From the Director

February 28, 2019

Dear Colleagues,

­­As winter quarter grinds to a soggy end, spring is bursting at PHS as many of seeds planted in months—even years—past begin to sprout. Three of the most exciting developments are highlighted in this month’s issue, but many more are about to bloom.

Air quality and health is at the front of our minds, and, after a recent convening this past quarter, the working group has seen a significant boost in momentum.  Spurred by the success of two PHS Faculty Fellows—Eran Bendavid and Marshall Burke, who published an award-winning Nature article demonstrating the impact of particulate matter in driving infant mortality in Africa, we are excited to see what new research directions, resources and impact this group will cultivate.  Additionally, generous support from Kari Nadeau’s lab and the Bravo Family Foundation has resulted in a post-doctoral fellowship to leverage the a new, rich aerial surveillance method to quantify local air quality as a means of assessing the health impact of California’s fire crisis.  Soon, we hope to be able to make the data widely available to our PHS users for similar studies of environmental impact on a vast array of health outcomes spanning the life course. The working group meets next on Thursday, March 7, 2019. Email Rita Lonhart for details.

From the outset PHS has had multiple global partners—notably in Denmark (Aarhus University and the Statens Serum Institut), the United Kingdom (Born in Bradford), Israel (Clalit), the Czech Republic (Recetox) and Taiwan—but our imminent launch in India represents a sea-change. Recently announced, PHS is developing an Indian satellite program, with a footprint in Mumbai.  From that Center we will be replicating the Data Core we have built on campus, amassing data sets and collaborating with partners including the Bill and Melinda Gates Foundation, Google, Indian Institute of Technology (IIT) bombay, PATH, Tata Trusts, WISH Foundation and Wadhwani AI, and both State and National governmental agencies. The resource will be widely available to faculty and trainees for studies of health and development, and we will soon have the ability to provide logistic support, data services and office space for Stanford researchers working in-country. The initial focus will be on maternal and child health, sanitation, health service and use of AI for social good, however we expect to facilitate data access in support of studies focusing on a wide range of soc­ial science, environmental and biomedical issues.

Another data asset available in increasingly robust and user-friendly form is the American Manufacturing Cohort. This database is comprised of multiple, linked datasets that collectively provide an invaluable resource for understanding work-life exposures, health, and economic outcomes in a cohort of over a quarter of a million U.S. light and specialty metals workers and their dependents. Extensive investigations of longitudinal occupational, environmental, social, economic and health exposures and outcomes over the life course have already generated nearly a hundred papers. Now, with extensive efforts in the conversion to a common data model, data cleaning and upgrades to supporting metadata, these data will become more available to the researchers across campus for appropriate studies. A new and exciting venture for PHS, a dedicated website is being developed (expected to go live in March 2019) to detail the history of the data, body of research to date, current collaborators, and facilitate access to data and documentation to a broader audience of investigators across disciplines. We hope this will serve as a model for things to come. For more information about accessing these data, please contact Erika Tribett or Emma Hallgren.

Which reminds me — in so many ways it’s all about the data. I am usually loathe to boast, but I could not resist sharing this email from a colleague recruited to UCLA:

With access to the PHS data these past few years, I feel I have been able to make meaningful contributions to the field of GI. My group has had multiple (I have lost count) oral and poster presentations at national/international conferences, been featured in specialty newsletters, and won a “Best Clinical Poster Award” at a national conference. I first-authored 2 publications in Gut (2nd highest impact factor for GI) and co-authored 3 publications in high-impact/well-known GI journals. All of this would not have been possible without the PHS data. So, I personally thank you and your wonderful staff for the incredible opportunity. Of note, my upcoming chief in GI and co-director at UCLA are well aware that this will be a resource I will greatly miss. There is no resource like Stanford PHS there or elsewhere.

But our data team never rests on its laurels. In the coming months we will be both expanding the range of data (stay tuned!) and undertaking projects to improve these data for researchers across campus. This includes further legal research to simplify the dreadful DUA process for new datasets; continued efforts to tame the complex legal and ethical landscapes complicating research projects; developing new, standard ontologies to allow harmonization of data of novel kinds; and, in a collaboration with Google of potentially game-changing scope, a project to allow linkage in common data models for our (mostly) “high-risk” data with the literally millions of low risk data sets through machine-learned common data models. And because we live in a world of collaborations, we are exploring with many of our peer institutions the possibility of a shared data platform in the months to come. So keep our links handy: phs.stanford.edu and phsdata.stanford.edu!

—Mark Cullen, MD, PHS Director
@MarkCullen_PHS