U.S. News Ranks Penn Bioengineering No. 4

U.S. NewsEvery year, U.S. News & World Report compiles the rankings of Bioengineering and Biomedical Engineering departments across the country. Today, U.S. News revealed its rankings for 2019. Penn Bioengineering placed 4th among almost two hundred programs. Tied now with programs that include MIT, UC Berkeley, and Stanford, Penn BE is the fastest rising program in the Top 10. The department also strengthened its position as the highest ranked science and engineering program at Penn in this year’s rankings.

“It was welcome news to know that we were evaluated so highly by our peers” says David Meaney, chair of Penn BE, “I really think it is a statement of the students we attract to Penn, our educational programs, and the cutting edge research done by our faculty”.

Penn Engineering also rose in the rankings, rising one spot to #18.  Computed based on scores from peers, recruiters, and research activity, the rankings show that Penn BE lives in a healthy engineering ecosystem!

Double Shelix: You Do Belong in Science

If you’ve listened to our podcasts, then you’ve heard the work of Kayla and Sally at Double Shelix. They’ll be running a special series of podcasts next month and are asking for readers’ help. Please read the below, and if you decide to participate, let them know that Penn Bioengineering sent you!


Double Shelix
You do belong in science – even if it doesn’t always seem like it. Penn Bioengineering‘s affiliate podcast, Double Shelix, is launching a special series on the theme You do Belong in Science. This series will bring together experts in science, education, and inclusion in conversation about creating STEM communities where all can feel belonging. 

As part of this, we are seeking stories from members of our STEM communities (including Penn Bioengineering!) about times when they felt like they did or didn’t belong in science. Sharing these stories can help all to feel that they are not alone in their occasional (or frequent!) feelings of imposter syndrome/isolation.

Call our voicemail at 415-895-0850 to share your story, or record yourself and email it to our podcast email, doubleshelixpodcast@gmail.com. Anonymous is ok! We may just feature you the podcast!

Prompts (Respond to whichever moves you! Questions are great too!)
– Is there a time when you felt like you did not belong in science? What happened and how did it make you feel?
– What would you say to someone who is experiencing dis-belonging?
– What can the scientific community (or your school/department/professors/peers) do to help people experience belonging?

Subscribe to Double Shelix now on iTunes or Google Play Music to catch the episodes when they launch in April! And a sneak peek trailer is coming soon! Also, the most recent episode in our feed is all about wellness in graduate school – and features some voices familiar to Penn Bioengineers! More info on our site – doubleshelix.com and our mailing list (sign up here).
Thanks a million and remember, you do belong in science!
Sally Winkler + Kayla Wolf
4th year PhD Students, UC Berkeley/UCSF Bioengineering
Founders, Double Shelix Podcast

Cell Phones: Is There a Link to Cancer?

cell phonesLast month, the National Toxicology Program (NTP), a division of the U.S. Department of Health and Human Services, announced the findings of a draft study in which it was shown that high exposure to radiofrequency radiation, similar to that caused by persistent use of cell phones, resulted in the formation of tumors in nerves surrounding the hearts of male rats — but not female rats or mice.  These are the final results of the study, the preliminary results of which were released in 2016. The study must still undergo peer review later this month.

Among the experts studying this question for the last decade is Kenneth R. Foster, Ph.D., Professor Emeritus of Bioengineering at the University of Pennsylvania. He’s not so sure that there’s really any link between the radiation emitted by cell phones and cancers. “People have been using cell phones for decades and so far there has been no noticeable increase in brain cancer,” Dr. Foster said. “This means that the risk, if it occurs at all, is too low to detect with any reliability.”

cell phones
Kenneth R. Foster, Ph.D.

Asked whether the findings of the NTP study could be generalized to people, Dr. Foster responded, “If you look at enough tissues and compare enough endpoints, you will pick up things that may just be one-off findings. Health agencies will have to assess the findings carefully in the light of the considerable previous literature of related studies. The results of the study are unlikely to change their previous assessments, which is that there is no clear evidence of health hazards from using cell phones.” The exposed rats in the NTP study consistently lived longer than the exposed rats, he added.

Dr. Foster noted that the exposure levels for the rats that developed tumors was far higher than safety limits for humans in terms of whole body exposure and not at all similar to the exposures that people receive from using cell phones. “Also,” he said, “people don’t use cell phones for nine hours a day for two years at a time, which were the exposures in the NTP study. After all of this research on the issue, my own view is that cell phones don’t cause brain cancer. But they do contribute to traffic accidents!”

Week in BioE (March 14, 2018)

Nanotube Yarn Used for Neurological Applications

Microscopic image of carbon nanotube yarn.

Tapping into the autonomous nervous system – the control center for things like heartbeat and breathing – is a relatively new part of neurostimulation technologies to both record and direct organ function. Implants designed for stimulating peripheral nerves often fail because the protective tissue surrounding nerve bundles (the perineurium) is difficult to penetrate, and the body’s immune response often builds a scar around the implanted device.

Now, a team of scientists from Case Western Reserve University (CWRUL) has used carbon nanotubes to overcome these obstacles, reporting their findings in Scientific Reports. The authors, led by Dominique M. Durand, Ph.D., Director of the Neural Engineering Center and El Lindseth Professor of Biomedical Engineering, Neurosciences, Physiology and Biophysics at CWRU, fabricated yarn made of carbon nanotubes that was 10 to 20 µm in diameter. The yarn was then used to create electrodes, which were implanted into rats to monitor activity of the glossopharyngeal and vagus nerves.

The authors found that they could use the implants to monitor nerve activity under conditions of hypoxia and stomach distention. They report that the success of their experiments likely derives from the similarity of the nanotube yarn to the actual neural tissue surrounding the implant. The implants are a long way from being tried in humans, but the large number of functions controlled by just these two nerves indicates that such implants could find use in an enormous number of diseases.

Better Screening of Nanoparticle Delivery

As we discussed last week, the development of gene-based therapies is hindered by the sheer size of the human genome. The immense volume of information involved can quickly become difficult to manage, so one way in which scientists “keep track” of genetic information during the process of introducing new genetic material into an organism is DNA barcoding. This process attaches a small piece of DNA to the gene being studied; if and when the gene causes cells to replicate, these cells will bear the barcode, thus allowing the observer to be certain of the gene identities the whole time.

Seeking to determine whether DNA barcoding of lipid nanoparticles for injection into living models would outperform in vitro testing, a team of investigators at Georgia Tech and Emory University conducted a comparison of the two techniques, reporting their findings in Nano Letters. The authors, led by James Dahlman, Ph.D., Assistant Professor of Biomedical Engineering at GT/Emory, found that in vitro testing did not predict in vivo delivery. Further, they were able to track several dozen barcodes delivered by nanoparticles to eight different cell lines.

The authors believe that their technique, which they call JOint Rapid DNA Analysis of Nanoparticles (JORDAN), is superior to in vitro screening of nanoparticles to predict successful transplantation. They are offering JORDAN online as open source software so other scientists can use the technology to more accurately screen nanomaterials.

Synthetic Biologists Create Gene Circuits

Among the many types of molecules that regulate genetic expression in the body are microRNAs, non-coding strands of RNA that are responsible for gene silencing and other forms of gene expression regulation. The ability to harness and control the functions of microRNAs could have important implications for disease prevention and treatment.

In a recent article in Systems Biology and Applications, researchers at the University of Texas, Dallas, report on their engineering of a microRNA-based genetic circuit and its deployment in living cells. They created the circuit using strands of RNA from a variety of organisms, including viruses and jellyfish. The authors, led by Leonidas Bleris, Ph.D., Associate Professor of Bioengineering at UT Dallas, used the circuits to better understand how microRNAs change gene expression under different conditions.

More importantly, the authors found that their circuit had the ability to outproduce types of gene expression, which decreased as the number of gene replications increased.  The authors believe that their discoveries could have applications in a number of genetic disorders.

Discouraging Smoking at the Level of the Brain

Cigarette smoking is the single greatest contributor to negative health outcomes in the population.  Nicotine addiction often appears during the teenage years, and aggressive advertising has been used for the last couple of decades to encourage people to quit smoking and younger people not to start. Despite the widespread use of advertising to change human behavior, remarkably little is known on how the brain responds to advertising messages.

Danielle S. Bassett, Ph.D., Eduardo D. Glandt Faculty Fellow and Associate Professor of Bioengineering at Penn, recently collaborated with faculty from Penn’s Annenberg School of Communication to determine the neuroscience underlying this outcome. The collaborators showed graphic warning labels to a cohort of smokers while they were subjected to functional magnetic resonance imaging, which images brain activity during specific tasks. They found that smokers whose brains showed greater coherence between regions in the valuation network were more likely to quit smoking. Determining why these brain regions acted as they did could yield even more effective smoking-cessation messaging.

Purdue Startup Working to Expand MRI

Engineers at Purdue, including Zhongming Liu, Ph.D., Assistant Professor of Biomedical Engineering and Electrical and Computer Engineering, have cofounded at startup company, called MR-Link, to develop and produce a coin-sized device that can be inserted into MRI machines, allowing them to perform multiple scans simultaneously.

The device could be useful in reducing the amount of electromagnetic force to which patients are exposed during an MRI scan. In addition, Dr. Liu and his colleagues believe the device will cost perhaps less than a tenth of what similar devices currently cost. Given the widespread use of MRI, the device could ultimately impact how a number of diseases and disorders are diagnosed and tracked.

Shoddy Science Uncovered in New Research

by Linda Tunesi

shoddy science
Konrad Kording, Ph.D.

Konrad Kording, professor in the Department of Bioengineering, and colleagues have a new technique for identifying fraudulent scientific papers by spotting reused images. Rather than scrap a failed study, for example, a researcher might attempt to pass off images from a different experiment to give the false impression that their own was a success.

Kording, a Penn Integrates Knowledge (PIK) Professor who also has an appointment in the Department of Neuroscience in Penn’s Perelman School of Medicine, and his collaborators developed an algorithm that can compare images across journal articles and detect such replicas, even if the image has been resized, rotated, or cropped.

They describe their technique in a paper recently published on the BioRxiv preprint server.

“Any fraudulent paper damages science,” Kording says. “In biology, many times fraud is detected when someone looks at a few papers and says ‘hey, these images look a little similar.’ We reckoned we could make an algorithm that does the same thing.”

“Science depends on building upon other people’s work,” adds Daniel Acuna, lead author on the paper, and a student in Kording’s lab at Northwestern University at the time the study was conducted. “If you cannot trust other people’s work, the scientific process collapses and, worse, the general public loses trust in us. Some websites were doing this, anonymously, but at a painstakingly slow rate.” Acuna is now an assistant professor in the School of Information Studies at Syracuse University.

While much of Kording’s work focuses on using data science to understand the brain, he is also curious about the process of research itself, or, as he puts it, “the science of science.” One of the Kording lab’s previous projects closely analyzed common methods of neuroscience research, and another turned a mirror on itself, describing how to structure a scientific paper.

Continued at the Penn Engineering Medium blog.

Thouron Award for Bioengineering Major Nicholas Stiansen

Nick Stiansen

Nicholas Stiansen, a senior Bioengineering major at Penn, is one of eight students and alumni receiving a Thouron Award. Nick will receive a full scholarship to cover tuition and fees, plus a stipend of £19,500 (approximately $27,000). He is still awaiting decisions from graduate programs, but his first choice is to study at Imperial College London (ICL) in the United Kingdom.

Named for Sir John Thouron, a British aristocrat and husband of Esther Driver du Pont, great-granddaughter of Alfred V. du Pont, founder of the chemical company, the Thouron Award is given to graduates of Penn and of universities in the U.K. Each year, a small number of Penn students receives awards, as well as a similar number of British students.  Previous awardees include: the current nominee to head the SEC, Jay Clayton; Pulitzer-prize winning novelist Jennifer Egan; and John J. Leonard, Professor of Mechanical and Ocean Engineering and Samuel C. Collins Professor at MIT.

In addition to majoring in Bioengineering, Nick works as an undergraduate research assistant in the Spine Pain Research Laboratory of Beth Winkelstein, Vice Provost for Education and Professor, and a teaching assistant for BE 310, the second half of the junior year bioengineering lab series. Plus, he holds or has held positions with the Engineering Deans’ Advisory Board and the Biomedical Engineering Society, and he is involved in the Theta Tau Professional Engineering Fraternity and Tau Beta Pi Engineering Honor Society. If he enrolls at ICL, Nick intends to study in the university’s Master’s program in Medical Device Design and Entrepreneurship.

“I am honored to be named a Thouron Scholar,” Nick says, “and I am extremely excited to continue my graduate studies in the U.K. I am eager to immerse myself in a new, vibrant culture and learn about medical technology from an entirely new perspective. This experience will be integral towards achieving my long-term goal of developing the next wave of innovative and accessible medical devices.”

Week in BioE (March 7, 2018)

Online Tool for 3D Visualization of Gene Mutations

DNA inside cell nuclei undergoing the process of mitosis.

Fifteen years ago marked a major milestone in the Human Genome Project: scientists successfully sequenced all of the base pairs in our 23 sets of chromosomes. Following this accomplishment, researchers assembled generations of mathematical models to understand how gene mutations result in disease. A key barrier in developing these models is the size of genome itself: a single human genome requires approximately 2 GB of storage, and many studies examine thousands of genomes to detect changes in a small number of patients. Both processing these large datasets and efficiently storing them create challenges. Making these model predictions accurate and complete is another challenge.

Scientists collaborating among several universities on three continents developed an online computational tool to help overcome these barriers. The scientists, who include Bernhard Palsson, Ph.D., Galletti Professor of Bioengineering at University of California, San Diego, as one of the lead authors, report on the resource in a recent issue of Nature Biotechnology.

Called Recon3D, the new resource provides a metabolic network model using approximately 17% of known human genes. The model combines data on the genes, metabolites, proteins, and metabolic reactions for human metabolism. In addition, as the model’s name implies, Recon3D accounts for the physical structure of model components, imporving significantly on past models that relied on linear, two-dimensional models. Although the model still has 83% of genes left to incorporate, it could ultimately unravel some of the mysteries underlying virtually any disease with a genetic cause, from inborn errors of metabolism to cancer.

Bioengineering for Refugees

As the war in Syria enters its seventh year, at least five million refugees have left the country to seek asylum elsewhere. Roughly 20% of the refugees are now in Lebanon, where many reside in refugee camps.  Although these refugees are now much safer than before, even in the best of circumstances, the conditions in refugee camps can compromise health and wellness.

Engineering can offer relief for some of these conditions. A three-week course offered in January at the American University of Beirut, co-designed and taught by Muhammad Zaman, Ph.D., Professor of Biomedical Engineering at Boston University, and entitled “Humanitarian Engineering: Designing Solutions for Health Challenges in Crises,” had students devising solutions to the issues facing these refugees.

Among the ideas generated by the students was “3D Safe Water” – a device designed to detect the contamination of water, decontaminate it, and deploy the technology in low resource settings. The device uses sensors to detect contamination and chlorine to decontaminate. With water-borne diseases taking an especially hard toll on camps like these, the device could significantly improve living conditions for refugees.

Placenta on a Chip

Organ-on-chip technologies use microfluidics to model organs or organ systems. So far, engineers have developed chip-based models of the lungs, heart, and kidneys, as well as the circulatory system.

The most recent addition to the organ-on-chip family is the placenta-on-a-chip, developed by Dan Huh, Ph.D., Wilf Family Term Assistant Professor of Bioengineering at the University of Pennsylvania. Modeling the organ that mediates and communicates between a pregnant woman and the fetus, Dr. Huh created a chip to study how drugs move from the bloodstream of the mother to the fetus. With this knowledge, one could determine more safely and more accurately how drugs taken by the mother can affect a pregnancy.

People and Places

Two colleges have announced new biomedical engineering programs.  George Fox University, a Christian college in Oregon, will offer a BME concentration for engineering majors starting this fall. On the other side of the country, Springfield Technical Community College in western Massachusetts will offer a two-year associate’s degree in BME technology.

The University of Arizona, in cooperation with the City of Phoenix, will launch a new medical technology accelerator program, to be called InnoVention. It will be located on UofA’s Phoenix Biomedical Campus. Frederic Zenhausern, PhD, MBA, Professor of Basic Medical Sciences and Director of the Center for Applied NanoBioscience and Medicine at Arizona, is among the people leading the effort.

Finally, Distinguished Professor Craig Simmons of the University of Toronto’s Institute of Biomaterials and Biomedical Engineering is among 10 awardees sharing a $3.5 million grant (approximately $2.7 million in U.S. currency) for the development of medical devices and technologies. Dr. Simmons, a former postdoc at Penn, will use his funding to investigate the use of stem cells to repair congenital heart defects in infants.

Podcast: Wellness in Graduate School

wellnessPenn Bioengineering PhD students Meagan Ita and Michael Magaraci join Sally and Kayla from Double Shelix to discuss wellness in graduate school. Going in, graduate students expect they’ll have to work hard, but most students are unprepared for the mental anguish that grad school can induce – especially when experiments aren’t going well, or when we compare to themselves to others’ successes. Meagan and Mike discuss the importance of actively taking charge of your own wellness, and what departments can do to support student wellness. Things also get real with discussions of the value therapy and/or medicine to address depression or anxiety, and we sound off on the harm caused by toxic mentor/mentee relationships. If you’ve struggled with being well, want to stay well, or want to support others on their journey to wellness, check this out!


Professor Arjun Raj’s blog – truly, a font of knowledge
UC Berkeley graduate student wellbeing survey results​
Fixyourrun.com and Philly Surge Running
Meagan’s Lab, the Spine Pain Research Lab
Mike’s Lab, the Chow Lab
7 Habits of Highly Effective People by Stephen Covey
Headspace – a meditation app
The Power of Now by Eckhart Tolle
The Subtle Art of Not Giving a F*ck  by Mark Manson

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Feedback? They love it! – doubleshelixpodcast@gmail.com