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Open Access Publications from the University of California

Scholarly Works (38 results)

  • Thesis
  • Peer Reviewed
UCLA Electronic Theses and Dissertations (2017)

Over the past decade there have been considerable research efforts directed at controlling spin dynamics in nanomagnets. Spin dynamics generally covers two regimes, one is large amplitude motion associated with equilibrium magnetization state change with storage media applications that use parallel and antiparallel magnetization configurations to represent “0” and “1” states of memory bits. The other type is small amplitude oscillation, wherein spin precesses around its equilibrium state within a small cone angle. This behavior is generally used to design radio frequency(RF) devices. One of the approaches to controlling spin dynamics in nanomagnets is to use strain-mediated multiferroic heterostructures that consist of a nanomagnet deposited on a piezoelectric substrate wherein the magnetic state in the nanomagnet can be altered by electric field induced piezo-strain in piezoelectric substrates. Three innovative applications of nanomagnets via this piezo-driven method for both types of spin dynamics are presented in this dissertation: perpendicular magnetic tunnel junctions (pMTJ) in magnetoresistive random access memory(MRAM), surface acoustic wave(SAW) driven spin wave resonance (SWR) devices for RF transducers design, and multiferroic multiband tunable filters. Finite element analysis (FEA) simulation results in this dissertation demonstrated a 180-degree magnetization switch in the free layer of a pMTJ in response to an in-plane effective magnetic field induced by strain. Experimental work on thin film characterization is discussed that provides PMA material candidates for future pMTJ designs. A longer distance travelling spin wave (up to 1200um) in a SAW driven SWR device was obtained through magnetoelastic coupling. Three factors that affect energy transmission rate in this device have been investigated, which are film size, SAW wave vector k and spin pumping effect. Furthermore, a new type of E-field tuning multiband filter based on multiferroic heterostructure was proposed in this dissertation, which exhibits multiple absorption peaks and a large E-field tunability resulting from the acoustic and optical modes of spin interaction in magnetic layered structures. This work provides valuable insights into spin dynamics in nanomagnets. It opens up a new design space for next generation spintronic devices.

    Cover page: Nanomagnet Applications in Multiferroic Heterostructures
    • Article
    • Peer Reviewed
    UC Berkeley Previously Published Works (2017)
    In this paper, we propose a cost-effective localization solution for land vehicles, which can simultaneously adapt to the uncertain noise of inertial sensors and bridge Global Positioning System (GPS) outages. First, three Unscented Kalman filters (UKFs) with different noise covariances are introduced into the framework of Interacting Multiple Model (IMM) algorithm to form the proposed IMM-based UKF, termed as IMM-UKF. The IMM algorithm can provide a soft switching among the three UKFs and therefore adapt to different noise characteristics. Further, two IMM-UKFs are executed in parallel when GPS is available. One fuses the information of low-cost GPS, in-vehicle sensors, and micro electromechanical system (MEMS)-based reduced inertial sensor systems (RISS), while the other fuses only in-vehicle sensors and MEMS-RISS. The differences between the state vectors of the two IMM-UKFs are considered as training data of a Grey Neural Network (GNN) module, which is known for its high prediction accuracy with a limited amount of samples. The GNN module can predict and compensate position errors when GPS signals are blocked. To verify the feasibility and effectiveness of the proposed solution, road-test experiments with various driving scenarios were performed. The experimental results indicate that the proposed solution outperforms all the compared methods.
      Cover page: A Cost-Effective Vehicle Localization Solution Using an Interacting Multiple Model−Unscented Kalman Filters (IMM-UKF) Algorithm and Grey Neural Network
      • Article
      • Peer Reviewed
      UC Irvine Previously Published Works (2015)
      Signal transductions are the basis of biological activities in all living organisms. Studying the signaling pathways, especially under physiological conditions, has become one of the most important facets of modern biological research. During the last decade, MS has been used extensively in biological research and is proven to be effective in addressing important biological questions. Here, we review the current progress in the understanding of signaling networks using MS approaches. We will focus on studies of protein-protein interactions that use affinity purification followed by MS approach. We discuss obstacles to affinity purification, data processing, functional validation, and identification of transient interactions and provide potential solutions for pathway-specific proteomics analysis, which we hope one day will lead to a comprehensive understanding of signaling networks in humans.
        Cover page: From pathways to networks: Connecting dots by establishing protein–protein interaction networks in signaling pathways using affinity purification and mass spectrometry
        • Article
        • Peer Reviewed
        UC Berkeley Previously Published Works (2006)

        This paper presents a simulation of a biological olfactory neural system with a KIII set, which is a high-dimensional chaotic neural network. The KIII set differs from conventional artificial neural networks by use of chaotic attractors for memory locations that are accessed by, chaotic trajectories. It was designed to simulate the patterns of action potentials and EEG waveforms observed in electrophysiological experiments, and has proved its utility as a model for biological intelligence in pattern classification. An application to recognition of handwritten numerals is presented here, in which the classification performance of the KIII network under different noise levels was investigated.

          Cover page: A study on a Bionic Pattern Classifier Based on Olfactory Neural System
          • Article
          • Peer Reviewed
          UC Irvine Previously Published Works (2014)
          The Hippo pathway, which is conserved from Drosophila to mammals, has been recognized as a tumor suppressor signaling pathway governing cell proliferation and apoptosis, two key events involved in organ size control and tumorigenesis. Although several upstream regulators, the conserved kinase cascade and key downstream effectors including nuclear transcriptional factors have been defined, the global organization of this signaling pathway is not been fully understood. Thus, we conducted a proteomic analysis of human Hippo pathway, which revealed the involvement of an extensive protein-protein interaction network in this pathway. The mass spectrometry data were deposited to ProteomeXchange with identifier PXD000415. Our data suggest that 550 interactions within 343 unique protein components constitute the central protein-protein interaction landscape of human Hippo pathway. Our study provides a glimpse into the global organization of Hippo pathway, reveals previously unknown interactions within this pathway, and uncovers new potential components involved in the regulation of this pathway. Understanding these interactions will help us further dissect the Hippo signaling-pathway and extend our knowledge of organ size control.
            Cover page: Defining the Protein–Protein Interaction Network of the Human Hippo Pathway*
            • Article
            • Peer Reviewed
            UC Davis Previously Published Works (2016)
            Substrate specificity studies of human FUT8 using 77 structurally-defined N-glycans as acceptors showed a strict requirement towards the α1,3-mannose branch, but a great promiscuity towards the α1,6-mannose branch. Accordingly, a chemoenzymatic strategy was developed for the efficient synthesis of core-fucosylated asymmetric N-glycans.
              Cover page: Substrate specificity of FUT8 and chemoenzymatic synthesis of core-fucosylated asymmetric N -glycans
              • Article
              • Peer Reviewed
              UC Irvine Previously Published Works (2022)
              Identification of protein interactors is fundamental to understanding their functions. Here, we describe a modified protocol for tandem affinity purification coupled with mass spectrometry (TAP/MS), which includes two-step purification. We detail the S-, 2×FLAG-, and Streptavidin-Binding Peptide (SBP)- tandem tags (SFB-tag) system for protein purification. This protocol can be used to identify protein interactors and establish a high-confidence protein-protein interaction network based on computational models. This is particularly useful for identifying bona fide interacting proteins for subsequent functional studies. For complete details on the use and execution of this protocol, please refer to Bian et al. (2021).
                Cover page: Protocol for establishing a protein-protein interaction network using tandem affinity purification followed by mass spectrometry in mammalian cells
                • Article
                • Peer Reviewed
                UC Irvine Previously Published Works (2022)
                Dysregulation of the Notch-RBPJ (recombination signal-binding protein of immunoglobulin kappa J region) signaling pathway has been found associated with various human diseases including cancers; however, precisely how this key signaling pathway is fine-tuned via its interactors and modifications is still largely unknown. In this study, using a proteomic approach, we identified F-box only protein 42 (FBXO42) as a previously unidentified RBPJ interactor. FBXO42 promotes RBPJ polyubiquitination on lysine-175 via lysine-63 linkage, which enhances the association of RBPJ with chromatin remodeling complexes and induces a global chromatin relaxation. Genetically depleting FBXO42 or pharmacologically targeting its E3 ligase activity attenuates the Notch signaling-related leukemia development in vivo. Together, our findings not only revealed FBXO42 as a critical regulator of the Notch pathway by modulating RBPJ-dependent global chromatin landscape changes but also provided insights into the therapeutic intervention of the Notch pathway for leukemia treatment.
                  Cover page: FBXO42 facilitates Notch signaling activation and global chromatin relaxation by promoting K63-linked polyubiquitination of RBPJ
                  • Article
                  • Peer Reviewed
                  UCLA Previously Published Works (2013)
                  Arabidopsis thaliana cryptochrome 2 (CRY2) mediates light control of flowering time. CIB1 (CRY2-interacting bHLH 1) specifically interacts with CRY2 in response to blue light to activate the transcription of FT (Flowering Locus T). In vitro, CIB1 binds to the canonical E-box (CACGTG, also referred to as G-box) with much higher affinity than its interaction with non-canonical E-box (CANNTG) DNA sequences. However, in vivo, CIB1 binds to the chromatin region of the FT promoter, which only contains the non-canonical E-box sequences. Here, we show that CRY2 also interacts with at least CIB5, in response to blue light, but not in darkness or in response to other wavelengths of light. Our genetic analysis demonstrates that CIB1, CIB2, CIB4, and CIB5 act redundantly to activate the transcription of FT and that they are positive regulators of CRY2 mediated flowering. More importantly, CIB1 and other CIBs proteins form heterodimers, and some of the heterodimers have a higher binding affinity than the CIB homodimers to the non-canonical E-box in the in vitro DNA-binding assays. This result explains why in vitro CIB1 and other CIBs bind to the canonical E-box (G-box) with a higher affinity, whereas they are all associated with the non-canonical E-boxes at the FT promoter in vivo. Consistent with the hypothesis that different CIB proteins play similar roles in the CRY2-midiated blue light signaling, the expression of CIB proteins is regulated specifically by blue light. Our study demonstrates that CIBs function redundantly in regulating CRY2-dependent flowering, and that different CIBs form heterodimers to interact with the non-canonical E-box DNA in vivo.
                    Cover page: Multiple bHLH Proteins form Heterodimers to Mediate CRY2-Dependent Regulation of Flowering-Time in Arabidopsis
                    • Article
                    • Peer Reviewed
                    UC San Diego Previously Published Works (2018)

                    Introduction

                    Superficial siderosis is a rare, neurodegenerative disease caused by toxic accumulation of hemosiderin on the surface of the brain and the spinal cord, most commonly from chronic subarachnoid hemorrhage.

                    Aims

                    The aim of this study was to assess the clinical and radiological outcomes of superficial siderosis patients using deferiprone, a cell permeant iron chelator. Subjects obtained pre- and post-treatment brain MRIs and weekly laboratory tests. Osirix software was used to develop a method of quantifying hemosiderin deposition. Three-dimensional whole brain images of gradient echo images were rendered and compared by dividing the mean T2 hyperintensity to the maximal cerebrospinal fluid signal.

                    Results

                    A total of 38 subjects completed the study, of which clinical and radiological data were available for 30. The average age was 64 years (range 37-86), 53% were male, 94% were white. Nineteen subjects (63%) reported either no progression of disease or an improvement in at least one neurological domain, with 40% of patients reporting a stabilization in hearing function and 30% reporting stable or improved coordination and walking. By MRI, there was an overall mean increase in T2 hyperintensity of the whole brain of 1%-13% over the 2-year time period in half of patients, indicating a reduction hemosiderosis. There were no cases of agranulocytosis, and declines of white blood cells counts and neutrophils averaged <10%. Fatigue was the most common side effect.

                    Conclusion

                    This is the first long-term prospective study of superficial siderosis on the iron chelator, deferiprone. MRI quantification of hemosiderin appears to demonstrate a measurable reduction in half of patients and this correlated with a stabilized or improving disease course. A future placebo-controlled trial is necessary to determine whether deferiprone is an effective therapy for superficial siderosis.
                      Cover page: Two‐year observational study of deferiprone in superficial siderosis
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