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Open Access Publications from the University of California

Scholarly Works (7 results)

  • Article
  • Peer Reviewed
UC Irvine Previously Published Works (2014)

The major removal processes for gaseous nitric acid (HNO3) in the atmosphere are dry and wet deposition onto various surfaces. The surface in the boundary layer is often covered with organic films, but the interaction of gaseous HNO3 with them is not well understood. To better understand the factors controlling the uptake of gaseous nitric acid and its dissociation in organic films, studies were carried out using single component and mixtures of C8 and C18 alkyl self-assembled monolayers (SAMs) attached to a germanium (Ge) attenuated total reflectance (ATR) crystal upon which a thin layer of SiOx had been deposited. For comparison, diffuse reflectance infrared Fourier transform spectrometry (DRIFTS) studies were also carried out using a C18 SAM attached to the native oxide layer on the surface of silicon powder. These studies show that the alkyl chain length and order/disorder of the SAMs does not significantly affect the uptake or dissociation/recombination of molecular HNO3. Thus, independent of the nature of the SAM, molecular HNO3 is observed up to 70-90% relative humidity. After dissociation, molecular HNO3 is regenerated on all SAM surfaces when water is removed. Results of molecular dynamics simulations are consistent with experiments and show that defects and pores on the surfaces control the uptake, dissociation and recombination of molecular HNO3. Organic films on surfaces in the boundary layer will certainly be more irregular and less ordered than SAMs studied here, therefore undissociated HNO3 may be present on surfaces in the boundary layer to a greater extent than previously thought. The combination of this observation with the results of recent studies showing enhanced photolysis of nitric acid on surfaces suggests that renoxification of deposited nitric acid may need to be taken into account in atmospheric models.

    Cover page: Interactions of gaseous HNO3 and water with individual and mixed alkyl self-assembled monolayers at room temperature.
    • Article
    • Peer Reviewed
    UC Irvine Previously Published Works (2014)

    The major removal processes for gaseous nitric acid (HNO3) in the atmosphere are dry and wet deposition onto various surfaces. The surface in the boundary layer is often covered with organic films, but the interaction of gaseous HNO3 with them is not well understood. To better understand the factors controlling the uptake of gaseous nitric acid and its dissociation in organic films, studies were carried out using single component and mixtures of C8 and C18 alkyl self-assembled monolayers (SAMs) attached to a germanium (Ge) attenuated total reflectance (ATR) crystal upon which a thin layer of SiOx had been deposited. For comparison, diffuse reflectance infrared Fourier transform spectrometry (DRIFTS) studies were also carried out using a C18 SAM attached to the native oxide layer on the surface of silicon powder. These studies show that the alkyl chain length and order/disorder of the SAMs does not significantly affect the uptake or dissociation/recombination of molecular HNO3. Thus, independent of the nature of the SAM, molecular HNO3 is observed up to 70-90% relative humidity. After dissociation, molecular HNO3 is regenerated on all SAM surfaces when water is removed. Results of molecular dynamics simulations are consistent with experiments and show that defects and pores on the surfaces control the uptake, dissociation and recombination of molecular HNO3. Organic films on surfaces in the boundary layer will certainly be more irregular and less ordered than SAMs studied here, therefore undissociated HNO3 may be present on surfaces in the boundary layer to a greater extent than previously thought. The combination of this observation with the results of recent studies showing enhanced photolysis of nitric acid on surfaces suggests that renoxification of deposited nitric acid may need to be taken into account in atmospheric models.

      Cover page: Interactions of gaseous HNO3 and water with individual and mixed alkyl self-assembled monolayers at room temperature.
      • Article
      • Peer Reviewed
      UC San Diego Previously Published Works (2020)

      Background

      A number of motor abnormalities have been reported in psychotic disorders, including dyskinesia and psychomotor slowing. There is also evidence for many of the same motor abnormalities in biological first-degree relatives and accruing evidence for motor abnormalities in bipolar disorder. In addition to motor dysfunction, there are also shared symptom domains amongst these populations.

      Objectives

      We explored the associations of (1) current and lifetime psychosis and mood symptom domains and (2) domains of psychosis proneness with various domains of motor function in a transdiagnostic sample (n = 149).

      Method

      Individuals with schizophrenia, schizoaffective disorder, or bipolar disorder, biological first-degree relatives of individuals with a psychotic disorder, and controls completed measures of psychomotor speed and movement fluidity, and neural activity related to motor preparation (stimulus-locked lateralized readiness potential, S-LRP) and execution (response-locked LRP) was assessed using EEG. All participants completed the Brief Psychiatric Rating Scale; patients were additionally assessed for lifetime psychosis and mood episode symptoms, and relatives and controls completed the Chapman psychosis proneness scales.

      Results

      Multiple regression revealed levels of current negative symptoms and mania were significantly positively associated with psychomotor slowing even after accounting for current antipsychotic medication dosage and duration of illness. S-LRP onset latency was significantly positively associated with magical ideation.

      Conclusion

      Domains of motor function are associated with various mood and psychosis symptom domains in a transdiagnostic sample, which may provide insight into brain abnormalities relevant to the expression of symptoms across disorders.
        Cover page: Exploring the Relationship of Transdiagnostic Mood and Psychosis Symptom Domains with Motor Dysfunction
        • Article
        • Peer Reviewed
        UC Irvine Previously Published Works (2017)
        It is now well established by numerous experimental and computational studies that the adsorption propensities of inorganic anions conform to the Hofmeister series. The adsorption propensities of inorganic cations, such as the alkali metal cations, have received relatively little attention. Here we use a combination of liquid-jet X-ray photoelectron experiments and molecular dynamics simulations to investigate the behavior of K+ and Li+ ions near the interfaces of their aqueous solutions with halide ions. Both the experiments and the simulations show that Li+ adsorbs to the aqueous solution-vapor interface, while K+ does not. Thus, we provide experimental validation of the "surfactant-like" behavior of Li+ predicted by previous simulation studies. Furthermore, we use our simulations to trace the difference in the adsorption of K+ and Li+ ions to a difference in the resilience of their hydration shells.
          Cover page: Specific cation effects at aqueous solution−vapor interfaces: Surfactant-like behavior of Li+ revealed by experiments and simulations
          • Article
          • Peer Reviewed
          UC San Francisco Previously Published Works (2022)

          Background

          Current TB treatment for children is not optimized to provide adequate drug levels in TB lesions. Dose optimization of first-line antituberculosis drugs to increase exposure at the site of disease could facilitate more optimal treatment and future treatment-shortening strategies across the disease spectrum in children with pulmonary TB.

          Objectives

          To determine the concentrations of first-line antituberculosis drugs at the site of disease in children with intrathoracic TB.

          Methods

          We quantified drug concentrations in tissue samples from 13 children, median age 8.6 months, with complicated forms of pulmonary TB requiring bronchoscopy or transthoracic surgical lymph node decompression in a tertiary hospital in Cape Town, South Africa. Pharmacokinetic models were used to describe drug penetration characteristics and to simulate concentration profiles for bronchoalveolar lavage, homogenized lymph nodes, and cellular and necrotic lymph node lesions.

          Results

          Isoniazid, rifampicin and pyrazinamide showed lower penetration in most lymph node areas compared with plasma, while ethambutol accumulated in tissue. None of the drugs studied was able to reach target concentration in necrotic lesions.

          Conclusions

          Despite similar penetration characteristics compared with adults, low plasma exposures in children led to low site of disease exposures for all drugs except for isoniazid.
            Cover page: Drug concentration at the site of disease in children with pulmonary tuberculosis
            • Article
            • Peer Reviewed
            UC Davis Previously Published Works (2021)
            We develop a generalizable AI-driven workflow that leverages heterogeneous HPC resources to explore the time-dependent dynamics of molecular systems. We use this workflow to investigate the mechanisms of infectivity of the SARS-CoV-2 spike protein, the main viral infection machinery. Our workflow enables more efficient investigation of spike dynamics in a variety of complex environments, including within a complete SARS-CoV-2 viral envelope simulation, which contains 305 million atoms and shows strong scaling on ORNL Summit using NAMD. We present several novel scientific discoveries, including the elucidation of the spike’s full glycan shield, the role of spike glycans in modulating the infectivity of the virus, and the characterization of the flexible interactions between the spike and the human ACE2 receptor. We also demonstrate how AI can accelerate conformational sampling across different systems and pave the way for the future application of such methods to additional studies in SARS-CoV-2 and other molecular systems.
              Cover page: AI-driven multiscale simulations illuminate mechanisms of SARS-CoV-2 spike dynamicsCreative Commons 'BY-SA' version 4.0 license
              • Article
              • Peer Reviewed
              UCLA Previously Published Works (2016)
              Protein-truncating variants protective against human disease provide in vivo validation of therapeutic targets. Here we used targeted sequencing to conduct a search for protein-truncating variants conferring protection against inflammatory bowel disease exploiting knowledge of common variants associated with the same disease. Through replication genotyping and imputation we found that a predicted protein-truncating variant (rs36095412, p.R179X, genotyped in 11,148 ulcerative colitis patients and 295,446 controls, MAF=up to 0.78%) in RNF186, a single-exon ring finger E3 ligase with strong colonic expression, protects against ulcerative colitis (overall P=6.89 × 10(-7), odds ratio=0.30). We further demonstrate that the truncated protein exhibits reduced expression and altered subcellular localization, suggesting the protective mechanism may reside in the loss of an interaction or function via mislocalization and/or loss of an essential transmembrane domain.
                Cover page: A protein-truncating R179X variant in RNF186 confers protection against ulcerative colitis.Creative Commons 'BY' version 4.0 license
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