Despite estimates that, each year, as many as 300 million dengue virus (DENV) infections result in either no perceptible symptoms (asymptomatic) or symptoms that are sufficiently mild to go ...undetected by surveillance systems (inapparent), it has been assumed that these infections contribute little to onward transmission. However, recent blood-feeding experiments with Aedes aegypti mosquitoes showed that people with asymptomatic and pre-symptomatic DENV infections are capable of infecting mosquitoes. To place those findings into context, we used models of within-host viral dynamics and human demographic projections to (1) quantify the net infectiousness of individuals across the spectrum of DENV infection severity and (2) estimate the fraction of transmission attributable to people with different severities of disease. Our results indicate that net infectiousness of people with asymptomatic infections is 80% (median) that of people with apparent or inapparent symptomatic infections (95% credible interval (CI): 0-146%). Due to their numerical prominence in the infectious reservoir, clinically inapparent infections in total could account for 84% (CI: 82-86%) of DENV transmission. Of infections that ultimately result in any level of symptoms, we estimate that 24% (95% CI: 0-79%) of onward transmission results from mosquitoes biting individuals during the pre-symptomatic phase of their infection. Only 1% (95% CI: 0.8-1.1%) of DENV transmission is attributable to people with clinically detected infections after they have developed symptoms. These findings emphasize the need to (1) reorient current practices for outbreak response to adoption of pre-emptive strategies that account for contributions of undetected infections and (2) apply methodologies that account for undetected infections in surveillance programs, when assessing intervention impact, and when modeling mosquito-borne virus transmission.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
To estimate PM2.5 concentrations, many parametric regression models have been developed, while nonparametric machine learning algorithms are used less often and national-scale models are rare. In ...this paper, we develop a random forest model incorporating aerosol optical depth (AOD) data, meteorological fields, and land use variables to estimate daily 24 h averaged ground-level PM2.5 concentrations over the conterminous United States in 2011. Random forests are an ensemble learning method that provides predictions with high accuracy and interpretability. Our results achieve an overall cross-validation (CV) R 2 value of 0.80. Mean prediction error (MPE) and root mean squared prediction error (RMSPE) for daily predictions are 1.78 and 2.83 μg/m3, respectively, indicating a good agreement between CV predictions and observations. The prediction accuracy of our model is similar to those reported in previous studies using neural networks or regression models on both national and regional scales. In addition, the incorporation of convolutional layers for land use terms and nearby PM2.5 measurements increase CV R 2 by ∼0.02 and ∼0.06, respectively, indicating their significant contributions to prediction accuracy. A pair of different variable importance measures both indicate that the convolutional layer for nearby PM2.5 measurements and AOD values are among the most-important predictor variables for the training process.
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IJS, KILJ, NUK, PNG, UL, UM
A carefully considered observational study estimates that up to 22% of infant deaths in sub-Saharan Africa could be prevented by improving air quality -- a value much higher than previous estimates.
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KISLJ, NUK, SBMB, UL, UM, UPUK
Staphylococcus aureus (S. aureus) is known to cause human infections and since the late 1990s, community-onset antibiotic resistant infections (methicillin resistant S. aureus (MRSA)) continue to ...cause significant infections in the United States. Skin and soft tissue infections (SSTIs) still account for the majority of these in the outpatient setting. Machine learning can predict the location-based risks for community-level S. aureus infections. Multi-year (2002-2016) electronic health records of children <19 years old with S. aureus infections were queried for patient level data for demographic, clinical, and laboratory information. Area level data (Block group) was abstracted from U.S. Census data. A machine learning ecological niche model, maximum entropy (MaxEnt), was applied to assess model performance of specific place-based factors (determined a priori) associated with S. aureus infections; analyses were structured to compare methicillin resistant (MRSA) against methicillin sensitive S. aureus (MSSA) infections. Differences in rates of MRSA and MSSA infections were determined by comparing those which occurred in the early phase (2002-2005) and those in the later phase (2006-2016). Multi-level modeling was applied to identify risks factors for S. aureus infections. Among 16,124 unique patients with community-onset MRSA and MSSA, majority occurred in the most densely populated neighborhoods of Atlanta's metropolitan area. MaxEnt model performance showed the training AUC ranged from 0.771 to 0.824, while the testing AUC ranged from 0.769 to 0.839. Population density was the area variable which contributed the most in predicting S. aureus disease (stratified by CO-MRSA and CO-MSSA) across early and late periods. Race contributed more to CO-MRSA prediction models during the early and late periods than for CO-MSSA. Machine learning accurately predicts which densely populated areas are at highest and lowest risk for community-onset S. aureus infections over a 14-year time span.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
The mosquito Aedes aegypti is the vector of a number of medically-important viruses, including dengue virus, yellow fever virus, chikungunya virus, and Zika virus, and as such vector control is a key ...approach to managing the diseases they cause. Understanding the impact of vector control on these diseases is aided by first understanding its impact on Ae. aegypti population dynamics. A number of detail-rich models have been developed to couple the dynamics of the immature and adult stages of Ae. aegypti. The numerous assumptions of these models enable them to realistically characterize impacts of mosquito control, but they also constrain the ability of such models to reproduce empirical patterns that do not conform to the models' behavior. In contrast, statistical models afford sufficient flexibility to extract nuanced signals from noisy data, yet they have limited ability to make predictions about impacts of mosquito control on disease caused by pathogens that the mosquitoes transmit without extensive data on mosquitoes and disease. Here, we demonstrate how the differing strengths of mechanistic realism and statistical flexibility can be fused into a single model. Our analysis utilizes data from 176,352 household-level Ae. aegypti aspirator collections conducted during 1999-2011 in Iquitos, Peru. The key step in our approach is to calibrate a single parameter of the model to spatio-temporal abundance patterns predicted by a generalized additive model (GAM). In effect, this calibrated parameter absorbs residual variation in the abundance time-series not captured by other features of the mechanistic model. We then used this calibrated parameter and the literature-derived parameters in the agent-based model to explore Ae. aegypti population dynamics and the impact of insecticide spraying to kill adult mosquitoes. The baseline abundance predicted by the agent-based model closely matched that predicted by the GAM. Following spraying, the agent-based model predicted that mosquito abundance rebounds within about two months, commensurate with recent experimental data from Iquitos. Our approach was able to accurately reproduce abundance patterns in Iquitos and produce a realistic response to adulticide spraying, while retaining sufficient flexibility to be applied across a range of settings.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Abstract
In this paper, we advocate and expand upon a previously described monitoring strategy for efficient and robust estimation of disease prevalence and case numbers within closed and enumerated ...populations such as schools, workplaces, or retirement communities. The proposed design relies largely on voluntary testing, which is notoriously biased (e.g., in the case of coronavirus disease 2019) due to nonrepresentative sampling. The approach yields unbiased and comparatively precise estimates with no assumptions about factors underlying selection of individuals for voluntary testing, building on the strength of what can be a small random sampling component. This component enables the use of a recently proposed “anchor stream” estimator, a well-calibrated alternative to classical capture-recapture (CRC) estimators based on 2 data streams. We show that this estimator is equivalent to a direct standardization based on “capture,” that is, selection (or not) by the voluntary testing program, made possible by means of a key parameter identified by design. This equivalency simultaneously allows for novel 2-stream CRC-like estimation of general mean values (e.g., means of continuous variables like antibody levels or biomarkers). For inference, we propose adaptations of Bayesian credible intervals when estimating case counts and bootstrapping when estimating means of continuous variables. We use simulations to demonstrate significant precision benefits relative to random sampling alone.
Coronavirus disease 2019 (COVID-19) testing is a critical component of public health surveillance and pandemic control, especially among the unvaccinated, as the nation resumes in-person activities. ...This study examined the relationships between COVID-19 testing rates, testing positivity rates, and vaccination coverage across US counties.
Data from the Health and Human Services' Community Profile Report and 2016-2020 American Community Survey 5-Year Estimates were used. A total of 3114 US counties were analyzed from January through September 2021. Associations among the testing metrics and vaccination coverage were estimated using multiple linear regression models with fixed effects for states and adjusted for county demographics. COVID-19 testing rates (polymerase chain reaction PCR testing per 1000), testing positivity (percentage of all PCR tests that were positive), and vaccination coverage (percentage of county population that was fully vaccinated) were determined.
Nationally, median daily COVID-19 testing rates were highest in January and September (35.5 and 34.6 tests per capita, respectively) and lowest in July (13.2 tests per capita). Monthly testing positivity was between 0.03 and 0.12 percentage points lower for each percentage points of vaccination coverage, and monthly testing rates were between 0.08 and 0.22 tests per capita higher for each percentage point of vaccination coverage.
The quantity of COVID-19 testing was associated with vaccination coverage, implying counties having populations with relatively lower protection against the virus are conducting less testing than counties with relatively more protection. Monitoring testing practices in relation to vaccination coverage may be used to monitor the sufficiency of COVID-19 testing based on population susceptibility to the virus.
•Synergistic effects of air pollution and neighborhood deprivation on cognition.•Inclusion of neighborhood deprivation (nSES) as co-exposure to account for synergy.•Complex nSES-air pollution ...relationship requires advanced mixture modelling.•Combination of several mixture methods for a holistic assessment of associations.
Air pollution and neighborhood socioeconomic status (nSES) have been shown to affect cognitive decline in older adults. In previous studies, nSES acts as both a confounder and an effect modifier between air pollution and cognitive decline.
This study aims to examine the individual and joint effects of air pollution and nSES on cognitive decline on adults 50 years and older in Metro Atlanta, USA.
Perceived memory and cognitive decline was assessed in 11,897 participants aged 50+ years from the Emory Healthy Aging Study (EHAS) using the cognitive function instrument (CFI). Three-year average air pollution concentrations for 12 pollutants and 16 nSES characteristics were matched to participants using census tracts. Individual exposure linear regression and LASSO models explore individual exposure effects. Environmental mixture modeling methods including, self-organizing maps (SOM), Bayesian kernel machine regression (BKMR), and quantile-based G-computation explore joint effects, and effect modification between air pollutants and nSES characteristics on cognitive decline.
Participants living in areas with higher air pollution concentrations and lower nSES experienced higher CFI scores (beta: 0.121; 95 % CI: 0.076, 0.167) compared to participants living in areas with low air pollution and high nSES. Additionally, the BKMR model showed a significant overall mixture effect on cognitive decline, suggesting synergy between air pollution and nSES. These joint effects explain protective effects observed in single-pollutant linear regression models, even after adjustment for confounding by nSES (e.g., an IQR increase in CO was associated with a 0.038-point lower (95 % CI: −0.06, −0.01) CFI score).
Observed protective effects of single air pollutants on cognitive decline can be explained by joint effects and effect modification of air pollutants and nSES. Researchers must consider nSES as an effect modifier if not a co-exposure to better understand the complex relationships between air pollution and nSES in urban settings.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Short-term exposure to ambient fine particulate matter (PM2.5) concentrations has been associated with increased mortality and morbidity. Determining which sources of PM2.5 are most toxic can help ...guide targeted reduction of PM2.5. However, conducting multicity epidemiologic studies of sources is difficult because source-specific PM2.5 is not directly measured, and source chemical compositions can vary between cities.
We determined how the chemical composition of primary ambient PM2.5 sources varies across cities. We estimated associations between source-specific PM2.5 and respiratory disease emergency department (ED) visits and examined between-city heterogeneity in estimated associations.
We used source apportionment to estimate daily concentrations of primary source-specific PM2.5 for four U.S. cities. For sources with similar chemical compositions between cities, we applied Poisson time-series regression models to estimate associations between source-specific PM2.5 and respiratory disease ED visits.
We found that PM2.5 from biomass burning, diesel vehicle, gasoline vehicle, and dust sources was similar in chemical composition between cities, but PM2.5 from coal combustion and metal sources varied across cities. We found some evidence of positive associations of respiratory disease ED visits with biomass burning PM2.5; associations with diesel and gasoline PM2.5 were frequently imprecise or consistent with the null. We found little evidence of associations with dust PM2.5.
We introduced an approach for comparing the chemical compositions of PM2.5 sources across cities and conducted one of the first multicity studies of source-specific PM2.5 and ED visits. Across four U.S. cities, among the primary PM2.5 sources assessed, biomass burning PM2.5 was most strongly associated with respiratory health. Citation: Krall JR, Mulholland JA, Russell AG, Balachandran S, Winquist A, Tolbert PE, Waller LA, Sarnat SE. 2017. Associations between source-specific fine particulate matter and emergency department visits for respiratory disease in four U.S. cities. Environ Health Perspect 125:97-103; http://dx.doi.org/10.1289/EHP271.
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CEKLJ, DOBA, IZUM, KILJ, NUK, OILJ, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK, VSZLJ
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