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Operation Outbreak simulation teaches students how pandemics spread

Source: Cell Press
Date: 9/3/2020
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In 2015, a team of specialists in modeling disease outbreaks got together with educators to create Operation Outbreak, an educational platform and simulation intended to teach high school and college students the fundamentals of responses to pandemics. The program, which is open source and freely available, was designed to simulate outbreaks with different variables (such as R0 and mode of transmission) and to generate data in the context of real human behavior. It includes a Bluetooth-based app that carries out contact tracing by recording transmission events between phones. The details are highlighted in a Commentary published August 31 in the journal Cell.

Operation Outbreak came about after Todd Brown, then a middle school teacher in Florida, contacted Pardis Sabeti (@PardisSabeti), a computational biologist at the Broad Institute of Harvard and MIT, after reading a profile of her in a magazine. He and his students were studying the ongoing Ebola outbreak in West Africa, and he was developing a simulation of how the virus spread using stickers.

As they continued to work together, Sabeti and her team, including Andrés Colubri (@codeanticode), at the time a computational scientist in her lab, began studying mumps outbreaks across Boston college campuses. The idea to create an educational app that “spread” viruses through Bluetooth was soon born. And as recently as December 2019, they were running simulations modeling the outbreak of a virus with a very similar modus operandi to SARS-CoV-2.

“We decided to use a SARS-like virus since it had been high on many pandemic researchers’ lists as a concern,” says Colubri, who is now at the University of Massachusetts Medical School. “To make the simulation more challenging, we included an element of asymptomatic spread. This was a natural concern that would elevate a pandemic’s potential even further.”

This summer, as the COVID-19 pandemic continued to spread, Operation Outbreak was rolled out to 2,000 students in Chicago who were participating as “social distancing ambassadors” as part of the One Summer Chicago program. Participants used the app to track and trace behaviors and learn how “infections” spread in different parts of the city.

“The platform and curriculum are very flexible from an academic and also an experiential learning standpoint,” Brown says. “We tried to gamify the education, so that players’ behaviors and decisions affect not only them, but the entire group they’re playing with.”

The simulation includes elements that have become a familiar part of our daily lives, like limitations in testing abilities and shortages of personal protective equipment (PPE). The program also offers the ability to simulate additional elements that could arise in the current pandemic or in future ones, such as other circulating viruses that can complicate diagnosis.

“We are in one of the most unique situations in the history of the world, by virtue of being able to engage students,” says Brown, who is now community outreach director at Sarasota Military Academy. “Kids are more primed to learn when something directly affects them and their families. This is a chance for future generations to become aware of how infections spread and to recognize warning signs.”

“I hope we can convey that we don’t have to wait for the next pandemic to learn how to respond to them,” Sabeti says. “Ultimately, we can exquisitely model every aspect of viruses and how they spread, even in the ways that we react through vaccines, protective gear, and diagnostics.”

The team has put together a scalable curriculum, including a textbook and series of educational videos, that can be integrated at schools around the country. The materials, which have been funded by philanthropy, are open source and are available for free.

This work is supported by the Gordon and Betty Moore Foundation and the Howard Hughes Medical Institute. Additional funding grants include L’Oreal USA Women in Science Changing the Face of STEM, Toshiba America Foundation, Florida Association of International Baccalaureate World Schools, and Voya Financial.

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Report cards on women in STEM fields finds much room for improvement

Source: Cell Press
Date: 09/05/2019
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Although women have made important contributions to science throughout history, they have consistently been underrepresented at all levels. Now, data from a four-year study of institutional “report cards” undertaken as part of the New York Stem Cell Foundation’s (NYSCF) Initiative on Women in Science and Engineering (IWISE) suggest that although a growing number of women are training in the sciences, efforts to promote and maintain women in more senior scientific roles are still largely inadequate. Additionally, the researchers report that not enough policies have been put in place to support women in science throughout their careers. The study is being reported September 5 in the journal Cell Stem Cell.

“The data suggest that we are making headway,” says Reshma Jagsi (@reshmajagsi), a radiation oncologist and director of the Center for Bioethics and Social Sciences in Medicine at the University of Michigan and one of the corresponding authors. “That said, there are still many institutions that have few women in senior-most faculty positions. There also remains quite a bit of room for improvement in certain areas, including the representation of women in certain roles, such as speaking at scientific meetings.”

The researchers obtained their data through the use of institutional report cards that were collected when individual researchers applied for grants from NYSCF. The report cards were part of a 2014 NYSCF project that put forward a number of strategies aimed at helping to achieve gender parity in science, technology, engineering, and math (STEM). Of the 1,287 report cards that were submitted, 741 provided complete information for a given year, and some included multiple years. Overall, the data in the paper represent 541 institutions in 38 countries in North America (72%) and Europe (18%).

The investigators found that although women made up more than half of the population among undergraduate, graduate, and post-graduate students, the picture became different as seniority increased. Women made up 42% of assistant professors, 34% of associate professors, and 23% of full professors. These rates varied greatly by institution: At about one-third of the institutions surveyed, women made up less than 10% of tenured faculty recruits.

“We expected to find that women would be better represented at more junior ranks compared with senior ranks,” Jagsi says. “But I found it noteworthy that there were regional differences. For example, institutions in Europe come closer to achieving gender parity.”

The researchers say their findings suggest that the primary issue is not recruiting women into STEM roles but retaining them and promoting them into more influential positions.

They also point out the important part that funding organizations can play. “Funding organizations are in a unique position to require institutional leaders to pay attention to equity, diversity, and inclusion within their organizations,” Jagsi says. “By requiring these report cards, they can promote actions that help all scientists thrive. We hope that other funding bodies, like the NIH, will adopt a similar report card.”

The next phase of IWISE will focus on highlighting best practices undertaken by institutions. This will provide comparative data and allow the researchers to monitor progress over time. The researchers will also look at other factors that may influence the recruitment and retention of women scientists, such as the presence of women in top leadership roles, the rates at which tenured women stay in their positions, and equity in salaries across gender, race, and ethnicity.

“For my own work, I plan to begin to focus more on issues of intersectionality,” Jagsi concludes. “A particularly understudied area involves the career experiences in women with other minority identities, such as race. Further research is needed to understand the challenges these women face.”

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This study was supported by the Doris Duke Charitable Foundation and the New York Stem Cell Foundation Research Institute.

Cell Stem Cell, Beeler et al. “Institutional Report Cards for Gender Equality Results of a 4-Year Pilot to Encourage Benchmarking for Women in STEM.” https://www.cell.com/cell-stem-cell/fulltext/S1934-5909(19)30345-5

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Quiz Yourself to Grow What You Know About Regeneration

Source: National Institute of General Medical Sciences - Biomedical Beat Blog
Date: 01/29/2020
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Regeneration is the natural process of replacing or restoring cells that have been lost or damaged due to injury or disease. A few animals can regrow entire organs or other body parts, but most have limited abilities to regenerate.

Scientists in the field of regenerative medicine study how some animals are able to rebuild lost body parts. By better understanding these processes and learning how to control them, researchers hope to develop new methods to treat injuries and diseases in people.

Take this quiz to test what you know about regeneration and regenerative medicine. Then check out our Regeneration fact sheet and the regeneration issue of Pathways , a teaching resource produced in collaboration with Scholastic.

1.) Which of these animals don’t have the ability to regenerate?

  • a.) Zebrafish
  • b.) Fruit flies
  • c.) Sea urchins
  • d.) Axolotls (Mexican salamanders)

2.) The human body can regenerate:

  • a.) Tooth enamel
  • b.) Toes
  • c.) Heart valves
  • d.) Bone tissue

3.) True or false: A planarian flatworm can regrow its entire body from one tiny piece of tissue.

  • a.) True
  • b.) False

4.) True or false: The same genes that some animals use to undergo extensive regeneration are also found in humans.

  • a.) True
  • b.) False

5.) Which of these is an achievement of regeneration research involving stem cells?

  • a.) A treatment for burn wounds that uses a spray gun to apply stem cells
  • b.) Creating a device that emits a light ray of stem cells and is passed through the chest to treat asthma
  • c.) A medication that completely stops a person from aging
  • d.) Cloning an entire human being
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Crowdsourcing Science: Using Competition to Drive Creativity

Source: National Institute of General Medical Sciences - Biomedical Beat Blog
Date: 02/05/2020
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Historically, crowdsourcing has played an important role in certain fields of scientific research. Wildlife biologists often rely on members of the public to monitor animal populations. Using backyard telescopes, amateur astronomers provide images and measurements that lead to important discoveries about the universe. And many meteorologists use data collected by citizen scientists to study weather conditions and patterns.

Now, thanks largely to advances in computing, researchers in computational biology and data science are harnessing the power of the masses and making discoveries that provide valuable insights into human health.

Tackling Data on Complex Diseases 

Trey Ideker, Ph.D. , a professor of medicine at the University of California, San Diego (UCSD), has used crowdsourcing in his graduate-level bioinformatics classes to analyze results from genome-wide association studies. These studies allow researchers to identify particular gene variations that are linked with a disease or another trait.

Some diseases are triggered by single gene mutations or changes, but most conditions are much more complex. A combination of gene variations as well as environmental and other factors influence disease development.

“Common diseases like diabetes, cancer, heart disease, and neurological and psychiatric disorders have hundreds or even thousands of genes that are contributing to them,” Dr. Ideker says. “When you have diseases that involve so many genes, and the massive amount of data that’s associated with those genes, it’s hard to find connections.”

Students in Dr. Ideker’s class applied a classroom approach to crowdsourcing for a project on schizophrenia. The challenge was to develop computer algorithms that could generate a ranked list of 100 genes associated with schizophrenia. Students were given data on gene variants from more than 51,000 individuals.

“Setting this up as a competition pushed the students to explore different methods,” says UCSD graduate student Samson Fong, the teaching assistant for the class. “In a regular lab setting, you might have one or two people working on a problem. In this case, we allowed the students to develop eight or nine different approaches, which we could compare side by side. We learned much more about which methods worked and which didn’t.”

Dr. Ideker adds that running a competition in a classroom setting, rather than within the scientific community, encouraged collaboration as well as competition.

Fong agrees, noting that students learned a lot from each other. Additionally, they were guided to take their projects in different directions, to ensure a wider range of solutions. He explains that because students worked on teams instead of individually, they tackled much more complex problems than they could have on their own.

Advancing Science with a Combination of Computational Methods

The winning method from the competition led to a computational approach, called Network-Assisted Genomic Association, published in iScience. This approach outperformed other methods in identifying known disease genes and in how well the results from the analysis could be replicated. Dr. Ideker has already used the competition framework in another class to develop algorithms related to computational challenges in structural biology.

“This is a field that’s evolving so quickly that for most problems, there is unlikely to be only one computational method that will work,” Dr. Ideker says. “With this classroom approach, we see how the research can benefit from sampling a bouquet of different ideas. You’re pushing science forward in a really nice way.”

Dr. Ideker’s work is supported by NIGMS grant P41GM103504.