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Open Access Publications from the University of California

Scholarly Works (23 results)

  • Thesis
  • Peer Reviewed
UC Riverside Electronic Theses and Dissertations (2024)

The critical intermediate produced in the ozonolysis of unsaturated volatile organic compounds (VOCs), Criegee intermediates (CIs), plays an important role in the production of hydroxyl radicals and secondary organic aerosols (SOA) in the troposphere. Due to the transient nature of CIs, decades of efforts on direct measurements of CIs in ozonolysis have proven its difficulty. This dissertation presents a comprehensive study on the kinetics and mechanisms of CIs produced in ozonolysis of a series of alkenes using cavity ringdown spectroscopy and a fast flow reactor. Chapters 2 to 5 of this dissertation investigated the nascent yield of stabilized Criegee intermediates (sCIs) produced in ozonolysis of alkenes using chemical titration with an excess amount of SO2 scavenger. These studies specifically examined ethene, propene, 1-butene, 1-pentene, 1-hexene, 1-heptene, 2-methylpropene, 2-methyl-1-butene, and 3-methyl-1-butene. The findings reveal a chain length dependence behavior of nascent sCI yields that increases with the addition of carbon atoms and eventually reached a plateau at around 31% for longer chain 1-alkenes. In particular, the fraction of stabilized CH2OO reached a plateau from propene, indicating that CH2OO was produced with nearly the same internal energy distribution from propene to 1-heptene and the increased chain in 1-alkenes was not effective in taking away the excess energy. The comparison between the experiments and RRKM calculations suggests that the dissociation of primary ozonide (POZ) of O3 + ethene and propene can be treated by statistical theory, while that of O3 + 1-butene to 1-heptene is non-statistical and intramolecular vibrational redistribution (IVR) of the initial energy on the 1,2,3-trioxolane of POZ throughout the molecule was incomplete on the dissociation time scale. Chapters 6 to 11 of this dissertation focus on the direct measurements and kinetic studies of the simplest CI (CH2OO) in ozonolysis of a series of terminal alkenes ranging from ethene to isoprene. Strong absorption features of CH2OO in near UV region corresponding to the B̃(1A′) ← X̃(1A′) transition were utilized to characterize and quantify the concentrations of CH2OO produced in ozonolysis of ethene, isoprene, propene, 1-butene, 1-pentene, and isobutene. Short residence times were used to generate sufficiently high concentrations of CH2OO. Kinetic studies based on experimental data and reaction network modeling allow the determination of sCI yields and the measurements on the rate coefficients of reactions between CH2OO and various species in ozonolysis, such as alkenes, O3, and aldehydes. Chapter 12 focuses on the direct measurements of CH3CHOO produced in ozonolysis of cis- and trans-2-butene. Branching ratios of syn- and anti-CH3CHOO in both systems were obtained from their spectra features.

    Creative Commons 'BY-NC-ND' version 4.0 license
    • Article
    • Peer Reviewed
    UC Irvine Previously Published Works (2014)
    Hemodynamic monitoring and optimization improve postoperative outcome during high-risk surgery. However, hemodynamic management practices among Chinese anesthesiologists are largely unknown. This study sought to evaluate the current intraoperative hemodynamic management practices for high-risk surgery patients in China. From September 2010 to November 2011, we surveyed anesthesiologists working in the operating rooms of 265 hospitals representing 28 Chinese provinces. All questionnaires were distributed to department chairs of anesthesiology or practicing anesthesiologists. Once completed, the 29-item questionnaires were collected and analyzed. Two hundred and 10 questionnaires from 265 hospitals in China were collected. We found that 91.4% of anesthesiologists monitored invasive arterial pressure, 82.9% monitored central venous pressure (CVP), 13.3% monitored cardiac output (CO), 10.5% monitored mixed venous saturation, and less than 2% monitored pulse pressure variation (PPV) or systolic pressure variation (SPV) during high-risk surgery. The majority (88%) of anesthesiologists relied on clinical experience as an indicator for volume expansion and more than 80% relied on blood pressure, CVP and urine output. Anesthesiologists in China do not own enough attention on hemodynamic parameters such as PPV, SPV and CO during fluid management in high-risk surgical patients. The lack of CO monitoring may be attributed largely to the limited access to technologies, the cost of the devices and the lack of education on how to use them. There is a need for improving access to these technologies as well as an opportunity to create guidelines and education for hemodynamic optimization in China.
      Cover page: Hemodynamic monitoring and management of patients undergoing high-risk surgery: a survey among Chinese anesthesiologistsCreative Commons 'BY' version 4.0 license
      • Article
      • Peer Reviewed
      UC Irvine Previously Published Works (2017)
      OBJECTIVE: The utility of biomedical information retrieval environments can be severely limited when users lack expertise in constructing effective search queries. To address this issue, we developed a computer-based query recommendation algorithm that suggests semantically interchangeable terms based on an initial user-entered query. In this study, we assessed the value of this approach, which has broad applicability in biomedical information retrieval, by demonstrating its application as part of a search engine that facilitates retrieval of information from electronic health records (EHRs). MATERIALS AND METHODS: The query recommendation algorithm utilizes MetaMap to identify medical concepts from search queries and indexed EHR documents. Synonym variants from UMLS are used to expand the concepts along with a synonym set curated from historical EHR search logs. The empirical study involved 33 clinicians and staff who evaluated the system through a set of simulated EHR search tasks. User acceptance was assessed using the widely used technology acceptance model. RESULTS: The search engines performance was rated consistently higher with the query recommendation feature turned on vs. off. The relevance of computer-recommended search terms was also rated high, and in most cases the participants had not thought of these terms on their own. The questions on perceived usefulness and perceived ease of use received overwhelmingly positive responses. A vast majority of the participants wanted the query recommendation feature to be available to assist in their day-to-day EHR search tasks. DISCUSSION AND CONCLUSION: Challenges persist for users to construct effective search queries when retrieving information from biomedical documents including those from EHRs. This study demonstrates that semantically-based query recommendation is a viable solution to addressing this challenge.
        Cover page: Development and empirical user-centered evaluation of semantically-based query recommendation for an electronic health record search engine.
        • Article
        • Peer Reviewed
        UC San Diego Previously Published Works (2016)

        Background

        Accurately assessing pain for those who cannot make self-report of pain, such as minimally responsive or severely brain-injured patients, is challenging. In this paper, we attempted to address this challenge by answering the following questions: (1) if the pain has dependency structures in electronic signals and if so, (2) how to apply this pattern in predicting the state of pain. To this end, we have been investigating and comparing the performance of several machine learning techniques.

        Methods

        We first adopted different strategies, in which the collected original n-dimensional numerical data were converted into binary data. Pain states are represented in binary format and bound with above binary features to construct (n + 1) -dimensional data. We then modeled the joint distribution over all variables in this data using the Restricted Boltzmann Machine (RBM).

        Results

        Seventy-eight pain data items were collected. Four individuals with the number of recorded labels larger than 1000 were used in the experiment. Number of avaliable data items for the four patients varied from 22 to 28. Discriminant RBM achieved better accuracy in all four experiments.

        Conclusion

        The experimental results show that RBM models the distribution of our binary pain data well. We showed that discriminant RBM can be used in a classification task, and the initial result is advantageous over other classifiers such as support vector machine (SVM) using PCA representation and the LDA discriminant method.
          Cover page: PATTERN: Pain Assessment for paTients who can’t TEll using Restricted Boltzmann machiNe
          • Article
          • Peer Reviewed
          UC Berkeley Previously Published Works (2024)
          Recent developments in intelligent robot systems, especially autonomous vehicles, put forward higher requirements for safety and comfort. Road conditions are crucial factors affecting the comprehensive performance of ground vehicles. Nonetheless, existing environment perception datasets for autonomous driving lack attention to road surface areas. In this paper, we introduce the road surface reconstruction dataset, providing multi-modal, high-resolution, and high-precision data collected by real-vehicle platform in diverse driving conditions. It covers common road types containing approximately 16,000 pairs of stereo images, point clouds, and ground-truth depth/disparity maps, with accurate data processing pipelines to ensure its quality. Preliminary evaluations reveal the effectiveness of our dataset and the challenge of the task, underscoring substantial opportunities of it as a valuable resource for advancing computer vision techniques. The reconstructed road structure and texture contribute to the analysis and prediction of vehicle responses for motion planning and control systems.
            Cover page: A road surface reconstruction dataset for autonomous driving.
            • Article
            • Peer Reviewed
            UC Berkeley Previously Published Works (2015)
            Although Mg(2+) is essential for a myriad of cellular processes, high levels of Mg(2+) in the environment, such as those found in serpentine soils, become toxic to plants. In this study, we identified two calcineurin B-like (CBL) proteins, CBL2 and CBL3, as key regulators for plant growth under high-Mg conditions. The Arabidopsis mutant lacking both CBL2 and CBL3 displayed severe growth retardation in the presence of excess Mg(2+), implying elevated Mg(2+) toxicity in these plants. Unexpectedly, the cbl2 cbl3 mutant plants retained lower Mg content than wild-type plants under either normal or high-Mg conditions, suggesting that CBL2 and CBL3 may be required for vacuolar Mg(2+) sequestration. Indeed, patch-clamp analysis showed that the cbl2 cbl3 mutant exhibited reduced Mg(2+) influx into the vacuole. We further identified four CBL-interacting protein kinases (CIPKs), CIPK3, -9, -23, and -26, as functionally overlapping components downstream of CBL2/3 in the signaling pathway that facilitates Mg(2+) homeostasis. The cipk3 cipk9 cipk23 cipk26 quadruple mutant, like the cbl2 cbl3 double mutant, was hypersensitive to high-Mg conditions; furthermore, CIPK3/9/23/26 physically interacted with CBL2/3 at the vacuolar membrane. Our results thus provide evidence that CBL2/3 and CIPK3/9/23/26 constitute a multivalent interacting network that regulates the vacuolar sequestration of Mg(2+), thereby protecting plants from Mg(2+) toxicity.
              Cover page: Tonoplast CBL–CIPK calcium signaling network regulates magnesium homeostasis in Arabidopsis
              • Article
              • Peer Reviewed
              UC Irvine Previously Published Works (2014)
              The I222K, I222R, and I222T substitutions in neuraminidase (NA) have been found in clinically derived 2009 pandemic influenza A/H1N1 viruses with altered susceptibilities to NA inhibitors (NAIs). The effects of these substitutions, together with the most frequently observed resistance-related substitution, H274Y, on viral fitness and resistance mechanisms were further investigated in this study. Reduced sensitivities to oseltamivir were observed in all three mutants (I222K, I222R, and I222T). Furthermore, the I222K and I222T substitutions had a combinational effect of further increasing resistance in the presence of H274Y, which might result from a conformational restriction in the NA binding site. Of note, by using molecular dynamics simulations, R152, the neighbor of T222, was observed to translate to a position closer to T222, resulting in the narrowing of the binding pocket, which otherwise only subtends the residue substitution of H274Y. Moreover, significantly attenuated NA function and viral growth abilities were found in the I222K+H274Y double mutant, while the I222T+H274Y double mutant exhibited slightly delayed growth but had a peak viral titer similar to that of the wild-type virus in MDCK cells. The relative growth advantage of the I222T mutant versus the I222K mutant and the higher frequency of I222T emerging in N1 subtype influenza viruses raise concerns necessitating close monitoring of the dual substitutions I222T and H274Y.
                Cover page: A Conformational Restriction in the Influenza A Virus Neuraminidase Binding Site by R152 Results in a Combinational Effect of I222T and H274Y on Oseltamivir Resistance
                • Article
                • Peer Reviewed
                UC San Diego Previously Published Works (2014)
                "Strain engineering" in functional materials has been widely explored to tailor the physical properties of electronic materials and improve their electrical and/or optical properties. Here, we exploit both in plane and out of plane uniaxial tensile strains in MoS2 to modulate its band gap and engineer its optical properties. We utilize X-ray diffraction and cross-sectional transmission electron microscopy to quantify the strains in the as-synthesized MoS2 nanosheets and apply measured shifts of Raman-active modes to confirm lattice strain modification of both the out-of-plane and in-plane phonon vibrations of the MoS2 nanosheets. The induced band gap evolution due to in-plane and out-of-plane tensile stresses is validated by photoluminescence (PL) measurements, promising a potential route for unprecedented manipulation of the physical, electrical and optical properties of MoS2.
                  Cover page: Lattice strain effects on the optical properties of MoS2 nanosheets
                  • Article
                  • Peer Reviewed
                  UC San Diego Previously Published Works (2022)
                  Therapeutic drug monitoring (TDM) with measurement of serum drug and antidrug antibodies (ADAb) is used widely to confirm therapeutic exposure, rule out immunogenicity, and optimize treatment of biologics in patients with inflammatory bowel diseases.1 A recent genome-wide association study found the variant HLA-DQA1∗05 to increase the risk of development of antibodies against infliximab (IFX) and adalimumab (ADM) 2-fold, regardless of concomitant immunomodulator use.2,3 However, there is currently limited evidence showing whether patients who develop antibodies to 1 anti-tumor necrosis factor (TNF) are prone to develop antibodies to the subsequent anti-TNF. Our aim was to investigate the risk of subsequent antibody development in cases (with ADAb to prior anti-TNF) versus control subjects (without ADAb to prior anti-TNF) using a large cohort of patients with inflammatory bowel diseases who underwent TDM with a drug-tolerant assay.
                    Cover page: Patients With Low Drug Levels or Antibodies to a Prior Anti–Tumor Necrosis Factor Are More Likely to Develop Antibodies to a Subsequent Anti–Tumor Necrosis Factor
                    • Article
                    • Peer Reviewed
                    UCLA Previously Published Works (2023)
                    OBJECTIVE: Evidence-based treatment options for late-life treatment-resistant depression (TRD) are limited. Ketamine is a promising treatment for TRD; however, there is a paucity of data on its safety and efficacy in older adults. METHODS: In this pilot clinical trial, 25 adults aged ≥60 years with TRD received IV ketamine openly twice a week for 4 weeks; partial responders at the end of this acute phase were eligible to receive weekly infusions for 4 more weeks in a continuation phase. Acceptability, tolerability, and safety, including adverse and serious adverse events (AEs and SAEs), blood pressure changes, dissociation, craving, in addition to rates of depression response and remission were evaluated. The NIH Toolbox Cognitive Battery was used to assess specific measures of executive function (EF) and overall fluid cognition. RESULTS: Completion rates were 88% for the acute phase and 100% for the continuation phase. No AEs resulted in participant discontinuation, and there were no SAEs. Treatment-emergent elevation of blood pressure, dissociation, and craving were transient and did not result in any participant discontinuation. Depressive symptoms improved significantly and 48% of participants responded. During the acute phase, the EF measures and the fluid cognition composite score improved (Cohens d = 0.61), and these improvements were sustained in the continuation phase. CONCLUSION: This pilot study suggests that repeated IV ketamine infusions are well-tolerated and are associated with improvement in depression and EF in older adults with TRD. These promising findings need to be confirmed and extended in a larger randomized controlled trial.
                      Cover page: Intravenous Ketamine for Late-Life Treatment-Resistant Depression: A Pilot Study of Tolerability, Safety, Clinical Benefits, and Effect on Cognition.
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