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New Health Data Science Course

Split Violin PlotDr. Saumyadipta Pyne, the Scientific Director of PHDL, will be teaching a new Biostatistics course in Fall 2019, BIOSTAT 2036: Introduction to Health Data Science. This course will teach students methods and concepts in data science that are motivated by real life problems in public health. Students will become familiar with data science terms and will learn the concepts of exploratory data analysis, data cleaning, data wrangling, and visualization. Students will learn the necessary skills to tidy, manage, and visualize data and communicate results. This course will mainly use the R programming language but will also teach certain concepts in SQL and Python. The course lectures will cover the following general themes: data structures and representation, data wrangling and processing, computational tools and techniques, and case studies illustrating steps of analysis of real data, including examples from public health.

BIOSTAT 2036 is a newly designed introduction to data science that will be one of the required courses in the soon to be formalized data science concentration of the MS degree in Biostatistics at Pitt Public Health though it will be open to any student. The prerequisite (co-requisite) is BIOST 2039 or permission of instructor. It will be offered in Fall 2019 on Tuesdays, 2:30-4:20 pm in Room A425 Public Health.

Pitt Public Health Leads New MIDAS Network Coordination Center

Wilbert van Panhuis

Pitt Public Health will lead a multidisciplinary group of computer scientists, biostatisticians and biomedical informatics experts to direct the inaugural Network Coordination Center for the Models of Infectious Disease Agent Study (MIDAS), a collaborative research network originally launched by the NIH in 2004 to assist the nation in preparing for infectious disease threats. Backed by a five-year, $6.7 million NIH grant, the University of Pittsburgh Graduate School of Public Health will support an open, community-driven discovery process where all scientists and the broader community have the chance to analyze datasets. Leading the new center is Wilbert van Panhuis, MD, PhD, assistant professor of epidemiology at Pitt Public Health and biomedical informatics at Pitt's School of Medicine. "The scientific community is increasingly recognizing that sharing research data and software not only benefits individual research projects, but increases the impact of science and innovation on the greater good. However, nobody's figured out exactly how to do this for global infectious diseases. What we're going to do is leverage that interest in 'open science' to create a framework that will make it easy to share, find and use research data and software to combat infectious diseases," said Van Panhuis. Click here to read the May 20, 2019 press release.

PHDL Participates in Modeling World’s Systems Conference

Mark Roberts, MD, MPP Wilbert van Panhuis, MD, PhD David Sinclair, PhD

The University of Pittsburgh, through its newly formed School of Computing and Information, leads an initiative to enhance the technological and policy aspects of modeling and managing the world's complicated, interacting systems. This goal – rational analysis and management of complicated systems – is shared by unusually diverse stakeholders from government, industry, non-profits, foundations and academics.

The 2019 conference will be held May 13-15 in Washington, DC and will feature refereed papers and posters in addition to invited sessions. This meeting is a convening of stakeholders, not an academic conference. It will recognize and mobilize a latent community of stakeholders, and organize a professional society and develop modes of communication, survey the state of the art in technologies for modeling and managing complicated systems, and discuss important applications.

Mark Roberts, MD, MPP, Wilbert van Panhuis, MD, PhD and David Sinclair, PhD, members of the Pitt Public Health Dynamics Lab (PHDL), will participate as conference committee members and panelists (Mark and Wilbert) and presenter (David).

Dean Burke Keynote Speaker at Harm Reduction Conference

Cato Institute LogoOn March 21, 2019, Donald S Burke, MD, Dean, University of Pittsburgh Graduate School of Public Health, will deliver the keynote address at the Cato Institute conference on Harm Reduction: Shifting from a War on Drugs to a War on Drug-Related Deaths. This conference, featuring clinical and research experts in epidemiology, public health, addiction treatment, and harm reduction, will examine the record of various harm-reduction modalities in the developed world and will consider their potential for improving the problems caused by drug prohibition. Dr. Burke will speak on "Changing dynamics of the drug overdose epidemic in the U.S. from 1979 through 2016". This event will be livestreamed at on Thursday, March 21 from 8:15am-3:15pm.

The Cato Institute, located in Washington, DC, is a public policy research organization dedicated to the principles of individual liberty, limited government, free markets, and peace. Its scholars and analysts conduct independent, nonpartisan research on a wide range of policy issues. The institute uses the most effective means to originate, advocate, promote, and disseminate applicable policy proposals that create free, open, and civil societies in the United States and throughout the world.

Dengue Immunity May Protect Against Zika

mosquitoAn international team of scientists led by the University of Pittsburgh Graduate School of Public Health, Yale School of Public Health, and the University of Florida reported in the February issue of Science that the higher a person's immunity to dengue virus, the lower their risk of Zika infection. The study, which followed nearly 1,500 people living in a poor neighborhood at the heart of the 2015 Zika outbreak in Brazil, also provides evidence that Brazil's Zika epidemic has largely petered out because enough people acquired immunity to reduce the efficiency of transmission. "Take that with a grain of salt, though. Our study was in a very small urban area, and it is likely that in other parts of Brazil, even different neighborhoods within the same city, people are still susceptible to Zika infection," said co-senior author Ernesto T.A. Marques, M.D., Ph.D., associate professor in Pitt Public Health's Department of Infectious Diseases and Microbiology and public health researcher at Fundação Oswaldo Cruz in Brazil.

Paradoxically, computational models by co-senior author Derek A.T. Cummings, PhD, professor of biology at the University of Florida, showed that participants who had a very recent dengue infection were actually more susceptible to Zika. Possible explanations include protective antibodies have not developed yet or there is something about the immune systems of these people that increases their risk of contracting Zika; or the mosquitoes that transmit dengue also transmit Zika, so a recent dengue infection could mean they are in a place where Zika transmission is active as well. Additional study is needed to determine how these findings could prove useful to clinicians.

PHDL Participates in Disease Modelling Meeting in India

DMPH Discussion Meeting Group Photo
DMPH Workshop Group Photo

Dr. Saumyadipta Pyne, Scientific Director of the Public Health Dynamics Lab (PHDL) at Pitt Public Health, was a co-organizer of a week long discussion meeting and workshop on Mathematical and Statistical Explorations in Disease Modelling and Public Health held in July in Bangalore, India. The aims of this meeting included: 1) exploring different mathematical, statistical and computational approaches to integrate experimental and clinical data, and; 2) discussion on how mathematical modeling can help to interpret and integrate experimental data, frame and test hypotheses, and suggest novel experiments allowing for more conclusive and quantitative interpretations of biological, immunological and disease-related processes.

Dr. David Sinclair, PHDL Post-doctoral Researcher, highlighted the PHDL's agent-based modeling system FRED (A Framework for Reconstructing Epidemiological Dynamics), in his July 1st presentation on "Forecasted size of measles outbreaks associated with vaccination exemptions for school children". Though measles was eliminated from the US in 2000, over the last decade outbreaks continue to occur due to international travel and exemptions from mandatory Measles immunization for all school children based on personal and or religious reasons. Dr. Sinclair discussed the efforts to estimate potential outbreak sizes using an agent-based model, populated with synthetic representation of the US state of Texas.

Dr. Saumyadipta Pyne delivered a virtual presentation on July 4th on "Hierarchical modeling of high-dimensional human immuno-phenotypic diversity". Dr. Pyne described the computational frameworks developed with a focus on fast and automatic modeling and identification of different cell populations, their hierarchical structures and inter-relationships under different biological conditions.


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