Skip to main content
eScholarship
Open Access Publications from the University of California

UC San Diego

UC San Diego Previously Published Works bannerUC San Diego
Cover page of Recent advances and applications of deep learning methods in materials science

Recent advances and applications of deep learning methods in materials science

(2022)

Deep learning (DL) is one of the fastest-growing topics in materials data science, with rapidly emerging applications spanning atomistic, image-based, spectral, and textual data modalities. DL allows analysis of unstructured data and automated identification of features. The recent development of large materials databases has fueled the application of DL methods in atomistic prediction in particular. In contrast, advances in image and spectral data have largely leveraged synthetic data enabled by high-quality forward models as well as by generative unsupervised DL methods. In this article, we present a high-level overview of deep learning methods followed by a detailed discussion of recent developments of deep learning in atomistic simulation, materials imaging, spectral analysis, and natural language processing. For each modality we discuss applications involving both theoretical and experimental data, typical modeling approaches with their strengths and limitations, and relevant publicly available software and datasets. We conclude the review with a discussion of recent cross-cutting work related to uncertainty quantification in this field and a brief perspective on limitations, challenges, and potential growth areas for DL methods in materials science.

Cover page of Hostile Ecologies: Navigating the Barriers to Community-Led Innovation

Hostile Ecologies: Navigating the Barriers to Community-Led Innovation

(2022)

This paper describes how the contemporary technology innovation ecology is hostile to community-driven design. These hostilities are important to understand if we want to intervene in the policy landscape of technology innovation to support viable alternatives to big tech consolidation and more democratic ways of developing and maintaining technology. We contribute a thick description of the hostile ecologies faced by transportation workers, community organizers, and allied technology researchers as they work toward building a cooperatively-owned taxi business with a digital dispatching technology. Our findings show that the hostile innovation ecology manifests as constrained access to resources, an inequitable regulatory framework, diminished agency in the software design process, and limits to the will of our community partners. We discuss the paths toward innovation for United Taxi Workers San Diego as compared with transportation network companies (e.g. Lyft, Uber) in terms of access to funding, regulation, labor, expertise, and market. We argue that a critical examination of institutions and policies in the innovation ecology is a necessary step toward charting fair, equitable, and community-strengthening pathways for technology innovation in the future.

Haunting melodies: Specific memories distort beat perception.

(2022)

How much does specific previous experience shape immediate perception? Top-down perceptual inference occurs in ambiguous situations. However, similarity-based accounts such as exemplar theory suggest that similar memories resonate with the percept, predicting that detailed previous experiences can shape perception even when bottom-up cues are unambiguous. The current study tests whether specific musical memories influence beat perception only under ambiguity, or more pervasively-that is, even when clear bottom-up beat cues are present. Listeners were exposed to 16 melodies, half in one meter, half in another. Later, each listener's perception of a specific melody's beat pattern was tested when that melody occurred in either its original meter or another meter. Ratings of metrical probes were influenced not only by fit with the current (test) meter, but also by fit with the meter previously experienced with that melody. Findings suggest that perception is routinely influenced by detailed top-down perceptual imagery.

Associations of chronotype and sleep patterns with metabolic syndrome in the Hispanic community health study/study of Latinos.

(2022)

Sleep duration, sleep efficiency, and sleep timing have been shown to have potential effects on metabolic functions relevant to circadian rhythms. It is not clear if the impact of sleep patterns on metabolic risk factors is through sociocultural and environmental factors or circadian misalignment. We investigated the associations of sleep patterns, chronotype, and social jet lag with metabolic syndrome among non-shift worker Hispanic/Latino adults. We used cross-sectional data from the Sueño Ancillary Study of The Hispanic Community Health Study/Study of Latinos (HCHS/SOL). Data from a subsample of 2189 participants aged 18-64 years were used in the analysis. Mean nightly sleep duration, mean sleep onset time, mean sleep offset time, mean sleep midpoint time, sleep efficiency, sleep variability (standard deviation (SD) of sleep duration, and SD of sleep midpoint), and time spent above light exposure threshold (1000 lux) in a day were assessed by wrist actigraphy (Acti-watch Spectrum). Chronotype was determined by the reduced Morningness-Eveningness Questionnaire. Medical conditions including dyslipidemia, hypertension, and diabetes mellitus were determined from a fasting blood specimen and physical exam at the baseline visit. To determine whether sleep patterns, light levels, chronotype, and social jetlag are associated with metabolic syndrome, multivariable logistic regression models were fitted, including variables with P < .15 in the univariate analysis. The results of the multivariable analysis demonstrated that in participants older than 40 years, intermediate chronotype (vs early) was significantly associated with a higher risk of metabolic syndrome (Odds ratio (95%CI): 1.33 (1.04,1.7)), while later chronotype (vs. early) in participants younger than 40 years was significantly associated with a lower risk of metabolic syndrome (Odds ratio (95%CI): 0.37 (0.14, 0.96)). Also, higher sleep efficiency was significantly associated with decreased odds of metabolic syndrome (Odds ratio (95%CI): 0.98 (0.96, 0.99)). Nightly sleep duration was not significantly different between two groups of participants with and without metabolic syndrome in multivariable analyses. There was no significant association between social jet lag and metabolic syndrome in multivariable analysis (p = .286). Moreover, there was no significant association between chronotype and social jet lag in multivariable analysis. The association between metabolic syndrome and chronotype is age-dependent. While early chronotype is associated with metabolic syndrome in younger individuals, it tended to be associated with lower odds for metabolic syndrome in older individuals.

Electrode biasing maintains the edge shear layer at high density in the J-TEXT tokamak

(2022)

Abstract Collapse of the edge flow shear as the line-averaged density approaches the Greenwald density limit has been observed as a precursor to the enhanced edge particle flux characteristic of proximity to the density limit regime. Here, we report the use of a biased electrode to sustain the edge shear layer in high density discharges, in which the shear layer would otherwise collapse. A stable increase in line-averaged density is observed along with a strong increase in edge density. These experiments were carried out on the J-TEXT tokamak. The Reynolds stress at the edge is enhanced, and the zonal flow sustained, while density perturbation levels, the flux of turbulence internal energy (i.e., turbulence spreading), and particle and heat flux all decrease significantly. Electron adiabaticity increases, and bias voltage modulation experiments show that an increase in the edge shear leads the increase in adiabaticity. These results suggest that external edge E × B flow shear drive may be of interest for sustaining edge plasma states at high density, and support the hypothesis that collapse of the edge shear layer triggers the onset of the strong transport and turbulence characteristic of the density limit regime.

Development of the HIV360 international core set of outcome measures for adults living with HIV: A consensus process.

(2022)

Objectives

HIV outcomes centre primarily around clinical markers with limited focus on patient-reported outcomes. With a global trend towards capturing the outcomes that matter most to patients, there is agreement that standardizing the definition of value in HIV care is key to their incorporation. This study aims to address the lack of routine, standardized data in HIV care.

Methods

An international working group (WG) of 37 experts and patients, and a steering group (SG) of 18 experts were convened from 14 countries. The project team (PT) identified outcomes by conducting a literature review, screening 1979 articles and reviewing the full texts of 547 of these articles. Semi-structured interviews and advisory groups were performed with the WG, SG and people living with HIV to add to the list of potentially relevant outcomes. The WG voted via a modified Delphi process - informed by six Zoom calls - to establish a core set of outcomes for use in clinical practice.

Results

From 156 identified outcomes, consensus was reached to include three patient-reported outcomes, four clinician-reported measures and one administratively reported outcome; standardized measures were included. The WG also reached agreement to measure 22 risk-adjustment variables. This outcome set can be applied to any person living with HIV aged > 18 years.

Conclusions

Adoption of the HIV360 outcome set will enable healthcare providers to record, compare and integrate standardized metrics across treatment sites to drive quality improvement in HIV care.

Financial toxicity impact on younger versus older adults with cancer in the setting of care delivery.

(2022)

Background

Young adults and other working-age adults with cancer are at risk for cancer-related financial toxicity (FT), including material hardships, depletion of coping resources, and psychological burden. This study compares FT domains in young adults (18-39 years old) (YAs), other working-age adults (40-64 years old), and older adults (≥65 years old) receiving cancer care.

Methods

A total of 311 adults were surveyed using the multi-domain Economic Strain and Resilience in Cancer instrument measuring FT (0-10 score indicating least to greatest FT; score ≥5 severe FT). Participants were receiving ambulatory care from March-September 2019. Associations of age with overall FT and material hardship, coping resource depletion, and psychological burden FT domains were tested using Kruskal-Wallis and χ2 tests and multivariable generalized linear models with gamma distribution.

Results

YAs (median age, 31.5 years) comprised 9.6% of the sample; other working-age adults comprised 56.9%. Overall, material, coping, and psychological FT scores were worse in younger age adults versus older adults (P < .001 in all multivariable models). Compared with older adults, younger age adults demonstrated worse material hardship (median scores, 3.70 vs 4.80 vs 1.30 for YAs, other working-age, and older adults, respectively; P < .001), coping resource depletion (4.50 vs 3.40 vs 0.80; P < .001), and psychological burden (6.50 vs 7.00 vs 1.00; P < .001). Fifty percent of YAs had severe overall FT versus 40.7% of other working-age adults and 9.6% of older adults (P < .001).

Conclusions

Younger age adults with cancer bore disproportionate FT. Interventions to address unmet needs are critical components for addressing FT in this population.

Cover page of Freshwater Input and Vertical Mixing in the Canada Basin’s Seasonal Halocline: 1975 versus 2006–12

Freshwater Input and Vertical Mixing in the Canada Basin’s Seasonal Halocline: 1975 versus 2006–12

(2022)

Abstract The Arctic seasonal halocline impacts the exchange of heat, energy, and nutrients between the surface and the deeper ocean, and it is changing in response to Arctic sea ice melt over the past several decades. Here, we assess seasonal halocline formation in 1975 and 2006–12 by comparing daily, May–September, salinity profiles collected in the Canada Basin under sea ice. We evaluate differences between the two time periods using a one-dimensional (1D) bulk model to quantify differences in freshwater input and vertical mixing. The 1D metrics indicate that two separate factors contribute similarly to stronger stratification in 2006–12 relative to 1975: 1) larger surface freshwater input and 2) less vertical mixing of that freshwater. The larger freshwater input is mainly important in August–September, consistent with a longer melt season in recent years. The reduced vertical mixing is mainly important from June until mid-August, when similar levels of freshwater input in 1975 and 2006–12 are mixed over a different depth range, resulting in different stratification. These results imply that decadal changes to ice–ocean dynamics, in addition to freshwater input, significantly contribute to the stronger seasonal stratification in 2006–12 relative to 1975. These findings highlight the need for near-surface process studies to elucidate the impact of lateral processes and ice–ocean momentum exchange on vertical mixing. Moreover, the results may provide insight for improving the representation of decadal changes to Arctic upper-ocean stratification in climate models that do not capture decadal changes to vertical mixing.

Cover page of Microbial DNA enrichment promotes liver steatosis and fibrosis in the course of non-alcoholic steatohepatitis.

Microbial DNA enrichment promotes liver steatosis and fibrosis in the course of non-alcoholic steatohepatitis.

(2022)

Aim

Low-grade inflammation is the hallmark of non-alcoholic fatty liver diseases (NAFLD) and non-alcoholic steatohepatitis (NASH). The leakage of microbiota-derived products can contribute to liver inflammation during NAFLD/NASH development. Here, we assessed the roles of gut microbial DNA-containing extracellular vesicles (mEVs) in regulating liver cellular abnormalities in the course of NAFLD/NASH.

Methods

We performed studies with Vsig4-/- , C3-/- , cGAS-/- , and their wild-type littermate mice. Vsig4+ macrophage population and bacterial DNA abundance were examined in both mouse and human liver by either flow cytometric or immunohistochemistry analysis. Gut mEVs were adoptively transferred into Vsig4-/- , C3-/- , cGAS-/- , or littermate WT mice, and hepatocyte inflammation and HSC fibrogenic activation were measured in these mice.

Results

Non-alcoholic fatty liver diseases and non-alcoholic steatohepatitis development was concomitant with a diminished liver Vsig4+ macrophage population and a marked bacterial DNA enrichment in both hepatocytes and HSCs. In the absence of Vsig4+ macrophages, gut mEVs translocation led to microbial DNA accumulation in hepatocytes and HSCs, resulting elevated hepatocyte inflammation and HSC fibrogenic activation. In contrast, in lean WT mice, Vsig4+ macrophages remove gut mEVs from bloodstream through a C3-dependent opsonization mechanism and prevent the infiltration of gut mEVs into hepatic cells. Additionally, Vsig4-/- mice more quickly developed significant liver steatosis and fibrosis than WT mice after Western diet feeding. In vitro treatment with NASH mEVs triggered hepatocyte inflammation and HSC fibrogenic activation. Microbial DNAs are key cargo for the effects of gut mEVs by activating cGAS/STING.

Conclusion

Accumulation of microbial DNAs fuels the development of NAFLD/NASH-associated liver abnormalities.