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Open Access Publications from the University of California

Scholarly Works (7 results)

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

Tumor grading is an important prognostic parameter for renal cell carcinoma (RCC). However, current grading schemes require an invasive surgical procedure, putting patients at risks including increased risk of hemorrhage, infection, renal failure, or death. Furthermore, low grade RCC is indolent with low mortality risk and may not require treatment. Therefore, a pre-operative and non-invasive assessment of malignancy grade may be beneficial and facilitate optimal timing of treatment. In recent years, deep learning-based image analysis has gained wide popularity in cancer prognosis and prediction. The goal of this study is to investigate the feasibility and performance of a deep-learning-based model for clear cell RCC grading prediction from contrast-enhance computed tomography (CECT). After institutional review board approval, an institutional pathology database was queried for all renal biopsies between December 2002 and October 2018. All included patients received a CT with a non-contrast and at least one post-contrast series. All patients have Fuhrman grade confirmation from surgical pathology, with CT scan prior to the procedure. Tumors were manually annotated by a radiologist on either the corticomedullary or nephrographic phase CECT. Rectangular regions of interest (ROI) were drawn on each slice throughout the tumor and used as inputs to the Deep CNN ResNet50. A binary label of low grade or high grade was assigned to each patient. Sensitivity, specificity, accuracy, and AUC were calculated based on a five-fold cross-validation. Preliminary results from a small subset of data suggests that a deep learning model can be used to predict clear cell RCC grading based on CT imaging prior to surgical procedures.

    Cover page: Clear Cell Renal Cell Carcinoma: Deep Learning-Based Prediction of Tumor Grade from Contrast-Enhanced CT
    • Article
    • Peer Reviewed
    UC Berkeley Previously Published Works (2023)
    A main challenge in Heat-Assisted Magnetic Recording technology is the build-up of contaminants called smear on the near field transducer. In this paper, we investigate the role of optical forces originating from the electric field gradient in the formation of smear. First, based on suitable theoretical approximations, we compare this force with air drag and the thermophoretic force in the head-disk interface for two smear nanoparticle shapes. Then, we evaluate the force fields sensitivity to the relevant parameter space. We find that the smear nanoparticles refractive index, shape, and volume significantly impact the optical force. Further, our simulations reveal that the interface conditions, such as spacing and the presence of other contaminants, also influence the magnitude of the force.
      Cover page: Optical forces in heat-assisted magnetic recording head-disk interface.
      • Article
      • Peer Reviewed
      UC Riverside Previously Published Works (2018)
      Phased, secondary siRNAs (phasiRNAs) represent a class of small RNAs in plants generated via distinct biogenesis pathways, predominantly dependent on the activity of 22-nt miRNAs. Most 22-nt miRNAs are processed by DCL1 from miRNA precursors containing an asymmetric bulge, yielding a 22/21-nt miRNA/miRNA* duplex. Here we show that miR1510, a soybean miRNA capable of triggering phasiRNA production from numerous nucleotide-binding leucine-rich repeat (NB-LRRs), previously described as 21 nt in its mature form, primarily accumulates as a 22-nt isoform via monouridylation. We demonstrate that, in Arabidopsis, this uridylation is performed by HESO1. Biochemical experiments showed that the 3' terminus of miR1510 is only partially 2'-O-methylated because of the terminal mispairing in the miR1510/miR1510* duplex that inhibits HEN1 activity in soybean. miR1510 emerged in the Phaseoleae ∼41-42 million years ago with a conserved precursor structure yielding a 22-nt monouridylated form, yet a variant in mung bean is processed directly in a 22-nt mature form. This analysis of miR1510 yields two observations: (i) plants can utilize postprocessing modification to generate abundant 22-nt miRNA isoforms to more efficiently regulate target mRNA abundances; and (ii) comparative analysis demonstrates an example of selective optimization of precursor processing of a young plant miRNA.
        Cover page: Biogenesis of a 22-nt microRNA in Phaseoleae species by precursor-programmed uridylation
        • Article
        • Peer Reviewed
        Advanced Light Source (2017)
        Most van der Waals crystals present highly anisotropic optical responses due to their strong in-plane covalent bonding and weak out-of-plane interactions. However, the determination of the polarization-dependent dielectric constants of van der Waals crystals remains a nontrivial task, since the size and dimension of the samples are often below or close to the diffraction limit of the probe light. In this work, we apply an optical nano-imaging technique to determine the anisotropic dielectric constants in representative van der Waals crystals. Through the study of both ordinary and extraordinary waveguide modes in real space, we are able to quantitatively determine the full dielectric tensors of nanometer-thin molybdenum disulfide and hexagonal boron nitride microcrystals, the most-promising van der Waals semiconductor and dielectric. Unlike traditional reflection-based methods, our measurements are reliable below the length scale of the free-space wavelength and reveal a universal route for characterizing low-dimensional crystals with high anisotropies.
          Cover page: Probing optical anisotropy of nanometer-thin van der waals microcrystals by near-field imaging
          • Article
          • Peer Reviewed
          Advanced Light Source (2020)
          Modern scattering-type scanning near-field optical microscopy (s-SNOM) has become an indispensable tool in material research. However, as the s-SNOM technique marches into the far-infrared (IR) and terahertz (THz) regimes, emerging experiments sometimes produce puzzling results. For example, "anomalies" in the near-field optical contrast have been widely reported. In this Letter, we systematically investigate a series of extreme subwavelength metallic nanostructures via s-SNOM near-field imaging in the GHz to THz frequency range. We find that the near-field material contrast is greatly impacted by the lateral size of the nanostructure, while the spatial resolution is practically independent of it. The contrast is also strongly affected by the connectivity of the metallic structures to a larger metallic "ground plane". The observed effect can be largely explained by a quasi-electrostatic analysis. We also compare the THz s-SNOM results to those of the mid-IR regime, where the size-dependence becomes significant only for smaller structures. Our results reveal that the quantitative analysis of the near-field optical material contrasts in the long-wavelength regime requires a careful assessment of the size and configuration of metallic (optically conductive) structures.
            • Article
            • Peer Reviewed
            UC San Francisco Previously Published Works (2014)
            The blood-brain barrier (BBB) remains a formidable obstacle in medicine, preventing efficient penetration of chemotherapeutic and diagnostic agents to malignant gliomas. Here, a transactivator of transcription (TAT) peptide-modified gold nanoparticle platform (TAT-Au NP) with a 5 nm core size is demonstrated to be capable of crossing the BBB efficiently and delivering cargoes such as the anticancer drug doxorubicin (Dox) and Gd(3+) contrast agents to brain tumor tissues. Treatment of mice bearing intracranial glioma xenografts with pH-sensitive Dox-conjugated TAT-Au NPs via a single intravenous administration leads to significant survival benefit when compared to the free Dox. Furthermore, it is demonstrated that TAT-Au NPs are capable of delivering Gd(3+) chelates for enhanced brain tumor imaging with a prolonged retention time of Gd(3+) when compared to the free Gd(3+) chelates. Collectively, these results show promising applications of the TAT-Au NPs for enhanced malignant brain tumor therapy and non-invasive imaging.
              Cover page: Blood-brain barrier permeable gold nanoparticles: an efficient delivery platform for enhanced malignant glioma therapy and imaging.
              • Article
              • Peer Reviewed
              UC Davis Previously Published Works (2018)
              We here describe a novel α-conopeptide, Eu1.6 from Conus eburneus, which exhibits strong anti-nociceptive activity by an unexpected mechanism of action. Unlike other α-conopeptides that largely target nicotinic acetylcholine receptors (nAChRs), Eu1.6 displayed only weak inhibitory activity at the α3β4 and α7 nAChR subtypes and TTX-resistant sodium channels, and no activity at TTX-sensitive sodium channels in rat dorsal root ganglion (DRG) neurons, or opiate receptors, VR1, KCNQ1, L- and T-type calcium channels expressed in HEK293 cells. However, Eu1.6 inhibited high voltage-activated N-type calcium channel currents in isolated mouse DRG neurons which was independent of GABAB receptor activation. In HEK293 cells expressing CaV2.2 channels alone, Eu1.6 reversibly inhibited depolarization-activated Ba2+ currents in a voltage- and state-dependent manner. Inhibition of CaV2.2 by Eu1.6 was concentration-dependent (IC50 ~1 nM). Significantly, systemic administration of Eu1.6 at doses of 2.5-5.0 μg/kg exhibited potent analgesic activities in rat partial sciatic nerve injury and chronic constriction injury pain models. Furthermore, Eu1.6 had no significant side-effect on spontaneous locomotor activity, cardiac and respiratory function, and drug dependence in mice. These findings suggest α-conopeptide Eu1.6 is a potent analgesic for the treatment of neuropathic and chronic pain and opens a novel option for future analgesic drug design.
                Cover page: A novel α-conopeptide Eu1.6 inhibits N-type (CaV2.2) calcium channels and exhibits potent analgesic activity.
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