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Open Access Publications from the University of California

Scholarly Works (239 results)

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

The ever-increasing demands of data-intensive applications and the rapid evolution of computer architectures have posed significant challenges in memory performance and energy efficiency. Efficient memory management is crucial to meet the requirements of these applications while optimizing the utilization of memory resources. Traditional approaches that rely on workload-specific optimizations and static memory configurations are no longer sufficient to address the dynamic nature of modern computing systems.

To overcome these challenges, the concept of computational self-awareness (CSA) has emerged as a promising approach. Computational self-awareness draws inspiration from psychology and neuroscience and aims to develop intelligent systems that can learn from past experiences, reason about their current state, and make informed decisions at runtime.

In this thesis, I explore the application of computational self-awareness in the context of memory management. I investigate the different degrees of self-awareness applied across the memory subsystem and examine their benefits on memory performance and energy consumption. The results highlight the potential of computational self-awareness in addressing the challenges posed by data-intensive applications and evolving computer architectures, paving the way for improved performance, energy efficiency, and bandwidth utilization in memory systems.

    Cover page: Self-aware Memory Management for Emerging Architectures
    • Article
    • Peer Reviewed
    UCLA Previously Published Works (2020)
    The dynamic signal encoding paradigm suggests that information flows from the extracellular environment into specific signaling patterns (encoding) that are then read by downstream effectors to control cellular behavior. Previous work empirically quantified the information content of dynamic signaling patterns. However, whether this information can be faithfully transmitted to the gene expression level is unclear. Here we used NFkB signaling as a model to understand the accuracy of information transmission from signaling dynamics into gene expression. Using a detailed mathematical model, we simulated realistic NFkB signaling patterns with different degrees of variability. The NFkB patterns were used as an input to a simple gene expression model. Analysis of information transmission between ligand and NFkB and ligand and gene expression allows us to determine information loss in transmission between receptors to dynamic signaling patterns and between signaling dynamics to gene expression. Information loss could occur due to biochemical noise or due to a lack of specificity. We found that noise-free gene expression has very little information loss suggesting that gene expression can preserve specificity in NFkB patterns. As expected, the addition of noise to the gene expression model results in information loss. Interestingly, this effect can be mitigated by a specific choice of parameters that can substantially reduce information loss due to biochemical noise during gene expression. Overall our results show that the cellular capacity for information transmission from dynamic signaling patterns to gene expression can be high enough to preserve ligand specificity and thereby the accuracy of cellular response to environmental cues.
      Cover page: Information transmission from NFkB signaling dynamics to gene expression
      • Article
      • Peer Reviewed
      The Proceedings of the International Plant Nutrition Colloquium XVI (2009)

      An experiment was undertaken at District Seed Farm of Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, Nadia, West Bengal, India to evaluate the F1 hybrids of okra under reduced level of chemical fertilizers (50% of recommended dose of fertilizers) with two sources of organic manures (Cow-dung manure @ 25 t/ha and neem cake @ 2.5 t/ha). The results indicated significant differences among the hybrids and between the sources of organic manures for both vegetative growth characters such as plant height, number of primary branches/plant and nodes/plant; reproductive behaviour of the plant, i.e. days to 50% flowering as well as fruit characters like fruit length, girth, weight, fruits/plant and marketable fruit yield. Based on the results it may be concluded that under the agro climatic conditions of West Bengal, the hybrids NOH-15, Makhamalli, Sun 40, Sun 08, Mahyco Bhendi No.12, Mahyco Bhendi No.10, Mahyco Bhendi No.1 as well as Vijaya (99.36 – 107.43 q/ha) can be recommended for commercial cultivation under reduced level of chemical fertilizers during summer. Application of neem cake @ 2.5 t/ha along with reduced level of fertilizer (50% RDF) is very much beneficial for better vegetative growth with increasing the yield in okra.

        Cover page: PERFORMANCE OF OKRA [Abelmoschus esculentus (L.) Moench] HYBRIDS UNDER REDUCED LEVEL OF CHEMICAL FERTILIZERS SUPPLEMENTED WITH ORGANIC MANURES
        • Article
        • Peer Reviewed
        The Proceedings of the International Plant Nutrition Colloquium XVI (2009)

        Balanced and integrated plant nutrient management is imperative in agricultural production system including its quality - more applicable to those of developing country in the world. Like arable land in wetland ecosystem, nitrogen and other essential key plant elements and its management is also an integral part for so many beneficial aquatic crops (food, non-food etc.). With this significant importance of IPNM, number of case studies were undertaken through TOT, TDET based integrated aquaculture research projects (NWDPRA, ICAR, DoLR, Govt. of India) suited to wetland ecosystem at different agro-climatic zones (NAZ, OAZ including Coastal zone) of Indian sub-continent. In field study, emphasize were paid for utilizing divergence of waste wetlands followed with adoption of improvised agro-techniques (IPN & its management) on nutritious, valuable and popular aquatic food crops [deep-water rice - Oryza sativa, water chestnut - Trapa bispinosa, makhana - Euryale ferox, water lily - Nymphaea and Colocasia] in rural farming community at different agro-zones. Major and other essential plant nutrients combined with organic (neem oilcake) and inorganic sources (N : P2O5 : K2O @ 20-60 : 30-40 : 20-40 kg ha–1) includes spray materials were considered in these extensive study. Production of rice grains (3.76 t ha–1), fresh nut of water chestnut (9.93 t ha–1), makhana seeds (3.24 t ha–1), stalks of water-lily (6.52 t ha–1) and corm includes stalk yield of Colocasia (86.8 t ha–1) including its nutritional quality was remarkably influenced with IPNM, even exhibited >2.5 folds, economically viable to the rural farming community.

          Cover page: Integrated plant nutrient management on diversified cropping system in aqua-terrestrial ecosystem for yield potentiality, quality and rural sustainability
          • Article
          • Peer Reviewed
          UC San Diego Previously Published Works (2022)
            • Article
            • Peer Reviewed
            UC Berkeley Previously Published Works (2015)
            Implant-associated inflammation and bacterial infection severely limit the functional performance of medical devices and are a major cause of implant failure. Therefore, it is crucial to develop methodologies to monitor/image implant-associated aseptic inflammation and bacterial infection in a minimally invasive manner. Here, we exploited near-infrared fluorescence (NIRF) molecular probes injected locally at the implant site to perform minimally invasive, simultaneous imaging of inflammation, and infection associated with implanted polymer disks. The hydro-sulfo-Cy5 (H-s-Cy5) probe detected reactive oxygen species associated with inflammatory responses to both aseptic and biofilm-containing implants, whereas diaminocyanine sulfonate selectively detected nitric oxide associated with a biofilm on the biomaterial at acute time points (<4 days). This imaging modality also allows longitudinal monitoring because of high specificity and fast clearance rate of the fluorescent probes. Taken together, these NIRF molecular probes represent a useful tool to directly image inflammatory responses and infections associated with implanted devices for the diagnosis of device-associated inflammation and infection as well as the development of effective therapies.
              Cover page: In vivo fluorescence imaging of biomaterial‐associated inflammation and infection in a minimally invasive manner
              • Article
              • Peer Reviewed
              UC San Diego Previously Published Works (2023)
              Organic anion transporter 1 (OAT1/SLC22A6, NKT) is a multispecific drug transporter in the kidney with numerous substrates, including pharmaceuticals, endogenous metabolites, natural products, and uremic toxins. Here, we show that OAT1 regulates levels of gut microbiome-derived metabolites. We depleted the gut microbiome of Oat1-KO and WT mice and performed metabolomics to analyze the effects of genotype (KO versus WT) and microbiome depletion. OAT1 is an in vivo intermediary between the host and the microbes, with 40 of the 162 metabolites dependent on the gut microbiome also impacted by loss of Oat1. Chemoinformatic analysis revealed that the altered metabolites (e.g., indoxyl sulfate, p-cresol sulfate, deoxycholate) had more ring structures and sulfate groups. This indicates a pathway from gut microbes to liver phase II metabolism, to renal OAT1-mediated transport. The idea that multiple gut-derived metabolites directly interact with OAT1 was confirmed by in vitro transport and magnetic bead binding assays. We show that gut microbiome-derived metabolites dependent on OAT1 are impacted in a chronic kidney disease (CKD) model and human drug-metabolite interactions. Consistent with the Remote Sensing and Signaling Theory, our results support the view that drug transporters (e.g., OAT1, OAT3, OATP1B1, OATP1B3, MRP2, MRP4, ABCG2) play a central role in regulating gut microbe-dependent metabolism, as well as interorganismal communication between the host and microbiome.
                Cover page: The kidney drug transporter OAT1 regulates gut microbiome–dependent host metabolism
                • Article
                • Peer Reviewed
                UC Berkeley Previously Published Works (2020)
                The expression of beta-lactamases in bacteria is a central cause of drug resistance. In this report, we present a beta-lactamase chemiluminescent probe, termed CCP, which can for the first time detect beta-lactamase activity via chemiluminescence and can detect beta lactamase with a sensitivity that is 4-orders of magnitude higher than the commercially available fluorescent lactamase substrate fluorocillin.
                  • Article
                  • Peer Reviewed
                  UC Irvine Previously Published Works (2013)
                  Key assays in enzymology for the biochemical characterization of proteins in vitro necessitate high concentrations of the purified protein of interest. Protein purification protocols should combine efficiency, simplicity and cost effectiveness. Here, we describe the GST-His method as a new small-scale affinity purification system for recombinant proteins, based on a N-terminal Glutathione Sepharose Tag (GST) and a C-terminal 10xHis tag, which are both fused to the protein of interest. The latter construct is used to generate baculoviruses, for infection of Sf9 infected cells for protein expression. GST is a rather long tag (29 kDa) which serves to ensure purification efficiency. However, it might influence physiological properties of the protein. Hence, it is subsequently cleaved off the protein using the PreScission enzyme. In order to ensure maximum purity and to remove the cleaved GST, we added a second affinity purification step based on the comparatively small His-Tag. Importantly, our technique is based on two different tags flanking the two ends of the protein, which is an efficient tool to remove degraded proteins and, therefore, enriches full-length proteins. The method presented here does not require an expensive instrumental setup, such as FPLC. Additionally, we incorporated MgCl2 and ATP washes to remove heat shock protein impurities and nuclease treatment to abolish contaminating nucleic acids. In summary, the combination of two different tags flanking the N- and the C-terminal and the capability to cleave off one of the tags, guaranties the recovery of a highly purified and full-length protein of interest.
                    Cover page: GST-His purification: a two-step affinity purification protocol yielding full-length purified proteins.
                    • Article
                    • Peer Reviewed
                    UC San Diego Previously Published Works (2022)
                    In light of the demonstrated antagonism of Wnt5A signaling toward the growth of several bacterial pathogens, it was important to study the influence of Wnt5A on gut-resident bacteria and its outcome. Here, we demonstrate that in contrast to inhibiting the survival of the established gut pathogen Salmonella enterica, Wnt5A clearly promotes the survival of the common gut commensals Enterococcus faecalis and Lactobacillus rhamnosus within macrophages through a self-perpetuating Wnt5A-actin axis. A Wnt5A-actin axis furthermore regulates the subsistence of the natural bacterial population of the Peyer's patches, as is evident from the diminution in the countable bacterial CFU therein through the application of Wnt5A signaling and actin assembly inhibitors. Wnt5A dependency of the gut-resident bacterial population is also manifested in the notable difference between the bacterial diversities associated with the feces and Peyer's patches of Wnt5A heterozygous mice, which lack a functional copy of the Wnt5A gene, and their wild-type counterparts. Alterations in the gut commensal bacterial population resulting from either the lack of a copy of the Wnt5A gene or inhibitor-mediated attenuation of Wnt5A signaling are linked with significant differences in cell surface major histocompatibility complex (MHC) II levels and regulatory versus activated CD4 T cells associated with the Peyer's patches. Taken together, our findings reveal the significance of steady state Wnt5A signaling in shaping the gut commensal bacterial population and the T cell repertoire linked to it, thus unveiling a crucial control device for the maintenance of gut bacterial diversity and T cell homeostasis. IMPORTANCE Gut commensal bacterial diversity and T cell homeostasis are crucial entities of the host innate immune network, yet the molecular details of host-directed signaling pathways that sustain the steady state of gut bacterial colonization and T cell activation remain unclear. Here, we describe the protective role of a Wnt5A-actin axis in the survival of several gut bacterial commensals and its necessity in shaping gut bacterial colonization and the associated T cell repertoire. This study opens up new avenues of investigation into the role of the Wnt5A-actin axis in protection of the gut from dysbiosis-related inflammatory disorders.
                      Cover page: Wnt5A Signaling Regulates Gut Bacterial Survival and T Cell Homeostasis
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