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Open Access Publications from the University of California

Scholarly Works (38 results)

  • Article
  • Peer Reviewed
UC San Francisco Previously Published Works (2024)
Natural language processing (NLP), a technology that translates human language into machine-readable data, is revolutionizing numerous sectors, including cancer care. This review outlines the evolution of NLP and its potential for crafting personalized treatment pathways for cancer patients. Leveraging NLPs ability to transform unstructured medical data into structured learnable formats, researchers can tap into the potential of big data for clinical and research applications. Significant advancements in NLP have spurred interest in developing tools that automate information extraction from clinical text, potentially transforming medical research and clinical practices in radiation oncology. Applications discussed include symptom and toxicity monitoring, identification of social determinants of health, improving patient-physician communication, patient education, and predictive modeling. However, several challenges impede the full realization of NLPs benefits, such as privacy and security concerns, biases in NLP models, and the interpretability and generalizability of these models. Overcoming these challenges necessitates a collaborative effort between computer scientists and the radiation oncology community. This paper serves as a comprehensive guide to understanding the intricacies of NLP algorithms, their performance assessment, past research contributions, and the future of NLP in radiation oncology research and clinics.
    Cover page: Natural Language Processing for Radiation Oncology: Personalizing Treatment Pathways.
    • Article
    • Peer Reviewed
    UC Riverside Previously Published Works (2021)
    Wastewater treatment plant (WWTP) upgrades can reduce both nutrient and micropollutant emissions into receiving rivers, thus modifying the composition and function of biological communities. However, how microbial communities vary and whether they can be restored to levels found in less-polluted rivers remains uncertain. Aquatic biofilms are sensitive to environmental change and respond rapidly to bottom-up pressure. Thus, we used 12 flumes configured in three experimental treatments to mimic the dynamic processes of biofilm microbial communities occurring in a wastewater-receiving river following WWTP upgrade, with rivers containing two levels of nutrients and micropollutants used as references. We compared the biofilm microbial biomass, carbon source utilization, and community composition among the three "blocks". Results showed that the metabolic patterns of the carbon sources and composition of the biofilm bacterial communities in the flumes mimicking a receiving river with WWTP upgrade recovered over time to those mimicking a less-disturbed river. The restoration of potential carboxylic acid-consuming denitrifying bacteria (i.e., Zoogloea, Comamonas, Dechloromonas, and Acinetobacter) likely played a significant role in this process. Combining quantitative analysis of the denitrification genes nirS and nosZ, we confirmed that the denitrification function of the river biofilms recovered after WWTP upgrade, consistent with our previous field investigation.
      Cover page: Recovery trajectories and community resilience of biofilms in receiving rivers after wastewater treatment plant upgradeCreative Commons 'BY-NC-ND' version 4.0 license
      • Article
      • Peer Reviewed
      UC San Diego Previously Published Works (2017)
      Insects rely on their sense of smell to guide a wide range of behaviors that are critical for their survival, such as food-seeking, predator avoidance, oviposition, and mating. Myriad chemicals of varying volatilities have been identified as natural odorants that activate insect Olfactory Receptor Neurons (ORNs). However, studying the olfactory responses to low-volatility odorants has been hampered by an inability to effectively present such stimuli using conventional odor-delivery methods. Here, we describe a procedure that permits the effective presentation of low-volatility odorants for in vivo Single-Sensillum Recording (SSR). By minimizing the distance between the odor source and the target tissue, this method allows for the application of biologically salient but hitherto inaccessible odorants, including palmitoleic acid, a stimulatory pheromone with a demonstrated effect on ORNs involved in courtship and mating behavior1. Our procedure thus affords a new avenue to assay a host of low-volatility odorants for the study of insect olfaction and pheromone communication.
        Cover page: Electrophysiological Recording from Drosophila Trichoid Sensilla in Response to Odorants of Low Volatility.
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        • Peer Reviewed
        UC Santa Cruz Previously Published Works (2017)

        We demonstrate transcutical structural and functional imaging of neurons labeled with genetically encoded red fluorescent proteins and calcium indicators in the living Drosophila brain with cellular and subcellular resolution.

          Cover page: Transcutical imaging with cellular and subcellular resolution.
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          • Peer Reviewed
          Faculty Publications (1997)

          Seasonal trade wind-induced upwelling along the southern margin of the Caribbean Sea occurs in response to the annual migration of the Intertropical Convergence Zone. Laminated, high deposition rate sediments of the Cariaco Basin, a small anoxic basin on the Venezuelan continental shelf, clearly record large changes in the past intensity of this upwelling. Because sediments of the Cariaco Basin are largely unbioturbated, they offer a natural opportunity to study the stable isotopic records of multiple planktonic foraminiferal taxa and to evaluate their sensitivity to both the modern hydrography and temporal changes in upwelling intensity and climate. Oxygen isotope data (δ18O) from four dominant foraminiferal taxa are presented for the time period covering the last 28 kyr. The δ18O data from Globigerina bulloides, after correction for nonequilibrium precipitation, are used as a monitor of sea surface conditions during the winter-spring upwelling season. The δ18O data from white Globigerinoides ruber are used as a measure of annual-average conditions in the near surface, while pink G. ruber data are consistent with use as an index of endmember conditions during the summer-fall nonupwelling season. Data from the deeper dwelling Neogloboquadrina dutertrei yield information on conditions near the base of the local thermocline. During the last glacial, δ18O data from G. ruber and generally reduced interspecific differences indicate cooling of surface waters over the Cariaco Basin by up to 4°C. This longer-term cooling does not appear to be related to changes in upwelling intensity along the coast but may instead reflect more regional cooling of the larger Caribbean. Superimposed on this pattern, between 12.6 and ∼10 ka, is a convergence of δ18O data between G. bulloides and N. dutertrei, implying much stronger upwelling during the last deglaciation. This scenario is consistent with other evidence for high productivity at this time. At ∼14 ka, a sharp δ18O depletion event observed in all taxa seems to have been produced by increased freshwater discharge to the southern Caribbean, suggesting either higher regional rainfall or the influence of glacial melting in the Andes. Minimum δ18O values of pink G. ruber around 6–7 ka record warmer summer sea surface temperatures and/or decreased salinity in the mid-Holocene.

            Cover page: Late Quaternary climate change from delta 13 O records of multiple species of planktonic foraminifera: High-resolution records from the Anoxic Cariaco Basin, VenezuelaCreative Commons 'BY' version 4.0 license
            • Article
            • Peer Reviewed
            UC Davis Previously Published Works (2015)
            We report engineering Neurospora crassa to improve the yield of cellobiose and cellobionate from cellulose. A previously engineered strain of N. crassa (F5) with six of seven β-glucosidase (bgl) genes knocked out was shown to produce cellobiose and cellobionate directly from cellulose without the addition of exogenous cellulases. In this study, the F5 strain was further modified to improve the yield of cellobiose and cellobionate from cellulose by increasing cellulase production and decreasing product consumption. The effects of two catabolite repression genes, cre-1 and ace-1, on cellulase production were investigated. The F5 Δace-1 mutant showed no improvement over the wild type. The F5 Δcre-1 and F5 Δace-1 Δcre-1 strains showed improved cellobiose dehydrogenase and exoglucanase expression. However, this improvement in cellulase expression did not lead to an improvement in cellobiose or cellobionate production. The cellobionate phosphorylase gene (ndvB) was deleted from the genome of F5 Δace-1 Δcre-1 to prevent the consumption of cellobiose and cellobionate. Despite a slightly reduced hydrolysis rate, the F5 Δace-1 Δcre-1 ΔndvB strain converted 75% of the cellulose consumed to the desired products, cellobiose and cellobionate, compared to 18% converted by the strain F5 Δace-1 Δcre-1.
              Cover page: Engineering Neurospora crassa for Improved Cellobiose and Cellobionate Production
              • Article
              • Peer Reviewed
              UC San Diego Previously Published Works (2022)
              Animals must set behavioural priority in a context-dependent manner and switch from one behaviour to another at the appropriate moment1-3. Here we probe the molecular and neuronal mechanisms that orchestrate the transition from feeding to courtship in Drosophila melanogaster. We find that feeding is prioritized over courtship in starved males, and the consumption of protein-rich food rapidly reverses this order within a few minutes. At the molecular level, a gut-derived, nutrient-specific neuropeptide hormone-Diuretic hormone 31 (Dh31)-propels a switch from feeding to courtship. We further address the underlying kinetics with calcium imaging experiments. Amino acids from food acutely activate Dh31+ enteroendocrine cells in the gut, increasing Dh31 levels in the circulation. In addition, three-photon functional imaging of intact flies shows that optogenetic stimulation of Dh31+ enteroendocrine cells rapidly excites a subset of brain neurons that express Dh31 receptor (Dh31R). Gut-derived Dh31 excites the brain neurons through the circulatory system within a few minutes, in line with the speed of the feeding-courtship behavioural switch. At the circuit level, there are two distinct populations of Dh31R+ neurons in the brain, with one population inhibiting feeding through allatostatin-C and the other promoting courtship through corazonin. Together, our findings illustrate a mechanism by which the consumption of protein-rich food triggers the release of a gut hormone, which in turn prioritizes courtship over feeding through two parallel pathways.
                Cover page: A nutrient-specific gut hormone arbitrates between courtship and feeding
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                • Peer Reviewed
                UC San Francisco Previously Published Works (2024)
                Purpose To evaluate and report the performance of the winning algorithms of the Radiological Society of North America Cervical Spine Fracture AI Challenge. Materials and Methods The competition was open to the public on Kaggle from July 28 to October 27, 2022. A sample of 3112 CT scans with and without cervical spine fractures (CSFx) were assembled from multiple sites (12 institutions across six continents) and prepared for the competition. The test set had 1093 scans (private test set: n = 789; mean age, 53.40 years ± 22.86 [SD]; 509 males; public test set: n = 304; mean age, 52.51 years ± 20.73; 189 males) and 847 fractures. The eight top-performing artificial intelligence (AI) algorithms were retrospectively evaluated, and the area under the receiver operating characteristic curve (AUC) value, F1 score, sensitivity, and specificity were calculated. Results A total of 1108 contestants composing 883 teams worldwide participated in the competition. The top eight AI models showed high performance, with a mean AUC value of 0.96 (95% CI: 0.95, 0.96), mean F1 score of 90% (95% CI: 90%, 91%), mean sensitivity of 88% (95% Cl: 86%, 90%), and mean specificity of 94% (95% CI: 93%, 96%). The highest values reported for previous models were an AUC of 0.85, F1 score of 81%, sensitivity of 76%, and specificity of 97%. Conclusion The competition successfully facilitated the development of AI models that could detect and localize CSFx on CT scans with high performance outcomes, which appear to exceed known values of previously reported models. Further study is needed to evaluate the generalizability of these models in a clinical environment. Keywords: Cervical Spine, Fracture Detection, Machine Learning, Artificial Intelligence Algorithms, CT, Head/Neck Supplemental material is available for this article. © RSNA, 2024.
                  Cover page: Performance of the Winning Algorithms of the RSNA 2022 Cervical Spine Fracture Detection Challenge.
                  • Article
                  • Peer Reviewed
                  UC San Diego Previously Published Works (2019)
                  Critical to evolutionary fitness, animals regulate social behaviors by integrating signals from both their external environments and internal states. Here, we find that population density modulates the courtship behavior of male Drosophila melanogaster in an age-dependent manner. In a competitive mating assay, males reared in a social environment have a marked advantage in courting females when pitted against males reared in isolation. Group housing promotes courtship in mature (7-day) but not immature (2-day) males; this behavioral plasticity requires the Or47b pheromone receptor. Using single-sensillum recordings, we find that group housing increases the response of Or47b olfactory receptor neurons (ORNs) only in mature males. The effect of group housing on olfactory response and behavior can be mimicked by chronically exposing single-housed males to an Or47b ligand. At the molecular level, group housing elevates Ca2+ levels in Or47b ORNs, likely leading to CaMKI-mediated activation of the histone-acetyl transferase CBP. This signaling event in turn enhances the efficacy of juvenile hormone, an age-related regulator of reproductive maturation in flies. Furthermore, the male-specific Fruitless isoform (FruM) is required for the sensory plasticity, suggesting that FruM functions as a downstream genomic coincidence detector in Or47b ORNs-integrating reproductive maturity, signaled by juvenile hormone, and population density, signaled by CBP. In all, we identify a neural substrate and activity-dependent mechanism by which social context can directly influence pheromone sensitivity, thereby modulating social behavior according to animals' life-history stage.
                    Cover page: Social Context Enhances Hormonal Modulation of Pheromone Detection in Drosophila
                    • Article
                    • Peer Reviewed
                    UC Davis Previously Published Works (2019)
                    Gluconic acid, an oxidized cellulose degradation product, could be produced from cellulosic biomass. Glycerol is an inexpensive and renewable resource for fuels and chemicals production and is available as a byproduct of biodiesel production. Gluconate is a more oxidized substrate than glucose, whereas glycerol is a more reduced substrate than glucose. Although the production of homoethanol from glucose can be achieved, the conversion of gluconate to ethanol is accompanied by the production of oxidized byproduct such as acetate, and reduced byproducts such as 1,3-propanediol are produced, along with ethanol, when glycerol is used as the carbon source. When gluconate and glycerol are used as the sole carbon source by Klebsiella oxytoca BW21, the ethanol yield is about 62 to 64%. Coutilization of both gluconate and glycerol in batch fermentation increased the yield of ethanol to about 78.7% and decreased by-product accumulation (such as acetate and 1,3-propanediol) substantially. Decreasing by-product formation by deleting the pta, frd, ldh, pflA, and pduC genes in strain BW21 increased the ethanol yield to 89.3% in the batch fermentation of a glycerol-gluconate mixture. These deletions produced the strain K. oxytoca WT26. However, the utilization rate of glycerol was significantly slower than that of gluconate in batch fermentation. In addition, substantial amounts of glycerol remain unutilized after gluconate was depleted in batch fermentation. Continuous fed-batch fermentation was used to solve the utilization rate mismatch problem for gluconate and glycerol. An ethanol yield of 97.2% was achieved in continuous fed-batch fermentation of these two substrates, and glycerol was completely used at the end of the fermentation.IMPORTANCE Gluconate is a biomass-derived degradation product, and glycerol can be obtained as a biodiesel byproduct. Compared to glucose, using them as the sole substrate is accompanied by the production of by-products. Our study shows that through pathway engineering and adoption of a fed-batch culture system, high-yield homoethanol production that usually can be achieved by using glucose as the substrate is achievable using gluconate and glycerol as cosubstrates. The same strategy is expected to be able to achieve homofermentative production of other products, such as lactate and 2,3-butanediol, which can be typically achieved using glucose as the substrate and inexpensive biodiesel-derived glycerol and biomass-derived gluconate as the cosubstrates.
                      Cover page: Homoethanol Production from Glycerol and Gluconate Using Recombinant Klebsiella oxytoca Strains.
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