Summary of Fall 2017 “Nectar Microbiome” class

20171025_130035-300x169.jpg

So last quarter we wrapped up the third in our series of “Swabs to Genomes” based courses at UC Davis.  As with every iteration there was the plan and there was the reality.  More on that below. The first version of class this was Swabs to Genomes in abalone which while scientifically awesome, was both …

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Summary of Fall 2017 “Nectar Microbiome” class

Exposure to Traffic Emissions and Fine Particulate Matter and Computed Tomography Measures of the Lung and Airways

Background:

Exposure to ambient air pollution has been associated with lower lung function in adults, but few studies have investigated associations with radiographic lung and airway measures.

Methods:

We ascertained lung volume, mass, density, visual emphysema, airway size, and airway wall area by computed tomography (CT) among 2,545 non-smoking Framingham CT sub-study participants. We examined associations of home distance to major road and PM2.5 (2008 average from a spatiotemporal model using satellite data) with these outcomes using linear and logistic regression models adjusted for age, sex, height, weight, census tract median household value and population density, education, packyears of smoking, household tobacco exposure, cohort, and date. We tested for differential susceptibility by sex, smoking status (former vs never), and cohort.

Results:

The mean participant age was 60.1 y (standard deviation 11.9). Median PM2.5 level was 9.7 µg/m3 (interquartile range 1.6). Living 400 m away. There was also a log-linear association between proximity to road and higher lung volume. There were no convincing associations of proximity to major road or PM2.5 with the other pulmonary CT measures. In subgroup analyses, road proximity was associated with lower lung density among men, and higher odds of emphysema among former smokers.

Conclusions:

Living near a major road was associated with higher average lung volume, but otherwise we found no association between ambient pollution and radiographic measures of emphysema or airway disease.

* Drs. Mittleman and Washko contributed equally to this study.

Statement on Conflict of Interest: The authors have no conflicts of interest to declare.

Sources of Financial Support: This results reported herein correspond to specific aim 1 of the National Institute for Environmental Health Sciences K23 ES026204 grant to Mary B. Rice. This work was also supported by the US Environmental Protection Agency (R832416, RD834798), and the National Heart, Lung and Blood Institute (the Framingham Heart Study Contract Nos. N01-HC-25195 and HHSN268201500001I, and T32HL007575), and National Institute of General Medical Sciences (1P20GM109036-01A1). This publication’s contents are solely the responsibility of the grantee and do not necessarily represent the official views of the US EPA; the National Heart, Lung, and Blood Institute; the National Institutes of Health; or the U.S. Department of Health and Human Services. Further, US EPA does not endorse the purchase of any commercial products or services.

Process to Replicate Results: Research applications can be submitted to the Framingham Heart Study Research Review Committees online at http://ift.tt/1mdm2Hk.

Acknowledgments: The authors wish to thank the Framingham Heart Study participants for their participation in the study.

Corresponding Author: Mary B. Rice, MD MPH, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02215, mrice1@bidmc.harvard.edu, Phone: 617-667-3258, Fax: 617-667-4849

Copyright © 2018 Wolters Kluwer Health, Inc. All rights reserved.

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Exposure to Traffic Emissions and Fine Particulate Matter and Computed Tomography Measures of the Lung and Airways

Intake of Sugar-sweetened Beverages and Fecundability in a North American Preconception Cohort

Dietary factors, including sugar-sweetened beverages, may have adverse effects on fertility. Sugar-sweetened beverages have been associated with poor semen quality in cross-sectional studies, and female soda intake has been associated with lower fecundability in some, but not all, studies. We evaluated the association of female and male sugar-sweetened beverage intake with fecundability among 3828 women planning pregnancy and 1045 of their male partners in a North American prospective cohort study. We followed participants enrolled between June 2013 and May 2017 until pregnancy or for up to twelve menstrual cycles. Eligible women were aged 21-45 years (male partners ≥21), attempting conception for ≤6 cycles, and not using fertility treatments. Participants completed a comprehensive baseline questionnaire, including questions on soda (sugar-sweetened and diet), fruit juice, energy, and sports drink consumption during the previous 4 weeks. We estimated time-to-pregnancy from follow-up questionnaires completed every 2 months by the female partner. We calculated adjusted fecundability ratios (FR) and 95% confidence intervals (CIs) according to intake of sugar-sweetened beverages using proportional probabilities regression. Both female and male intakes of sugar-sweetened beverages were associated with reduced fecundability (FR= 0.81; 95% CI: 0.70, 0.94 and 0.78; 95% CI: 0.63, 0.95 for ≥ 7 sugar-sweetened beverages per week compared with none, for females and males, respectively). Fecundability was further reduced among those who drank ≥7 servings per week of sugar-sweetened sodas (FR= 0.75, 95% CI: 0.59, 0.95 for females and 0.67, 95% CI: 0.51, 0.89 for males). Diet soda had little association with fecundability.

The authors declare that they have no conflict of interest. The computing code and de-identified data are available by contacting the first or last author.

Sources of funding: This research was supported by NICHD (R21-HD072326, R01-HD086742, R03-HD090315, and T32-HD052458).

Acknowledgements: We acknowledge the contributions of PRESTO participants and staff. We thank Mr. Michael Bairos for technical support in developing the study’s web-based infrastructure and Drs. Amy Subar and Ken Bishop for assistance with the National Cancer Institute Food Frequency Questionnaire.

Copyright © 2018 Wolters Kluwer Health, Inc. All rights reserved.

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Intake of Sugar-sweetened Beverages and Fecundability in a North American Preconception Cohort

Exploring the subtleties of inverse probability weighting and marginal structural models

Since being introduced to epidemiology in 2000, marginal structural models have become a commonly used method for causal inference in a wide range of epidemiologic settings. In this brief report, we aim to explore three subtleties of marginal structural models. First, we distinguish marginal structural models from the inverse probability weighting estimator, and we emphasize that marginal structural models are not only for longitudinal exposures. Second, we explore the meaning of the word ‘marginal’ in ‘marginal structural model.’ Lastly, we show that the specification of a marginal structural model can have important implications for the interpretation of its parameters. Each of these concepts have important implications for the use and understanding of marginal structural models, and thus providing detailed explanations of them may lead to better practices for the field of epidemiology

Conflicts of interest: The authors declare no conflicts of interest

Financial support: This work was supported by National Institutes of Health grants R01AI100654 (SRC) and DP2HD084070 (DW).

Correspondence to: Alexander Breskin, Department of Epidemiology, University of North Carolina at Chapel Hill, CB 7435 McGavran-Greenberg Hall, Chapel Hill, NC 27599, abreskin@unc.edu, (917) 593 9004

Copyright © 2018 Wolters Kluwer Health, Inc. All rights reserved.

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Exploring the subtleties of inverse probability weighting and marginal structural models

The Effects of Long-Term Storage on Commonly Measured Serum Analyte Levels

Background:

Cohort studies typically bank biospecimens for many years prior to assay and investigators do not know whether levels of analytes have degraded.

Methods:

We collected control samples from 22 non-study participants using the same enrollment criteria and specimen collection, processing, and storage protocols as The Sister Study. Serum samples were assayed for 21 analytes at collection and 6 years later. For each sample, the difference between the result at baseline and at 6 years was calculated for each analyte.

Results:

Some of the analytes experienced a marked decrease in concentration after six years of frozen storage in liquid nitrogen vapor, compared to their baseline value. The confidence interval for the mean paired difference excluded 0 for 8 of the 21 analytes tested (aspartate transaminase, total cholesterol, estradiol, glucose, HDL cholesterol, luteinizing hormone, protein, and triglycerides). Two analytes, lactate dehydrogenase and sex hormone binding globulin, increased substantially in concentration over time (confidence interval excluded 0). For compounds substantially affected by storage time, the internal laboratory control variance was greater than the estimated mean percent change for HDL cholesterol and luteinizing hormone, indicating that extent of degradation for these analytes did not exceed technical variation.

Conclusions:

Despite evidence for systematic changes over long-term storage, correlations between baseline and later measures were high with little relation between size of the correlation and estimated mean difference across time points. QC experiments to assess the impact of long-term storage on anticipated analytes of interest are important in planning cohort studies with banked samples.

Acknowledgments:The authors thank Quest Diagnostics, Inc. for testing the samples, providing the results, and providing quality control variance data. We thank Kristie Dantzler for laboratory coordination of sample collection, storage, transfer, and returned results.

Conflicts of Interest and Source of Funding: Supported by the Intramural Research Program of the National Institutes of Health, National Institute of Environmental Health Sciences. The authors report no conflicts of interest.

Correspondence: Cynthia Kleeberger, 1007 Slater Road, Durham, NC 27703. Email: ckleeberger@s-3.com.

Copyright © 2018 Wolters Kluwer Health, Inc. All rights reserved.

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The Effects of Long-Term Storage on Commonly Measured Serum Analyte Levels

Exposure to Traffic Emissions and Fine Particulate Matter and Computed Tomography Measures of the Lung and Airways

Background:

Exposure to ambient air pollution has been associated with lower lung function in adults, but few studies have investigated associations with radiographic lung and airway measures.

Methods:

We ascertained lung volume, mass, density, visual emphysema, airway size, and airway wall area by computed tomography (CT) among 2,545 non-smoking Framingham CT sub-study participants. We examined associations of home distance to major road and PM2.5 (2008 average from a spatiotemporal model using satellite data) with these outcomes using linear and logistic regression models adjusted for age, sex, height, weight, census tract median household value and population density, education, packyears of smoking, household tobacco exposure, cohort, and date. We tested for differential susceptibility by sex, smoking status (former vs never), and cohort.

Results:

The mean participant age was 60.1 y (standard deviation 11.9). Median PM2.5 level was 9.7 µg/m3 (interquartile range 1.6). Living 400 m away. There was also a log-linear association between proximity to road and higher lung volume. There were no convincing associations of proximity to major road or PM2.5 with the other pulmonary CT measures. In subgroup analyses, road proximity was associated with lower lung density among men, and higher odds of emphysema among former smokers.

Conclusions:

Living near a major road was associated with higher average lung volume, but otherwise we found no association between ambient pollution and radiographic measures of emphysema or airway disease.

* Drs. Mittleman and Washko contributed equally to this study.

Statement on Conflict of Interest: The authors have no conflicts of interest to declare.

Sources of Financial Support: This results reported herein correspond to specific aim 1 of the National Institute for Environmental Health Sciences K23 ES026204 grant to Mary B. Rice. This work was also supported by the US Environmental Protection Agency (R832416, RD834798), and the National Heart, Lung and Blood Institute (the Framingham Heart Study Contract Nos. N01-HC-25195 and HHSN268201500001I, and T32HL007575), and National Institute of General Medical Sciences (1P20GM109036-01A1). This publication’s contents are solely the responsibility of the grantee and do not necessarily represent the official views of the US EPA; the National Heart, Lung, and Blood Institute; the National Institutes of Health; or the U.S. Department of Health and Human Services. Further, US EPA does not endorse the purchase of any commercial products or services.

Process to Replicate Results: Research applications can be submitted to the Framingham Heart Study Research Review Committees online at http://ift.tt/1mdm2Hk.

Acknowledgments: The authors wish to thank the Framingham Heart Study participants for their participation in the study.

Corresponding Author: Mary B. Rice, MD MPH, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02215, mrice1@bidmc.harvard.edu, Phone: 617-667-3258, Fax: 617-667-4849

Copyright © 2018 Wolters Kluwer Health, Inc. All rights reserved.

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Exposure to Traffic Emissions and Fine Particulate Matter and Computed Tomography Measures of the Lung and Airways

Intake of Sugar-sweetened Beverages and Fecundability in a North American Preconception Cohort

Dietary factors, including sugar-sweetened beverages, may have adverse effects on fertility. Sugar-sweetened beverages have been associated with poor semen quality in cross-sectional studies, and female soda intake has been associated with lower fecundability in some, but not all, studies. We evaluated the association of female and male sugar-sweetened beverage intake with fecundability among 3828 women planning pregnancy and 1045 of their male partners in a North American prospective cohort study. We followed participants enrolled between June 2013 and May 2017 until pregnancy or for up to twelve menstrual cycles. Eligible women were aged 21-45 years (male partners ≥21), attempting conception for ≤6 cycles, and not using fertility treatments. Participants completed a comprehensive baseline questionnaire, including questions on soda (sugar-sweetened and diet), fruit juice, energy, and sports drink consumption during the previous 4 weeks. We estimated time-to-pregnancy from follow-up questionnaires completed every 2 months by the female partner. We calculated adjusted fecundability ratios (FR) and 95% confidence intervals (CIs) according to intake of sugar-sweetened beverages using proportional probabilities regression. Both female and male intakes of sugar-sweetened beverages were associated with reduced fecundability (FR= 0.81; 95% CI: 0.70, 0.94 and 0.78; 95% CI: 0.63, 0.95 for ≥ 7 sugar-sweetened beverages per week compared with none, for females and males, respectively). Fecundability was further reduced among those who drank ≥7 servings per week of sugar-sweetened sodas (FR= 0.75, 95% CI: 0.59, 0.95 for females and 0.67, 95% CI: 0.51, 0.89 for males). Diet soda had little association with fecundability.

The authors declare that they have no conflict of interest. The computing code and de-identified data are available by contacting the first or last author.

Sources of funding: This research was supported by NICHD (R21-HD072326, R01-HD086742, R03-HD090315, and T32-HD052458).

Acknowledgements: We acknowledge the contributions of PRESTO participants and staff. We thank Mr. Michael Bairos for technical support in developing the study’s web-based infrastructure and Drs. Amy Subar and Ken Bishop for assistance with the National Cancer Institute Food Frequency Questionnaire.

Copyright © 2018 Wolters Kluwer Health, Inc. All rights reserved.

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Intake of Sugar-sweetened Beverages and Fecundability in a North American Preconception Cohort