PIK Professor Kevin Johnson named University Professor

Johnson, who has appointments in the Perelman School of Medicine and the School of Engineering and Applied Science, and a secondary appointment in the Annenberg School for Communication, will become the David L. Cohen University Professor.

Penn Integrates Knowledge Professor Kevin Johnson, a pediatrician who has pioneered the use of clinical information systems and artificial intelligence to improve medical research and patient care, has received a named University professorship.

Kevin Johnson, a Penn Integrates Knowledge University Professor whose work as a physician-scientist has led to medical information technologies that improve patient safety, has been named the David L. Cohen University Professor. The announcement was made today by President Amy Gutmann.

“David Cohen’s extraordinary leadership at the University and Penn Medicine, and longtime dedication to Philadelphia, has without a doubt shaped the booming campus, health system, and city we so much enjoy today,” says Gutmann. “His dedication is mirrored by the extraordinarily influential, innovative, and committed Dr. Kevin Johnson, whose university professorship will now bear Ambassador Cohen’s name.”

Johnson joined Penn this year from the Vanderbilt University School of Medicine. A board-certified pediatrician and leading medical informaticist, he holds faculty appointments in the Department of Biostatistics, Epidemiology, and Informatics in the Perelman School of Medicine and the Department of Computer and Information Science in the School of Engineering and Applied Science. He is also vice president for applied informatics at the University of Pennsylvania Health System and has secondary faculty appointments in the Perelman School of Medicine’s Department of Pediatrics and in the Annenberg School for Communication.

Cohen has served for two decades on Penn’s Board of Trustees and recently concluded a 12-year term as chair. He was confirmed by the U.S. Senate last month as United States Ambassador to Canada, bringing to the role decades of experience as a senior executive at Comcast Corp., chair of the Ballard Spahr law firm, chief of staff to Philadelphia Mayor Ed Rendell, trustee chair at Penn, and major player in a number of other business, civic, political, and philanthropic venues.

In addition to serving as a Trustee, Cohen is a Penn alum, having graduated from what is now the University of Pennsylvania Carey School of Law in 1981. His wife and son also attended the Law School. Cohen’s leadership in the University has been credited with helping guide the growth and advancement of both the University and Health System, in close partnership with both President Gutmann and her predecessor, Judith Rodin.

“It’s an honor to hold a professorship named after Mr. Cohen,” Johnson says. “Throughout his career, he has provided inspired leadership across Penn and our city and region. He is a passionate believer in uniting the public, private, and nonprofit sectors to tackle complex challenges and strengthen communities. Those who know me know that I’ve played a similar role as a pediatrician who works with technology, and who uses digital media to communicate to lay audiences about both. His passion for this city and our University’s educational mission are inspiring.”

N.B.: Johnson also holds a secondary appointment in the Department of Bioengineering. Read his full appointment announcement here.

Penn Researchers Show ‘Encrypted’ Peptides Could be Wellspring of Natural Antibiotics

by Melissa Pappas

César de la Fuente, Ph.D.

While biologists and chemists race to develop new antibiotics to combat constantly mutating bacteria, predicted to lead to 10 million deaths by 2050, engineers are approaching the problem through a different lens: finding naturally occurring antibiotics in the human genome.

The billions of base pairs in the genome are essentially one long string of code that contains the instructions for making all of the molecules the body needs. The most basic of these molecules are amino acids, the building blocks for peptides, which in turn combine to form proteins. However, there is still much to learn about how — and where — a particular set of instructions are encoded.

Now, bringing a computer science approach to a life science problem, an interdisciplinary team of Penn researchers have used a carefully designed algorithm to discover a new suite of antimicrobial peptides, hiding deep within this code.

The study, published in Nature Biomedical Engineering, was led by César de la Fuente, Presidential Assistant Professor in Bioengineering, Microbiology, Psychiatry, and Chemical and Biomolecular Engineering, spanning both Penn Engineering and Penn Medicine, and his postdocs Marcelo Torres and Marcelo Melo. Collaborators Orlando Crescenzi and Eugenio Notomista of the University of Naples Federico II also contributed to this work.

“The human body is a treasure trove of information, a biological dataset. By using the right tools, we can mine for answers to some of the most challenging questions,” says de la Fuente. “We use the word ‘encrypted’ to describe the antimicrobial peptides we found because they are hidden within larger proteins that seem to have no connection to the immune system, the area where we expect to find this function.”

Read the full story in Penn Engineering Today.

Using Big Data to Measure Emotional Well-being in the Wake of George Floyd’s Murder

by Melissa Pappas

George Floyd’s murder had an undeniable emotional impact on people around the world, as evidenced by this memorial mural in Berlin, but quantifying that impact is challenging. Researchers from Penn Engineering and Stanford have used a computational approach on U.S. survey data to break down this emotional toll along racial and geographic lines. Their results show a significantly larger amount of self-reported anger and sadness among Black Americans than their White counterparts. (Photo: Leonhard Lenz)

The murder of George Floyd, an unarmed Black man who was killed by a White police officer, affected the mental well-being of many Americans. The effects were multifaceted as it was an act of police brutality and example of systemic racism that occurred during the uncertainty of a global pandemic, creating an even more complex dynamic and emotional response.

Because poor mental health can lead to a myriad of additional ailments, including poor physical health, inability to hold a job and an overall decrease in quality of life, it is important to understand how certain events affect it. This is especially critical when the emotional burden of these events  falls most on demographics affected by systemic racism. However, unlike physical health, mental health is challenging to characterize and measure, and thus, population-level data on mental health has been limited.

To better understand patterns of mental health on a population scale, Penn Engineers Lyle H. Ungar, Professor of Computer and Information Science (CIS), and Sharath Chandra Guntuku, Research Assistant Professor in CIS, take a computational approach to this challenge. Drawing on large-scale surveys as well as language analysis in social media through their work with the World Well-Being Project, they have developed visualizations of these patterns across the U.S.

Their latest study involves tracking changes in emotional and mental health following George Floyd’s murder. Combining polling data from the U.S. Census and Gallup, Guntuku, Ungar and colleagues have shown that Floyd’s murder spiked a wave of unprecedented sadness and anger across the U.S. population, the largest since relevant data began being recorded in 2009.

Read the full story in Penn Engineering Today.

N.B. Lyle Ungar is also a member of the Penn Bioengineering Graduate Group.

The Pioneering Career of Norman Badler

by Ebonee Johnson

The retiring CIS professor chats about his recent ACM SIGGRAPH election and his expansive computer graphics path.

Norman Badler, Ph.D. (Image credit: Penn CIS)

Norman Badler’s election into the 2021 ACM SIGGRAPH Academy Class is right on time. After nearly five decades of teaching and trailblazing in the Penn community, the Rachleff Family Professor in the Department of Computer and Information Sciences retired at the end of the spring semester.

When he arrived at the University in 1974, CIS itself was only about 2 years old, and there was virtually no computer graphics focus or program at all. Badler had no intention to teach it.

“At that time, I was actually a computer vision researcher, but I was also working a little bit in natural language,” says Badler. “So I was literally brought in to fit between the chair, Aravind Joshi, who was a natural language person, and the computer vision person. It wasn’t until about three or four years after I came here that I switched over to computer graphics. Mostly because there was a vacuum and a need and an excitement.”

Several years after completing his dissertation in computer vision and forming a career path to head in that direction, Badler “started getting serious about computer graphics.” An organization that was getting its start around the same time as his Penn career would play a major role: ACM SIGGRAPH (the Association for Computing Machinery’s Special Interest Group on Computer Graphics and Interactive Techniques).

Read the full story in the CIS Blog.

N.B.: Badler was a member of the Penn Bioengineering Graduate Group.

Bioengineering Contributes to “New COVID-19 Testing Technology at Penn”

César de la Fuente, Ph.D., a Presidential Assistant Professor in Psychiatry, Microbiology, and Bioengineering, is leading a team to develop an electrode that can be easily printed at low cost to provide COVID-19 test results from your smart phone.

A recent Penn Medicine blog post surveys the efforts across Penn and the Perelman School of Medicine to develop novel says to detect SARS-CoV-2 and features several Department of Bioengineering faculty and Graduate Group members, including César de la Fuente, Presidential Assistant Professor in Psychiatry, Microbiology, and Bioengineering; Arupa Ganguly, Professor in Genetics; A.T. Charlie Johnson, Rebecca W. Bushnell Professor in Physics and Astronomy; Lyle Ungar, Professor in Computer and Information Science; and Ping Wang, Associate Professor in Pathology and Laboratory Medicine.

Read “We’ll Need More than Vaccines to Vanquish the Virus: New COVID-19 Testing Technology at Penn” by Melissa Moody in Penn Medicine News.

Kevin Johnson Appointed Penn Integrates Knowledge University Professor

Ron Ozio

Kevin Johnson, Penn’s 27th Penn Integrates Knowledge University Professor.

Kevin Johnson has been named the University of Pennsylvania’s 27th Penn Integrates Knowledge University Professor.

The announcement was made by Penn President Amy Gutmann and Provost Wendell Pritchett.

A pioneer of medical information technologies to improve patient safety, Johnson will hold joint appointments in the Department of Biostatistics, Epidemiology, and Informatics in the Perelman School of Medicine and the Department of Computer and Information Science in the School of Engineering and Applied Science, with secondary appointments in the Annenberg School for Communication and in the Department of Bioengineering. He will also serve as vice president for applied informatics in the University of Pennsylvania Health System and professor of pediatrics at the Children’s Hospital of Philadelphia.

“Kevin Johnson is a gifted physician-scientist,” Gutmann said, “who has harnessed and aligned the power of medicine, engineering, and technology to improve the health of individuals and communities. He has championed the development and implementation of clinical information systems and artificial intelligence to drive medical research, encouraged the effective use of technology at the bedside, and empowered patients to use new tools to better understand how medications and supplements may affect their health. He is a board-certified pediatrician, and his commitment to patient health and welfare knows no age limits. In so many different settings, Kevin’s work is driving progress in patient care and improving our health care system. He is a perfect fit for Penn, where our goal is to create a maximally inclusive and integrated academic community to spur unprecedented global impact.”

Johnson is currently the Cornelius Vanderbilt Professor and chair of the Department of Biomedical Informatics at the Vanderbilt University School of Medicine, where he has taught since 2002. He is a world-renowned innovator in developing clinical information systems that improve best practices in patient safety and compliance with medical practice guidelines, especially the use of computer-based documentation systems and other digital technologies. His research bridges biomedical informatics, bioengineering, and computer science. As senior vice president for health information technology at the Vanderbilt University Medical Center from 2014 to 2019, he led the development of clinical systems that enabled doctors to make better treatment and care decisions for individual patients, in part by alerting patients as to how medications or supplements might affect their body chemistry, as well as new systems to integrate artificial intelligence into patient care workflows and to unify and simplify all the Medical Center’s clinical and administrative systems.

The author of more than 150 publications, books, or book chapters, Johnson has held numerous leadership positions in the American Medical Informatics Association and the American Academy of Pediatrics, leads the American Board of Pediatrics Informatics Advisory Committee, directs the Board of Scientific Counselors of the National Library of Medicine, and is a member of the NIH Council of Councils. He has been elected to the National Academy of Medicine (Institute of Medicine), American College of Medical Informatics, and Academic Pediatric Society and has received awards from the Robert Wood Johnson Foundation and American Academy of Pediatrics, among many others.

“Kevin Johnson exemplifies our most profound Penn values,” Pritchett said. “He is a brilliant innovator committed to bringing together disciplines across traditional boundaries. Yet he always does so in the service of helping others, finding technological solutions that can make a tangible impact on improving people’s lives. He will be an extraordinary colleague, teacher and mentor across multiple areas of our campus in the years to come.”

Johnson earned an M.D. from the Johns Hopkins University School of Medicine, an M.S. in medical informatics from Stanford University, and a B.S. with honors in biology from Dickinson College. He became the first Black chief resident in pediatrics at Johns Hopkins in 1992, and was a faculty member in both pediatrics and biomedical information sciences at Johns Hopkins until 2002.

The Penn Integrates Knowledge program was launched by Gutmann in 2005 as a University-wide initiative to recruit exceptional faculty members whose research and teaching exemplify the integration of knowledge across disciplines and who are appointed in at least two Schools at Penn.

Originally posted in Penn Today.

An ‘Electronic Nose’ to Sniff Out COVID-19

by Erica K. Brockmeier

Postdoc Scott Zhang at work in the Johnson lab. (Photo: Eric Sucar, University Communications)

Even as COVID-19 vaccines are being rolled out across the country, the numerous challenges posed by the pandemic won’t all be solved immediately. Because herd immunity will take some time to reach and the vaccine has not yet been approved for some groups, such as children under 16 years of age, the coming months will see a continued need for tools to rapidly track the disease using real-time community monitoring.

A team of Penn researchers is working on a new “electronic nose” that could help track the spread of COVID-19. Led by physicist Charlie Johnson, the project, which was recently awarded a $2 million grant from the NIH, aims to develop rapid and scalable handheld devices that could spot people with COVID-19 based on the disease’s unique odor profile.

Dogs and devices that can detect diseases

Long before “coronavirus” entered into the vernacular, Johnson was collaborating with Cynthia Otto, director of the Penn Vet Working Dog Center, and Monell Chemical Senses Center’s George Preti to diagnose diseases using odor. Diseases are known to alter a number of physical processes, including body odors, and the goal of the collaboration was to develop new ways to detect the volatile organic compounds (VOCs) that were unique to ovarian cancer.

The next step is to scale down the current device, and the researchers are aiming to develop a prototype for testing on patients within the next year.

Since 2012, the researchers have been developing new ways to diagnose early-stage ovarian cancer. Otto trained dogs to recognize blood plasma samples from patients with ovarian cancer using their acute sense of smell. Preti, who passed away last March, was looking for the specific VOCs that gave ovarian cancer a unique odor. Johnson developed a sensor array, an electronic version of the dog’s nose, made of carbon nanotubes interwoven with single-stranded DNA. This device binds to VOCs and can determine samples that came from patients with ovarian cancer.

Last spring, as the pandemic’s threat became increasingly apparent, Johnson and Otto shifted their efforts to see if they could train their disease-detecting devices and dogs to spot patients with COVID-19.

Continue reading at Penn Today.

N.B.: A.T. Charlie Johnson, Rebecca W. Bushnell Professor of Physics and Astronomy at the Penn School of Arts & Sciences, and Lyle Ungar, Professor in Computer and Information Science at Penn Engineering and Psychology at the School of Arts & Sciences, are both members of the Penn Bioengineering Graduate Group.

BE Seminar: “Emerging Technologies for Detection of Early Stage Bladder Cancer” (Audrey Bowden)

Audrey Bowden, PhD, Associate Professor of Biomedical Engineering. (Vanderbilt University / Steve Green)

Speaker: Audrey Bowden, Ph.D.
Dorothy J. Wingfield Phillips Chancellor’s Faculty Fellow and Associate Professor of Biomedical Engineering and Electrical Engineering & Computer Science
Vanderbilt University

Date: Thursday, November 19, 2020
Time: 3:00-4:00 PM EST
Zoom – check email for link or contact ksas@seas.upenn.edu

Title: “Emerging Technologies for Detection of Early Stage Bladder Cancer”

Abstract:

Bladder cancer (BC) —  the 4th most common cancer in men and the most expensive cancer to treat over a patient’s lifetime — is a lifelong burden to BC patients and a significant economic burden to the U.S. healthcare system. The high cost of BC stems largely from its high recurrence rate (>50%); hence, BC management involves frequent surveillance. Unfortunately, the current in-office standard-of-care tool for BC surveillance, white light cystoscopy (WLC), is limited by low sensitivity and specificity for carcinoma in situ (CIS), a high-grade carcinoma with high potential to metastasize. Early detection and complete eradication of CIS are critical to improve treatment outcomes and to minimize recurrence. The most promising macroscopic technique to improve sensitivity to CIS detection, blue light cystoscopy (BLC), is costly, time-intensive, has low availability and a high false-positive rate. Given the limitations of WLC, we aim to change the paradigm around how BC surveillance is performed by validating new tools with high sensitivity and specificity for CIS that are appropriate for in-office use. In this seminar, I discuss our innovative solutions to improve mapping the bladder for longitudinal tracking of suspicious lesions and to create miniature tools for optical detection based on optical coherence tomography (OCT). OCT and its functional variant, cross-polarized OCT, can detect early-stage BC with better sensitivity and specificity than WLC. We discuss the critical technical innovations necessary to make OCT and CP-OCT a practical tool for in-office use, and new results from recent explorations of human bladder samples that speak to the promise of this approach to change the management of patient care.

Bio:

Audrey K. Bowden is the Dorothy J. Wingfield Phillips Chancellor Faculty Fellow and Associate Professor of Biomedical Engineering (BME) and of Electrical Engineering and Computer Science (EECS) at Vanderbilt University. Prior to this, she served as Assistant and later Associate Professor of Electrical Engineering and Bioengineering at Stanford University. Dr. Bowden received her BSE in Electrical Engineering from Princeton University, her PhD in BME from Duke University and completed her postdoctoral training in Chemistry and Chemical Biology at Harvard University. During her career, Dr. Bowden served as an International Fellow at Ngee Ann Polytechnic in Singapore. From 2007-2008, she was the Arthur H. Guenther Congressional Fellow sponsored by the OSA and SPIE and served as a Legislative Assistant in the United States Senate through the AAAS Science and Technology Policy Fellows Program. Dr. Bowden is a Fellow of SPIE, a Fellow of AIMBE and is the recipient of numerous awards, including the Air Force Young Investigator Award, the NSF Career Award, the Hellman Faculty Scholars Award, the Phi Beta Kappa Teaching Award, Ford Foundation Postdoctoral Fellowship, and the NSBE Golden Torch Award. She is a former Associate Editor of IEEE Photonics Journal, former Lead Guest Editor of a Biomedical Optics Express Special Issue and is a member of numerous professional committees. Her research interests include biomedical optics – particularly optical coherence tomography and near infrared spectroscopy – microfluidics, and point of care diagnostics.

Meet Bioengineering Sophomore and SNF Paideia Fellow Catherine Michelutti

Catherine Michelutti (BSE, BS ’23)

Rising Bioengineering Sophomore Catherine Michelluti (BSE 2023) has been featured on Penn’s SNF Paideia Program Instagram which discusses her diverse interests in machine learning in medicine, computer science, playing the violin and more. Catherine is a pre-med student who is pursuing an uncoordinated dual degree between the School of Engineering and Applied Science and the Wharton School of Business (BS in Economics 2023). She is also an incoming fellow in the SNF Paideia Program, which is supported by the Stavros Niarchos Foundation, is an interdisciplinary program which “encourage[s] the free exchange of ideas, civil and robust discussion of divergent views, and the integration of individual and community wellness, service, and citizenship through SNF Paideia designated courses, a fellows program, and campus events” (SNF Paideia website).

Read more about Catherine and other Fellows on the SNF Paideia Instagram.

Lyle Ungar: ‘Philadelphia Needs More Contact Tracers’

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

In May, Lyle Ungar, Professor of Computer and Information Science and Angela Duckworth, Rosa Lee and Egbert Chang Professor in Penn Arts & Sciences and the Wharton School, contributed to a New York Times op-ed on how to slow the COVID-19 pandemic through a culture of mask-wearing.

As infections continue to rise, Ungar and Duckworth are following up with another op-ed. Writing in the Philadelphia Inquirer, they outline the need to rapidly ramp-up the city and state’s contact tracing capacity:

Guidelines from health officials suggest Pennsylvania needs about 4,000 contact tracers, including 2,000 for the Philadelphia metro area. Our state has been operating with fewer than 200.

Continue reading Ungar and Duckworth’s op-ed at the Philadelphia Inquirer.

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

Lyle Ungar is a Professor of Computer and Information Science (CIS) and a member of the Penn Bioengineering Graduate Group. Read more stories about the coronavirus pandemic written by Lyle Ungar here.