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Open Access Policy Deposits

This series is automatically populated with publications deposited by UC Berkeley School of Public Health 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.

Evaluating the robustness of targeted maximum likelihood estimators via realistic simulations in nutrition intervention trials.

(2022)

Several recently developed methods have the potential to harness machine learning in the pursuit of target quantities inspired by causal inference, including inverse weighting, doubly robust estimating equations and substitution estimators like targeted maximum likelihood estimation. There are even more recent augmentations of these procedures that can increase robustness, by adding a layer of cross-validation (cross-validated targeted maximum likelihood estimation and double machine learning, as applied to substitution and estimating equation approaches, respectively). While these methods have been evaluated individually on simulated and experimental data sets, a comprehensive analysis of their performance across real data based simulations have yet to be conducted. In this work, we benchmark multiple widely used methods for estimation of the average treatment effect using ten different nutrition intervention studies data. A nonparametric regression method, undersmoothed highly adaptive lasso, is used to generate the simulated distribution which preserves important features from the observed data and reproduces a set of true target parameters. For each simulated data, we apply the methods above to estimate the average treatment effects as well as their standard errors and resulting confidence intervals. Based on the analytic results, a general recommendation is put forth for use of the cross-validated variants of both substitution and estimating equation estimators. We conclude that the additional layer of cross-validation helps in avoiding unintentional over-fitting of nuisance parameter functionals and leads to more robust inferences.

Barriers and Facilitators to the Implementation of a Community Doula Program for Black and Pacific Islander Pregnant People in San Francisco: Findings from a Partnered Process Evaluation.

(2022)

Introduction

Increasingly, community-based models of doula care are receiving attention as possible interventions to address racial inequities in maternal health care experiences and outcomes. In 2018, community-based organization SisterWeb launched to provide free culturally congruent community doula care to advance birth equity for Black and Pacific Islander pregnant people, with funding from the San Francisco Department of Public Health. We conducted a process evaluation of SisterWeb's first 1.5 years of existence to identify multilevel barriers and facilitators to implementation of their programs.

Methods

Guided by the Equitable Evaluation Framework™, we conducted 46 in-depth interviews with individuals from 5 groups: SisterWeb leadership, doulas, doula mentors, and clients, and external stakeholders.

Results

Barriers included having diverse clientele groups with unique needs, an ineffective payment model, and simultaneously building an organization and developing and implementing programs. Facilitators included the presence of established strategic partnerships, positive reception of services due to an unmet need for culturally and linguistically congruent pregnancy and birth support among SisterWeb's clients, a clear organizational vision and mission, and a unique doula cohort model.

Discussion

Our findings suggest developing community doula programs pay close attention to the difference between launching a program versus an organization, including the required resources of each, the sustainability of payment models for community doulas, and the provision of culturally relevant, needed services within priority communities. Furthermore, strategic partnerships with maternal health stakeholders in birthing sites, particularly hospitals, are vital to the success of a community doula program.

All-cause mortality during the COVID-19 pandemic in Chennai, India: an observational study.

(2022)

Background

India has been severely affected by the ongoing COVID-19 pandemic. However, due to shortcomings in disease surveillance, the burden of mortality associated with COVID-19 remains poorly understood. We aimed to assess changes in mortality during the pandemic in Chennai, Tamil Nadu, using data on all-cause mortality within the district.

Methods

For this observational study, we analysed comprehensive death registrations in Chennai, from Jan 1, 2016, to June 30, 2021. We estimated expected mortality without the effects of the COVID-19 pandemic by fitting models to observed mortality time series during the pre-pandemic period, with stratification by age and sex. Additionally, we considered three periods of interest: the first 4 weeks of India's first lockdown (March 24 to April 20, 2020), the 4-month period including the first wave of the pandemic in Chennai (May 1 to Aug 31, 2020), and the 4-month period including the second wave of the pandemic in Chennai (March 1 to June 30, 2021). We computed the difference between observed and expected mortality from March 1, 2020, to June 30, 2021, and compared pandemic-associated mortality across socioeconomically distinct communities (measured with use of 2011 census of India data) with regression analyses.

Findings

Between March 1, 2020, and June 30, 2021, 87 870 deaths were registered in areas of Chennai district represented by the 2011 census, exceeding expected deaths by 25 990 (95% uncertainty interval 25 640-26 360) or 5·18 (5·11-5·25) excess deaths per 1000 people. Stratified by age, excess deaths numbered 21·02 (20·54-21·49) excess deaths per 1000 people for individuals aged 60-69 years, 39·74 (38·73-40·69) for those aged 70-79 years, and 96·90 (93·35-100·16) for those aged 80 years or older. Neighbourhoods with lower socioeconomic status had 0·7% to 2·8% increases in pandemic-associated mortality per 1 SD increase in each measure of community disadvantage, due largely to a disproportionate increase in mortality within these neighbourhoods during the second wave. Conversely, differences in excess mortality across communities were not clearly associated with socioeconomic status measures during the first wave. For each increase by 1 SD in measures of community disadvantage, neighbourhoods had 3·6% to 8·6% lower pandemic-associated mortality during the first 4 weeks of India's country-wide lockdown, before widespread SARS-CoV-2 circulation was underway in Chennai. The greatest reductions in mortality during this early lockdown period were observed among men aged 20-29 years, with 58% (54-62) fewer deaths than expected from pre-pandemic trends.

Interpretation

Mortality in Chennai increased substantially but heterogeneously during the COVID-19 pandemic, with the greatest burden concentrated in disadvantaged communities. Reported COVID-19 deaths greatly underestimated pandemic-associated mortality.

Funding

National Institute of General Medical Sciences, Bill & Melinda Gates Foundation, National Science Foundation.

Translation

For the Hindi translation of the abstract see Supplementary Materials section.

Cover page of Neighborhood Contexts and Breast Cancer Among Asian American Women.

Neighborhood Contexts and Breast Cancer Among Asian American Women.

(2022)

Background

This study examines how neighborhood socioeconomic status (nSES) and ethnic composition are associated with breast cancer risk for Asian American women.

Methods

We linked individual level data from a population-based case-control study of breast cancer among Asian American women with neighborhood level data in the Greater San Francisco Bay Area (cases: n = 118, controls: n = 390). Multivariable logistic regression models examined the association between nSES, ethnic composition, and odds of having breast cancer.

Results

Asian American women living in neighborhoods with high nSES and high ethnic composition had the highest odds of breast cancer, compared to those living in neighborhoods with high nSES and low ethnic composition (OR = 0.34, 95% CI [0.16-0.75]) or in neighborhoods with low nSES and high ethnic composition (OR = 0.37, 95% CI [0.17-0.83]).

Discussion

Neighborhood socioeconomic and ethnic contexts are associated with breast cancer for Asian American women. We discuss explanations and avenues for future research.

Pandemic-related financial hardship and disparities in sugar-sweetened beverage consumption and purchasing among San Francisco Bay Area residents during COVID-19.

(2022)

Some reports suggest that the COVID-19 pandemic resulted in shifts to unhealthier diets. These unhealthier diets may include sugar-sweetened beverages (SSBs), which strongly contribute to diabetes and other chronic diseases. Using cross-sectional surveys in the San Francisco Bay Area, California, USA we sought to assess self-reported SSB consumption during the pandemic's shelter-in-place and self-reported changes in SSB purchasing from before to during the pandemic's shelter-in-place, stratifying by indices of pandemic-related financial hardship. Nearly 60% of our diverse sample (N = 943) reported that it was harder to pay for basics (like food and utilities) during shelter-in-place. Among those who found it harder to pay for basics and received financial assistance during shelter-in-place, we found a ten-fold higher frequency of daily SSB consumption compared to those not facing new financial hardship (2.76 [95% CI: 1.78, 3.74] versus 0.30 [95% CI: 0.23, 0.37] times/day). There were no statistically significant increases in reported purchasing of any SSB, but those with new financial hardship during shelter-in-place reported greater purchasing of regular soda relative to those with no new hardship (0.20 on a 3-point scale [95% CI: 0.03, 0.37]). Our findings suggest that new hardship may increase unhealthy behaviors and worsen existing disparities in SSB consumption. Such disparities are a reminder of the urgent need to reduce economic inequity and improve the quality of our emergency food system in order to mitigate the impact of public health crises like the COVID-19 pandemic.

Increases in ambient air pollutants during pregnancy are linked to increases in methylation of IL4, IL10, and IFNγ.

(2022)

Background

Ambient air pollutant (AAP) exposure is associated with adverse pregnancy outcomes, such as preeclampsia, preterm labor, and low birth weight. Previous studies have shown methylation of immune genes associate with exposure to air pollutants in pregnant women, but the cell-mediated response in the context of typical pregnancy cell alterations has not been investigated. Pregnancy causes attenuation in cell-mediated immunity with alterations in the Th1/Th2/Th17/Treg environment, contributing to maternal susceptibility. We recruited women (n = 186) who were 20 weeks pregnant from Fresno, CA, an area with chronically elevated AAP levels. Associations of average pollution concentration estimates for 1 week, 1 month, 3 months, and 6 months prior to blood draw were associated with Th cell subset (Th1, Th2, Th17, and Treg) percentages and methylation of CpG sites (IL4, IL10, IFNγ, and FoxP3). Linear regression models were adjusted for weight, age, season, race, and asthma, using a Q value as the false-discovery-rate-adjusted p-value across all genes.

Results

Short-term and mid-term AAP exposures to fine particulate matter (PM2.5), nitrogen dioxide (NO2) carbon monoxide (CO), and polycyclic aromatic hydrocarbons (PAH456) were associated with percentages of immune cells. A decrease in Th1 cell percentage was negatively associated with PM2.5 (1 mo/3 mo: Q < 0.05), NO2 (1 mo/3 mo/6 mo: Q < 0.05), and PAH456 (1 week/1 mo/3 mo: Q < 0.05). Th2 cell percentages were negatively associated with PM2.5 (1 week/1 mo/3 mo/6 mo: Q < 0.06), and NO2 (1 week/1 mo/3 mo/6 mo: Q < 0.06). Th17 cell percentage was negatively associated with NO2 (3 mo/6 mo: Q < 0.01), CO (1 week/1 mo: Q < 0.1), PM2.5 (3 mo/6 mo: Q < 0.05), and PAH456 (1 mo/3 mo/6 mo: Q < 0.08). Methylation of the IL10 gene was positively associated with CO (1 week/1 mo/3 mo: Q < 0.01), NO2 (1 mo/3 mo/6 mo: Q < 0.08), PAH456 (1 week/1 mo/3 mo: Q < 0.01), and PM2.5 (3 mo: Q = 0.06) while IL4 gene methylation was positively associated with concentrations of CO (1 week/1 mo/3 mo/6 mo: Q < 0.09). Also, IFNγ gene methylation was positively associated with CO (1 week/1 mo/3 mo: Q < 0.05) and PAH456 (1 week/1 mo/3 mo: Q < 0.06).

Conclusion

Exposure to several AAPs was negatively associated with T-helper subsets involved in pro-inflammatory and anti-inflammatory responses during pregnancy. Methylation of IL4, IL10, and IFNγ genes with pollution exposure confirms previous research. These results offer insights into the detrimental effects of air pollution during pregnancy, the demand for more epigenetic studies, and mitigation strategies to decrease pollution exposure during pregnancy.

Epigenome-wide association study and epigenetic age acceleration associated with cigarette smoking among Costa Rican adults.

(2022)

Smoking-associated DNA methylation (DNAm) signatures are reproducible among studies of mostly European descent, with mixed evidence if smoking accelerates epigenetic aging and its relationship to longevity. We evaluated smoking-associated DNAm signatures in the Costa Rican Study on Longevity and Healthy Aging (CRELES), including participants from the high longevity region of Nicoya. We measured genome-wide DNAm in leukocytes, tested Epigenetic Age Acceleration (EAA) from five clocks and estimates of telomere length (DNAmTL), and examined effect modification by the high longevity region. 489 participants had a mean (SD) age of 79.4 (10.8) years, and 18% were from Nicoya. Overall, 7.6% reported currently smoking, 35% were former smokers, and 57.4% never smoked. 46 CpGs and five regions (e.g. AHRR, SCARNA6/SNORD39, SNORA20, and F2RL3) were differentially methylated for current smokers. Former smokers had increased Horvath's EAA (1.69-years; 95% CI 0.72, 2.67), Hannum's EAA (0.77-years; 95% CI 0.01, 1.52), GrimAge (2.34-years; 95% CI1.66, 3.02), extrinsic EAA (1.27-years; 95% CI 0.34, 2.21), intrinsic EAA (1.03-years; 95% CI 0.12, 1.94) and shorter DNAmTL (- 0.04-kb; 95% CI - 0.08, - 0.01) relative to non-smokers. There was no evidence of effect modification among residents of Nicoya. Our findings recapitulate previously reported and novel smoking-associated DNAm changes in a Latino cohort.

Longitudinal social contacts among school-aged children during the COVID-19 pandemic: the Bay Area Contacts among Kids (BACK) study.

(2022)

Background

The San Francisco Bay Area was the first region in the United States to enact school closures to mitigate SARS-CoV-2 transmission. The effects of closures on contact patterns for schoolchildren and their household members remain poorly understood.

Methods

We conducted serial cross-sectional surveys (May 2020, September 2020, February 2021) of Bay Area households with children to estimate age-structured daily contact rates for children and their adult household members. We examined changes in contact rates over the course of the COVID-19 pandemic, including after vaccination of household members, and compared contact patterns by household demographics using generalized estimating equations clustered by household.

Results

We captured contact histories for 1,967 households on behalf of 2,674 children, comprising 15,087 non-household contacts over the three waves of data collection. Shortly after the start of shelter-in-place orders in May 2020, daily contact rates were higher among children from Hispanic families (1.52 more contacts per child per day; [95% CI: 1.14-2.04]), households whose parents were unable to work from home (1.82; [1.40-2.40]), and households with income < $150,000 (1.75; [1.33-2.33]), after adjusting for other demographic characteristics and household clustering. Between May and August 2020, non-household contacts of children increased by 145% (ages 5-12) and 172% (ages 13-17), despite few children returning to in-person instruction. Non-household contact rates among children were higher-by 1.75 [1.28-2.40] and 1.42 [0.89-2.24] contacts per child per day in 5-12 and 13-17 age groups, respectively, in households where at least one adult was vaccinated against COVID-19, compared to children's contact rates in unvaccinated households.

Conclusions

Child contact rates rebounded despite schools remaining closed, as parents obtained childcare, children engaged in contact in non-school settings, and family members were vaccinated. The waning reductions observed in non-household contact rates of schoolchildren and their family members during a prolonged school closure suggests the strategy may be ineffective for long-term SARS-CoV-2 transmission mitigation. Reductions in age-assortative contacts were not as apparent amongst children from lower income households or households where adults could not work from home. Heterogeneous reductions in contact patterns raise concerning racial, ethnic and income-based inequities associated with long-term school closures as a COVID-19 mitigation strategy.

Household air pollution and COPD: cause and effect or confounding by other aspects of poverty?

(2022)

SETTING: Household air pollution (HAP) and chronic obstructive pulmonary disease (COPD) are both major public health problems, reported to cause around 4 million and 3 million deaths every year, respectively. The great majority of these deaths, as well as the burden of disease during life is felt by people in low- and middle-income countries (LMICs).OBJECTIVE and DESIGN: The extent to which HAP causes COPD is controversial; we therefore undertook this review to offer a viewpoint on this from the Global Initiative for COPD (GOLD).RESULTS: We find that while COPD is well-defined in many studies on COPD and HAP, there are major limitations to the definition and measurement of HAP. It is thus difficult to disentangle HAP from other features of poverty that are themselves associated with COPD. We identify other limitations to primary research studies, including the use of cross-sectional designs that limit causal inference.CONCLUSION: There is substantial preventable morbidity and mortality associated with HAP, COPD and poverty, separately and together. Although it may not be possible to define clear causal links between HAP and COPD, there is a clear urgency to reduce the avoidable burden of disease these inflict on the world´s poor.

Cover page of Structural competency and global health education.

Structural competency and global health education.

(2022)

Structural competency is a new curricular framework for training health professionals to recognise and respond to disease and its unequal distribution as the outcome of social structures, such as economic and legal systems, healthcare and taxation policies, and international institutions. While extensive global health research has linked social structures to the disproportionate burden of disease in the Global South, formal attempts to incorporate the structural competency framework into US-based global health education have not been described in the literature. This paper fills this gap by articulating five sub-competencies for structurally competent global health instruction. Authors drew on their experiences developing global health and structural competency curricula-and consulted relevant structural competency, global health, social science, social theory, and social determinants of health literatures. The five sub-competencies include: (1) Describe the role of social structures in producing and maintaining health inequities globally, (2) Identify the ways that structural inequalities are naturalised within the field of global health, (3) Discuss the impact of structures on the practice of global health, (4) Recognise structural interventions for addressing global health inequities, and (5) Apply the concept of structural humility in the context of global health.