New NIH Grant to Identify HIV MicroEpidemics in Lima, Peru

A new CFAR Supplement grant from the NIH will examine spatial-genetic clustering of HIV infections among males who have sex with other males (MSM) in Lima, Peru.

The study will make use of state of the art genetic markers to identify recent infections within the MSM population — so-called “HIV MicroEpidemics”.  Spatial analyses will be conducted to identify neighborhoods and social venues — the places that are most associated with these MicroEpidemics.  And, the study will be able to assess the role that certain risk factors, such numbers of sexual partners and alcohol and drug use, play in MicroEpidemic transmission.

Dr. Edmund Seto will serve as the new study’s director.  His research group in the Department of Environmental & Occupational Health Sciences at the University of Washington will contribute to the spatial-genetic analyses for this study. The research builds off the Center for AIDS Research (CFAR) at the University of Washington led by King Holmes,  the ongoing ¿Sabes? research study collaboration between Ann Duerr’s group at Fred Hutchinson Cancer Research Center at Manual Villaran at Impacta in Peru, as well as work on HIV genetics by Joshua Herbeck in the Department of Global Health at the University of Washington.


New Phased Innovation Grant from NIEHS to Develop Next Generation Exposure Assessment Device

In collaboration with other UW collaborators, my research group will receive a new 5-year phased innovation grant from the NIEHS. Under the funding opportunity (RFA-ES-13-013), the intent is “to facilitate the translation of prototype devices for characterization of personal exposures into field use by supporting a phased validation effort involving a partnership between tool developers and environmental epidemiologists”.  The new grant will support much needed pilot-stage iterative prototyping, refinement, and usability testing of new exposure devices, which will demonstrate device reliability and data quality, and usefulness in real-world settings. The later stages of the grant will support larger scale deployment in a large epidemiological study to improve science and to refine associations between environmental exposures and health outcomes.  This new grant will utilize my new rapid prototyping lab at UW — a newly renovated space for collaborative design, engineering, and testing of new exposure assessment tools.


New P01 Center To Examine the Role of Human Mobility in Infectious Disease Transmission

My group will be working with researchers from UC Davis on a newly awarded NIH P01 Center Grant, “Quantifying Heterogeneities in Dengue Virus Transmission Dynamics”, a 5-year $7.3 million study that will examine as one of its aims, the role of human mobility on contributing to virus transmission and spread.  The study builds upon previous studies conducted by UC Davis researchers on dengue transmission in Iquitos, Peru.  My group is involved in the data core project for the new center.


Congratulations — David Holstius graduates

Congratulations to David Holstius, who graduated over the weekend with a PhD in Environmental Health Sciences.  David’s dissertation, entitled “Monitoring Particulate Matter with Commodity Hardware”, describes work he’s done to develop and utilize lower-cost PM instruments for improved exposure assessment and environmental epidemiological studies.

New Study to Develop Methods to Analyze Ecological Momentary Assessment Data

Just heard, NIH NHLBI will fund a new study with collaborators from USC (Genevieve Dunton, Mary Ann Pentz, and Chih-Ping Chou), UC Berkeley (Michael Jerrett), and Northeastern (Stephen Intille), and UW (Edmund Seto) to develop new statistical modeling approaches to analyze large data from Ecological Momentary Assessment (EMA) studies.

This new study builds upon the work we’ve done with the CalFit system, using smartphone-based EMAs to study the associations between mood, physical activity, and a person’s environment.

NOx dispersion modeling for the Black Women’s Study

For the NIH-funded Black Women’s Health Study, my group is estimating exposures to traffic-related air and noise pollution.  Previously, the traffic noise modeling was described here.

I now have preliminary results for NOx (NO and NO2) traffic air pollution dispersion model.  The model uses the best available roadway geometries, and traffic data, and emissions modeling to derive estimates of exposures.  Moreover, the exposure assessment methodology can be run anywhere in the U.S.  The figure shown is a coarse resolution example of the model applied to 5 boroughs of New York City. But, the model is being run to estimate NOx concentrations at the exact residential address of each person in the Black Women’s Health Study.

Currently the model makes use of parallel computing on a high performance cluster so that hundreds of thousands of exposures can be estimated in reasonable amounts of time.

For another application of our traffic air pollutant model see this, as well as recent the publication in Circulation, and conference proceeding from the 2013 Air & Waste Management Association 106th Annual Conference.


New paper on air quality modeling using real-time traffic data — NOKIA ClearSky project

Over the last couple years, UC Berkeley researchers (Professors Bayen, Glaser, and Seto) have collaborated with NOKIA on the ClearSky project to use state of the art traffic data from sensors and models to estimate air pollution in metropolitan areas. This builds off of progress our group has made towards the development of flexible interfaces to traffic pollution models.  In particular, the ClearSky project makes use of the Rcaline package developed by PhD student, David Holstius.  This forthcoming paper describes how various data and models are integrated into the ClearSky system:

Samaranayake S, Holstius D, Monteil J, Tracton K, Glaser S, Seto E, Bayen A (accepted) Real-time estimation of pollution emissions and dispersion from highway traffic.Computer-aided Civil and Infrastructure Engineering



The Health Effects Institute Funding Near Roadway Monitoring and Exposure Assessment Study

My group at UW will be funded next spring by the Health Effects Institute (HEI) to conduct a 2-year study in which we will deploy over 60 traffic-related real-time air pollution monitors throughout Alameda County.  The first study of its kind, the dense monitoring network will provide crucial information on the ebb and flow of traffic related air pollution at extremely fine spatial and temporal scales.  The network will enable exposure assessment experiments within Alameda County, which will also be conducted as part of the HEI-funded study.  For more information contact me:


NIH to Fund our Study of Children’s Obesity in LA using Systems Science Approach

Just heard good news!  NIH is funding our study with Professors May Wang and Mike Prelip at UCLA to apply Systems Science modeling approaches to data from the Women, Infants, and Children (WIC) program in Los Angeles.  This study will evaluate the efficacy of community-based strategies to reduce obesity in this large cohort.  This new study will build upon causal inference modeling approaches my group has been applying with the help of Biostats Professor Alan Hubbard at Berkeley.  I look forward to working with the many collaborators from UCLA, UCB, Center for Weight and Health, PHFE WIC, LA County Public Health, and Samuels and Associates.