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Nine MIT students awarded 2021 Paul and Daisy Soros Fellowships for New Americans

Tue, 04/13/2021 - 12:00am

An MIT senior and eight MIT graduate students are among the 30 recipients of this year’s P.D. Soros Fellowships for New Americans. In addition to senior Fiona Chen, MIT’s newest Soros winners include graduate students Aziza Almanakly, Alaleh Azhir, Brian Y. Chang PhD ’18, James Diao, Charlie ChangWon Lee, Archana Podury, Ashwin Sah ’20, and Enrique Toloza. Six of the recipients are enrolled at the Harvard-MIT Program in Health Sciences and Technology.

P.D. Soros Fellows receive up to $90,000 to fund their graduate studies and join a lifelong community of new Americans from different backgrounds and fields. The 2021 class was selected from a pool of 2,445 applicants, marking the most competitive year in the fellowship’s history.

The Paul & Daisy Soros Fellowships for New Americans program honors the contributions of immigrants and children of immigrants to the United States. As Fiona Chen says, “Being a new American has required consistent confrontation with the struggles that immigrants and racial minorities face in the U.S. today. It has meant frequent difficulties with finding security and comfort in new contexts. But it has also meant continual growth in learning to love the parts of myself — the way I look; the things that my family and I value — that have marked me as different, or as an outsider.”

Students interested in applying to the P.D. Soros fellowship should contact Kim Benard, assistant dean of distinguished fellowships in Career Advising and Professional Development.

Aziza Almanakly

Aziza Almanakly, a PhD student in electrical engineering and computer science, researches microwave quantum optics with superconducting qubits for quantum communication under Professor William Oliver in the Department of Physics. Almanakly’s career goal is to engineer multi-qubit systems that push boundaries in quantum technology.

Born and raised in northern New Jersey, Almanakly is the daughter of Syrian immigrants who came to the United States in the early 1990s in pursuit of academic opportunities. As the civil war in Syria grew dire, more of her relatives sought asylum in the U.S. Almanakly grew up around extended family who built a new version of their Syrian home in New Jersey.

Following in the footsteps of her mathematically minded father, Almanakly studied electrical engineering at The Cooper Union for the Advancement of Science and Art. She also pursued research opportunities in experimental quantum computing at Princeton University, the City University of New York, New York University, and Caltech.

Almanakly recognizes the importance of strong mentorship in diversifying engineering. She uses her unique experience as a New American and female engineer to encourage students from underrepresented backgrounds to enter STEM fields.

Alaleh Azhir

Alaleh Azhir grew up in Iran, where she pursued her passion for mathematics. She immigrated with her mother to the United States at age 14. Determined to overcome strict gender roles she had witnessed for women, Azhir is dedicated to improving health care for them. 

Azhir graduated from Johns Hopkins University in 2019 with a perfect GPA as a triple major in biomedical engineering, computer science, and applied mathematics and statistics. A Rhodes and Barry Goldwater Scholar, she has developed many novel tools for visualization and analysis of genomics data at Johns Hopkins University, Harvard University, MIT, the National Institutes of Health, and laboratories in Switzerland. 

After completing a master’s in statistical science at Oxford University, Azhir began her MD studies in the Harvard-MIT Program in Health Sciences and Technology. Her thesis focuses on the role of X and Y sex chromosomes on disease manifestations. Through medical training, she aims to build further computational tools specifically for preventive care for women. She has also founded and directs the nonprofit organization, Frappa, aimed at mentoring women living in Iran and helping them to immigrate abroad through the graduate school application process. 

Brian Y. Chang PhD ’18

Born in Johnson City, New York, Brian Y. Chang PhD ’18 is the son of immigrants from the Shanghai municipality and Shandong Province in China. He pursued undergraduate and master’s degrees in mechanical engineering at Carnegie Mellon University, graduating in a combined four years with honors.

In 2018, Chang completed a PhD in medical engineering at MIT. Under the mentorship of Professor Elazer Edelman, Chang developed methods that make advanced cardiac technologies more accessible. The resulting approaches are used in hospitals around the world. Chang has published extensively and holds five patents.

With the goal of harnessing the power of engineering to improve patient care, Chang co-founded X-COR Therapeutics, a seed-funded medical device startup developing a more accessible treatment for lung failure with the potential to support patients with severe Covid-19 and chronic obstructive pulmonary disease.

After spending time in the hospital connecting with patients and teaching cardiovascular pathophysiology to medical students, Chang decided to attend medical school. He is currently a medical student in the Harvard-MIT Program in Health Sciences and Technology. Chang hopes to advance health care through medical device innovation and education as a future physician-scientist, entrepreneur, and educator.

Fiona Chen

MIT senior Fiona Chen was born in Cedar Park, Texas, the daughter of immigrants from China. Witnessing how her own and many other immigrant families faced significant difficulties finding work and financial stability sparked her interest in learning about poverty and economic inequality.

At MIT, Chen has pursued degrees in economics and mathematics. Her economics research projects have examined important policy issues — social isolation among students, global development and poverty, universal health-care systems, and the role of technology in shaping the labor market.

An active member of the MIT community, Chen has served as the officer on governance and officer on policy of the Undergraduate Association, MIT’s student government; the opinion editor of The Tech student newspaper; the undergraduate representative of several Institute-wide committees, including MIT’s Corporation Joint Advisory Committee; and one of the founding members of MIT Students Against War. In each of these roles, she has worked to advocate for policies to support underrepresented groups at MIT.

As a Soros fellow, Chen will pursue a PhD in economics to deepen her understanding of economic policy. Her ultimate goal is to become a professor who researches poverty and economic inequality, and applies her findings to craft policy solutions.

James Diao

James Diao graduated from Yale University with degrees in statistics and biochemistry and is currently a medical student at the Harvard-MIT Program in Health Sciences and Technology. He aspires to give voice to patient perspectives in the development and evaluation of health-care technology.

Diao grew up in Houston’s Chinatown, and spent summers with his extended family in Jiangxian. Diao’s family later moved to Fort Bend, Texas, where he found a pediatric oncologist mentor who introduced him to the wonders of modern molecular biology.

Diao’s interests include the responsible development of technology. At Apple, he led projects to validate wearable health features in diverse populations; at PathAI, he built deep learning models to broaden access to pathologist services; at Yale, where he worked on standardizing analyses of exRNA biomarkers; and at Harvard, he studied the impacts of clinical guidelines on marginalized groups.

Diao’s lead author research in the New England Journal of Medicine and JAMA systematically compared race-based and race-free equations for kidney function, and demonstrated that up to 1 million Black Americans may receive unequal kidney care due to their race. He has also published articles on machine learning and precision medicine.

Charlie ChangWon Lee

Born in Seoul, South Korea, Charlie ChangWon Lee was 10 when his family immigrated to the United States and settled in Palisades Park, New Jersey. The stress of his parents’ lack of health coverage ignited Lee’s determination to study the reasons for the high cost of health care in the U.S. and learn how to care for uninsured families like his own.

Lee graduated summa cum laude in integrative biology from Harvard College, winning the Hoopes Prize for his thesis on the therapeutic potential of human gut microbes. Lee’s research on novel therapies led him to question how newly approved, and expensive, medications could reach more patients.

At the Program on Regulation, Therapeutics, and Law (PORTAL) at Brigham and Women’s Hospital, Lee studied policy issues involving pharmaceutical drug pricing, drug development, and medication use and safety. His articles have appeared in JAMA, Health Affairs, and Mayo Clinic Proceedings.

As a first-year medical student at the Harvard-MIT Health Sciences and Technology program, Lee is investigating policies to incentivize vaccine and biosimilar drug development. He hopes to find avenues to bridge science and policy and translate medical innovations into accessible, affordable therapies.

Archana Podury

The daughter of Indian immigrants, Archana Podury was born in Mountain View, California. As an undergraduate at Cornell University, she studied the neural circuits underlying motor learning. Her growing interest in whole-brain dynamics led her to the Princeton Neuroscience Institute and Neuralink, where she discovered how brain-machine interfaces could be used to understand diffuse networks in the brain.

While studying neural circuits, Podury worked at a syringe exchange in Ithaca, New York, where she witnessed firsthand the mechanics of court-based drug rehabilitation. Now, as an MD student in the Harvard-MIT Health Sciences and Technology program, Podury is interested in combining computational and social approaches to neuropsychiatric disease.

In the Boyden Lab at the MIT McGovern Institute for Brain Research, Podury is developing human brain organoid models to better characterize circuit dysfunction in neurodevelopmental disorders. Concurrently, her work in the Dhand Lab at Brigham and Women’s Hospital applies network science tools to understand how patients’ social environments influence their health outcomes following acute neurological injury.

Podury hopes that focusing on both neural and social networks can lead toward a more comprehensive, and compassionate, approach to health and disease.

Ashwin Sah ’20

Ashwin Sah ’20 was born and raised in Portland, Oregon, the son of Indian immigrants. He developed a passion for mathematics research as an undergraduate at MIT, where he conducted research under Professor Yufei Zhao, as well as at the Duluth and Emory REU (Research Experience for Undergraduates) programs.

Sah has given talks on his work at multiple professional venues. His undergraduate research in varied areas of combinatorics and discrete mathematics culminated in the Barry Goldwater Scholarship and the Frank and Brennie Morgan Prize for Outstanding Research in Mathematics by an Undergraduate Student. Additionally, his work on diagonal Ramsey numbers was recently featured in Quanta Magazine.

Beyond research, Sah has pursued opportunities to give back to the math community, helping to organize or grade competitions such as the Harvard-MIT Mathematics Tournament and the USA Mathematical Olympiad. He has also been a grader at the Mathematical Olympiad Program, a camp for talented high-school students in the United States, and an instructor for the Monsoon Math Camp, a virtual program aimed at teaching higher mathematics to high school students in India.

Sah is currently a PhD student in mathematics at MIT, where he continues to work with Zhao.

Enrique Toloza

Enrique Toloza was born in Los Angeles, California, the child of two immigrants: one from Colombia who came to the United States for a PhD and the other from the Philippines who grew up in California and went on to medical school. Their literal marriage of science and medicine inspired Toloza to become a physician-scientist.

Toloza majored in physics and Spanish literature at the University of North Carolina at Chapel Hill. He eventually settled on an interest in theoretical neuroscience after a summer research internship at MIT and completing an honors thesis on noninvasive brain stimulation.

After college, Toloza joined Professor Mark Harnett’s laboratory at MIT for a year. He went on to enroll in the Harvard-MIT MD/PhD program, studying within the Health Sciences and Technology MD curriculum at Harvard and the PhD program at MIT. For his PhD, Toloza rejoined Harnett to conduct research on the biophysics of dendritic integration and the contribution of dendrites to cortical computations in the brain.

Toloza is passionate about expanding health care access to immigrant populations. In college, he led the interpreting team at the University of North Carolina at Chapel Hill’s student-run health clinic; at Harvard Medical School, he has worked with Spanish-speaking patients as a student clinician.

With “Choctaw Animals” for piano, Charles Shadle honors his Native American heritage

Tue, 04/13/2021 - 12:00am

Charles Shadle was just 10 years old when he was entrusted with a precious family heirloom: a book of music that his great-great-great-grandmother had brought with her on the Trail of Tears, the forced removal of Native Americans to Oklahoma from their southeastern homelands beginning in the 1830s.

Today, this extraordinary gift remains a symbol of two significant threads interwoven in Shadle’s life: music and his Choctaw heritage. “There was usually a person in every generation that music was important to, and I was the one in my generation,” says Shadle, a senior lecturer in music at MIT and an enrolled Oklahoma Choctaw.

The fact that his ancestor carried the book on the journey illustrates the importance of music to the Choctaw, Shadle explains. “I think it’s true of any immigrants,” he says. “Once you get past the essentials, what you take with you has real cultural significance.”

Now an accomplished composer, Shadle has received commissions from many institutions over the years, including Lake George Opera Festival, the Handel and Haydn Society, the Syracuse Symphony Orchestra, and the Rockport Chamber Music Festival. But recently, he created a simpler series of compositions that he hopes will provide an accessible introduction both to music and to Choctaw traditions.

“I have written a number of pieces that explore aspects of my Choctaw heritage, such as ‘Limestone Gap,’ ‘Red Cedar,’ and ‘The Old Place’ (all commissioned by the London-based ensemble Lontano), but these works tend to be rather difficult, requiring numerous highly accomplished players. Since this naturally limits the number of people who can experience my music, I decided to compose a set of much more accessible piano pieces,” he says.

Choctaw Animals” is a series of four pieces intended for pianists of all ages and abilities. “My thought was that they could be played by young people taking piano lessons,” Shadle says. “They’re as simple as I could make them and still have them sound like my music.”

Inspired by tradition

With titles in Choctaw, each piece reflects the character of a particular creature, Shadle says. For example, “Chulhkvn” (pronounced choth-kan), or “Spider,” is a piece that weaves together musical lines the way a spider might weave silk. “Issuba,” which means “pony,” features a rhythm reminiscent of hoof beats. The other two pieces are “Nvni,” which means “fish,” and “Nashoba,” which means “wolf.”

Listen to the recordings: “Chulhkvn” | “Nvni” | “Nashoba” | “Issuba

Some of the creatures have strong ties to Choctaw heritage — the spider, for example, is credited in folklore with bringing fire to the people — but Shadle says he chose others primarily because it was enjoyable to represent the animals musically. “Maybe the wolf is my favorite,” he says, describing the piece as quiet and mysterious. “It’s almost as if we never see the wolf, we just sort of sense that it’s there.”

In all cases, Shadle says, the compositions draw on elements of Choctaw music-making, notably the tribe’s tradition of social dance. “I focused on using melodic patterns and rhythmic configurations that are inspired by this tradition, without ever quoting any of the actual dance songs,” Shadle says. While reimagining traditional songs can be very successful artistically, he explains, “among the people whose music is used, that can feel like a violation, like something taken from them. I didn’t want to participate in that.”

An identity connected to the land

Shadle says he hopes his work will provide performers and listeners with some insight into Choctaw traditions and perhaps even introduce them to a part of the country they don’t know. “My corner of Oklahoma isn’t a part that most people think about very much,” he says, explaining that his music is deeply rooted in the landscape. “That connection with place, with land, with heritage, are always inextricably linked. ... That feels to me to come from a singularly Choctaw part of myself.”

And, while that might seem strange, given that the Choctaws were forced off their ancestral lands, Shadle says he thinks the traumatic move to Oklahoma (which led to the deaths of an estimated 4,000 of the 20,000 Choctaw who were relocated) actually deepened the tribe’s connection to the land. “The Choctaw had mostly owned land communally before the 19th century. When they got to Oklahoma, they had the sense they had to hold onto the land,” he says, noting that members of the tribe now own land as individuals. “Our identity is connected to the land because it was taken from us at one point.”

Building connections

Ultimately, Shadle hopes his work builds connections — between music and his Choctaw heritage, between classical music and traditional music, and between generations of Choctaw. “I want to make sure I’m acting as a conduit for people who may come after me,” he says, noting that he is arguably the most visible living classical composer in the Choctaw tribe, and he does not want to be the last. “I’m interested in the young Choctaw girl or boy in some rural community,” he says. “To some extent, I can say, you could be a composer too. Your voice can be heard.”

Shadle is also happy to have the opportunity to share his heritage with MIT, since he is one of just two Native Americans on the faculty; the other is David Robertson, a senior lecturer in the MIT Sloan School of Management, who is Cherokee. "David and I are the only two people who have ever taught full time at MIT who are Native American. There has never been a tenured faculty member,” Shadle says. However, there is a Native American Student Association on campus, and Shadle sees efforts to give that group meeting space as a sign of progress for a broad and diverse group of people that includes the Choctaw and hundreds of other tribes.

“If a group gets space at MIT, they count — and I think we’re seeing that happening for Indigenous students.”

Story by SHASS Communications
Editorial and design director: Emily Hiestand
Senior writer: Kathryn O’Neill

Talking outside the tower

Mon, 04/12/2021 - 3:50pm

Walking into MIT can feel like entering a foreign country — one with a number for every building and an unwieldy acronym for every organization. Deeper conversations are even more opaque, as fields and sub-fields command their own complex scientific argot. But if the Covid-19 pandemic has taught us anything, it’s that bridging the gap between scientists and their wider society is more important than ever. The School of Engineering's EECS Communication Lab, in partnership with the MIT Libraries, is working to bridge that communications gap and help research scientists translate their findings for lay audiences in a series of talks called “Science Snippets.”

“A lot of our work is scientist-to-scientist communication, such as invited talks, poster presentation, thesis defenses, etc., but I also have experience in teaching researchers to communicate with lay audiences,” says Deanna Montgomery, the manager of the EECS Communication Lab and the mastermind behind the Science Snippets talks and related Independent Activities Period (IAP) workshop. “There are skills that overlap, but we wanted to focus on outreach: How do we get outside MIT and the ivory tower?”

For the lab’s first major venture in teaching outside-of-field communications, Montgomery decided to implement a subset of a larger curriculum designed at the University of Michigan by an organization called RELATE. “The workshop was the Communication Lab’s first real venture into teaching researchers how to communicate with people outside their field,” says Montgomery, who co-taught the series with Rachel Yang, an electrical engineering and computer science PhD student, and Jim Clark, a recent PhD graduate in aeronautics and astronautics.

But where to find a willing audience? Montgomery approached Phoebe Ayers, MIT's librarian for electrical engineering and computer science and mathematics, who looped in Nina Davis-Millis, the MIT Libraries director of community engagement. Davis-Millis had an immediate idea: “I have a master’s degree in gifted education, so when we were thinking about an audience, I thought immediately about AP high school students with a hunger for science.” Davis-Millis envisioned finding an audience of students who might not have access to high-quality science labs or expensive learning equipment. “I got all fired up about this and then got off the Zoom and thought, 'What did I just do? Now I am on the hook to find these people!'”

By posting to websites aimed at gifted students and their families, Davis-Millis was able to find not only AP students enrolled in schools down the Eastern Seaboard, but also several home-schooled students who were interested in learning about science from current MIT students. “I felt that this was a program where we provided the right kind of audience for the people who took that workshop, and it was a win-win all around,” says Davis-Millis.

The two sets of mini-lectures, given over Zoom on March 2 and March 9, gave a tantalizing hint of the breadth and depth of research occurring at MIT. “We’re just beginning to introduce the idea of using bacteria to digest plastic, which is not as easy as it sounds, because bacteria have very hyper-specific types of enzymes that are only prepared to digest certain kinds of molecular structures, much like a key can only fit into one kind of lock,” said biological engineering graduate student Mirna Kheir Gouda, deploying a carefully chosen metaphor in her talk on new ideas in plastic waste management. The metaphor was specifically crafted for her high school-aged audience. “These speakers were not just repurposing a conference talk,” points out Montgomery. “They needed to choose language appropriately to reduce jargon, think intentionally about the analogies and metaphors they would use, and choose words carefully for the audience.”

That careful consideration was on display when postdoc Ahmed Alade “Tia” Tiamiyu titled his talk “Bounce, stick, bury: different behaviors when tiny particles take a hit.” By classifying the behaviors of microscopic particles being sprayed at a substrate with familiar playground terms like “splat” and “stickiness”, Tiamiyu made mindbogglingly tiny particles — which, he reminded his audience, were seven times smaller than the width of an average human hair — feel familiar. “Given the depth and complexity of the topics, I was very impressed at how well they avoided jargon and assumptions of previous knowledge,” says Davis-Millis. “That’s hard to do!”

The success of the talks was partially rooted in the diverse backgrounds of students enrolled in Montgomery’s IAP course. “Our discussion- and activity-based curriculum worked really well because we had people from a variety of disciplines. Say you have an aero-astro student working with a bioengineering student,” says Montgomery. “Both might be engineers, but they don’t know each other’s field jargon, so they make good stand-ins for a lay audience.”

The course’s diversity mirrors the EECS Communication Lab’s open-door policy. “Anyone affiliated with Course 6 in any way can make a one-on-one appointment to get coaching on any communications task,” stresses Montgomery. “You don’t have to be a Course 6 major! You could be a minor, or your advisor could be a Course 6 faculty member. We seriously help with anything: writing, speaking, grad school applications, conference talks, posters, graphics, all the kinds of communications which MIT students have to do.”

Davis-Millis reported that the MIT Libraries share the Communication Lab’s desire to help MIT students tackle any challenge: “I wish people would feel more comfortable about asking librarians to find information. If you learn nothing else from me, remember this: Don’t ever pay for information. We will get it for you. It’s pretty rare that in your MIT career, you don’t need help in something, and there’s an awful lot of help available, whether it’s mental health support or grant application support, or spiritual support, or library support, and I wish more students felt entitled to ask for the support and resources that we are all eager to give them.”

Now those resources include training to share science — its possibility and its excitement — with the world beyond MIT.

MIT Press launches open access collection of 34 classic architecture and urban studies titles

Mon, 04/12/2021 - 3:30pm

The MIT Press has launched MIT Press Open Architecture and Urban Studies, a robust digital collection of classic and previously out-of-print architecture and urban studies books, on their digital book platform MIT Press Direct. The collection was funded by a grant from the Andrew W. Mellon Foundation as part of the Humanities Open Book Program, which they co-sponsored with the National Endowment for the Humanities.

For years, the MIT Press has fielded requests for e-book editions of classic, out-of-print works, like the two volumes of “The Staircase,” by John Templer; “On Leon Battista Alberti: His Literary and Aesthetic Theories,” by Mark Jarzombek; “Possible Palladian Villas: (Plus a Few Instructively Impossible Ones),” by George L. Hersey and Richard Freedman, and “Making a Middle Landscape,” by Peter Rowe. Many of these foundational texts were published before the advent of e-books and remained undigitized because of complex design requirements and the prohibitive cost of image permissions.

Now, with funding from the Mellon Foundation and the efforts of an open-access-savvy digitization team, the MIT Press was able to not only secure image permissions, but also to solicit fresh forewords that bring new insights to bear on many of these classic texts. Many of the titles will also be made available on the open access platform PubPub, where readers will be able to interact with and annotate the works with contemporary context and related readings.

Representing the breadth and depth of the MIT Press’s architecture and urban studies publishing program, the collection is a quintessential blend of theory, practice, history, and technology. 

“The books in this collection are drawn from an absolutely formative period in the discourse of architectural and urban history and theory,” explains Timothy Hyde, associate professor in the MIT Department of Architecture. “These are essential publications to have available again, as they represent to some degree the founding of an independent discipline.”

Explicitly global and timeless, the collection features texts such as Constantinos Doxiadis’s “Architectural Space in Ancient Greece,” Jean Gottman’s “Megalopolis: The Urbanized Northeastern Seaboard of the United States,” and four volumes of the “Survey of the Architectural History of Cambridge” series. And the major figures and movements that have shaped the modern built world are well represented by books like Donald Leslie Johnson’s “Frank Lloyd Wright vs. America: The 1930s;” Gilbert Herbert’s “The Dream of the Factory-Made House,” by Walter Gropius and Konrad Wachsmann; and Moshe Safdie’s “Beyond Habitat.”

This initiative combines two of the MIT Press’s core strengths — its legacy of publishing titles of the greatest importance and highest quality in architecture and urban studies and its longstanding support for open access publishing — according to MIT Press Director Amy Brand.

“The MIT Press is committed to reimagining daily what academic publishing can be,” says Brand. “This partnership with the Humanities Open Book Program not only gives these important works a second life and introduces them to new generations of scholars and readers, it also reaffirms our commitment to making scholarship available as widely and openly as possible.”

Task Force 2021 and Beyond moves into new phase

Mon, 04/12/2021 - 9:00am

Task Force 2021 and Beyond is entering the next major phase of its work to position MIT for the post-Covid world, co-chairs Rick Danheiser and Sanjay Sarma announced today in a letter to the MIT community.

In the first phase of the task force’s work, which ran from last June through December, nearly 200 MIT faculty, staff, and students served in working groups that generated more than 50 discrete ideas intended to help MIT emerge strong from the disruption of Covid-19.

“We have spent the past three months developing a plan and a structure to advance these ideas,” wrote Danheiser, chair of the faculty and Arthur C. Cope Professor of Chemistry, and Sarma, vice president for open learning and Fred Fort Flowers and Daniel Fort Flowers Professor of Mechanical Engineering. “Today we launch the second phase of Task Force 2021 and Beyond, focused on refining these ideas and planning for their implementation.”

In this next phase, different groups — known as Refinement and Implementation Committees (RICs) — will determine how best to make progress on 16 sets of ideas and proposals put forth during the previous phase.

“Some of these ideas emerged from Phase 1 in well-developed form, and in these cases only one or two meetings of the relevant RIC may be necessary,” Danheiser wrote in a recent Faculty Newsletter column. “Other RICs are expected to meet throughout the spring semester and in these cases meetings with students and colleagues via forums will likely be appropriate.”

Efforts to refine and implement ideas

The RICs are organized into five pillars, representing the broad themes that emerged from last year’s work. Those five pillars are:

1. Rethink how and where we work and revamp employee development and spaces, leveraging what we’ve learned about remote teaching, learning, and working during the pandemic.

Specific RICs under this pillar seek to:

  • Plan and pilot flexible work practices and policies, as well as platforms, data, and systems to support such practices. Consider short-, medium-, and long-term needs, carefully weighing flexibility, sustainability, and our community’s needs.
  • Establish integrated opportunities for all employees to develop skills for mentorship, management of teams, and career advancement through tools, training, and support of career pathways and networks at MIT.
  • Consider how changing technology and work practices affect our needs for space, including academic classrooms, community spaces, research spaces, outdoor spaces, work spaces, and flexible spaces. Consider also an expanded definition of campus, including locations outside of Cambridge.

2. Review our classroom education in light of evolving curricula, the increasing necessity for lifelong learning, and possibilities created by leveraging technology.

Specific RICs under this pillar seek to:

  • Review how best to leverage digital technologies in pedagogy and how best to use class time for that which can best be done in person.
  • Consider opportunities for incorporating education experiences involving social responsibility, public service, sustainability, and appreciation of structural, systemic, and institutional hierarchies.
  • Articulate a future view for community and outdoor spaces, classrooms, and other academic spaces.

3. Increase the scope and intensity of our holistic learning and training, developing each member of the MIT community to foster the ability and passion to work wisely, creatively, and effectively for the betterment of humankind.

Specific RICs under this pillar seek to:

  • Review and recommend ways to enhance undergraduate advising, mentoring, and development.
  • Consider models for holistic graduate education and recommend professional development opportunities.
  • Review and recommend ways to enhance the scope and effectiveness of graduate advising and mentorship.
  • Review and provide concrete recommendations for career paths and support for postdocs, research scientists, and instructional staff.

4. Articulate our public responsibilities and imbue these ideals in our community and culture, infusing them more deeply in our student education and human resources.

Specific RICs under this pillar seek to:

  • Define our public responsibilities globally and locally, and integrate these responsibilities into our student education and organizational structure.
  • Enact a plan that attracts, acculturates, develops, rewards, and retains exceptional individuals and reflects our aspirations for diversity, equity, and inclusion.
  • Provide recommendations to support research collaborations, including multidisciplinary collaborations to solve large, pressing problems; share research data, equipment, and other resources; and foster industry and international collaborations.

5. Modernize our data, systems, processes, and financial models to serve future economic realities and our evolving needs.

Specific RICs under this pillar seek to:

  • Address concerns related to under-recovery funding levels and processes.
  • Provide more financial support to residential students with greater needs.
  • Develop a new financial model for the Institute, reflecting more diverse and multifaceted sources of funding.
  • Support transformational internal projects with a new cross-functional team and digitized data-sharing practices across departments, labs, and centers.
  • Develop a plan to address the high costs of graduate students at MIT.

Some of the RICs have already held initial meetings, and the rest will convene soon. Each includes relevant task force members who were involved in generating the initial ideas, as well as others who will be involved in implementing those ideas. Most of the RICs will develop goals and metrics for tracking progress over the next few years.

The MIT community is encouraged to provide input to each of the RICs via the Task Force 2021 and Beyond website.

Julie Soriero inducted into National Association of Collegiate Directors of Athletics Hall of Fame

Fri, 04/09/2021 - 4:50pm

Former MIT Director of Athletics and head of the MIT Department of Athletics, Physical Education and Recreation Julie Soriero has been inducted into the National Association of Collegiate Directors of Athletics (NACDA) Hall of Fame, as announced by the NACDA National Office. The seven-member class of inductees will be recognized in conjunction with the 56th Annual NACDA and Affiliates Convention, which will be held virtually on July 27-28.

“When I think about what this honor means to me, the first thought that comes to mind is appreciation,” says Soriero. “I start with my family and my appreciation for their understanding of the late hours, weekends of work, travel, phone calls at all hours, and the pride they shared in the successes of the teams at the institutions I worked for as championships were won and tournament play unfolded. As a coach and as an administrator, I have always been passionate about the inherent lessons we are able to teach through intercollegiate athletics. I am therefore appreciative of the opportunities I have had in being named as the director of athletics to the various institutions I have been able to lead and serve.” 

Soriero arrived at MIT in July 2007 as the director of athletics and the head of DAPER. Retiring in January 2020, she led MIT intercollegiate athletics through a transformation into one of the top intercollegiate athletic programs in the United States.

“Working in higher education is a privilege, and I have been fortunate to have worked alongside so many talented leaders and have enjoyed a career that has been demanding, challenging, and rewarding — all elements anyone would appreciate in a job,” Soriero says. “I also have a very deep appreciation for the many wonderful, dedicated, and talented people who I worked alongside in implementing creative ideas, developing solutions to problems, and moving a vision of excellence forward. NACDA does so many important things for professional growth in the world of collegiate athletics and to be recognized by this organization is truly an honor.”

Boasting one the largest athletics programs in the country with 33 varsity sports, under her leadership MIT captured numerous New England Women's and Men's Athletic Conference (NEWMAC) championships and was awarded both the men’s and women’s NEWMAC President's Cups from 2016-17 through 2018-19. Competitively, MIT finished consistently in the top 10 in the Learfield IMG College Directors' Cup during much of her tenure, including an Institute-record second-place finish in 2017-18.

MIT also sits as the leader in NCAA Division III for Academic All-Americans. In addition to their competitive success, Soriero also focused on student development and initiated a leadership program for student athletes titled a “Culture of Care,” which focused on sexual assault prevention, mental health, diversity, and inclusion and secured an endowment fund to support these efforts and programming.

Since her initial arrival at MIT, Soriero was a tireless and successful fundraiser. Over her MIT career, she raised well over $25 million for a variety of capital project improvements or new construction. Additionally, Soriero raised funds for four head coaching endowments ($2 million), two director-level endowments ($2.5 million), and completed the fund-raising for two coaching endowments that were initiated prior to her arrival.

In 2018, Soriero received the prestigious NCAA President's Pat Summitt Award, which honors the recipient for significant lifetime achievement in demonstrating a devotion to the development of student-athletes and making a positive impact on their lives. She has received additional recognition for her leadership, including the 2014-15 Division III Under Armour Athletics Director of the Year by NACDA and the 2012 Division III Administrator of the Year by Women Leaders in College Sports.

She came to MIT from Colorado College, where she spent nine years overall that included four as the director of athletics. Before Colorado College, Soriero was the women's basketball head coach at the University of Pennsylvania for 10 years, and overall she coached for 21 years before transitioning into her career as a full-time administrator.

Soriero has been invited to conduct numerous intercollegiate program reviews on other campuses and is currently a consultant with SHIFT Executive Coaching with a focus on intercollegiate athletics administration mentoring, leadership and career development.

NACDA, now in its 56th year, is the professional and educational association for more than 22,000 college athletics administrators at more than 2,200 institutions throughout the United States, Canada, and Mexico. More than 6,500 athletics administrators annually attend NACDA and Affiliates Convention Week. Additionally, NACDA manages 17 professional associations and four foundations.

One-stop machine learning platform turns health care data into insights

Fri, 04/09/2021 - 3:40pm

Over the past decade, hospitals and other health care providers have put massive amounts of time and energy into adopting electronic health care records, turning hastily scribbled doctors' notes into durable sources of information. But collecting these data is less than half the battle. It can take even more time and effort to turn these records into actual insights — ones that use the learnings of the past to inform future decisions.

Cardea, a software system built by researchers and software engineers at MIT's Data to AI Lab (DAI Lab), is built to help with that. By shepherding hospital data through an ever-increasing set of machine learning models, the system could assist hospitals in planning for events as large as global pandemics and as small as no-show appointments.

With Cardea, hospitals may eventually be able to solve "hundreds of different types of machine learning problems," says Kalyan Veeramanchaneni, principal investigator of the DAI Lab and a principal research scientist in MIT's Laboratory for Information and Decision Systems (LIDS). Because the framework is open-source, and uses generalizable techniques, they can also share these solutions with each other, increasing transparency and enabling teamwork.

Automated for the people

Cardea belongs to a field called automated machine learning, or AutoML. Machine learning is increasingly common, used for everything from drug development to credit card fraud detection. The goal of AutoML is to democratize these predictive tools, making it easier for people — including, eventually, non-experts — to build, use, and understand them, says Veeramachaneni.

Instead of requiring people to design and code an entire machine learning model, AutoML systems like Cardea surface existing ones, along with explanations of what they do and how they work. Users can then mix and match modules to accomplish their goals, like going to a buffet rather than cooking a meal from scratch.

For instance, data scientists have built a number of machine learning tools for health care, but most of them aren't very accessible — even to experts. "They're written up in papers and hidden away," says Sarah Alnegheimish, a graduate student in LIDS. To build Cardea, she and her colleagues have been unearthing these tools and bringing them together, aiming to form "a powerful reference" for hospital problem-solvers, she says.

Step by step

To turn reams of data into useful predictions, Cardea walks users through a pipeline, with choices and safeguards at each step. They are first greeted by a data assembler, which ingests the information they provide. Cardea is built to work with Fast Healthcare Interoperability Resources (FHIR), the current industry standard for electronic health care records.

Hospitals vary in exactly how they use FHIR, so Cardea has been built to "adapt to different conditions and different datasets seamlessly," says Veeramachaneni. If there are discrepancies within the data, Cardea's data auditor points them out, so that they can be fixed or dismissed.

Next, Cardea asks the user what they want to find out. Perhaps they would like to estimate how long a patient might stay in the hospital. Even seemingly small questions like this one are crucial when it comes to day-to-day hospital operations — especially now, as health care facilities manage their resources during the Covid-19 pandemic, says Alnegheimish. Users can choose between different models, and the software system then uses the dataset and models to learn patterns from previous patients, and to predict what could happen in this case, helping stakeholders plan ahead.

Currently, Cardea is set up to help with four types of resource-allocation questions. But because the pipeline incorporates so many different models, it can be easily adapted to other scenarios that might arise. As Cardea grows, the goal is for stakeholders to eventually be able to use it to "solve any prediction problem within the health care domain," Alnegheimish says.

The team presented their paper describing the system at the IEEE International Conference on Data Science and Advanced Analytics in October 2020. The researchers tested the accuracy of the system against users of a popular data science platform, and found that it out-competed 90 percent of them. They also tested its efficacy, asking data analysts to use Cardea to make predictions on a demo health care dataset. They found that Cardea significantly improved their efficiency — for example, feature engineering, which the analysts said usually takes them an average of two hours, took them five minutes instead.

Trust the process

Hospital workers are often tasked with making high-stakes, critical decisions. It's vital that they trust any tools they use along the way, including Cardea. It's not enough for users to plug in some numbers, press a button, and get an answer: "They should get some sense of the model, and they should know what is going on," says Dongyu Liu, a postdoc in LIDS.

To build in even more transparency, Cardea's next step is a model audit. Like all predictive apparatuses, machine learning models have strengths and weaknesses. By laying these out, Cardea gives the user the ability to decide whether to accept this model's results, or to start again with a new one.

Cardea was released to the public earlier this year. Because it's open source, users are welcome to integrate their own tools. The team also took pains to ensure that the software system is not only available, but understandable and easy to use. This will also help with reproducibility, Veeramachaneni says, so that predictions made on models built with the software can be understood and checked by others.  

The team also plans to build in more data visualizers and explanations, to provide an even deeper view, and make the software system more accessible to non-experts, Liu says.

"The hope is for people to adopt it, and start contributing to it," Alnegheimish says. "With the help of the community, we can make it something much more powerful." 

Standing in solidarity with the AAPI community

Fri, 04/09/2021 - 3:15pm

On Saturday, April 3, members of the community — students, staff, faculty, and affiliates — with COVIDPass eligibility were invited to reflect, mourn, and show their solidarity with the MIT Asian American and Pacific Islander (AAPI) community. A total of 3,795 battery-operated candles were lit up on Kresge Oval to recognize the 3,795 reported — and countless unreported — anti-AAPI hate incidents over the last year alone. 

Following recent murders in Georgia and the growing wave of anti-Asian hate incidents across the United States, the installation was intended to contextualize the magnitude of the impact that anti-Asian violence has on the AAPI community. Each candle represents victims who have experienced racism or discrimination during the pandemic and the growing wave of hurt, fear, and anxiety the AAPI community has endured. The number of lit candles reemphasize the work there is left to do to combat racist acts of violence and xenophobia against Asian Americans.

“To see the number of lights on Kresge and realize that each one represents an Asian American enduring a hate incident this past year is incredibly startling,” says Yu Jing Chen, vice president of the Undergraduate Association (UA) and junior in the School of Architecture and Planning. “I hope that this installation speaks to people and helps them realize that even one candle out there is too many.”

Led by a group of AAPI student leaders and volunteers, a Covid-19-safe candlelight vigil took place on Friday evening on Killian Court as a symbolic and artistic expression opposing the surge of anti-Asian violence across the United States.

“As I’ve learned more about the history of the AAPI community in the United States, the purpose of a hate crime is to instill fear, keep people quiet, and make them feel alone and insignificant,” says Lily Cheng Zedler, one of the event organizers and graduate student in Sloan School of Management. “I hope members of the AAPI community who came to the candlelight installation took away the message that, ‘You are seen. You matter. You belong here.’”

Racism is nothing new to the AAPI community; it existed long before the coronavirus pandemic thrust it into the national spotlight. The installation is just the starting point for community members to stand in solidarity with the AAPI community. MIT community members are encouraged to continue amplifying and supporting AAPI organizations and community groups, to check in on friends and loved ones, and to continue to condemn all acts of hate and violence towards the Asian community.

At MIT, Institute Discrimination and Harassment Response (idhr@mit.edu) can help anyone in the community, whether you seek support or would like to report an incident.

National organizations and resources include the Stop AAPI Hate reporting site, Stand Against Hatred reporting site, Asian Americans Advancing Justice, and the Asian American Organizing Project.

“Timber Wars” from Oregon Public Broadcasting wins McElheny Award for local science reporting

Thu, 04/08/2021 - 5:35pm

The Knight Science Journalism Program at MIT has named Oregon Public Broadcasting’s “Timber Wars” podcast as 2021 winner of the prestigious Victor K. McElheny Award for local and regional science journalism. The seven-part series tells the story of how a group of activists and scientists turned a fight over logging and animal protection into one of the biggest environmental conflicts of the 20th century — a conflict that still resonates in culture wars today. The podcast is the first work of audio journalism to win the McElheny Award in the competition’s three-year history.

Judges praised “Timber Wars” for its rigorous reporting, artful storytelling, and deft handling of intricate science. “It ticks all the boxes: superb craftsmanship and storytelling; delightful science that is explained without pedantry; and real impact,” said the jury. “They really dug into the history and were able to connect it to the current day.” The podcast also resonated with policymakers. Oregon State Representative Dacia Grayber called it “the best history and take on this I’ve ever heard.”

“Timber Wars” was conceived and executive produced by Ed Jahn, of Oregon Public Broadcasting’s Science and Environment team. Aaron Scott, a producer and reporter for “Oregon Field Guide,” was the podcast’s reporter, writer, host, and lead producer. David Steves, Peter Frick-Wright, Robbie Carver, and Laura Gibson contributed to editing, production, sound design, and music composition.

The winning entry topped a large and highly competitive field of submissions from media outlets across the country. Also making the short list of finalists were: The Boston Globe’s “The Virus's Tale,” a day-by-day account of the handling of the city’s first Covid-19 cases; an investigation by The Detroit Free Press and Type Investigations into Detroit housing demolitions and their potential role in child lead poisoning; a feature by Boston-based WBUR on the quest to return loons to their native Massachusetts habitats; and a series from The Arizona Republic that chronicles how Indigenous Hopi are grappling with climate change and vanishing water sources.

"It was really a stellar year for local science reporting,” says Knight Science Journalism Program director Deborah Blum. “It was heartening to see so many insightful and beautifully told stories across such a range of environmental issues. These works are a reminder of just how integral science is to our everyday lives, and how crucial it is that local journalists receive support to tell these stories."

Named after the Knight Science Journalism Program’s founding director, the Victor K. McElheny Award was established to honor outstanding coverage of science, public-health, technology, and environmental issues at the local and regional level. Members of the winning “Timber Wars” team will receive the award’s $5,000 prize. Due to the pandemic, the Knight Science Journalism Program will not hold an in-person award ceremony this year.

The Knight Science Journalism Program extends a special thanks to the award’s jury: Rachel Ehrenberg, Knowable Magazine; Sujata Gupta, Science News; Eric Hand, Science; Emily Laber-Warren, Craig Newmark Graduate School of Journalism at CUNY; Dave Spratt, Institute for Journalism & Natural Resources, and screeners. The McElheny Award is made possible by generous support from Victor K. McElheny, Ruth McElheny, and the Rita Allen Foundation.

The 2021 McElheny Award honorees:

Winner:

  • "Timber Wars" (Episodes 1 and 2), Oregon Public Broadcasting. (Ed Jahn, Aaron Scott, David Steves, Peter Frick-Wright, Robbie Carver, and Laura Gibson)

Finalists:

The Knight Science Journalism Program at MIT, founded more than 30 years ago, seeks to nurture and enhance the ability of journalists from around the world to accurately document and illuminate the often complex intersection of science, technology, and human culture. It does so through an acclaimed fellowship program — which hosts 10 or more journalists every academic year — and also through
science-focused seminars, skills-focused master classes, workshops, and publications. Since it began, the program has hosted more than 300 fellows, who continue to cover science across a range of platforms in the United States, including The New York Times, The Wall Street Journal, Forbes, Time, Scientific American, Science, the Associated Press, and broadcast outlets ranging from ABC News to CNN, as well as in numerous other countries.

SMART researchers develop 15-minute immune-profiling assay

Thu, 04/08/2021 - 5:10pm

Researchers from Critical Analytics for Manufacturing Personalized-Medicine (CAMP), an interdisciplinary research group at the Singapore-MIT Alliance for Research and Technology (SMART), MIT’s research enterprise in Singapore, have developed a new label-free immune profiling assay that profiles the rapidly changing host immune response in case of infection, in a departure from existing methods that focus on detecting the pathogens themselves, which can often be at low levels within a host. This novel technology presents a host of advantages over current methods, being much faster, more sensitive, and more accurate.

The new assay is described in a paper titled, “Label-free biophysical markers from whole blood microfluidic immune profiling reveals severe immune response signatures”, published recently in Small, a weekly peer-reviewed scientific journal covering nanotechnology, and included a pilot study of 85 donors recruited from the National University Hospital (NUH) emergency department. The paper was led by Kerwin Kwek Zeming, senior postdoc at SMART CAMP, and co-authored by Professor Jongyoon Han, principal investigator at SMART CAMP and professor of biological engineering and electrical engineering at MIT, and Win Sen Kuan, research director, Emergency Medicine Department, NUH.

In many cases, the main culprit behind disease manifestation, severity of infection, and patient mortality is an overly aggressive host immune response. For instance, the Spanish flu pandemic of 1918 resulted in a disproportionately high number of deaths among otherwise-healthy young adults. This has been attributed to the now well-studied phenomenon of cytokine storms, which precipitate the rapid release of immune cells and inflammatory molecules and are brought on by a hyper-aggressive host immune response. In a more recent example, cases of severe Covid-19 infection often result in death via sepsis and a dysregulated immune response, while current risk stratification methods based on age and comorbidity remain a significant challenge and can be inaccurate. Moreover, current Covid-19 testing does not prognose the severity of the immune response, and can thus lead to inefficient deployment of resources in health-care settings.

In cases of acute infection, the status of a patient’s immune response can often be volatile and may change within minutes. Hence, there exists a pressing need for assays that are able to rapidly and accurately inform on the state of the immune system. This is particularly vital in early triage among patients with acute infection, and for predicting subsequent deterioration of disease. In turn, this will better empower medical personnel to make more accurate initial assessments and deliver the appropriate medical response. This can ensure timely intervention in the emergency department and prevent admission to the intensive care unit (ICU).

The new assay developed by SMART researchers focuses on profiling the rapidly changing host inflammatory response, which, in a hyper-aggressive state, can lead to sepsis and death. A 15-minute label-free immune profiling assay from 20 microliters (µL) of unprocessed blood using unconventional L and inverse-L shaped pillars of DLD microfluidic technology was developed, functioning as a sensitive and quantitative assay of immune cell biophysical signatures in relation to real-time activation levels of white blood cells (WBCs). As WBCs are activated by various internal or external triggers, the assay can sensitively measure both the extent and direction of these changes, which in turn reflect a patient’s current immune response state. As such, the new assay developed by SMART researchers is able to accurately and quickly assess patients’ immune response states by profiling immune cell size, deformability, distribution, and cell counts.

Significantly, the new assay provides considerable advantages over existing methods of profiling the immune system and its activity. These include measuring leukocyte gene expression, cell-surface biochemical markers, and blood serum cytokine profile. Notably, these current methods require sample dilution or pre-processing steps, as well as labor-intensive, expensive equipment and antibody labeling procedures. As a result, these methods generally require a few hours, at minimum, to return results. This is a key pain point and drawback in triage and the emergency department, where clinicians need to make accurate clinical assessments as early as possible. The labor- and time-intensive nature of these current methods significantly limits their clinical utility for rapid triage and prevents their wider implementation within the emergency room (ER) or ICU.

In contrast, as this new SMART assay takes only 15 minutes, uses only 20 µL of whole blood, and only requires video capture frame rates of up to 150 frames per second, there is considerable potential for the technology to be developed into a portable unit that can perform point-of-care blood-sparing assays that could significantly improve the diagnosis and differentiation of patients in the ER and other primary or critical-care settings. This application will enable clinicians to be able to quickly identify at-risk patients and take immediate action to mitigate or prevent organ dysfunction and other adverse effects of a hyper-aggressive immune response.

Lead author Kerwin Kwek says, “Our new DLD assay will help address an unmet need in the ER and ICU by significantly reducing waiting time for accurate patient assay results. This could lead to more effective triage decision-making and more appropriate and timely treatment, which are critical to saving lives. More generally, this groundbreaking technology provides new insights into both the engineering of precision microfluidics and clinical research.”

Jongyoon Han adds, “In the wake of lessons learnt in emergency rooms in hospitals across the world, especially during the Covid-19 pandemic, where medical professionals have been faced with making difficult and at times life-or-death decisions in triage, this new technology represents a hugely exciting and significant breakthrough. By reducing the time taken for assay results from hours to a matter of minutes, SMART CAMP’s new assay could help save lives as we continue to combat the scourge of pathogens and infectious diseases. The assay will also have wider applications, giving clinicians a new and more effective tool in the ER and ICU.”

The research is carried out by SMART and supported by the National Research Foundation (NRF) Singapore under its Campus for Research Excellence And Technological Enterprise (CREATE) program.

CAMP is a SMART interdisciplinary research group launched in June 2019. It focuses on better ways to produce living cells as medicine, or cellular therapies, to provide more patients access to promising and approved therapies. The investigators at CAMP address two key bottlenecks facing the production of a range of potential cell therapies: critical quality attributes (CQA) and process analytic technologies (PAT). Leveraging deep collaborations within Singapore and MIT in the United States, CAMP invents and demonstrates CQA/PAT capabilities from stem to immune cells. Its work addresses ailments ranging from cancer to tissue degeneration, targeting adherent and suspended cells, with and without genetic engineering.

CAMP is the R&D core of a comprehensive national effort on cell therapy manufacturing in Singapore.

SMART is MIT’s research enterprise in Singapore, established in partnership with the NRF in 2007. SMART is the first entity in CREATE developed by NRF. SMART serves as an intellectual and innovation hub for research interactions between MIT and Singapore, undertaking cutting-edge research projects in areas of interest to both Singapore and MIT. SMART currently comprises an Innovation Center and five interdisciplinary research groups: Antimicrobial Resistance, CAMP, Disruptive and Sustainable Technologies for Agricultural Precision, Future Urban Mobility, and Low Energy Electronic Systems.

SMART research is funded by the NRF under the CREATE program.

A better nasal swab for Covid-19 testing

Thu, 04/08/2021 - 12:00am

Over nearly seven years researching 3D printing systems in MIT’s Media Lab, Jifei Ou SM ’14, PhD ’19 began to suspect the work could lead to better products. He never could have imagined it would help address supply shortages caused by a global pandemic.

Since March of last year, Ou’s company, OPT Industries, has been working with hospitals to deliver a new type of nasal swab for Covid-19 testing. The swabs make use of thin, hairlike structures Ou developed while at MIT. Tiny woven lattices within OPT’s swabs allow them to absorb and release more fluid than conventional swabs.

The MIT spinout uses a continuous manufacturing approach that allows it to scale up printer production with demand. To date, it has supplied over 800,000 swabs to a number of health care and at-home testing organizations, helping to meet a shortage that had threatened hospitals’ testing capacity.

In the 12 months since Ou realized OPT could play a role in the pandemic response, the company’s small team has multiplied its manufacturing and distribution capabilities, partnered with large health care organizations like Kaiser Permanente, and begun developing other products that could benefit from the company’s design process.

“It’s very meaningful to be part of this effort,” Ou says. “It also feels particularly good because we’ve been developing materials with hairlike structures for a long time, so it’s like, ‘Aha, our expertise finally put to use!’”

An innovation leaves the lab

Ou’s time as a research assistant in the Media Lab’s Tangible Media Group culminated in a PhD for which he created new ways to design and 3D print intricate microstructures. The work required his team to build its own 3D printer, create design software, and develop special polymers to meet high durability and resolution requirements.

Ou received support from MIT Sandbox and the E14 Fund, a Media Lab-focused investment firm. Ou also credits MIT’s Industrial Liaison Program for helping him secure industry connections. Since leaving MIT, Ou’s team has improved the throughput of the machines, enabling continuous printing that led the company to focus on creating flexible, textile-like materials.

In March last year, as hospitals around the country began running out of the nasal swabs needed to test for Covid-19, Ramy Arnaout ’97, a director at Beth Israel's clinical microbiology laboratories and an associate professor at Harvard Medical School, sent an email to his network at MIT and beyond looking for help.

The following day, Ou walked into Arnaout’s office at Beth Israel with a prototype nasal swab his team had put together overnight. The visit was notable not only for the quick turnaround, but also for the precision with which the prototype was made.

OPT’s products are designed using algorithms that attempt to optimize each fiber placement. The company’s swabs feature porous microstructures within their heads that are tuned to collect and retain fluid, then quickly release that fluid when it enters a test vial.

“When it came to the swabs we thought, ‘Hey, that’s a great fit!’” Ou recalls. “Swabs need to be soft, flexible, the structures on the tip need to be very intricate. That’s what we do.”

Ou worked with members of MIT’s Center for Bits and Atoms and an external microbiology lab to compare OPT’s swabs with traditional, Q-tip-like cotton swabs. The tests showed that OPT’s swabs released 20 times the amount of bacteria for testing. That’s important because more specimens increases the sensitivity of tests, particularly rapid tests, according to Ou.

Moving forward

OPT’s additive manufacturing system can produce the company’s hairlike microstructures in a highly automated way that allows OPT to compete on price with traditional swab makers. The company currently is able to produce 80,000 swabs a day in its facility, and Ou says OPT is building newer versions of its machines that can produce products even more quickly.

OPT has secured partnerships with large health care organizations such as the distributor Henry Schein to get its swabs into hospitals, health clinics, and at-home testing kits.

The startup is also developing other medical sampling devices that use its high bacterial collection rate to test for other diseases. In May, OPT will move into a new office in Medford, Massachusetts, that will bring together its lab and production teams. Ou says the goal is to speed up the cycle from product ideation to design, prototype, optimization, and production.

“We’re trying to be like [the multinational products company] 3M in additive manufacturing,” Ou says. “Everyone knows 3M because they have a lot of different products that are essential to daily life. That’s the model we’re going after. We have other medical and cosmetic products under development — the swab is just the beginning.”

School of Science announces 2021 Infinite Mile awards

Tue, 04/06/2021 - 4:55pm

The MIT School of Science has recognized 13 staff members with the 2021 Infinite Mile Award.

Staff are nominated for Infinite Mile Awards, presented annually since their creation in 2001, by their peers for going above and beyond in their roles and making MIT a better place. Their support for the School of Science, and the Institute community as a whole, has been invaluable, especially as we pass the one-year mark of work-from-home and social distancing due to the Covid-19 pandemic.

The following are the 2021 School of Science Infinite Mile winners.

  • Rebecca Chamberlain, administrative officer in the Department of Biology, was nominated by Professor Stephen Bell because Chamberlain “makes things easier for everyone in the department and this has never been more true than in this trying year. Even as she has taken on so much more, she has continued to maintain a friendly, patient, and unflappable attitude that makes her all the more remarkable.”
  • Janice Chang, academic administrator in the Department of Biology, was nominated by MIT Human Resources administrator Helene Kelsey because Chang is “truly exceptional, strives for perfection, and her skills and work ethic are recognized throughout the department. Janice has embraced the associated challenges with wisdom, a common-sense approach, dedication, goodwill, and a willingness to devote endless additional hours to the tasks at hand.”
  • Emma Dunn, undergraduate programs assistant in the Department of Physics, was nominated by Academic Administrator Catherine Modica because, when campus closed, “it was Emma who came up with all the ideas we used to try to reach out to our students, […] tracking their arrivals at home to make sure they were safe, and creating and sending shipments of care packages to every undergraduate major to remind them that we were […] thinking about them and standing ready to help.”
  • Jennifer Fentress, communications officer in the Department of Earth, Atmospheric and Planetary Sciences, was nominated by professor of physics and department head Robert van der Hilst; associate professor of physics David McGee; and staff colleagues Julia Keller, Megan Jordan, Angela Ellis, Maggie Cedarstrom, Brandon Milardo, and Scott Wade because Fentress “has helped advance the work of the school and MIT more broadly. At every opportunity, she ensures that the voices of EAPS research scientists are well-represented.”
  • Laura Frawley, a lecturer in the Department of Brain and Cognitive Sciences, was nominated by Professor Michale Fee and staff colleagues Kate White and Kimberli DeMayo because Frawley “has dedicated so much time and effort into learning all the new tools and resources available to help faculty convert to remote learning. […] All in all, Laura has been a savior this year!”
  • Brittany Greenough, an events planning assistant in the Picower Institute for Learning and Memory, was nominated by Picower Institute director and professor of brain and cognitive sciences Li-Huei Tsai and Administrative Officer William Lawson because, “[i]n this new, virtual environment, Brittany has taken it upon herself to be the resident expert with transitioning events to online formats.”
  • Chhayfou Hong, a financial assistant in the Laboratory for Nuclear Science, was nominated by professors of physics Jesse Thaler, Mike Williams, Joseph Formaggio, and Philip Harris because “without Chai’s herculean efforts here, the IAIFI [NSF AI Institute for Artificial Intelligence and Fundamental Interactions] would not exist, and MIT would have missed out on housing one of the inaugural NSF AI institutes — and on $20 million in revenue over the next five years.”
  • Beverly La Marr, a test engineer in the MIT Kavli Institute for Astrophysics and Space Research, was nominated by Kavli Institute director and professor of physics Robert Simcoe and principal research scientists Marshall Bautz, Ronald Remillard, and Gregory Prigozhin because La Marr “has played an essential part in MKI’s success in space with flagships, mid-sized, and small missions; and in fact, at this moment, three missions bearing her intellectual ‘fingerprints’ are all producing exciting scientific data from space. Her contributions to her colleagues are no less significant.”
  • Brian Pretti, a facilities and operations administrator in the Department of Chemistry, was nominated by professor and department head Troy Van Voorhis and administrative officer Richard Wilk because Pretti “is someone who goes far above and beyond his usual call of duty. He is also a joy to work with, no matter the stress or difficulty of the situation. Brian exemplifies all of the qualities of someone who truly cares about the quality of his work and those individuals he supports. He has demonstrated an incredible commitment to the Department, and it is a better place because of him.”
  • Alison Salie, senior fiscal officer in the Department of Biology, was nominated by professor and department head Alan Grossman because Salie “is a top-notch employee, well-respected across the department and Institute, and valued for her knowledge and expertise, common-sense approach, willingness to provide support and guidance at every turn, persistence, and never-ending goal to keep work flowing smoothly with limited administrative burden on faculty.”
  • Amanda Trainor, a technical associate in the Department of Chemistry, was nominated by colleagues John Dolhun, Brian Pretti, Scott Ide, John Grimes, and graduate student Axel Vera because her “work on all aspects of various lab functions has been outstanding, from finishing her assigned responsibilities, to taking on unassigned work that needed to be done, [and] demonstrating a strong commitment to the well-being of the MIT community by going countless extra miles.”
  • Joshua Wolfe, a technical instructor in the Department of Physics, was nominated by postdoc Alex Shvonski and lecturer Michelle Tomasik because Wolfe “goes above and beyond his prescribed duties because he cares holistically about creating an effective learning environment in our classes.”
  • Macall Zimmerman, senior financial officer in the Department of Chemistry, was nominated by professor and department head Troy Van Voorhis and staff colleagues Richard Wilk and Tyler Brezler because Zimmerman “is someone who goes far above and beyond her usual call of duty. She is an excellent leader, manager, and mentor. She demonstrates an exceptional commitment to every aspect of her work and the staff whom she mentors. Our department is a better place with her in it.”

The 2021 Infinite Mile Award winners receive a monetary award. An in-person celebration will be held in their honor, as well as the 2021 Infinite Expansion Award winners, at a later date with their families, friends, and nominators.

The MIT Press launches MIT Open Publishing Services

Tue, 04/06/2021 - 4:40pm

The MIT Press has announced the launch of MIT Open Publishing Services, a scholar-focused, MIT-branded hosting and publishing services operation.

MIT Open Publishing Services (MITops), working with its partner the Knowledge Futures Group, provides a portfolio of services to mission-aligned partners, including peer review support and editorial development; professional copy editing and design; marketing and publicity; and hosting on the PubPub open source platform.  

The MIT Press believes that the full potential of institutionally owned and managed infrastructure will be realized by pairing publishing technology innovation with economic incentives that will make it possible for the academy to reclaim the marketplace for scholarly communications. “This model will accelerate the shift away from the academy’s growing dependence on large multinational information service providers,” says Amy Brand, director and publisher of the MIT Press. “Because we are mission-aligned with the institutional environments that we serve, we can meet the needs of researchers, authors, and readers ‘where they are.’”  

One of the first projects published with support from the MITops program is a new case studies series that examines the social, ethical, and policy challenges of present-day efforts in computing. Published as part of the Social and Ethical Responsibilities of Computing (SERC) cross-cutting program within the MIT Stephen A. Schwarzman College of Computing and edited by associate deans David Kaiser and Julie Shah, the series aims to facilitate the development of responsible “habits of mind and action” for those who create and deploy computing technologies. 

The inaugural set of cases in the series places readers in various settings that challenge them to consider the social and ethical implications of computing technologies, such as how social media services and surveillance tools are built; the racial disparities that can arise from deploying facial recognition technology in unregulated, real-world settings; the biases of risk prediction algorithms in the criminal justice system; and the politicization of data collection. New sets of case studies will be published twice a year on the PubPub platform.

“It has been such a pleasure working with the MITops team to launch our new peer-reviewed, open-access MIT Case Studies series in Social and Ethical Responsibilities of Computing,” notes David Kaiser, Germeshausen Professor of the History of Science and professor of physics at MIT. “The PubPub platform is easy to use and embodies many of the values we aim to highlight in SERC. More than that, the MITops team is passionate about enabling equitable, accessible scholarly publishing — of finding new, sustainable ways to share hard-won knowledge broadly. I am thrilled that Issue 1 is now available, and I look forward to working with the team for Issue 2 and beyond.” 

How MIT OpenCourseWare became an educational resource to millions around the world

Tue, 04/06/2021 - 12:00pm

“It is typical of our faculty to come up with something as bold and innovative as this," said then-MIT president Charles Vest at a special gathering of community members and press in April 2001. “OpenCourseWare looks counterintuitive in a market-driven world. It goes against the grain of current material values. But it really is consistent with what I believe is the best about MIT ... It expresses our belief in the way education can be advanced — by constantly widening access to information and by inspiring others to participate."

In the 20 years since it began, MIT OpenCourseWare has become a pillar of the open education community, an exemplar of the MIT ethos, and an invaluable resource to millions of learners around the world. People of all ages and all walks of life have used the lectures, videos, problem sets, and other content to pursue their curiosity and passions, improve their careers, and get a leg up in their studies. Now, the team looks to the future with a clear sense of purpose, informed by the learning needs underscored by the Covid-19 pandemic. 

OpenCourseWare launched during the early days of Web 2.0 and a growing — but highly commercialized — interest in e-learning. Charles Vest had commissioned the Lifelong Learning Committee, asking its members to propose an educational technology project that would extend MIT's reach beyond classrooms. That committee’s recommendation was to launch OpenCourseWare, a website offering all of MIT’s course materials, available for free to anyone. Within one year, OCW had published a pilot website with 50 courses and attracted worldwide acclaim. Today, OCW offers materials from over 2,570 courses spanning the MIT graduate and undergraduate curriculum, from 1,735 MIT faculty and lecturers​ from 33 academic units across all five schools, including syllabi, lecture notes, problem sets, assignments, and audiovisual content including recorded lectures. To date, OCW has been a resource for over 210 million unique users, with over 70 percent of users in 2020 coming from outside the United States.

Professor Dick KP Yue, who chaired the Lifelong Learning Committee, described the impetus for the project in the proposal: "In the digital age, institutions like MIT have a responsibility — and an opportunity — to impact learners far beyond their campuses. OCW embodies MIT's commitment to constantly widening access to knowledge."

The value of that commitment is borne out by learners who have shared their stories over the years — from Tooba Siddiqui in Pakistan, who had access to education through OCW when other doors were closed to her, to Anita Moreno in Nevada, who used OCW to keep up with her studies following a brain aneurysm. “I cannot emphasize enough how this site has boosted my confidence, that I am still able to comprehend and succeed in an engineering program,” says Moreno. 

Today, Professor Krishna Rajagopal, dean for digital learning, says, “It was the best thing MIT could have done at that moment for MIT and for the world."

A revolution in the making

From its modest and experimental beginning, OCW sparked a new era in the growing open-education movement. Beyond the courses themselves, OCW has had a broad impact on the way online learning resources have evolved in higher education, setting the template for other colleges and universities undertaking similar efforts and helping launch the open education resources (OER) revolution. 

”Free access to knowledge is a powerful foundation for progress,” says OCW Director Curt Newton, “but it’s not the whole picture. OER that lifts up everyone’s right to contribute to shared knowledge, and builds everyone’s capacity to extend that knowledge, is creating new paths for us to work together on the world’s most important, complex, and rapidly evolving challenges.”

It helps that OCW and Creative Commons share family bonds. Launched the same year, electrical engineering and computer science Professor Hal Abelson was a member of the founding teams for both, and helped arrange for OCW to be the first institutional project to use Creative Commons licenses, In turn, OCW’s early adoption of Creative Commons licenses helped demonstrate their usefulness and lent credence to the burgeoning open movement. 

In 2005, OCW helped launch the OpenCourseWare Consortium (now Open Education Global), whose network of over 300 higher education institutions and related organizations have freely shared many thousands of courses, open textbooks, and other resources, and collaborated to foster widespread adoption of OERs.

At MIT, OCW has paved the way for other innovative new learning platforms, such as MITx and MicroMasters, Open Learning Library, and professional and executive learning programs. 

Integrating teachers into the experience of OCW was a key priority very early on. (Indeed, the faculty committee originally envisioned OCW as being used by educators almost exclusively — its widespread popularity among students and lifelong learners was a welcome surprise.) Educators around the world have shared their experiences of using OCW to master new content or inspire and engage students. In 2013, the team launched the OCW Educator program; now, hundreds of OCW courses include Instructor Insights sections where faculty share how they have taught their courses through text, video, and most recently, through the Chalk Radio podcast. 

“A core tenet of MIT’s mission is to create and share knowledge, empowering our own community and myriad others to bring this knowledge to bear on the world’s great challenges. From its inception, OpenCourseWare has offered a new and substantial way of realizing that mission in the 21st century,” says Rajagopal. “For individual learners, OCW is a means to expand understanding and satisfy curiosity, to support personal and professional goals, or change in their communities; for educators, it's a resource library to help augment and strengthen their curricula, enriching the experience of so many students; for educational organizations, it’s an invitation to nurture a shared commitment to open knowledge. OCW provides invaluable resources for millions and paves the way for others to contribute in their own ways to sharing and using knowledge for the betterment of humankind.”

Living legacy

The courses on OCW have also come to reflect the way that MIT, and its relationship with the world, has grown and changed over the last two decades. Perhaps it’s no surprise that 6.0001 (Introduction to Computer Science and Programming in Python) and 18.06 (Linear Algebra) are consistently among the most-viewed courses. But the ebb and flow of traffic on OpenCourseWare reflects topics in the zeitgeist, too. When Esther Duflo and Abhijit Banerjee won the Nobel Prize for Economics in 2019, Duflo’s OCW course “The Challenge of World Poverty” spiked in popularity as people all over the world sought to understand her worldview and learn from her. A similar spike occurred with Professor Gary Gensler’s graduate-level course “Blockchain and Money” when he was nominated to serve in the Biden administration earlier this year. 

As MIT faculty have endeavored to offer students a nuanced understanding of our complex world, so too have the materials on OCW grown more expansive. Learners around the world can now delve into “Ethics for Engineers: Artificial Intelligence,” “Queer Cinema and Visual Culture,” and “Black Matters: Introduction to Black History” alongside engineering, math, and science standbys. 

“As instructors, we’re excited about what we get to do in the classroom with our students, and also it’s wonderful to have the opportunity to expand beyond the classroom, and to actually make the material that we develop for students available more broadly,” says Amah Edoh, assistant professor of anthropology and African studies and a member of the OCW Faculty Advisory Committee, whose courses “Africa and the Politics of Knowledge” and “Global Africa: Creative Cultures” are on OCW.

She also appreciates the role OCW plays in sharing MIT expertise with the world beyond engineering and science. “My particular investment in this has been around making African studies more visible at MIT ... It really changes the image, the idea that others have of MIT. I think it’s particularly important to show that we also have courses in African studies specifically. Oftentimes Africa, African countries, African people are seen not as agents, but rather as a space where you go to solve problems. So to show that we can engage knowledge production in and on Africa critically, to me is very important.” 

In capturing course materials and videos, OCW does more than open windows into MIT for global learners; it also provides a unique, living archive of teaching at MIT. Alumni can revisit favorite classes or share them with colleagues, peers, or kids looking into college. High-schoolers can get a sense of what courses in different fields will entail. Faculty whose course materials are preserved on OCW have an artifact of their teaching legacy, for everyone, forever. Consider “How to Speak,” a OCW video of the late Professor Patrick Winston’s beloved Independent Activities Period course, which he taught for 40 years before passing away in 2019; posted in December 2019, it has now been viewed 3.3 million times.

Looking forward

OpenCourseWare enters its third decade on the heels of unprecedented global disruption. During the first months of the Covid-19 pandemic, when schools and businesses closed and billions of people around the world sheltered in place at home, traffic to OCW spiked to 2.2 million visits a month, a 75 percent increase from 2019. Since then, site visits have settled into a 15 percent uptick in use. More importantly, the massive shift to remote and hybrid learning over the past year has brought into sharp relief both the opportunities of online education and the disparities of access, technology, and equity for learners everywhere. In charting a course for the future, the OCW team has the opportunity to draw on 20 years of experience in addressing the issues brought to the fore in 2020. 

“The first years of OCW have been primarily about the power of access,” says Newton. “A core principle of where we’re heading in our upcoming program is the progression from giving access to knowledge to really driving towards educational equity.”

Later this year, OpenCourseWare will launch its NextGen platform and program. Its three principal aims are offering a vibrant reflection of MIT education as it evolves, delivering a more user-focused design and experience, and broadening access and usability to a larger global population. The NextGen platform will support a more dynamic experience of OCW’s robust multimedia content, allowing users to seamlessly search, browse, download, remix, and redistribute all materials more easily. Individuals can get a sneak peek of the new OCW and sign up to be a beta tester.

Another major pillar of the NextGen platform is mobile optimization, a user-friendly interface to provide readable, searchable content on any device. With 92.6 percent of internet users around the world using mobile devices at least some of the time, and with smartphone use growing at a rate of 7 percent per year, this change represents not only a catch-up to current need but also a purposeful approach to finding and engaging with future learners. 

“As we look at the next year, five years, 20 years of OpenCourseWare, our goal is to keep pace with the evolving artifacts of MIT teaching and learning, offering the best possible experience to our growing community of learners,” says Newton. “We are also committed to continually reinvesting in the OER community — working collaboratively to share resources and engage with the people and organizations at the vanguard of access and equity in education.”

MIT Open Learning will host an online celebration of OpenCourseWare’s 20th anniversary on Wednesday, April 7, from noon to 1 p.m. EDT featuring OCW leadership, MIT faculty, and learners sharing stories and ideas about the past, present, and future of open education, at MIT and beyond.

Seeking the cellular mechanisms of disease, with help from machine learning

Tue, 04/06/2021 - 12:00am

Caroline Uhler’s research blends machine learning and statistics with biology to better understand gene regulation, health, and disease. Despite this lofty mission, Uhler remains dedicated to her original career passion: teaching. “The students at MIT are amazing,” says Uhler. “That’s what makes it so fun to work here.”

Uhler recently received tenure in the Department of Electrical Engineering and Computer Science. She is also an associate member of the Broad Institute of MIT and Harvard, and a researcher at the MIT Institute for Data, Systems, and Society, and the Laboratory for Information and Decision Systems.

Growing up along Lake Zurich in Switzerland, Uhler knew early on she wanted to teach. After high school, she spent a year gaining classroom experience — and didn’t discriminate by subject. “I taught Latin, German, math, and biology,” she says. But by year’s end, she found herself enjoying teaching math and biology best. So she enrolled at ETH Zurich to study those subjects and earn a master’s of education that would allow her to become a full-time high school teacher.

But Uhler’s plans changed, thanks to a class she took from a visiting professor from the University of California at Berkeley named Bernd Sturmfels. “He taught a course called algebraic statistics for computational biology,” says Uhler. The course title alone may sound like a mouthful, but to Uhler, the class was an elegant link between her passions for math and biology. “It basically connected everything that I liked in one course,” she recalls.

Algebraic statistics provided Uhler with a unique set of tools for representing the mathematics of complex biological systems. She was so intrigued she decided to postpone her dreams of teaching and pursue a PhD in statistics.

Uhler enrolled at UC Berkeley, completing her dissertation with Sturmfels as her advisor. “I loved it,” Uhler says of her time at Berkeley, where she dove deeper into the nexus of math and biology using algebra and statistics. “Berkeley was very open in the sense that you can take all kinds of courses,” she says, “and really pursue your diverse research interests early on. It was a great experience.”

Much of her work was theoretical, attempting to answer questions about network models in statistics. But toward the end of her PhD, her questions took on a more applied approach. “I got really interested in causality and gene regulation — how can we learn something about what is going on in the cell?” Uhler says gene regulation provides ample opportunities to apply causal analysis, because changes in one gene can have cascading effects on the expression of genes downstream.

She carried these causality questions forward to MIT, where she accepted a role as assistant professor in 2015. Her first impressions of the Institute? “The place was very collaborative and a hub for machine learning and genomics,” says Uhler. “I was excited to find a place with so many people working in my field. Here, everyone wants to discuss research. It’s just really, really fun.”

The Broad Institute, which uses genomics to better understand the genetic basis of disease and seek solutions, has also been a good fit for Uhler’s academic interests and her cooperative approach to research. The Broad announced last month that Uhler will co-direct its new Eric and Wendy Schmidt Center, which will promote interdisciplinary research between the data and life sciences.

Uhler now works to synthesize two distinct types of genomic information: sequencing and the 3D packing of DNA. The nucleus of each cell in a person’s body contains an identical sequence of DNA, but the physical arrangement of that DNA — how it kinks and winds — varies among cell types. “In understanding gene regulation, it’s becoming clear that the packing of the DNA matters very much,” says Uhler. “If some genes in the DNA are not used, you can just close them off and pack them very densely. But if you have other genes that you need often in a particular cell, you’ll have them open and maybe even close together so they can be co-regulated.”

Learning the interplay of the genetic code and the 3D packing of the DNA could help reveal how a particular disease impacts the body on a cellular level, and it could help point to targeted treatments. To achieve this synthesis, Uhler develops machine-learning methods, in particular based on autoencoders, which can be used to integrate sequencing data and packing data to generate a representation of a cell. “You can represent the data in a space where the two modalities are integrated,” says Uhler. “It’s a question I’m very excited about because of its importance in biology as well as my background in mathematics. It’s an interesting packing problem.”

Recently, Uhler has focused on one disease in particular. Her research group co-authored a paper that uses autoencoders and causal networks to identify drugs that could be repurposed to fight Covid-19. The approach could help pinpoint drug candidates to be tested in clinical trials, and it is adaptable to other diseases where detailed gene expression data are available.

Research accomplishments aside, Uhler hasn’t relinquished her earliest career aspirations to be a teacher and mentor. In fact, it’s become one of her most cherished roles at MIT. “The students are incredible,” says Uhler, highlighting their intellectual curiosity. “You can just go up to the whiteboard and start a conversation about research. Everyone is so driven to learn and cares so deeply.”

A safer way to deploy bacteria as environmental sensors

Mon, 04/05/2021 - 4:00pm

In recent years, scientists have developed many strains of engineered bacteria that can be used as sensors to detect environmental contaminants such as heavy metals. If deployed in the natural environment, these sensors could help scientists track how pollutant levels change over time, over a wide geographic area.

MIT engineers have now devised a way to make this kind of deployment safer, by encasing bacterial sensors in a tough hydrogel shell that prevents them from escaping into the environment and potentially spreading modified genes to other organisms.

“Right now there are a lot of whole-cell biosensors being developed, but applying them in the real world is a challenge because we don’t want any genetically modified organisms to be able to exchange genetic material with wild-type microbes,” says MIT graduate student Tzu-Chieh Tang, one of the lead authors of the new study.

Tang and his colleagues showed that they could embed E. coli into hydrogel spheres, allowing them to detect the contaminants they’re looking for while remaining isolated from other organisms. The shells also help to protect the sensors from environmental damage.

Timothy Lu, an MIT associate professor of electrical engineering and computer science and of biological engineering, and Xuanhe Zhao, an MIT professor of mechanical engineering and of civil and environmental engineering, are the senior authors of the study, which appears today in Nature Chemical Biology. Along with Tang, Eleonore Tham PhD ’18 and MIT graduate student Xinyue Liu are also lead authors of the paper.

Physical containment

By engineering bacteria to express genetic circuits that they don’t normally have, researchers can enable them to detect a variety of different molecules. Often, the circuits are designed so that detection of the target triggers production of green fluorescent protein or bioluminescence. In other circuits, a memory of the event is recorded in the cells’ DNA.

The genetic circuits that go into these bacteria often include genes for antibiotic resistance, which enables the researchers to ensure that their genetic circuit has been correctly inserted into the bacterial cells. However, those genes could be harmful if released into the environment. Many bacteria and other microbes are able to exchange genes, even between different species, using a process called horizontal gene transfer.

To try to prevent this kind of gene exchange, researchers have used a strategy called “chemical containment,” which involves designing the bacterial sensors so they require an artificial molecule that they can’t get in the wild. However, in a very large population of bacteria, there is a chance that a small number will acquire mutations that allow them to survive without that molecule.

Another option is physical containment, achieved by encapsulating bacteria within a device that prevents them from escaping. However, the materials that have been tried so far, such as plastic and glass, don’t work well because they form diffusion barriers preventing bacteria from interacting with the molecules they are designed to detect.

In this study, the researchers decided to try encapsulating bacterial sensors in hydrogels. These are stretchy materials that can be formed from a variety of different building blocks. Many naturally occurring hydrogels, such as alginate, which is derived from algae, are too fragile to protect cells in an outdoor environment. However, Zhao’s lab has previously developed some very tough, stretchy hydrogels, which the researchers believed could be suitable for encapsulating bacteria.

To make the protective spheres, the researchers first embedded bacteria in alginate, along with some essential nutrients. These spheres were then coated with one of Zhao’s tough hydrogels, which is made from a combination of alginate and polyacrylamide. This external layer has pores that range from 5 to 50 nanometers in diameter, which allows molecules such as sugars or heavy metals to pass through. However, DNA and larger proteins cannot go through.

Detecting pollution

The spheres that the researchers constructed for this study are about 5 millimeters in diameter and can carry up to 1 billion bacterial cells. The researchers used the spheres to encapsulate E. coli bacteria that were designed to detect cadmium, a heavy metal.

To test the sensors, the researchers placed them into water samples collected from the Charles River. To determine whether the sensors could detect pollutants from inside their spheres, the researchers added cadmium to the samples and found that the bacteria could accurately detect it. The researchers also showed that the bacteria did not escape from the sphere or leak any genetic material.

The researchers demonstrated that their encapsulation technique also worked with a different strain of E. coli that was engineered to be dependent on an artificial molecule — an amino acid not found in nature.

“We are trying to come up with a solution to see if we can combine chemical and physical containment. That way, if either one of them failed, the other one can keep things in check,” Tang says.

In future studies, the researchers hope to test the sensors in a model environment that would simulate real-world conditions. In addition to detecting environmental contaminants, this type of sensor could potentially be used for medical applications such as detecting bleeding in the digestive tract, the researchers say.

Other authors of the paper include Kevin Yehl, a former MIT postdoc; Alexis Rovner, a former postdoc at Harvard Medical School; Hyunwoo Yuk, an MIT graduate student; Cesar de la Fuente-Nunez, a former MIT postdoc and an assistant professor of bioengineering at the University of Pennsylvania; and Farren Isaacs, an associate professor of molecular, cellular, and developmental biology at Yale School of Medicine.

The research was funded by the National Institutes of Health, the U.S. Office of Naval Research, the Defense Advanced Research Projects Agency, the National Science Foundation, the U.S. Army Research Office through MIT’s Institute for Soldier Nanotechnologies, and the Abdul Latif Jameel Water and Food Systems Laboratory (J-WAFS) Graduate Student Fellowship.

What has the pandemic revealed about the US health care system — and what needs to change?

Mon, 04/05/2021 - 9:45am

With vaccinations for Covid-19 now underway across the nation, MIT SHASS Communications asked seven MIT scholars engaged in health and health care research to share their views on what the pandemic has revealed about the U.S. health care system — and what needs to change. Representing the fields of medicine, anthropology, political science, health economics, science writing, and medical humanities, these researchers articulate a range of opportunities for U.S. health care to become more equitable, more effective and coherent, and more prepared for the next pandemic.

Dwaipayan Banerjee, associate professor of science, technology, and society

On the heels of Ebola, Covid-19 put to rest a persistent, false binary between diseases of the rich and diseases of the poor. For several decades, health care policymakers have labored under the impression of a great epidemiological transition. This theory holds that the developed world has reached a stage in its history that it no longer needs to worry about communicable diseases. These "diseases of the poor" are only supposed to exist in distant places with weak governments and struggling economies. Not here in the United States.

On the surface, Covid-19 made clear that diseases do not respect national boundaries. More subtly, it tested the hypothesis that the global north no longer need concern itself with communicable disease. And in so doing, it undermined our assumptions about global north health-care infrastructures as paradigmatically more evolved.

Over the last decades, the United States has been focused on developing increasingly sophisticated drugs. While this effort has ushered in several technological breakthroughs, a preoccupation with magic-bullet cures has distracted from public health fundamentals. The spread of the virus revealed shortages in basic equipment and hospitals beds, the disproportionate effects of disease on the marginalized, the challenge of prevention rather than cure, the limits of insurance-based models to provide equitable care, and our unacknowledged dependence on the labor of underpaid health care workers.

To put it plainly, the pandemic did not create a crisis in U.S. health care. For many in the United States, crisis was already a precondition of care, delivered in emergency rooms and negotiated through denied insurance claims. As we begin to imagine a "new normal," we must ask questions about the old. The pandemic made clear that the "normal" had been a privilege only for a few well-insured citizens. In its wake, can we imagine a health-care system that properly compensates labor and recognizes health care as a right, rather than a privilege only available to the marginalized when an endemic crisis is magnified by a pandemic emergency? 

Andrea Campbell, professor of political science

No doubt, the pandemic reveals the dire need to invest in public-health infrastructure to better monitor and address public-health threats in the future, and to expand insurance coverage and health care access. To my mind, however, the pandemic’s greatest significance is in revealing the racism woven into American social and economic policy.

Public policies helped create geographic and occupational segregation to begin with; inadequate racist and classist public policies do a poor job of mitigating their effects. Structural racism manifests at the individual level, with people of color suffering worse housing and exposure to toxins, less access to education and jobs, greater financial instability, poorer physical and mental health, and higher infant mortality and shorter lifespans than their white counterparts. Residential segregation means many white Americans do not see these harms.

Structural racism also materializes at the societal level, a colossal waste of human capital that undercuts the nation’s economic growth, as social and economic policy expert Heather McGhee shows in her illuminating book, "The Sum of Us." These society-wide costs are hidden as well; it is difficult to comprehend the counterfactual of what growth would look like if all Americans could prosper.

My hope is that the pandemic renders this structural inequality visible. There is little point in improving medical or public-health systems if we fail to address the structural drivers of poor health. We must seize the opportunity to improve housing, nutrition, and schools; to enforce regulations on workplace safety, redlining, and environmental hazards; and to implement paid sick leave and paid family leave, among other changes. It has been too easy for healthy, financially stable, often white Americans to think the vulnerable are residual. The pandemic has revealed that they are in fact central. It’s time to invest for a more equitable future.

Jonathan Gruber, Ford Professor of Economics

The Covid-19 pandemic is the single most important health event of the past 100 years, and as such has enormous implications for our health care system. Most significantly, it highlights the importance of universal, non-discriminatory health insurance coverage in the United States. The primary source of health insurance for Americans is their job, and with unemployment reaching its highest level since the Great Depression, tens of millions of workers lost, at least temporarily, their insurance coverage.

Moreover, even once the economy recovers, millions of Americans will have a new preexisting condition, Covid-19. That’s why it is critical to build on the initial successes of the Affordable Care Act to continue to move toward a safety net that provides insurance options for all without discrimination.

The pandemic has also illustrated the power of remote health care. The vast majority of patients in the United States have had their first experience with telehealth during the pandemic and found it surprisingly satisfactory. More use of telehealth can lead to increased efficiency of health care delivery as well as allowing our system to reach underserved areas more effectively.

The pandemic also showed us the value of government sponsorship of innovation in the health sciences. The speed with which the vaccines were developed is breathtaking. But it would not have been possible without decades of National Institute of Health investments such as the Human Genome Project, nor without the large incentives put in place by Operation Warp Speed. Even in peacetime, the government has a critical role to play in promoting health care innovation

The single most important change that we need to make to be prepared for the next pandemic is to recognize that proper preparation is, by definition, overpreparation. Unless we are prepared for the next pandemic that doesn’t happen, we won’t possibly be ready for the next pandemic that does.

This means working now, while the memory is fresh, to set up permanent, mandatorily funded institutions to do global disease surveillance, extensive testing of any at-risk populations when new diseases are detected, and a permanent government effort to finance underdeveloped vaccines and therapeutics.

Jeffrey Harris, professor emeritus of economics and a practicing physician

The pandemic has revealed the American health care system to be a non-system. In a genuine system, health care providers would coordinate their services. Yet when Elmhurst Hospital in Queens was overrun with patients, some 3,500 beds remained available in other New York hospitals. In a genuine system, everyone would have a stable source of care at a health maintenance organization (HMO). While our country has struggled to distribute the Covid-19 vaccine efficiently and equitably, Israel, which has just such an HMO-based system, has broken world records for vaccination.

Germany, which has all along had a robust public health care system, was accepting sick patients from Italy, Spain, and France. Meanwhile, U.S. hospitals were in financial shock and fee-for-service-based physician practices were devastated. We need to move toward a genuine health care system that can withstand shocks like the Covid-19 pandemic. There are already models out there to imitate.

We need to strengthen our worldwide pandemic and global health crisis alert systems. Despite concerns about China’s early attempts to suppress the bad news about Covid-19, the world was lucky that Chinese investigators posted the full genome of SARS-CoV-2 in January 2020 — the singular event that triggered the search for a vaccine. With the recurrent threat of yet another pandemic — after H1N1, SARS, MERS, Ebola, and now SARS-Cov-2 — along with the anticipated health consequences of global climate change, we can’t simply cross our fingers and hope to get lucky again.

Erica Caple James, associate professor of medical anthropology and urban studies

The coronavirus pandemic has revealed some of the limits of the American medical and health care system and demonstrated many of the social determinants of health. Neither the risks of infection nor the probability of suffering severe illness are equal across populations. Each depends on socioeconomic factors such as type of employment, mode of transportation, housing status, environmental vulnerability, and capacity to prevent spatial exposure, as well as “preexisting” health conditions like diabetes, obesity, and chronic respiratory illness.

Such conditions are often determined by race, ethnicity, gender, and “biology,” but also poverty, cultural and linguistic facility, health literacy, and legal status. In terms of mapping the prevalence of infection, it can be difficult to trace contacts among persons who are regular users of medical infrastructure. However, it can be extraordinarily difficult to do so among persons who lack or fear such visibility, especially when a lack of trust can color patient-clinician relationships.

One’s treatment within medical and health care systems may also reflect other health disparities — such as when clinicians discount patient symptom reports because of sociocultural, racial, or gender stereotypes, or when technologies are calibrated to the norm of one segment of the population and fail to account for the severity of disease in others.

The pandemic has also revealed the biopolitics and even the “necropolitics” of care — when policymakers who are aware that disease and death fall disproportionately in marginal populations make public-health decisions that deepen the risks of exposure of these more vulnerable groups. The question becomes, “Whose lives are deemed disposable?” Similarly, which populations — and which regions of the world — are prioritized for treatment and protective technologies like vaccines and to what degree are such decisions politicized or even racialized?

Although no single change will address all of these disparities in health status and access to treatment, municipal, state, and federal policies aimed at improving the American health infrastructure — and especially those that expand the availability and distribution of medical resources to underserved populations — could greatly improve health for all.

Seth Mnookin, professor of science writing

The Covid-19 pandemic adds yet another depressing data point to how the legacy and reality of racism and white supremacy in America is lethal to historically marginalized groups. A number of recent studies have shown that Black, Hispanic, Asian, and Native Americans have a significantly higher risk of infection, hospitalization, and death compared to white Americans.

The reasons are not hard to identify: Minority populations are less likely to have access to healthy food options, clean air and water, high-quality housing, and consistent health care. As a result, they’re more likely to have conditions that have been linked to worse outcomes in Covid patients, including diabetes, hypertension, and obesity.

Marginalized groups are also more likely to be socioeconomically disadvantaged — which means they’re more likely to work in service and manufacturing industries that put them in close contact with others, use public transportation, rely on overcrowded schools and day cares, and live in closer proximity to other households. Even now, more vaccines are going to wealthier people who have the time and technology required to navigate the time-consuming vaccine signup process and fewer to communities with the highest infection rates.

This illustrates why addressing inequalities in Americans’ health requires addressing inequalities that infect every part of society. Moving forward, our health care systems should take a much more active role in advocating for racial and socioeconomic justice — not only because it is the right thing to do, but because it is one of the most effective ways to improve health outcomes for the country as a whole.

On a global level, the pandemic has illustrated that preparedness and economic resources are no match for lies and misinformation. The United States, Brazil, and Mexico have, by almost any metric, handled the pandemic worse than virtually every other country in the world. The main commonality is that all three were led by presidents who actively downplayed the virus and fought against lifesaving public health measures. Without a global commitment to supporting accurate, scientifically based information, there is no amount of planning and preparation that can outflank the spread of lies.

Parag Pathak, Class of 1922 Professor of Economics
 
The pandemic has revealed the strengths and weaknesses of America’s health care systems in an extreme way. The development and approval of three vaccines in roughly one year after the start of the pandemic is a phenomenal achievement. At the same time, there are many innovations for which there have been clear fumbles, including the deployment of rapid tests and contact tracing.  

The other aspect the pandemic has made apparent is the extreme inequality in America’s health systems. Disadvantaged communities have borne the brunt of Covid-19 both in terms of health outcomes and also economically. I’m hopeful that the pandemic will spur renewed focus on protecting the most vulnerable members of society.

A pandemic is a textbook situation in economics of externalities, where an individual’s decision has external effects on others. In such situations, there can be major gains to coordination. In the United States, the initial response was poorly coordinated across states. I think the same criticism applies globally. We have not paid enough attention to population health on a global scale.

One lesson I take from the relative success of the response of East Asian countries is that centralized and coordinated health systems are more equipped to manage population health, especially during a pandemic. We’re already seeing the need for international cooperation with vaccine supply and monitoring of new variants. It will be imperative that we continue to invest in developing the global infrastructure to facilitate greater cooperation for the next pandemic.

Prepared by MIT SHASS Communications
Editor and designer: Emily Hiestand
Consulting editor: Kathryn O'Neill

Ancient atmospheric oxygen sleuthing with ocean chromium

Mon, 04/05/2021 - 9:15am

Found in jewelry, car parts, pigments, and industrial chemical reactions, the metal chromium and its compounds are often employed for their color, finish, and anti-corrosive and catalytic properties. Currently, geoscientists and paleoceanographers from MIT and the Woods Hole Oceanographic Institution (WHOI) are looking to add another use to that list: as a way to examine chemical shifts in ancient Earth’s oceans and atmosphere that are preserved in the seafloor’s paleorecord. More specifically, they want to reconstruct rising atmospheric oxygen levels, which began around 2.4 billion years ago, and their effect on the seas. Since biology and the environment are intimately intertwined, this information could help illuminate how the Earth’s life and climate evolved.

While researchers have widely applied chromium as a tool to understand the rock record around this global transition, they’re still working out what different chemical signals mean. This is especially true for evaluating ocean sediments, which could reveal where and when oxygen began penetrating and was being formed in the oceans. However, paleoscientists have largely lacked an understanding of how trace amounts of chromium mechanistically interact and cycle in modern, oxygenated seas, let alone the early oceans — a key component needed for any interpretation — until now.

Research recently published in the Proceedings of the National Academy of Sciences and led by MIT-Woods Hole Oceanographic Institution Joint Program graduate student Tianyi Huang investigated the trace metal’s promise as a paleoproxy for oxygen. For this, the team tracked how oxygen-sensitive chromium isotopes circulated and how they were chemically oxidized or reduced within an oxygen-deficient patch of water in the tropical Pacific Ocean, an analog for early, anaerobic seas. Their findings help validate chromium tracking as a reliable instrument in geology toolbox.

“People have seen the that chromium isotopes in the geological records kind of track the atmospheric oxygen levels. But, because you're using something that is buried in the sediments to interpret what is happening in the atmosphere, there's a missing link in between, and that is the ocean,” says Huang. Further, “how that chromium cycles might change our interpretations of geological records.”

“The evolution of oxygen on Earth is only known in a coarse fashion, but it is crucial to the development and survival of complex multicellular life," says Ed Boyle, professor of ocean geochemistry of MIT’s Department of Earth, Atmospheric and Planetary Sciences (EAPS); MIT-WHOI Joint Program director; and study co-author, along with Simone Moos PhD ’18 of the Elementar Corporation. "In addition, there is ongoing concern about the past few decades of decreasing oceanic oxygen levels in the ocean, and we need tools to better understand the ocean’s oxygen dynamics.” 

Bridging a gap

Billions of years ago, when Earth and its atmosphere were essentially devoid of molecular oxygen (O2), chemical reactions and biological metabolisms would have occurred in a chemically reduced, anaerobic environment. During the Great Oxidation Event, which occurred over the course of millions of years, oxygen levels rose planet-wide, and life transitioned accordingly. Further, the environment largely became an oxidized one that grappled with stress processes like rusting and free radicals.

Some evidence has shown that chemical reactions involving chromium track this process, through effects on its isotopes, chromium-52 and chromium-53, and their oxidation states, primarily the trivalent, reduced form Cr (III) and a hexavalent, oxidized one Cr (VI). The latter is more likely to be found in oxygenated, surface seawater and is considered a health and environmental hazard. Previous studies have shown that the upper ocean tends to have more of the heavier isotope than the lighter one, suggesting some preferential uptake by marine microorganisms. The problem, Huang notes, is that after chromium enters the oceans from rivers, scientists don’t really know the mechanisms behind these observations and if the trends are consistent. In today’s oxygen-deficient waters, she says, “chromium could potentially be reduced, and we want to know the isotope signal of that and other chromium processes that might leave an isotope fingerprint.”

To investigate these phenomena, Huang joined two research cruises to the eastern tropical North Pacific Ocean’s oxygen-deficient zone (ODZ) and gathered vertical profiles of seawater samples down to 3,500 meters from across a transect of sea. Some of these seawater samples were frozen to be analyzed for concentrations of trivalent and hexavalent chromium. After being shipped back to the lab, these samples were thawed and purified. The team analyzed the isotope composition of the Cr (III) samples. They then acidified the Cr (VI) samples to convert them to Cr (III) before performing the same isotope analysis as before. The researchers also measured the total chromium in the samples to be able to account for any chemical transformations or migration within the ODZ. With the addition of data from another cruise, Boyle, Moos, and Huang examined the fraction of each isotope over the depth range, compared to an average partitioning, to see if there was any enrichment in a particular area of the ODZ and which oxidation state it existed in. They charted this against the samples’ oxygen levels and put the results in context of known ocean features to help explain how chromium is cycling.

A ground truth for chromium cycling

The oceanographers found a pattern. In surface, oxygenated ocean, hexavalent chromium was consumed, likely by microbial life, and transported deeper, into the ODZ. Around the 200-meter mark, the metal began to accumulate in the seawater, and the lighter isotope, chromium-52, was preferentially reduced. This depth happens to coincide with anaerobic, denitrifying microbes that produce nitrite. Huang says that this could be a sign that nitrogen and chromium cycling are entangled, but that doesn’t rule out other biotic or abiotic mechanisms, like reduction by iron, that could be affecting ocean sediment records.

Chromium doesn’t linger here forever, though. While data showed that most of it remained in oxygen-deficient zone, which extends from 90 to 800 meters, for about 20-50 years, a small portion of it attached to sinking particles, sank into the deep ocean where there is more dissolved oxygen, and later oxidized back to hexavalent chromium. Here, it could begin incorporating and interacting with sediments.

“I think it is exciting that we could determine the chromium [oxidation] species, and from that, we could calculate its isotope fractionation,” says Huang. “Nobody has done that in this way before.”

Their work, Huang says, helps validate chromium as an indicator of different redox environments. “We're seeing this signal and it’s not vanishing.” Further, it seems consistent over the seasons. However, the team isn’t convinced yet. They plan to test this in other oxygen-deficient zones around the world to see if a similar chromium signature pops up, as well as investigate the composition of the sinking particles carrying the trivalent chromium and the surface of ocean sediments, in order to get a more complete picture of the ocean’s involvement.

For now, they advise against drawing conclusions, but are guardedly optimistic about its potential. “I think people need to interpret this proxy with more caution,” says Huang. “It might not be purely the atmospheric oxygen that is determining the measurement, but there could be other [biotic or abiotic] processes in the ocean that could alter their paleorecords.” So, they suggest not to read into the chromium signals in the paleorecord too much, yet.

This research was supported, in part, by the National Science Foundation.

Study reveals uncertainty in how much carbon the ocean absorbs over time

Mon, 04/05/2021 - 12:00am

The ocean’s “biological pump” describes the many marine processes that work to take up carbon dioxide from the atmosphere and transport it deep into the ocean, where it can remain sequestered for centuries. This ocean pump is a powerful regulator of atmospheric carbon dioxide and an essential ingredient in any global climate forecast.

But a new MIT study points to a significant uncertainty in the way the biological pump is represented in climate models today. Researchers found that the “gold standard” equation used to calculate the pump’s strength has a larger margin of error than previously thought, and that predictions of how much atmospheric carbon the ocean will pump down to various depths could be off by 10 to 15 parts per million.

Given that the world is currently emitting carbon dioxide into the atmosphere at an annual rate of about 2.5 parts per million, the team estimates that the new uncertainty translates to about a five-year error in climate target projections.

“This larger error bar might be critical if we want to stay within 1.5 degrees of warming targeted by the Paris Agreement,” says Jonathan Lauderdale, a research scientist in MIT’s Department of Earth, Atmospheric and Planetary Sciences. “If current models predict we have until 2040 to cut carbon emissions, we’re expanding the uncertainty around that, to say maybe we now have until 2035, which could be quite a big deal.”

Lauderdale and former MIT graduate student B.B. Cael, now at the National Oceanography Center in Southampton, U.K., have published their study today in the journal Geophysical Research Letters.

Snow curve

The marine processes that contribute to the ocean’s biological pump begin with phytoplankton, microscopic organisms that soak up carbon dioxide from the atmosphere as they grow. When they die, phytoplankton collectively sink through the water column as “marine snow,” carrying that carbon with them.

“These particles rain down like white flaky snow that is all this dead stuff falling out of the surface ocean,” Lauderdale says.

At various depths the particles are consumed by microbes, which convert the particles’ organic carbon and respire it into the deep ocean in an inorganic, mineral form, in a process known as remineralization.

In the 1980s, researchers collected marine snow at locations and depths throughout the tropical Pacific. From these observations they generated a simple power law  mathematical relationship — the Martin curve, named after team member John Martin — to describe the strength of the biological pump, and how much carbon the ocean can remineralize and sequester at various depths.

“The Martin curve is ubiquitous, and it’s really the gold standard [used in many climate models today],” Lauderdale says.

But in 2018, Cael and co-author Kelsey Bisson showed that the power law derived to explain the Martin curve was not the only equation that could fit the observations. The power law is a simple mathematical relationship that assumes that particles fall faster with depth. But Cael found that several other mathematical relationships, each based on different mechanisms for how marine snow sinks and is remineralized, could also explain the data.

For instance, one alternative assumes that particles fall at the same rate no matter the depth, while another assumes that particles with heavy, less-consumable phytoplankton shells fall faster than those without.

“He found that you can’t tell which curve is the right one, which is a bit troubling, because each curve has different mechanisms behind it,” Lauderdale says. “In other words, researchers might be using the ‘wrong’ function to predict the strength of the biological pump. These discrepancies could snowball and impact climate projections.”

A curve, reconsidered

In the new study, Lauderdale and Cael looked at how much difference it would make to estimates of carbon stored deep in the ocean if they changed the mathematical description of the biological pump.

They started with the same six alternative equations, or remineralization curves, that Cael had previously studied. The team looked at how climate models’ predictions of atmospheric carbon dioxide would change if they were based on any of the six alternatives, versus the Martin curve’s power law.

To make the comparison as statistically similar as possible, they first fit each alternative equation to the Martin curve. The Martin curve describes the how much marine snow reaches various depths through the ocean. The researchers entered the data points from the curve into each alternative equation. They then ran each equation through the MITgcm, a general circulation model that simulates, among other processes, the flux of carbon dioxide between the atmosphere and the ocean.

The team ran the climate model forward in time to see how each alternative equation for the biological pump changed the model’s estimates of carbon dioxide in the atmosphere, compared with the Martin curve’s power law. They found that the amount of carbon that the ocean is able to draw down and sequester from the atmosphere varies widely, depending on which mathematical description for the biological pump they used.

“The surprising part was that even small changes in the amount of remineralization or marine snow making it to different depths due to the different curves can lead to significant changes in atmospheric carbon dioxide,” Lauderdale says.

The results suggest that the ocean’s pumping strength, and the processes that govern how fast marine snow falls, are still an open question.  

“We definitely need to make many more measurements of marine snow to break down the mechanisms behind what’s going on,” Lauderdale adds. “Because probably all these processes are relevant, but we really want to know which are driving carbon sequestration.”

This research was supported, in part, by the National Science Foundation, the Simons Collaboration on Computational Biogeochemical Modeling of Marine Ecosystems, and the UK National Environmental Research Council.

An artificial intelligence tool that can help detect melanoma

Fri, 04/02/2021 - 4:30pm

Melanoma is a type of malignant tumor responsible for more than 70 percent of all skin cancer-related deaths worldwide. For years, physicians have relied on visual inspection to identify suspicious pigmented lesions (SPLs), which can be an indication of skin cancer. Such early-stage identification of SPLs in primary care settings can improve melanoma prognosis and significantly reduce treatment cost.

The challenge is that quickly finding and prioritizing SPLs is difficult, due to the high volume of pigmented lesions that often need to be evaluated for potential biopsies. Now, researchers from MIT and elsewhere have devised a new artificial intelligence pipeline, using deep convolutional neural networks (DCNNs) and applying them to analyzing SPLs through the use of wide-field photography common in most smartphones and personal cameras.

DCNNs are neural networks that can be used to classify (or “name”) images to then cluster them (such as when performing a photo search). These machine learning algorithms belong to the subset of deep learning.

Using cameras to take wide-field photographs of large areas of patients’ bodies, the program uses DCNNs to quickly and effectively identify and screen for early-stage melanoma, according to Luis R. Soenksen, a postdoc and a medical device expert currently acting as MIT’s first Venture Builder in Artificial Intelligence and Healthcare. Soenksen conducted the research with MIT researchers, including MIT Institute for Medical Engineering and Science (IMES) faculty members Martha J. Gray, W. Kieckhefer Professor of Health Sciences and Technology, professor of electrical engineering and computer science; and James J. Collins, Termeer Professor of Medical Engineering and Science and Biological Engineering.

Soenksen, who is the first author of the recent paper, “Using Deep Learning for Dermatologist-level Detection of Suspicious Pigmented Skin Lesions from Wide-field Images,” published in Science Translational Medicine, explains that “Early detection of SPLs can save lives; however, the current capacity of medical systems to provide comprehensive skin screenings at scale are still lacking.”

The paper describes the development of an SPL analysis system using DCNNs to more quickly and efficiently identify skin lesions that require more investigation, screenings that can be done during routine primary care visits, or even by the patients themselves. The system utilized DCNNs to optimize the identification and classification of SPLs in wide-field images.

Using AI, the researchers trained the system using 20,388 wide-field images from 133 patients at the Hospital Gregorio Marañón in Madrid, as well as publicly available images. The images were taken with a variety of ordinary cameras that are readily available to consumers. Dermatologists working with the researchers visually classified the lesions in the images for comparison. They found that the system achieved more than 90.3 percent sensitivity in distinguishing SPLs from nonsuspicious lesions, skin, and complex backgrounds, by avoiding the need for cumbersome and time-consuming individual lesion imaging. Additionally, the paper presents a new method to extract intra-patient lesion saliency (ugly duckling criteria, or the comparison of the lesions on the skin of one individual that stand out from the rest) on the basis of DCNN features from detected lesions.

“Our research suggests that systems leveraging computer vision and deep neural networks, quantifying such common signs, can achieve comparable accuracy to expert dermatologists,” Soenksen explains. “We hope our research revitalizes the desire to deliver more efficient dermatological screenings in primary care settings to drive adequate referrals.”

Doing so would allow for more rapid and accurate assessments of SPLS and could lead to earlier treatment of melanoma, according to the researchers.

Gray, who is senior author of the paper, explains how this important project developed: "This work originated as a new project developed by fellows (five of the co-authors) in the MIT Catalyst program, a program designed to nucleate projects that solve pressing clinical needs. This work exemplifies the vision of HST/IMES devotee (in which tradition Catalyst was founded) of leveraging science to advance human health.” This work was supported by Abdul Latif Jameel Clinic for Machine Learning in Health and by the Consejería de Educación, Juventud y Deportes de la Comunidad de Madrid through the Madrid-MIT M+Visión Consortium.

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