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Open Access Publications from the University of California

Scholarly Works (25 results)

  • Thesis
  • Peer Reviewed
UC Davis Electronic Theses and Dissertations (2023)

Reaction wheels play an essential role in the attitude control of small satellites; however, the trade-off between cost and reliability of commercial and in-house manufactured reaction wheels is a common pain point for small satellite developers. Hard disk drives (HDDs) repurposed as reaction wheels (HDD-RWs) are a low-cost, commercial-off-the-shelf (COTS) solution to the cost versus reliability trade-off for small satellite reaction wheels - they are one to three orders of magnitude less expensive than commercial reaction wheels and demonstrate competitive performance. HDD-RWs have the potential to dramatically lower barriers to entry, allowing resource-constrained organizations to develop CubeSat missions with reliable attitude control.

This thesis presents the research efforts to develop, test, and demonstrate the HDD-RW technology. Lab testing of the HDD-RW was performed to identify a working hardware configuration for the HDD-RWs and develop an actuator model. Preliminary environmental testing was conducted to ensure the HDD-RW can survive vibration loads and a vacuum environment. Single-axis ground testing of the attitude controller using the HDD-RWs was performed to verify its performance. Demonstration of three-axis attitude control using the HDD-RWs was performed through microgravity parabolic flight testing. Successful demonstrations of stabilization and pointing of a HDD-RW CubeSat testbed in microgravity environment raised the Technology Readiness Level (TRL) of the HDD-RW technology from TRL 4 to TRL 6. Data from parabolic flight testing is used to perform system identification of the HDD-RWs and CubeSat system. Simulation results based on the system model further demonstrates pointing control with the HDD-RWs for various target attitudes and stabilization from various initial rotation rates. A guide for using HDD-RWs and developing a controller is presented. Recommendations and lessons learned are provided, and next steps for the HDD-RW technology are discussed.

    Cover page: CubeSat Attitude Control Using Hard Disk Drives as Reaction Wheels
    • Thesis
    • Peer Reviewed
    UC Santa Cruz Electronic Theses and Dissertations (2023)

    Easy access to powerful computational resources (cloud platforms and supercomputers) has revolutionized scientific research in the 21st century. However, these resources are often under-utilized, resulting in sub-optimal performance and increased operational costs. But, improving application performance is a complex task, as various factors such as mismatch between hardware configuration, runtime environment, and source code can contribute to sub-optimal performance.

    To address these challenges, our study describes a `profile-and-optimize' approach that leverages profiling data obtained by running applications on supercomputing systems. By systemically analyzing this data and modifying both the runtime environment and source code, we aim to improve application performance and scalability. We apply our methodology to four case studies and showcase performance improvements by comparing baseline results with optimized results obtained through our approach. Through our methods and the insights gained from the case studies, we provide a valuable resource for optimizing similar applications. By following our process, researchers and developers can reduce application runtime, maximize the utilization of computational resources, and run finer-grained simulations.

      Cover page: A Systems-Centric Approach for Improving Scientific Simulation PerformanceCreative Commons 'BY' version 4.0 license
      • Article
      • Peer Reviewed
      UC Riverside Previously Published Works (2021)
      The E3 ubiquitin ligases have been known to intrigue many researchers to date, due to their heterogenicity and substrate mediation for ubiquitin transfer to the protein. HECT (Homologous to the E6-AP Carboxyl Terminus) E3 ligases are spatially and temporally regulated for substrate specificity, E2 ubiquitin-conjugating enzyme interaction, and chain specificity during ubiquitylation. However, the role of the HECT E3 ubiquitin ligase in plant development and stress responses was rarely explored. We have conducted an in-silico genome-wide analysis to identify and predict the structural and functional aspects of HECT E3 ligase members in tomato. Fourteen members of HECT E3 ligases were identified and analyzed for the physicochemical parameters, phylogenetic relations, structural organizations, tissue-specific gene expression patterns, and protein interaction networks. Our comprehensive analysis revealed the HECT domain conservation throughout the gene family, close evolutionary relationship with different plant species, and active involvement of HECT E3 ubiquitin ligases in tomato plant development and stress responses. We speculate an indispensable biological significance of the HECT gene family through extensive participation in several plant cellular and molecular pathways.
        Cover page: Genome-wide analysis of HECT E3 ubiquitin ligase gene family in Solanum lycopersicum.
        • Article
        • Peer Reviewed
        UC Riverside Previously Published Works (2023)

        Key message

        F-box E3-ubiquitin ligases regulate critical biological processes in plant development and stress responses. Future research could elucidate why and how plants have acquired a large number of F-box genes. The ubiquitin-proteasome system (UPS) is a predominant regulatory mechanism employed by plants to maintain the protein turnover in the cells and involves the interplay of three classes of enzymes, E1 (ubiquitin-activating), E2 (ubiquitin-conjugating), and E3 ligases. The diverse and most prominent protein family among eukaryotes, F-box proteins, are a vital component of the multi-subunit SCF (Skp1-Cullin 1-F-box) complex among E3 ligases. Several F-box proteins with multifarious functions in different plant systems have evolved rapidly over time within closely related species, but only a small part has been characterized. We need to advance our understanding of substrate-recognition regulation and the involvement of F-box proteins in biological processes and environmental adaptation. This review presents a background of E3 ligases with particular emphasis on the F-box proteins, their structural assembly, and their mechanism of action during substrate recognition. We discuss how the F-box proteins regulate and participate in the signaling mechanisms of plant development and environmental responses. We highlight an urgent need for research on the molecular basis of the F-box E3-ubiquitin ligases in plant physiology, systems biology, and biotechnology. Further, the developments and outlooks of the potential technologies targeting the E3-ubiquitin ligases for developing crop improvement strategies have been discussed.
          Creative Commons 'BY' version 4.0 license
          • Article
          • Peer Reviewed
          UCLA Previously Published Works (2024)
          INTRODUCTION: We aimed to investigate the impact of reduced contact prenatal care necessitated by the COVID-19 pandemic on meeting standards of care and perinatal outcomes. METHODS: This was a retrospective case-control study of patients in low-risk obstetrics clinic at a tertiary care county facility serving solely publicly insured patients comparing reduced in-person prenatal care (R) over 12 weeks with a control group (C) receiving traditional prenatal care who delivered prior. RESULTS: Total 90 patients in reduced contact (R) cohort were matched with controls (C). There were similar rates of standard prenatal care metrics between groups. Gestational age (GA) of anatomy ultrasound was later in R (p = 0.017). Triage visits and missed appointments were similar, though total number of visits (in-person and telehealth) was higher in R (p = 0.043). R group had higher GA at delivery (p = 0.001). Composite neonatal morbidity and length of stay were lower in R (p = 0.017, p = 0.048). Maternal and neonatal outcomes did not otherwise differ between groups. Using Kotelchuck Adequacy of Prenatal Care Utilization index, R had higher rates of adequate prenatal care (45.6% R vs. 24.4% C, p = 0.005). DISCUSSION: Our study demonstrates the non-inferiority of a hybrid, reduced schedule prenatal schedule to traditional prenatal scheduling. In a reduced contact prenatal care model, more patients met criteria for adequate prenatal care, likely due to higher attendance of telehealth visits. These findings raise the question of revising the prenatal care model to mitigate disparities in disadvantaged populations.
            Cover page: Evaluating Standard of Care and Obstetrical Outcomes in a Reduced Contact Prenatal Care Model in the COVID-19 Pandemic.
            • Article
            • Peer Reviewed
            UCLA Previously Published Works (2023)
            The present study investigates whether less computer access is associated with an increase or decrease in cyberbullying and face-to-face bullying victimization. Data were derived from the 2009-2010 Health Behavior in School-Aged Children U.S. Study, consisting of 12,642 adolescents aged 11, 13, and 15 years (Mage = 12.95). We found that less computer usage was negatively associated with cyberbullying victimization and face-to-face bullying victimization. The findings from the study have implications for research and practice.
              Cover page: Less Computer Access: Is It a Risk or a Protective Factor for Cyberbullying and Face-to-Face Bullying Victimization among Adolescents in the United States?
              • Article
              • Peer Reviewed
              UC San Diego Previously Published Works (2014)
              Over the last 60 years, the use of hexachlorocyclohexane (HCH) as a pesticide has resulted in the production of >4 million tons of HCH waste, which has been dumped in open sinks across the globe. Here, the combination of the genomes of two genetic subspecies (Sphingobium japonicum UT26 and Sphingobium indicum B90A; isolated from two discrete geographical locations, Japan and India, respectively) capable of degrading HCH, with metagenomic data from an HCH dumpsite (∼450 mg HCH per g soil), enabled the reconstruction and validation of the last-common ancestor (LCA) genotype. Mapping the LCA genotype (3128 genes) to the subspecies genomes demonstrated that >20% of the genes in each subspecies were absent in the LCA. This includes two enzymes from the 'upper' HCH degradation pathway, suggesting that the ancestor was unable to degrade HCH isomers, but descendants acquired lin genes by transposon-mediated lateral gene transfer. In addition, anthranilate and homogentisate degradation traits were found to be strain (selectively retained only by UT26) and environment (absent in the LCA and subspecies, but prevalent in the metagenome) specific, respectively. One draft secondary chromosome, two near complete plasmids and eight complete lin transposons were assembled from the metagenomic DNA. Collectively, these results reinforce the elastic nature of the genus Sphingobium, and describe the evolutionary acquisition mechanism of a xenobiotic degradation phenotype in response to environmental pollution. This also demonstrates for the first time the use of metagenomic data in ancestral genotype reconstruction, highlighting its potential to provide significant insight into the development of such phenotypes.
                Cover page: Reconstructing an ancestral genotype of two hexachlorocyclohexane-degrading Sphingobium species using metagenomic sequence data
                • Article
                • Peer Reviewed
                UC Davis Previously Published Works (2022)
                The soil-borne pathogens, particularly Fusarium oxysporum f. sp. niveum (FON) and southern root-knot nematode (RKN, Meloidogyne incognita) are the major threats to watermelon production in the southeastern United States. The role of soil micronutrients on induced resistance (IR) to plant diseases is well-documented in soil-based media. However, soil-based media do not allow us to determine the contribution of individual micronutrients in the induction of IR. In this manuscript, we utilized hydroponics-medium to assess the effect of controlled application of micronutrients, including iron (Fe), manganese (Mn), and zinc (Zn) on the expression of important IR genes (PR1, PR5, and NPR1 from salicylic acid (SA) pathway, and VSP, PDF, and LOX genes from jasmonic acid (JA) pathway) in watermelon seedlings upon inoculation with either FON or RKN or both. A subset of micronutrient-treated plants was inoculated (on the eighth day of micronutrient application) with FON and RKN (single or mixed inoculation). The expression of the IR genes in treated and control samples was evaluated using qRT-PCR. Although, significant phenotypic differences were not observed with respect to the severity of wilt symptoms or RKN galling with any of the micronutrient treatments within the 30-day experimental period, differences in the induction of IR genes were considerably noticeable. However, the level of gene expression varied with sampling period, type and concentration of micronutrients applied, and pathogen inoculation. In the absence of pathogens, micronutrient applications on the seventh day, in general, downregulated the expression of the majority of the IR genes. However, pathogen inoculation preferentially either up- or down-regulated the expression levels of the IR genes at three days post-inoculation depending on the type and concentration of micronutrients. The results demonstrated here indicate that micronutrients in watermelon may potentially make watermelon plants susceptible to infection by FON and RKN. However, upon infection the IR genes are significantly up-regulated that they may potentially aid the prevention of further infection via SA- and JA-pathways. This is the first demonstration of the impact of micronutrients affecting IR in watermelon against FON and RKN infection.
                  Cover page: Micronutrients Affect Expression of Induced Resistance Genes in Hydroponically Grown Watermelon against Fusarium oxysporum f. sp. niveum and Meloidogyne incognita
                  • Article
                  • Peer Reviewed
                  UC San Diego Previously Published Works (2020)
                  Compassion meditation (CM) is a contemplative practice that is intended to cultivate the ability to extend and sustain compassion toward self and others. Although research documents the benefits of CM in healthy populations, its use in the context of psychopathology is largely unexamined. The purpose of this study was to refine and initially evaluate a CM protocol, Cognitively Based Compassion Training (CBCT®), for use with Veterans with PTSD. To this end, our research team developed and refined a manualized protocol, CBCT-Vet, over 4 sets of groups involving 36 Veterans. This protocol was delivered in 8-10 sessions, each lasting 90-120 min and led by a CBCT®-trained clinical psychologist. Quantitative and qualitative data were used to identify areas to be improved and to assess change that occurred during the treatment period. Based on pooled data from this series of groups, CM appears to be acceptable to Veterans with PTSD. Group participation was associated with reduced symptoms of PTSD (partial eta squared = .27) and depression (partial eta squared = .19), but causality should not be inferred given the nonrandomized design. No change was observed in additional outcomes, including positive emotion and social connectedness. The results of this open trial support additional exploration of CM as part of the recovery process for Veterans with PTSD.
                    Cover page: Compassion Meditation for Veterans with Posttraumatic Stress Disorder (PTSD): a Nonrandomized Study
                    • Article
                    • Peer Reviewed
                    UC San Diego Previously Published Works (2016)
                    Guard cells form epidermal stomatal gas-exchange valves in plants and regulate the aperture of stomatal pores in response to changes in the carbon dioxide (CO2) concentration ([CO2]) in leaves. Moreover, the development of stomata is repressed by elevated CO2 in diverse plant species. Evidence suggests that plants can sense [CO2] changes via guard cells and via mesophyll tissues in mediating stomatal movements. We review new discoveries and open questions on mechanisms mediating CO2-regulated stomatal movements and CO2 modulation of stomatal development, which together function in the CO2 regulation of stomatal conductance and gas exchange in plants. Research in this area is timely in light of the necessity of selecting and developing crop cultivars that perform better in a shifting climate.
                      Cover page: CO2 Sensing and CO2 Regulation of Stomatal Conductance: Advances and Open Questions
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