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Open Access Publications from the University of California

Open Access Policy Deposits

This series is automatically populated with publications deposited by UC Irvine Donald Bren School of Information and Computer Sciences Department of Computer Science researchers in accordance with the University of California’s open access policies. For more information see Open Access Policy Deposits and the UC Publication Management System.
Cover page of Neurodatascience: Past, Present, and Future

Neurodatascience: Past, Present, and Future

(2026)

The study of the brain is a compelling example of the power of convergent science. Over the last few decades, advances in neuroscience techniques and experimentation, as well as in data science tools to analyze the resulting data, have dramatically furthered our understanding of fundamental brain functions. Historically, it has been common for analytical approaches to have a considerable lag in development following the availability of new neuroscience techniques. However, this relationship has not simply been unidirectional, as there have been examples in which analytical developments have directly led to new scientific questions and experiments. Here we review how this interplay between neuroscience and data science advances has unfolded in the past and into the present, with a focus on electrophysiology and calcium imaging. Applying lessons learned from the past and present, we then discuss expected developments, challenges, and opportunities in the future. We end by providing recommendations on how to foster the necessary team science approach to continue the advancement of research at the intersection of neuroscience and data science, which we call neurodatascience, toward a sustainable future.

Cover page of Retinal nerve fibre layer optical texture analysis: retinal nerve fibre bundle defect patterns and the extent of macular involvement across different stages of glaucoma

Retinal nerve fibre layer optical texture analysis: retinal nerve fibre bundle defect patterns and the extent of macular involvement across different stages of glaucoma

(2026)

BACKGROUND/AIMS: To apply retinal nerve fibre layer (RNFL) optical texture analysis (ROTA) to investigate (1) the patterns of RNFL bundle defects, and (2) the frequency of papillomacular and papillofoveal bundle involvement across early, moderate and advanced glaucoma. METHODS: All eyes underwent 24-2 visual field (VF) testing and optical coherence tomography (OCT) for ROTA. The borders of RNFL defects were delineated from ROTA, and the involvement of the arcuate, papillomacular and papillofoveal bundles was determined for each eye. 24-2 VF stimulus projections were mapped onto the corresponding topographic areas of ROTA images. Multilevel logistic regression analysis was applied to evaluate the structure-function association. RESULTS: Papillomacular bundle defects were highly prevalent in glaucoma, increasing from 87.7% in early to 95.35% in moderate and 100% in advanced glaucoma. Papillofoveal bundle defects were also common, increasing from 29.7% in early to 36.05% in moderate and 60.98% in advanced glaucoma. Central four 24-2 test locations that projected onto the trajectories of papillomacular or papillofoveal RNFL bundle defects demonstrated significantly increased likelihood of VF sensitivity abnormality (ORs of 22.42 at PDP<5% and 20.26 at TDP<5%, respectively, p<0.001 for both). CONCLUSION: ROTA uncovers a wide spectrum of RNFL bundle defects spanning the entire glaucoma continuum. It also provides visualisation of the preserved RNFL bundles in advanced glaucoma. Papillomacular and papillofoveal RNFL bundle defects are present in a considerable proportion of eyes with early, moderate and advanced glaucoma, and, when detected, they significantly increase the likelihood of abnormality in the corresponding central 24-2 test locations.

FamilyBloom: Examining Ecologies of Collaboration in Family-Centered Health Tracking

(2026)

Family health informatics tools can help support well-being with shared data tracking. Prior work typically focused on shared data review, but often in specific moments, like bedtime, or centered on caregiving of children or elderly members. To investigate how tracking can support mutual health collaboration between family members pervasively across daily contexts, we designed and deployed FamilyBloom, a glanceable smartwatch and home display system for mood and goal tracking. Twelve families with both neurotypical and ADHD members used FamilyBloom for three months on average. Our findings reveal how family-centered tracking created collaboration opportunities and tensions across multiple ecological systems: individual self-regulation, collaborations within family dynamics, involvement of care networks with varying trust levels, institutional school constraints and cultural stigma, and temporality of regular routines and crisis periods. We discuss an ecosystem-aware approach to family informatics, wherein design can attend to how families navigate multiple contexts while sustaining family-level collaboration.

Cover page of Computed tomography staging of colon cancer: improved patient selection for neoadjuvant therapy with combined radiologic tumor and nodal staging.

Computed tomography staging of colon cancer: improved patient selection for neoadjuvant therapy with combined radiologic tumor and nodal staging.

(2026)

BACKGROUND: Patient selection for neoadjuvant therapy in colon cancer (CC) needs to be improved as utilizing computed tomography (CT) tumor (T) staging alone is associated with overstaging and overtreatment. Therefore, we sought to identify specific nodal imaging features that can be combined with radiologic T staging to improve patient selection. METHODS: Pre-operative CTs of stage I-III CC patients treated with upfront resection (2018–2023) were assessed by an expert abdominal radiologist blinded to the histopathologic staging. Radiologic T and node (N) staging based on five imaging features (single lymph node (LN) > 1 cm, ≥ 3 prominent LNs, irregular borders, heterogenous enhancement, and extramural venous invasion) were compared to the pathologic staging, grouped by proficient or deficient mismatch repair status (pMMR vs. dMMR). RESULTS: Of the 177 patients, 147 and 30 had pMMR and dMMR CC, respectively. The overstaging rate for pathologic T staging was 6.1% pMMR vs. 6.7% dMMR CC (p = 0.91). The overstaging rate for pathologic N disease by any imaging feature was 17.0% pMMR vs. 33.3% dMMR (p = 0.04) but improved to 4.8% pMMR vs. 6.7% dMMR (p = 0.67) with irregular borders and/or heterogenous enhancement alone. Compared to radiologic T staging only, the addition of N staging (any feature) to T staging resulted in decreased overstaging rates of stage I/low-risk stage II to high-risk stage II/III CC from 25.2% to 15.6% for pMMR CC and 60.0% to 33.3% for dMMR CC. Overstaging rates further decreased to 4.8% for pMMR and 16.7% for dMMR CC with the combination of radiologic T and N staging by irregular borders and/or heterogenous enhancement specifically. CONCLUSION: Combining radiologic T and N stage based on any of the five imaging features resulted in lower overstaging rates than radiologic T staging alone, but overstaging rates continued to improve when only irregular borders and heterogenous enhancement were used to assess nodal disease. These results can be used as an initial framework for combining CT T and N staging for CC and improve patient selection for neoadjuvant treatment.

The Energy Exascale Earth System Model Version 3: 2. Overview of the Coupled System

(2026)

Abstract The Energy Exascale Earth System Model version 3 (E3SMv3) represents the latest advancement in Earth system modeling developed by the U.S. Department of Energy (DOE). Building upon previous versions, E3SMv3 introduces significant updates across its coupled components to enhance capability and improve fidelity. The atmosphere component incorporates advancements in chemistry, aerosol‐cloud interactions, convection, and microphysics. The ocean features a new time‐stepping scheme and a higher‐resolution unstructured mesh with sub‐ice‐shelf cavities, while the sea ice model integrates advanced snow and ice physics for more realistic cryospheric simulations. The land model introduces prognostic vegetation dynamics and a new sub‐grid topographic treatment of solar radiation. A new tri‐grid configuration harmonizes the horizontal grids of the land and river components for improved process coupling. It is enabled by a new non‐linear remapping between the atmosphere and land. E3SMv3 underwent extensive testing through a comprehensive simulation campaign, including pre‐industrial control, idealized experiments, and historical simulations spanning 1850–2024. The model demonstrates significant improvements in simulating the evolution of the historical surface temperature, particularly addressing the “pothole cooling” bias in earlier versions. Reduced aerosol‐related forcing contributes to more realistic radiative forcing and better alignment with the observational record. Ocean heat content (OHC) and sea ice trends are also improved as a result. Plain Language Summary The Energy Exascale Earth System Model version 3 (E3SMv3), developed by the U.S. Department of Energy, is a state‐of‐the‐science tool designed to advance our understanding of the Earth and energy systems. This model simulates interactions between the atmosphere, land, rivers, oceans, and sea ice to predict Earth system changes and their impacts. E3SMv3 includes major improvements, such as enhanced representations of atmospheric chemistry, clouds, aerosols, sea ice, and vegetation dynamics. It also introduces refined marine and land grids to improve the accuracy of how these components interact. E3SMv3 was evaluated through simulations of past and historical conditions, totaling over 5,000 years. The model successfully resolved a major issue leading to unrealistic cooling trends during the mid‐20th century. E3SMv3 now provides more accurate predictions of surface temperatures, ocean heat content, and sea ice changes, closely matching observed data. Key Points E3SMv3 introduces major updates to the atmosphere, sea ice, and land components, enhancing capability and improving fidelity E3SMv3 increases resolution in the ocean‐sea ice mesh and unifies land and river grids for tighter coupling within and between components Reduced aerosol forcing in E3SMv3 resolves mid‐20th century cooling biases, aligning historical temperature trends with observations

Cover page of Evaluating the potential of acupuncture for Alzheimer’s disease treatment: A meta-analysis and systematic review of mouse model studies

Evaluating the potential of acupuncture for Alzheimer’s disease treatment: A meta-analysis and systematic review of mouse model studies

(2026)

Acupuncture is an ancient practice that was developed within the framework of traditional Chinese medicine. While acupuncture has been recently proposed as a therapy for Alzheimer’s disease (AD), acupuncture effects are not well understood in terms of neural mechanisms. Here, we review and examine the studies that used AD mouse models and analyze the experiments where researchers administered electroacupuncture (EA) to AD mice to assess the potential therapeutic impact of acupuncture on disease pathology and cognitive function in controlled laboratory settings. We analyzed 29 relevant PubMed articles published between January 2014 and July 2025. Our results reveal that EA significantly reduces both amyloid-beta (Aβ) and phosphorylated tau (p-tau) levels and neuroinflammatory biomarkers, including molecular signatures for activated microglia and astrocytes in the brain. EA also enhances cognitive functions. While no study directly compared acupoint strategies, the indirect comparisons in our network analysis suggest that GV20 has potential as a therapeutic target for AD. Our present meta-analysis and review of literature add to the evidence of integrative health practices for acupuncture-based Alzheimer’s disease treatment.

Cover page of Enhancing Detection of Message Intents in a Mobile Health Smoking-Cessation Intervention Using Large Language Model Fine-Tuning, Data Downsampling, and Error Correction: Algorithm Development and Validation

Enhancing Detection of Message Intents in a Mobile Health Smoking-Cessation Intervention Using Large Language Model Fine-Tuning, Data Downsampling, and Error Correction: Algorithm Development and Validation

(2026)

Background: Although smoking-cessation aids such as support groups and nicotine replacement therapy (NRT) can help people quit, quit rates remain low. Mobile health interventions can boost accessibility and engagement, especially with NRT, but require ongoing effort to deliver timely responses. Accurate intent detection is crucial for identifying user needs and delivering timely, appropriate chatbot responses. Recent large language model advancements in natural language processing and artificial intelligence (AI) have shown promise. However, these systems often struggle with many intent categories, complex language, and imbalanced data, reducing recognition accuracy. Objective: The main goal of this study was to develop an AI tool, a large language model that could accurately detect people's message intents, despite dataset imbalances and complexities. In our application, the messages came from a smoking-cessation support-group intervention and often involved the use of NRT provided as part of that intervention. Methods: We consistently used a state-of-the-art public domain large language model, Llama-3 8B (8 billion parameters) from Meta. First, we used the model off-the-shelf. Second, we fine-tuned it on our annotated dataset with 25 intent categories. Third, we also downsampled the predominant intent category to reduce model bias. Finally, we combined downsampling with corrected human annotations, creating a cleaned dataset for a new round of fine-tuning. Results: Without fine-tuning, the model achieved unweighted and weighted F1-scores (overall performance) of 0.41 and 0.38, respectively, on the downsampled corrected test dataset, and 0.29 and 0.35 on the full test dataset. Fine-tuning improved performance to 0.77 and 0.80 on the downsampled corrected dataset, and 0.72 and 0.86 on the full dataset. Fine-tuning with downsampling attained the best F1-scores, 0.88 and 0.91 on the downsampled corrected dataset, though performance dropped on the full test dataset (0.58 unweighted, 0.66 weighted) due to the predominance of the off-topic intent category, while unweighted recall remained high (0.80). The final method combining fine-tuning, downsampling, and error correction achieved 0.86 unweighted and 0.90 weighted F1-scores on the downsampled corrected dataset, and 0.57 and 0.65 on the full dataset with unweighted recall improving to 0.82. Conclusions: Large language models performed poorly without fine-tuning, highlighting the need for domain-specific training. Even with fine-tuning, performance was limited by a highly imbalanced dataset. Downsampling before fine-tuning moderately improved performance but still left room for improvement and concerns about dataset noise. A careful review of model-human disagreement cases helped identify human annotation errors. After error correction, the method without error correction still achieved slightly higher precision and F1-score on the corrected test dataset. While error correction slightly improved recall on noisy data, automated downsampling alone may be sufficient, making manual correction a more resource-intensive option with limited added benefit.