In the latest podcast from Double Shelix and produced by Penn Bioengineering, Julea Vlassakis, mentorship expert and Bioengineering PhD Candidate, joins Kayla and Sally to talk mentoring in academia and beyond. Learn how to establish productive mentor/mentee relationships and cultivate the next generation of scientists — yourself included! Beginning mentees and seasoned mentors alike will learn something new from Julea’s wisdom. Discover strategies for breaking out of the cycle of mediocre mentorship, how to deal with underperforming mentees, tips for cultivating a community of mentors within your field, and how to get a mentor to step up for your career goals. Stay tuned to the end for Julea’s list of mentor and mentee responsibilities — supported by peer-reviewed literature, of course! This is next-level mentorship.
Spoiler alert: Mentor/Mentee Responsibility Number Zero is “Establish clear goals and expectations!”
As new technologies emerge, whether related to health care, artificial intelligence, or other aspects of society, they bring with them new ethical challenges.
The topic of the future of technology was front and center on day three of the Penn Teach-in March 18-22. The series of free public events convened by the faculty senate aims to bring the academic community together with the broader community to engage in wide-ranging discussions on topics of social importance.
Robots have come a long way in the past few decades, but we’re still a long way off from one that can move like animals and humans. To date, programming movement for robots uses instructions to individual mechanical parts to mimic muscle activity. The main challenge is that the number of small, coordinated muscle movements in walking requires an enormous number of instructions to program. In addition, these instructions are often not very good at accommodating for different surfaces or changing landscapes.
One way around this issue might be to focus less on “muscles” and more on neurons for creating the instructions of walking. This is the approach being taken in the lab of Francisco Valero-Cuevas, PhD, Professor of Biomedical Engineering at the University of Southern California. A recent feature at Wired magazine details their construction of a robotic cat based on a network of artificial neurons.
The USC model uses reinforcement learning, which is a system whereby neurons of the spinal cord form networks on the basis of trial and error, using random firing of neurons until motion is produced. In this way, the need for an algorithm or complicated programming is eliminated. The cat, called Kleo, is a long way off from being able to land on its feet or use a litter box, but it might give us insight into new technologies that will help people with disabilities from spinal cord injury or motor neuron disease.
Less Neuronal Flexibility With Learning
One of the primary tasks of the brain is learning, but there’s still a lot we don’t know about what happens in the brain as learning occurs. Much of the past research examined changes at the level of individual neurons to explain learning. Newer research, however, has indicated that it is more insightful to examine larger populations of neurons during tasks to get a deeper insight into how the brain learns.
Using this principle, a team of engineers and scientists collaborating between Carnegie Mellon and the University of Pittsburgh submitted rhesus monkeys to a learning task and obtained neural recordings to determine how the task affected neuron populations. Their study, led by Steven Chase, PhD, and Byron Yu, PhD, both associate professors of biomedical engineering at CMU, was published in Nature Neuroscience. Drs. Matthew Golub and Penn alumnus Aaron Batista were also coauthors.
Contrary to previous thinking, the authors found the brain is less flexible during learning tasks. In part, this lack of flexibility explains why certain tasks take a long time to learn. The authors state that it remains unclear whether the brain changes detected occur at the level of the cortex or subcortex, so additional research will be necessary.
Preventing Bad Science
Academic science remains largely an environment of publish or perish, and this pressure on scientists has unfortunately resulted in an increased incidence of academic fraud. One form of fraud is recycling old images from past publications of successful experiments while presenting the results of newer research.
Recognizing that data science could be used to detect such episodes of fraud, Konrad Kording, PhD, a Penn Integrates Knowledge (PIK) Professor with appointments in the Departments of Bioengineering and Neuroscience, and his collaborators developed an algorithm that can compare images across journal articles and detect whether images have been repeated across two articles, even if they have been resized, rotated, or cropped. They describe their technique in a paper recently published on the BioRxiv preprint server. Among the next moves the authors are considering is licensing the algorithm to academic publishers, with the caveat that the possibility of false positive accusations has not been eliminated.
People and Places
Congratulations go to Judy Cezeaux, PhD, who has been named Dean of the Arkansas Tech University College of Engineering and Applied Sciences. A biomedical engineer with degrees from Carnegie-Mellon and Rensselaer Polytechnic Institute, Dr. Cezeaux was most recently chair of the Department of Biomedical Engineering at Western New England University.
Growing up and living in rural, upstate New York, there are a lot of things that stay off of your radar. I was always interested in science, technology, and medicine, but had very little exposure to the world of engineering until about four years ago.
As a competitive tennis player, my drive to be a college athlete steered much of my college search. Additionally, I knew that I wanted to go to a small school and to make an impact on the community, leading me to seek out liberal arts schools. I was recruited to Hobart and William Smith Colleges (HWS) in the Finger Lakes region of New York, and was excited to jump into the scientific community there. Though it was strong in traditional sciences, HWS did not have an engineering program. I majored in biology and was a pre-med student until I realized it was not for me. Trying my hand in molecular genetics research didn’t seem to click either, so I took a step away from science.
I loved being part of such an intimate community at HWS and wanted to give back to the school, so after I graduated I worked full-time for the admissions department and assistant-coached for men’s tennis for two years. I knew this was only temporary; I missed working in STEM!
After months of exploration, I discovered bioengineering — the perfect combination of biology, medicine, and technology. I was ready for the career switch and excited at the possibility. After applying to several schools with limited familiarity of what I was up against, University of Pennsylvania accepted me into the master’s program and I could not turn down the opportunity. Additionally, my brother was accepted into the Robotics Master’s program at the same time! As one can imagine, this was particularly exciting for my parents, as their years of love and support resulted in two of their children attending excellent programs together.
Every 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!
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!
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.
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
Last 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.”
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!”
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.
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.
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.”