difficult posterior distributions, e.g., multimodal distributions, in a highly structured model with complex data collection mechanisms. Markov chain Monte Carlo (MCMC) methods have been widely explored in such tasks. However, traditional MCMC methods suffer from slow convergence incurred by the local trap problem. In this thesis, we propose a general population-based MCMC strategy, which is able to speed up convergence significantly. Specifically, we initialize multiple chains from dispersed starting values and perform a two-step jump with our proposed between-chain jump. The novel between-chain jumping proposal tries to move to the neighborhood of the iterate in another chain, which encourages full exploration of the parameter space. As for the numerical illustration, we apply the proposed method to fit thermal models to Capella data. The results indicate that our method is effective in two aspects. First, it can be applied in Bayesian model selection to decide which mixture model is more appropriate; secondly, it can be served as an exploratory step to identify modes. The strength shown from the second aspect can help determine the importance of those temperature components and decide upon the relative proportion among those modes. In addition, we show that our method is also useful in other applications including Bayes factor computation for Bayesian model selection, variance component estimation in mixed effect models, and sensor network localization.

    Cover page: A New Population-based MCMC MethodCreative Commons 'BY' version 4.0 license
    • Thesis
    • Peer Reviewed
    UCLA Electronic Theses and Dissertations (2012)

    Computed Tomography (CT) has been used for medical diagnosis for the past four decades and has made significant contributions to patient healthcare by providing fast and accurate diagnostic information. Besides the extraordinary medical benefits it has brought to society, it delivers radiation dose to the patients, which can be potentially hazardous. Therefore, it has been a significant interest in both scientific research and clinical practice to reduce radiation dose to the patients during CT scans, while still maintaining the diagnostic performance, so that the information provided through this procedure is not compromised and appropriate medical determinations can be made at the minimum cost.

    In this research work, a Monte Carlo based simulation package was used to estimate radiation dose to individual radiosensitive organs of patients with a range of body habitus. This package is exam and protocol specific, and it takes into account technical details of CT scanners such as spectra, bowtie filtration, and beam geometry. Modifications were made to the Monte Carlo simulation package to perform detailed radiation dose assessments for both patients and phantoms. These include the estimate of radiation dose to individual organs, the peak radiation dose to a wide spread tissue (such as peak skin dose), and surface dose distribution in a complex CT irradiation environment. Meanwhile, the effect of a variety of traditional dose reduction methods, such as tilting the gantry in brain perfusion scans, was also investigated.

    In addition to the traditional dose reduction techniques that are already being utilized in the clinic, an innovative method to reduce organ dose while maintaining image quality was investigated. The distribution of radiation dose within the scan volume was demonstrated to be dependent on the Tube Start Angle (TSA). A change of TSA can cause a shift of dose distribution along the longitudinal axis. This results in variations in the measurement of surface dose during helical scans. This dose variation along the longitudinal direction for patients in CT imaging inspired a novel innovation to reduce organ dose while maintaining image quality by adjusting the TSA and table height in CT exams. Monte Carlo simulations were performed to demonstrate the effectiveness of this method for different patients under various scenarios, including conventional fixed tube current CT scans, and tube current modulated (TCM) scans. Besides the dose benefit this new method brings, its effect on image quality was investigated and demonstrated that there was no significant compromise on the image quality.

    Despite the efforts to reduce radiation dose while maintaining image quality, the ultimate tradeoff in the goal of maximizing the benefit to risk ratio in CT examinations is the tradeoff between radiation dose and diagnostic outcome. As radiation dose is decreased, the image quality may be degraded. However, the diagnostic outcome does not necessarily have to be compromised. In other words, the image quality used for specific CT clinical tasks today may have room to be degraded and still be able to maintain accuracy of diagnostic outcomes. In order to investigate this tradeoff between radiation dose and diagnostic outcome for a specific clinical task (appendicitis was selected in this dissertation), a preliminary observer study was conducted to determine the difference of diagnostic performance at various dose levels. Images at reduced radiation dose levels were simulated by adding noise to the projection data using a calibrated method. These methods were employed for a group of patients with right lower quadrant pain who were scanned because of a suspected appendicitis. The results of Receiver Operation Characteristic (ROC) analysis suggested that there was no significant difference between radiation dose levels of 100%, 70% and 50%. Detailed analysis of patient organ (liver) dose demonstrated that the diagnostic performance is nearly perfect when the liver dose is higher than 10mGy. The interrelationship between a simple image quality metric (noise), organ dose, and patient size was also investigated.

    In summary, this work assessed dose reduction tools available today that do not affect image quality, proposed a new method to reduce organ dose while maintaining image quality, and evaluated the method to reduce radiation dose, which affects image quality but could maintain diagnostic outcome by investigating the tradeoff between radiation dose and diagnostic outcome, as well as their correlation with image quality metrics (noise).

      Cover page: Reduction of radiation dose to radiosensitive organs and its tradeoff with image quality in Computed Tomography
      • Article
      • Peer Reviewed
      UC Davis Previously Published Works (2020)
      This study uses online survey data from the United States and China to examine how contradictory information and social norms regarding HPV vaccines obtained through social media are related to young women's attitudes and intentions surrounding HPV vaccination. The results show that exposure to contradictory information on social media had a greater negative association with intentions to receive HPV vaccination among the United States participants than among the Chinese participants, while social norms supporting HPV vaccines had a stronger positive association with intentions to receive HPV vaccination among the Chinese participants than among the United States participants. These findings extend the literature on social media communication regarding HPV vaccination and contribute to our knowledge of cultural contexts that influence intentions to receive HPV vaccination.
        Cover page: Caught in the Crossfire: How Contradictory Information and Norms on Social Media Influence Young Women’s Intentions to Receive HPV Vaccination in the United States and China
        • Article
        • Peer Reviewed
        UC Irvine Previously Published Works (2018)
        Reservoirs and dams are vital human-built infrastructures that play essential roles in flood control, hydroelectric power generation, water supply, navigation, and other functions. The realization of those functions requires efficient reservoir operation, and the effective controls on the outflow from a reservoir or dam. Over the last decade, artificial intelligence (AI) techniques have become increasingly popular in the field of streamflow forecasts, reservoir operation planning and scheduling approaches. In this study, three AI models, namely, the backpropagation (BP) neural network, support vector regression (SVR) technique, and long short-term memory (LSTM) model, are employed to simulate reservoir operation at monthly, daily, and hourly time scales, using approximately 30 years of historical reservoir operation records. This study aims to summarize the influence of the parameter settings on model performance and to explore the applicability of the LSTM model to reservoir operation simulation. The results show the following: (1) for the BP neural network and LSTM model, the effects of the number of maximum iterations on model performance should be prioritized; for the SVR model, the simulation performance is directly related to the selection of the kernel function, and sigmoid and RBF kernel functions should be prioritized; (2) the BP neural network and SVR are suitable for the model to learn the operation rules of a reservoir from a small amount of data; and (3) the LSTM model is able to effectively reduce the time consumption and memory storage required by other AI models, and demonstrate good capability in simulating low-flow conditions and the outflow curve for the peak operation period.
          Cover page: Modeling and simulating of reservoir operation using the artificial neural network, support vector regression, deep learning algorithmCreative Commons 'BY' version 4.0 license
          • Article
          • Peer Reviewed
          UCLA Previously Published Works (2017)
          Gene synthesis, the process of assembling gene-length fragments from shorter groups of oligonucleotides (oligos), is becoming an increasingly important tool in molecular and synthetic biology. The length, quality and cost of gene synthesis are limited by errors produced during oligo synthesis and subsequent assembly. Enzymatic error correction methods are cost-effective means to ameliorate errors in gene synthesis. Previous analyses of these methods relied on cloning and Sanger sequencing to evaluate their efficiencies, limiting quantitative assessment. Here, we develop a method to quantify errors in synthetic DNA by next-generation sequencing. We analyzed errors in model gene assemblies and systematically compared six different error correction enzymes across 11 conditions. We find that ErrASE and T7 Endonuclease I are the most effective at decreasing average error rates (up to 5.8-fold relative to the input), whereas MutS is the best for increasing the number of perfect assemblies (up to 25.2-fold). We are able to quantify differential specificities such as ErrASE preferentially corrects C/G transversions whereas T7 Endonuclease I preferentially corrects A/T transversions. More generally, this experimental and computational pipeline is a fast, scalable and extensible way to analyze errors in gene assemblies, to profile error correction methods, and to benchmark DNA synthesis methods.
            Cover page: A systematic comparison of error correction enzymes by next-generation sequencing
            • Article
            • Peer Reviewed
            UC Berkeley Previously Published Works (2021)
            Among metals used for CO2 electroreduction in water, Cu appears to be unique in its ability to produce C2+ products like ethylene. Bimetallic combinations of Cu with other metals have been investigated with the goal of steering selectivity via creating a tandem pathway through the CO intermediate or by changing the surface electronic structure. Here, we demonstrate a facile cation exchange method to synthesize Ag/Cu electrocatalysts for CO2 reduction using Cu sulfides as a growth template. Beginning with Cu2−xS nanosheets (C?nano-0, 100 nm lateral dimension, 10 nm thick), varying the Ag+ concentration in the exchange solution produces a gradual change in crystal structure from Cu7S4 to Ag2S, as the Ag/Cu mass ratio varies from 0.1 to 10 (CA-nano-x, x indicating increasing Ag fraction). After cation exchange, the nanosheet morphology remains but with increased shape distortion as the Ag fraction is increased. Interestingly, the control (C-nano-0) and cation exchanged nanosheets have very high Faradaic efficiency for producing formate at low overpotential (−0.2 V vs. RHE). The primary effect of Ag incorporation is increased production of C2+ products at −1.0 V vs. RHE compared with C-nano-0, which primarily produces formate. Cation exchange can also be used to modify the surface of Cu foils. A two-step electro-oxidation/sulfurization process was used to form Cu sulfides on Cu foil (C-foil-x) to a depth of a few 10s of microns. With lower Ag+ concentrations, cation exchange produces uniformly dispersed Ag; however, at higher concentrations, Ag particles nucleate on the surface. During CO2 electroreduction testing, the product distribution for Ag/Cu sulfides on Cu foil (CA-foil-x-y) changes in time with an initial increase in ethylene and methane production followed by a decrease as more H2 is produced. The catalysts undergo a morphology evolution towards a nest-like structure which could be responsible for the change in selectivity. For cation-exchanged nanosheets (CA-nano-x), pre-reduction at negative potentials increases the CO2 reduction selectivity compared to tests of as-synthesized material, although this led to the aggregation of nanosheets into filaments. Both types of bimetallic catalysts are capable of selective reduction of CO2 to multi-carbon products, although the optimal configurations appear to be metastable.
              • Article
              • Peer Reviewed
              UCLA Previously Published Works (2010)
              The increasing use of serial PET/CT scans in the management of pediatric malignancies raises the important consideration of radiation exposure in children. To estimate the cumulative radiation dose from PET/CT studies to children with malignancy and to compare with the data in literature. Two hundred forty-eight clinical PET/CT studies performed on 78 patients (50 boys/28 girls, 1.3 to 18 years old from December 2002 to October 2007) were retrospectively reviewed under IRB approval. The whole-body effective dose (ED) estimates for each child were obtained by estimating the effective dose from each PET/CT exam performed using the ImPACT Patient Dosimetry Calculator for CT and OLINDA for PET. The average number of PET/CT studies was 3.2 per child (range: 1 to 14 studies). The average ED of an individual CT study was 20.3 mSv (range: 2.7 to 54.2), of PET study was 4.6 mSv (range: 0.4 to 7.7) and of PET/CT study was 24.8 mSv (range: 6.2 to 60.7). The average cumulative radiation dose per patient from CT studies was 64.4 mSv (range: 2.7 to 326), from PET studies was 14.5 mSv (range: 2.8 to 73) and from PET/CT studies was 78.9 mSv (range: 6.2 to 399). The radiation exposure from serial PET/CT studies performed in pediatric malignancies was considerable; however, lower doses can be used for both PET and CT studies. The ALARA principle must be applied without sacrificing diagnostic information.
                Cover page: Estimated cumulative radiation dose from PET/CT in children with malignancies: a 5-year retrospective review
                • Article
                • Peer Reviewed
                UC Berkeley Previously Published Works (2021)
                Among metals used for CO2 electroreduction in water, Cu appears to be unique in its ability to produce C2+ products like ethylene. Bimetallic combinations of Cu with other metals have been investigated with the goal of steering selectivity via creating a tandem pathway through the CO intermediate or by changing the surface electronic structure. Here, we demonstrate a facile cation exchange method to synthesize Ag/Cu electrocatalysts for CO2 reduction using Cu sulfides as a growth template. Beginning with Cu2-x S nanosheets (C-nano-0, 100 nm lateral dimension, 14 nm thick), varying the Ag+ concentration in the exchange solution produces a gradual change in crystal structure from Cu7S4 to Ag2S, as the Ag/Cu mass ratio varies from 0.3 to 25 (CA-nano-x, x indicating increasing Ag fraction). After cation exchange, the nanosheet morphology remains but with increased shape distortion as the Ag fraction is increased. Interestingly, the control (C-nano-0) and cation exchanged nanosheets have very high faradaic efficiency for producing formate at low overpotential (-0.2 V vs. RHE). The primary effect of Ag incorporation is increased production of C2+ products at -1.0 V vs. RHE compared with C-nano-0, which primarily produces formate. Cation exchange can also be used to modify the surface of Cu foils. A two-step electro-oxidation/sulfurization process was used to form Cu sulfides on Cu foil (C-foil-x) to a depth of a few 10 s of microns. With lower Ag+ concentrations, cation exchange produces uniformly dispersed Ag; however, at higher concentrations, Ag particles nucleate on the surface. During CO2 electroreduction testing, the product distribution for Ag/Cu sulfides on Cu foil (CA-foil-x-y) changes in time with an initial increase in ethylene and methane production followed by a decrease as more H2 is produced. The catalysts undergo a morphology evolution towards a nest-like structure which could be responsible for the change in selectivity. For cation-exchanged nanosheets (CA-nano-x), pre-reduction at negative potentials increases the CO2 reduction selectivity compared to tests of as-synthesized material, although this led to the aggregation of nanosheets into filaments. Both types of bimetallic catalysts are capable of selective reduction of CO2 to multi-carbon products, although the optimal configurations appear to be metastable.
                  Cover page: Copper sulfide as the cation exchange template for synthesis of bimetallic catalysts for CO 2 electroreduction
                  • Article
                  • Peer Reviewed
                  UCLA Previously Published Works (2013)

                  Purpose

                  CT neuroperfusion examinations are capable of delivering high radiation dose to the skin or lens of the eyes of a patient and can possibly cause deterministic radiation injury. The purpose of this study is to: (a) estimate peak skin dose and eye lens dose from CT neuroperfusion examinations based on several voxelized adult patient models of different head size and (b) investigate how well those doses can be approximated by some commonly used CT dose metrics or tools, such as CTDIvol, American Association of Physicists in Medicine (AAPM) Report No. 111 style peak dose measurements, and the ImPACT organ dose calculator spreadsheet.

                  Methods

                  Monte Carlo simulation methods were used to estimate peak skin and eye lens dose on voxelized patient models, including GSF's Irene, Frank, Donna, and Golem, on four scanners from the major manufacturers at the widest collimation under all available tube potentials. Doses were reported on a per 100 mAs basis. CTDIvol measurements for a 16 cm CTDI phantom, AAPM Report No. 111 style peak dose measurements, and ImPACT calculations were performed for available scanners at all tube potentials. These were then compared with results from Monte Carlo simulations.

                  Results

                  The dose variations across the different voxelized patient models were small. Dependent on the tube potential and scanner and patient model, CTDIvol values overestimated peak skin dose by 26%-65%, and overestimated eye lens dose by 33%-106%, when compared to Monte Carlo simulations. AAPM Report No. 111 style measurements were much closer to peak skin estimates ranging from a 14% underestimate to a 33% overestimate, and with eye lens dose estimates ranging from a 9% underestimate to a 66% overestimate. The ImPACT spreadsheet overestimated eye lens dose by 2%-82% relative to voxelized model simulations.

                  Conclusions

                  CTDIvol consistently overestimates dose to eye lens and skin. The ImPACT tool also overestimated dose to eye lenses. As such they are still useful as a conservative predictor of dose for CT neuroperfusion studies. AAPM Report No. 111 style measurements are a better predictor of both peak skin and eye lens dose than CTDIvol and ImPACT for the patient models used in this study. It should be remembered that both the AAPM Report No. 111 peak dose metric and CTDIvol dose metric are dose indices and were not intended to represent actual organ doses.
                    • Article
                    • Peer Reviewed
                    UCLA Previously Published Works (2019)
                    Aluminum oxide based optically stimulated luminescent dosimeters (OSLD) have been recognized as a useful dosimeter for measuring CT dose, particularly for patient dose measurements. Despite the increasing use of this dosimeter, appropriate dosimeter calibration techniques have not been established in the literature; while the manufacturer offers a calibration procedure, it is known to have relatively large uncertainties. The purpose of this work was to evaluate two clinical approaches for calibrating these dosimeters for CT applications, and to determine the uncertainty associated with measurements using these techniques. Three unique calibration procedures were used to calculate dose for a range of CT conditions using a commercially available OSLD and reader. The three calibration procedures included calibration (a) using the vendor-provided method, (b) relative to a 120 kVp CT spectrum in air, and (c) relative to a megavoltage beam (implemented with 60 Co). The dose measured using each of these approaches was compared to dose measured using a calibrated farmer-type ion chamber. Finally, the uncertainty in the dose measured using each approach was determined. For the CT and megavoltage calibration methods, the dose measured using the OSLD nanoDot was within 5% of the dose measured using an ion chamber for a wide range of different CT scan parameters (80-140 kVp, and with measurements at a range of positions). When calibrated using the vendor-recommended protocol, the OSLD measured doses were on average 15.5% lower than ion chamber doses. Two clinical calibration techniques have been evaluated and are presented in this work as alternatives to the vendor-provided calibration approach. These techniques provide high precision for OSLD-based measurements in a CT environment.
                      Cover page: Calibration strategies for use of the nanoDot OSLD in CT applications
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