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Open Access Publications from the University of California

Scholarly Works (13 results)

  • Article
SEMM Reports Series (2015)
    Cover page: Lyapunov stability and accuracy of direct integration algorithms in nonlinear dynamic problems and considering the strict positive real lemma
    • Thesis
    • Peer Reviewed
    UC Berkeley Electronic Theses and Dissertations (2016)

    The performance-based earthquake engineering (PBEE) approach, developed at the Pacific Earthquake Engineering Research (PEER) Center, aims to robustly decompose the performance assessment and design process into four logical stages that can be studied and resolved in a systematic and consistent manner. However, two key challenges are experienced in this approach, namely the accurate seismic structural analysis and the selection and modification of ground motions (GMs). This dissertation investigates these two challenges with application to reinforced concrete (RC) bridge systems.

    In nonlinear structural dynamics, the most accurate analytical simulation method is the nonlinear time history analysis (NTHA). It involves the use of different types of direct integration algorithms and nonlinear equation solvers where their stability performance and convergence behaviors are of great significance. Lyapunov stability theory, the most complete framework for stability analysis of dynamical systems, is introduced in this study. Based on this theory, a new nonlinear equation solver is developed and its convergence performance was theoretically formulated and verified by several examples. Stability is one of the most important properties of direct integration algorithms that must be considered for efficient and reliable NTHA simulations. Two Lyapunov-based approaches are proposed to perform stability analysis for nonlinear structural systems. The first approach transforms the stability analysis to a problem of existence, that can be solved via convex optimization. The second approach is specifically applicable to explicit algorithms for nonlinear single-degree of freedom and multi-degree of freedom systems considering strictly positive real lemma. In this approach, the stability analysis of the formulated nonlinear system is transformed to investigating the strictly positive realness of its corresponding transfer function matrix.

    Ground motion selection and modification (GMSM) procedures determine the necessary input excitations to the NTHA simulations of structures. Therefore, proper selection of the GMSM procedures is vital and an important prerequisite for the accurate and robust NTHA simulation and thus for the entire PBEE approach. Although many GMSM procedures are available, there is no consensus regarding a single accurate method and many studies focused on evaluating these procedures. In this dissertation, a framework for probabilistic evaluation of the GMSM procedures is developed in the context of a selected large earthquake scenario with bidirectional GM excitations.

    In urban societies, RC highway bridges, representing key components of the transportation infrastructure systems, play a significant role in transporting goods and people around natural terrains. Therefore, they are expected to sustain minor damage and maintain their functionality in the aftermath of major earthquakes, which commonly occur in California due to many active faults. Accurate seismic structural analysis of existing and newly designed RC highway bridges is fundamental to estimate their seismic demands. As such important lifeline structures, RC highway bridge systems are investigated as an application of the previously discussed theoretical developments proposed in this dissertation to address the two key challenges in the PEER PBEE approach.

      Cover page: Performance-Based Robust Nonlinear Seismic Analysis with Application to Reinforced Concrete Bridge Systems
      • Article
      • Peer Reviewed
      UC Davis Previously Published Works (2014)
      In order to improve the analytic quality of respiratory specimens collected from cattle for nucleic acid-based diagnosis, a study was undertaken to verify realtime PCR efficiency of specimens collected and stabilized on FTA Cards™, filter paper which is treated chemically. Nucleic acids collected using FTA Cards without the need for a cold-chain or special liquid media handling provided realtime PCR results consistent (96.8% agreement, kappa 0.923 [95% CI=0.89-0.96]) with the same specimens collected using traditional viral transport media and shipped on ice using the U.S. Department of Transportation mandated liquid handling requirements. Nucleic acid stabilization on FTA Cards was evaluated over a temperature range (-27 °C to +46 °C) for up to 14 days to mimic environmental conditions for diagnostic sample handling between collection and processing in a routine veterinary laboratory. No significant difference (P≥0.05) was observed in realtime PCR cycle threshold values over the temperature range and time storage conditions for Bovine Viral Diarrhea virus, Bovine Respiratory Syncytial virus, Bovine Coronavirus, and Bovine Herpesvirus I. The four viruses evaluated in the study are associated with Bovine Respiratory Disease Complex where improvements in ease and reliability of specimen collection and shipping would enhance the diagnostic quality of specimens collected in the field, and ultimately improve diagnostic efficiency.
        Cover page: Evaluation of Fast Technology Analysis (FTA) Cards as an improved method for specimen collection and shipment targeting viruses associated with Bovine Respiratory Disease Complex
        • Article
        • Peer Reviewed
        UC San Diego Previously Published Works (2014)

        Background

        Platelet-derived growth factor C (PDGF-C) has been reported to promote angiogenesis independently of vascular endothelial growth factor (VEGF), although its significance in postnatal angiogenesis in vivo remains poorly understood. VEGF has been employed as a major molecular tool to induce therapeutic angiogenesis. However, VEGF therapy is not very effective in models of cardiovascular diseases associated with diabetes, and the mechanisms of this phenomenon still remain to be elucidated.

        Methods

        We used a murine model of hind limb ischemia and of streptozotocin-induced diabetes.

        Results

        Expression of PDGF-C and its receptor PDGFR-α were markedly upregulated in ischemic limbs. Treatment with a neutralizing antibody against PDGF-C significantly impaired blood flow recovery and neovascularization after ischemia almost to the same extent as a VEGF-neutralizing antibody. Mice deficient in PDGF-C exhibited reduced blood flow recovery after ischemia compared with wild-type mice, confirming a strong proangiogenic activity of PDGF-C. Next, we injected an expression vector encoding PDGF-C into ischemic limbs. Blood flow recovery and neovascularization after ischemia were significantly improved in the groups treated with PDGF-C compared with controls. Attenuation of angiogenic responses to ischemia has been reported in patients with diabetes even after VEGF treatment, although a precise mechanism remains unknown. We hypothesized that PDGF-C might relate to the impaired angiogenesis of diabetes. We tested this hypothesis by inducing diabetes by intraperitoneal injection of streptozotocin. Expression levels of PDGF-C at baseline and after ischemia were significantly lower in limb tissues of diabetic mice than in those of control mice, whereas expression levels of other members of the PDGF family and VEGF were not changed or were even higher in diabetic mice. Introduction of VEGF complementary DNA expression plasmid vector into ischemic limbs did not improve blood flow recovery. However, these changes were effectively reversed by additional introduction of the PDGF-C complementary DNA plasmid vector.

        Conclusions

        These results indicate that downregulation of PDGF-C expression in limb tissues of diabetic mice contributes to impaired angiogenesis and suggest that introduction of PDGF-C might be a novel strategy for therapeutic angiogenesis, especially in the diabetic state.

        Clinical relevance

        Angiogenesis and arteriogenesis after ischemia are attenuated in most diabetic patients, although the precise mechanisms remain unclear. Platelet-derived growth factors (PDGFs) have a variety of functions on many cell types, and PDGF-C stimulates angiogenesis and revascularizes ischemic tissues. This study indicates the role for PDGF-C as a critical regulator of impaired angiogenesis of diabetes and suggests that PDGF-C might be a novel target for the treatment of ischemic cardiovascular diseases in diabetes.
          Cover page: Platelet-derived growth factor C promotes revascularization in ischemic limbs of diabetic mice
          • Article
          • Peer Reviewed
          UC San Francisco Previously Published Works (2018)
          Hypoxia-inducible factor 1α (HIF1α) is a key regulator of oxygen homeostasis, and its target genes mediate adaptive, protective, and pathological processes. The role of HIF1α in neuronal survival is controversial and the brain maturation stage is important in determining its function in brain ischemia or hypoxia-ischemia (HI). In this study, we used neuron-specific HIF1α knockout mice at postnatal day 9 (P9), and immature cortical neurons (days 7-8 in vitro) treated with the HIF1α inhibitor 2-methoxyestradiol (2ME2) or stabilizer dimethyloxalylglycine (DMOG), to examine the function of neuronal HIF1α in neonatal HI in vivo (Vannucci model) and in vitro (oxygen glucose deprivation, OGD). Inhibition of HIF1α with 2ME2 in primary neurons or deletion of neuronal HIF1α in P9 mice increased both necrotic and apoptotic cell death following HI, as evaluated by the protein levels of 145/150-kDa and 120-kDa spectrin breakdown products 24 h after HI. DMOG attenuated neuronal death right after OGD. Acute pharmacological manipulation of HIF1α synchronously regulated the expression of its targets, vascular endothelial growth factor (VEGF) and erythropoietin (Epo), in the same manner. The in vivo findings agree with our previous data using the same HIF1α-deficient mice at an earlier age. This study confirms the role of neuronal HIF1α signaling in the endogenous protective responses following HI in the developing brain.
            Cover page: HIF1α Signaling in the Endogenous Protective Responses after Neonatal Brain Hypoxia-Ischemia
            • Article
            • Peer Reviewed
            UCLA Previously Published Works (2019)
            Inferior charge transport in insulating and bulk discharge products is one of the main factors resulting in poor cycling stability of lithium-oxygen batteries with high overpotential and large capacity decay. Here we report a two-step oxygen reduction approach by pre-depositing a potassium carbonate layer on the cathode surface in a potassium-oxygen battery to direct the growth of defective film-like discharge products in the successive cycling of lithium-oxygen batteries. The formation of defective film with improved charge transport and large contact area with a catalyst plays a critical role in the facile decomposition of discharge products and the sustained stability of the battery. Multistaged discharge constructing lithium peroxide-based heterostructure with band discontinuities and a relatively low lithium diffusion barrier may be responsible for the growth of defective film-like discharge products. This strategy offers a promising route for future development of cathode catalysts that can be used to extend the cycling life of lithium-oxygen batteries.
              Cover page: Multistaged discharge constructing heterostructure with enhanced solid-solution behavior for long-life lithium-oxygen batteries
              • Article
              • Peer Reviewed
              UC San Francisco Previously Published Works (2018)
              The N-methyl-d-aspartate-type glutamate receptor (NMDAR)-associated multiprotein complexes are indispensable for synaptic plasticity and cognitive functions. While purification and proteomic analyses of these signaling complexes have been performed in adult rodent and human brain, much less is known about the protein composition of NMDAR complexes in the developing brain and their modifications by neonatal hypoxic-ischemic (HI) brain injury. In this study, the postsynaptic density proteins were prepared from postnatal day 9 naïve, sham-operated and HI-injured mouse cortex. The GluN2B-containing NMDAR complexes were purified by immunoprecipitation with a mouse GluN2B antibody and subjected to mass spectrometry analysis for determination of the GluN2B binding partners. A total of 71 proteins of different functional categories were identified from the naïve animals as native GluN2B-interacting partners in the developing mouse brain. Neonatal HI reshaped the postsynaptic GluN2B interactome by recruiting new proteins, including multiple kinases, into the complexes; and modifying the existing associations within 1h of reperfusion. The early responses of postsynaptic NMDAR complexes and their related signaling networks may contribute to molecular processes leading to cell survival or death, brain damage and/or neurological disorders in term infants with neonatal encephalopathy.
                Cover page: Hypoxia-ischemia modifies postsynaptic GluN2B-containing NMDA receptor complexes in the neonatal mouse brain
                • Article
                • Peer Reviewed
                UC Berkeley Previously Published Works (2023)
                The extraordinary work hardening ability and fracture toughness of the face-centered cubic (fcc) high-entropy alloys render them ideal candidates for many structural applications. Here, the deformation and failure mechanisms of an equiatomic CrCoNi medium-entropyalloy (MEA) were investigated by powerful laser-driven shock experiments. Multiscale characterization demonstrates that profuse planar defects including stacking faults, nanotwins, and hexagonal nanolamella were generated during shock compression, forming a three-dimensional network. During shock release, the MEA fractured by strong tensile deformation and numerous voids was observed in the vicinity of the fracture plane. High defect populations, nanorecrystallization, and amorphization were found adjacent to these areas of localized deformation. Molecular dynamics simulations corroborate the experimental results and suggest that deformation-induced defects formed before void nucleation govern the geometry of void growth and delay their coalescence. Our results indicate that the CrCoNi-based alloys are impact resistant, damage tolerant, and potentially suitable in applications under extreme conditions.
                  Cover page: Deformation and failure of the CrCoNi medium-entropy alloy subjected to extreme shock loading
                  • Article
                  • Peer Reviewed
                  UC Irvine Previously Published Works (2020)
                  High-resolution imaging techniques capable of detecting identifiable endogenous fluorophores in the eye along with genetic testing will dramatically improve diagnostic capabilities in the ophthalmology clinic and accelerate the development of new treatments for blinding diseases. Two-photon excitation (TPE)-based imaging overcomes the filtering of ultraviolet light by the lens of the human eye and thus can be utilized to discover defects in vitamin A metabolism during the regeneration of the visual pigments required for the detection of light. Combining TPE with fluorescence lifetime imaging (FLIM) and spectral analyses offers the potential of detecting diseases of the retina at earlier stages before irreversible structural damage has occurred. The main barriers to realizing the benefits of TPE for imaging the human retina arise from concerns about the high light exposure typically needed for informative TPE imaging and the requirement to correlate the ensuing data with different states of health and disease. To overcome these hurdles, we improved TPE efficiency by controlling temporal properties of the excitation light and employed phasor analyses to FLIM and spectral data in mouse models of retinal diseases. Modeling of retinal photodamage revealed that plasma-mediated effects do not play a role and that melanin-related thermal effects are mitigated by reducing pulse repetition frequency. By using noninvasive TPE imaging we identified molecular components of individual granules in the retinal pigment epithelium and present their analytical characteristics.
                    Cover page: Noninvasive two-photon optical biopsy of retinal fluorophores
                    • Article
                    • Peer Reviewed
                    UC Berkeley Previously Published Works (2024)
                    Transition-metal-catalyzed carbene insertion reactions of a nitrogen-hydrogen bond have emerged as robust and versatile methods for the construction of C-N bonds. While significant progress of homogeneous catalytic metal carbene N-H insertions has been achieved, the control of chemoselectivity in the field remains challenging due to the high electrophilicity of the metal carbene intermediates. Herein, we present an efficient strategy for the synthesis of a rhodium single-atom-site catalyst (Rh-SA) that incorporates a Rh atom surrounded by three nitrogen atoms and one phosphorus atom doped in a carbon support. This Rh-SA catalyst, with a catalyst loading of only 0.15 mol %, exhibited exceptional catalytic performance for heterogeneous carbene insertion with various anilines and heteroaryl amines in combination with diazo esters. Importantly, the heterogeneous catalyst selectively transformed aniline derivatives bearing multiple nucleophilic moieties into single N-H insertion isomers, while the popular homogeneous Rh2(OAc)4 catalyst produced a mixture of overfunctionalized side products. Additionally, similar selectivities for N-H bond insertion with a set of stereoelectronically diverse diazo esters were obtained, highlighting the general applicability of this heterogeneous catalysis approach. On the basis of density functional theory calculations, the observed selectivity of the Rh-SA catalyst was attributed to the insertion barriers and the accelerated proton transfer assisted by the phosphorus atom in the support. Overall, this investigation of heterogeneous metal-catalyzed carbene insertion underscores the potential of single-atom-site catalysis as a powerful and complementary tool in organic synthesis.
                      Cover page: Heterogeneous Rhodium Single-Atom-Site Catalyst Enables Chemoselective Carbene N–H Bond Insertion
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