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Open Access Publications from the University of California

Scholarly Works (4 results)

  • Thesis
  • Peer Reviewed
UC Santa Barbara Electronic Theses and Dissertations (2024)

This thesis reports a search for anomalous production of inclusive single photon events from neutrino interactions using the Wire-Cell event reconstruction package in the MicroBooNE experiment, which is motivated by the previous observation of a low-energy excess (LEE) of electromagnetic events from the MiniBooNE experiment.

In the last few decades, multiple short-baseline experiments have reported anomalies in their measurements of neutrino interactions. Among them is the MiniBooNE experiment, which has reported a 4.8$\sigma$ excess of single electromagnetic shower events in the low energy region ($E_\nu \sim$100--800 MeV), commonly referred to as the MiniBooNE Low-Energy Excess (LEE)\cite{mb:2021}. However, the nature of these events remains unknown due to MiniBooNE's inability to distinguish between electron- and photon-induced showers. The Short-Baseline Neutrino (SBN) Program at Fermilab aims to shine light on the nature and origin of the MiniBooNE anomaly.

Running from 2015 to 2021, MicroBooNE was the first SBN detector to collect data and has already begun to probe the MiniBooNE anomaly. In MicroBooNE's first round of LEE results, which consisted of both electron-like and photon-like excess searches, no significant excess was seen in events with a single electron-like or single photon-like electromagnetic shower in the final state~\cite{uB_eLEE_PRL,uB_gLEE}. However, unlike the electron-like LEE searches, which covered a wide range of final states and possible processes, the photon-like LEE search only focused on one specific model, that of \ncdeltaNgamma{} decays. Given these results, a more general search for photon-like events was needed to complete a model-independent investigation of the MiniBooNE anomaly. This thesis describes such a model-independent analysis searching for events from neutrino interactions that result in a single photon, above 20 MeV kinetic energy, inside the MicroBooNE detector volume, with no charged leptons and any number of hadrons.

A selection of inclusive single photon final-state interactions using the Wire-Cell event reconstruction package, with a final selection efficiency of 7.0\% and purity of 40.2\%, is described. Systematic uncertainties and statistical treatments are also discussed. Sidebands to provide measurements of \numuCC{} and \ncpio{} interactions are created and used to constrain signal and background predictions and reduce uncertainties for the rare single photon interactions. A blind analysis was performed using a data set collected from Feb 2016 to July 2018, corresponding to an exposure of 6.34$\times$10$^{20}$ protons on target from the Booster Neutrino Beam (BNB) at FNAL. In the full signal region, we observe an excess of single-photon events with a significance of less than 2.0$\sigma$. In a subsample of these events containing no observed protons, we observe an excess of $92.8$ events above prediction, corresponding to a 2.0$\sigma$ significance, concentrated mostly in shower energies below 600 MeV.

Additionally, the final detector of the SBN program, SBND, is planned to begin physics data-taking in 2024. It expects to acquire orders of magnitude more neutrino data that can be used for future expansions of this investigation. Work on the commissioning of SBND is presented.

    Cover page: A Search for Anomalous Single Photon Production in Neutrino Interactions with the MicroBooNE Detector
    • Article
    • Peer Reviewed
    UCLA Previously Published Works (2023)
    MOTIVATION: In recent years, high-throughput sequencing technologies have made large-scale protein sequences accessible. However, their functional annotations usually rely on low-throughput and pricey experimental studies. Computational prediction models offer a promising alternative to accelerate this process. Graph neural networks have shown significant progress in protein research, but capturing long-distance structural correlations and identifying key residues in protein graphs remains challenging. RESULTS: In the present study, we propose a novel deep learning model named Hierarchical graph transformEr with contrAstive Learning (HEAL) for protein function prediction. The core feature of HEAL is its ability to capture structural semantics using a hierarchical graph Transformer, which introduces a range of super-nodes mimicking functional motifs to interact with nodes in the protein graph. These semantic-aware super-node embeddings are then aggregated with varying emphasis to produce a graph representation. To optimize the network, we utilized graph contrastive learning as a regularization technique to maximize the similarity between different views of the graph representation. Evaluation of the PDBch test set shows that HEAL-PDB, trained on fewer data, achieves comparable performance to the recent state-of-the-art methods, such as DeepFRI. Moreover, HEAL, with the added benefit of unresolved protein structures predicted by AlphaFold2, outperforms DeepFRI by a significant margin on Fmax, AUPR, and Smin metrics on PDBch test set. Additionally, when there are no experimentally resolved structures available for the proteins of interest, HEAL can still achieve better performance on AFch test set than DeepFRI and DeepGOPlus by taking advantage of AlphaFold2 predicted structures. Finally, HEAL is capable of finding functional sites through class activation mapping. AVAILABILITY AND IMPLEMENTATION: Implementations of our HEAL can be found at https://github.com/ZhonghuiGu/HEAL.
      Cover page: Hierarchical graph transformer with contrastive learning for protein function prediction.Creative Commons 'BY' version 4.0 license
      • Article
      • Peer Reviewed
      UC San Diego Previously Published Works (2010)
      Abstract Background The current paradigm for cord blood transplantation is that HLA matching and immune suppression are strictly required to prevent graft versus host disease (GVHD). Immunological arguments and historical examples have been made that the use of cord blood for non-hematopoietic activities such as growth factor production, stimulation of angiogenesis, and immune modulation may not require matching or immune suppression. Methods 114 patients suffering from non-hematopoietic degenerative conditions were treated with non-matched, allogeneic cord blood. Doses of 1-3 × 107 cord blood mononuclear cells per treatment, with 4-5 treatments both intrathecal and intravenously were performed. Adverse events and hematological, immunological, and biochemical parameters were analyzed for safety evaluation. Results No serious adverse effects were reported. Hematological, immunological, and biochemical parameters did not deviate from normal ranges as a result of therapy. Conclusion The current hematology-based paradigm of need for matching and immune suppression needs to be revisited when cord blood is used for non-hematopoietic regenerative purposes in immune competent recipients.
        Cover page: Safety evaluation of allogeneic umbilical cord blood mononuclear cell therapy for degenerative conditions
        • Article
        • Peer Reviewed
        UC Davis Previously Published Works (2020)
        Rationale: Dysregulation of arachidonic acid (ARA) metabolism results in inflammation; however, its role in acute lung injury (ALI) remains elusive. In this study, we addressed the role of dysregulated ARA metabolism in cytochromes P450 (CYPs) /cyclooxygenase-2 (COX-2) pathways in the pathogenesis of lipopolysaccharide (LPS)-induced ALI in mice. Methods: The metabolism of CYPs/COX-2-derived ARA in the lungs of LPS-induced ALI was investigated in C57BL/6 mice. The COX-2/sEH dual inhibitor PTUPB was used to establish the function of CYPs/COX-2 dysregulation in ALI. Primary murine macrophages were used to evaluate the underlying mechanism of PTUPB involved in the activation of NLRP3 inflammasome in vitro. Results: Dysregulation of CYPs/COX-2 metabolism of ARA occurred in the lungs and in primary macrophages under the LPS challenge. Decrease mRNA expression of Cyp2j9, Cyp2j6, and Cyp2j5 was observed, which metabolize ARA into epoxyeicosatrienoic acids (EETs). The expressions of COX-2 and soluble epoxide hydrolase (sEH), on the other hand, was significantly upregulated. Pre-treatment with the dual COX-2 and sEH inhibitor, PTUPB, attenuated the pathological injury of lung tissues and reduced the infiltration of inflammatory cells. Furthermore, PTUPB decreased the pro-inflammatory factors, oxidative stress, and activation of NACHT, LRR, and PYD domains-containing protein 3 (NLRP3) inflammasome in LPS-induced ALI mice. PTUPB pre-treatment remarkably reduced the activation of macrophages and NLRP3 inflammasome in vitro. Significantly, both preventive and therapeutic treatment with PTUPB improved the survival rate of mice receiving a lethal dose of LPS. Conclusion: The dysregulation of CYPs/COX-2 metabolized ARA contributes to the uncontrolled inflammatory response in ALI. The dual COX-2 and sEH inhibitor PTUPB exerts anti-inflammatory effects in treating ALI by inhibiting the NLRP3 inflammasome activation.
          Cover page: A COX-2/sEH dual inhibitor PTUPB alleviates lipopolysaccharide-induced acute lung injury in mice by inhibiting NLRP3 inflammasome activationCreative Commons 'BY' version 4.0 license
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