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Open Access Publications from the University of California

Scholarly Works (31 results)

  • Thesis
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UC Berkeley Electronic Theses and Dissertations (2014)

The present work comprises a detailed study of specific terms of discourse in the pre-twelfth century sources of esoteric "Tantric" Shaivism, both scriptural and exegetical, some of which are still unpublished and others of which are published only in the original Sanskrit. As a dissertation in South Asian Studies using the philological method, the primary purpose of the study is to ascertain the range of meanings of certain technical terms of great importance to the theology and practice of the Shaiva religion, namely avesa, samavesa, and saktipata. The work focuses on both the independent meaning and the intersection of these key terms, incorporating also the terms diksa and vedha in the latter endeavor. The intersection of these terms constitutes a complex set of relationships, a nexus of ideas that lie at the very heart of the Shaiva tradition and which, due to the latter's widespread influence, came to be important in Tantric Buddhism and later forms of Hinduism as well. This thesis contends that samavesa--meaning the fusion or commingling of one's self with the energy of one's deity and/or the consciousness of one's guru--is the key term that distinguishes Tantric Shaivism from mainstream (esp. Vaidika) Indian religion. This constitutes a reinterpretation and overcoding of the earlier meaning of avesa, i.e. self-induced controlled possession by a deity.

Samavesa is important to all forms of Shaivism, whether dualistic and ritualized (the Siddhanta) or nondual subitist charismatic forms (the Kaula). This thesis further contends that a philological study of samavesa and related terms like saktipata demonstrates that religious experience (or evidence thereof) was considered central and indispensable to initiatory Shaivism throughout the medieval period. Saktipata was requisite to receive the basic level of initiation, and in the Kaula branch of the tradition, samavesa denoted forms of religious experience that were necessary for aspirants to demonstrate in order to receive higher-level initiations. The former term is still commonly used in many Hindu communities today to designate a "spiritual awakening" or initiatory experience that is transmitted by a qualified guru.

Part One of this work is a comprehensive overview of the nature and structure of the Shaiva religion, providing important context to what follows. Part Two studies the key terms of (sam)avesa, saktipata, etc. in a) early Sanskrit literature generally, b) Shaiva scriptures, and c) the abundant exegetical literature based on those scriptures.

    Cover page: To Enter, to be entered, to merge: The role of religious experience in the traditions of Tantric Shaivism
    • Article
    • Peer Reviewed
    UC Davis Previously Published Works (2022)
    We have recently developed a low-cost spark-induced breakdown spectroscopy (SIBS) instrument for in-situ analysis of toxic metal aerosol particles that we call TARTA (toxic-metal aerosol real time analyzer). In this work, we applied machine learning methods to improve the quantitative analysis of elemental mass concentrations measured by this instrument. Specifically, we applied least absolute shrinkage and selection operator (LASSO), partial least squares (PLS) regression, principal component regression (PCR), and support vector regression (SVR) to develop multivariate calibration models for 13 metals (e.g., Cr, Cu, Mn, Fe, Zn, Co, Al, K, Be, Hg, Cd, Pb, and Ni), some of which are included on the US EPA hazardous air pollutants (HAPS) list. The calibration performance, adjusted coefficient of determination (R2) and normalized root mean square error (RMSE), and limit of detection (LOD) of the proposed models were compared to those of univariate calibration models for each analyte. Our results suggest that machine learning models tend to have better prediction accuracy and lower LODs than conventional univariate calibration, of which the LASSO approach performs the best with R2 > 0.8 and LODs of 40-170 ng m-3 at a sampling time of 30 min and a flow rate of 15 l min -1. We then assessed the applicability of the LASSO model for quantifying elemental concentrations in mixtures of these metals, serving as independent validation datasets. Ultimately, the LASSO model developed in this work is a very promising machine learning approach for quantifying mass concentration of metals in aerosol particles using TARTA.
      Cover page: Improving quantitative analysis of spark-induced breakdown spectroscopy: Multivariate calibration of metal particles using machine learning
      • Article
      • Peer Reviewed
      UC Davis Previously Published Works (2023)
      BACKGROUND: Quantifying the dose and distribution of tobacco smoke in the respiratory system is critical for understanding its toxicity, addiction potential, and health impacts. Epidemiologic studies indicate that the incidence of lung tumors varies across different lung regions, suggesting there may be a heterogeneous deposition of smoke particles leading to greater health risks in specific regions. Despite this, few studies have examined the lobar spatial distribution of inhaled particles from tobacco smoke. This gap in knowledge, coupled with the growing popularity of little cigars among youth, underscores the need for additional research with little cigars. RESULTS: In our study, we analyzed the lobar deposition in rat lungs of smoke particles from combusted regular and mentholated Swisher Sweets little cigars. Twelve-week-old male and female Sprague-Dawley rats were exposed to smoke particles at a concentration of 84 ± 5 mg/m3 for 2 h, after which individual lung lobes were examined. We utilized Inductively Coupled Plasma Mass Spectrometry to quantify lobar chromium concentrations, serving as a smoke particle tracer. Our findings demonstrated an overall higher particle deposition from regular little cigars than from the mentholated ones. Higher particle deposition fraction was observed in the left and caudal lobes than other lobes. We also observed sex-based differences in the normalized deposition fractions among lobes. Animal study results were compared with the multi-path particle dosimetry (MPPD) model predictions, which showed that the model overestimated particle deposition in certain lung regions. CONCLUSIONS: Our findings revealed that the particle deposition varied between different little cigar products. The results demonstrated a heterogenous deposition pattern, with higher particle deposition observed in the left and caudal lobes, especially with the mentholated little cigars. Additionally, we identified disparities between our measurements and the MPPD model. This discrepancy highlights the need to enhance the accuracy of models before extrapolating animal study results to human lung deposition. Overall, our study provides valuable insights for estimating the dose of little cigars during smoking for toxicity research.
        Cover page: Heterogeneous deposition of regular and mentholated little cigar smoke in the lungs of Sprague-Dawley rats.
        • Article
        • Peer Reviewed
        UC Davis Previously Published Works (2021)
        To meet the demand for identifying and controlling toxic air contaminants in environmental justice communities, we have recently developed a cost-effective spark-induced breakdown spectroscopy (SIBS) instrument for detecting and quantifying toxic metal air pollutants. We characterized the detection limit and linearity of this SIBS instrument by analyzing nebulized elemental standard solutions. The experimental parameters affecting SIBS performance were optimized, including the time delay to observation, the distance between electrodes, and the ablation voltage. The instrument successfully detected Cr, Cu, Mn, Fe, Zn, Co, and Ni, with limits of detection ranged from 0.05 μg m-3 to 0.81 μg m-3 at a flow rate of 15 l min-1 and a 30 min sampling duration. Similar to other investigations using ion breakdown spectroscopy, we did not observe strong emissions lines for As, Sb, Se, Hg, Pb, and Cd, which were likely due to spectral overlap, matrix effects, and the limited detection range of the optical components. Overall, SIBS is a promising technique for field measurements of toxic metals for environmental justice, industrial and urban applications.
          Cover page: The performance of an inexpensive spark-induced breakdown spectroscopy instrument for near real-time analysis of toxic metal particles
          • Article
          • Peer Reviewed
          UC Berkeley Previously Published Works (2024)
          Genome editing tools, particularly the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) systems (e.g., CRISPR/Cas9), and their repurposing into epigenetic editing platforms, offer enormous potential as safe and customizable therapies for cancer. Specifically, various transcriptional abnormalities in human malignancies, such as silencing of tumor suppressors and ectopic re-expression of oncogenes, have been successfully targeted with virtually no off-target effects using CRISPR activation and repression systems. In these systems, the nuclease-deactivated Cas9 protein (dCas9) is fused to one or more domains inducing selective activation or repression of the targeted genes. Despite these advances, the efficient in vivo delivery of these molecules into the target cancer cells represents a critical barrier to accomplishing translation into a clinical therapy setting for cancer. Major obstacles include the large size of dCas9 fusion proteins, the necessity of multimodal delivery of protein and gRNAs, and the potential of these formulations to elicit detrimental immune responses.In this context, viral methods for delivering CRISPR face several limitations, such as the packaging capacity of the viral genome, the potential for integration of the nucleic acids into the host cells genome, and immunogenicity of viral proteins, posing serious safety concerns. The rapid development of mRNA vaccines in response to the COVID-19 pandemic has rekindled interest in mRNA-based approaches for CRISPR/dCas9 delivery. Simultaneously, due to their high loading capacity, scalability, customizable surface modification for cell targeting, and low immunogenicity, lipid nanoparticles (LNPs) have been widely explored as nonviral vectors. In this chapter, we first describe the design of optimized dCas9-effector mRNAs and gRNAs for epigenetic editing. We outline formulations of LNPs suitable for dCas9 mRNA delivery. Additionally, we provide a protocol for the co-encapsulation of the dCas9-effector mRNAs and gRNA into these LNPs, along with detailed methods for delivering these formulations to both cell lines (in vitro) and mouse models of breast cancer (in vivo).
            Cover page: Protocol for Delivery of CRISPR/dCas9 Systems for Epigenetic Editing into Solid Tumors Using Lipid Nanoparticles Encapsulating RNA
            • Article
            • Peer Reviewed
            UC Davis Previously Published Works (2023)
            Smoke plumes emitted from wildland-urban interface (WUI) wildfires contain toxic chemical substances that are harmful to human health, mainly due to the burning of synthetic components. Accurate measurement of these air toxics is necessary for understanding their impacts on human health. However, air pollution is typically measured using ground-based sensors, manned airplanes, or satellites, which all provide low-resolution data. Unmanned Aerial Vehicles (UAVs) have the potential to provide high-resolution spatial and temporal data due to their ability to hover in specific locations and maneuver with precise trajectories in 3-D space. This study investigates the use of an octocopter UAV, equipped with a customized air quality sensor package and a volatile organic compound (VOC) air sampler, for the purposes of collecting and analyzing air toxics data from wildfire plumes. The UAV prototype developed has been successfully tested during several prescribed fires conducted by the California Department of Forestry and Fire Protection (CAL FIRE). Data from these experiments were analyzed with emphasis on the relationship between the air toxics measured and the different types of vegetation/fuel burnt. BTEX compounds were found to be more abundant for hardwood burning compared to grassland burning, as expected.
              Cover page: UAV-Based Wildland Fire Air Toxics Data Collection and Analysis
              • Article
              • Peer Reviewed
              UC Riverside Previously Published Works (2016)
              Potato psyllid (Bactericera cockerelli) is an important pest of potato, tomato and pepper. Not only could a toxin secreted by nymphs results in serious phytotoxemia in some host plants, but also over the past few years B. cockerelli was shown to transmit "Candidatus Liberibacter solanacearum", the putative bacterial pathogen of potato zebra chip (ZC) disease, to potato and tomato. ZC has caused devastating losses to potato production in the western U.S., Mexico, and elsewhere. New knowledge of the genetic diversity of the B. cockerelli is needed to develop improved strategies to manage pest populations. Mitochondrial genome (mitogenome) sequencing provides important knowledge about insect evolution and diversity in and among populations. This report provides the first complete B. cockerelli mitogenome sequence as determined by next generation sequencing technology (Illumina MiSeq). The circular B. cockerelli mitogenome had a size of 15,220 bp with 13 protein-coding gene (PCGs), 2 ribosomal RNA genes (rRNAs), 22 transfer RNA genes (tRNAs), and a non-coding region of 975 bp. The overall gene order of the B. cockerelli mitogenome is identical to three other published Psylloidea mitogenomes: one species from the Triozidae, Paratrioza sinica; and two species from the Psyllidae, Cacopsylla coccinea and Pachypsylla venusta. This suggests all of these species share a common ancestral mitogenome. However, sequence analyses revealed differences between and among the insect families, in particular a unique region that can be folded into three stem-loop secondary structures present only within the B. cockerelli mitogenome. A phylogenetic tree based on the 13 PCGs matched an existing taxonomy scheme that was based on morphological characteristics. The available complete mitogenome sequence makes it accessible to all genes for future population diversity evaluation of B. cockerelli.
                Cover page: The Complete Mitochondrial Genome Sequence of Bactericera cockerelli and Comparison with Three Other Psylloidea Species
                • Article
                • Peer Reviewed
                UC Davis Previously Published Works (2017)
                Grapevine trunk diseases cause important economic losses in vineyards worldwide. Neofusicoccum parvum, one of the most aggressive causal agents of the trunk disease Botryosphaeria dieback, colonizes cells and tissues of the grapevine wood, leading to the formation of an internal canker. Symptoms then extend to distal shoots, with wilting of leaves and bud mortality. Our aim was to characterize the transcriptional dynamics of grapevine genes in the woody stem and in the leaves during Neofusicoccum parvum colonization. Genome-wide transcriptional profiling at seven distinct time points (0, 3, and 24 hours; 2, 6, 8, and 12 weeks) showed that both stems and leaves undergo extensive transcriptomic reprogramming in response to infection of the stem. While most intense transcriptional responses were detected in the stems at 24 hours, strong responses were not detected in the leaves until the next sampling point at 2 weeks post-inoculation. Network co-expression analysis identified modules of co-expressed genes common to both organs and showed most of these genes were asynchronously modulated. The temporal shift between stem vs. leaf responses affected transcriptional modulation of genes involved in both signal perception and transduction, as well as downstream biological processes, including oxidative stress, cell wall rearrangement and cell death. Promoter analysis of the genes asynchronously modulated in stem and leaves during N. parvum colonization suggests that the temporal shift of transcriptional reprogramming between the two organs might be due to asynchronous co-regulation by common transcriptional regulators. Topology analysis of stem and leaf co-expression networks pointed to specific transcription factor-encoding genes, including WRKY and MYB, which may be associated with the observed transcriptional responses in the two organs.
                  Cover page: Neofusicoccum parvum Colonization of the Grapevine Woody Stem Triggers Asynchronous Host Responses at the Site of Infection and in the LeavesCreative Commons 'BY-NC-ND' version 4.0 license
                  • Article
                  • Peer Reviewed
                  UC Davis Previously Published Works (2017)
                    Cover page: Neofusicoccum parvum colonization of the grapevine woody stem triggers asynchronous host responses at the site of infection and in the leaves
                    • Article
                    • Peer Reviewed
                    UC Davis Previously Published Works (2020)

                    Background

                    Traffic-related air pollution (TRAP) is made up of complex mixtures of particulate matter, gases and volatile compounds. However, the effects of TRAP on the cardiopulmonary system in most animal studies have been tested using acute exposure to singular pollutants. The cardiopulmonary effects and molecular mechanisms in animals that are chronically exposed to unmodified air pollution as a whole have yet to be studied. Additionally, sex-dependent toxicity of TRAP exposure has rarely been evaluated.

                    Objectives

                    This study sought to assess the cardiopulmonary effect of chronic exposure to unmodified, real-world TRAP in both female and male rats.

                    Methods

                    Four-week-old male and female rats were exposed to TRAP or filtered air for 14 months in a novel facility drawing air from a major freeway tunnel system in Northern California. Inflammation and oxidative stress markers were examined in the lung, heart, spleen, and plasma, and TRAP deposits were quantified in the lungs of both male and female rats.

                    Results

                    Elemental analysis showed higher levels of eight elements in the female lungs and one element in the male lungs. Expression of genes related to fibrosis, aging, oxidative stress, and inflammation were higher in the rat hearts exposed to TRAP, with female rats being more susceptible than males. Enhanced collagen accumulation was found only in the TRAP-exposed female hearts. Plasma cytokine secretion was higher in both female and male rats, but inflammatory macrophages were higher only in TRAP-exposed male spleens.

                    Discussion

                    Our results in rats suggest pathological consequences from chronic TRAP exposure, including sex differences indicating females may be more susceptible to TRAP-induced cardiac fibrosis. https://doi.org/10.1289/EHP7045.
                      Cover page: Pathological Cardiopulmonary Evaluation of Rats Chronically Exposed to Traffic-Related Air Pollution
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