Developing new soft materials requires new data-driven research techniques, such as autonomous experimentation. Data regarding nanometer-scale material structure, taken by X-ray measurements at a synchrotron, can be fed into an algorithm that identifies the most relevant features, represented here as red dots. The algorithm then determines the optimum conditions for the next set of measurements and directs their execution without human intervention. Brookhaven National Laboratory’s Kevin Yager, who helped develop this technique, will co-teach a course on it as part of a new Penn project on Data Driven Soft Materials Research.
The National Science Foundation’s Research Traineeship Program aims to support graduate students, educate the STEM leaders of tomorrow and strengthen the national research infrastructure. The program’s latest series of grants are going toward university programs focused on artificial intelligence and quantum information science and engineering – two areas of high priority in academia, industry and government.
Chinedum Osuji, Eduardo D. Glandt Presidential Professor and Chair of the Department of Chemical and Biomolecular Engineering (CBE), has received one of these grants to apply data science and machine learning to the field of soft materials. The grant will provide five years of support and a total of $3 million for a new Penn project on Data Driven Soft Materials Research.
Osuji will work with co-PIs Russell Composto, Professor and Howell Family Faculty Fellow in Materials Science and Engineering, Bioengineering, and in CBE, Zahra Fakhraai, Associate Professor of Chemistry in Penn’s School of Arts & Sciences (SAS) with a secondary appointment in CBE, Paris Perdikaris, Assistant Professor in Mechanical Engineering and Applied Mechanics, and Andrea Liu, Hepburn Professor of Physics and Astronomy in SAS, all of whom will help run the program and provide the connections between the multiple fields of study where its students will train.
These and other affiliated faculty members will work closely with co-PI Kristin Field, who will serve as Program Coordinator and Director of Education.
CPE4H is one of the focal points of Penn Engineering signature initiative on Engineering Health.
The Penn Center for Precision Engineering for Health (CPE4H) was established late last year to accelerate engineering solutions to significant problems in healthcare. The center is one of the signature initiatives for Penn’s School of Engineering and Applied Science and is supported by a $100 million commitment to hire faculty and support new research on innovative approaches to those problems.
Acting on that commitment, CPE4H solicited proposals during the spring of 2022 for seed grants of $80K per year for two years for research projects that address healthcare challenges in several key areas of strategic importance to Penn: synthetic biology and tissue engineering, diagnosis and drug delivery, and the development of innovative devices. While the primary investigators (PIs) for the proposed projects were required to have a primary faculty appointment within Penn Engineering, teams involving co-PIs and collaborators from other schools were eligible for support. The seed program is expected to continue for the next four years.
“It was a delight to read so many novel and creative proposals,” says Daniel A. Hammer, Alfred G. and Meta A. Ennis Professor in Bioengineering and the Inaugural Director of CPE4H. “It was very hard to make the final selection from a pool of such promising projects.”
Judged on technical innovation, potential to attract future resources, and ability to address a significant medical problem, the following research projects were selected to receive funding.
Evolving and Engineering Thermal Control of Mammalian Cells
Led by Lukasz Bugaj, Assistant Professor in Bioengineering, this project will engineer molecular switches that can be toggled on and off inside mammalian cells at near-physiological temperatures. Successful development of these switches will provide new ways to communicate with cells, an advance that could be used to make safer and more effective cellular therapies. The project will use directed evolution to generate and find candidate molecular tools with the desired properties. Separately, the research will also develop new technology for manipulating cellular temperature in a rapid and programmable way. Such devices will enhance the speed and sophistication of studies of biological temperature regulation.
A Quantum Sensing Platform for Rapid and Accurate Point-of-Care Detection of Respiratory Viral Infections
Combining microfluidics and quantum photonics, PI Liang Feng, Professor in Materials Science and Engineering and Electrical and Systems Engineering, Ritesh Agarwal, Professor in Materials Science Engineering, and Shu Yang, Joseph Bordogna Professor in Materials Science and Engineering and Chemical and Biomolecular Engineering, are teaming up with Ping Wang, Professor of Pathology and Laboratory Medicine in Penn’s Perelman School of Medicine, to design, build and test an ultrasensitive point-of-care detector for respiratory pathogens. In light of the COVID-19 pandemic, a generalizable platform for rapid and accurate detection of viral pathogenesis would be extremely important and timely.
Versatile Coacervating Peptides as Carriers and Synthetic Organelles for Cell Engineering
PI Amish Patel, Associate Professor in Chemical and Biomolecular Engineering, and Matthew C. Good, Associate Professor of Cell and Developmental Biology in the Perelman School of Medicine and in Bioengineering, will design and create small proteins that self-assemble into droplet-like structures known as coacervates, which can then pass through the membranes of biological cells. Upon cellular entry, these protein coacervates can disassemble to deliver cargo that modulates cell behavior or be maintained as synthetic membraneless organelles. The team will design new chemistries that will facilitate passage across cell membranes, and molecular switches to sequester and release protein therapeutics. If successful, this approach could be used to deliver a wide range of macromolecule drugs to cells.
Towards an Artificial Muscle Replacement for Facial Reanimation
Cynthia Sung, Gabel Family Term Assistant Professor in Mechanical Engineering and Applied Mechanics and Computer Information Science, will lead a research team including Flavia Vitale, Assistant Professor of Neurology and Bioengineering, and Niv Milbar, Assistant Instructor in Surgery in the Perelman School of Medicine. The team will develop and validate an electrically driven actuator to restore basic muscle responses in patients with partial facial paralysis, which can occur after a stroke or injury. The research will combine elements of robotics and biology, and aims to produce a device that can be clinically tested.
“These novel ideas are a great way to kick off the activities of the center,” says Hammer. “We look forward to soliciting other exciting seed proposals over the next several years.”
In a new book ‘Curious Minds: The Power of Connection,’ Penn’s Dani S. Bassett and twin sibling Perry Zurn weave together history, linguistics, network science, neuroscience, and philosophy to unpack the concept of curiosity.
Twin siblings and scholars Dani S. Bassett of Penn and Perry Zurn of American University collaborated over half a dozen years to write “Curious Minds: The Power of Connection.” (Image: Tony and Tracy Wood Photography)
Bugs. Sometimes, something just bugs you. A worm in your ear. We have all had the experience. You are going about your day, and something prompts you to wonder. You mull it over. You try on this explanation, or that one. And then you get distracted, and you move on. Or maybe you don’t, and the worm digs in deeper. Or maybe you do, but the worm returns to its wriggling later that night. You can’t shake it off. Maybe you pull out your phone or strike a few keys—or turn to a colleague or ping a friend. Gosh, now you really want to know! Perhaps you hit a few walls—paywalls or prejudices, differences of opinion or the limits of science, or even congenial scoffing at your pet project. Depending on who you are, you might also encounter outright sexism or racism, classism or ableism—all ways of telling you your bug is a bust. Forget this fleeting interest and focus on something that matters.
Regardless, let’s say, you carry on. Maybe the kids are screaming, or you are in a meeting, or you drive to the store for milk. Despite bombastic blasts from every corner, you hold on to what’s bugging you, refusing to let it bugger off. And then it happens … your mind begins to dance and to weave. Collecting the bits of things that might be relevant and stitching them together. So builds the briefest of webs. Perhaps it was a silkworm after all! Now you are really getting somewhere. This is your brain on curiosity.
And you are in good company. Rewind back to 1928, if you will. Virginia Woolf is sitting on the banks of a river (the Thames, the Cam, the Isis), and she has a worm in her ear: women and fiction. What even are they? she wonders. “Questions,” she calls them, “unsolved problems.” She finds herself walking and thinking, calmly at first and then feverishly. Crisscrossing the Brontë sisters and George Eliot, Charles Lamb and William Thackeray, she wonders not only about women and about fiction, but about their relation and the several ways in which it can be characterized. She strides by the nearby university, a place filled—as she puts it—with obsolete old minds, bereft of body and free of fact, loosed from the roughshod rambling toward truth she is currently undertaking. And then there it is!
Thought—to call it by a prouder name than it deserved—had let its line down into the stream. It swayed, minute after minute, hither and thither, among the reflections and the weeds, letting the water lift it and sink it, until—you know the little tug—the sudden conglomeration of an idea at the end of one’s line….
Dani S. Bassett is the J. Peter Skirkanich Professor at the University of Pennsylvania with a primary appointment in the School of Engineering and Applied Science’s Department of Bioengineering and secondary appointments in the School of Arts & Sciences’ Department of Physics & Astronomy, SEAS’ Department of Electrical and Systems Engineering, and the Perelman School of Medicine’s Departments of Neurology and Psychiatry.
Perry Zurn is an associate professor and director of undergraduate studies in philosophy at American University in the College of Arts and Sciences’ Department of Philosophy and Religion.
In 2005, John Ioannidis published a bombshell paper titled “Why Most Published Research Findings Are False.” In it, Ioannidis argued that a lack of scientific rigor in biomedical research — such as poor study design, small sample sizes and improper assessment of the significance of data— meant that a large percentage of experiments would not return the same results if they were conducted again.
Since then, researchers’ awareness of this “replication crisis” has grown, especially in fields that directly impact the health and wellbeing of people, where lapses in rigor can have life-or-death consequences. Despite this attention and motivation, however, little progress has been made in addressing the roots of the problem. Formal training in rigorous research practices remains rare; while mentors advise their students on how to properly construct and conduct experiments to produce the most reliable evidence, few educational resources exist to support them.
Konrad Kording, a Penn Integrates Knowledge Professor with appointments in the Departments of Bioengineering and Computer and Information Science in Penn Engineering and the Department of Neuroscience in Penn’s Perelman School of Medicine, has been awarded one of the initiative’s first five grants.
“The replication crisis is real,” says Kording. “I’ve tried to replicate the research of others and failed. I’ve reanalyzed my own data and found major mistakes that needed to be corrected. I was never properly taught how to do rigorous science, and I want to improve that for the next generation.”
Therapies that use engineered cells to treat diseases, infections and chronic illnesses are opening doors to solutions for longstanding medical challenges. Lukasz Bugaj, Assistant Professor in Bioengineering, has been awarded a National Science Foundation CAREER Award for research that may be key to opening some of those doors.
Such cellular therapies take advantage of the complex molecular mechanisms that cells naturally use to interact with one another, enabling them to be more precise and less toxic than traditional pharmaceutical drugs, which are based on simpler small molecules. Cellular therapies that use engineered immune system cells, for example, have recently been shown to be highly successful in treating certain cancers and protecting against viral infections.
However, there is still a need to further fine-tune the behavior of cells in these targeted therapies. Bugaj and colleagues are addressing that need by developing new ways to communicate with engineered cells once they are in the body, such as turning molecular events on and off at specific times.
The research team recently discovered that both temperature and light can act as triggers of a specific fungal protein, dynamically controlling its location within a mammalian cell. By using light or temperature to instruct that protein to migrate toward or away from the cell’s membrane, Bugaj and his colleagues showed how it could serve as a key component in controlling the behavior of human cells.
Penn Health-Tech director Katie Reuther (center) with Glory Durham, director of operations, Penn Health-Tech (at left), and Courtney Houtsma, program manager, Penn Health-Tech (at right), at a recent symposium.
A new interview in Penn Medicine News examines Penn Health-Tech (PHT) five years after its founding. PHT began as an experimental collaborative effort between the Perelman School of Medicine, the School of Engineering and Applied Science, and the Office of the Vice Provost for Research to provide funding, advising, and resources to empower innovators to develop transformative devices and technologies in the Penn community. Specifically, PHT specializes in connecting innovators from across Penn’s campus and schools to connect and to develop technology and medical devices to answer some of the most pressing needs in healthcare. Katherine (Katie) Reuther, Practice Associate Professor in Bioengineering, was appointed Executive Director of PHT in 2021 and is leading this venture into the next phase of its growth. Reuther, an alumna of Penn Bioengineering, followed up her doctoral studies with a M.B.A. from Columbia University and subsequently stayed at Columbia as Senior Lecturer in Design, Innovation, and Entrepreneurship in the Department of Biomedical Engineering. As such, her experience and expertise in the fields of both biomedical engineering and entrepreneurship position her well to shepherd PHT into its fullest potential:
“What appealed to me most about the position was a strong foundation, deep resources, and the potential and room to do more, including the opportunity to elevate Penn and Philadelphia as a national hub for health-technology innovation.”
Controlled and actuated by magnetic fields, these mircrorobots are capable of precisely targeting the apical region — the opening where blood vessels and nerve enter the tooth — in a root canal.
With its irregularities and anatomical complexities, the root canal system is one of the most clinically challenging spaces in the oral cavity. As a result, biofilm not fully cleared from the nooks and crannies of the canals remains a leading cause of treatment failure and persistent endodontic infections, and there are limited means to diagnose or assess the efficacy of disinfection. One day, clinicians may have a new tool to overcome these challenges in the form of microrobots.
In a proof-of-concept study, researchers from Penn Dental Medicine and its Center for Innovation & Precision Dentistry (CiPD), have shown that microrobots can access the difficult to reach surfaces of the root canal with controlled precision, treating and disrupting biofilms and even retrieving samples for diagnostics, enabling a more personalized treatment plan. The Penn team shared their findings on the use of two different microrobotic platforms for endodontic therapy in the August issue of the Journal of Dental Research;the work was selected for the issue’s cover.
“The technology could enable multimodal functionalities to achieve controlled, precision targeting of biofilms in hard-to-reach spaces, obtain microbiological samples, and perform targeted drug delivery, ” says Dr. Alaa Babeer, lead author of the study and a Penn Dental Medicine Doctor of Science in Dentistry (DScD) and endodontics graduate, who is now within the lab of Dr. Michel Koo, co-director of the CiPD .
In both platforms, the building blocks for the microrobots are iron oxide nanoparticles (NPs) that have both catalytic and magnetic activity and have been FDA approved for other uses. In the first platform, a magnetic field is used to concentrate the NPs in aggregated microswarms and magnetically control them to the apical area of the tooth to disrupt and retrieve biofilms through a catalytic reaction. The second platform uses 3D printing to create miniaturized helix-shaped robots embedded with iron oxide NPs. These helicoids are guided by magnetic fields to move within the root canal, transporting bioactives or drugs that can be released on site.
“This technology offers the potential to advance clinical care on a variety of levels,” says Dr. Koo, co-corresponding author of the study with Dr. Edward Steager, a senior research investigator in Penn’s School of Engineering and Applied Science. “One important aspect is the ability to have diagnostic as well as therapeutic applications. In the microswarm platform, we can not only remove the biofilm, but also retrieve it, enabling us identify what microorganisms caused the infection. In addition, the ability to conform to the narrow and difficult-to-reach spaces within the root canal allows for a more effective disinfection in comparison to the files and instrumentation techniques presently used.”
Michel Koo is a professor in the Department of Orthodontics and divisions of Community Oral Health and Pediatric Dentistry in Penn Dental Medicine and co-director of the Center for Innovation & Precision Dentistry. He is a member of the Penn Bioengineering Graduate Group.
Combining optical measurements with ultrasound, an interdisciplinary team from the School of Arts & Sciences, Perelman School of Medicine, and CHOP developed a device to better measure blood flow and oxygenation in the placenta. (Image: Lin Wang)
A study published in Nature Biomedical Engineering details a novel method for imaging the placenta in pregnant patients as well as the results of a pilot clinical study. By combining optical measurements with ultrasound, the findings show how oxygen levels can be monitored noninvasively and provides a new way to generate a better understanding of this complex, crucial organ. This research was the result of a collaboration of the groups of the University of Pennsylvania’s Arjun Yodh and Nadav Schwartz with colleagues from the Children’s Hospital of Philadelphia (CHOP) and was led by postdoc Lin Wang.
Schwartz describes the placenta as the “engine” of pregnancy, an organ that plays a crucial role in delivering nutrients and oxygen to the fetus. Placental dysfunction can lead to complications such as fetal growth restriction, preeclampsia, and stillbirth. To increase knowledge about this crucial organ, the National Institute of Child Health and Human Development launched the Human Placenta Project in 2014. One focus of the program is to develop tools to assess human placental structure and function in real time, including optical devices.
For three years, the researchers optimized the design of their instrument and tested it in preclinical settings. The process involved integrating optical fibers with ultrasound probes, exploring various ultrasound transducers, and improving the multimodal technology so that measurements were stable, accurate, and reproducible while collecting data at the bedside. The resulting instrumentation now enables researchers to study the anatomy of the placenta while also collecting detailed functional information about placenta blood flow and oxygenation, capabilities that existing commercially devices do not have, the researchers say.
Because the placenta is located far below the body’s surface, one of the key technical challenges addressed by Wang, a postdoc in Yodh’s lab, was reducing background noise in the opto-electronic system. Light is scattered and absorbed when it travels through thick tissues, Yodh says, and the key for success was to reduce background interference so that the small amount of light that penetrates deep into the placenta and then returns is still large enough for a high-quality measurement.
“We’re sending a light signal that goes through the same deep tissues as the ultrasound. The extremely small amount of light that returns to the surface probe is then used to accurately assess tissue properties, which is only possible with very stable lasers, optics, and detectors,” says Yodh. “Lin had to overcome many barriers to improve the signal-to-noise ratio to the point where we trusted our data.”
The authors are Lin Wang, Jeffrey M. Cochran, Kenneth Abramson, Lian He, Venki Kavuri, Samuel Parry, Arjun G. Yodh, and Nadav Schwartz from Penn; Tiffany Ko, Wesley B. Baker, and Rebecca L. Linn from the Children’s Hospital of Philadelphia, and David R. Busch, previously a research associate at Penn and now at the University of Texas Southwestern Medical School.
This research was supported by National Institutes of Health grants F31HD085731, R01NS113945, R01NS060653, P41EB015893, P41EB015893, T32HL007915, and U01HD087180.
Though the technology for brain-computer interfaces (or BCI’s) has existed for decades, recent strides have been made to create BCI devices which are safer, smaller, and more effective. Konrad Kording, Nathan Francis Mossell University Professor in Bioengineering, Neuroscience, and Computer and Information Science, helps to elucidate the potential future of this technology in a recent feature in Wired. In the article, he discusses the “invasive” aspects of previous BCI technology, in contrast to recent innovations, such as a new device by Synchron, which do not require surgery and are consequently much less risky:
“The device, called a Stentrode, has a mesh-like design and is about the length of a AAA battery. It is implanted endovascularly, meaning it’s placed into a blood vessel in the brain, in the region known as the motor cortex, which controls movement. Insertion involves cutting into the jugular vein in the neck, snaking a catheter in, and feeding the device through it all the way up into the brain, where, when the catheter is removed, it opens up like a flower and nestles itself into the blood vessel’s wall. Most neurosurgeons are already up to speed on the basic approach required to put it in, which reduces a high-risk surgery to a procedure that could send the patient home the very same day. ‘And that is the big innovation,” Kording says.
Congratulations to Kevin B. Johnson, David L. Cohen University Professor, on his recent appointed as a Senior Fellow in the Leonard Davis Institute of Health Economics at the University of Pennsylvania (Penn LDI). Johnson, an expert in health care innovation and health information technology, holds appointments in Biostatistics, Epidemiology and Informatics in the Perelman School of Medicine and Computer and Information Science in the School of Engineering and Applied Science. He also holds secondary appointments in Bioengineering, Pediatrics, and in the Annenberg School of Communication and is Vice President for Applied Informatics in the University of Pennsylvania Health System.
Penn LDI is Penn’s hub for health care delivery, health policy, and population health, we connect and amplify experts and thought-leaders and train the next generation of researchers. Johnson joins over 500 Fellows from across all of Penn’s schools, the University of Pennsylvania Health System, and the Children’s Hospital of Philadelphia. Johnson brings expertise in Health Care Innovation, Health Information Technology, Medication Adherence, and Social Media to his new fellowship and has extensively studied healthcare informatics with the goal of improving patient care.
