What do ‘Bohemian Rhapsody,’ ‘Macbeth,’ and a list of Facebook Friends All Have in Common?

New research finds that works of literature, musical pieces, and social networks have a similar underlying structure that allows them to share large amounts of information efficiently.

Examples of statistical network analysis of characters in two of Shakespeare’s tragedies. Two characters are connected by a line, or edge, if they appear in the same scene. The size of the circles that represent these characters, called nodes, indicate how many other characters one is connected to. The network’s density relates to how complete the graph is, with 100% density meaning that it has all of the characters are connected. (Image: Martin Grandjean)

 

By Erica K. Brockmeier

To an English scholar or avid reader, the Shakespeare Canon represents some of the greatest literary works of the English language. To a network scientist, Shakespeare’s 37 plays and the 884,421 words they contain also represent a massively complex communication network. Network scientists, who employ math, physics, and computer science to study vast and interconnected systems, are tasked with using statistically rigorous approaches to understand how complex networks, like all of Shakespeare, convey information to the human brain.

New research published in Nature Physics uses tools from network science to explain how complex communication networks can efficiently convey large amounts of information to the human brain. Conducted by postdoc Christopher Lynn, graduate students Ari Kahn and Lia Papadopoulos, and professor Danielle S. Bassett, the study found that different types of networks, including those found in works of literature, musical pieces, and social connections, have a similar underlying structure that allows them to share information rapidly and efficiently.

Technically speaking, a network is simply a statistical and graphical representation of connections, known as edges, between different endpoints, called nodes. In pieces of literature, for example, a node can be a word, and an edge can connect words when they appear next to each other (“my” — “kingdom” — “for” — “a” — “horse”) or when they convey similar ideas or concepts (“yellow” — “orange” — “red”).

The advantage of using network science to study things like languages, says Lynn, is that once relationships are defined on a small scale, researchers can use those connections to make inferences about a network’s structure on a much larger scale. “Once you define the nodes and edges, you can zoom out and start to ask about what the structure of this whole object looks like and why it has that specific structure,” says Lynn.

Building on the group’s recent study that models how the brain processes complex information, the researchers developed a new analytical framework for determining how much information a network conveys and how efficient it is in conveying that information. “In order to calculate the efficiency of the communication, you need a model of how humans receive the information,” he says.

Continue reading at Penn Today.

Dan Huh Receives Chan Zuckerberg Initiative Grant for Placenta-on-a-chip Research

CRI huh
Dan Huh, Ph.D.

The Chan Zuckerberg Initiative (CZI) has announced $14 million in funding to support 29 interdisciplinary teams who are investigating the role of inflammation in disease. Among these recipients is Dan Huh, Associate Professor in Bioengineering, whose placenta-on-a-chip research will “explore how maternal and fetal cells respond to specific inflammatory signals and analyze the network of placental cells and immune cells that impact pregnancy outcomes in chronic inflammatory diseases.”

Kellie Ann Jurado, Presidential Assistant Professor in the Perelman School of Medicine’s Department of Microbiology, will lead the research team. She and Huh will collaborate with Monica Mainigi, William Shippen, Jr. Assistant Professor of Human Reproduction in Penn Medicine.

A version of the Huh Lab’s placenta-on-a-chip from 2018

Huh’s placenta-on-a-chip consists of a small block of silicone containing microfluidic channels separated by a membrane of human cells. Variations in designs and cell types allow researchers to study how different molecules cross that barrier, allowing for experiments that would be otherwise impossible or unethical. For example, Huh and his group previously used a placenta-on-a-chip designed to model the placental barrier to research the effect of maternally-administered medications on the fetal bloodstream.

In this new study, Huh, Jurando and Mainigi were motivated by even more fundamental questions of pregnancy.

“It has been known for quite some time that women with chronic inflammatory diseases are at increased risk of developing various complications during pregnancy,” Huh says. “Despite accumulating clinical evidence, we understand little about how inflammation contributes to adverse pregnancy outcomes.”

Read the full story on the Penn Engineering blog.

Bridging the Communication Divide for Deaf and Hard-of-hearing Communities

Clear-fronted face masks, better and more frequent interpreters, and amped up involvement from local organizations have made a big difference during the COVID-19 pandemic.

By Michele Berger

Since April 23, when bioengineering alum Kate Panzer (above) and her partners at the Deaf-Hearing Communication Centre started taking orders for masks with clear fronts, they’ve shipped about 450, with a backlog of requests for hundreds more. (Image: Courtesy Kate Panzer)

Because COVID-19 spreads via respiratory droplets that disperse through sneezes and coughs, shielding the mouth and nose is an important weapon against the virus. But it can also hinder conversations for people who rely on reading lips. “Communication barriers are already difficult sometimes, and this makes it more difficult,” says linguist , director of ’s .

It’s one of the trickiest aspects of this pandemic for those in the Deaf and hard-of-hearing communities, Fisher says. The challenge doesn’t stem just from misunderstandings due to wearing masks. It’s also about the dissemination of accurate and timely information, knowing who to rely on and how to assess what’s being said.

Trusted sources like the Swarthmore, Pennsylvania–based nonprofit Deaf-Hearing Communication Centre (DHCC), a Penn community partner, have filled that gap, frequently updating information on its social media channels and websites. Governors and mayors are more frequently using Certified Deaf Interpreters (CDI) during press briefings, and Penn alum Kate Panzer, who graduated in 2018, started a project with DHCC to sew masks with clear fronts to offer both lip-reading access and protection.

Innovative masks

Like much of the country, Panzer has stayed inside for the past several months. When the pandemic started to worsen, she temporarily left a research position in Michigan and returned to her childhood home in Media, Pennsylvania. And like many people, she wanted to give back.

At Penn, she’d taken several American Sign Language classes through the program Fisher runs, so when she read an article about a student in Kentucky making clear-fronted masks, it piqued her interest. She reached out to Fisher, who connected her with Kyle Rosenberg, DHCC’s community development and outreach coordinator.

As a volunteer, she shared her mask idea with Rosenberg. “Even in normal times, the Deaf community really struggles with clear communication,” says Rosenberg, who is himself deaf. “ASL is very visual. It relies on body language. Covering up the mouth with a mask makes communication 10 times harder.”

Rosenberg helped Panzer tweak a design and create a process to reach the community, and they took their first order on April 23. Since then, they’ve shipped about 450 masks, with a backlog of requests for hundreds more.

Though the response has been overwhelmingly positive, when constructive feedback comes in, they do take it to heart, Panzer says. For example, when mask-wearers told them that the elastic bands they’d been using rubbed uncomfortably against hearing aids, they switched to fabric ties that go around the back of the head. The masks are not medical grade, so they can’t be used in a hospital setting, but Panzer says her goal was to improve everyday interactions.

“When you can only see the eyes, it takes a lot out of expressive communication for Deaf people,” says Fisher, whose parents and one brother are deaf. “It’s really important that they be able to more fully convey facial expressions and mouth movements that influence meaning.” Masks with clear fronts help.

Continue reading at .

Kate Panzer earned her bachelor’s degree in 2018 from the Department of Bioengineering in the School of Engineering and Applied Science at the University of Pennsylvania. She is currently a disability health and family medicine research assistant at Michigan Medicine at the University of Michigan. 

NB: Kate has done prior work with ASL during her time at Penn Bioengineering. Kate’s 2018 Senior Design team created a two-way interface to help communication between deaf patients and hearing medical professionals called MEDISIGN. Fellow team members included fellow BE alumni Jackie Valeri, Nick Stiansen, and Karol Szymula. Watch their presentation on the Penn Engineering youtube channel.

Lyle Ungar on Normalizing Face Masks

As scientists continue to battle the novel coronavirus, public health officials maintain that wearing a face mask is a powerful way to curb the spread of the virus and keep communities safe. However, America has struggled to adopt this change, as compared to other countries that have made wearing a face mask an unremarkable aspect of their culture.

Lyle Ungar, Ph.D.

In an opinion piece for the New York Times, Lyle Ungar, Professor of Computer and Information Science, Angela Duckworth, Rosa Lee and Egbert Chang Professor in Penn Arts & Sciences and the Wharton School, and Ezekiel J. Emanuel, Professor of Medical Ethics and Health Policy in Penn’s Perelman School of Medicine, propose a new approach to increase consistent face mask use among Americans: make wearing a mask “easy,” “understood,” and “expected.”

In their article, Ungar, Duckworth, and Emanuel make reference to communities that provided face masks free of charge for residents and note the decrease in infection in these areas. In addition, they point out how uncertainty about the necessity of face masks in the U.S. has led to public confusion which inhibits trust and use of masks. Finally, the three researchers push for a shift in social norms to embrace wearing a face mask as standard in America for the near future.

Some of Ungar’s recent research is also focused on the pandemic, including a “COVID Twitter map,” created with colleagues at the World Well-Being Project and Penn Medicine’s Center for Digital Health. Their map helps show, in real time, how people across the country perceive the virus and how it is affecting their mental health.

Read more about Ungar, Duckworth, and Emanuel’s strategy for normalizing face masks in their opinion piece for the New York Times.

Originally posted on the Penn Engineering blog.

Lyle Ungar is a Professor of Computer and Information Science (CIS) and a member of the Penn Bioengineering Graduate Group.

How Penn’s Medical Device Development Course Adapted to the COVID-19 Pandemic

Though BE 472 was able to quickly pivot to an entirely online curriculum, some in-person aspects of the course were unfortunately lost. Pictured: BE 472’s Spring 2019 MedTech panel discussion with industry leaders Katherine High, MD (President of Spark Therapeutics), Lucas Rodriguez, PhD (CEO of CerSci Therapeutics), and Penn BE alumnus Brianna Wronko (CEO of Group K Diagnostics) (credit: Lauren McLeod BE 2020).

by Sophie Burkholder

Given the closing of schools in response to the coronavirus pandemic, professors teaching lab-based courses were forced to make some changes. One such course, the Department of Bioengineering’s Medical Device Development (BE 472) taught by Matthew R. Maltese, Ph.D., usually requires students to develop a medical device and learn how to lead a startup venture for it. Over the semester, students design prototypes for unmet needs in the medical device community, and then go on to learn about business-related aspects of the project, like fundraising, regulations, teamwork, and leadership. Maltese often encourages junior engineering students to take the course, in the hopes that their projects might become launchpads for their senior design projects the following year.

But with the pandemic’s interruptions to education restricting access to the lab, or even to some of the schematics for their earlier designs, Maltese’s Spring 2020 students had to re-focus on the business side of their projects.

Fortunately, the shift to online learning came late enough in the semester that most students had already come up with solid project ideas. Maltese then shifted gears to the less hands-on parts of the course. “There’s lots of elements to this course that are not focused on putting hands on hardware,” he says. “They’re focused on distilling and disseminating information about your endeavor to people that are interested.”

While some of those more hands-off assignments originally had some face-to-face aspects, like the final pitch competition, they’re also easy to transition to an online format. Maltese had students record videos of their pitches, which he notes is perhaps more akin to what they might have to do for external pitch competitions. And even though students couldn’t make their physical prototypes, Maltese says that they were all able to make virtual prototypes through CAD or other modeling software.

In his opinion, this renewed focus on out-of-lab prototype models might be a good thing for real-world experience. Investors and stakeholders often want the full picture of a device or startup before they even have to start working with physical material, for the sake of cost efficiency.

Students had already been working on their projects for a couple of months before the pandemic started to affect classes, so most of them stuck to their original ideas instead of adapting them to meet the needs of the current medical crisis. “Next year, I think we’re going to focus the class on COVID-19 ideas though,” says Maltese.

In fact, Medical Device Development will likely be one of many Penn Bioengineering courses that adapts its curriculum to the challenges the pandemic presented. “As a medical device community, a pharmaceutical community, a healthcare community, we were not ready for this,” Maltese notes, “but history teaches us that some of our greatest innovations emerge from our greatest trials.”  He is excited for the future.

A Message to the Penn Bioengineering Community

A message to the Penn Bioengineering community from BE leadership:

Dear BE Nation,

We wanted you to know that we in BE fully stand behind and reiterate the message from President Gutmann in full support of our Black students, postdocs, staff, colleagues, and friends.

As noted by President Gutmann, we all are feeling outrage, anger, grief, and myriad other emotions. We are at a loss to comprehend and to process the magnitude and implications of the brutality, oppression, and injustice that have come to light once again following the horrific event of George Floyd’s murder.

Several students and colleagues have reached out expressing their desires to contribute actively to effect a positive and progressive change. Our President Gutmann and Provost Pritchett have summarized some of the Penn initiatives towards our local communities in their message linked above. Numerous others are proactively contributing large and small. While we may not agree on many things, we can all agree that a lot remains to be done, and it will take time and sustained effort and commitment on our part. We are committed to the cause: to effect continual and progressive change for nurturing equality and cultural sensitivity as we build a diverse academic ecosystem, and this includes BE, Penn, and our surrounding community. It is our commitment to our Black friends and colleagues.

We take this opportunity to share this article sent by Denise Lay: Answering the Question, ‘What Can I Do?’ and this document compiled by BE Ph.D. student Lasya Sreepada created to share resources and opportunities for members of the University of Pennsylvania community to help their local communities.

Also, here are a  few resources to help cope:

Racial Justice and Equity (from Bucketlisters): A listing of resources, organizations and actions, including Philadelphia specific organizations.

Coping with Racial Trauma (recommended by Penn’s Counseling and Psychological Services [CAPS]): A mental, emotional, physical and spiritual toolkit for coping with racial trauma which provides a window into the personal cost of systemic racism, discrimination and inequality.

Mostly and immediately, we write this note to reiterate that we stand with and support our Black students, postdocs, staff, colleagues, and friends in this difficult period.

Sincerely yours,

Undergraduate Chair Andrew Tsourkas
Graduate Chair Yale Cohen
Department Chair Ravi Radhakrishnan

Connecting Communities Impacted by COVID-19

Three Penn seniors combine their desire to help with their unique skill sets to create Corona Connects, an online platform that connects volunteers with organizations in need of support.

Developed by (from left) Steven Hamel from the School of Engineering and Applied Science, Megan Kyne from the Wharton School, and Hadassah Raskas from the College of Arts & Sciences, Corona Connects bridges the gap between those looking for ways to help and organizations in need of support.

by Erica K. Brockmeier

With college campuses shut due to the novel coronavirus, many students with new-found time on their hands have found themselves asking, “What can I do to help?”

To connect people with organizations that need support, three students have combined their desire to help with the skills they’ve learned both inside and outside the classroom. Developed by Penn seniors Steven Hamel from the School of Engineering and Applied Science, Megan Kyne from the Wharton School, and Hadassah Raskas from the College of Arts & Sciences, the online platform Corona Connects bridges the gap between people looking for ways to help and organizations looking for support.

After returning to her hometown of Silver Spring, Maryland, Raskas was eager to find some way to help but noticed that it was difficult to find opportunities online. With friends and colleagues voicing similar struggles, Raskas reached out to University of Maryland junior Elana Sichel and started putting together a list of organizations in need of help. Then, after reaching out on the Class of 2020 Facebook page about the project, Hamel, from Philadelphia, and Kyne, from Pittsburgh, offered their support to get an online platform up and running.

The team of students quickly realized that there was both a large number of individuals who wanted to find ways to help alongside an unprecedented level of need from numerous types of organizations. “We knew there was need, and we knew there was an availability of people, but the connection was missing, so we built Corona Connects to bridge this gap,” says Raskas.

Continue reading on Penn Today.

Steven Hamel graduated with his B.S.E. in Bioengineering and a Math minor in in 2020 and is currently pursuing a Master’s in Bioengineering.

To Err is Human, to Learn, Divine

Researchers develop a new model for how the brain processes complex information: by striking a balance between accuracy and simplicity while making mistakes along the way.

By Erica K. Brockmeier

New research finds that the human brain detects patterns in complex networks by striking a balance between simplicity and complexity, much like how a pointillist painting can be viewed up close to see the finer details or from a distance to see its overall structure.

The human brain is a highly advanced information processor composed of more than 86 billion neurons. Humans are adept at recognizing patterns from complex networks, such as languages, without any formal instruction. Previously, cognitive scientists tried to explain this ability by depicting the brain as a highly optimized computer, but there is now discussion among neuroscientists that this model might not accurately reflect how the brain works.

Now, Penn researchers have developed a different model for how the brain interprets patterns from complex networks. Published in Nature Communications, this new model shows that the ability to detect patterns stems in part from the brain’s goal to represent things in the simplest way possible. Their model depicts the brain as constantly balancing accuracy with simplicity when making decisions. The work was conducted by physics Ph.D. student Christopher Lynn, neuroscience Ph.D. student Ari Kahn, and Danielle Bassett, J. Peter Skirkanich Professor in the departments of Bioengineering and Electrical and Systems Engineering.

This new model is built upon the idea that people make mistakes while trying to make sense of patterns, and these errors are essential to get a glimpse of the bigger picture. “If you look at a pointillist painting up close, you can correctly identify every dot. If you step back 20 feet, the details get fuzzy, but you’ll gain a better sense of the overall structure,” says Lynn.

To test their hypothesis, the researchers ran a set of experiments similar to a previous study by Kahn. That study found that when participants were shown repeating elements in a sequence, such as A-B-C-B, etc., they were automatically sensitive to certain patterns without being explicitly aware that the patterns existed. “If you experience a sequence of information, such as listening to speech, you can pick up on certain statistics between elements without being aware of what those statistics are,” says Kahn.

To understand how the brain automatically understands such complex associations within sequences, 360 study participants were shown a computer screen with five gray squares corresponding to five keys on a keyboard. As two of the five squares changed from gray to red, the participants had to strike the computer keys that corresponded to the changing squares. For the participants, the pattern of color-changing squares was random, but the sequences were actually generated using two kinds of networks.

The researchers found that the structure of the network impacted how quickly the participants could respond to the stimuli, an indication of their expectations of the underlying patterns. Responses were quicker when participants were shown sequences that were generated using a modular network compared to sequences coming from a lattice network.

Continue reading on Penn Today.

This paper was also profiled on the website Big Think.

Language in Tweets Offers Insight Into Community-level Well-being

In a Q&A, researcher Lyle Ungar discusses why counties that frequently use words like ‘love’ aren’t necessarily happier, plus how techniques from this work led to a real-time COVID-19 wellness map.

By Michele W. Berger

Lyle Ungar, Ph.D. (Photo: Eric Sucar)

People in different areas across the United States reacted differently to the threat of COVID-19. Some imposed strict restrictions, closing down most businesses deemed nonessential; others remained partially open.

Such regional distinctions are relatively easy to quantify, with their effects generally understandable through the lens of economic health. What’s harder to grasp is the emotional satisfaction and happiness specific to each place, a notion ’s has been working on for more than five years.

In 2017, the group published the , a free, interactive tool that displays characteristics of well-being by county based on Census data and billions of tweets. Recently, WWBP partnered with ’s Center for Digital Health to create a , which reveals in real time how people across the country perceive COVID-19 and how it’s affecting their mental health.

That map falls squarely in line with a paper published this week in the by computer scientist , one of the principal investigators of the World Well-Being Project, and colleagues from Stanford University, Stony Brook University, the National University of Singapore, and the University of Melbourne.

By analyzing 1.5 billion tweets and controlling for common words like “love” or “good,” which frequently get used to connote a missing aspect of someone’s life rather than a part that’s fulfilled, the researchers found they could discern subjective well-being at the county level. “We have a long history of collecting people’s language and asking people who are happier or sadder what words they use on Facebook and on Twitter,” Ungar says. “Those are mostly individual-level models. Here, we’re looking at community-level models.”

In a conversation with Penn Today, Ungar describes the latest work, plus how it’s useful in the time of COVID-19 and social distancing.

Read Ungar’s Q&A at .

Dr. Lyle Ungar is a Professor of Computer and Information Science and a member of the Department of Bioengineering Graduate Group.

David Meaney on Responding to the COVID-19 Crisis

David F. Meaney, the Senior Associate Dean of Penn Engineering and Solomon R. Pollack Professor of Bioengineering, is known for his scholarship and innovation in neuroengineering and concussion science, his leadership as former Chair of the Department of Bioengineering, and for his marshaling of interdisciplinary research between Penn Engineering and the University’s health schools.

The Penn Engineering community has sprung into action over the course of the past few weeks in response to COVID-19. Meaney shared his perspective on those efforts and the ones that will come online as the pandemic continues to unfold.

David F. Meaney, Ph.D.

It is remarkable to think that a little more than a month ago I was saying an early goodbye to students for their spring break. In the first week of March, I was wishing everyone a happy and safe break, emphasizing safe, not knowing how prophetic that word would be. I was also looking forward to my own spring break, traveling for the first time in many years over this part of the academic calendar.

And then our campus — and world — changed.

COVID-19 is among us, in ways that we can’t exactly measure. It is among us in ways that we feel — we probably know someone that has tested positive for the virus, and others that are living with someone that is sick. And we all realize the virus will be with us for some time; the exact amount we don’t know.

Which brings up the question — what can we do to fight this pandemic? Many of us are trying to find ways to keep our connections with others vibrant and strong in the world of Zoom, Hangout, and BlueJeans. That is important. Let me also say that I can’t wait to reconnect with everyone in person, and close my laptop for a week.

But staying connected is what everyone should do. I often think about what can engineers do?

As the Senior Associate Dean, I want to let you know what I’m seeing on a quiet, but not shuttered, Penn campus. Examples of our response to the pandemic include our faculty designing personal protective equipment for health care workers, and our students, faculty and staff volunteering to assemble it. Other faculty are inventing COVID-19 test kits that can be completed at home, with the results available in less than an hour. Professors are sharing their creative mask designs with the world, for free, to make sure that we can all feel comfortable walking outside. And yet others that are collaborating to make a vaccine that will help us put COVID-19 behind us, permanently.

All of this is happening at speeds we have never seen before. Ideas move to prototypes and testing in days, not months, and to product in a week. We are not alone — our colleagues across campus are working at light speed to generate better tests, treatments, and models to fight COVID-19. This time, Nature has given us the problem. Time for us to solve it.

It’s more important than ever that we amplify one another’s voices and we want to hear from you. Learn more about Penn Engineering’s Share Your Story project here, and read entries here. You can also keep up-to-date on Penn Engineering’s pandemic response efforts here.

Originally posted on the Penn Engineering blog. Media contact Evan Lerner.

Learn more about the Department of Bioengineering’s COVID-19 projects in our recent blog post.