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Open Access Publications from the University of California

Scholarly Works (6 results)

  • Thesis
  • Peer Reviewed
UC Riverside Electronic Theses and Dissertations (2014)

There is a long history for differential equations to be utilized to model dynamic pro- cesses in many disciplines such as physics, engineering, computer science, Finance, Biology, etc.. Most original efforts have been devoted to simulating the dynamic process for given parame- ters that characterize the differential equations. In recent years, more and more attention has been given by scientists, especially statisticians who considered the problem inversely, that is, using the experimental data to recover the values of parameters that specifically describe the experimental process trajectory.

In this dissertation, we introduced a general Integro-ordinary differential equation that describes a reaction diffusion process for the tip growth of pollen tubes and proposed a constrained nonlinear mixed effects model for the dynamic response. Accordingly, we developed two estimation procedures to estimate this model, Constrained Method of Moments (CMM) and Constrained Restricted Maximum Likelihood (CREML). The advantages and disadvantages of the two procedures were investigated. Simulation studies and a real data analysis demonstrated that both estimation procedures could provide accurate estimates for the parameters.

As an extension, the parameter estimation for Integro-partial differential equation of multiple dimension would also be discussed.

    Cover page: Parameter Estimation in Differential Equation Based Models
    • Article
    • Peer Reviewed
    Technical Reports (2006)
    Given a sparse binary matrix A and a sparse query vector x, can we efficiently identify the large entries of the matrix-vector product Ax? This problem occurs in document comparison, spam filtering, network intrusion detection, information retrieval, as well as other areas. We present an exact deterministic algorithm that takes advantage of the sparseness of A and x. Although in the worst case, the query complexity is linear in the number of rows of A, the amortized query complexity for a sequence of several similar queries depends only logarithmically on the size of A when the non-zero entries of A and the queries are distributed uniformly.

    Pre-2018 CSE ID: CS2006-0866

      Cover page: Incremental Sparse Binary Vector Similarity Search in High-Dimensional Space
      • Article
      • Peer Reviewed
      UC Irvine Previously Published Works (2015)
      The Hippo pathway was discovered as a conserved tumour suppressor pathway restricting cell proliferation and apoptosis. However, the upstream signals that regulate the Hippo pathway in the context of organ size control and cancer prevention are largely unknown. Here, we report that glucose, the ubiquitous energy source used for ATP generation, regulates the Hippo pathway downstream effector YAP. We show that both the Hippo pathway and AMP-activated protein kinase (AMPK) were activated during glucose starvation, resulting in phosphorylation of YAP and contributing to its inactivation. We also identified glucose-transporter 3 (GLUT3) as a YAP-regulated gene involved in glucose metabolism. Together, these results demonstrate that glucose-mediated energy homeostasis is an upstream event involved in regulation of the Hippo pathway and, potentially, an oncogenic function of YAP in promoting glycolysis, thereby providing an exciting link between glucose metabolism and the Hippo pathway in tissue maintenance and cancer prevention.
        Cover page: AMPK modulates Hippo pathway activity to regulate energy homeostasis
        • Article
        • Peer Reviewed
        UC Riverside Previously Published Works (2017)
        Many tip-growing cells are capable of responding to guidance cues, during which cells precisely steer their growth toward the source of guidance signals. Though several players in signal perception have been identified, little is known about the downstream signaling that controls growth direction during guidance. Here, using combined modeling and experimental studies, we demonstrate that the growth guidance of Arabidopsis pollen tubes is regulated by the signaling network that controls tip growth. Tip-localized exocytosis plays a key role in this network by integrating guidance signals with the ROP1 Rho GTPase signaling and coordinating intracellular signaling with cell wall mechanics. This model reproduces the high robustness and responsiveness of pollen tube guidance and explains the connection between guidance efficiency and the parameters of the tip growth system. Hence, our findings establish an exocytosis-coordinated mechanism underlying the cellular pathfinding guided by signal gradients and the mechanistic linkage between tip growth and guidance.
          Cover page: Exocytosis-coordinated mechanisms for tip growth underlie pollen tube growth guidance
          • Article
          • Peer Reviewed
          UC Irvine Previously Published Works (2016)
          Long non-coding RNAs (lncRNAs) have emerged as critical regulators in various cellular processes. However, the potential involvement of lncRNAs in kinase signalling remains largely unknown. AMP-activated protein kinase (AMPK) acts as a critical sensor of cellular energy status. Here we show that the lncRNA NBR2 (neighbour of BRCA1 gene 2) is induced by the LKB1-AMPK pathway under energy stress. On energy stress, NBR2 in turn interacts with AMPK and promotes AMPK kinase activity, thus forming a feed-forward loop to potentiate AMPK activation during energy stress. Depletion of NBR2 attenuates energy-stress-induced AMPK activation, resulting in unchecked cell cycling, altered apoptosis/autophagy response, and increased tumour development in vivo. NBR2 is downregulated and its low expression correlates with poor clinical outcomes in some human cancers. Together, the results of our study uncover a mechanism coupling lncRNAs with metabolic stress response, and provides a broad framework to understand further the regulation of kinase signalling by lncRNAs.
            Cover page: LncRNA NBR2 engages a metabolic checkpoint by regulating AMPK under energy stress.
            • Article
            • Peer Reviewed
            UC Irvine Previously Published Works (2016)
            Long non-coding RNAs (lncRNAs) have emerged as critical regulators in various cellular processes. However, the potential involvement of lncRNAs in kinase signalling remains largely unknown. AMP-activated protein kinase (AMPK) acts as a critical sensor of cellular energy status. Here we show that the lncRNA NBR2 (neighbour of BRCA1 gene 2) is induced by the LKB1-AMPK pathway under energy stress. On energy stress, NBR2 in turn interacts with AMPK and promotes AMPK kinase activity, thus forming a feed-forward loop to potentiate AMPK activation during energy stress. Depletion of NBR2 attenuates energy-stress-induced AMPK activation, resulting in unchecked cell cycling, altered apoptosis/autophagy response, and increased tumour development in vivo. NBR2 is downregulated and its low expression correlates with poor clinical outcomes in some human cancers. Together, the results of our study uncover a mechanism coupling lncRNAs with metabolic stress response, and provides a broad framework to understand further the regulation of kinase signalling by lncRNAs.
              Cover page: LncRNA NBR2 engages a metabolic checkpoint by regulating AMPK under energy stressCreative Commons 'BY' version 4.0 license
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