Tag: big data

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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.

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Week in BioE (February 28, 2019)

by Sophie Burkholder

Louisiana Tech Sends First All-Female Team to RockOn

A team of faculty and students from Louisiana Tech University will participate in RockOn, a NASA-sponsored workshop on rocketry and engineering. Mechanical Engineering Lecturer Krystal Corbett, Ph.D., and Assistant Professor of bioengineering Mary Caldorera-Moore, Ph.D., will work together to lead the university’s first team of three all-female students at the event. At the program, they will have the chance to work on projects involving components of spacecraft systems, increasing students’ experience in hands-on activities and real-world engineering.

Refining Autism Treatments Using Big Data

Though treatments like therapy and medication exist for patients with autism, one of the biggest challenges that those caring for these patients face is in measuring their effects over time. Many of the markers of progress are qualitative, and based on a given professional’s opinion on a case-by-case basis. But now, a team of researchers from Rensselaer Polytechnic Institute (RPI) hopes to change that with the use of big data.

Juergen Hahn, Ph. D., and his lab recently published a paper in Frontiers in Cellular Neuroscience discussing their findings in connecting metabolic changes with behavioral improvements in autistic patients. Their analysis looks for multiple chemical and medical markers simultaneously in data from three distinct clinical trials involving metabolic treatment for patients. Being able to quantitatively describe the effects of current autism treatments would revolutionize clinical trials in the field, and lead to overall better patient care.

Penn Engineers Can Detect Ultra Rare Proteins in Blood Using a Cellphone Camera

One of the frontiers of medical diagnostics is the race for more sensitive blood tests. The ability to detect extremely rare proteins could make a life-saving difference for many conditions, such as the early detection of certain cancers or the diagnosis of traumatic brain injury, where the relevant biomarkers only appear in vanishingly small quantities. Commercial approaches to ultrasensitive protein detection are starting to become available, but they are based on expensive optics and fluid handlers, which make them relatively bulky and expensive and constrain their use to laboratory settings.

Knowing that having this sort of diagnostic system available as a point-of-care device would be critical for many conditions — especially traumatic brain injury — a team of engineers led by Assistant Professor in the Department of Bioengineering, David Issadore, Ph.D., at the University of Pennsylvania have developed a test that uses off-the-shelf components and can detect single proteins with results in a matter of minutes, compared to the traditional workflow, which can take days.

Read the full story on Penn Engineering’s Medium blog.

Treating Cerebral Palsy with Battery-Powered Exoskeletons

Cerebral palsy is one of the most common movement disorders in the United States. The disorder affects a patient’s control over even basic movements like walking, so treatments for cerebral palsy often involve the use of assistive devices in an effort to give patients better command over their muscles. Zach Lerner, Ph.D., is an Assistant Professor of Mechanical Engineering and faculty in Northern Arizona University’s Center for Bioengineering Innovation whose research looks to improve these kinds of assistive devices through the use of battery-powered exoskeletons.

Lerner and his lab recently received three grants, one each from the National Institute of Health (NIH), the National Science Foundation (NSF), and the Arabidopsis Biological Resource Center, to continue their research in developing these exoskeletons. Their goal is to create devices with powered assistance at joints like the ankle or knee to help improve patient gait patterns in rehabilitating the neuromuscular systems associated with walking. The team hopes that their work under these new grants will help further advance treatment for children with cerebral palsy, and improve overall patient care.

People & Places

David Aguilar, a 19-year-old bioengineering student at Universitat Internacional de Catalunya made headlines recently for a robotic prosthetic arm that he built for himself using Lego pieces. Due to a rare genetic condition, Aguilar was born without a right forearm, a disability that inspired him to play with the idea of creating his own prosthetic arm from age nine. His design includes a working elbow joint and grabber that functions like a hand. In the future, Aguilar hopes to continue improving his own prosthetic designs, and to help create similar versions of affordable devices for other patients who need them.

This week, we would like to congratulate two recipients of the National Science Foundation’s Career Awards, given to junior faculty that exemplify the role of teacher-scholars in their research. The first recipient we’d like to acknowledge is the University of Arkansas’ Kyle Quinn, Ph.D., who received the award for his work in developing new image analysis methods and models using the fluorescence of two metabolic cofactors. Dr. Quinn completed his Ph.D. here at Penn in Dr. Beth Winkelstein’s lab, and received the Solomon R. Pollack Award for Excellence in Graduate Bioengineering Dissertation Research for his work.

The second recipient of the award we wish to congratulate is Reuben Kraft, Ph.D., who is an Assistant Professor in Mechanical and Biomedical Engineering at Penn State. Dr. Kraft’s research centers around developing computational models of the brain through linking neuroimaging and biomechanical assessments. Dr. Kraft also collaborates with Kacy Cullen, Ph.D., who is a secondary faculty member in Penn’s bioengineering department and a member of the BE Graduate Group faculty.

Finally, we’d like to congratulate Dawn Elliott, Ph.D., on being awarded the Orthopaedic Research Society’s Adele L. Boskey, PhD Award, awarded annually to a member of the Society with a commitment to both mentorship and innovative research. Dr. Elliott’s spent 12 years here at Penn as a member of the orthopaedic surgery and bioengineering faculty before joining the University of Delaware in 2011 to become the founding director of the bioengineering department there. Her research focuses primarily on the biomechanics of fibrous tissue in tendons and the spine.

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Penn Engineers Develop “WorMotel”

The roundworm C. elegans is one of the most important model organisms in biological research. With a transparent, millimeter-long body containing only about a thousand cells and a lifespan of a few weeks, there is no better way of deciphering the role of a given gene on a living creature’s anatomy or behavior. In addition, many of the genes discovered in the worm have been shown to have similar roles in other animals and humans.

In the era of big data, however, a single worm isn’t enough. Thousands upon thousands of individual organisms are necessary to compare many different genes and ensure the reliability of experimental results.

Engineers at the University of Pennsylvania have taken strides to make this type of high-throughput experiment feasible by developing a system they have dubbed “the WorMotel.” To demonstrate its effectiveness, the researchers have studied the role of a set of mutations and stress-inducing drugs on the aging of 1,935 of these organisms, specifically, what percentage of their lifespans they remain healthy and active.

The WorMotel system features index-card-sized plates made out of a transparent polymer. Each plate features 240 individual wells, in which a single worm lives its entire life. Automated systems keep them fed and stimulated while machine vision algorithms track and record their behavior.

The WorMotel system is also designed to be highly scalable. Robotic carousels can automatically swap hundreds of WorMotel plates in and out of analysis chambers, studying up to 57,600 worms in a single experiment. 

WorMotel
Christopher Fang-Yen, Ph.D.

The study, published in the journal eLife, was led by Christopher Fang-Yen, Wilf Family Term Assistant Professor in Bioengineering in Penn’s School of Engineering and Applied Science, and Matthew Churgin, a former graduate student (now a postdoctoral fellow) in his lab. They collaborated with David Raizen, an Associate Professor of Neurology in Penn’s Perelman School of Medicine. Former Fang-Yen lab members Sang-Kyu Jung, Chih-Chieh (Jay) Yu, and Xiangmei Chen also contributed to the research.

 

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Week in BioE (July 20, 2017)

science
Adenocarcinoma of the pancreas, stained and viewed under a microscope.

How smartphones reveal the world of physical activity

We all know lack of exercise adversely affects our health. Policy experts often cite that exercise is such an infrequent part of people’s lives that it now constitutes a public health crisis. However, we never had a global view on how physical activity differs among all of us.

In an article recently published in Nature, scientists used smartphones to collect data on how much variation occurs in the daily activity of people from more than 100 countries.  Bioengineering professor Scott Delp and his team from Stanford used smartphones to collect 68 million days of physical activity from 717,527 people living in 111 countries.

Some of the conclusions made intuitive sense, which is always good when dealing with large data sets. For example, inactivity was strongly predictive of obesity, and this correlation was stronger in women than in men. In addition, people walked more in countries where the terrain was easier to navigate. When people were more physically active in a country, the differences in obesity rates between men and women decreased. All of this means that if it is easier to walk, people will walk, and the gender disparity in activity will shrink. Geographic data also produced interesting findings, with East Asian countries (China and Japan) walking the most, and countries near the equator walking less.  Perhaps the most significant finding is the importance of the activity gap within a country’s population, defined as the difference between highly active and inactive individuals within a country. The larger the gap, the higher likelihood for high obesity rates.  Unfortunately, the US ranks among the highest in activity gap among its population and, in turn, among the highest in national obesity rates.

While we all ponder little tricks to make us walk more (at Penn we schedule classes across campus to make the professors get up at least once a day), other work is making the task of climbing stairs easier.  Reporting in PLOS One, Lena Ting and her team from Georgia Tech developed energy-conserving stairs, using springs that store and release energy when the user ascends. Their design means that someone can save 40% energy going up their flight of stairs when compared to the traditional design. Innovations like these could be a real help to people recovering from surgeries or with age-related joint deterioration.

Networking a human

As we start to unleash the power of smartphones on health and wellness, many predict the next disruption is networking inexpensive monitoring technologies together for a single person via their smartphone. One main benefit of creating a ‘networked human’ is to monitor an individual continuously for the earliest signs of health trouble, rather than waiting for the individual to experience a significant health episode (e.g., heart attack) and unleash the powerful (but expensive) army of technologies and people for saving their life. A recent symposium was held at Northwestern University discuss the future of wearable electronics in this future. Inevitably, this will evolve the Internet of Things (IoT) into the ‘Internet of Me’ for health technologies. John Rogers of Northwestern gave a presentation showing the wearable wireless electronics he developed to monitor bodily functions in babies. The adhesive devices, which resemble temporary tattoos, are far more comfortable than many monitoring devices. Other presentations at the symposium showcased technologies for monitoring concussion, cellphone apps to facilitate psychotherapy, and more intuitive touch screens for electronics.

A Blood Test for Early Pancreatic Cancer

Pancreatic cancer is one of the deadliest cancers because it is usually only detected after it has become too advanced to treat efficaciously. However, a collaboration between Penn and Mayo Clinic scientists may have made a key advance in mitigating this threat.

A team led by Kenneth S. Zaret, Ph.D., of Penn’s Institute for Regenerative Medicine reports in Science Translational Medicine that they were able to identify thrombospondin-2, a protein, as a biomarker of pancreatic cancer. Most impressively, plasma measurements of the protein detected cancer in patients in stage I of the disease, when it can still be treated surgically. The predictive power of the biomarker test increased significantly when combined with measurements of a previously identified marker, cancer antigen 19-9, to detect pancreatic cancer at a much earlier stage.

People in the News

Our colleagues at Carnegie Mellon named a new chair of their Department of Biomedical Engineering: Bin He, Ph.D.. His appointment begins February 1, 2018. Closer to home, the Rutgers Biomedical Engineering named David I. Shreiber as its new chair. Dr. Shreiber earned his Ph.D. in Bioengineering from Penn in 1998. Congratulations to Drs. He and Shreiber!

Speaking of Penn alums, we’d like to congratulate Dr. Spencer Szczesny, who was hired as a new assistant professor at Penn State to start in the fall 2017 semester. We’re very proud of Spencer and wish him the best of luck.

Last not but not least, if you’ve flown in or out of Washington’s Dulles Airport recently, you might have seen the exhibit Life: Magnified, selections of which are available online. One of the images featured, showing skin cancer cells connected by actin, a normally occurring protein that also facilitates cancer metastasis, was created by Dr. Catherine Galbraith, who earned her BS (1986) and MS (1985) in Penn Bioengineering. Congratulations to Cathy for such wonderful visibility!