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Open Access Publications from the University of California

Scholarly Works (2 results)

  • Thesis
  • Peer Reviewed
UC Merced Electronic Theses and Dissertations (2020)

We report the development of a modular multiphysics computational framework for performing continuum simulations of low-temperature plasmas. The primary goal of this work is to discuss the features of this framework along with representative results provided as examples for a range of operating conditions and geometries. This includes plasma and plasma-dielectric systems operating in direct current, radio frequency, and microwave regimes from pressures as low as 100 mTorr to atmospheric pressure. The code has several useful features including the ability to run massively parallel simulations using arbitrary geometries, structured/unstructured meshes, choice of various models such as drift-diffusion/full-momentum at runtime, and species-dependent timesteps to name a few. The verification/validation studies presented include comparison with previously published continuum and kinetic simulations with experiments. The performance of the code is also discussed with serial and distributed memory parallel runs with scaling demonstrated up to 512 cores. The design and implementation of the code can be expected to play an important role in computational studies of low-temperature plasmas in academic and industry. As part of the dissertation research, the framework was also used to study direct current and microwave microplasmas with the goal of quantifying the accuracy of continuum simulations in comparison with fundamental kinetic simulations. These results will enable decision-making in the context of choice of simulation strategy while modeling various microplasma devices.

    Cover page: Computational Modeling of Low Temperature Microplasmas and ApplicationsCreative Commons 'BY-NC-ND' version 4.0 license
    • Article
    • Peer Reviewed
    UCLA Previously Published Works (2021)

    Background & aims

    Alterations in microRNA (miRNA) and in the intestinal barrier are putative risk factors for irritable bowel syndrome (IBS). We aimed to identify differentially expressed colonic mucosal miRNAs, their targets in IBS compared to healthy controls (HCs), and putative downstream pathways.

    Methods

    Twenty-nine IBS patients (15 IBS with constipation [IBS-C], 14 IBS with diarrhea [IBS-D]), and 15 age-matched HCs underwent sigmoidoscopy with biopsies. A nCounter array was used to assess biopsy specimen-associated miRNA levels. A false discovery rate (FDR) < 10% was considered significant. Real-time polymerase chain reaction (PCR) was used to validate differentially expressed genes. To assess barrier function, trans-epithelial electrical resistance (TEER) and dextran flux assays were performed on Caco-2 intestinal epithelial cells that were transfected with miRNA-inhibitors or control inhibitors. Protein expression of barrier function associated genes was confirmed using western blots.

    Results

    Four out of 247 miRNAs tested were differentially expressed in IBS compared to HCs (FDR < 10%). Real-time PCR validation suggested decreased levels of miR-219a-5p and miR-338-3p in IBS (P = .026 and P = .004), and IBS-C (P = .02 and P = .06) vs. HCs as the strongest associations. Inhibition of miR-219a-5p resulted in altered expression of proteasome/barrier function genes. Functionally, miR-219a-5p inhibition enhanced the permeability of intestinal epithelial cells as TEER was reduced (25-50%, P < .05) and dextran flux was increased (P < .01). Additionally, inhibition of miR-338-3p in cells caused alterations in the mitogen-activated protein kinase (MAPK) signaling pathway genes.

    Conclusion

    Two microRNAs that potentially affect permeability and visceral nociception were identified to be altered in IBS patients. MiR-219a-5p and miR-338-3p potentially alter barrier function and visceral hypersensitivity via neuronal and MAPK signaling and could be therapeutic targets in IBS.
      Cover page: The Colonic Mucosal MicroRNAs, MicroRNA-219a-5p, and MicroRNA-338-3p Are Downregulated in Irritable Bowel Syndrome and Are Associated With Barrier Function and MAPK Signaling
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