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Open Access Publications from the University of California

Scholarly Works (40 results)

  • Thesis
  • Peer Reviewed
UCLA Electronic Theses and Dissertations (2022)

To build up large-scale quantum systems, four challenges in the existing hardware realization need to be addressed: (1) I/O management, (2) latency and phase matching in a large system footprint, (3) the heat and power dissipation as the qubit count scales up, and (4) transmission of delicate quantum information. To minimize these issues, there are efforts using different architectures, such as CryoCMOS, 3D stacking, and Josephson-Junction-based (JJ-based) approach. Superconducting Silicon Interconnect Fabric (Superconducting-IF) is yet another promising approach, which is an advanced fine-pitch and wafer-scale cryogenic packaging platform. The proposed architecture, which aims to co-integrate superconducting qubit control/readout with qubits in a compact way, and the demonstration of the Superconducting-IF are detailed. The key enabler of Superconducting-IF is the low-temperature assembly technology, the Au interlayer bonding method, which is demonstrated to be fine-pitch (≤ 10 um), mechanically robust (> 30 MPa), electrically reliable, and quantum-compatible (< 150℃). The Au interlayer with Nb superconducting interconnects has a transition temperature at 9 K and is demonstrated to be a low-temperature-compatible process having a high critical current for integrated superconducting processing applications. On the Superconducting-IF platform, heterogeneity and flexibility are both demonstrated regarding the die sizes, the inter-die spacing, and the configuration. For future transmission of delicate quantum information, Superconducting RF optimization, including insertion loss and crosstalk, is implemented. All the simulated and measured results on short superconducting links (≤ 500 um) with 2 and 5 um line/space are far below the quantum limitation, meaning the superconducting interconnects are suitable to carry future inter-dielet delicate quantum communication. This dissertation achieves the following intellectual contributions: (1) the first combination of heterogeneous integration and advanced packaging with quantum applications, (2) the first proposal of the architecture of integrated system-on-wafer quantum hardware, (3) the first demonstration of the Au interlayer bonding to be fine-I/O pitch, mechanically robust, electrically reliable, and quantum compatible, and (4) the first achievement of low-loss, low-crosstalk, and 20 GHz-broadband RF capability on superconducting short links through advanced packaging. To sum up, it is promising to use the Superconducting-IF for future large-scale quantum systems to realize the full strength of quantum computing.

    Cover page: Niobium-based Superconducting Silicon Interconnect Fabric for Future Cryogenic Applications
    • Article
    • Peer Reviewed
    UC Davis Previously Published Works (2014)
    Amphiphilic gold nanoparticles (amph-NPs), composed of gold cores surrounded by an amphiphilic mixed organic ligand shell, are capable of embedding within and traversing lipid membranes. Here we describe a strategy using crosslink-stabilized lipid nanocapsules (NCs) as carriers to transport such membrane-penetrating particles into tumor cells and promote their transfer to intracellular membranes for enhanced radiotherapy of cancer. We synthesized and characterized interbilayer-crosslinked multilamellar lipid vesicles (ICMVs) carrying amph-NPs embedded in the capsule walls, forming Au-NCs. Confocal and electron microscopies revealed that the intracellular distribution of amph-NPs within melanoma and breast tumor cells following uptake of free particles vs Au-NCs was quite distinct and that amph-NPs initially delivered into endosomes by Au-NCs transferred over a period of hours to intracellular membranes through tumor cells, with greater intracellular spread in melanoma cells than breast carcinoma cells. Clonogenic assays revealed that Au-NCs enhanced radiotherapeutic killing of melanoma cells. Thus, multilamellar lipid capsules may serve as an effective carrier to deliver amphiphilic gold nanoparticles to tumors, where the membrane-penetrating properties of these materials can significantly enhance the efficacy of frontline radiotherapy treatments.
      Cover page: Enhancing Radiotherapy by Lipid Nanocapsule-Mediated Delivery of Amphiphilic Gold Nanoparticles to Intracellular Membranes
      • Article
      • Peer Reviewed
      UC Riverside Previously Published Works (2020)
      Despite many studies on the toxicity of nanoplastic particles (NPPs) to aquatic invertebrates, the effects of ecological constituents such as humic substances (HSs) are often neglected. In our study, Daphnia magna was used to evaluate the effects of three HSs, natural organic matter (NOM), fulvic acid (FA), and humic acid (HA), on NPP toxicity and corona formation. Acute toxicities of NPPs were reduced by all HSs at environmentally relevant concentrations. NPPs elicited the upregulation of all genes related to detoxification, oxidative stress, and endocrine activity after 7 days of exposure. The presence of NOM or HA resulted in the mitigation of gene expression, whereas significantly higher upregulation of all of the genes was observed with FA. The presence of FA led to increased protein adsorption on NPPs in D. magna culture medium (eco-corona, EC) and homogenates (protein corona, PC), while there was less adsorption in the presence of HA. The highly abundant proteins identified in EC are involved in immune defense, cell maintenance, and antipredator response, while those in PC are responsible for lipid transport, antioxidant effects, and estrogen mediation. Our findings revealed the key influence of HSs on the toxicity of NPPs and provide an analytical and conceptual foundation for future study.
        Cover page: Eco-Corona vs Protein Corona: Effects of Humic Substances on Corona Formation and Nanoplastic Particle Toxicity in Daphnia magnaCreative Commons 'BY' version 4.0 license
        • Article
        • Peer Reviewed
        Dermatology Online Journal, Volume 19, Issue 7 (2013)
        This is the report of a 76-year-old male with typical lesions of acanthosis nigricans maligna (ANM), florid cutaneous papillomatosis (FCP), and tripe palms (TP) for 2 years. He did not have any gastrointestinal complaints. Pathologic findings of skin supported the diagnosis of ANM. Because gastric adenocarcinoma is the most common neoplasm associated with these paraneoplastic dermatoses, further tests were carried out. Endoscopic examination was performed and an adenocarcinoma of the esophagogastric junction was confirmed. Meanwhile, multiple small polyps in the middle and the lower thirds of the esophagus were observed. The patient was referred for further evaluation and subsequent surgical resection of the tumor.Acanthosis nigricans (AN) is a hyperkeratotic mucocutaneous eruption of heterogenous etiology, which is characterized by hyperpigmentation, velvety cutaneous thickening, intensified skin markings, and development of verrucous excrescences typically involving the intertriginous areas. AN is classified into benign and malignant forms on the basis of clinical associations. Malignant acanthosis nigricans (MAN) tends to be extensive and involves mucosal surfaces, mostly in elderly people. Florid cutaneous papillomatosis (FCP), also known as the Schwartz-Burgess syndrome, is characterized by the rapid appearance of multiple verrucous lesions that are clinically indistinguishable from common warts [1]. Tripe palms (TP) is characterized by diffuse, yellowish palmar hyperkeratosis, with enhancement of the epidermal ridges on the hands (dermatoglyphics), resembling intestinal villosities [1]. The association of these three paraneoplastic dermatoses (FCP, ANM and TP) in the same patient has been reported. Herein, we report an elderly male with three paraneoplastic dermatoses for two years. On the initial presentation, he did not report any systemic complaints; diagnostic tests confirmed the presence of a gastric adenocarcinoma.
          Cover page: Three paraneoplastic signs in the same patient with gastric adenocarcinomaCreative Commons 'BY-NC-ND' version 4.0 license
          • Article
          • Peer Reviewed
          UC Riverside Previously Published Works (2019)
          With worldwide environmental accumulation of plastics and their recognized degradation into smaller particles, attention to their impacts on ecological systems and humans has been increasing recently. However, environmental factors and their impacts are seldom considered during their eco-toxicity evaluation. In this study, D. magna neonates were used to assess and compare the acute toxicities of polystyrene microplastic particles (MPPs) and nanoplastic particles (NPPs) in the absence and presence of humic acids (HAs), an important environmental factor in aquatic systems. Four stress response and detoxification genes (CAT, GST, HSP70, and P-GP) were used to characterize the toxic response of the neonates to the exposure. Our results showed that NPPs were much more toxic than MPPs in that 10 mg L-1 NPPs induced over 70% of death in 96 h but MPPs (as high as 400 mg L-1) caused no mortality under all tested conditions. More importantly, we revealed a potent protective role of HA against NPP toxicity at environmentally relevant concentrations. The effect was concentration dependent, as 50 mg L-1 HA subdued the NPP (400 mg L-1) toxicity effect completely. NPPs elicited the up-regulation of all examined genes while HA diminished the change appreciably, further confirming its detoxifying role against NPP toxicity. Through fluorescence and dynamic light scattering measurements, we found that HA was adsorbed on NPPs and formed a corona, without causing agglomeration or precipitation, but changed NPP distribution in the D. magna neonates in a way similar to that of MPPs, leading to alleviated toxicity. Our results suggest that it is essential to consider environmental factors in evaluating and monitoring NPP toxicity as this presents a more relevant exposure state.
            Cover page: Humic acid alleviates the toxicity of polystyrene nanoplastic particles to Daphnia magnaCreative Commons 'BY' version 4.0 license
            • Article
            • Peer Reviewed
            UC Davis Previously Published Works (2017)
            Pharmacological preconditioning reduces myocardial infarct size in ischaemia-reperfusion (I-R) injury. Dexmedetomidine, a selective α2 -adrenoceptor agonist, has a proven cardioprotective effect when administered prior to I-R, although the underlying mechanisms for this effect are not fully understood. We evaluated whether dexmedetomidine preconditioning could induce a myocardio-protective effect against I-R injury by inhibiting associated inflammatory processes through downregulation of the high mobility group box 1 (HMGB1)-toll-like receptor 4 (TLR4)-nuclear factor κB (NF-κB) signalling pathway. Seventy rats were randomly assigned to seven groups: a control and six test groups, involving I-R for 30 and 120 minutes, respectively, in isolated rat hearts and different pretreatment protocols with dexmedetomidine (10 nmol/L) as well as yohimbine (1 μmol/L) and recombinant HMGB1 peptide (rHMGB1; 20 μg/L), alone or in combination with dexmedetomidine. Cardiac function was recorded; myocardial HMGB1, TLR4, and NF-κB activities and levels of tumour necrosis factor-α (TNF-α) and interleukin-6 (IL-6) were measured as were lactate dehydrogenase (LDH) and creatine kinase (CK) in coronary outflow. Dexmedetomidine preconditioning significantly improved cardiac function (P<.05), downregulated the expression of HMGB1-TLR4-NF-κB, reduced levels of TNF-α and IL-6 in isolated ventricles during I-R injury, and significantly reduced CK and LDH levels in coronary outflow (P<.05). All of these effects were partially reversed by yohimbine (P<.05) or rHMGB1 (P<.05). Dexmedetomidine preconditioning alleviated myocardial I-R injury in rats through inhibition of inflammatory processes associated with downregulation of the HMGB1-TLR4-NF-κB signalling pathway via activation at α2 -adrenergic receptors.
              Cover page: Dexmedetomidine preconditioning for myocardial protection in ischaemia‐reperfusion injury in rats by downregulation of the high mobility group box 1‐toll‐like receptor 4‐nuclear factor κB signalling pathway
              • Article
              • Peer Reviewed
              UCLA Previously Published Works (2023)
              Spin glasses are disordered magnets with random interactions that are, generally, in conflict with each other. Finding the ground states of spin glasses is not only essential for understanding the nature of disordered magnets and many other physical systems, but also useful to solve a broad array of hard combinatorial optimization problems across multiple disciplines. Despite decades-long efforts, an algorithm with both high accuracy and high efficiency is still lacking. Here we introduce DIRAC - a deep reinforcement learning framework, which can be trained purely on small-scale spin glass instances and then applied to arbitrarily large ones. DIRAC displays better scalability than other methods and can be leveraged to enhance any thermal annealing method. Extensive calculations on 2D, 3D and 4D Edwards-Anderson spin glass instances demonstrate the superior performance of DIRAC over existing methods. The presented framework will help us better understand the nature of the low-temperature spin-glass phase, which is a fundamental challenge in statistical physics. Moreover, the gauge transformation technique adopted in DIRAC builds a deep connection between physics and artificial intelligence. In particular, this opens up a promising avenue for reinforcement learning models to explore in the enormous configuration space, which would be extremely helpful to solve many other hard combinatorial optimization problems.
                Cover page: Searching for spin glass ground states through deep reinforcement learning.
                • Article
                • Peer Reviewed
                UCLA Previously Published Works (2017)
                Distinguishing cell states based only on gene expression data remains a challenging task. This is true even for analyses within a species. In cross-species comparisons, the results obtained by different groups have varied widely. Here, we integrate RNA-seq data from more than 40 cell and tissue types of four mammalian species to identify sets of associated genes as indicators for specific cell states in each species. We employ a statistical method, TROM, to identify both protein-coding and non-coding indicators. Next, we map the cell states within each species and also between species using these indicator genes. We recapitulate known phenotypic similarity between related cell and tissue types and reveal molecular basis for their similarity. We also report novel associations between several tissues and cell types with functional support. Moreover, our identified conserved associated genes are found to be a good resource for studying cell differentiation and reprogramming. Lastly, long non-coding RNAs can serve well as associated genes to indicate cell states. We further infer the biological functions of those non-coding associated genes based on their co-expressed protein-coding genes. This study demonstrates that combining statistical modeling with public RNA-seq data can be powerful for improving our understanding of cell identity control.
                  Cover page: Large-scale mapping of mammalian transcriptomes identifies conserved genes associated with different cell states
                  • Article
                  • Peer Reviewed
                  UCLA Previously Published Works (2015)
                  Cell identity (or cell state) is established via gene expression programs, represented by ???associated genes??? with dynamic expression across cell identities. Here we integrate RNA-seq data from 40 tissues and cell types from human, chimpanzee, bonobo, and mouse to investigate the conservation and differentiation of cell states. We employ a statistical tool, ???Transcriptome Overlap Measure??? (TROM) to first identify cell-state-associated genes, both protein-coding and non-coding. Next, we use TROM to comprehensively map the cell states within each species and also between species based on the cell-state-associated genes. The within-species mapping measures which cell states are similar to each other, allowing us to construct a human cell differentiation tree that recovers both known and novel lineage relationships between cell states. Moreover, the between-species mapping summarizes the conservation of cell states across the four species. Based on these results, we identify conserved associated genes for different cell states and annotate their biological functions. Interestingly, we find that neural and testis tissues exhibit distinct evolutionary signatures in which neural tissues are much less enriched in conserved associated genes than testis. In addition, our mapping demonstrate that besides protein-coding genes, long non-coding RNAs serve well as associated genes to indicate cell states. We further infer the biological functions of those non-coding associated genes based on their co-expressed protein-coding associated genes. Overall, we provide a catalog of conserved and species-specific associated genes that identifies candidates for downstream experimental studies of the roles of these candidates in controlling cell identity.
                    Cover page: Comprehensive mapping of mammalian transcriptomes identifies conserved genes associated with different cell differentiation states
                    • Article
                    • Peer Reviewed
                    UC Davis Previously Published Works (2014)
                    Controlling large natural and technological networks is an outstanding challenge. It is typically neither feasible nor necessary to control the entire network, prompting us to explore target control: the efficient control of a preselected subset of nodes. We show that the structural controllability approach used for full control overestimates the minimum number of driver nodes needed for target control. Here we develop an alternate 'k-walk' theory for directed tree networks, and we rigorously prove that one node can control a set of target nodes if the path length to each target node is unique. For more general cases, we develop a greedy algorithm to approximate the minimum set of driver nodes sufficient for target control. We find that degree heterogeneous networks are target controllable with higher efficiency than homogeneous networks and that the structure of many real-world networks are suitable for efficient target control.
                      Cover page: Target control of complex networks
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