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News Release

New drug screening method answers why Alzheimer's drugs fail, suggests new targets

January 27, 2022 -- By analyzing disease mechanisms in human neurons, researchers led by the University of California San Diego developed a new method to screen drugs for treating Alzheimer’s disease. Their work sheds light on why Alzheimer’s drugs so far have been ineffective at curing or reversing the disease and identifies new targets for drug development.

The findings, reported in a paper published Jan. 27 in Alzheimer’s & Dementia: The Journal of the Alzheimer’s Association, could help pave the way for radically new therapeutic approaches to treating Alzheimer’s.

Drug development for Alzheimer’s has long been driven by the hypothesis that amyloid plaques—formed by the buildup of amyloid-beta proteins in the brain—are what kill neurons and cause Alzheimer’s. As a result, many research efforts have focused on designing drugs that clear out these plaques.

“But this approach has not led to a cure or improved dementia in patients. Sometimes it has made the disease worse,” said senior author Shankar Subramaniam, a professor of bioengineering at the UC San Diego Jacobs School of Engineering.

To understand why, Subramaniam and his collaborators developed a drug screening method that looks at what disease mechanisms, or endotypes, change in patients’ neurons as a result of treatment. The most widely studied Alzheimer’s endotype is amyloid plaque formation. But there are other endotypes—reported for the first time by Subramaniam and colleagues in a previous study—that also warrant attention. These include de-differentiation of neurons to an earlier “non-neuron” cell state; suppression of neuronal genes; and loss of synaptic connections.

“This is a new test for measuring whether an Alzheimer’s drug works,” said Subramaniam. “The key here is that we are using the endotypes that we discovered to see how current drugs fail. When drugs interact with human neurons, what endotypes do the drugs fix, and what endotypes do they not fix in the process?”

What’s also special about this method is that it screens drugs on actual patient cells. “The power of this is that you can do precision medicine and have a good model system to study Alzheimer’s,” said Subramaniam.

The method involves taking human induced pluripotent stem cells derived from patients with familial Alzheimer’s disease, which is a hereditary form of Alzheimer’s, and transforming them into neurons. The researchers treat these neurons with drugs and use next generation sequencing techniques to evaluate what endotypes change before and after treatment. The researchers also perform this drug screen on neurons derived from healthy individuals as a control experiment.

In this study, the researchers screened two experimental Alzheimer’s drugs that were designed to reduce or prevent growth of amyloid plaques. One was a drug candidate developed by Eli Lilly, called semagacestat, which had failed late-stage clinical trials. The other was a drug candidate developed by Subramaniam’s collaborator and co-author on the study, Steven Wagner, who is a professor of neurosciences at UC San Diego School of Medicine.

The researchers found that the drugs only fix some endotypes, such as the formation of amyloid plaques. The drugs also partly fix the de-differentiation endotype, by triggering “non-neuron” cells to transform back into neurons. However, this transformation is not complete, noted Subramaniam, because the neurons still lack synaptic connections and therefore cannot communicate with each other.

“Now we have a prescription for what endotypes to target during drug screening,” said Subramaniam. “What we are seeing is that fixing amyloid plaque formation does not reverse the disease in any way. It turns out that this endotype is way downstream, so it’s too late. Once neurons de-differentiate into non-neurons, they lose their synaptic connections, which leads to loss of memory and cognition and as a consequence, dementia.”

”I am very excited to use these novel screening strategies for the Alzheimer’s drugs that are being developed in my laboratory,” added Wagner. “In my experience in industry and now academia, this is the first effort to use multiple endotypes for overcoming the failures of drugs targeted only at amyloid plaques.”

Next, the researchers will evaluate their drug screening method on brain organoids. “We want to take this a step further to screen drugs on more realistic tissues, not just neurons in a dish,” said Subramaniam. The team will also work on developing new Alzheimer’s drug candidates and screening them with their method.

Paper: “Endotype reversal as a novel strategy for screening drugs targeting familial Alzheimer’s disease.”

This study was supported by the Alzheimer’s Association New Investigator Research Award (NIRG-14-322164), the National Institutes of Health (grants P50 AGO5131, U01 NS 074501-05, U01 AG048986, R01 LM012595, U01 CA198941, U01 DK097430, R01 DK109365, R01 HD084633 and R01 HL108735), the National Science Foundation (grant STC CCF-0939370), the Joan and Irwin Jacobs Endowment; the Cure Alzheimer’s Fund (CAF), the Veterans Affairs (RR&D 1I01RX002259), and the Chen Foundation.

Two Jacobs School Researchers Named AAAS Fellows

Olivia Graeve (left) and Shirley Meng. 

Jan. 26, 2022 -- Two Jacobs School of Engineering material scientists have been elected as fellows of the American Society for the Advancement of Science), the largest general science organization in the United States and publisher of the journal Science.

 Professor Shirley Meng, a batteries expert, and Professor Olivia Graeve, an expert on materials for extreme environments and an advocate for engineering education for underrepresented students, join a total of 564 other scientists and physicians across the country recognized this year for work deemed scientifically or socially distinguished, advancing science or its applications.

Four other UC San Diego researchers also have been recognized: Dr. Gary Firestein and Dr. Victor Nizet from UC San Diego Health Sciences, Brian Palenik from the Scripps Institution of Oceanography and Michael Kalichman, who unti recently headed the campus’ research ethics program. 

Shirley Meng
Shirley Meng, an adjunct professor in the UC San Diego Department of Nanoengineering, was cited for "innovative and original discovery of interfacial sciences in energy storage materials that has led to improved battery technologies." Her research group – the Laboratory for Energy Storage and Conversion (LESC) – focuses on functional nano and micro-scale materials for energy storage and conversion. Her research focus includes the design, synthesis, processing, and operating characterization of energy storage materials in advanced rechargeable batteries; new intercalation materials for sodium ion batteries; and advanced flow batteries for large scale storage on the grid. 

Olivia Graeve

Olivia Graeve, a professor in the Department of Mechanical and Aerospace Engineering, was cited for "distinguished contributions to the field of material science, particularly materials for extreme environments and for leadership in engineering education for underrepresented students." Her area of research focuses on the design and processing of new materials for extreme environments, including extremes of temperature, pressure, and radiation. She heads the CaliBaja Center for Resilient Materials and Systems, a cross-border collaboration in materials science research and manufacturing. Graeve also spearheads the CaliBaja Education Consortium, which brings together high schools and higher education institutions on both sides of the U.S.-Mexico border. Graeve also earned a bachelor's degree in structural engineering from UC San Diego in 1995. 

New fellows are nominated by the steering group of their respective AAAS sections, by three existing fellows or by AAAS’s chief executive officer. Each steering group reviews the nominations of individuals within its respective section and a final list is forwarded to the AAAS Council, which votes on the aggregate list.

News Obituary: Remembering Paul A. Libby, founding
UC San Diego faculty member

Paul A. Libby, a UC San Diego founding faculty member, passed away on Nov. 2. 2021 at the age of 100 in La Jolla, Calif.

Jan. 31, 2022 -- Paul A. Libby, Professor Emeritus in the Department of Mechanical and Aerospace Engineering  (MAE) at the University of California San Diego, passed away on Nov. 2, 2021, at the age of 100 in La Jolla, Calif. An international expert in turbulence and combustion, Libby was recruited in 1964 by Professor Stanford “Sol” Penner as one of 10 founding faculty members of the Department of Applied Mechanics and Engineering Science (AMES) at the newly formed campus in La Jolla.

During his 65 years of research in the field of aerodynamics, Libby made foundational contributions to the fields of supersonic and hypersonic flight, with important applications that include improved heat protection of re-entry vehicles through ablative shielding. He collaborated in the fields of fluid mechanics and combustion with an impressive array of prominent scientists in the United States and abroad. He also served as the U.S. member of the Fluid Dynamics Panel of the Advisory Group for Aerospace Research and Development (AGARD), an agency of NATO, and on other U.S. governmental panels.  

He  was elected to the National Academy of Engineering in 1999 “for contributions as a researcher, author, and educator who advanced knowledge of fluid dynamics, turbulence, and combustion through theoretical analyses.”  

Libby produced more than 200 journal publications and authored a monograph on turbulence,  publishing his last paper in 2017 with his longtime collaborators Professors Michel Champion of the University of Poitiers, France, and K.N.C. Bray of the University of Cambridge. This collaboration led, among other things, to the highly cited Bray-Champion-Libby model of turbulent combustion. In addition, the Homann-Libby flow is named after Libby for his work on the axisymmetric stagnation point flows. These contributions aid in the development of improved aircraft and missile propulsion engines as well as ground-based industrial and transportation processes.

Libby received a Guggenheim Fellowship in 1972 and a Royal Society Guest Fellowship in 1982, both to support extended stays at the Imperial College of London as a visiting researcher. 

"Beyond the impact of his own personal research, as one of the earliest faculty members in the Department, Paul played a key role in building a Department and School with deep roots in the engineering sciences, thereby providing our students with the skills they need to make critical contributions in their chosen application areas; as a result, his legacy will continue to be felt for many years to come,” said George Tynan, chair of the UC San Diego Department of Mechanical and Aerospace Engineering. 

At UC San Diego, Libby held various administrative positions, including Associate Dean of Graduate Affairs, Acting Dean of Graduate Affairs, Chair of the AMES Department, and Interim Dean of the Engineering Division. He taught graduate and undergraduate engineering classes and served on numerous academic committees, including the UC San Diego Design Review Board.  Throughout his career, Libby also enjoyed mentoring  graduate students and became lifelong friends with many of them. 

Libby was born on Sept. 4, 1921 in Mineola, New York. He received his degrees from the Polytechnic Institute of Brooklyn, a bachelor’s degree in aeronautical engineering in 1942 and a PhD degree in applied mechanics in 1949. Libby also worked as an apprentice engineer with Chance Vought Aircraft and served as an officer in the Navy Bureau of Aeronautics. 

In the 1950s, Libby was appointed to the faculty of the Polytechnic Institute of Brooklyn, where he became a tenured professor, collaborating  with Professor Antonio Ferri on the development of experimental supersonic and hypersonic research facilities. This effort involved an extended collaboration with Theodore Von Kàrmàn, a leading figure in 20th century aerodynamics, at the California Institute of Technology, .

Outside of his academic pursuits, Libby was an avid tennis player, retiring from tennis only in his eighties, and an excellent cook. He was a lifelong enthusiast of gardening, classical music, modern architecture, history, and politics.

A memorial organized by Libby’s family will take place from 2 to 5 p.m. Saturday, March 5, 2022 at the Ida and Cecil Green Faculty Club on the UC San Diego campus. RVSPs due by Feb. 18, 2022 at  Libbymemorial@gmail.com. Guests must be vaccinated and boosted. 

Libby was preceded in death by his wife Petrina, and is survived by his son John Libby, daughter Patricia Libby Thvedt, and numerous grand-children. The family has requested that remembrances be made in the form of contributions to the UC San Diego Foundation fund designated as “The Dr. Paul A. Libby and Petrina M.C. Libby Endowed Scholarship in Engineering at UC San Diego."  Donations may be made  online at https://giveto.ucsd.edu/giving/home/gift-referral/4e375052-6bd8-4ba3-8c70-b2ac42fde0d5/, or by calling UC San Diego Gift Processing at 858-534-4493, or mailing a check (made payable to the UC San Diego Foundation) with "Libby Endowed Scholarship (Fund No. 7230)" on the memo line to UC San Diego Gift Services, 9500 Gilman Dr. Mail Code 0940, La Jolla, CA 92093 - 0940.  

Gifts may also be made in Libby’s memory to his beloved KUSC Radio at KUSC.org





 

Computers in a Jazz Ensemble? Inventing Improvisational AI

UC San Diego Professor Shlomo Dubnov is among the researchers who recently received a European Research Council Advanced Grant to teach computers how to improvise, musically.

January 20, 2022-- Go to any jazz club and watch the musicians. Their performances are dynamic and improvisational; they’re inventing as they go along, having entire conversations through their instruments. Can we give computers the same capabilities? 

To answer that question, University of California San Diego Professor Shlomo Dubnov, who has appointments in the departments of Computer Science and Engineering and Music and UC San Diego’s Qualcomm Institute, and Gérard Assayag, a researcher at the Institute for Research and Coordination in Acoustics/Music in Paris, recently received a €2.4 million (around $2.8 million) European Research Council Advanced Grant. The grant will fund Project REACH: Raising Co-creativity in Cyber-Human Musicianship, which is teaching computers how to improvise, musically.

The Conversation

Almost all human interactions are improvisational, with each party modifying their responses based on real-time feedback. But computers, even with the most sophisticated AI, are constrained by their programming. And while chatbots and other online tools are getting better at conversing fluidly, they can hardly improvise on the fly.

“There are various machine learning applications today to create art,” said Dubnov. “The question is: Can we go beyond these tools and generate some sort of autonomous creativity?”

In this scenario, computers would do more than learn musical styles and replicate them. They would innovate on their own, produce longer and more complex sounds and make their own decisions based on the feedback they are receiving from other musicians.

“Not only should the human musician be interested in what the machine is doing; the machine should be interested in what the person is doing,” said Dubnov. “It needs to be able to analyze what’s happening and decide when it’s going to improvise with its human partners and when it’s going to improvise on its own. It needs agency.”

The Struggle to Define Music

The REACH project falls broadly under reinforcement learning, a form of machine learning that gives computers a sense of reward to incentivize them; however, that requires qualitative labels. For example: What makes music good?

In other words, REACH needs to teach computers an aesthetic, something humans don’t fully comprehend. Musically, what is good or bad? What makes Miles Davis’s Kind of Blue, Beethoven’s Ninth Symphony and the Beatles’ Abbey Road so engaging?

“If we produce sounds with the intent to make music, that is music,” said Dubnov. “That means that, to become musical, the computer must have its own intent.”

In a sense, the project is all about self-discovery. By teaching machines how to improvise well, the REACH group will be inventing more precise definitions of music for themselves. This all circles back to the methods behind reinforcement learning. The team will have to teach computers to make good choices. 

“That will be our greatest scientific challenge,” said Dubnov. “How do we give the machine intrinsic motivation when it’s so difficult to specify what constitutes good?” 

 

From coffee cart to educational computing platform

January 20, 2022 San Diego CA: 

In classic UC San Diego fashion, an overheard conversation at a campus coffee cart has turned into an interdisciplinary project that's making computing-intensive coursework more exciting while saving well over one million dollars so far. The effort gives UC San Diego graduate and undergraduate students – and their professors – better hardware and software ecosystems for exploring real-world, data-intensive and computing-intensive projects and problems in their courses. 

Larry Smarr UC San Diego professor of computer science
Larry Smarr, Distinguished Professor Emeritus, Department of Computer Science and Engineering at the UC San Diego Jacobs School of Engineering.

It all started while UC San Diego computer science and engineering professor Larry Smarr was waiting for coffee in the "Bear" courtyard at the Jacobs School of Engineering a little more than three years ago. In line, Smarr overheard a student say, "I can't get a job interview if I haven't run TensorFlow on a GPU on a real problem."

While this one student's conundrum may sound extremely technical and highly specific, Smarr heard a general need; and he saw an opportunity. In particular, Smarr realized that innovations coming out of a U.S. National Science Foundation (NSF) funded research project he leads – the Pacific Research Platform (PRP) – could be leveraged to create better computing infrastructure for university courses that rely heavily on machine learning, data visualizations, and other topics that require significant computer resources. This infrastructure would make it easier for professors to offer courses that challenge students to solve real-world data- and computation- intensive problems, including things like what he heard at the coffee cart: running TensorFlow on a GPU on a real problem.

Fast forward to 2022, and Smarr's spark of an idea has grown into a cross-campus collaboration called the UC San Diego Data Science/Machine Learning Platform or the UC San Diego JupyterHub. Through this platform, the inexpensive, high-performance computational building blocks combining hardware and software that Smarr and his PRP collaborators designed for use in computation-intensive research across the country are now also the backbone of dynamic computing ecosystems for UC San Diego students and professors who use machine learning, data visualization, and other computing- and data- intensive tools in their courses. The Platform has been widely used in every Division on campus, with courses taught in biological sciences, cognitive science, computer science, data science, engineering, health sciences, marine sciences, medicine, music, physical sciences, public health and more. See a list of Jacobs School affiliated faculty and the names of the courses they have taught using the UC San Diego Data Science/Machine Learning Platform.

It's a unique, collaborative project that leverages Federally funded computing research innovations for classroom use. To make the jump from research to classroom applications, a creative and hardworking interdisciplinary team at UC San Diego came together. UC San Diego's IT Services / Academic Technology Services stepped up in a big way. Senior architect Adam Tilghman and chief programmer David Andersen led the implementation effort, with leadership and funding support from UC San Diego CIO Vince Kellen and Academic Technology Senior Director Valerie Polichar. The project has already helped the campus avoid well over one million dollars in cloud-computing spend, according to Kellen.

Usage patterns for the UC San Diego Data Science/Machine Learning Platform. The green regions respresent available capacity for non-coursework use. 

 

Examples of the software that students are able to run on the UC San Diego Data Science/Machine Learning Platform

At the same time, the project gives the UC San Diego community tools to encourage the back-and-forth flow of students and ideas between classroom projects and follow-on research projects. 

"Our students are getting access to the same level of compte capacity that normally only a researcher using an advanced system like a supercomputer would get. The students are exploring much more complex data problems because they can," said Smarr, who was also the founding Director of the California Institute for Telecommunications and Information Technology (Calit2), a UC San Diego / UC Irvine partnership. 

Personal genomics 

One of the many professors from all across campus using the UC San Diego Data Science / Machine Learning Platform for courses is Melissa Gymrek, who is a professor in both the Department of Computer Science and Engineering and the Department of Medicine's Division of Genetics.

Her students write and run code in a software environment called Jupyter Notebooks that runs on the UC San Diego platform. "They can write code in the notebook and press execute and see the results. They can build figures to visualize data. We focus a lot more now on data visualizations," said Gymrek. 

Xuan Zhang (UC San Diego Chemistry PhD, '21) is one of the tens of thousands of UC San Diego students and young researchers who has used the UC San Diego Data Science/Machine Learning Platform extensively in courses.
Xuan Zhang (UC San Diego Chemistry PhD, '21) is one of the tens of thousands of UC San Diego students and young researchers who has used the UC San Diego Data Science/Machine Learning Platform extensively in courses.

One of the thousands of UC San Diego students who has used the platform extensively is Xuan Zhang. Through the data- and visualization- intensive coursework in CSE 284, Zhang realized that the higher order genetic structures at the center of her chemistry Ph.D. dissertation – R-Loops – could be regulated by the short tandem repeats (STRs) that are at the center of much of the research in Gymrek's lab. Without the computing-infrastructure for real-world coursework problems, Zhang believes she would not have made the research connection. 

After taking Gymrek's course, Zhang also realized that she could apply to obtain her own independent research profile on the UC San Diego Data Science / Machine Learning Platform in order to retain access to all her coursework and to keep building on it. (When Jupyter Notebooks are hosted on the commercial cloud, students generally lose access to their data-intensive coursework when the class ends, unless they download the data themselves.)

"I thought it was just for the course, but then I realized that Jupyter Notebooks are available for research, without losing access through the UC San Diego Jupyterhub," said Zhang. 

This educational infrastructure has added benefits for professors as well.

"With these Jupyter Notebooks, you can automatically embed the grading system. It saves a lot of work," said Gymrek. You can designate how many points a student gets if they get the code right, she explained. Before using this system, students sent PDFs of their problem sets which made grading more time intensive. "It was hard to go past a dozen students. Now, you can scale," said Gymrek. In fact, she has been able to expand access to her personal genomics graduate class to more than 50 students, up from a dozen before she had access to these new tools. 

Direct uploading of assignments and grades to the campus learning management system, Canvas, is also now available.

“The platform is truly transforming education. Unlike many learning technology innovations, classes in every division at UC San Diego have used the Data Science/Machine Learning Platform. Many thousands of students use it every year. It’s innovation with real impact, preparing our students in many — sometimes unexpected — fields to be leaders and innovators when they graduate,” said Polichar. 

Professors and students from all six departments at the UC San Diego Jacobs School of Engineering are making great use of the UC San Diego Data Science/Machine Learning Platform. The numbers on each stacked bar represent the number of students in that Department using the DSMLP in that quarter.

 

Courses from all six departments at the UC San Diego Jacobs School of Engineering are run on the UC San Diego Data Science/Machine Learning Platform. See a list of the courses taught on the platform by faculty affiliated with the UC San Diego Jacobs School of Engineering.

 

Commodity hardware for research and education

"If you build your distributed supercomputer, like the PRP, on commodity hardware then you can ride Moore's Law," explained Smarr. 

UC San Diego ITS senior architect Adam Tilghman poses with some of the innovative computing hardware that has opened the door to more data-intensive and computing-intensive coursework for UC San Diego students. These PCs run a wide range of leading-edge software to help students program the system, record their results in Jupyter notebooks, and execute a variety of data analytic and machine learning algorithms on their problems.
UC San Diego ITS senior architect Adam Tilghman poses with some of the innovative computing hardware that has opened the door to more data-intensive and computing-intensive coursework for UC San Diego students. These racked PCs, hosted in a San Diego Supercomputer Center machine room at UC San Diego, run a wide range of leading-edge software (earlier figure).

Following this commodity hardware strategy, Smarr and his PRP collaborators developed hardware designs where performance goes up while prices go down over time. The computational building blocks developed by the PRP, that were repurposed by UC San Diego’s ITS, are rack-mounted PCs, containing multi-core CPUs, eight Graphics Processing Units (GPUs), and optimized for data-intensive projects, including accelerating machine learning on the GPUs. These PCs run a wide range of leading-edge software to help students program the system, record their results in Jupyter Notebooks, and to execute a variety of data analytic and machine learning algorithms on their problems.

Building on this commodity hardware approach to high performance computing has allowed UC San Diego to build a dynamic and innovative "on premises" ecosystem for data- and computing- intensive coursework, rather than relying solely on commercial cloud computing services.

"The commercial cloud doesn't provide an ecosystem that gives students the same platform from course to course, or the same platform they have in their courses as they have in their research," said Tilghman. "This is especially true in the graduate area where students are starting work in a course context and then they continue that work in their research. It's that continuity, even starting as a lower division undergraduate, all the way up. I think that's one of the innovative advantages that we give at UC San Diego."

UC San Diego professors and students interested in learning more about the Data Science / Machine Learning Platform can find additional details and contact information on their website.

"I've been at this for 50 years," said Smarr. "I don't know of many examples where I've seen such a close linking of research and education all the way around, in a circle." 

This alignment of research and education feeds into UC San Diego's culture of innovation and relevance. 

"It's essential for the nation that students all across campus learn and work on computing infrastructure that is relevant for their future, whether it's in industry, academia or the public sector," said Albert P. Pisano, Dean of the UC San Diego Jacobs School of Engineering. "These information technology ecosystems being created and deployed on campus are critical for empowering our students to leverage innovations to serve society." 

Pacific Research Platform

Click here for a video gives an overview of the Pacific Research Platform (PRP) and includes a sampling of research projects the platform has enabled. 

Larry Smarr serves as Principal Investigator on the PRP and allied grants (NSF Awards OAC-1541349, OAC-1826967, CNS-1730158, CNS-2100237) which are administered through the Qualcomm Institute, which is the UC San Diego Division of Calit2.

UC San Diego Receives $14M to Drive Precision Nutrition with Gut Microbiome Data

National Institutes of Health establishes Microbiome and Metagenomics Center at UC San Diego, part of new effort to predict individual responses to food and inform personalized nutrition recommendations

A student processes microbiome samples in the UC San Diego School of Medicine lab of Rob Knight, PhD.
Photo credit: Erik Jepsen/UC San Die

January 20, 2022--The National Institutes of Health (NIH)’s All of Us Research Program is a national effort to build a large, diverse database of 1 million or more people whom researchers can use to study health and disease.

The NIH is now awarding $170 million in grant funding to centers across the country to create a new consortium known as Nutrition for Precision Health, powered by the All of Us Research Program®. The consortium will recruit a diverse pool of 10,000 All of Us Research Program participants to develop algorithms to predict individual responses to food and inform more personalized nutrition recommendations. 

The Nutrition for Precision Health consortium includes $14.55 million to launch a new Microbiome and Metagenomics Center at UC San Diego. The center will analyze the microbiomes — communities of microbes and their genetic material — found in the stool samples of nutrition study participants. 

A current challenge in precision nutrition is the inability to combine the many factors that affect how individuals respond to diet into a personalized nutrition regimen. These potential factors include the microbiome, metabolism, nutritional status, genetics and the environment. The way these factors interact to affect health is still poorly understood. 

The Microbiome and Metagenomics Center at UC San Diego will help address some of these gaps.

“Our new center will deploy more than a decade of research and development for the NIH’s most exciting exploration yet, combining our understanding of the microbiome and human genetics with our groundbreaking technical and informatics advances to rapidly explore next-generation disease treatments based on precision nutrition,” said Microbiome and Metagenomics Center co-leader Jack Gilbert, professor at UC San Diego School of Medicine and Scripps Institution of Oceanography. 

The Microbiome and Metagenomics Center will be led by Gilbert and Rob Knight, who holds appointments in the UC San Diego Department of Computer Science and Engineering and School of Medicine, along with co-investigators Andrew Bartko; Rebecca Fielding-Miller; Kathleen Fisch; Maryam Gholami David Gonzalez Kristen Jepsen; Daniel McDonald; Camille Nebeker; Pavel Pevzner, professor in the Department of Computer Science and Engineering; and Karsten Zengler all at UC San Diego. The team will also collaborate closely with researchers at Duke University. 

“The center will build on what we have learned in other large-scale activities, including the Human Microbiome Project, the Earth Microbiome Project and the American Gut Project. It leverages many of the faculty and strengths brought together in the Center for Microbiome Innovation, as well as the cross-disciplinary microbiome community we have built here at UC San Diego,” said Knight, professor and director of the Center for Microbiome Innovation at UC San Diego School of Medicine and Jacobs School of Engineering. 

“Bringing this expertise and technology to bear on the incredibly challenging problem of nutrition and health will enable a whole new level of precision in answering the age-old question of ‘what should I eat today’?’ We are just starting to understand how the microbiome can answer this with a surprising level of individual detail, not just broad-strokes generalizations for the whole population.”

Nutrition for Precision Health will collect new microbiome and metagenomics data, along with other potentially predictive factors, and combine it with existing data in the All of Us database to develop a more complete picture of how individuals respond to different foods or dietary routines. The data will be integrated into the All of Us Researcher Workbench and made widely available, providing greater opportunities for researchers to make discoveries that could improve health and prevent or treat diseases and conditions affected by nutrition. 

“We know that nutrition, just like medicine, isn’t one-size-fits-all,” said Holly Nicastro, PhD, MPH, a coordinator of Nutrition for Precision Health at NIH. “Nutrition for Precision Health will take into account an individual’s genetics, gut microbes and other lifestyle, biological, environmental or social factors to help each individual develop eating recommendations that improve overall health.”

All of Us opened for enrollment in 2018 and UC San Diego Health co-leads the program’s implementation in California, where more than 37,000 people have already signed up to participate. To learn more about the All of Us Research Program and how to join, please visit JoinAllofUs.org.

The Microbiome and Metagenomics Center at UC San Diego is supported by the NIH Common Fund’s Nutrition for Precision Health, powered by the All of Us Research Program grant 1 U24 DK131617-01. Nutrition for Precision Health, powered by All of Us Research Program, and All of Us are service marks of the U.S. Department of Health and Human Services (HHS).

New sensor grids record human brain signals in record-breaking resolution

High-resolution recordings of electrical signals from the surface of the brain could improve neurosurgeons' ability to remove brain tumors and treat epilepsy, and could open up new possibilities for medium- and longer- term brain-computer interfaces.

January 19, 2022 -- A team of engineers, neurosurgeons and medical researchers has published data from both humans and rats demonstrating that a new array of brain sensors can record electrical signals directly from the surface of the human brain in record-breaking detail. The new brain sensors feature densely packed grids of either 1,024 or 2,048 embedded electrocorticography (ECoG) sensors. The paper was published by the journal Science Translational Medicine on January 19, 2022. 

These thin, pliable grids of ECoG sensors, if approved for clinical use, would offer neurosurgeons brain-signal information directly from the surface of the brain's cortex in 100 times higher resolution than what is available today. Access to this highly detailed perspective on which specific areas of the tissue at the brain’s surface, or cerebral cortex, are active, and when, could provide better guidance for planning surgeries to remove brain tumors and surgically treat drug-resistant epilepsy. Longer term, the team is working on wireless versions of these high resolution ECoG grids that could be used for up to 30 days of brain monitoring for people with intractable epilepsy. The technology also holds potential for permanent implantation to improve the quality of life of people who live with paralysis or other neurodegenerative diseases that can be treated with electrical stimulation such as in Parkinson’s disease, essential tremor, and the neurological movement disorder called dystonia.

The project is led by electrical engineering professor Shadi Dayeh at the University of California San Diego Jacobs School of Engineering. The team of engineers, neurosurgeons and medical researchers hails from UC San Diego; Massachusetts General Hospital; and Oregon Health & Science University.

Next-generation electrocorticography

Recording brain activity from grids of sensors placed directly on the surface of the brain – electrocorticography (ECoG) – is already in common use as a tool by neurosurgeons performing procedures to remove brain tumors and treat epilepsy in people who do not respond to drugs or other treatments. The new work in Science Translational Medicine provides a wide range of peer-reviewed data demonstrating that grids with 1,024 or 2,048 sensors can be used to reliably record and process electrical signals directly from the surface of the brain in both humans and rats. For comparison, the ECoG grids most commonly used in surgeries today typically have between 16 and 64 sensors, although research grade grids with 256 sensors can be custom made. 

Being able to record brain signals at such high resolution could improve neurosurgeons' ability to remove as much of a brain tumor as possible while minimizing damage to healthy brain tissue. In the case of epilepsy, higher resolution brain-signal recording capacity could improve a neurosurgeon's ability to precisely identify the regions of the brain where the epileptic seizures are originating, so that these regions can be removed without touching nearby brain regions not involved in seizure initiation. In this way, these high resolution grids may enhance preservation of normal, functioning brain tissue.

Demonstrating that ECoG grids with sensors in the thousands function well also opens new opportunities in neuroscience for uncovering a deeper understanding of how the human brain functions. Basic science advances, in turn, could lead to improved treatments grounded in enhanced understanding of brain function. 

One millimeter vs one centimeter spacing

A thin, plastic-like square of electronic sensors is held up by tweezers.
A new array of brain sensors can record electrical signals directly from the surface of the human brain in record-breaking detail. The new brain sensors feature thin, flexible and densely packed grids of either 1,024 or 2,048 embedded electrocorticography (ECoG) sensors. Photos by David Baillot/UC San Diego Jacobs School of Engineering

Recording brain signals at higher resolution is attributable to the team's ability to place individual sensors significantly closer to each other without creating problematic interference between nearby sensors. For example, the team's three-centimeter-by-three-centimeter grid with 1,024-sensors recorded signals directly from the brain tissue of 19 people who agreed to participate in this project during the "downtime" of their already scheduled brain surgeries related to either cancer or epilepsy. In this grid configuration, the sensors are one millimeter apart from each other. In contrast, the ECoG grids already approved for clinical use typically have sensors that are placed one centimeter apart. This provides the new grids 100 sensors per unit area compared to 1 sensor per unit area for clinically used grids, offering 100 times better spatial resolution in interpreting brain signals.

Sensors made with platinum nano-rods

While using platinum-based sensors for recording electrical activity from neurons in the brain is not new, the research team is using platinum in a novel way: nanoscale platinum rods. The nano-rod shape offers more sensing surface area than flat platinum sensors, which helps to make the sensors more sensitive. The sensing system is based on the fact that the electron count in the platinum nano-rods changes in response to neurons firing in the brain.

Charged ions move in and out of a neuron when it fires. This movement of charged ions causes changes in the voltage potential in the cerebrospinal fluid that the neurons are bathed in. These changes in voltage potential in the brain tissue and cerebrospinal fluid change the population count of electrons in the platinum nano-rods by charge screening processes. In this way, the firing of neurons at or near the surface of the cerebral cortex is recorded by the platinum nanorods in near real time and with high precision.

Thin and pliable grids of sensors in various sizes

Thin, transparent, plastic-like square of electronic sensors being bent by a person's fingers.

The human brain is always moving. With each heartbeat, for example, the brain moves with the pulsating blood flowing through it. The platinum nano-rod based sensor grids are thinner and more flexible than today's clinically approved ECoG grids. The thinness and flexibility allows the sensor grids to move with the brain, enabling a closer connection and better readings. In addition, the grids are manufactured with small, ring-shaped holes that allow cerebral spinal fluid to pass through. In this way, these perfusion holes support a better interface between the sensor grid and the brain surface by allowing the sensor to easily and safely displace the fluid.  

The new platinum nano-rod brain sensor grids are ten micrometers thick, approximately one tenth the size of a human hair and 100 times thinner than the one millimeter thick and clinically approved ECoG grids. The nano-rods are embedded in a transparent, soft and flexible biocompatible material called parylene which is in direct contact with the surface of the brain. The electrical signals travel from the brain, through the cerebrospinal fluid, and reach the exposed surfaces of the platinum nano-rods which are recessed within the parylene. This design yields a sensor grid that forms a close and stable connection with the surface of the brain, improving signal quality. 

The manufacturing process used also allows for a wide variety of sizes and shapes, which opens up new possibilities for greater and more customized cortical coverage. Collecting signals from larger areas of the brain at the same time could unlock more of the brain's mysteries.

Through close collaboration between engineers led by electrical engineering professor Dayeh at UC San Diego and clinicians led by neurosurgeon Ahmed Raslan at Oregon Health & Science University, the team has implemented design improvements geared specifically for clinical use. For example, customized sensor grids can be printed with specialized holes that allow neurosurgeons to insert probes at exactly the right spot and apply electrical stimulation directly to brain tissue at specific locations. With the goal of getting higher-resolution ECoG grids approved for clinical use, Dayeh, Raslan and co-first author Youngbin Tchoe have co-founded a startup called Precision Neurotek Inc. 

More precise functional mapping

One of the challenges of removing brain tumors is that the presence of the tumor triggers changes in the brain, including changing what areas of the brain are involved in what functions. These changes make it critical for the surgical team to make a personalized map of the patient's brain – "functional maps" – in order to decide where to cut and where not to cut while removing as much of the tumor as possible. 

Four scientists in a lab huddled around a model of a human brain.
The three co-first authors and senior author on the Science Translational Medicine paper. L-R: Daniel R. Cleary, Andrew M. Bourhis, Shadi A. Dayeh and Youngbin Tchoe.

The authors of the Science Translational Medicine paper demonstrated that these functional maps can be made extremely precise using their platinum nano-rod ECoG sensors. In particular, the team developed functional maps in four different people of a boundary in the brain called the central sulcus. The central sulcus divides the brain's somatomotor cortex from the somatosensory cortex. In these four individuals, the researchers placed the platinum nano-rod grids on the surfaces of the subjects’ brains and asked them to do a number of activities, including hand grasping. With this information, the researchers reconstructed the actual location of this key landmark in the brain as well as the neural correlates in the brain that correspond to finger sensation and hand grasping. The results from the platinum nano-rod grids aligned with the results from the lower-resolution ECoG grids already approved for clinical use, but with more precision about exactly where this critical functional boundary is between the somatomotor cortex and the somatosensory cortex. The newly delineated curvilinear functional boundary unique to each patient’s brain is superior to the often extrapolated and linear boundary that is determined from today's one-centimeter-spaced clinical grids.

Neuroscience insights

Some of the team's newly published data from studies in rats also demonstrate the utility of the grids for opening new avenues in fundamental neuroscience research. The Science Translational Medicine paper, for example, includes what the researchers believe is the first mapping of a cortical column in a rat from brain-surface recordings. In the past, the mapping of cortical columns has only been done by placement of an individual needle at the surface of the brain and sequential electrical stimulation and movement of the needle across the brain surface. More generally, the fact that the platinum nano-rod grids provide high resolution data in both time and space opens up many new possibilities for uncovering new knowledge about how the brain works.

Another observation enabled by the new grids is uncovering the short and local as well as long and broad range brain waves associated with brain function all at the same time. This high- spatial and time-varying (dynamic) picture of the brain activity was documented in several supplementary movies associated with the Science Translational Medicine paper and was used to interpret hand motion in new ways utilizing brain wave patterns.

Next steps 

The team is working on a range of initiatives in parallel to advance these grids so that they are eligible for review for approval for short-, medium- and longer-term use. For example, the team, led by UC San Diego electrical engineering professor Shadi Dayeh, was awarded a $12.25 Million NIH Brain Research Through Advancing Innovative Neurotechnologies® (BRAIN) Initiative grant focused on developing the sensing system to the point that the next step will be a clinical trial for people with treatment-resistant epilepsy. This grant also funds efforts to make the system wireless, which would be important for creating implantable grids for medium- and longer- term use.

To accelerate the translation of these implants for broader clinical use, UC San Diego is establishing a current good manufacturing practice (cGMP) laboratory co-led by professors Dayeh and Alexander Khalessi, who is the Don and Karen Cohn Chancellor’s Endowed Chair in Neurosurgery and chair of the Department of Neurological Surgery at UC San Diego Health. This cGMP will regulate the manufacture of these grids to attain FDA approvals for use in small clinical trials.

Collaborations

The project is led by electrical engineering professor Shadi Dayeh at the University of California San Diego Jacobs School of Engineering. The team of engineers, neurosurgeons and medical researchers hails from UC San Diego; Massachusetts General Hospital; and Oregon Health & Science University, where the majority of the human surgeries were performed by neurosurgery professor Ahmed Raslan. In addition to the Dayeh-Raslan collaboration, the development of the grids has spanned many years of collaboration between Dayeh and clinical partners spearheaded by Daniel Cleary of UC San Diego Health’s Department of Neurological Surgery, and by Angelique Paulk and Jimmy Yang of Massachusetts General Hospital, and under the supervision of Sharona Ben-Haim and Eric Halgren of UC San Diego and Sydney Cash of Massachusetts General Hospital, and by Brittany Stedelin of Oregon Health & Science University under Raslan’s supervision. Scaling of the grids and their interconnects were led by Dayeh’s postdoctoral fellow Youngbin Tchoe and graduate student Andrew Bourhis who is co-advised by Dayeh and Ian Galton of UC San Diego. 

Technology transfer

UC San Diego has filed multiple patent applications on the manufacture of the multi-thousand channel PtNRGrids. Shadi Dayeh, Ahmed Raslan, and Youngbin Tchoe co-founded Precision Neurotech Inc. to support the commercialization of the PtNRGrids.

Funding

This work was supported by the National Institutes of Health Awards No. NIBIB DP2-EB029757, the NIH Brain Initiative R01NS123655-01, UG3NS123723-01 and NIDA R01-DA050159 and the National Science Foundation (NSF) Awards No. 1728497 and CAREER No. 1351980 to S.A.D., F32 postdoctoral fellowship to D.C. award # MH120886-01, and an NSF Graduate Research Fellowship Program No. DGE-1650112 to A.M.B. 

Authors and Institutions

Co-First authors

Youngbin Tchoe, Andrew M. Bourhis, and Daniel R. Cleary from the Integrated Electronics and Biointerfaces Laboratory, Department of Electrical and Computer Engineering at the University of California San Diego Jacobs School of Engineering. Daniel Cleary is an MD/PhD whose primary appointment is in the Department of Neurological Surgery at UC San Diego Health.

Corresponding author

Shadi A. Dayeh, who leads the Integrated Electronics and Biointerfaces Laboratory, Department of Electrical and Computer Engineering at the University of California San Diego Jacobs School of Engineering

Full Article Author List (by institution)

University of California San Diego
Youngbin Tchoe, Andrew M. Bourhis, Daniel R. Cleary, Jihwan Lee, Karen J. Tonsfeldt, Hongseok Oh, Yun Goo Ro, Keundong Lee, Samantha Russman, Mehran Ganji, Ian Galton, Sharona Ben-Haim, and Shadi A. Dayeh

Oregon Health & Science University
Brittany Stedelin, Erik C. Brown, Dominic Siler and Ahmed M. Raslan

Massachusetts General Hospital
Angelique C. Paulk, and Jimmy C. Yang

Two UC San Diego Computer Scientists Named as 2021 Fellows for Prestigious Computing Association

The Association for Computing Machinery has selected 70 Fellows for Computing Advances that are Driving Innovation

Tajana Rosing Ranjit Jhala

January 19, 2022-- Two computer scientists from the University of California San Diego have been elected as fellows of the Association for Computing Machinery (ACM), the association announced today. They are among the 70 new fellows recognized by the ACM, the world’s largest educational and scientific computing society.

The ACM Fellows program recognizes the top 1% of ACM Members for their outstanding accomplishments in computing and information technology and/or outstanding service to ACM and the larger computing community. The 2021 Fellows represent universities, corporations, and research centers in Belgium, China, France, Germany, India, Israel, Italy, and the United States.

The 2021 UC San Diego ACM Fellows are:

  • Ranjit Jhala, for contributions to software verification
  • Tajana Simunic Rosing, for contributions to power, thermal, and reliability management

“Ranjit and Tajana truly represent our department’s commitment to conducting impactful research and education. We are incredibly proud of their accomplishments, which benefit our community and the world, and are pleased they are being recognized with such a great honor,” said UC San Diego Department of Computer Science and Engineering Chair Sorin Lerner. 

Ranjit Jhala’s research interests include programming languages and software engineering to develop techniques for building reliable computer systems. His work draws from, combines and contributes to the areas of: Type Systems, Model Checking, Program Analysis and Automated Deduction. He is part of the Programming Systems Group in the Department of Computer Science and Engineering, which focuses on developing new languages, compilers, program analysis techniques and development environments for making software systems easier to build, maintain and understand. He joined UC San Diego in 2005.

Tajana Simunic Rosing is the director of the System Energy Efficiency Lab at UC San Diego. Her research interests are energy efficient computing, cyber-physical and distributed systems. The projects she leads include efforts funded by the Defense Advanced Research Projects Agency (DARPA) and the Semiconductor Research Corporation (SRC) that focus on design of accelerators for analysis of big data; a project focused on developing artificial intelligence systems in support of healthy living; an SRC-funded project on the Internet of Things system reliability and maintainability; and a National Science Foundation- funded project on the design and calibration of air-quality sensors. She joined UC San Diego in 2006. 

The addition of Jhala and Rosing brings to 13 the number of ACM Fellows among active faculty in the CSE department. Prior honorees included professors Victor Vianu (2006), Pavel Pevzner (2010), Stefan Savage (2010), Dean Tullsen (2011), Andrew Kahng (2012), Yuanyuan Zhou (2013), Mihir Bellare (2013), Rajesh Gupta (2016) and Ravi Ramamoorthi, Alexander Vardy and Geoffrey Voelker (2017).


 

 

 

 

 

 





 

UC Riverside Joins UC San Diego, UC Irvine in Multidisciplinary Research Institute Calit2

Ramesh Rao, a professor in the Department of Electrical and Computer Engineering and the current director of the UC San Diego division of Calit2 – known as the Qualcomm Institute – has been appointed interim director of Calit2. 

Jan. 18, 2022-- The California Institute for Telecommunications and Information Technology, or Calit2, is expanding to include a third University of California campus. The UC Office of the President has approved a plan for University of California Riverside to join founding members UC San Diego and UC Irvine in the multidisciplinary research institute. Calit2 was created by the state of California over 20 years ago to ensure the state remains on the leading edge of information technology, communications, and other 21st-century technologies.

UC San Diego Chancellor Pradeep K. Khosla also announced that Ramesh Rao, a professor in the Department of Electrical and Computer Engineering and the current director of the UC San Diego division of Calit2 – known as the Qualcomm Institute – has been appointed interim director of the three-campus institute. 

“This expansion of Calit2 to include UC Riverside will allow us to leverage new opportunities and synergies in Southern California, bringing UC Riverside’s unique perspective and talent into an already dynamic multidisciplinary research enterprise,” said Khosla, who is also the principal investigator of Calit2. “We look forward to their contributions.”

UC Irvine Chancellor Howard Gillman, co-principal investigator of Calit2, also welcomed the new partner campus, noting that “the addition of UC Riverside will help us reinforce a more powerful technology ecosystem stretching across four contiguous counties in southern California.”  

“With its location and rapid growth in research relevant to Calit2, UC Riverside is equipped to be a strong partner for the institute’s divisions in San Diego and Irvine,” said Vice President of Research and Innovation in the UC Office of the President Theresa A. Maldonado. “The addition of Riverside means that all 10 UC campuses are now members of the four Governor Gray Davis Institutes for Science and Innovation for the first time since their founding. These institutes continue to make significant impacts on California and society at large.”

UC Riverside has grown to include 22 research centers, a school of medicine, more than 26,000 students, and faculty that includes 26 members of the National Academies and two Nobel laureates. UC Riverside is the primary research university serving California’s Inland Empire– the fastest growing region in the nation, projected to grow 44% by 2050.

“We have focused research areas that are complementary to existing research and faculty strengths at UC San Diego and UC Irvine,” noted UC Riverside Chancellor Kim A. Wilcox. “These areas are of critical importance to the future of all Californians, including clean transportation and infrastructure, clean energy and fuels, agriculture technology and food security, as well as natural resource management.”

“Our membership in Calit2 will further crystallize already existing synergies between the three campuses,” said Rodolfo H. Torres, UC Riverside vice chancellor for Research and Economic Development. “In collaboration with my counterparts, Vice Chancellor Corinne Peek-Asa at UC San Diego and Vice Chancellor Pramod Khargonekar at UC Irvine, we will continue to explore and support the exciting research opportunities our partnership brings.”

As the first UC campus to become a Hispanic Serving Institution, UC Riverside has one of the state’s most diverse student populations, with nearly 40% of graduate and undergraduate students Hispanic or Latino.

“Our campus brings to Calit2 not only our track record in student social mobility, inclusion, and equity, but also broad expertise in sustainable research and innovation,” said Gillian Wilson, UC Riverside senior associate vice chancellor for Research and Economic Development and professor of Physics and Astronomy. Wilson has been appointed director of Calit2 at UC Riverside.

Faculty and students at UC Riverside will benefit from access to shared-use Calit2 facilities in San Diego and Irvine, including specialized labs, world-class nanotechnology facilities, wired and wireless infrastructure, and other technical resources.

The three Calit2 campuses will work closely to coordinate joint research and development projects, as well as short-term exchanges of engineers and scientists and access to temporary workspace to enhance collaboration among researchers from the participating campuses. 

 

 

Armor Lab is using motion capture data to develop next-gen wearables

Introducing the second cohort of Racial Equity Fellows

January 10, 2022--Seven UC San Diego Jacobs School of Engineering students have been selected to serve as Racial Equity Fellows. In this role, they will act as student advocates on the Jacobs School Student and Faculty Racial Equity Task Force, each bringing their demonstrated interest in diversity, equity and inclusion to the Task Force. These students represent undergraduate and graduate perspectives from all six academic departments at the Jacobs School.  

The 2021 Jacobs School Racial Equity Fellows

The goal of the Jacobs School Student and Faculty Racial Equity Task Force is to make the Jacobs School a truly inclusive community. The Task Force, which kicked off in 2020 along with the first cohort of Racial Equity Fellows, is tasked with developing a comprehensive understanding of existing programs and resources in place to reach this goal, and suggesting solutions where gaps exist. The Task Force is working on such issues as improving retention and time-to-degree for Black, Latinx and Native American students, and recruitment and retention of faculty from these same groups underrepresented in engineering. Among its activities last year, the task force helped launch several new recruiting events for admitted Black, Latinx and Native American students that resulted in an increase of newly admitted undergraduate engineering students from those groups.

The seven new Racial Equity Fellows will bring student concerns and suggestions to the larger Task Force group. The students receive a $1,000 stipend for the yearlong fellowship. In addition to these seven Racial Equity Fellows, the Task Force also includes a faculty representative from each department; a representative from the IDEA Engineering Student Center; the Associate Deans for Students and for Faculty Affairs; and the Jacobs School Faculty Equity Advisor. 

This year the task force will build on the work that was started last year.  At the student level, a central focus will be on classroom and research lab climate, and building community among students from racial and ethnic groups that are underrepresented in engineering and computer science.  

“I’m excited about what the Task Force accomplished last year," said Christine Alvarado, Associate Dean for Students and a computer science professor at the Jacobs School who co-led the creation of the Student and Faculty Racial Equity Task Force. "The undergraduate student recruiting efforts that we launched were so successful that we plan to repeat them every year. The perspective and energy that the 2020 Racial Equity Fellows brought to the Task Force was critical to the success of our efforts, and I look forward to learning from and working with the 2021 Fellows.” 

2021 Racial Equity Fellows:

Mariam Abdu:
Mariam Abdu is an undergraduate structural engineering student, and a member of the National Society of Black Engineers and the National Society of Leadership and Success. A refugee from Kenya, Abdu said showing up fully as herself is an important part of making campus more welcoming. 

“It is important that I take up space, speaking in my native Arabic tongue and dressing in my religious garment, because I want other students to feel comfortable occupying a space that they are underrepresented in,” she said.

Abdu also works as an administrative assistant with the Division of Biological Sciences, managing the Biology Bulletin and weekly newsletter, where she shares campus resources with students. 

“As a Triton who transferred from social science to engineering, I want all students to feel confident pursuing STEM. A fundamental part of getting a diverse population of students in STEM is prioritizing a welcoming and informative environment. I look forward to upholding racial equity in the Jacobs School of Engineering by serving as an envoy between students and administration. As a Jacobs School Racial Equity Fellow, I envision a sincere celebration of students' unique backgrounds while getting them acquainted and excited in STEM.”

 

Jennifer Hernandez-Mora:
Jennifer Hernandez-Mora is an undergraduate mechanical engineering student, and president of the UC San Diego chapter of the Society of Hispanic Professional Engineers. She is also a member of the Students for the Exploration and Development of Space organization (SEDS at UC San Diego), where she helped develop a female mentorship program that increased the number of underrepresented women in the club threefold. A first-generation student, Hernandez encourages students to take advantage of the existing resources campus has to offer, while pushing to expand these support networks, such as the IDEA Engineering Student Center. 

 

 

 

Alexander Perez de Leon:
Undergraduate nanoengineering student Alexander Perez de Leon is all about action. A Latinx student who conducted research as a McNair Scholar and serves as a mentor to five students through the Mentorship Collective, Perez de Leon aims to help the Task Force bring tangible changes to student life.

“I am particularly interested in how we can help students and administrators take advantage of the resources and infrastructure UC San Diego has. In other words, I want to serve the students by helping admin serve students better," he said. “I hope to balance our strong sense of idealism with an equal amount of pragmatism. Tangible impact, I believe, is the most fulfilling and also the most important to administration and students. With all this said I am enthusiastic to meet my peers and create a welcoming environment for all perspectives and ideas.”

He demonstrated what he means by action during COVID-19, developing next-generation solar cells and light-emitting diodes for cheap energy generation and consumption. He also worked with his local hospital and earplug manufacturers to provide the night shift nurses with custom earplugs, helping to improve the nurses' rest during the day.

 

Mary Anne Smart:
Mary Anne Smart, a PhD student in computer science, plans to bring what she’s learned as a Cultural Competence in Computing (3C) Fellow to the Task Force. 3C is a professional development program aiming to help computing professionals learn about racism, bias, discrimination and intersectionality. Smart aims to not only work toward a more diverse body of researchers, but also to push for more of a focus on the impact of racism within technologies themselves. 

“With a few notable exceptions, the impact of racism in the development of technology is rarely mentioned in engineering classes. Furthermore, the Jacobs School should highlight and support research projects examining the role of racism in engineering education, in the development of technology, and in other aspects of university life. The Jacobs School Racial Equity Task Force has the opportunity to make meaningful changes to advance racial equity at UC San Diego.”

Among the ideas Smart will bring to the Task Force for consideration are opportunities for more partnerships with Historically Black Colleges and Universities, and to strengthen recruiting efforts for both undergraduate and graduate students from backgrounds underrepresented in engineering and computer science.

 

Marco Paredes:
Undergraduate electrical engineering student Marco Paredes knows first-hand how valuable student diversity organizations can be. A first-generation Latinx student and Vice President External of the UC San Diego chapter of the Society of Hispanic Professional Engineers, Paredes hopes to increase support for these groups.

“As a first-generation minority student at UC San Diego, I am committed to increasing the number of underrepresented students in STEM as well as providing a safe space for these students to succeed academically and professionally. A student can thrive more in a diverse space; having each diversity organization prosper will help every student (including those who are not minorities) become more comfortable. With that, as VP External ( of the UC San Diego chapter of the Society of Hispanic Professional Engineers), I will be moving towards not only inviting more companies to work with SHPE at UC San Diego, but also further developing partnerships between the diversity organizations and working together to organize workshops.”

 

Rayyan Gorashi:
Rayyan Gorashi is a bioengineering PhD student with a goal of increasing support for students from underrepresented backgrounds. She hopes to ensure that this support stays active within academic settings, not separate from them. She’s already doing this as a member of the Jacobs Undergraduate Mentorship Program (JUMP) and the Bioengineering Graduate Society (BEGS), and plans to continue this advocacy as a Racial Equity Fellow.

“While offices like the Black Resource Center are incredible resources in and of themselves, I strongly believe that there is much work needed to be done to bring an equitable amount of support for Black and LatinX students in the academic setting. As an undergraduate, I realized that the racial disparities in academia were going to last for the entirety of my higher education. As tough as this realization was, knowing that there was minimal support from academic departments felt even tougher. The initiation of this Racial Equity Task Force, as well as its inclusion of both undergraduate and graduate students presents a big step in the right direction towards support for students from underrepresented backgrounds."

"Ultimately, I hope to increase the visibility of students from underrepresented backgrounds in STEM. I also hope to provide better support to students as they transition to UC San Diego through additional orientation programming and continued mentorship for the duration of their graduate careers.”

As an undergraduate, Gorashi led the Johns Hopkins chapter of the National Society of Black Engineers where she developed an engineering outreach program with an all-girls high school in Baltimore. She’s continuing her involvement in outreach elementary through undergraduate students through BEGS and JUMP.
 

Sheron Tavares:
Sheron Tavares, a doctoral student in the materials science and engineering program in the Department of Mechanical and Aerospace Engineering, came to UC San Diego from Brazil. Her father worked in the blast furnace of a steel manufacturer, which piqued Tavares’ interest in steel. After working at the steel plant herself, she realized she would need an advanced degree to make the type of research contributions she wanted. While earning her undergraduate and master’s degrees in metallurgical engineering in Brazil, Tavares taught math and Portuguese classes for extremely poor students from favelas, an experience that has shaped her outlook on racial equity. 

“I believe that knowledge is the greatest wealth we can have,” she said. “Nobody can take it from you.”

In addition to finding ways to better support underrepresented students once they’re on campus, Tavares hopes to find ways to increase the number of these students interested in and attending UC San Diego, noting, for example, that the number of Black students on campus doesn’t reflect the Black community in San Diego.

“From my point of view, developing socioeconomic policies is an alternative [for] attracting Black and African American students to UC San Diego. I think that the creation of a space to honor Black personalities on the campus will make the students feel more comfortable. In addition, this homage will demonstrate that UC San Diego is concerned about the racial issue. I think that the university needs to promote more activities to the students, independent of their nationality, race, or religion. These activities should encourage deeper interaction between students of all backgrounds.” 

"I'm so happy to recognize the important work of the students as Racial Equity Fellows here at the Jacobs School," said Albert P. Pisano, Dean of the UC San Diego Jacobs School of Engineering. "Engineering and computer science for the public good is the bedrock value of the Jacobs School. Fully delivering on this promise requires that each and every one of our students, faculty and staff has the material and social support necessary to thrive. The Racial Equity Fellows program is an important step in this direction, with a particular focus on students."  

Proposed Updates to Steel Building Standard Could Enhance Earthquake Resilience

Before 1994, the webs of steel columns were often relatively shallow (right) in buildings with steel frames. But since then, building designers have satisfied drift requirements by selecting columns with longer, or deeper, webs (left) to boost their lateral stiffness.

Credit: NIST

Jan. 7, 2022-- Since the mid-1990s, a type of steel column that commonly features slender cross-sectional elements has become more prevalent in buildings along the West Coast of the United States and in other seismically active regions. Although these columns have complied with modern design standards, our understanding of how they would perform during an earthquake has been limited by a lack of full-scale testing.

Using an earthquake-simulating device known as a shake table, researchers at the National Institute of Standards and Technology (NIST) and the University of California San Diego (UC San Diego) identified deficiencies in the performance of these columns, with many buckling prematurely. Based on the results, documented in a NIST report, and a detailed analysis of the test data, the researchers devised new limits for column slenderness, described in a paper published in the Journal of Structural Engineering last April. The American Institute of Steel Construction (AISC), a standards organization, has adopted the proposed limits in a draft for public feedback of the 2022 edition of AISC 341, a standard that provides guidance on designing earthquake-resistant steel buildings. 

“A lot of current design provisions are based on scaled-down column tests or a very small number of full-scale tests. But the full-scale testing we conducted here has allowed us to begin filling in the knowledge gap regarding the performance of these kinds of columns under extreme loading conditions,” said NIST structural engineer John Harris. “The results have supported the development of enhanced guidance for new buildings and could inform decision making on modifying columns in existing structures.” 

Throughout the 1990s, engineers gained substantial insight into the way structures respond to real earthquakes, such as the 1994 Northridge earthquake, which devastated the greater Los Angeles area. As a result, building codes began to impose strict requirements on the degree that buildings could sway during earthquakes — a measure known as story drift.

Steel columns in multistory buildings, with cross sections shaped like a capital “I,” are good at supporting the downward forces created by the weight of the floors and roof resting upon them. But a shaking ground can introduce additional forces in all directions, potentially causing columns to sway laterally, contributing to story drift. Before 1994, the middle part of columns’ I-shaped cross sections, known as webs, were often relatively short in buildings with steel frames. But since then, building designers have satisfied story drift requirements by selecting columns with longer, or deeper, and typically more slender webs to boost their lateral stiffness.

According to the current building standards, these deep columns were acceptable to use as long as their web dimensions did not surpass certain depth-to-width ratios — known as a slenderness limit — meant to reduce the risk of columns losing their capability to carry weight during earthquakes, Harris said. However, some engineers were unsure of how these columns would hold up against real earthquake motions.

When the slenderness limits were developed decades ago, engineers did not have the capability of testing the seismic performance of full-scale columns like those actually used in buildings. Instead, they based the limits on reduced-scale model columns, creating some uncertainty about their effectiveness in reality. But full-scale tests have since become possible with the availability of very powerful facilities, known as shake tables, designed to put full-scale structural components through the seismic gauntlet.

To assess the slenderness limits, Harris worked with fellow structural engineering experts at the Jacobs School of Engineering at UC San Diego, with access to one of the campus’ shake tables, called the Caltrans Seismic Response Modification Device (SRMD) Test Facility.


The researchers fastened 48 steel columns of varying dimensions into a hydraulic system called the Seismic Response Modification Device (SRMD), which thrusted one end of each column back and forth, replicating the shaking motions of an earthquake.

Photo: UC San Diego Caltrans SRMD Test Facility

The researchers tested 48 deep columns — donated by AISC and the Herrick Corporation, a steel fabricator — each 5 1/2 meters long and with webs of varying slenderness. Using the SRMD, they recreated the effects of earthquakes (which can differ greatly from quake to quake) on the columns. 

The machine simulated the weight of buildings on the columns by applying either constant or fluctuating compression, the latter representing the forces that pulse through the structure as the building sways back and forth. By jolting one end of the column back and forth with the SRMD’s hydraulic system, the team simulated a range of quake-induced lateral motions, the degree of which, in reality, depend on a building’s distance from the fault line that earthquake ground motions emanate from. 

The team measured the response of each column during the test, taking note of any permanent changes to its shape. In addition, they coated the columns in a layer of white paint that would begin to chip off as the steel bent, making permanent deformation more visually apparent. They tested every column until it could no longer oppose the forces exerted by the machine, driving some to buckle near their ends and others to contort along their entire length. Among the deformed columns, they picked up on a telling pattern.

“We noticed that, as the columns became stockier and less slender, they can more easily go through the entire loading protocol without losing a significant amount of their capability to withstand the earthquake motions,” Harris said.

Their findings suggested that the previous small-scale tests were not painting a complete picture of deep column performance and that column webs meeting the limits prescribed by today’s codes may still be too slender.

Keeping the story drift requirements in mind, Harris and his research partners at UC San Diego were able to propose new slenderness limits with the data from the full-scale experiments. Columns with webs sized according to the new limit could potentially meet drift and stability requirements at the same time. 

The researchers brought the revised limits before the AISC for review, which resulted in the organization including the limits in a draft of the 2022 edition of AISC 341. When the new version is published this December, the more stringent limits on steel column webs could soften the blow of earthquakes, potentially saving newly designed buildings from unnecessary damage or partial collapse. 

In the future, the researchers aim to incorporate the limits into standards for evaluating existing buildings as well, enabling engineers to identify deep columns in need of corrective actions such as the addition of bracing. But for now, AISC is accepting public feedback until Feb. 21, 2022 on their draft standard, which is available for download on their site. 

Paper: G. Ozkula, C.-M. Uang, and J. Harris. Development of Enhanced Seismic Compactness Requirements for Webs in Wide-Flange Steel Columns. Journal of Structural Engineering. Published April 29, 2021. DOI: 10.1061/(ASCE)ST.1943-541X.0003036

 

UH, UC San Diego students to compete in driverless car racing event at Consumer Electronics Show

A new method to make AI-generated voices more expressive

 

 Jan.4, 2022-- Researchers have found a way to make AI-generated voices, such as digital personal assistants, more expressive, with a minimum amount of training. The method, which translates text to speech, can also be applied to voices that were never part of the system’s training set.

The team of computer scientists and electrical engineers from the University of California San Diego presented their work at the ACML 2021 conference, which took place online recently. 

In addition to personal assistants for smartphones, homes and cars, the method could help improve voice-overs in animated movies, automatic translation of speech in multiple languages–and more.The method could also help create personalized speech interfaces that empower individuals who have lost the ability to speak, similar to the computerized voice that Stephen Hawking used to communicate, but far more expressive. 

“We have been working in this area for a fairly long period of time,” said Shehzeen Hussain, a Ph.D. student at the UC San Diego Jacobs School of Engineering and one of the paper’s lead authors. “We wanted to look at the challenge of not just synthesizing speech but of adding expressive meaning to that speech.” 

Existing methods fall short of this work in two ways. Some systems can synthesize expressive speech for a specific speaker by using several hours of training data for that speaker. Others can synthesize speech from only a few minutes of speech data from a speaker never encountered before; but they are not able to generate expressive speech and only translate text to speech. By contrast, method developed by the UC San Diego team is the only one that can generate with minimal training expressive speech for a subject that has not been part of its training set. 

The researchers flagged the pitch and rhythm of the speech in training samples, as a proxy for emotion. This allowed their cloning system to generate expressive speech with minimal training, even for voices it had never encountered before. 

“We demonstrate that our proposed model can make a new voice express, emote, sing or copy the style of a given reference speech,” the researchers write. 

Their method can learn speech directly from text; reconstruct a speech sample from a target speaker; and transfer the pitch and rhythm of speech from a different expressive speaker into cloned speech for the target speaker. 

The team is aware that their work could be used to make deepfake videos and audio clips more accurate and persuasive. As a result, they plan to release their code with a watermark that will identify the speech created by their method as cloned. 

“Expressive voice cloning would become a threat if you could make natural intonations,” said Paarth Neekhara, the paper’s other lead author and a Ph.D. student in computer science at the Jacobs School. “The more important challenge to address is detection of these media and we will be focusing on that next.” 

The method itself still needs to be improved. It is biased toward English speakers and struggles with speakers with a strong accent.

Expressive Neural Voice Cloning

https://arxiv.org/pdf/2102.00151.pdf

Paarth Neekhara, Shehzeen Hussain, Shlomo Dubnov, Farinaz Koushanfar, Julian McAuley, University of California San Diego

The expressive voice cloning modelk the researchers used. 
Audio examples:  https://expressivecloning.github.io/

 

Long-reads and powerful algorithms identify "invisible" microbes

New technique, developed by an international research team, could provide tremendous insights into health and disease.

January 3, 2022-- Microbes are everywhere – in our guts, on our skin, permeating the environments around us. Studying these microbial communities has delivered tremendous insights into disease and good health, but identifying all the distinct species in a sample can be challenging. 

Now, a study by an international research team has shown that highly accurate, long-read genomic sequencing technology (HiFi) can shine a light on this previously hidden biology.

Researchers at the University of California San Diego Department of Computer Science and Engineering, the U.S. Department of Agriculture, the biotechnology company Pacific Biosciences and labs in Russia, Israel and the Netherlands have shown that HiFi, combined with advanced algorithms, can differentiate between nearly identical organisms, allowing researchers to more completely catalogue microbial communities. The study was published in Nature Biotechnology .

“This HiFi technology, developed by Pacific Biosciences, is revolutionizing the field,” said Pavel Pevzner, the Ronald R. Taylor Distinguished Professor of Computer Science at UC San Diego and co-senior author on the paper. “Here, we provide complete or nearly complete bacterial genomes, distinguishing very similar bacterial strains from a single sample. This is no small thing: Some E. coli strains are harmless, others are deadly.” 

HiFi recently helped sequence a complete human genome, a feat that had evaded scientists since the Human Genome Project produced an incomplete version 20 years ago. 

This paper builds on those findings, showing that long-reads can shine a light on previously invisible organisms. Short-reads, the most common genomic sequencing technique, analyze brief DNA fragments (100 to 300 base pairs) and have trouble assembling complete genomes and differentiating between genomically-similar microbes.

Long-read technologies, such as HiFi, generate much larger DNA fragments (greater than 15,000 base pairs) and have emerged as a potential solution. As long-read accuracy has increased, the technology has revealed hidden genomic features in amazing detail. In this case, HiFi easily differentiated microbes with only minor genomic variations.

“We can now sequence complete genomes of nearly all abundant bacteria in a microbiome,” said first author Mikhail Kolmogorov, a former UC San Diego postdoctoral fellow and now a Stadtman Investigator at the National Cancer Institute. “Short-read studies rarely provided complete sequences of even a single microbe.”

Long Reads From sheep guts 

In this study, the research team used HiFi long-reads to sequence the microbial metagenome in sheep guts. Their goal was to create complete reference genomes for unique microbial species (metagenome-assembled genomes or MAGs).

They found HiFi and associated algorithms identified the genomes from 428 species with greater than 90 percent completeness. Many of these had been invisible to short-read technologies. These findings could be a tremendous boon for microbiome researchers and other scientists, providing new and powerful tools to fully delineate a sample’s microbial complement.

“Characterizing microbiomes of ruminant livestock, like sheep, can be used to develop methods to reduce disease, environmental impact and greenhouse gas emissions, while improving productivity,” said Timothy Smith, a research chemist at the USDA’s Meat Animal Research Center and co-senior author on the paper.  “Strain-level genome resolution will help track genes related to antimicrobial resistance and determine the extent animal husbandry might be contributing to the rise of antibiotic resistance in human and animal diseases.”

The applications for this work are quite broad, as the ability to precisely delineate specific microbial species in complex samples could inform many scientific endeavors.

“Although this study focuses on microbes in the sheep gut, the potential is tremendous because microbes inhabit so many places on human, animal and plant bodies and throughout the environment,” said Rob Knight, director of UC San Diego’s Center for Microbiome Innovation and a professor in the departments of Computer Science and Engineering, Bioengineering and Pediatrics and a co-founder of the American Gut Project.

“Having better ways to read genomes in complex environments sets the stage for improved efforts to write the genomes we need to solve many of society’s most pressing problems,” said Knight, who is not an author on this study. 

These advances should be quite useful in medicine, including UC San Diego’s groundbreaking phage therapy (IPATH) and antimicrobial (CHARM) programs. Microbes may also help diagnose cancer, decipher red tides, study plastic biodegradation in the ocean and measure carbon release and capture.  

“Rather than combining similar organisms into one bucket, we can now differentiate them and get a true metagenomic picture of complex bacterial communities,” said Pevzner. “Like complete genomics, which is already being applied to rare disease diagnostics, complete metagenomics may soon make its way into medicine and many other disciplines.”

Other researchers included: Sung Bong Shin, USDA Meat Animal Research Center; Derek, M. Bickhart and Kevin Panke-Buisse, USDA Dairy Forage Research Center; Elizabeth Tseng and Daniel M. Portik, Pacific Biosciences; Anton Korobeynikov and Ivan Tolstoganov, St. Petersburg State University; Gherman Uritskiy, Amazon; Ivan Liachko and Shawn T. Sullivan, Phase Genomics; Alvah Zorea and Itzhak Mizrahi, Ben Gurion University of the Negev; Victòria Pascal Andreu and Marnix H. Medema, Wageningen University.

 

'Pop-up' electronic sensors could detect when individual heart cells misbehave

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SEM image of the “pop-up” sensors that directly measure speed and movement of electrical signals inside heart cells. Credit: Yue Gu

December 23, 2021 -- Engineers at the University of California San Diego have developed a powerful new tool that monitors the electrical activity inside heart cells, using tiny “pop-up” sensors that poke into cells without damaging them. The device directly measures the movement and speed of electrical signals traveling within a single heart cell—a first—as well as between multiple heart cells. It is also the first to measure these signals inside the cells of 3D tissues.

The device, published Dec. 23 in the journal Nature Nanotechnology, could enable scientists to gain more detailed insights into heart disorders and diseases such as arrhythmia (abnormal heart rhythm), heart attack and cardiac fibrosis (stiffening or thickening of heart tissue).

“Studying how an electrical signal propagates between different cells is important to understand the mechanism of cell function and disease,” said first author Yue Gu, who recently received his Ph.D. in materials science and engineering at UC San Diego. “Irregularities in this signal can be a sign of arrhythmia, for example. If the signal cannot propagate correctly from one part of the heart to another, then some part of the heart cannot receive the signal so it cannot contract.”

“With this device, we can zoom in to the cellular level and get a very high resolution picture of what’s going on in the heart; we can see which cells are malfunctioning, which parts are not synchronized with the others, and pinpoint where the signal is weak,” said senior author Sheng Xu, a professor of nanoengineering at the UC San Diego Jacobs School of Engineering. “This information could be used to help inform clinicians and enable them to make better diagnoses.”

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Illustration of the device interfacing with heart cells (top). The sensors can monitor electrical signals in multiple single cells at once (bottom left) and at two sites in one cell (bottom right). Image adapted from Nature Nanotechnology

The device consists of a 3D array of microscopic field effect transistors, or FETs, that are shaped like sharp pointed tips. These tiny FETs pierce through cell membranes without damaging them and are sensitive enough to detect electrical signals—even very weak ones—directly inside the cells. To evade being seen as a foreign substance and remain inside the cells for long periods of time, the FETs are coated in a phospholipid bilayer. The FETs can monitor signals from multiple cells at the same time. They can even monitor signals at two different sites inside the same cell.

“That’s what makes this device unique,” said Gu. “It can have two FET sensors penetrate inside one cell—with minimal invasiveness—and allow us to see which way a signal propagates and how fast it goes. This detailed information about signal transportation within a single cell has so far been unknown.”

To build the device, the team first fabricated the FETs as 2D shapes, and then bonded select spots of these shapes onto a pre-stretched elastomer sheet. The researchers then loosened the elastomer sheet, causing the device to buckle and the FETs to fold into a 3D structure so that they can penetrate inside cells.

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SEM images of the device in its 2D form (left) and folded into its 3D structure (right). Image adapted from Nature Nanotechnology

“It’s like a pop-up book,” said Gu. “It starts out as a 2D structure, and with compressive force it pops up at some portions and becomes a 3D structure.”

The team tested the device on heart muscle cell cultures and on cardiac tissues that were engineered in the lab. The experiments involved placing either the cell culture or tissue on top of the device and then monitoring the electrical signals that the FET sensors picked up. By seeing which sensors detected a signal first and then measuring the times it took for other sensors to detect the signal, the team could determine which way the signal traveled and its speed. The researchers were able to do this for signals traveling between neighboring cells, and for the first time, for signals traveling within a single heart muscle cell.

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Device with a scaled-up FET sensor array for measuring electrical signals in a 3D cardiac tissue construct. Credit: Yue Gu

What makes this even more exciting, said Xu, is that this is the first time that scientists have been able to measure intracellular signals in 3D tissue constructs. “So far, only extracellular signals, meaning signals that are outside of the cell membrane, have been measured in these types of tissues. Now, we can actually pick up signals inside the cells that are embedded in the 3D tissue or organoid,” he said.

The team’s experiments led to an interesting observation: signals inside individual heart cells travel almost five times faster than signals between multiple heart cells. Studying these kinds of details could reveal insights on heart abnormalities at the cellular level, said Gu. “Say you’re measuring the signal speed in one cell, and the signal speed between two cells. If there’s a very big difference between these two speeds—that is, if the intercellular speed is much, much smaller than the intracellular speed—then it’s likely that something is wrong at the junction between the cells, possibly due to fibrosis,” he explained.

Biologists could also use this device to study signal transportation between different organelles in a cell, added Gu. A device like this could also be used for testing new drugs and seeing how they affect heart cells and tissues.

The device would also be useful for studying electrical activity inside neurons. This is a direction that the team is looking to explore next. Down the line, the researchers plan to use their device to record electrical activity in real biological tissue in vivo. Xu envisions an implantable device that can be placed on the surface of a beating heart or on the surface of the cortex. But the device is still far from that stage. To get there, the researchers have more work to do including fine-tuning the layout of the FET sensors, optimizing the FET array size and materials, and integrating AI-assisted signal processing algorithms into the device.

Paper: “Three-dimensional transistor arrays for intra- and inter-cellular recording.” Co-authors include Chunfeng Wang, Namheon Kim, Jingxin Zhang, Tsui Min Wang, Jennifer Stowe, Jing Mu, Muyang Lin, Weixin Li, Chonghe Wang, Hua Gong, Yimu Chen, Yusheng Lei, Hongjie Hu, Yang Li, Lin Zhang, Zhenlong Huang, Pooja Banik, Liangfang Zhang and Andrew D. McCulloch, UC San Diego; Rohollah Nasiri, Samad Ahadian and Ali Khademhosseini, Terasaki Institute for Biomedical Innovation; Jinfeng Li and Peter J. Burke, UC Irvine; Leo Huan-Hsuan Hsu, Xiaochuan Dai and Xiaocheng Jiang, Tufts University; Zheyuan Liu, Massachusetts Institute of Technology; and Xingcai Zhang, Harvard University.

This work was supported by the National Institutes of Health (1 R35 GM138250 01).

Europe's Earliest Female Infant Burial Reveals a Mesolithic Society that Honored Its Youngest Members

December 21, 2021--Researchers based at the UC San Diego Qualcomm Institute (QI) and Jacobs School of Engineering have digitally recreated, in painstaking detail, the oldest documented European burial of an infant female. The interactive 3D excavation site, included last week in an article with Scientific Reports (Nature), is being used by an international team to learn more about burial practices, gender-based status and other social behaviors of ancient hunter-gatherer groups.

Cross-section screen capture showing Neve’s burial site within the Arma Veirana cave in Liguria, Italy. Archaeologists can use the digital excavation created by UC San Diego researchers to revisit and study Neve’s resting grounds from anywhere in the world.

Archaeologists discovered the burial site in 2017 during an ongoing excavation at Arma Veirana, a cave in modern-day Italy. Led by the University of Colorado, Denver and the University of Colorado School of Medicine, the team discovered that the infant, nicknamed “Neve” by researchers, died at 40-50 days old approximately 10,000 years ago, during the early Mesolithic period. Buried with her were more than 60 pierced shell beads, four pendants and an eagle-owl talon.

Prior to advances in 3D scanning technology, archaeologists would have had to go to lengths to document an intact excavation site, including removing entire blocks of substrate for closer study. Now, UC San Diego’s interactive 3D reconstruction of the excavation offers archaeologists a reliable record that can be studied in perpetuity.

“During an excavation, archaeologists really have to pay attention to context and details, like forensic agents trying to recreate a crime scene,” said Dominique Meyer, co-author on the paper, QI engineer and alumnus of the UC San Diego Computer Science and Engineering Department. “The key to the digital reconstruction of the infant burial site was how it related to the context of the cave. This gives answers to the archaeological significance which would otherwise have been forever lost during the excavation process.”

The start of many discoveries

Meyer joined other QI researchers and UC San Diego undergraduate student Danylo Drohobytsky at Arma Veirana from 2017-2019. Over three field seasons, the team collected data and 3D imagery of both the surrounding landscape and burial site using drones and precise laser measurements. They then recreated the landscape and excavation, including Neve’s remains and accompanying artifacts, through a data reconstruction technique that pulls 3D information from photographs.

“Throughout this international and highly interdisciplinary research collaboration, our student-driven team had the opportunity to advance our vision of creating a deep-time archive and ‘digital twin’ of complex archaeological sites,” said Falko Kuester, co-author on the paper and director of the Cultural Heritage Engineering Initiative (CHEI) at QI. “The site’s ‘digital twin’ preserves it as it was originally discovered, making it accessible to future generations.”

Already, Neve’s discovery and preservation represent a meaningful addition to scientists’ understanding of burial practices from the early Mesolithic. Well-documented burials from the time period are extremely rare. Studying the fine details of Neve’s final resting place, from her position in relation to the artifacts to the significant wear and signs of use marking those same ornaments, offers potential insight into gender-based social status and personhood among early peoples.

In the future, scientists may be able to glean more knowledge from the Arma Veirana burial using virtual reality environments at UC San Diego. High-definition facilities like the WAVE, an immersive walk-in VR environment, enable researchers to effectively travel directly to the site as it was, and walk again through the excavation from its start to its current state.

Such collaborations are part of a larger effort at QI to advance fields like archaeology with new and emerging technologies. The CHEI team heads multiple related projects, including the study of submerged archaeological sites in the Yucatán peninsulaIce Age fossils and the bones of an early American in an underwater cave and delicate coral reef ecosystems.

Researchers Propose New Building Design Limits to Enhance Earthquake Resilience

Dec. 21, 2021-- Since the mid-1990s, a type of steel column that commonly features slender cross-sectional elements has become more prevalent in buildings along the West Coast of the United States and in other seismically active regions. Although these columns comply with modern design standards, our understanding of how they would perform during an earthquake has been limited by a lack of full-scale testing — until now.

Using an earthquake-simulating device called a shake table, researchers at the National Institute of Standards and Technology (NIST) and the University of California San Diego identified deficiencies in the performance of these columns, with many buckling prematurely. In a paper published in the Journal of Structural Engineering, the researchers propose new limits for column slenderness as a way to reduce the likelihood of column failure during an earthquake.

“Significant earthquake ground motions could create problems for an older building with these deep, slender columns that we've used in this research,” said NIST structural engineer John Harris, a co-author of the study. “This means that there is a risk of partial failure in parts of a building that are supported by these types of columns.”

The researchers fastened 48 steel columns of varying dimensions into a hydraulic system called the Seismic Response Modification Device (SRMD), which thrusted one end of each column back and forth, replicating the shaking motions of an earthquake.
Credit: UC San Diego Caltrans SRMD Test Facility

You can view the experiments in this playlist 

Throughout the 1990s, engineers gained substantial insight into the way structures respond to real earthquakes, such as the 1994 Northridge earthquake, which devastated the greater Los Angeles area. As a result, building codes began to impose strict requirements on the degree that buildings could sway during earthquakes — a measure known as story drift.

Steel columns in multistory buildings, with cross sections shaped like an upper case “L” are good at supporting the downward forces of the floors and roof resting upon them. But a shaking ground can introduce additional forces in all directions, potentially causing columns to deflect laterally, contributing to story drift. Before 1994, the middle part of columns’ I-shaped cross sections, known as webs, were often relatively short in buildings with steel frames. But since then, building designers have satisfied drift requirements by selecting columns with longer, or deeper, and typically more slender webs to boost their lateral stiffness.

These deep columns were OK to use as long as their web dimensions did not surpass certain depth-to-width ratios — known as a slenderness limit — meant to reduce the risk of columns losing their capability to carry weight during earthquakes, Harris said. However, some engineers were unsure of how these columns would hold up against real earthquake motions.

When the slenderness limits were developed decades ago, engineers did not have the facilities to test the seismic performance of full-scale columns like those actually used in buildings. Instead, they based the limits on reduced-scale model columns, creating some uncertainty about their effectiveness in reality. Full-scale tests have recently become possible with the availability of a very powerful shake table test facility, called Caltrans Seismic Response Modification Device (SRMD), at UC San Diego.

To assess the slenderness limits, Harris worked with fellow structural engineering experts at UC San Diego, with access to a shake table designed to put full-scale structural components through the seismic wringer.

Before 1994, the webs of steel columns were often relatively shallow (right) in buildings with steel frames. But since then, building designers have satisfied drift requirements by selecting columns with longer, or deeper, webs (left) to boost their lateral stiffness.
Credit: NIST

The researchers tested 48 deep columns, each 5 1/2 meters long and with webs of varying slenderness. The machine recreated the effects of earthquakes on columns by applying compressive forces to simulate the weight of the buildings and thrusting one end of the column back and forth with a hydraulic system, representing the lateral loads produced by a quake.

Because the effects of earthquakes can vary so greatly, the researchers used an assortment of loading protocols, which jolted and pressed on the columns in different ways. For certain columns, they applied a steady amount of compression, while varying compression that simulated the overturning effect of the building during an earthquake was used for other columns. The test specimens were also subjected to earthquake-induced lateral movements to simulate columns of steel buildings that were located either near or far away from the fault line. 

The team measured the response of each column during the test, taking note of any permanent changes to its shape. They coated the column ends in a layer of white paint that would begin to chip off as the steel bent, making permanent deformation more visually apparent. They tested every column until it could no longer oppose the forces exerted by the machine, driving some to buckle near their ends and others to contort along their entire length. Among the deformed columns, they picked up on a telling pattern.

“We noticed that, as the columns became stockier and less slender, they can more easily go through the entire loading protocol without losing a significant amount of their capability to withstand the earthquake motions,” Harris said.

Their results suggested that the previous small-scale tests were not painting a complete picture of deep column performance and that column webs meeting the limits prescribed by today’s codes may still be too slender.

Keeping the story drift requirements in mind, Harris and his research partners at UC San Diego were able to propose new slenderness limits with the data from the full-scale experiments. Columns with webs sized according to the new limit could potentially meet drift and stability requirements at the same time. 

The researchers recently brought the revised limits before the American Institute of Steel Construction, a standards organization, for review. If adopted, the more stringent limits on steel column webs could soften the blow of earthquakes, potentially saving newly designed buildings from unnecessary damage or partial collapse. 

The new limits could be incorporated into standards for evaluating existing buildings as well, enabling engineers to identify deep columns in need of corrective actions such as the addition of bracing.

Paper: G. Ozkula, C.-M. Uang, and J. Harris. Development of Enhanced Seismic Compactness Requirements for Webs in Wide-Flange Steel Columns. Journal of Structural Engineering. Published Oct. XX, 2020. DOI: XXX

 

Our 2021 Research Headlines

December 20, 2021-- From research into new ways to detect and preventCOVID-19, to new treatments for heart conditions and technology to combat natural disasters and climate change, it has been a busy year at the UC San Diego Jacobs School of Engineering. Here is a snapshot of research that made headlines this year, thanks to the dedicated work of our faculty, graduate and undergraduate student researchers, research and administrative staff, and campus and community partners. Delve deeper in press coverage in 2021 on our press coverage page

Fighting COVID-19

Niema Moshiri, a computer science teaching professor, was part of a UC San Diego team that used genetic sequencing to show that SARS COV-2 circulated in China as early as October 2019. The study received both national and international coverage, including CNN, the South China Morning Post and Yahoo News

A new tool for monitoring COVID-19 may one day be right under your nose. Researchers at UC San Diego are developing a color-changing test strip that can be stuck on a mask and used to detect SARS-CoV-2 in a person’s breath or saliva. The project is aimed at providing simple, affordable and reliable surveillance for COVID-19 infections that can be done daily and easily implemented in resource-poor settings. See news coverage in LA Times, Wall Street Journal, San Diego Union Tribune, Telemundo and ABC 10News.

Rapid COVID-19 tests are on the rise to deliver results faster to more people, and scientists need an easy, foolproof way to know that these tests work correctly and the results can be trusted. Nanoparticles that pass detection as the novel coronavirus could be just the ticket. Such coronavirus-like nanoparticles, developed by nanoengineers at UC San Diego, would serve as something called a positive control for COVID-19 tests.

Nanoengineers at UC San Diego have developed COVID-19 vaccine candidates that can take the heat. Their key ingredients? Viruses from plants or bacteria. In mice, the vaccine candidates triggered high production of neutralizing antibodies against SARS-CoV-2, the virus that causes COVID-19. If they prove to be safe and effective in people, the vaccines could be a big game changer for global distribution efforts, including those in rural areas or resource-poor communities. See news coverage in Fast Company.

Health research

A gene therapy for chronic pain could offer a safer, non-addictive alternative to opioids. By temporarily repressing a gene involved in sensing pain, the treatment increased pain tolerance in mice, lowered their sensitivity to pain and provided months of pain relief without causing numbness – and without permanently altering the genome. See news coverage in Science Magazine, Nature, C&EN, Medium (Future Human) and Gizmodo.

Bioengineers and physicians developed a bio-inspired hydrogel that forms a barrier to keep heart tissue from adhering to surrounding tissue after surgery. The team tested the hydrogel in rodents and conducted a pilot study on porcine hearts, with promising results. The work was covered in New Atlas and other outlets. 

UC San Diego engineers developed a soft, stretchy ultrasound patch that can be worn on the skin to monitor blood flow through vessels deep inside the body. Such a device can make it easier to detect cardiovascular problems, like blockages in the arteries that could lead to strokes or heart attacks. See news coverage in Physics World and Yahoo! News.

How do different parts of the brain communicate with each other during learning and memory formation? A study by researchers at UC San Diego takes a first step at answering this fundamental neuroscience question, thanks to a neural implant that monitors multiple brain regions at the same time.

Natural disasters and climate change

As California reacts to a record-breaking fire season, a backcountry observation network has  reached a milestone of installing more than 610 cameras across the state. The cameras are part of the ALERTWildfire camera network, built by UC San Diego, the University of Nevada, Reno and the University of Oregon. The network has become a vital firefighting tool helping first responders confirm and monitor wildfires from ignition through containment. Structural engineering professor Falko Kuester plays a key role in the system’s data collection and visualization. 

The UC San Diego shake table, the world’s largest outdoor earthquake simulator, is almost done with a $16.3 million upgrade. When the work is complete, the table will go from one dimension to three–or from one degree of freedom to three. The upgraded facility will be better able to replicate complex earthquake motions and will reopen in summer 2022 by putting to the test a full-scale, 10-story timber building. The upgrade work has been covered by the American Society of Civil Engineers, among others. 

Research into solid-state, silicon-based batteries took a significant step with a paper led by nanoengineering professor Shirley Meng, in collaboration with LG Energy Solutions, and published in Science. The work was broadly covered, including in Business Korea, Engadget and Yahoo! News

Cybersecurity and wireless communications

Deian Stefan and his research group have been hard at work making web browsers safer. A tool they designed in collaboration with Mozilla and UT Austin is now part of the latest version of Firefox. The story received broad coverage, including in The Verge and Engadget. Stefan’s team also developed tools that are part of the security-focused Brave browser. https://jacobsschool.ucsd.edu/news/release?id=3364 The team received a $3 million grant from the National Science Foundation, in conjunction with UT Austin.

A new technology developed by electrical engineers at UC San Diego might one day allow more people to have access to 5G connectivity that provides ultra-fast download speeds along with widespread, reliable coverage—all at the same time. See news coverage in Hackster and Interesting Engineering.

 

Robots for good

Roboticists led by computer science professor Laurel Riek built a navigation system that will allow robots to better negotiate busy clinical environments in general and emergency departments more specifically. The researchers have also developed a dataset of open source videos to help train robotic navigation systems in the future. The work was featured in PC Mag and United.AI

Roboticists led by professor Michael Tolley and PhD student Dylan Drotman developed a robot that doesn’t need electronics to function, and uses air pressure instead. The robot was quite popular with media outlets as well as YouTubers, including the Veritasium YouTube channel, which has 11 million subscribers. The video has more than 3.8 million views. Other outlets included IEEE Spectrum, CNet and MSN News

Wearables and more

A new wearable device turns the sweat and press of a fingertip into a source of power for small electronics and sensors. This sweat-fueled device is the first to generate power even while the wearer is asleep—no exercise or movement required. See news coverage in Science Magazine, Nature, CNET, New Scientist, ABC 10News and Ars Technica.

It is possible to re-create a bird’s song by reading only its brain activity, shows a first proof-of-concept study from the University of California San Diego. The study is an early step toward building vocal prostheses for humans who have lost the ability to speak. See news coverage in Salon, Miami Herald, BBC Science Focus and Psychology Today.

How do pelicans manage to glide above the waves? And why? Researchers in the Department of Mechanical and Aerospace Engineering and the Scripps Institution of Oceanography found an answer by modeling how the birds, the wind and the ocean interact. Their work was featured in The Washington Post and the Los Angeles Times

 

News Obituary: Remembering Paul A. Libby, founding UC San Diego faculty member

Professor Emeritus Paul A. Libby was a UC San Diego faculty member. 

December 20, 2021-- Paul A. Libby, Professor Emeritus in the Department of Mechanical and Aerospace Engineering  (MAE) at the University of California San Diego, passed away on Nov. 2, 2021, at the age of 100 in La Jolla, Calif. An international expert in turbulence and combustion, Libby was recruited in 1964 by Professor Stanford “Sol” Penner as one of 10 founding faculty members of the Department of Applied Mechanics and Engineering Science (AMES) at the newly formed campus in La Jolla.

During his 65 years of research in the field of aerodynamics, Libby made foundational contributions to the fields of supersonic and hypersonic flight, with important applications that include improved heat protection of re-entry vehicles through ablative shielding. He collaborated in the fields of fluid mechanics and combustion with an impressive array of prominent scientists in the United States and abroad. He also served as the U.S. member of the Fluid Dynamics Panel of the Advisory Group for Aerospace Research and Development (AGARD), an agency of NATO, and on other U.S. governmental panels.  

He  was elected to the National Academy of Engineering in 1999 “for contributions as a researcher, author, and educator who advanced knowledge of fluid dynamics, turbulence, and combustion through theoretical analyses.”  

Libby produced more than 200 journal publications and authored a monograph on turbulence,  publishing his last paper in 2017 with his longtime collaborators Professors Michel Champion of the University of Poitiers, France, and K.N.C. Bray of the University of Cambridge. This collaboration led, among other things, to the highly cited Bray-Champion-Libby model of turbulent combustion. In addition, the Homann-Libby flow is named after Libby for his work on the axisymmetric stagnation point flows. These contributions aid in the development of improved aircraft and missile propulsion engines as well as ground-based industrial and transportation processes.

Libby received a Guggenheim Fellowship in 1972 and a Royal Society Guest Fellowship in 1982, both to support extended stays at the Imperial College of London as a visiting researcher. 

"Beyond the impact of his own personal research, as one of the earliest faculty members in the Department, Paul played a key role in building a Department and School with deep roots in the engineering sciences, thereby providing our students with the skills they need to make critical contributions in their chosen application areas; as a result, his legacy will continue to be felt for many years to come,” said George Tynan, chair of the UC San Diego Department of Mechanical and Aerospace Engineering. 

At UC San Diego, Libby held various administrative positions, including Associate Dean of Graduate Affairs, Acting Dean of Graduate Affairs, Chair of the AMES Department, and Interim Dean of the Engineering Division. He taught graduate and undergraduate engineering classes and served on numerous academic committees, including the UC San Diego Design Review Board.  Throughout his career, Libby also enjoyed mentoring  graduate students and became lifelong friends with many of them. 

Libby was born on Sept. 4, 1921 in Mineola, New York. He received his degrees from the Polytechnic Institute of Brooklyn, a bachelor’s degree in aeronautical engineering in 1942 and a PhD degree in applied mechanics in 1949. Libby also worked as an apprentice engineer with Chance Vought Aircraft and served as an officer in the Navy Bureau of Aeronautics. 

In the 1950s, Libby was appointed to the faculty of the Polytechnic Institute of Brooklyn, where he became a tenured professor, collaborating  with Professor Antonio Ferri on the development of experimental supersonic and hypersonic research facilities. This effort involved an extended collaboration with Theodore Von Kàrmàn, a leading figure in 20th century aerodynamics, at the California Institute of Technology, .

Outside of his academic pursuits, Libby was an avid tennis player, retiring from tennis only in his eighties, and an excellent cook. He was a lifelong enthusiast of gardening, classical music, modern architecture, history, and politics.

Libby was preceded in death by his wife Petrina, and is survived by his son John Libby, daughter Patricia Libby Thvedt, and numerous grand-children. The family has requested that remembrances be made in the form of contributions to the UC San Diego Foundation fund designated as “The Dr. Paul A. Libby and Petrina M.C. Libby Endowed Scholarship in Engineering at UC San Diego."  Donations may be made  online at https://giveto.ucsd.edu/giving/home/gift-referral/4e375052-6bd8-4ba3-8c70-b2ac42fde0d5/, or by calling UC San Diego Gift Processing at 858-534-4493, or mailing a check (made payable to the UC San Diego Foundation) with "Libby Endowed Scholarship (Fund No. 7230)" on the memo line to UC San Diego Gift Services, 9500 Gilman Dr. Mail Code 0940, La Jolla, CA 92093 - 0940.  

Gifts may also be made in Libby’s memory to his beloved KUSC Radio at KUSC.org





 

Jacobs School of Engineering institutional highlights 2021

December 16, 2021--As we prepare to hit the ground running in 2022, we're looking back at all that our students, staff, faculty and partners accomplished last year toward our mission to leverage engineering and computer science for the public good. Here are a few of our UC San Diego Jacobs School of Engineering highlights from 2021, including launching new programs and research centers, welcoming new faculty, and preparing our new building.

Check out our 2021 research highlights here. 

#9 ranking: For the second year in a row, the UC San Diego Jacobs School of Engineering was ranked the #9 engineering school in the nation, according to the U.S. News & World Report Rankings of Best Engineering Schools. This #9 ranking is up from #11 two years ago, #12 three years ago, #13 four years ago, and #17 five years ago. “Ranking ninth in the nation is a tribute to the hard work, grit and excellence of our students, staff, faculty, industry partners, collaborators and friends," said Albert P. Pisano, Dean of the UC San Diego Jacobs School of Engineering. "I look at rankings as recognition rather than definition. It's wonderful to be recognized for some of the ways we are strengthening and growing as a school and as a community."

Franklin Antonio Hall nears completion: Franklin Antonio Hall is expected to be open and operational in the spring of 2022. The facility will serve as a model for how to build innovation ecosystems with physical roots and virtual infrastructure that extend opportunities well beyond the walls of the building. The diverse yet complementary research teams in the 180,000SF building will develop platform technologies that can be pivoted from one application to another to rapidly respond to the needs of the country. Jacobs School Dean Albert P. Pisano shares his vision for Franklin Antonio Hall in this video.

New Faculty: The Jacobs School hired 27 new faculty in the past two years. These professors are among the nearly 140 faculty who have joined the UC San Diego Jacobs School of Engineering in the last eight years. These new faculty and the bold research they pursue will further the Jacobs School’s mission of leveraging engineering and computer science for the public good. “We are a young, powerful school because we have added cohort after cohort of energetic, imaginative, bold new faculty. I am very much looking forward to seeing the impact they will make,” said Pisano. 

Highly Cited researchers: UC San Diego is home to the 9th largest number of highly cited researchers in the world. The Jacobs School is proud of the 10 engineers and computer scientists who were named among the world's most influential researchers in their fields according to the 2021 Clarivate listing of Most Highly Cited Researchers in the World.

NextProf Pathfinder: In an effort to diversify the ranks of engineering faculty, the Jacobs School partnered with the University of Michigan to strengthen the NextProf Pathfinder program. The two-day program is aimed at first and second-year PhD students, as well as students in masters programs, in an effort to keep them pursuing careers in academia. The two schools will partner on the NextProf Pathfinder program going forward, with the institutions swapping hosting duties each year; UC San Diego will host the workshop in 2022.

Veteran Forge: The Jacobs School of Engineering launched Veteran Forge, a new program designed to connect US government agencies, defense contractors, and National Laboratories with military veterans earning engineering and computer science degrees at UC San Diego. The program aims to provide a job upon graduation at one of the Veteran Forge partner organizations to qualifying student veterans at the Jacobs School, while at the same time offering partner organizations access to top talent that is qualified for required security clearances.

Power Management Integration Center: Innovations in power electronics systems will enable the mobile/IoT devices, EVs, data centers & energy grids of the future. UC San Diego is helping drive these innovations as a new member of an industry-university partnership called the Power Management Integration Center. Directed by Dartmouth College, PMIC is innovating power electronics that support higher efficiency, smaller size and reduced cost. UC San Diego joined PMIC as the second university site. The expanded center has attracted five new industry partners: Allegro MicroSystems, Efficient Power Conversion, Intel Corporation, Meta (formerly The Facebook company) and Qualcomm.


New Large Campus-wide Research Centers

TILOS: The National Science Foundation awarded $20 million for the creation of The Institute for Learning-enabled Optimization (TILOS), headquartered at UC San Diego. The institute will pursue foundational breakthroughs at the nexus of artificial intelligence and optimization to transform chip design, robotics, and communication networks. TILOS includes researchers from MIT, San Diego-based National University, U. of Pennsylvania, UT Austin, and Yale; partial support is from Intel. TILOS is led by Andrew Kahng, a world-renowned expert in the field of chip design and professor of computer science and electrical engineering at UC San Diego. The Institute will be housed at the Halicioglu Data Science Institute (HDSI), UC San Diego’s campus hub for data science and artificial intelligence.

Wu Tsai Human Performance Alliance: UC San Diego was one of six institutions invited to participate in the Wu Tsai Human Performance Alliance, a scientific collaboration that aims to transform human health and well-being on a global scale through the discovery and translation of the biological principles underlying peak human performance. The Alliance was created through a $220M philanthropic investment from the Joe and Clara Tsai Foundation. Partner institutions include Stanford; Boston Children’s Hospital, a Harvard Medical School Affiliate; U. of Kansas; U. of Oregon; and the Salk Institute for Biological Studies. The UC San Diego arm of the Alliance is led by Andrew McCulloch, a professor in the departments of Bioengineering and Medicine at UC San Diego and director of UC San Diego’s campus-wide Institute of Engineering in Medicine.

Center for Admixture Science: Disease prevalence and severity can vary considerably across racial and ethnic groups due to genetic and social factors. However, most of what we know about the genetics of human disease comes from datasets of predominantly white, European people. To address this issue, researchers at University of California San Diego, including computer science professor Melissa Gymrek, have been awarded $11.7 million to launch the Genetic & Social Determinants of Health: Center for Admixture Science and Technology.

Treating drug-resistant epilepsy: The National Institutes of Health has awarded a $12.25 million grant to the University of California San Diego to develop and enhance brain-sensing and brain-stimulating platform technologies to enable treatment of drug-resistant epilepsy. The project is led by UC San Diego electrical engineering professor Shadi Dayeh who leads the Integrated Electronics and Biointerfaces Laboratory and brings together expertise from all across UC San Diego, including the Jacobs School of Engineering and Health Sciences. The nation-wide team includes researchers and longtime collaborators of Dayeh at Massachusetts General Hospital led by Dr. Sydney Cash and Oregon Health & Sciences University led by Dr. Ahmed Raslan.

 

The router in your home might be intercepting some of your Internet traffic--but it may be for your own good

December 15, 2021-- The router in your home might be intercepting some of your Internet traffic and sending it to a different destination. Specifically, the router can intercept the Domain Name System traffic --the communications used to translate human-readable domain names (for example www.google.com) into the numeric Internet Protocol (IP) addresses that the Internet relies on.  That’s the finding from a team of computer scientists at the University of California San Diego, which they presented at the Internet Measurement Conference on November 3, 2021. 

Why does this matter? 

“The primary concern is privacy,” said Audrey Randall, a Ph.D. student in computer science at the University of California San Diego and first author of a paper on this subject. “When you visit a web site, you first have to do a DNS lookup for that site.  So whoever gets your DNS traffic gets to see all the sites that you’re visiting. In principle, you get to choose who performs your DNS lookups and you might pick a company that you trust not to sell your data or a company that uses robust security to protect their logs.  But if your DNS traffic is being silently intercepted and routed elsewhere, then someone else gets to see all that information.”

Many cases of DNS interception are not malicious, Randall pointed out. Often, interception is used by Internet Service Providers (ISPs) to protect users from malware that contacts particular Domain Name System (DNS) resolvers, which are essentially the Internet’s phone books. These resolvers transform the website URL users enter into a browser into an IP address for the servers that store the website’s content. In this case, interception can be helpful, by preventing malware from harming a user’s computer.

Researchers even found one instance of interception that was neither malicious nor benign: it was a simple bug. The UC San Diego team disclosed this bug to two Internet service providers. Both said they would work to fix issues. However, DNS queries also provide valuable data about users’ behavior that can be sold to advertisers, which might provide a less altruistic motive for some companies to intercept them.

The phenomenon of DNS interception has been studied in recent years, but little was known about where in the network interception takes place--until now. It turns out that in a surprising number of cases, users’ own home routers are the culprit. 

These routers don’t send DNS queries to the target DNS resolver that the user specified. Instead, the software reroutes them to an alternate resolver. The query response is then modified so that it appears to come from the original target resolver. This modification makes the interception “transparent” to the user, and therefore very difficult to detect.

Determining where transparent interception takes place is difficult. But researchers were able to do this by devising an innovative and clever methodology. They first made use of special DNS queries that were invented as debugging tools, but they found that no single query could give enough information to pinpoint an interceptor’s location. The key turned out to be to compare the responses from two special queries: the responses were identical if the interceptor was the home router, but different if the interceptor was elsewhere in the network.

Even though DNS interception is often used to foil malware, the fact remains that users have no idea that their traffic is being redirected, or where it’s redirected to. “If you are concerned enough about who sees your data and who sells your data to advertisers, you want to make sure that the company handling it is actually who they say they are,” said Randall. “When this type of transparent interception is used, you think you have control over your traffic, but you don’t.”

Researchers caution that their study has some limitations. For example, the platform they used to conduct their study is not representative of all interception cases, because it over-represents certain Internet service providers, countries, or demographics. 

Funding for this work was provided in part by National Science Foundation grants CNS-1629973 and CNS-1705050, the Irwin Mark and Joan Klein Jacobs Chair in Information and Computer Science at UC San Diego, and support from Google.

Home is Where the Hijacking is: Understanding DNS Interception by Residential Routers

Audrey Randall, Enze Liu, Ramakrishna Padmanabhan, Gautam Akiwate, Geoffrey M. Voelker, Stefan Savage and Aaron Schulman, University of California San Diego



 

Einstein wins again

The theory of general relativity passes a range of precise tests set by pair of extreme stars

December 13, 2021 -- An international team of researchers, including electrical engineers at the University of California San Diego, has conducted a 16-year long experiment to challenge Einstein’s theory of general relativity with some of the most rigorous tests yet. Their study of a unique pair of extreme stars, so called pulsars, involved seven radio telescopes across the globe and revealed new relativistic effects that were expected and have now been observed for the first time. Einstein’s theory, which was conceived when neither these types of extreme stars nor the techniques used to study them could be imagined, agrees with the observation at a level of at least 99.99%.

The results are published in Physical Review X.

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Artistic impression of the Double Pulsar system, where two active pulsars orbit each other in just 147 min. The orbital motion of these extremely dense neutrons star causes a number of relativistic effects, including the creation of ripples in spacetime known as gravitational waves. The gravitational waves carry away energy from the systems which shrinks by about 7mm per days as a result. The corresponding measurement agrees with the prediction of general relativity within 0.013%. Credit: Michael Kramer/MPIfR

More than 100 years after Albert Einstein presented his theory of gravity, scientists around the world continue their efforts to find flaws in general relativity. The observation of any deviation from General Relativity would constitute a major discovery that would open a window on new physics beyond our current theoretical understanding of the Universe.

“We studied a system of compact stars that is an unrivalled laboratory to test gravity theories in the presence of very strong gravitational fields," said lead investigator Michael Kramer, a professor at the Max Planck Institute for Radio Astronomy (MPIfR) in Bonn, Germany. "To our delight we were able to test a cornerstone of Einstein’s theory, the energy carried by gravitational waves, with a precision that is 25 times better than with the Nobel-Prize winning Hulse-Taylor pulsar, and 1000 times better than currently possible with gravitational wave detectors.” He explains that the observations are not only in agreement with the theory, “but we were also able to see effects that could not be studied before''.

“We follow the propagation of radio photons emitted from a cosmic lighthouse, a pulsar, and track their motion in the strong gravitational field of a companion pulsar," said Ingrid Stairs, a professor at the University of British Columbia at Vancouver. "We see for the first time how the light is not only delayed due to a strong curvature of spacetime around the companion, but also that the light is deflected by a small angle of 0.04 degrees that we can detect. Never before has such an experiment been conducted at such a high spacetime curvature.”

This cosmic laboratory known as the “Double Pulsar” was discovered by members of the team in 2003. It consists of two radio pulsars which orbit each other in just 147 min with velocities of about 1 million km/h. One pulsar is spinning very fast, about 44 times a second. The companion is young and has a rotation period of 2.8 seconds. It is their motion around each other which can be used as a near perfect gravity laboratory.

“Such fast orbital motion of compact objects like these - they are about 30% more massive than the Sun but only about 24 km across - allows us to test many different predictions of general relativity - seven in total!" said Dick Manchester, a professor at Australia's national science agency, CSIRO. "Apart from gravitational waves, our precision allows us to probe the effects of light propagation, such as the so-called “Shapiro delay” and light-bending. We also measure the effect of  “time dilation” that makes clocks run slower in gravitational fields. We even need to take Einstein's famous equation E = mc2 into account when considering the effect of the electromagnetic radiation emitted by the fast-spinning pulsar on the orbital motion. This radiation corresponds to a mass loss of 8 million tonnes per second! While this seems a lot, it is only a tiny fraction - 3 parts in a thousand billion billion(!) - of the mass of the pulsar per second.”

The researchers also measured - with a precision of 1 part in a million(!) - that the orbit changes its orientation, a relativistic effect also well known from the orbit of Mercury, but here 140,000 times stronger. They realized that at this level of precision they also need to consider the impact of the pulsar’s rotation on the surrounding spacetime, which is “dragged along” with the spinning pulsar. “Physicists call this the Lense-Thirring effect or frame-dragging. In our experiment it means that we need to consider the internal structure of a pulsar as a neutron star. Hence, our measurements allow us for the first time to use the precision tracking of the rotations of the neutron star, a technique that we call pulsar timing to provide constraints on the extension of a neutron star,” explained Norbert Wex from the MPIfR, another main author of the study. 

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The seven radio telescopes used for observations of the double pulsar PSR J0737-3039. Clockwise from upper left: Effelsberg Radio Telescope (Germany), Nançay Radio Telescope (NRT, France), Westerbork Synthesis Radio Telescope (WSRT, The Netherlands), Parkes Radio Telescope (Australia), Jodrell Bank Telescope (UK), Very Long Baseline Array (VLBA, U.S.), Green Bank Telescope (GBT, U.S.). Credit: Norbert Junkes/MPIfR (Effelsberg), Letourneur and Nançay Observatory (NRT), ASTRON (WSRT), ATNF/CSIRO (Parkes), Anthony Holloway (Jodrell Bank), NRAO/AUI/NSF (VLBA), NSF/AUI/Green Bank Observatory (GBT).

The technique of pulsar timing was combined with careful interferometric measurements of the system to determine its distance with high resolution imaging, resulting in a value of 2400 light years with only 8% error margin. “It is the combination of different complementary observing techniques that adds to the extreme value of the experiment," said Adam Deller, a professor at Swinburne University in Australia who was responsible for this part of the experiment. "In the past similar studies were often hampered by the limited knowledge of the distance of such systems.”

This is not the case here, where in addition to pulsar timing and interferometry also the information gained from effects due to the interstellar medium were carefully taken into account. “We gathered all possible information on the system and we derived a perfectly consistent picture, involving physics from many different areas, such as nuclear physics, gravity, interstellar medium, plasma physics and more," said William Coles, professor emeritus of electrical and computer engineering at the UC San Diego Jacobs School of Engineering. "This is quite extraordinary.”

“Our results are nicely complementary to other experimental studies which test gravity in other conditions or see different effects, like gravitational wave detectors or the Event Horizon Telescope. They also complement other pulsar experiments, like our timing experiment with the pulsar in a stellar triple system, which has provided an independent (and superb) test of the universality of free fall”, said Paulo Freire, also from MPIfR.

“We have reached a level of precision that is unprecedented," said Kramer. "Future experiments with even bigger telescopes can and will go still further. Our work has shown the way such experiments need to be conducted and which subtle effects now need to be taken into account. And, maybe, we will find a deviation from general relativity one day.”

News release adapted from: Max Planck Institute for Radio Astronomy

UC San Diego engineering professors inducted into National Academy of Inventors

December 7, 2021 -- Two professors at the UC San Diego Jacobs School of Engineering have been named 2021 fellows of the National Academy of Inventors (NAI).

Shaochen Chen, professor and chair of nanoengineering, and Tse Nga (Tina) Ng, professor of electrical and computer engineering, were among the 164 fellows announced by the NAI this year who have demonstrated a spirit of innovation in creating or facilitating outstanding inventions that have made a tangible impact on the quality of life, economic development, and the welfare of society. Election to NAI Fellow is the highest professional distinction accorded solely to academic inventors.

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Shaochen Chen is recognized for his innovative 3D bioprinting technology, which rapidly reproduces detailed structures that mimic the complex designs and functions of living biological tissues. Chen’s lab has used this technology to create lifelike liver tissue, networks of blood vessels, coral reef structures, and patient-specific spinal cord implants for treating severe spinal cord injury. What’s also noteworthy about Chen’s 3D bioprinting technology is that it prints structures with micrometer-scale resolution at an unprecedented speed of just mere seconds.

“My goal is to use our engineering talents to develop tools and technology to advance healthcare—specifically in the areas of tissue engineering and drug discovery,” said Chen. “In the tissue engineering area, we are developing our bioprinting technology to help overcome big bottlenecks in creating organ transplants, which are in high demand but in short supply. In the drug discovery area, we are developing our technology to mass-produce human tissue models, which pharmaceutical companies could use to test millions of drug candidates immediately for efficacy and toxicity. This will provide better prediction for the outcomes of human trials; significantly reduce the risk of later stage drug failure, saving millions of dollars during drug discovery; and speed up the drug development process to hopefully save more lives.”

Chen holds 18 patents and provisional patents. He is the co-founder of the startup company, Allegro 3D, which licensed the bioprinting technology and has produced a commercial 3D bioprinter (Stemaker™ Model D) that is currently being used by biotechnology, pharmaceutical and university research labs worldwide.

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Tse Nga (Tina) Ng is a leader in the field of flexible printed electronics. She is recognized for engineering additive manufacturing processes to create large-area optical and mechanical sensor systems. One example of such a system is a thin, compact infrared imager that Ng’s lab recently developed. This infrared imager has one of the largest display areas of infrared imagers to date and is fabricated using thin film processes, so it is easy and inexpensive to scale up to make even larger displays for biomedical imaging, silicon wafer inspection, and defense applications.

Ng hold 39 U.S. patents—some of which have been licensed to the U.S. Army and the Department of Energy, and others are in use at Palo Alto Research Center (PARC, a subsidiary of Xerox). The patents enable low-cost additive printing of sensors, memory elements and transistor circuits for Internet-of-Things devices and wearable systems. The patents were instrumental in the commercialization of Xerox’s printed electronic labels technology, which is used in the smart packaging and printed electronics industries.

“I am fortunate to work with great students at the Jacobs School to advance the mission of engineering for the public good,” said Ng. “In addition to producing peer-reviewed publications, my students and I engage in patent applications to facilitate technology translation to commercial partners. Coming in with my industrial research background, I can share my experience to help students understand the patent process—which is very different from academic publishing—so that they, too, can contribute to technology translation.”

This framework will improve the security of all Firefox users

Computer scientists develop a framework to protect browsers from zero-day vulnerabilities in third-party libraries

Dec. 6, 2021--Researchers from the University of California San Diego, the University of Texas at Austin, and Mozilla have designed a new framework, called RLBox, to make the Firefox browser more secure. Mozilla has started deploying RLBox on all Firefox platforms this week

RLBox increases browser security by separating third-party libraries that are vulnerable to attacks from the rest of the browser to contain potential damage—a practice called sandboxing.

Browsers, like Firefox, rely on third-party libraries to support different functionalities—from XML parsing, to spell checking and font rendering. These libraries are often written in low-level programming languages, like C, and, unfortunately, introducing vulnerabilities in C code is extremely easy. RLBox protects users from inevitable vulnerabilities in these libraries and supply-chain attacks that exploit these libraries. 

“Well funded attackers are exploiting zero-day vulnerabilities and supply chains to target real users”, said Deian Stefan, an assistant professor in UC San Diego’s Computer Science and Engineering department. “To deal with such sophisticated attackers we need multiple layers of defense and new techniques to minimize how much code we need to trust (to be secure). We designed RLBox exactly for this.”

The team’s effort to deploy RLBox on all Firefox platforms is detailed in a recent Mozilla Hacks blog post.

With RLBox, developers can retrofit systems like Firefox to put modules, like third-party libraries, in a fine-grained software sandbox. Like process-based sandboxing, which browsers use to isolate one site from another, software sandboxing ensures that bugs in the sandboxed module will not create security vulnerabilities—bugs are contained to the sandbox. “Unlike process-based sandboxing, though, RLBox’s sandboxing technique makes it possible for developers to isolate tightly coupled modules like Graphite and Expat without huge engineering or performance costs,” said Shravan Narayan, the UC San Diego computer science PhD student leading the project.

WebAssembly and sandboxing

At its core, the RLBox framework consists of two components. The first is the sandboxing technique itself: RLBox uses WebAssembly (Wasm). Specifically, RLBox compiles modules to WebAssembly and then compiles Wasm to native code using the fast and portable wasm2c compiler. “By compiling to Wasm before native code, we get sandboxing for free: We can ensure that all memory access and control flow will be instrumented to be confined to the module boundary,” said Narayan.

Wasm also makes it possible for RLBox to optimize calls into and out of sandboxed code into simple function calls. In an upcoming study, to be published in the proceedings of the 2022 ACM SIGPLAN Principles of Programming Languages Symposium, the researchers show that this is safe because Wasm satisfies a set of theoretical conditions called  “zero-cost conditions.” This is unlike most other sandboxing techniques, which require glue code at the sandbox-application boundary to be secure. This glue code is error-prone and, in some cases, contributes to large performance overheads—the team’s Wasm compiler elides this glue code, its complexity, and its overhead.

Tainted type system

The second key component of RLBox is its tainted type system. Sophisticated attackers can break out of the Wasm sandbox if the code interfacing with the sandboxed code—the Firefox code—does not carefully validate all the data that comes out of the sandbox. RLBox’s type system, which is implemented using C++ metaprogramming, prevents such attacks by marking all data coming out of the sandbox as “tainted” and ensuring, through compiler errors, that developers sanitize potentially unsafe data before using it. “Without such a type system, it would be extremely difficult to ensure that developers put all the right checks in all the right places,” said Stefan.

“RLBox is a big win for Firefox and our users,” said Bobby Holley, Distinguished Engineer at Mozilla. “It protects our users from accidental defects as well as supply-chain attacks, and it reduces the need for us to scramble when such issues are disclosed upstream.”

The team’s original work on RLBox was published in the proceedings of the USENIX Security Symposium last March. Since then they’ve been working on bringing RLBox to all Firefox users. RLBox will ship on all Firefox platforms, desktop and mobile, sandboxing five different modules: Graphite, Hunspell, Ogg, Expat and Woff2. The team is actively working on sandboxing more modules in future versions of Firefox and supporting use cases beyond Firefox.

This work was supported in part by gifts from Mozilla, Intel, and Google; by the National Science Foundation  under grant numbers CCF-1918573  and CAREER CNS-2048262; and, by the CONIX Research Center, one of six centers in JUMP, a Semiconductor Research Corporation (SRC) program sponsored by DARPA.

 

Who's got your mail? Google and Microsoft, mostly

Concentration of email service providers increases impact of service failures and data breaches

Top providers and the number and percentage of domains using these companies in different sets of domain names

December 6, 2021-- Who really sends, receives and, most importantly perhaps, stores your business’ email? Most likely Google and Microsoft, unless you live in China or Russia. And the market share for these two companies keeps growing. 

That’s the conclusion reached by a group of computer scientists at the University of California San Diego, who studied the email service providers used by hundreds of thousands of Internet domains-- between 2017 and 2021. 

“Our research team empirically showed the extent to which email has been outsourced and concentrated to a small number of providers and service providers,” said Stefan Savage, a professor in the UC San Diego Department of Computer Science and Engineering and one of the paper’s senior authors. 

The team presented their findings at the Internet Measurement Conference 2021, which took place virtually Nov. 2 to 4, 2021.

This concentration has several consequences: it increases the impact of service failures and data breaches; and it exposes companies and users outside the United States to potential subpoenas from U.S. government agencies. 

A quick explainer of the difference between domains and service providers: The second half of your email address is your company or agency's domain--for example, ucsd.edu is the domain for the University of California San Diego. The email service provider is the company that, behind the scenes, provides the infrastructure that allows you to send and receive email and stores your messages--so ucsd.edu’s email service is provided by a combination of Google and Microsoft mail services.

As of June 2021, Google and Microsoft are the dominant providers among popular domains, with 28.5% and 10.8% market share, respectively. In comparison, GoDaddy leads the market of providing services for smaller domains, with a 29% market share. The authors also observed a higher level of concentration over time: Google and Microsoft’s market share increased by 2.3% and 2.9%, respectively, since June 2017. 

Some of the growth comes from smaller domains that used to host their own emails. “While self-hosted domains switched to providers across all categories, more than a quarter of them changed their mail provider to Google and Microsoft,” said Alex Liu, a UC San Diego computer science Ph.D. student and the paper’s lead author. 

More affected during outages, data breaches

Concentration of email service providers has led to much bigger service outages. In August and December 2020, global outages affected Gmail and Drive--Gmail alone has an estimated 1.5 billion users. Outlook most recently suffered an outage in October 2021-- an estimated 400 million people use the service. 

The concentration of email service providers also puts more people at risk in the event of a data breach. One often-cited example is the Yahoo data breach that exposed at least 500 million user accounts. Recently, a flaw in a Microsoft Exchange protocol has been shown to have leaked hundreds of thousands of credentials. 

Legal impact

Mail provider preferences by country

Google and Microsoft, the two dominant US-based email service providers, appear to be in wide use by organizations outside the United States — particularly across Europe, North America, South America, large parts of Asia and, to a lesser extent, Russia. For example, 65% of Brazilian domains in the researchers’ dataset host email with Google or Microsoft. But they are not used in China. 

However, outsourcing email service to US companies can also have legal implications. Under the 2018 CLOUD Act, US-based providers can be legally compelled to provide stored customer data, including e-mail, to US law enforcement agencies, regardless of the location of the data, or of the nationality or residency of the customer using the data. 

Perhaps as a result, Tencent has an overwhelming market share in China, with 41%, as does Yandex in Russia, with 32 %. Both countries have shown that they prefer to keep control over data access. 

In addition, an increasing number of email domains contract with email security providers, such as ProofPoint and Mimecast. These companies can operate as a third-party filter for inbound emails, removing the need to manage security locally. These companies have almost a 7% market share for large commercial companies; and a 17.5% market share for .gov domains. 

The research was funded by the National Science Foundation, the University of California San Diego, the EU H2020 CONCORDIA project and Google. 

 

 

 

UC San Diego joins Dartmouth in industry-university collaboration to take power electronics to the next level

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L-R: Hanh-Phuc Le and Patrick Mercier


December 6, 2021 -- Smartphones that last for days on a single charge and are still thin, compact and lightweight. Electric vehicles that drive further with their existing batteries and are affordable. Data centers that meet the growing demands of seven billion internet-connected devices and counting while cutting down their carbon emissions and use of space. For these to become reality, electrified systems need cutting-edge upgrades in the hardware that manages and distributes the power in these systems.

This is a challenge that the University of California San Diego is helping to tackle as a new member of the Power Management Integration Center (PMIC)—a partnership directed by Dartmouth that brings industry and university members together to innovate power electronics technologies that support higher efficiency, smaller size and reduced cost.

Such innovations will be transformative for a wide range of applications such as battery-powered mobile and IoT devices; electrified transportation; renewable energy systems; 5G and 6G communications; and artificial intelligence and machine learning.

“Power management is a big bottleneck in basically every electronic system you can imagine,” said Patrick Mercier, a professor of electrical and computer engineering at the UC San Diego Jacobs School of Engineering and co-director of the university’s PMIC effort. There are fundamental limitations to how small the power management hardware can be miniaturized, he explained. And these, in turn, limit what kinds of improvements can be made to the size, cost, performance and battery life of the entire system.

“To get around some of these fundamental limitations, we have to be clever about how we architect our circuits and systems,” said Mercier. “At PMIC, we are working to achieve this goal by designing and creating new circuit topologies and using energy storage elements in new and interesting ways.”

PMIC is an Industry-University Cooperative Research Center (IUCRC) funded by the National Science Foundation. The center, founded in 2018, was a partnership between Dartmouth and five of the nation’s leading electrical tech companies: Analog Devices, Empower Semiconductor, Enphase Energy, Infineon Technologies and West Coast Magnetics.

UC San Diego recently joined PMIC as the second university site. The expanded center has attracted five new industry partners: Allegro MicroSystems, Efficient Power Conversion (EPC), Intel, Meta (formerly The Facebook company) and Qualcomm.

Mercier, along with UC San Diego electrical and computer engineering professor Hanh-Phuc Le, are the co-directors of the center’s UC San Diego site.

“We have a very strong team here that combines diverse expertise in the area of power management integration,” said Le.

Le, for example, is an expert at developing integrated power converters for data centers and mobile devices. His lab also designs power management integrated circuits for wireless and robotic systems. Meanwhile, Mercier brings in expertise in creating ultra-low power, miniaturized integrated circuits for sensors, wearables and IoT devices.

Other members of the UC San Diego team include: Tajana Rosing, a professor of computer science and engineering, who is an expert in energy efficient computing and power management in computing systems, with a focus on machine learning and artificial intelligence; Shadi Dayeh, a professor of electrical and computer engineering, who is an expert at developing next-generation materials for power management, namely gallium nitride semiconductors and transistors for 5G and 6G communications; and Peter Asbeck, a professor of electrical and computer engineering, who is an expert in high frequency semiconductors and high efficiency power amplifiers for 5G and 6G wireless technologies.

UC San Diego is also bringing its strong connection to industry to PMIC. The team’s faculty members have extensive experience recruiting and retaining corporate members to sponsor and collaborate on university projects—these include projects at the UC San Diego Center for Wearable Sensors and Center for Wireless Communications, for example. The UC San Diego team also consists of faculty members who are co-founders of startup companies.

“A big strength of our team is that we have a good understanding of what various tech companies actually need, and that’s what enables us to bring these companies on board with what we’re doing,” said Le.

PMIC serves as a collaborative research ecosystem where academia and industry can come together to solve fundamental problems and develop next-generation technologies that will advance the field of integrated power electronics. The NSF funding supports the partnership, in which the universities provide the research infrastructure and talent, and industry partners provide research funding and guidance. All industry members vote on the research areas the center should pursue.

Integrating plant molecular farming and materials research for next-generation vaccines

Once again, NASA chooses a UC San Diego graduate for astronaut training

The Core of Powerful, Power-Efficient Processors

Team from UC San Diego and HP Labs has been honored with a Test of Time award for creating a novel processor architecture

December 3, 2021

The high-performance yet low-power processors running billions of today’s laptops and mobile devices come thanks to research by computer scientists at the University of California San Diego and HP Labs.

Their work, which began nearly two decades ago, has influenced the design of many modern processors such as ARM's big.Little, Qualcomm’s Snapdragon, Intel's Alder Lake and Apple’s flagship Apple M1, including the recently announced M1Pro and M1 Max.

Dean Tullsen

“Nearly everyone probably has one running something in their lives,” said Dean Tullsen, a UC San Diego Computer Science and Engineering professor who was part of the team who set the foundation for a new way of thinking about processors.

Now, the paper that led to a novel processor architecture that would provide significant energy benefits has been recognized for its lasting impact with a MICRO Test of Time Award.

The paper, “Single-ISA Heterogenous Multi-Core Architectures: The Potential for Processor Power Reduction” published in 2003, has since been cited more than 1,000 times and spawned several impactful academic and industrial projects on heterogeneous systems.

 

“This simple, but powerful idea now drives a large number of computer systems,” said Luiz Barroso, a Google Fellow and head of the Office of Cross-Google Engineering, who nominated the paper.

At the time their paper was published, processors were increasing in performance and speed, resulting in challenges with power consumption and heat dissipation in designing future high-performance systems.

Multicores, which mean more than one processor core on a single chip, were just starting to enter the market. However, all commercial designs, and in fact all roadmaps from the processor vendors, assumed all cores were identical (as virtually all multi-chip multiprocessors had been before that).  The team challenged that assumption and pointed out that if the cores were different, they could better address the variation in program behavior and changes in environment.

Rakesh Kumar 

They proposed a new architecture for processors that would switch among cores to optimize energy and performance. Their multi-core model would allow software to evaluate the resource requirements of an application (or part of an application) and choose the core that would best meet the requirements while minimizing energy consumption.

“Contrary to homogeneous multi-cores, which were state-of-art then, the paper showed that putting cores with different power-performance characteristics on the same die with intelligent application mapping produces large improvements in energy efficiency,” said Barroso.

Powerful Collaborations
The paper’s lead author, Rakesh Kumar, then a Ph.D. student in the Department of Computer Science and Engineering who was being mentored by Tullsen, took a summer internship at HP Labs to begin the project. Kumar and Tullsen formed a partnership with Norman Jouppi, Parthasarathy Ranganathan, and Keith Farkas from HP.

The team continued their research for several years, publishing seven papers on the topic. This turned out to be quite an influential group, as they went on to amass numerous Test of Time awards on various topics: five for Tullsen, four for Norman Jouppi of HP Labs (now Google), and two for Kumar, who is now an associate professor at University of Illinois, Urbana-Champaign. Ranganathan is currently a vice president at Google and Farkas is currently with VMWare.

“This ended up being one of my favorite research projects ever,” said Tullsen. “Not just because of the widespread impact it had, but because of the amazing group of people I got to work with.”

Developing Sex-specific Treatments for Heart Disease

UC San Diego bioengineer advances equity in science, and among scientists

Bioengineering graduate students Nicole Felix-Velez and Talia Baddour work with Professor Brian Aguado to understand sex-based differences in cardiovascular diseases. Photos by David Baillot/UC San Diego Jacobs School of Engineering


December 2, 2021--As a heart fails, a woman's ventricular wall increases in thickness relative to a man's. And in heart valve disease, men show more calcified tissue growth, while women develop more fibrotic, scar-like tissue. Yet, treatments for both diseases remain strikingly similar for both men and women, despite the differences in disease progression.

Brian Aguado, a professor of bioengineering at the University of California San Diego, aims to change that. He is studying sex-specific differences in disease—starting with cardiovascular disease—from the molecular scale all the way up to the organism level. He uses bioengineering tools to develop more relevant, sex-specific models and treatments for cardiovascular disease, enabling better clinical outcomes for patients who have long been ignored.

“Cardiovascular disease is the leading cause of death in men and women, but we still don’t fully understand the mechanisms that cause it—especially in women—simply because our models for understanding disease are largely male biased,” said Aguado, one of the 27 new faculty who joined the Jacobs School of Engineering in the last two years. “This has created a gap in understanding as far as what makes men and women go through cardiovascular disease differently and how we can address that head on.”

And Aguado doesn’t just focus on equity in his research. He’s also a strong advocate of equity and diversity among the researchers doing this work, and co-founded the LatinX in Biomedical Engineering (LatinXinBME) community to support diversity within the scientific community.

“In academic spaces, I feel like a lot of folks are encouraged to assimilate—to adopt the current average,” said Aguado. “I think it's super important to bring your whole self to the workplace, and hope that my lab can inspire populations historically excluded from the sciences to do work that supports their respective communities.”

Diversifying the biomedical field and workforce

Aguado co-founded the LatinxinBME community with friend and fellow scientist of Colombian descent Ana Maria Porras, now a professor at the University of Florida, after a conference in 2018 helped them realize the value of community in fighting feelings of isolation. What started as a small Slack group to help these LatinX researchers keep in touch has now grown to a community of more than 300 members from around the country, seeking mentorship, advice, and a sense of inclusion.

Aguado, a first-generation Colombian American, co-founded the LatinX in Biomedical Engineering group to support diversity within the scientific community.

“We try to help each other through key transition points in our careers: from undergraduate to grad school; grad school to postdocs; postdocs to faculty; we share with each other what life is like, and any advice we can give. It’s been a beautiful tool and community for mentorship and helping each other through academic and industry careers,” said Aguado.

The group has now established an executive board, and holds regular research symposia along with social and mentorship events. The sense of inclusion he found through LatinXinBME was also one reason Aguado felt UC San Diego was the best place for his research, and himself, to thrive.

“I’m first-generation Colombian American, so I've just always been immersed in Colombian culture at home, but at the same time have come to realize that it’s a rarity in academic spaces,” he said. “The fact that I have colleagues here at UC San Diego that speak Spanish, it means a lot. That feeling of inclusion just has helped me in so many ways that it feels like LatinXinBME is a way I can create space to welcome people to academic spaces and help them feel like they are not alone.”

Aguado said it’s no accident that he’s working toward equity through his scientific and outreach efforts.

“I see this marriage between the diversity work I do with LatinXinBME and increasing equity in science through social means, but then also increasing it in science through my lab. That’s another reason UC San Diego is such a good fit for me, because I feel that both of these aspects are valued in this academic community.”

One-size-fits-all vs. precision medicine

Aguado’s scientific goal sits in between two healthcare paradigms: one-size-fits-all treatments that ignore differences based on sex, race, and age; and precision medicine, with treatments tailored down to the individual level. While the goals of precision medicine are worth exploring, Aguado said he has concerns about how accessible this level of care will be to the general population, and in particular, to underserved communities.

He envisions a more effective middle ground.

“My long-term vision is to not just focus on sex as a variable; I think we can also incorporate age and ancestry into our models, really embracing the whole idea of precision medicine but not making it so specific to individual patients. Instead, we could think of how we can stratify patients into groups and take into account what makes us unique biologically, so that we can better cater treatments to certain populations.”

Gender is another variable that Aguado considers, particularly as it relates to transgender people’s health outcomes with everything from hormone therapy treatments, to molecular differences impacting cardiovascular disease outcomes.

His current work on sex-specific differences in cardiovascular disease is a first step toward this larger goal. To understand how and why heart diseases affect men and women differently, and how we can develop more tailored treatments for them, Aguado and his team of student researchers study sex-based differences at a variety of scales, from within single cells, to the extracellular matrix, and to the immune system, tissue and organism level.

Studying sex-based differences

The Aguado lab studies sex-specific differences in disease from the molecular scale all the way up to the organism level.

At the smallest scale, Aguado and his team recently found that cells taken from the heart valve tissues of men and women with aortic valve disease respond very differently to the same drug. Using hydrogel biomaterials developed in his lab, they were able to tie some of these differences in response to genes on the cell’s X chromosome, explaining why female cells—which have two X chromosomes—express increased activity. They’re now working to understand how genetic and epigenetic changes caused by these sex chromosomes can lead to changes in cell behavior, and ultimately study how these changes could be harnessed to impact healing after a cardiac event.

Moving up from understanding the cellular to the extracellular level—the complex cocktail of proteins, hormones and biochemicals that surround cells—Aguado collaborates with cardiologists to collect serum samples from patients with aortic valve disease. He found that using this extracellular serum to culture cells resulted in cells with different behaviors based on the sex of the patient.

“We have provided this really nice bridge between in vitro disease modeling and in vivo patient outcomes, simply by taking into account these sex-specific extracellular components,” he said.

While understanding what underpins these differences is a scientific challenge, the biggest hurdle is simply making it a priority to incorporate both male and female models into research.

“It’s not hard, you just need to think about it,” said Aguado. “For example, in my previous lab work, we would isolate cells from pig hearts, but we did not know the biological sex of the hearts. After consulting the literature and recognizing sex differences in the heart, I called up the meat company that sent the hearts, and asked if they could ship separate boxes of male and female hearts. To my surprise, they said, “no problem.” It just takes initiative to acknowledge that there are these clinical differences between the sexes, and incorporate that into your studies.”

Developing new treatments

All this information that Aguado and other researchers are learning about sex-specific differences at the cellular, extracellular, immune system and organ levels, is setting the stage to not only prescribe existing treatments more effectively based on sex, but to also develop new ones.

For example, one project that Aguado plans to tackle is developing polymer scaffolds—sponge-like biomaterials—that have been engineered to recruit certain populations of immune cells as a strategy to control the male or female immune response after cardiac injury, and improve tissue regeneration after a heart attack.

Modulating the immune system in this way to encourage optimum healing based on what we know about how sex impacts cardiovascular disease and healing would be a crowning achievement.

“I believe we can find a middle ground between something that might work for large groups of people but is missing certain populations—like cardiovascular disease which has been largely based on male animal models—versus a completely customized approach that might not be accessible for every patient. If my work can show that there are more effective ways to treat certain groups of patients, then I’ll feel like I made an impact. Because at the very least we’re not ignoring 50 percent of the population with our research.”

Donors committed to student success bring Minerva's Cafe and Charles Lee Powell Foundation Terrace to Franklin Antonio Hall

A rendering of Franklin Antonio Hall


December 2, 2021--Located on the first floor of UC San Diego’s new Franklin Antonio Hall engineering facility, Minerva’s Café and the Charles Lee Powell Foundation Terrace will play a key role in enriching the university experience for generations of students – the future technology leaders who will tackle society’s toughest challenges.

The café and adjoining terrace will be at the heart of Franklin Antonio Hall (FAH), where donor support through the Campaign for UC San Diego is helping to create the capacity for world-changing innovation. The 186,000-square-foot facility, projected to be completed in early 2022, is designed for collaborative research, active learning, industry engagement, and commercialization of discoveries for the global good.

Two philanthropic groups will be recognized through naming the café and the outdoor terrace at FAH – both inspired by a commitment to supporting student success through gifts for programmatic expansion of the Jacobs School of Engineering.

The naming of Minerva’s Café is a tribute to ten women – technology leaders and science enthusiasts – who joined together to make a collective impact with a gift of $500,000. Minerva’s Café promises to be a popular gathering spot for sustenance, convening and conversation.

The Charles Lee Powell Foundation Terrace naming honors a steadfast champion of the Jacobs School of Engineering for nearly four decades – and their continuing support for student resources with a pledge of $250,000. The Powell Terrace will serve as a premier space for outdoor dining, events, and a central hub for activity and engagement.

The first floor of FAH will be an energetic center for education and student engagement, with more than 450 students per hour from across campus circulating through enhanced learning spaces. Minerva’s Café and the Charles Lee Powell Foundation Terrace will also draw faculty, students, researchers and industry partners enroute to FAH’s 13 collaboratories, Executive Outreach and Learning Center, and Institute for the Global Entrepreneur.

Campus and community members will gather at the café and terrace for meals, coffee breaks, networking, events, socializing and relaxing – while enjoying stunning views of the natural canyon landscape and eucalyptus grove, and the iconic Geisel Library. 

Minerva’s Café

A rendering of Minerva's Cafe and the adjoining Charles Lee Powell Foundation Terrace.

The idea to bring together ten women leaders in technology and STEM fields for collective philanthropic impact was the brainchild of Martha Dennis, a long-time friend of UC San Diego and member of dean’s advisory councils at both the Jacobs School and the Rady School of Management.

In the male-dominated field of technology engineering, Dennis paved the way for other women. She earned a Harvard PhD, raised a family, and built a remarkable career as a technology and software engineer, entrepreneur and CEO. Motivated by a desire to make life easier through technology, she takes pride in being part of a team that developed the groundbreaking idea of data service for cell phones.

Dennis took the lead in identifying and securing philanthropic commitments from nine women leaders in the community who are equally passionate about supporting student resources at UC San Diego. Each member of this accomplished group contributed $50,000 toward the $500,000 gift, and together they came up with the name Minerva’s Café, inspired by the Roman goddess for wisdom and community. 

The group of women includes some who are Jacobs School alumni, and nearly all are first-time donors. Many were inspired by Dennis, and credit her with making an impact on their professional growth. What unites them is their deep desire to support student success and diversity, and to inspire others to give. 

Minerva’s Cafe was made possible by Martha Dennis, Ambassador Diana L Dougan, Arlene Harris, Yvonne Hildebrand, Kristi Jaska, Peggy Johnson, Vera Kripalani, Anna Scipione, Jan Talbot and Susan Tousi.

Charles Lee Powell Foundation Terrace

The Charles Lee Powell Foundation’s support for UC San Diego spans nearly 40 years, with more than $35 million in philanthropic contributions to the Jacobs School. The foundation is the longest-running and top donor of graduate fellowship support to the university, and has also provided support for endowed chairs, the Powell Structures Lab in the campus engineering complex, and the Powell Focht Bioengineering Building.

The foundation’s recent pledge of $250,000 toward programmatic expansion underscores their continuing support for the vision of the Dean of the Jacobs School of Engineering Albert P. Pisano, who is dedicated to preparing the next generation of engineering and technology leaders. These future leaders include students such as Powell Fellows, who will have the opportunity to connect with campus and community members on the Charles Lee Powell Foundation Terrace. 

Nourishing people and conversation

“Franklin Antonio Hall is the place where we’re cooking up our future,” said Pisano. “And we’re not just cooking up ideas, we’re cooking up food.”

The kitchen is the center of the home in many cultures, he said, and Minerva’s Café and the Powell Terrace are the center of FAH in many ways. “A great kitchen facilitates conversation, because you put the people, the nourishment, the excitement, the energy – all in that place and watch the magic happen.”

In this way, the café and terrace will serve as an essential part of the FAH ecosystem for the innovators who will share meals and dynamic conversations. The rich array of first-floor student resources – such as the Learning Innovation Studio – are also designed to stimulate conversation, the key to the future of learning at the Jacobs School. In fact, the entire building is designed to facilitate the easy flow of people and ideas, and many architectural features draw the eye to the outside – underscoring the university’s message that impact occurs when ideas are shared with the world.

“The circulation of people and ideas is how you keep an ecosystem healthy, dynamic and strong,” said Pisano. “It’s how you drive the education and research of the future. It’s how you reinvent the world.”

Pisano envisions limitless possibilities at Minerva’s Café and the Charles Lee Powell Foundation Terrace. “Looking toward the west, imagine the sun going down, the sky becoming orange. You’ve got everything you need to stimulate the new ideas that are going to cook up the future. Including Wi-Fi, good colleagues, the right ecosystem . . . and probably the best cup of espresso you’re going to get this side of downtown.”

About the Campaign for UC San Diego

At the University of California San Diego, challenging convention is our most cherished tradition. Through the Campaign for UC San Diego – our university-wide comprehensive fundraising effort concluding in 2022 – we are enhancing student support, ensuring student success, transforming our campus, connecting our community, and redefining medicine and health care on a global scale. Together with our philanthropic partners, we will continue our nontraditional path toward revolutionary ideas, unexpected answers, lifesaving discoveries, and planet-changing impact.

 

10 Jacobs School faculty among 2021 list of most highly cited researchers in the world

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November 30, 2021 -- Ten professors at the University of California San Diego Jacobs School of Engineering are among the world’s most influential researchers in their fields, according to the 2021 Clarivate listing of Most Highly Cited Researchers in the World.

The Jacobs School of Engineering faculty members are among 51 professors and researchers at UC San Diego named in the prestigious list of Highly Cited Researchers in 2021. Researchers earned this distinction by producing multiple publications that rank in the top 1% by citations in their field over the past decade. UC San Diego was ranked 9th globally for institutions with the most highly cited researchers. The 2021 list identified some 6,600 researchers from around the world.

“UC San Diego’s 9th place ranking, out of 1,300 research institutions globally, shines a bright and well-deserved light on the groundbreaking, multi-disciplinary research taking place across our university,” said UC San Diego Chancellor Pradeep K. Khosla. “Regularly cited by colleagues around the globe, the work of our respected faculty experts is advancing human knowledge and addressing some of the world’s most pressing challenges.”

The ten Highly Cited Jacobs School researchers are listed below.

Ludmil Alexandrov, professor of bioengineering. Alexandrov maps the mutational processes in cancer and devises better strategies for cancer prevention and treatment.

Most cited paper: “Signatures of mutational processes in human cancer,” published in Nature, 2013.

Trey Ideker, professor of genetics and bioengineering. Ideker seeks to comprehensively map connections between the many genes and proteins in a cell and how these connections trigger or prevent disease. His current work focuses on DNA mutations that cause cancer.

A recent paper: “Interpretation of cancer mutations using a multiscale map of protein synthesis,” published in Science, 2021.

Rob Knight, professor of pediatrics, bioengineering, computer science and engineering, and director of the Center for Microbiome Innovation. Knight studies microbiomes in a range of settings, including but not limited to the human body, and how they can be manipulated to benefit health and the environment. Recently, Knight has been involved in campus programs performing COVID-19 clinical testing and wastewater detection of SARS-CoV-2.

Most cited paper: “QIIME allows analysis of high-throughput community sequencing data,” published in Nature Methods, 2010.

Prashant Mali, professor of bioengineering. Mali’s expertise is in the fields of genome engineering and regenerative medicine. He has helped develop CRISPRs and ADARs as powerful tools for DNA and RNA editing, with wide applications in both basic biology and human therapeutics.

A recent paper: “Peptide tiling screens of cancer drivers reveal oncogenic protein domains and associated peptide inhibitors,” published in Cell Systems, 2021.

Ying Shirley Meng, Zable Endowed Chair in Energy Technologies, professor of nanoengineering and director of the Institute for Materials Discovery and Design. Meng’s research focuses on functional nano- and micro-scale materials for energy storage and conversion—especially for batteries of all shapes and sizes.

Recent highly cited paper: “Pathways for practical high-energy long-cycling lithium metal batteries,” published in Nature Energy, 2019.

Shyue Ping Ong, professor of nanoengineering. Ong focuses on the intersection between materials science, computer science and data science. By building sophisticated automation software frameworks, Ong generates materials data at unprecedented scales to discover and design new materials for batteries, LEDs and aerospace applications. Ong also develops cutting edge machine learning methods to maximize the return on materials data. Ong is a firm advocate for open data and software to enable reproducible innovation in the materials research community.

A recent paper: “Learning properties of ordered and disordered materials from multi-fidelity data,” published in Nature Computational Science, 2021.

Bernhard O. Palsson, Galletti Professor of Bioengineering, professor of pediatrics and Director of the Center for Biosustainability. Palsson’s research focuses on developing experimental and computational models of the red blood cell, E. coli, CHO cells, and several human pathogens to establish their systems biology. His Systems Biology Research Group leverages high-power computing to build interactive databases of biological information and is increasingly focused on Genome Design and Engineering.

A highly cited paper: “BiGG models: A platform for integrating, standardizing and sharing genome-scale models,” published in Nucleic Acids Research, 2016.

Joseph Wang, SAIC Endowed Chair, distinguished professor of nanoengineering, director of the Center for Wearable Sensors and co-director of the Institute of Engineering in Medicine Center for Mobile-Health Systems and Applications. Wang’s research focuses on developing micro- and nanomotors and wearable sensors for medical, military, security and environmental applications.

A highly cited paper: “Electrochemical glucose biosensors,” published in Chemical Reviews, 2008.

Sheng Xu, professor of nanoengineering. Xu engineers soft, flexible and stretchable electronics that can be comfortably worn on the human body and perform just as well as conventional (hard) electronic devices. His contributions to novel materials and microfabrication strategies earned him the biennial Materials Research Prize for Young Investigators from ETH Zurich in 2021. Xu’s innovative work on wearable ultrasound technology has allowed noninvasive monitoring of tissue far below the skin surface. He also developed new growth methods for perovskite materials used in flexible high-performance electronics.

A recent paper: “Materials and structures towards soft electronics,” published in Advanced Materials, 2018.

Liangfang Zhang, professor of nanoengineering, co-director of the Center for Nano-Immuno Engineering and faculty member of the Institute of Engineering in Medicine. Zhang’s revolutionary work in the field of nanomedicine focuses on developing nanoparticles that perform therapeutic tasks in the body without being rejected by the immune system. He invented a technology to disguise synthetic nanoparticles in the skins of natural cells (i.e. red blood cells, platelets, white blood cells, cancer cells and others). These cell-mimicking nanoparticles have shown promise in fighting drug-resistant bacterial infections and viral infections; training the immune system to fight cancer; and treating rheumatoid arthritis and other diseases.

A highly cited paper: “Erythrocyte membrane-camouflaged polymeric nanoparticles as a biomimetic delivery platform,” published in Proceedings of the National Academy of Sciences, 2011.

ServiceNow supports student scholarships, computer science at UC San Diego with $1.25M gift

November 30, 2021--Software company ServiceNow, which was founded in San Diego in 2004, is now investing in the local computer science and engineering talent ecosystem through a $1.25 million gift to the University of California San Diego Jacobs School of Engineering. With Chancellor's Scholarship matching funds, the total impact of the gift is $1.75 million. 

Jacobs School of Engineering students participate in the IDEA Center's Summer Engineering Institute. ServiceNow Scholars will be encouraged to particiapte in IDEA Center programming.

ServiceNow is a Fortune500 company which develops cloud computing platforms to help companies manage digital workflows for enterprise operations. Hundreds of students from the UC San Diego Jacobs School of Engineering have played a role in its success as employees and interns, both here in San Diego where the company was founded, and at the current headquarters in the San Francisco Bay Area. 

To further advance educational opportunities for computer science students at the Jacobs School of Engineering, ServiceNow has donated $1 million to create an endowed ServiceNow Scholarship. In addition, ServiceNow has donated $250,000 to support the broader programmatic expansion of the Jacobs School of Engineering, which will be recognized through the naming of the ServiceNow Terrace in Franklin Antonio Hall. 

“The fact that we go back to UC San Diego year after year is a testament to the value that the UC San Diego students and graduates bring to our company,” said Magaly Drant, Vice President of Developer Productivity at ServiceNow. “We find in those students the right combination between a solid understanding of the fundamentals and an appetite for discovery and challenge that thrives in our complex, fast-paced and ever evolving environment. We are excited to contribute to making access to this education a reality for even more talented students.”

The new ServiceNow Scholarship is part of a larger effort within the UC San Diego Jacobs School of Engineering to strengthen financial support for students. Many engineering and computer science students at UC San Diego and around the country face a combination of  challenges inside and outside the classroom that make completing STEM degrees particularly challenging. 

"It's critical that we ensure all our students have the resources they need to thrive at the Jacobs School of Engineering. As a society, we need our technical workforce to reflect the diversity of our city, region, state and country. To do that, we need to increase support for students. I'm thrilled that ServiceNow has stepped up to strengthen our ability to provide the support our students need," said Albert P. Pisano, Dean of the UC San Diego Jacobs School of Engineering. 

Comprehensive support for Jacobs School students

Dean Pisano launched the Jacobs School of Engineering Dean’s Scholars of Excellence scholarship program to encourage and inspire the larger community to step up and work together to advance equal access to a Jacobs School education. This includes creating new scholarships to support students with outstanding academic merit, including students who have made or show potential to contribute to diversity, equity and inclusion; first generation; and low-income students. The new ServiceNow Scholarship is the newest part of this Jacobs School of Engineering Dean’s Scholars of Excellence effort. 

The students who receive these scholarships are encouraged to get involved with the IDEA Engineering Student Center here at the Jacobs School. The IDEA Engineering Student Center, which recently celebrated its 10-year anniversary, runs a wide range of programming designed to support engineering and computer science students as they work toward their degree, through summer prep and mentorship programs, peer-led engineering learning communities, support for student diversity organizations, and more.

"I can't overestimate the value and impact of scholarships in engineering and computer science. We have so many stellar students who are burning the candle at both ends. Scholarships that give students a little more leeway to join an engineering team project or get involved in research can truly be career- and life- changing," said Darren Lipomi, a nanoengineering professor and faculty director of the IDEA Engineering Student Center. 

This ServiceNow scholarship gift is being amplified by a $500,000 match through the Chancellor’s Scholarship and Fellowship Challenge, with a $1 match for every $2 given. This means a combined $1.5 million toward scholarships for undergraduate computer science students. The first cohort of ServiceNow Scholars is expected to be announced in fall quarter of the 2022 academic year.  

The ServiceNow Terrace in Franklin Antonio Hall will facilitate relationships between industry partners and academic researchers.

ServiceNow Terrace in Franklin Antonio Hall

In recognition of their $250,000 gift toward the programmatic expansion of engineering and computer science on campus, the fourth floor terrace in the new Franklin Antonio Hall will be named the ServiceNow Terrace. 

Franklin Antonio Hall opens in spring 2022. It has been designed from the ground up to facilitate cross-discipline and university-industry collaborations that are critical for solving the toughest health, energy, autonomy, security, communications, and materials challenges facing society. 

“I can’t stress enough how crucial our ties to industry are, not only in ensuring we’re working on solving relevant research challenges, but also in helping prepare our students to meet the technological demands of the workplace of the future,” said Albert P. Pisano, Dean of the Jacobs School of Engineering. “I’m grateful to the team at ServiceNow for also recognizing the value of these relationships, and supporting the Jacobs School of Engineering and our students in our mission to leverage engineering and computer science for the public good.”

The 186,000-square-foot building will house a wide range of multidisciplinary research “collaboratories,” as well as spaces to facilitate interactions between faculty, students and industry partners. 

“Technology is evolving faster than ever, and if we don’t build strong ties between industry and academia, we cannot hope to train tomorrow’s workforce to the skills and technologies that will matter in the future,” said Drant. “As for how to build such ties, there is nothing more powerful than in-person sharing, which spaces such as this ServiceNow Terrace make possible.”

The ServiceNow gift contributes to the Campaign for UC San Diego—a university-wide comprehensive fundraising effort concluding June 30, 2022. Together with philanthropic partners, UC San Diego will continue its nontraditional path toward revolutionary ideas, unexpected answers, lifesaving discoveries and planet-changing impact. To learn more, visit the Campaign for UC San Diego website.

Flu virus shells could improve delivery of mRNA into cells

November 30, 2021 -- Nanoengineers at the University of California San Diego have developed a new and potentially more effective way to deliver messenger RNA (mRNA) into cells. Their approach involves packing mRNA inside nanoparticles that mimic the flu virus—a naturally efficient vehicle for delivering genetic material such as RNA inside cells.

The new mRNA delivery nanoparticles are described in a paper published recently in the journal Angewandte Chemie International Edition.

The work addresses a major challenge in the field of drug delivery: getting large biological drug molecules safely into cells and protecting them from organelles called endosomes. These tiny acid-filled bubbles inside the cell serve as barriers that trap and digest large molecules that try to enter. In order for biological therapeutics to do their job once they are inside the cell, they need a way to escape the endosomes.

“Current mRNA delivery methods do not have very effective endosomal escape mechanisms, so the amount of mRNA that actually gets released into cells and shows effect is very low. The majority of them are wasted when they get administered,” said senior author Liangfang Zhang, a professor of nanoengineering at the UC San Diego Jacobs School of Engineering.

Achieving efficient endosomal escape would be a game changer for mRNA vaccines and therapies, explained Zhang. “If you can get more mRNA into cells, this means you can take a much lower dose of an mRNA vaccine, and this could reduce side effects while achieving the same efficacy.” It could also improve delivery of small interfering RNA (siRNA) into cells, which is used in some forms of gene therapy.

In nature, viruses do a very good job of escaping the endosome. The influenza A virus, for example, has a special protein on its surface called hemagglutinin that, when activated by acid inside the endosome, triggers the virus to fuse its membrane with the endosomal membrane. This opens up the endosome, enabling the virus to release its genetic material into the host cell without getting destroyed.

ALT TEXT
Illustration of a flu virus-mimicking nanoparticle entering and releasing mRNA into a host cell (top). A special protein on the nanoparticle’s surface triggers it to fuse with the endosomal membrane, allowing its mRNA cargo to safely escape into the host cell (bottom). Image adapted from Angewandte Chemie International Edition

 

Zhang and his team developed mRNA delivery nanoparticles that mimic the flu virus’s ability to do this. To make the nanoparticles, the researchers genetically engineered cells in the lab to express the hemagglutinin protein on their cell membranes. They then separated the membranes from the cells, broke them into tiny pieces, and coated them onto nanoparticles made from a biodegradable polymer that has been pre-packed with mRNA molecules inside.

The finished product is a flu virus-like nanoparticle that can get into a cell, break out of the endosome, and free its mRNA payload to do its job: instruct the cell to produce proteins.

The researchers tested the nanoparticles in mice. The nanoparticles were packed with mRNA encoding for a bioluminescent protein called Cypridina luciferase. They were administered both through the nose—the mice inhaled droplets of a nanoparticle-containing solution applied at the nostrils—and via intravenous injection. The researchers imaged the noses and assayed the blood of the mice and found a significant amount of bioluminescence signal. This was evidence that the flu virus-like nanoparticles effectively delivered their mRNA payloads into cells in vivo.

The researchers are now testing their system for delivery of therapeutic mRNA and siRNA payloads.

Paper: “Virus-Mimicking Cell Membrane-Coated Nanoparticles for Cytosolic Delivery of mRNA.” Co-authors include Joon Ho Park, Animesh Mohapatra, Jiarong Zhou, Maya Holay, Nishta Krishnan, Weiwei Gao and Ronnie H. Fang, UC San Diego.

This work is supported by the Defense Threat Reduction Agency Joint Science and Technology Office for Chemical and Biological Defense (grant HDTRA1-18-1-0014 and HDTRA1-21-1-0010).

How well do wet masks contain droplets?

Study shows damp masks still stop respiratory droplet penetration

November 22, 2021-- After studying the effectiveness of varying layers of masks in stopping respiratory droplets from escaping face masks, a team of international researchers has now turned their attention to modeling what happens to droplets when they come in contact with wet masks. Their results show that damp masks are still effective at stopping these droplets from escaping the mask and being atomized into smaller, easier-to-spread aerosolized particles. 

This study only investigated the effects of wet masks on droplet penetration; the researchers note that people should follow public health guidance to change their mask if it is wet, since wet masks are harder to breathe through, less efficient at filtering inhaled air, and can vent more around the edge of the mask than dry masks.

Images from the high-speed footage showing what happens as droplets hit an increasingly damp surgical mask; the respiratory droplets form small beads on the mask’s surface, providing additional resistance for the impacted droplets against possible penetration. 

“While the efficacies of various dry face masks have been explored, a comprehensive investigation of wet masks is lacking. Yet, users wear masks for long periods of time, and during this time the mask matrix becomes wet due to respiratory droplets released from breathing, coughing, sneezing etc,” wrote the team of engineers from the University of California San Diego, Indian Institute of Science, and University of Toronto. The researchers presented their findings on Nov. 21 at the American Physical Society’s 74th Annual Meeting of the APS Division of Fluid Dynamics. The same paper will be published in Physical Review Fluids on Dec. 7. 

They found that, perhaps counterintuitively, wet masks actually make it more difficult for these respiratory droplets to penetrate and escape the mask, splintering into smaller, aerosolized particles; research has shown that these smaller particles are more likely to spread the SARS-CoV-2 virus by lingering in the air longer than the larger droplets that fall to the ground. In modeling the physics behind why this happens, they discovered that two very different mechanisms are present for hydrophobic masks like common surgical masks, versus hydrophilic masks like the cloth varieties.

To study exactly how wetness impacts droplet penetration, the researchers generated mock respiratory droplets using a syringe pump, which slowly pushed liquid through a needle and onto one of three types of mask materials: a surgical mask, and two cloth masks of different thicknesses. The researchers recorded what happened as the droplets hit the mask using a high-speed camera capturing the impact at 4,000 frames per second, and continued to study it as the mask became damp. 

They found that droplets from a cough or sneeze have to be traveling at a higher velocity to be pushed through a mask when wet, compared to when it’s dry. On hydrophobic masks with low absorptivity,like surgical masks, the respiratory droplets form small beads on the mask’s surface, providing additional resistance for the impacted droplets against possible penetration. 

The hydrophilic cloth masks do not exhibit this beading; instead, the cloth absorbs the liquid, with the wetted area spreading as the mask absorbs more volume. The porous matrix of these cloth masks become filled with liquid, and the droplets are therefore required to displace a larger volume of liquid to penetrate the mask. Due to this additional resistance, penetration is weaker. 

Primary components of the experimental setup, not to scale.

“In summary, we showed that wet masks are capable of restricting ballistic respiratory droplets better than dry masks,” said Sombuddha Bagchi,  first author of the paper and a mechanical engineering PhD student at the Jacobs School of Engineering at UC San Diego.

 “However, we also need to pay attention to side leakage and breathability of wet masks, which were not investigated in our study”, added Abhishek Saha, a co-author and professor of  Mechanical and Aerospace Engineering at UC San Diego.

The team of engineers— which also includes Professors Swetaprovo Chaudhuri from University of Toronto, and Saptarshi Basu of the Indian Institute of Science— were well-versed in this type of experiment and analysis, though they were used to studying the aerodynamics and physics of droplets for applications including propulsion systems, combustion, or thermal sprays. They turned their attention to respiratory droplet physics last year when the COVID-19 pandemic started, and since then, have been studying the transport of these respiratory droplets and their roles in transmission of Covid-19 type diseases.

In March 2021, this same team published a paper in Science Advances detailing the effectiveness of dry masks of one, two, and three layers in stopping respiratory droplets from penetrating the mask. Using a similar methodology to this wet mask experiment, they showed that three-layered surgical masks are most effective at stopping large droplets from a cough or sneeze from getting atomized into smaller droplets. These large cough droplets can penetrate through the single- and double-layer masks and atomize to much smaller droplets, which is particularly crucial since these smaller aerosol droplets are able to linger in the air for longer periods of time.

 

This tool protects your private data while you browse

A high-level illustration that shows how SugarCoat modified code within API to protect private data. 

November 18, 2021--A team of computer scientists at the University of California San Diego and Brave Software Inc. have developed a tool that will increase protections for users’ private data while they browse the web.

The tool, named SugarCoat, targets scripts that harm users’ privacy -- for example, by tracking their browsing history around the Web -- yet are essential for the websites that embed them to function. SugarCoat replaces these scripts with scripts that have the same properties, minus the privacy-harming features. SugarCoat is designed to be integrated into existing privacy-focused browsers like Brave, Firefox, and Tor, and browser extensions like uBlock Origin. SugarCoat is open source and is currently being integrated into the Brave browser.

"SugarCoat is a practical system designed to address the lose-lose dilemma that privacy-focused tools face today: Block privacy-harming scripts, but break websites that rely on them; or keep sites working, but give up on privacy," said Deian Stefan, an assistant professor in the UC San Diego Department of Computer Science and Engineering. "SugarCoat eliminates this trade-off by allowing the scripts to run, thus preserving compatibility, while preventing the scripts from accessing user-private data."

The researchers will describe their work at the ACM Conference on Computer and Communications Security (CCS) taking place in Seoul, Korea, Nov. 14 to 19, 2021.

"SugarCoat integrates with existing content-blocking tools, like ad blockers, to empower users to browse the Web without giving up their privacy," said Michael Smith, a PhD student in Stefan’s research group, who is leading the project.

Most existing content-blocking tools make very coarse-grained decisions: They either totally block or totally allow a script to run, based on whether it appears on a public list of privacy-harming scripts.  In practice, though, some scripts are both privacy-harming and necessary for websites to function -- and most tools inevitably choose to make an exception and allow these scripts to run. Today, there are more than 6,000 exception rules letting through these privacy-harming scripts.

There is a better approach, though. Instead of blocking a script entirely or allowing it to run, content-blocking tools can replace its source code with an alternative privacy-preserving version. For example, instead of loading popular website analytics scripts which also track users, content-blocking tools replace these scripts with fake versions that look the same. This ensures that the content-blocking tools are not breaking web pages that embed these scripts and that the scripts can’t access private data (and thus report it back to the analytics companies). To date, crafting such privacy-preserving replacement scripts has been a slow, manual task even for privacy engineering experts. uBlock Origin, for example, maintains replacements for only 27 scripts, compared to the over 6,000 exception rules.

How SugarCoat changes the game

The researchers developed SugarCoat precisely to address this gap by automatically generating privacy-preserving replacement scripts.  The tool uses the PageGraph tracing framework--Smith was key to the development of the framework--to follow the behavior of privacy-harming scripts throughout the browser engine.  

SugarCoat scans this data to identify when and how the scripts talk to Web Platform APIs that expose privacy-sensitive data.  SugarCoat then rewrites the scripts’ source code to talk to fake “SugarCoated” APIs instead, which look like the Web Platform APIs but don't actually expose any private data. 

To evaluate the impact of SugarCoat on Web functionality and performance, the team integrated the rewritten scripts into the Brave browser; they found that SugarCoat effectively protected users’ private data without impacting functionality or page load performance. SugarCoat is now being deployed in production at Brave.

“Brave is excited to start deploying the results of the year-long SugarCoat research project,” said Peter Snyder, senior privacy researcher and director of privacy at Brave Software. “SugarCoat gives Brave and other privacy projects a powerful, new capability for defeating online trackers, and helps keep users in control of the Web.

This work was supported by the NSF under grant numbers CCF-1918573 and CAREER CNS-2048262, by a gift from Brave Software, and by an NSF Graduate Research Fellowship. 

 

SugarCoat: Programmatically Generating Privacy-Preserving, Web-Compatible Resource Replacements for Content Blocking

 

Michael Smith and Deian Stefan, University of California San Diego

Benjamin Livshits, Imperial College of London

Peter Snyder, Brave Software

 

A Brief History of Minimal Surfaces and the Ants that Love Them

The research describes a new algorithm that solves a classical geometry problem: find a surface of minimal area bordered by an arbitrarily prescribed boundary curve. 

Nov. 18, 2021--Consider a soap bubble. The way it contains the minimal possible surface area is surprisingly efficient. This is not a trivial issue. Mathematicians have been looking for better ways to calculate minimal surfaces for hundreds of years. Recently, Computer Science and Engineering Department Assistant Professor Albert Chern, and postdoctoral researcher Stephanie Wang, added a new page to this book with their paper: Computing Minimal Surfaces with Differential Forms, which was recently published by ACM.

“Other than modeling soap films, these shapes are the foundation for many micro structures, such as in tissues in biology,” said Chern. “If you zoom into bone structures, you'll see these membranes that tend to form minimal surfaces. Basically, the surface tension on either side of the membrane is canceling itself out.”

These measurements can also be applied to architecture. Chern points to the Olympic Park in Munich, which was inspired by minimal surfaces. Regardless of the application, finding the most efficient method to determine minimal surfaces is a valuable proposition.

Plateau’s Problem

Calculating a minimal surface within a boundary curve – the path around its edge – is called Plateau’s problem, after Joseph Plateau, who was born in 1801 and liked to experiment with soap bubbles. As new technologies have emerged, our ability to solve for minimal surfaces has slowly improved. Most recently, mathematicians have used an old approach called gradient descent (not to be confused with the machine learning algorithm), which until recently was state of the art. 

Oddly enough, Chern got into this area, to some degree, because of ants. “I was looking at optimal transport problems,” says Chern. “Let’s say you have an ant hill and a little ways away you have a pile of food. What is the optimal path for the ants to take to get that food and bring it back to their anthill?” 

In real life, ants can’t do the math, but they have still figured out the problem, creating optimal paths to food sources. No doubt, this ability evolved as a survival mechanism to gain the greatest nutritional benefit at the least metabolic cost. Chern saw the similarities between this optimal transport problem and minimal surfaces and, in a sense, combined them.

One of the advantages of Chern’s new method is that it doesn’t care about variations in a shape’s topology. Previous methods, such as using triangle mesh, required different approaches based on topology. As a result, handling varied surface topologies has become much easier.

“It’s a completely different approach to looking at minimal surface problems – generalizing this interesting optimal transport problem,” said Chern. “And then it suddenly becomes this big, well-known mathematical problem and that gives it a very different flavor.”

AI-powered personalized recommendation system helps lower blood pressure

Clinical trial data show tailored recommendations improve health outcomes

An example of a personalized recommendation provided to a patient.

November 15, 2021--Engineers at UC San Diego have developed an artificial intelligence platform that fuses data from disparate health and lifestyle sensors, wearables and apps into one site, using this combined data stream to paint a broader picture of a user’s health, and make personalized recommendations for them to improve a specified health outcome. In a clinical trial with hypertensive patients, those using the P3.AI platform saw their systolic and diastolic blood pressure decrease by 3.8 and 2.3 points respectively, compared to 0.3 and 0.9 points for subjects in the control group who did not receive personal recommendations.

Researchers detailed the early findings of the Proactive, Personalized and Precise Insights and Recommendations using AI project, or P3.AI, in the IEEE Journal of Translational Engineering in Health and Medicine.

In addition to the clinical trial with hypertensive patients, this P3.AI platform powered the eCOVID app used in a clinical trial of patients with moderate cases of COVID-19 in San Diego. The same methodology, though a slightly different platform, was used to predict depression and recommend personalized mental health treatment, to participants in a UC San Diego School of Medicine study.

“This personalized model is not just a trove of data--its much smarter than that,” said Sujit Dey, professor of electrical and computer engineering at UC San Diego, and director of the Center for Wireless Communication, who is leading this P3.AI (Proactive, Personalized and Precise Insights and Recommendations using AI) project. “It’s trying to learn your habits in terms of sleep, activities, nutrition, stress level and mood, and how this is all correlated to your mental health or chronic conditions like blood pressure.”

Early results demonstrate the power of personalized recommendations in healthcare.

“Instead of telling you 10 different generic things to do, and encouraging you to totally change your life-- which is often what hypertensive patients are currently told-- this system will recommend one or two specific actions for you to take that would be most effective for you, and will show you with easy to interpret data how effective the changes are. Since your model will keep changing with your lifestyle changes and personal conditions, the specific recommendations may also change over time. We’ve seen again and again that general guidance leads to poor compliance; this system is capable of providing the personalized, explainable recommendations needed.”

Eventually, the goal is for patients and their doctors to be able to use this AI platform to improve any number of health conditions through personalized, data-driven recommendations. The platform can be integrated with electronic health records using APIs, enabling healthcare providers to get a more accurate and holistic picture of patients’ well being through a personalized dashboard for each patient. Healthcare providers can receive notifications if certain metrics hit a specified level, but are not bogged down by sifting through and interpreting the data.

A larger clinical trial of the P3.AI personalized recommendation system for hypertensive patients began in October through UC San Diego Health’s Population Health Services. 

“Getting patients engaged in evidence-based priorities by using this AI hypertension platform to better manage their lifestyle and environmental factors seems to help improve their cardiovascular health,” said Dr. Parag Agnihotri, Chief Medical Officer of the Population Health Services Organization at UC San Diego Health. “This collaborative project between the Jacobs School of Engineering and UC San Diego Health to test the P3.AI integrated hypertension care platform has the potential to help prevent avoidable heart attacks and strokes in our community.”

The platform and research challenges 

The platform works by fusing together data from a variety of sources-- fitness trackers, sleep trackers, mobile apps and questionnaires, blood pressure cuffs and more-- transmitted  at a variety of timescales, from every millisecond to daily or weekly-- and in a variety of modes, including numerical data points, photos, written text, and more. Finding a way to sync all of this data into one site and make it interpretable was one of three key challenges that engineers tackled when developing P3.AI.

Once the data is in one place, the researchers had to develop an AI system capable of fusing the multi-modal data and creating a personalized model of the user, constantly learning about the user’s lifestyle and habits and their impact, and updating the model. The model also reveals the top factors that influence the patient’s blood pressure, so that precise insights into the patient’s health can be generated.  

The third significant challenge that the team is now working through, is developing an AI system capable of interacting with a human, and able to translate the data and insights into recommendations in a way the user would understand and be more willing to comply with.

“An AI system directly collaborating with a patient is uncharted territory,” said Dey. “We keep learning about it, the job is not complete yet, but we’re getting positive results. That can be exciting, but we know we still have a lot of learning left to do.”

While clinical trials for the personalized health app for hypertensive patients continue to scale up, the initial results of this AI-patient teaming are promising. In the clinical trial of 25 patients, 83% of the subjects in the experimental group improved their mean systolic blood pressure, compared to only 47% of subjects in the control group, while 100% of the experimental group improved their mean diastolic blood pressure, compared to 53% of people in the control group. 

Similarly, all subjects in the experimental group improved their maximum systolic and diastolic, compared to only 63% and 58% of the subjects in the control group respectively. Finally, in the last 30 days, the blood pressure trend of subjects in the control group was relatively flat, while a decreasing trend was observed in the experimental group.   
 

Connected Health

This AI platform for personalized health is one of several projects at the UC San Diego Center for Wireless Communications focused on applying advances in wireless technologies to Connected Health challenges. The P3.AI platform underpins the Personalized Hypertension Care project, as well as the eCOVID monitoring and guidance project, and was crucial to the Personalized Machine Learning of Depressed Mood effort. 

In addition, engineers and physicians at the Center for Wireless Communications are working to advance an on-demand virtual physical therapy system; developing an Image Processing Platform for MRI-based Rectal Cancer Diagnosis; and are working to reduce the power constraints and advance the communication capabilities of Internet of Medical Things devices. 

“While amazing discoveries keep on happening on the pharmaceutical side, the surgery side, on using various kinds of sensors, yet health and health care have become more and more elusive to large swaths of populations,” said Dey. “When you hear ‘virtual healthcare,’ people often think of an inferior version of what you do at the clinic. But what we’re working on here is truly proactive and personalized care, empowering patients, with insights from their doctors, to make changes in their daily lives.”

UC San Diego Jacobs School of Engineering launches pilot program to connect veterans with careers in national security and at National Labs

November 11, 2021--United States government agencies, defense contractors and National Labs regularly report shortages of U.S. graduates with STEM degrees who can work in areas requiring security clearances. At the same time, the process of transitioning from military service to a STEM degree program and then to a job in a national security area is often not simple. The Jacobs School of Engineering at the University of California San Diego is working to address these challenges through a new pilot program called the Veteran Forge, which it announced on Nov. 11, 2021. 

The Veteran Forge program is designed to support qualifying veterans working toward an engineering or computer science degree at UC San Diego on their path to employment in national security careers. The hope is to provide a job upon graduation at one of the Veteran Forge partner organizations. At the same time, the program offers these organizations access to top talent from the #9 engineering school in the nation, knowing that these veterans are qualified for the required security clearances. 

“The Veteran Forge program will be a great resource for our student veterans," said Albert P. Pisano, dean of the UC San Diego Jacobs School of Engineering. "I anticipate that this program, by facilitating connections between our student veterans and employers in the defense space and at National Labs, will further establish UC San Diego as a destination for world class education and top engineering talent and leadership for all those involved." 

In its initial rollout as a pilot, the Veteran Forge program will be open to veterans currently enrolled in master’s degree programs at the UC San Diego Jacobs School of Engineering. If accepted into the program, student veterans will participate in a soft-skill curriculum, as well as a paid summer internship at one of the partnering institutions. Students and partners will participate in a match program similar to that used for medical school residency, to place students into careers at participating employers upon graduation. 

"There are so many opportunities for veterans to go on to further serve our country through civilian national security roles,” said Pisano. “I’m proud and excited that the Jacobs School can provide this needed support to our veterans, while at the same time helping our defense and National Lab partners find the right people for these crucial jobs.”

Launching a pilot allows the Jacobs School to grow the program as it works out the fine details and looks to offer the ability to include student veterans from undergraduates to doctoral students, from across campus. Another goal is to open the program to a wider variety of employers. Additionally, the vision is for Veteran Forge to assist community college student veterans, and individuals nearing separation from the service, with their education and career goals. 

"This program aims to provide the support structure and job outcomes that will enable our veterans to thrive, while providing defense organizations the uniquely qualified talent they need,” said Lon McPhail, himself a Navy veteran, director of corporate research partnerships at the UC San Diego Jacobs School of Engineering, and inaugural Veteran Forge executive director. 

With the pilot phase ramping up, there will be a limited number of slots for employers in the defense space and at National Labs to participate. Participating organizations will each commit to hosting students for summer internships; providing input in the soft-skills component of the program; mentoring participating student veterans; and hiring several Veteran Forge graduates each year.

UC San Diego is a natural fit for this program, as the region is home to the nation’s largest military community, housing one out of every four US. Marines, and one out of every six sailors. San Diego is also home to more than 2,000 defense companies, as well as the UC San Diego Jacobs School of Engineering, the largest engineering school on the west coast. 

The new program is designed to complement existing services offered by UC San Diego's Student Veterans Resource Center

Javier Garay, Associate Dean for Research and professor in the Department of Mechanical and Aerospace Engineering, is the Faculty Director of the Veteran Forge pilot program. 

To get involved as a participating hiring entity, please contact Lon McPhail at lmcphail@eng.ucsd.edu

 

UC San Diego team develops new point-of-care analyzer for human milk

ALT TEXT
Illustration of proposed human milk assay. Image adapted from Analytical and Bioanalytical Chemistry

November 10, 2021 -- Measuring human milk oligosaccharides (HMOs) at the point of care, in the NICU, in milk banks, at home or even on your cell phone may soon be possible, thanks to a new device developed by researchers at the University of California San Diego.

The device is a biosensor that tests for maternal secretor status and measures concentrations of the HMO 2’-fucosyllactose (2’FL) in a drop of human milk in just 35 minutes.

The work, led by postdoctoral researcher Saeromi Chung and Professor Drew Hall in the Department of Electrical and Computer Engineering at UC San Diego, is described in a paper published Nov. 5 in the journal Analytical and Bioanalytical Chemistry. The team included Lars Bode, a professor of pediatrics at UC San Diego School of Medicine and director of the Larsson-Rosenquist Foundation Mother-Milk-Infant Center of Research Excellence (MOMI CORE).

High concentration of 2’FL in human milk has been linked to infant growth, improved neurodevelopment, and protection from infectious diarrhea, which is one of the major causes of infant death worldwide. However, there is currently no technology to analyze the presence and concentration of HMOs such as 2’FL in human milk at the point of care.

The lack of such technology “represents a major impediment to advancing human milk research and improving maternal-infant health,” the researchers wrote.

The new technology developed at UC San Diego will be a game changer for research, donor milk banking and clinical applications, the researchers said. It consists of a simple biosensor, made of an electrode containing molecules that selectively bind to 2’FL. Place a drop of human milk sample on the electrode tip and within 35 minutes, it produces an electrochemical readout of the 2’FL concentration.

The team is improving the device so that it can communicate with and display readings on smartphones.

Paper: “Point-of-care human milk testing for maternal secretor status.”

This work was supported by pilot grants from the MOMI CORE Seeds program and the Altman Clinical and Translational Research Institute (ACTRI) at UC San Diego.

Want to throw off your chatbot? Use figurative language

An example of how the researcher's script helps make figurative speech literal so it can be more easily understood by dialog systems. 

November 8, 2021-- Computer scientists recently examined the performance of dialog systems, such as personal assistants and chatbots designed to interact with humans. The team found that when these systems are confronted with dialog that includes idioms or similes, their performance drops to between 10 and 20 percent. 

The research team also developed a partial remedy. They wrote a simple script that identifies figurative phrases and replaces those with their literal meaning. As a result, the performance of dialog systems improved by up to 15 percent.

The researchers are presenting their findings at the 2021 Conference on Empirical Methods in Natural Language Processing, which takes place Nov. 7 to 11, 2021. 

Applications for this work include not only personal assistants, but also systems that are designed to summarize information, such as the box summarizing search results at the top of a Google page. Automated systems that need to answer questions, for example when a bill needs to be paid or an appointment to be made, would also benefit from this work. 

“We want to enable more natural conversations between people and dialog systems,” said Harsh Jhamtani, the paper’s first author. 

Jhamtani is a Ph.D. student at Carnegie Mellon University and is currently working as a visiting researcher with senior author Taylor Berg-Kirkpatrick, a faculty member in the UC San Diego Department of Computer Science and Engineering.

The study was inspired by Jhamtani’s own struggles with figurative language. He is a native Hindi speaker and also speaks English, India’s other official language. But he had to learn the many U.S. idioms and metaphors his colleagues use. 

For example, he panicked when a colleague said they were starving because in Hindi that might indicate a medical emergency. His colleague then explained it just meant he was hungry. By then Jhamtani was wondering if artificial dialog systems would have the same issue he did.

In the study, researchers tested five different systems designed to talk  with humans, including GPT-2, which is trained to predict the next word in 40GB of Internet text and was developed by research company OpenAI. 

Researchers first ran the dialog systems through a dataset of 13.1K conversations on colloquial topics like tourism, health and so on. They then extracted the conversations that included figurative language from the dataset and ran the systems through those only. They observed a drop in performance ranging from 10 to 20 percent. 

They then wrote a script that allowed the systems to quickly check dictionaries that translate figurative speech into literal speech. This is faster and more efficient than re-training systems to learn the complete content of these dictionaries. Researchers observed that performance improved by as  much as 15 percent. 

The researchers still had to partially rely on human observers to identify figurative language within the dataset, before the text could be converted. Further study is needed in this area. 

It will take several iterations before the algorithms the researchers developed will be ready for implementation. For example, they found that in some rare cases, replacing the figurative language with literal language distorted the grammar of a sentence to the point where the dialog systems couldn’t no longer understand. 

Another example of literalized text  

Investigating Robustness of Dialog Models to Popular Figurative Language Constructs

Harsh Jhamtani, Varun Gangal, Eduard Hovy, School of Computer Science, Carnegie Mellon University

Taylor Berg-Kirkpatrick, Department of Computer Science and Engineering, University of California San Diego

 




 

 

ROSE YU HEADS MAJOR SCIENTIFIC MACHINE LEARNING PROJECT

Interdisciplinary team receives $3.6 million Department of Energy grant to develop scientific machine learning methods that will glean actionable information from complex climate datasets

November 5, 2021

Researchers at UC San Diego, UC Irvine and Columbia University have received a $3.6 million Department of Energy (DOE) grant to develop new machine learning methods to understand climate data and predict its ramifications on a warming world.

CSE Assistant Professor Rose Yu is the lead investigator on a new Department of Energy project

“We want to understand what is driving extreme heat in Houston or blizzards in Boston,” says CSE Assistant Professor Rose Yu, principal investigator on the project. “Climate studies often focus on short-range correlations, like the atmospheric dynamics near Texas that drive extreme heat. But what about the long-range pieces, like phenomena in the middle of the Pacific that change climate dynamics worldwide?”

Big, Big Data

The project, which includes CSE Assistant Professor Yian Ma, in the Halıcıoğlu Data Science Institute, and CSE Professor Lawrence Saul, will advance machine learning approaches to better handle the many large datasets that contribute to the overall climate picture.

“We want to combine simulation and observational data,” said Yu. “Traditionally in climate science, people develop simulation models but the process is very slow and has limited resolution – about a 100 to 150 square kilometer range. That's just not enough to understand the hidden drivers that lead to major events, such as extreme heat or hurricanes.”

The group will incorporate data from satellite images data, climate stations, ocean-deployed sensors and other sources. Each of these contribute enormous amounts of data, so the team will have to devise new ways to trim that down for analysis.

Yu and colleagues will develop a machine learning framework, based on latent variable models, which creates mathematical models to infer information from unobservable events. Using this approach, they intend to map super-complex information from climate models and observational data to create simpler forms that can be more readily interpreted.

Ironically, the datasets are both large and small: Overall climate information is massive, but extreme climate events can be quite rare. One of the many challenges the group will face is teaching the algorithm, even when data points are unavoidably sparse and unbalanced.

The Physical World

Yu notes the group will have to customize existing algorithms to make them more science-focused. Specifically, the team will embed principles from physics and other disciplines to better define data parameters.

“Climate science is driven by physical principles,” said Yu. “If we just use an off-the-shelf machine learning model, it's predictions may not adhere to physical laws. Such models would not make any sense to our end users, which are climate scientists.”

While challenging, incorporating physics in machine learning will improve predictions by adding explicit constraints. For example, there’s no chance the temperature will hit 200 degrees Fahrenheit. The hybrid model will also account for the constant uncertainty in climate data – it’s not a single temperature but rather a temperature range.

The seven investigators on the grant bring a wide range of expertise to solve these and other problems and better capture the nuances associated with climate change. They hope their results will inform better policy. In addition, the methods they develop could provide other, ongoing benefits to the broader science community.

“I'm really excited because we can potentially demonstrate the huge impact of AI to improve our fundamental understanding and accelerate scientific discoveries.,” said Yu. “We need advanced machine learning technologies, and these can have a broader impact on many fields beyond climate science.”

$6M IARPA grant to secure wireless data communication

November 3, 2021 -- A team co-led by the University of California San Diego has been awarded a $6 million grant from the Intelligence Advanced Research Projects Activity (IARPA) to secure classified data transmissions using smart radio technology. The researchers will partner with JASR systems, a San Diego-based company focused on advanced remote sensing and navigation technologies.

The grant is part of a new program by IARPA—dubbed Securing Compartmented Information with Smart Radio Systems (SCISRS)—that aims to protect sensitive data communications from being breached in government facilities and “in the wild.” 

ALT TEXT
Dinesh Bharadia

“The project funded by IARPA would not only help develop solutions for intelligence and defense agencies, but also for everyday people since most of our communications today are wireless,” said Dinesh Bharadia, a professor of electrical and computer engineering at the UC San Diego Jacobs School of Engineering. “Wireless systems, including 5G systems, are long overdue for security and privacy features, which are currently non-existent. It is very easy today for anyone to mimic your Wi-Fi Access Point, know everything you send over the world wide web, and worse yet, get access to all your data, and you wouldn’t even know it.” 

The goal of the project is to develop smart radio systems to detect and characterize suspicious radiofrequency signals, or RF anomalies, in complex RF environments. These RF anomalies include: 

- Low probability of intercept signals (signals that are hard to see because they are buried in noise and masked by stronger signals)

- Altered or mimicked signals (these signals attempt to appear benign—for example, they can look like signals from a cell tower or your neighbor’s Wi-Fi—but are actually soliciting communication with your devices)

- Unintended emissions (signals that are not meant to be transmitted and inadvertently carry sensitive information; sources for these emissions include screens, video monitors, computer mice and KVM switches on keyboards)

The UC San Diego team will design and build algorithms that can identify RF anomalies by continuously scanning a wide range of radio wavelengths in near real-time and with high accuracy. The team’s approach will involve using frequency and spatial channelization techniques to suppress interfering background signals and expose weak, anomalous RF signals. The researchers will also use deep learning techniques and large-array sensor data that they developed to sense the environment, and extract and classify signals from noise. 

UC San Diego researchers will work with JASR Systems, which will develop an efficient implementation of the algorithms, then test the implementation of these systems on the RF testbed at UC San Diego. 

Bharadia, who is a faculty member of the university’s Center for Wireless Communications and director of the Wireless Communication, Sensing and Networking Group (WCSNG), is a co-principal investigator on the project along with Jinendra Ranka, CEO of JASR Systems. Other investigators on the team include: Fredric J. Harris, an expert in digital signal processing and adjunct professor of electrical and computer engineering at UC San Diego; and Peter Gerstoft, a machine learning expert and data scientist at Scripps Institution of Oceanography at UC San Diego and adjunct professor of electrical and computer engineering (lab website: Noiselab).

“This partnership between UC San Diego and JASR Systems will work toward securing our everyday communications by developing world class solutions for identifying malicious and nefarious behavior with our wireless communications. As a future extension, we also hope to develop a low-cost solution that anyone can readily acquire to detect such nefarious activities,” said Bharadia.

Making Voice Assistants Accessible for Older Patients

November 2, 2021-- Voice assistants such as Amazon’s Alexa and Apple’s Siri have tremendous potential to help people manage their health as they age. Using these eye- and hands-free tools, patients could make appointments, confer with clinicians, receive medication reminders and perform other tasks. Unfortunately, current devices have not been designed with older patients, or even healthcare, in mind.  

Now, researchers at UC San Diego’s Qualcomm Institute, the Human-centered eXtended Intelligence Research Lab and other programs in UC San Diego’s Computer Science and Engineering Department and Department of Medicine, are taking a hard look at whether older adults are using (or not using) this technology and how it can be improved. Their project is called Voice Assistant for Quality of Life and Healthcare Improvement in Aging Populations, or VOLI, and the voice assistant that resulted is being tested in homes beginning this month as part of a feasibility study. 

“Voice assistants have become ubiquitous and could really improve wellbeing for older adults,” said VOLI principal investigator Emilia Farcas, an assistant research scientist at the Qualcomm Institute. “There are many services and products out there, but their adoption is really questionable because you can't just develop something, put it out there and hope it will be used.”

Technological Barriers

The prototyped voice skill will be used to examine the feasibility of using voice assistants for Ecological Momentary Assessment (EMA). The skill could run across different devices, including user-detached voice-only (a-b), voice-first speakers (c-d), user-attached smartphone (e-f), and watch (g-h).

Farcas, co-investigator Nadir Weibel, a Computer Science and Engineering professor who heads the Human-centered eXtended Intelligence Research Lab, and colleagues have been assessing the many barriers that reduce effectiveness. In a paper presented at the 23rd International ACM SIGACCESS Conference on Computers and Accessibility (ASSETS'21), the team explored the different issues older people face when using voice assistants.

“We tried to connect to older adults’ real lives,” said Computer Science and Engineering Ph.D. student Chen Chen, first author on the paper. “We wanted to pinpoint their daily life and healthcare management routines – contacting doctors, scheduling appointments, recording their vital signs and submitting them through MyChart (UC San Diego’s electronic health record system) – and we identified some of the problems they are facing.”

The team interviewed 16 people ages 68 to 90, two geriatricians and three nurses to understand how virtual assistants can be useful and where they fall short. They found current devices are poorly designed to manage most healthcare needs. 

Tracking medication compliance is just one example. Sometimes patients forget to take their medicines and compound the problem by taking time-sensitive medications whenever they remember, which can lead to bad results. Throughout the study, patients described the functions they wanted.

“I have to weigh myself every day and take my blood pressure and my sugar and keep all that down,” said one study participant. “And my friend said it would be a great thing for me to be able to have Alexa keep that information and then just be able to transfer to MyChart instead of me having that typed all in for the doctors.”

New Designs, New Devices

The VOLI team envisions devices that are more user-friendly and useful to better support older patients. Health-focused voice assistants could prevent emergency room visits and hospitalizations, generally improve quality of life and act as extra sets of eyes and ears for clinicians and concerned family members.

“We need to think about these systems from a more holistic perspective,” said Weibel. “The patient may be the only one actually talking to the device, but we must also consider clinicians and family. What are their needs and how can we support them?”

The group is custom designing its own voice assistants and anticipate placing them in households this month. This feasibility study will assess the technology’s effectiveness and provide feedback to continuously refine it. VOLI will initially enroll 10 participants and then scale up to 50. Each participant will receive two devices to test assistant efficacy both with and without a screen.

“This will be an iterative project, during which we test new designs in patients’ homes and see how they work,” said Farcas. “We can then use that information to redesign the devices to make them more effective and give patients, doctors and family members better value.”

VOLI’s interdisciplinary team also includes UC San Diego Department of Medicine co-investigators Alison Moore, the Larry L. Hillblom Chair in Geriatric Medicine and Professor and chief of the Division of Geriatrics and Gerontology, and Michael Hogarth, Professor in the Division of Biomedical Informatics, Director of Biomedical Informatics at the Altman Clinical Translational Science Institute (ACTRI) and Chief Clinical Research Information Officer for UC San Diego Health, as well as Ndapa Nakashole, an assistant professor in the Department of Computer Science and Engineering and a member of the UC San Diego Artificial Intelligence Group.






 

 


 

Making Space Travel Inclusive for All

UC San Diego researchers participate in zero gravity flight to understand ability, disability in space

AstroAccess Ambassador Mary Cooper, an aerospace engineering student at Stanford and below-the-knee amputee, experiences a weightless, microgravity environment on the Zero-G Flight. Photo credit: Al Powers for Zero Gravity Corporation.

By Kiran Kumar

October 28, 2021--In a weightless, microgravity environment like space, what do ability and disability look like? How can someone with partial sight or impaired mobility navigate in a confined space like the space station? As scientists and innovators continue to push the boundaries of spaceflight and the possibility of human life on other planets, how can we build space infrastructure that is inclusive of all humans?

The Mission: AstroAccess project aims to answer these questions, starting with a historic parablic flight that took off from Long Beach on Oct. 17, 2021. A group of 12 disabled scientists, veterans, students, athletes and artists launched into a zero-gravity environment as a first step toward understanding what is needed to make space inclusive for all.

Dr. Eric Viirre (right) served as chief medical officer on Stephen Hawking's microgravity flight in 2007, and was medical and flight operations lead for this AstroAccess flight. Viirre directs The Arthur C. Clarke Center for Human Imagination at UC San Diego and is a neurologist at UC San Diego Health.

“The whole point of this project is to demonstrate that people with disabilities are able to fly safely into space,” said Dr. Erik Viirre, director of The Arthur C. Clarke Center for Human Imagination at the University of California San Diego, and a neurologist at UC San Diego Health. Viirre served as medical and flight operations lead for the AstroAccess flight, ensuring a safe environment for all 12 AstroAccess Ambassadors and their partners on board. "What we're working on in this initial flight are demonstrations of a variety of different tasks that our Ambassadors will have to carry out, including navigating up, down, left and right; clear communication; and being able to move to a set location."

In addition to Viirre, aerospace engineering student Brenda Williamson, the former president of the UC San Diego chapter of the American Institute of Aeronautics and Astronautics (AIAA), served as head of the logistics committee in preparation for the flight.

The AstroAccess project is led by a group of scientists, engineers, and social workers with a common goal: inclusive space exploration. In the United States, 26% of the population has a disability, yet people with disabilities make up only 8.4% of the country’s employed scientists and engineers. AstroAccess wants to make STEM, and space, accessible to this large portion of the population.

To get a better idea of what is needed for more inclusive space travel, AstroAccess plans to conduct a series of follow-on parabolic flights after this inaugural launch. On these flights, conducted by the Zero Gravity Corporation (Zero-G), a plane equipped with a special padded section flies up to an altitude of around 32,000 feet and then begins a rapid descent at about 4 miles per second. This quick descent creates a free fall, or microgravity, weightless effect lasting roughly 30 seconds. Afterwards, the plane climbs back up to a stable altitude, and repeats the process again. On the Oct. 17 flight, the process was repeated roughly 15 times.

AstroAccess Ambassador Azubuike "Zuby" Onwuta is a Harvard-MIT trained innovator and U.S. Army veteran who is legally blind. Viirre braces himself behind Onwuta, as he ensures a safe on-board experience for all participants. Photo credit: Al Powers for Zero Gravity Corporation.

The 12 AstroAccess Ambassadors selected for this first microgravity flight included four blind or low-vision Ambassadors; two deaf or hard-of-hearing Ambassadors; and six Ambassadors with mobility disabilities, all carrying out a variety of tasks and challenges in the weightless environment. One of the challenges was seeing whether all crew members could perform basic safety and operational tasks, like navigating to oxygen masks. The crew also tested a procedure to see whether sound beacons can be used for blind members to orient themselves, and the effectiveness of haptic devices in communicating commands. They’re also investigating how American Sign Language will be impacted by microgravity.

When it comes to the physiology of microgravity and understanding how the human body is affected, Viirre has a wealth of information and experience. This wasn’t his first flight with Zero-G; Viirre was also the chief medical officer in charge of Stephen Hawking’s microgravity flight in 2007, and has served as CMO on several gravity-free flights for people with disabilities since. The Arthur C. Clarke Center for Human Imagination at UC San Diego is an official sponsor of the AstroAccess program.

“We still have lots of things to learn about traveling in space,” he said “Our destiny really is out there.”

Brenda Williamson, an aerospace engineering student at UC San Diego, served as head of the AstroAccess logistics committee in preparation for the flight.

Williamson, an aerospace engineering student at UC San Diego, has been involved with the project for months now, working to ensure the October launch went off without a hitch.

“As the lead of logistics, I manage all of the nitpicky details we need to know for our five-day trip in Long Beach, including transportation, food, catering, ASL interpreters and company tours,” Williamson said. “We’re doing quite a bit these few days and it’s my job to make sure we make that all happen.”

As former president of the AIAA chapter at UC San Diego, Williamson was responsible for hosting events with guest speakers, organizing club trips, and planning events to help prepare students for graduate school or industry jobs. She believes that this helped her prepare for her role with AstroAccess. For her, contributing to AstroAccess’ goal is also personal.

“My whole career goal is to make the average person able to go to outer space, where you don’t have to be a crazy trained astronaut with impeccable physical abilities and health to visit outer space,” she said. “I grew up on Star Trek, so the idea of exploration is really important to me.”

Williamson and Viirre are enabling a path for more Tritons to join the storied history of UC San Diego alumni in space. UC San Diego is home to a number of astronaut alumni and faculty members, including Sally Ride, former professor of physics at UC San Diego and the first American woman in space; and current NASA astronauts Megan Mcarthur, an alumna of the Scripps Institution of Oceanography, and Kate Rubins, a biology alumni of UC San Diego.

Cars, Start Your Engines!

UC San Diego joins the University of Hawai'i to compete at the first autonomous car race at famed Indianapolis Motor Speedway

The AI Racing Tech team, representing the University of Hawai'i and UC San Diego, stand behind the autonomous race car they developed, at the Indianapolis Motor Speedway. UC San Diego students Siddharth Saha and Haoru Xue are fifth and sixth from the left. Photo credit: Indy Autonomous Challenge.

 

October 21, 2021--On October 23, nine race cars will take to the famed Indianapolis Motor Speedway, home to the Indy 500, to await the most famous words in racing: Drivers, start your engines! But at this race, there’s something missing: the drivers.

For the first time, autonomous cars will race 20 laps around the 2.5-mile track at speeds of up to 200 miles per hour, without any physical driver. Each of the full-sized race cars will be equipped with computer and software systems designed by teams of university students from around the world, including engineering and data science students from the University of California San Diego. At stake? A $1.5 million prize pool, and the title of champion of the inaugural Indy Autonomous Challenge.

UC San Diego, through its Contextual Robotics Institute, is a partner institution with the University of Hawai'i at the Indy Autonomous Challenge.

The Indy Autonomous Challenge (IAC) is a collaborative effort that brings together public, private and academic institutions to challenge university students around the world to imagine, invent and prove a new generation of automated vehicle software and inspire the next generation of STEM talent.

UC San Diego, through its Contextual Robotics Institute, is an associate institution partner with the University of Hawaii’s AI Racing Tech Team, sponsored by GAIA Platform; two UC San Diego students have been in Indianapolis working on their autonomous race car since July.

Each team has transformed a Dallara AV-21 race car into an autonomous vehicle over the course of several months, developing perception, navigation, and control systems with support from IAC sponsor companies, in order for the car to function completely autonomously.

“The name of the competition really describes what we’re doing: it’s the Indy Autonomous Challenge, and it truly has been a challenge,” said Haoru Xue, an undergraduate electrical engineering student at the Jacobs School of Engineering at UC San Diego, and a member of the team. “There's so many challenges before we can get the cars to be controlled autonomously that all the teams are actually helping each other out as we get our cars up and running, before even getting to the competition aspect.”

The competition will feature 21 universities from nine countries that have formed 10 teams.

The students they’re collaborating with, and competing against, come from universities including MIT, Purdue, Korea Advanced Institute of Science and Technology, ETH Zurich, Technische Universität München and more; most of the nine teams are collaborative efforts between multiple universities, as is the case with the University of Hawai’i and UC San Diego partnership.

A neuro-symbolic AI approach

Once they get the race cars up and running, the real fun begins as each team develops its own approach to adding autonomy to the physical car, including cameras, radar and lidar systems, and the software to control it all. All teams start with the same physical car, and build their autonomy systems on top of the same Dallara car frame.

The students transformed a Dallara AV-21 race car into an autonomous vehicle.

“The approach we’re using is best described as neuro-symbolic AI, a hybrid version becoming more common for increasing the robustness of AI in many industries,” said Siddharth Saha, a recent UC San Diego data science graduate now earning a master’s in computer science at UC San Diego. “The idea is you feed in neural inputs into a mostly rule- and structure-based algorithm, and that enhances its robustness. The main advantage of this approach is it’s no longer a huge black box where we don’t know why something different than what we expected came out. Since the core decision making aspect of our data pipeline is rule-based, we can see the input and know what’s coming out, because we coded it.”

This makes it easier to trace back decisions to understand why the car performed a certain way, helping to eliminate the uncertainties which could be race-ending at these speeds. Though the cars are capable of speeds up to 200 mph, Xue said he expects most teams will stick in the 160-170 mph range, to try and reduce the possibility of collisions.

An autonomous vehicle pipeline

UC San Diego electrical engineering student Haoru Xue sits on a race car frame.

Participating in this competition is the next step in the students’ progression from small scale robocar to go-kart to real deal race car. Xue got his start in the autonomous car space by taking the Introduction to Autonomous Vehicles course at UC San Diego, building 1/10 scale autonomous cars and racing them on a tape-lined track on campus. Next, he and Saha moved up to working on autonomous go-karts, and were part of the UC San Diego Triton AI team that took 3rd place at the autonomous division of the evGrandPrix race earlier this year.

“I always see flashbacks when I see the car running on the track,” said Xue. “Only one year ago, we were only racing these mini robocars on the UC San Diego Warren Mall track, and now we’re dealing with full size autonomous cars.”

Through the Indy Autonomous Challenge, the students had the opportunity to test their car on the Indianapolis Motor Speedway, work on their car in the Juncos Racing factory, and collaborate with industry professionals from top companies in the field. But for Saha, the best moments have been some of the simplest.

“I personally think the coolest thing is when you get your engine starting and you’re right next to it,” he said. “When the engine starts right next to you and your ears are ringing, that’s been a defining moment for me.”

For the UC San Diego contingent’s advisor, being able to offer unique opportunities like this is already a win, regardless of the results on race day.

“For me, this project feels like going back to graduate school where I had a chance to participate in a few high-profile field robotics missions for NASA,” said Jack Silberman, a lecturer from UC San Diego’s Contextual Robotics Institute and one of the group’s advisors, as well as the instructor of the autonomous vehicle course. “I can’t express the satisfaction that I have by offering back to students similar academic and career opportunities. We can already see the growing number of students interested in joining our autonomous Triton AI evGoKart race team, so I consider the team’s accomplishments over these few months a victory already. I can’t wait to see where these students will be in a few years and hopefully engage back with us to help other students succeed.”

These opportunities could continue to involve partnership with The University of Hawai’i, whose team principal, Gary Passon, said the partnership has been a fruitful way to exchange knowledge and work collaboratively between the two universities. The team was sponsored by GAIA, ADLINK, and the Maui Robotics Vehicle Association (MRVA), with the support of UC San Diego's Jacobs School of Engineering and HalıcıoÄŸlu Data Science Institute (HDSI).

The Indy Autonomous Challenge is a full day affair scheduled for October 23, with the race beginning at 1:30 pm EDT. The race will be livestreamed to the IAC homepage beginning at 1 p.m. EDT.

Graduate Women in Computing Wins International Award to Boost Diversity and Engagement in CS

GradWIC takes full advantage of UC San Diego’s proximity to La Jolla Shores by hosting beach bonfires with smores and more (June 2021).

October 21, 2021--The Graduate Women in Computing organization (GradWIC) at UC San Diego is one of seven universities in the world to be selected for this year’s Xilinx Women in Technology University Grant Program. The program seeks to increase the representation, participation and entrepreneurial skills and abilities of women and other underrepresented minorities in computing related fields.

“GradWIC's primary focus is to build the community, both here at UC San Diego and beyond. This gift will enable us to continue our mentorship program for graduate students in computing across campus, as well as our collaborations with the undergraduate computing organizations,” said GradWIC’s president Jennifer Chien, a Ph.D. student in the Department of Computer Science and Engineering.

Jennifer Chien, GradWIC’s president

UC San Diego’s GradWIC works to create an innovative, informative and inclusive environment to help graduate students achieve their goals and succeed in their program. Focusing on those who identify as women and underrepresented minorities in computing fields, GradWIC’s membership of 400-plus students spans nine departments across the university.

It fills an important need. The underrepresentation—and importance—of women and minority voices in science, engineering and technology fields has long been known.

“GradWIC’s initiatives strive to build a more connected community so that minority voices can focus less on ‘fitting in’ and more on ‘belonging,’ ” Chien said. “This helps empower students to succeed in their career goals, lead by example and pay it forward for incoming students. These pipelines are essential to both recruitment and retention of women and minorities in computing, and beyond.”

From 2015 to 2021, GradWIC has hosted more than 375 students in mentorship programs, funded over 75 students to attend the annual Grace Hopper and ACM Richard Tapia Celebration of Diversity in Computing conferences and organized more than 25 professional development talks and workshops.

The award of $25,000 will help GradWIC develop its new or growing initiatives, such as the Graduate School Application Workshop Series, sexual assault and sexual harassment bystander training, professional development and resilience workshops and more, said Chien.

“We are also currently in the midst of developing an outreach program for underserved children at local schools helping them to see that they too have a future and belong in computing!” they said.

This year, GradWIC hosted a new student field trip to help incoming students become acquainted with the bus system and necessities in the La Jolla area. GradWIC Board Officers shown: Sophia Sun and Hema Thota (September 2021).

Coming out of four quarters of virtual classes into a hybrid fall quarter, GradWIC’s initiatives are more important than ever before, said Chien. “We will continue hosting mentorship programs, workshops and talks but are also expanding new outreach initiatives to help navigate students returning to in-person learning and work environments and to foster a greater sense of community,” they said.

UC adopts recommendations for the responsible use of artificial intelligence

Oct. 20, 2021-- The University of California has adopted a set of recommendations to guide the safe and responsible deployment of artificial intelligence in UC operations and three researchers at UC San Diego were involved with the effort. 

UC becomes one of the first universities in the nation to establish overarching principles for the responsible use of artificial intelligence (AI) and a governance process that prioritizes transparency and accountability in decisions about when and how AI is deployed.

The recommendations were developed by the University of California Presidential Working Group on Artificial Intelligence. The group was launched in 2020 by UC President Michael V. Drake and former UC President Janet Napolitano to assist UC in determining a set of responsible principles to guide procurement, development, implementation, and monitoring of artificial intelligence (AI) in UC operations.

The group included three UC San Diego faculty. Nadia Henninger is an associate professor whose work focuses on cryptography and security. Lawrence Saul is a professor whose research interests are machine learning and data analysis. Camille Nebeker is a professor who co-founded and directs the Research Center for Optimal Digital Ethics Health at UC San Diego.

The working group developed a set of UC Responsible AI Principles and explored four high-risk application areas: health, human resources, policing, and student experience. Nebeker and Saul were part of the group focusing on health, while Heninger worked on policing considerations. The group has published a final report that explores current and future applications of AI in these areas and provides recommendations for how to operationalize the UC Responsible AI Principles. The report concludes with overarching recommendations to help guide UC’s strategy for determining whether and how to responsibly implement AI in its operations.

UC will now take steps to operationalize the Working Group’s key recommendations:

  • Institutionalize the UC Responsible AI Principles in procurement and oversight practices;
  • Establish campus-level councils and systemwide coordination to further the principles and guidance from the working group;
  • Develop a risk and impact assessment strategy to evaluate AI-enabled technologies during procurement and throughout a tool’s operational lifetime;
  • Document AI-enabled technologies in a public database to promote transparency and accountability.

Using ultrasound to activate ion channels in brain cells

 

Oct. 19, 2021-- Researchers have discovered the mechanism that causes ion channels in brain cells to switch open after the cells are exposed to ultrasound waves. The discovery could have applications in the development of non-invasive, non-pharmacological treatments of neurological conditions. 

The team, which is composed of researchers from the MADLab at University of California San Diego and the Chalasani lab at the Salk Institute for Biological Studies, presents its results in the Nov. 7 issue of the journal Advanced Science.

“No one has seen the cell membrane move like this before,” said James Friend, a professor in the UC San Diego Department of Mechanical and Aerospace Engineering.

The researchers discovered that the thin membranes of neuronal and fibroblast cells are deformed by incident ultrasound, which causes these membranes to stretch. This is surprising because the cell membranes are roughly 10 nanometers thick, or 10,000 times smaller than a human hair's width. In addition, the liquid on both sides of the membranes is roughly the same composition. Researchers observed that the stretch is caused by the reflection of a small portion of the ultrasound from the membrane, deforming and stretching it. 

When the membrane stretches, its capacitance changes. Because there is already a voltage difference from the inside of the cell to the outside (due to chemical differences), a capacitance change in the presence of this voltage difference causes current to flow.

“This may prove effective in triggering specific ion channels, such as TRPA1, an ion channel often used in sonogenetics research,” said Aditya Vasan, the paper’s first author and a Ph.D. student in Friend’s research group. 

This ion channel is already expressed in important cells in some organs, making this type of ultrasound intervention possible. As a result, this mechanism could also be used in treatments used on the heart, liver, pancreas, gall bladder and other organs that either have TRPA1 or could be added later.

A unique system

A unique high-speed, digital, holographic microscope allowed researchers to observe this stretching mechanism for the first time. Researchers were able to use the instrument to confirm the amplitude of the cell membrane's deformation and its dynamic response to ultrasound exposure. 

The microscope marries a 1-million frame-per-second camera to a laser-driven microscope that uses holography — the interference between light passed through a measurement sample and light that goes around that sample. The holographic method produces a measurement of the deformation of a surface—whether a fluid-air surface or the surface of a cell membrane—without scanning.

Most models of cell membranes use static analyses, ignoring the dynamics of that model. The team’s results suggest ignoring the dynamics may be a mistake. Their model is dynamic, and includes mechanical and electrical information to form a complete picture. It is also nonlinear. The results are similar to what was observed in experiments for similar ultrasound exposure values. The nonlinearity and the dynamics are both important parts in modeling.

This work was completed in in vitro neurons and HEK cells. Next steps include investigating in mice whether TRPA1 and potentially other channels can be used to provide targeted actuation of cells in the brain of live, freely moving mice.

The research was funded by a SERF grant from the W.M. Keck Foundation, the National Institutes of Health and the National Science Foundation. 




 

Researchers determine optimum pressure to improve the performance of lithium metal batteries

Top row: top view and cross sections of deposited lithium at 70 kilo-Pascal or kPa (less than one atmosphere)
Bottom row: top view and cross sections of deposited lithium at 350 kPa, or 3.5 atmospheres
The higher pressure causes the lithium particles to deposit in neatly stacked columns, which  increases the volume of lithium deposited and prevents porosity

Oct.18, 2021-- A team of materials scientists  and chemists has determined the proper stack pressure that lithium metal batteries, or LMBs, need to be subjected to during battery operation in order to produce optimal performance. 

The team, which includes researchers from the University of California San Diego, Michigan State University, Idaho National Laboratory and the General Motors Research and Development Center, presents their findings in the Oct. 18 issue of Nature Energy.

Using lithium metal to replace the graphite for battery anodes is the ultimate goal for part of the battery R&D field; these lithium-metal batteries (LMBs) have the potential to double the capacity of today’s best lithium-ion technologies. For example, lithium metal battery-powered electric vehicles would have twice the range of lithium-ion battery-powered vehicles, for the same battery weight. 

Despite this advantage over lithium-ion batteries, LMBs are not considered a viable option to power electric vehicles or electronics, because of their short lifespan and potential safety hazards, specifically short circuits caused by lithium dendrite growth. Researchers and technologists had noticed that subjecting LMBs to pressure during battery cycling increases performance and stability, helping to solve this lifespan challenge. But the reasons behind this were not fully understood.

“We not only answered this scientific question, but also identified the optimum pressure needed,” said Shirley Meng, a professor in the UC San Diego Department of NanoEngineering and the paper’s senior author. “We also proposed new testing protocols for maximum LMB performance.”

In the Nature Energy study, researchers used several characterization and imaging techniques to study LMB morphology and quantify performance when the batteries were subjected to different pressures. 

They found that higher pressure levels force lithium particles to deposit in neat columns, without any porous spaces in between. The pressure required to achieve this result is 350 kilo Pascal (roughly 3.5 atmospheres). By contrast, batteries subjected to lower levels of pressure are porous and lithium particles deposit in a disorderly fashion, leaving room for dendrites to grow. 

Researchers also showed that the process doesn’t affect the solid electrolyte interphase (SEI) structure of the batteries’ electrolytes. 

But manufacturing facilities for LMBs would have to be retooled for this new technique to be applied.

Another way to boost performance is to not completely discharge the battery while it cycles. Instead, the researchers keep a reservoir of lithium where re-nucleation can occur. 

The researchers’ findings were validated at the General Motors Research and Development Center in Michigan. 

Separately, researchers at Idaho National Laboratory use molecular dynamics simulations to understand the stack pressure range used in this work, which is much less than that expected based on macroscopic mechanical models. Researchers explained the mechanistic origin of this unique process.

“Research institutions should keep collaborating with national laboratories and industries to solve practical problems in the battery field,” said Chengcheng Fang, the paper’s first author, who earned her Ph.D. in Meng’s research group and is now on faculty at Michigan State University. 

Pressure-tailored lithium deposition and dissolution in lithium metal batteries

Chengcheng Fang, Bingyu Lu, Minghao Zhang, Diyi Cheng, Miguel Ceja, Jean-Marie Doux and Y. Shirley Meng, Department of NanoEngineering, University of California San Diego

Chengcheng Fang, Department of Chemical Engineering and Materials Science, Michigan State University

Gorakh Pawar and Boryann Liaw, Energy and Environmental Science & Technology, Idaho National Laboratory

Shuru Chen and Mei Cai, General Motors Research and Development Center 




 

Computer Scientist's Work Passes the Test of Time, Again

Second test of time award honors AspectJ, which makes it easier to write code for complex applications

UC San Diego computer science professor William Griswold has received his second test of time award for work that has had a major impact on the field

Oct. 13, 2021-- UC San Diego computer science professor William Griswold has received his second test of time award for groundbreaking work. This time, he was honored by the Association Internationale pour les Technologies Objets (AITO) for his 2001 paper on the AspectJ programming language, an aspect-oriented extension of Java. The test of time award recognizes work that has had a major impact on the field.

The seminal paper, An Overview of AspectJ, described ways to extend Java, the most popular programming language at the time, and has been cited more than 4,000 times. The paper transformed aspect-oriented programming (AOP) into a mature research topic, influencing context-oriented programming, feature-oriented programming and software product line techniques. The award was presented at the 2001 European Conference on Object-Oriented Programming (ECOOP).

This is the second test of time award for Griswold, a professor in UC San Diego Computer Science and Engineering Department. In 2013, he and colleagues received the ACM SIGSOFT Impact Paper Award for Dynamically Discovering Likely Program Invariants to Support Program Evolutionwhich broke new ground in software engineering.

In the ECOOP paper, Griswold and co-authors describe a way interrelated program components can talk to each other and still remain independent. This has obvious advantages, such as being able to add or extend one component without having to think about or update others.

“Let’s say I’m running a bank, and I want my clients to accrue interest, or I want them to accrue mortgage interest that they have to pay off,” said Griswold. “Those little increments of new functionality now become an interesting part of a much larger thing.”

The key is managing the linkages between components. Accruing interest in a savings account is like a deposit but happens on a regular basis. A timer program tells the interest calculating program when to do its job. The two need to interact – the interest piece must listen for the timer – but they also need to be kept apart or decoupled.

In this way, “the timer only knows about signaling the time’s up,” said Griswold. “It doesn’t know about updating interest. Likewise, the interest calculator doesn’t know about a timer.  We broke these two concerns apart. AspectJ makes the introduction of this listening functionality easy. You can tap into a very large number of events very concisely, rather than having to specify every last detail.”

This advance made it much easier to write code for complex applications, while reducing the risk that changes to one component could interfere with the other. “Banking is always coming up with new interest-bearing instruments,” said Griswold. “Some compound monthly, some compound by the minute – it’s confusing, you have to connect a lot of timers to different activities. Giving the programmer aspect-oriented support to respond to requests for new functionality is critical.”

Computer scientists part of NSF grant to make browsers safer

Computer scientist Deian Stefan is part of a $3M NSF grant to make web browsers safer. 

Oct. 12, 2021-- Computer scientists at the University of California San Diego are part of a $3 million grant from the National Science Foundation to make web browsers safer. 

At UC San Diego, the effort will be headed by Deian Stefan, an assistant professor in the Department of Computer Science and Engineering. The grant’s principal investigator is Hovav Shacham, a professor at The University of Texas at Austin. Shacham, Stefan and other members of the team, including Fraser Brown at Stanford, Isil Dillig at UT Austin, UC San Diego professors Ranjit Jhala and Sorin Lerner, have extensive experience in the field of browser security.

Last year,  the team developed a framework, called RLBox, that increases browser security by separating third-party libraries that are vulnerable to attacks from the rest of the browser to contain potential damage—a practice called sandboxing. The RLBox framework was integrated into Firefox to complement Firefox’s other security-hardening efforts. Now, the team is expanding their focus to the other huge attack vector: the browser’s JavaScript just-in-time (JIT) compiler.

Browser JITs turn web application code, written in JavaScript, into optimized machine code. Browser JITs are highly tuned and complex systems. Unfortunately, browser JITs also have bugs, and attackers have figured out how to take advantage of those bugs to take over the computers of users who visit their malicious websites.  Journalists and dissidents have been targeted by attackers using browser JIT bugs.

“We need to rethink the way browsers execute JavaScript programs from the ground up, by designing and building new JavaScript interpreters and compilers that are extensible, maintainable, and verified secure,” Stefan said. 

The goal of the NSF project is to build and deploy more secure JavaScript JITs. To this end, the team will develop new techniques, frameworks, and principles that help browser developers build JIT compilers that are provably secure and don't incur the high costs and development timelines traditionally associated with high-assurance software. 

 

“Everyone should be able to browse the web without worrying that clicking the wrong link will cause their computer to be compromised,” Shacham said.  “We hope our project can help make that goal a reality.”

 

Low-performing computer science students face wide array of struggles

October 12, 2021--Researchers at the University of California San Diego conducted a broad student experience survey to learn which factors most impact student success in early computing courses, a field that has historically seen high failure rates and poor student retention. They found that lower performing students reported higher stress levels on multiple factors— including cognitive, socio-economic, and personal—than higher performing students, indicating that when students struggle, they are often facing headwinds on multiple fronts.  

While previous research has studied one or two factors impacting computer science student success, this is one of the first studies that takes a holistic view of the student experience. The results suggest that successful interventions should target multiple areas of student stress, instead of focusing only on addressing a single issue. 

The computer scientists presented their findings at the Association for Computing Machinery Conference on International Computing Education Research

“Students are struggling with a lot of things across the board, it’s not just a single issue like ‘I’m confused with the material or I feel I don’t belong,’” said Adrian Salguero, a computer science PhD student at UC San Diego and first author of the paper. “Many students, especially those who are lower performing, appear to be struggling with more issues apart from just not understanding the material. They're also reporting things like work obligations, feeling like they don’t belong, or don’t have the confidence to feel comfortable in the class; it’s more than just not understanding the material.”

Salguero and computer science education researchers analyzed surveys distributed to a total of nearly 1,700 students across four introductory computer science courses at UC San Diego in 2019. The weekly and bi-weekly surveys asked the students questions about their sense of belonging in the course; their level of in-class confusion; their personal obligations including work and family requirements; and their level of confidence and interest in the coursework.

Over 70% of students in the lowest quartile of final exam performance reported high levels of stress due to at least one of the four identified factors, compared with just 30% in the highest performing quartile. Over 50% of students in the lowest quartile report high levels of stress for two or more factors. By comparison, half as many students in the next higher quartile report struggling with multiple factors. 

The issue of struggle across multiple factors was particularly prevalent for students from groups traditionally underrepresented in computing—including women, Latinx and Black students. This is important to consider as the computer science field aims to rectify its low levels of retention of women students, and Black and Latinx students : less than 20% of computer science bachelor’s degree recipients in the nation are women, while 10.1% are Latino and 8.9% are Black.

Exposing students to computing prior to college is one step that could help diversify the field; the researchers’ results showed that students with no prior computing experience reported considerably more struggle than students with prior experience, across all levels of exam performance. And previous research has shown that students from groups underrepresented in computing are less likely to have access to these computer science experiences and courses prior to college.

“We as instructors or staff want to help students who are struggling, and our interventions are done with great intentions and a lot of hard work, but sometimes they may not be enough,” said Salguero. “You can imagine a student who doesn’t feel they belong in the course and has all these obligations outside of the course; perhaps an intervention changing the way the material is taught isn’t going to be sufficient to help that student. It begs the question of how can we start helping these students succeed?”

This paper focused on understanding student stress and not on actionable steps for instructors to take, but the researchers do note that increased flexibility of timing and assignments in the course may be one way to help these struggling students cope with their various stressors and still learn the material. Grander scale solutions, such as not tying financial aid to a set number of courses but rather to course difficulty level, may make sense as well, along with offering computer science courses and camps at the K-12 level. 

Ultimately, Salguero said that something as simple as asking students to complete these surveys could be a first step to help students feel that their instructor cares about their success and well-being, while also identifying students who may need more support. 

“What Adrian’s work has shown to the community is that struggling students often face a combination of challenges that may be impeding their success,” said paper co-author Leo Porter, a professor of computer science at UC San Diego and Salguero’s advisor. “This might help explain why interventions that seemed like they should have a larger impact have failed to improve student outcomes. As such, I’m hopeful that these findings will usher in a new era of study focused on holistic interventions that address a combination of students’ cognitive, social, and personal needs.”

This research is part of the team’s larger goal of studying how to help struggling students succeed in learning computer science. 

New Research Center Brings Genomic Medicine to Individuals of Admixed Ancestry

Researchers at UC San Diego School of Medicine awarded $11.7 million by National Institutes of Health to identify genomic and socioeconomic factors contributing to health and disease in admixed individuals

October 12, 2021--One way to make health care more personalized is to use a person’s DNA sequence — or genome — to predict their risk of disease. But as the field of precision medicine grows, so have concerns that we may be leaving a large fraction of Americans out.

Disease prevalence and severity can vary considerably across racial and ethnic groups due to genetic and social factors. However, most of what we know about the genetics of human disease comes from datasets of predominantly white, European people. This lack of genomic data from people of other backgrounds makes it harder to accurately predict their health outcomes. Even less is known about the genomes of “admixed” individuals whose DNA reflect multiple ancestries.

From left: Dr. Lucila Ohno-Machado, Kelly Frazer and Melissa Gymrek are principal investigators of the new genomics center at UC San Diego.

So the question is: How do we ensure that advancements in genomic medicine will be accessible to all?

Researchers at University of California San Diego School of Medicine have been awarded $11.7 million to launch the Genetic & Social Determinants of Health: Center for Admixture Science and Technology (CAST) to address this issue. CAST will use the largest genomic datasets of individuals with diverse ancestry, in combination with socioeconomic data, to better predict health and disease in admixed individuals.

Historical and recent mixing of Europeans, Native Americans, Africans and Asians has resulted in a relatively large number of admixed individuals in the U.S. Their genomes are a patchwork of DNA segments associated with different races and ethnicities, and may reflect ancestries outside of the individual’s self-identified race. The issue is physicians do not yet know how these DNA segments interact with each other to shape health outcomes, so these genomes are more difficult for them to interpret.

CAST is one of the latest additions to the renowned Centers of Excellence in Genomic Science (CEGS) funded by the National Institutes of Health (NIH). Each center focuses on a unique aspect of genomics research with the intention of blazing new trails in our understanding of human biology and disease.

“To bring the CEGS program to our campus is a huge honor, and a national recognition of UC San Diego as a major player in genomics,” said Lucila Ohno-Machado, MD, PhD, Distinguished Professor of Medicine at UC San Diego School of Medicine, chair of the Department of Biomedical Informatics at UC San Diego Health, and founding faculty of the Halicioglu Data Science Institute. Ohno-Machado will lead the center with Kelly Frazer, PhD, professor of pediatrics and director of the Institute for Genomic Medicine at UC San Diego School of Medicine, and Melissa Gymrek, PhD, assistant professor at UC San Diego School of Medicine and Jacobs School of Engineering.

Researchers need data on many people’s genomes and health outcomes in order to find consistent relationships among them. The health of individuals from different racial and ethnic groups is also affected by social factors, so this information must be included in models of disease. To do all this, CAST will develop computational tools to combine, protect and analyze data from two national studies: All of Us Research Program and the Million Veterans Program. These projects aim to recruit one million participants each, equipping CAST with an unprecedentedly large and diverse pool of data.

Their ultimate goal is for anyone to be able to visit their physician, have their genome sequenced, and learn not only if they are at higher risk for any particular disease, but also which prevention and treatment plans are best suited for them.

“As it stands, white people will be able to do this, but our existing knowledge may not be useful to most others,” said Gymrek. “We want to bring the genomic revolution to everyone.”

“People may not realize that a large number of people living in America are likely admixed, so we would be excluding a large portion of our community if we were not taking these mixed genomes into account,” said Ohno-Machado.

CAST will use advanced approaches to study admixed genomes. Their models will consider each individual’s unique patchwork of ancestry, rather than grouping individuals into established categories like “white” or “Asian.” And while most groups focus on changes in individual DNA nucleotides, known as single nucleotide polymorphisms (SNPs), the CAST team will consider a much broader spectrum of genetic variation. This includes investigating tandem repeats, or short lengths of DNA that are repeated at different frequencies in each person, and a region called the major histocompatibility complex (MHC). The MHC is one of the most diverse sections of the genome across races, in part because it is related to immune function, which is tailored to each population’s local environment.

CAST will also innovate the way large-scale and complex data is processed. The team will develop privacy-preserving algorithms that consult the data in the All of Us and the Million Veterans enclaves without needing to centralize the data in a single place. They will also use natural language processing to extract information on social determinants of health from patients’ clinical notes. These innovations will come from collaborations between informatics researchers at UC San Diego, the Broad Institute, University of Texas Health, Indiana University and the Veterans Administration.

“I really think we have the dream team here,” said Frazer. “We’re excited to use our complementary expertise to push the limits of genomic medicine at UC San Diego and beyond.”

Co-investigators at the Center for Admixture Science and Technology include: Lisa Madlensky, PhD, Cheryl Anderson, PhD, MPH, Cinnamon Bloss, PhD, Vineet Bafna, PhD, Niema Moshiri, PhD, Tim Kuo, PhD, Olivier Harismendy, PhD, Matteo D’Antonio, PhD, and Jihoon Kim, MS, of UC San Diego. Principal collaborators include Hoon Cho, PhD, of the Broad Institute, Hua Xu, PhD, of University of Texas Health, Haixu Tang, PhD, of Indiana University and Philip Tsao, PhD, of the Veterans Administration.

Students make it to finals of first autonomous EV GrandPrix race

September 30, 2021-- A group of UC San Diego engineering and data science students was one of three teams to make it to the final round of the inaugural autonomous EV GrandPrix go-kart race hosted by Purdue University in Indianapolis on Sept. 17. The team, spearheaded by student organization Triton AI, was among 12 university teams who registered to compete with an autonomous go-kart. 

The International Electric Go Kart Racing event began in 2010, originally with students building electric go-karts and driving them around a curvy course. This year was the first time that the event included an autonomous version of the race, with students implementing autonomous perception, navigation, and control systems to see which kart could complete roughly one-third of a mile lap on the race track in the fastest time, all on its own. 

“The whole concept of it is we build a robot from bottom up-- we just get a go-kart frame and we wire everything together. Then add lidar, add cameras, add radar, and make sure it’s all a  complete stack. We built a smaller scale car, basically,” said UC San Diego computer engineering student Jose Jimenez-Olivas.

Along with Jimenez-Olivas, UC San Diego electrical engineering students Jesus Fausto and Dallas Dominguez spent six weeks in Indianapolis this summer developing their go-kart. In addition, Triton AI members Siddharth Saha, Vladimir Rubtsov, Chris Jensen, Andrew Britten, David He and Haoru Xue (all data science or engineering students and recent graduates) provided key support leading up to the race. 

To qualify for the final race day, teams had to demonstrate that their go-kart could autonomously complete three laps around the race track. On Sept. 17, the three teams that qualified took turns racing a lap for the fastest time. During the race, the UC San Diego robot’s steering mechanism broke, leading to a third place finish. Though this wasn’t their desired outcome, the students said it highlighted how tricky this competition was; while previous human-driven races have focused on edging out the competition by margins of less than a second, this autonomous version posed more of a challenge.

The students developed an autonomous go-kart, no driver required.

“Part of what is exciting about this is that stuff usually doesn’t work,” said Fausto. “Especially since this is the first year it’s autonomous, it’s alright how much of this is gonna work, how much is not gonna go well. That’s kind of exciting. Because rather than going to a competition where every year everyone is going to complete this and it’s all gonna go perfectly, we’re all hacking it together as we go.”

Fausto and Dominguez got their start in this space as students in the Introduction to Autonomous Vehicles course at UC San Diego, where students build small autonomous cars, and race them around short tracks on campus. Jimenez-Olivas never took the course, but has a strong personal interest in cars and autonomy, even turning a go-kart frame he found at the dump into an autonomous vehicle on his own. Even with all this previous experience, the students said this EV GrandPrix competition was a step up. 

“The 1/10 scale cars we built during the Intro to Autonomous Vehicles course worked; you knew it would work based on previous quarters reports,” said Fausto. “Here, half the challenge is just getting the kart to work, before we even start making updates.”

 “The class was level one, learning how it all worked; this is like we skipped level two and went right to level three,” said Dominguez. “We’re learning on the fly, but there are skills from the class that we’ve used a lot, like how to navigate a linux environment and how to run certain scripts, so the class did pay off.”

The students designed the go-kart to use GPS waypoint navigation to maneuver around the course. They added radar and lidar systems to the chassis, so that it’s able to detect and avoid objects in its path if it goes off course. The students then programmed an embedded GPU with artificial intelligence to compute the optimal speed and orientation of the go-kart. Once the speed and orientation were calculated in the navigation stack, a controller area network (CAN) message is sent to the hardware stack to actuate the go-kart electronically. The students also programmed an industry grade engine control unit (ECU) with software to receive artificial intelligent CAN messages to communicate to the kart’s electrical nervous system to steer, brake, or accelerate. 

“From the bottom stack which we’re working on, these CAN frames say, ‘Based on the perception stack, we want the throttle to be at 50 percent, or we have to turn the steering wheel 30 degrees.’ We’re teaching the robot to do all this autonomously through coding,” said Jimenez-Olivas.

The students say they’ve learned a lot through the months-long process, including the importance of documentation. 

“A huge theme we’ve been pushing is the fact that this is the first year of the competition, which makes us the people whose shoulders everyone is going to stand on. We’re making documentation really nice to try and make things easier for whatever aspiring engineering students come next, so they don’t have to start from scratch,” said Dominguez.

The UC San Diego Triton AI team with their autonomous go-kart.

“Our Triton AI members were extremely committed and determined to win any placement and represent UC San Diego, additionally becoming the first UC San Diego organization to attend the EVGrandPrix competition,” said Andrew Britten, cofounder of Triton AI and a recent electrical engineering graduate. “It was a great teamwork experience that we all can definitely look back on, and we plan to try again in the future. I personally am very proud of my organization and how far we have come with my best UC San Diego Tritons.” 

According to Jack Silberman, a lecturer from UC San Diego’s Contextual Robotics Institute and the group’s advisor, the robot’s challenges were part of what made this such an excellent learning experience. 

“You usually do not learn these types of things in a classroom,” said Silberman. “Field robotics competitions represent unique opportunities for students to experience the real-world challenges they will most likely face on their next step outside UC San Diego. We will keep building upon the foundations we laid preparing for the 2021 EV GrandPrix. In fact, we are already preparing to participate in the next autonomous robotics competitions.”

Students interested in getting involved with autonomous robotics can reach out to the Triton AI student organization: https://tritonai.org.

DOE awards UC San Diego nanoengineers $1.25M to improve batteries for EVs

Sept. 28, 2021-- The U.S. Department of Energy (DOE) has awarded $1.25 million to nanoengineers at the University of California San Diego to improve the electrolytes that carry ions in lithium-sulfur batteries. The researchers will partner with General Motors and Ampcera Inc, a solid-state battery materials and technology company. 

The grant is part of a $60 million investment by the DOE for 24 research and development projects aimed at reducing carbon dioxide emissions from passenger cars and light- and heavy-duty trucks. The projects will help decarbonize the transportation sector and enhance the infrastructure needed to support the growing adoption of zero-emission vehicles—crucial to reaching the Biden-Harris Administration’s ambitious goal of a net-zero emissions economy by 2050.  

“Fossil-fuel powered cars and trucks are a leading cause of air pollution and carbon emissions, and that is why we are focusing on decarbonizing the transportation sector to achieve President Biden’s climate goals,” said Secretary of Energy Jennifer M. Granholm. “Partnering with industry and leading research universities, DOE’s investment in these 24 projects will create technologies and techniques that will cut vehicle greenhouse emissions and boost America’s competitiveness in the global clean energy market.”  

The projects, funded through DOE’s Office of Energy Efficiency and Renewable Energy (EERE) Vehicles Technology Office (VTO), address the two largest contributors to transportation sector emissions: passenger cars and light-duty trucks account for nearly 60% of emissions and medium- and heavy-duty trucks account for nearly 25%.

Specifically, the UC San Diego team, led by Professor Shirley Meng, in the Department of NanoEngineering at the Jacobs School of Engineering, will investigate how to enable what is known as lean electrolytes in pouch lithium-sulfur batteries. These batteries typically require a high amount of electrolytes, which in turn lower the battery’s energy density. That is where lean electrolyte technology comes in to increase the energy density and lower the cost. 

The team proposes using a polymer made of macromolecules that is highly dense and redox active to reduce the amount of electrolyte needed. Using this material leads to a substantial reduction in porosity in the battery--the amount of space between molecules inside the device’s materials. “The high S loading and preliminary cycling performance presents a promising and practical pathway to achieve the energy density goal of 500Wh/kg,” the researchers write. 

In addition, the true nature of the lithium-sulfur reaction is still not fully understood, so researchers will need to develop new tools to provide qualitative and quantitative understanding to further improve the device performance. The researchers plan to enable sulfur imaging at the nanospace to investigate lithium and sulfur loss in the batteries. 

The team also plans to optimize the materials for scale-up and pouch cell prototyping, in collaboration with industry partners Ampcera and GM. 

The UC San Diego award is one of across 12 projects that will focus on developing next generation lithium batteries with improved lifespan, safety, and affordability, improving the performance and durability of electrolytes that carry ions within batteries, and increasing the power density of electric drive systems. These advancements would increase the useful life of EVs and enable more affordable, better performing vehicles.
 

$5 million NSF grant supports data-friendly research platform

UC San Diego computer scientists will help develop the National Research Platform to create a data freeway system to accelerate research

Professor Tajana Rosing, in the Department of Computer Science and Engineering at the Jacobs School, is a co-PI on the project to prototype the National Research Platform (NRP), an actual information superhighway

Sept. 27, 2021--The San Diego Supercomputer Center (SDSC) has received a $5 million grant from the National Science Foundation’s Office of Advanced Cyberinfrastructure to prototype the (NRP), an actual information superhighway. Several members of the UC San Diego Department of Computer Science and Engineering will lend their expertise to the project.

The grant funds efforts at SDSC, the Massachusetts Green High Performance Computing Center and the University of Nebraska–Lincoln to build a high-performance platform, optimizing equipment, configurations and security to support data-intensive science projects. The NRP will give research collaborators new opportunities to share data and work simultaneously on complex projects.

COVID Analysis

One of the many beneficiaries will be UC San Diego Computer Science and Engineering Professor Tajana Rosing, who is trying to solve several high-data problems.

“I have been working with a couple of different teams on biology-related applications,” said Rosing. “For example, we're trying to accelerate the COVID 19 genomics pipeline, creating a phylogenetic tree of life of all the different mutations of COVID-19 to track viral evolution. Right now, that takes a really long time.”

Working with Rob Knight, a professor of pediatrics and computer science, Niema Moshiri, a computer science assistant teaching professor , and others, Rosing is using programmable hardware, called field-programmable gate arrays (FPGAs), to accelerate the process. So far, the analysis pipeline works great until the last step, actually creating the phylogenetic tree. That’s where the National Research Platform comes in.

“We will need many FPGAs to run in parallel, and that’s what the NRP platform does for us,” said Rosing. “The FPGAs must be connected with high bandwidth and low latency because we're moving a lot of data around.”

Molecular Dynamics

Rosing is also using the NRP on a collaboration with the Lawrence Livermore Laboratory to model molecular dynamics to enhance drug discovery. The team is trying to analyze the physical movements of atoms and molecules, another data-intensive task, and using a similar parallel FPGA setup to gain the necessary speed.

“It’s massive amounts of data and it’s interactive data,” said Rosing. “We’re trying to simulate interactions that happen in femtoseconds (one quadrillionth of a second), and need this very parallel system to get there.”

The end goal is to use this computer modeling to determine which molecules have the greatest potential to become medicines. While chemists can create a seemingly endless number of molecules, only a few go on to become safe and effective therapies. Physically testing these molecules is both time-consuming and expensive.

“The nice thing about simulating these interactions in the computer is that we don't have to run cell-based tests in the lab on every compound,” said Rosing. “We can use the model to weed out the ones that won’t work and only move forward with the ones that show promise, dramatically reducing the amount of time it takes to develop new medicines.”

A new solid-state battery surprises the researchers who created it

Engineers create a high performance all-solid-state battery with a pure-silicon anode

Sept. 23, 2021--Engineers created a new type of battery that weaves two promising battery sub-fields into a single battery. The battery uses both a solid state electrolyte and an all-silicon anode, making it a silicon all-solid-state battery. The initial rounds of tests show that the new battery is safe, long lasting, and energy dense. It holds promise for a wide range of applications from grid storage to electric vehicles. 

The battery technology is described in the Sept. 24, 2021 issue of the journal Science. University of California San Diego nanoengineers led the research, in collaboration with researchers at LG Energy Solution. 

Silicon anodes are famous for their energy density, which is 10 times greater than the graphite anodes most often used in today's commercial lithium ion batteries. On the other hand, silicon anodes are infamous for how they expand and contract as the battery charges and discharges, and for how they degrade with liquid electrolytes. These challenges have kept all-silicon anodes out of commercial lithium ion batteries despite the tantalizing energy density. The new work published in Science provides a promising path forward for all-silicon-anodes, thanks to the right electrolyte.

"With this battery configuration, we are opening a new territory for solid-state batteries using alloy anodes such as silicon," said Darren H. S. Tan, the lead author on the paper. He recently completed his chemical engineering PhD at the UC San Diego Jacobs School of Engineering and co-founded a startup UNIGRID Battery that has licensed this technology. 

Next-generation, solid-state batteries with high energy densities have always relied on metallic lithium as an anode. But that places restrictions on battery charge rates and the need for elevated temperature (usually 60 degrees Celsius or higher) during charging. The silicon anode overcomes these limitations, allowing much faster charge rates at room to low temperatures, while maintaining high energy densities. 

The team demonstrated a laboratory scale full cell that delivers 500 charge and discharge cycles with 80% capacity retention at room temperature, which represents exciting progress for both the silicon anode and solid state battery communities.

1) The all solid-state battery consists of a cathode composite layer, a sulfide solid electrolyte layer, and a carbon free micro-silicon anode.
2) Before charging, discrete micro-scale Silicon particles make up the energy dense anode. During battery charging, positive Lithium ions move from the cathode to the anode, and a stable 2D interface is formed.
3) As more Lithium ions move into the anode, it reacts with micro-Silicon to form interconnected Lithium-Silicon alloy (Li-Si) particles. The reaction continues to propagate throughout the electrode.
4) The reaction causes expansion and densification of the micro-Silicon particles, forming a dense Li-Si alloy electrode. The mechanical properties of the Li-Si alloy and the solid electrolyte have a crucial role in maintaining the integrity and contact along the 2D interfacial plane.

Silicon as an anode to replace graphite

Silicon anodes, of course, are not new. For decades, scientists and battery manufacturers have looked to silicon as an energy-dense material to mix into, or completely replace, conventional graphite anodes in lithium-ion batteries. Theoretically, silicon offers approximately 10 times the storage capacity of graphite. In practice however, lithium-ion batteries with silicon added to the anode to increase energy density typically suffer from real-world performance issues: in particular, the number of times the battery can be charged and discharged while maintaining performance is not high enough.  

Much of the problem is caused by the interaction between silicon anodes and the liquid electrolytes they have been paired with. The situation is complicated by large volume expansion of silicon particles during charge and discharge. This results in severe capacity losses over time. 

“As battery researchers, it's vital to address the root problems in the system. For silicon anodes, we know that one of the big issues is the liquid electrolyte interface instability," said UC San Diego nanoengineering professor Shirley Meng, the corresponding author on the Science paper, and director of the Institute for Materials Discovery and Design at UC San Diego. “We needed a totally different approach,” said Meng.

Indeed, the UC San Diego led team took a different approach: they eliminated the carbon and the binders that went with all-silicon anodes. In addition, the researchers used micro-silicon, which is less processed and less expensive than nano-silicon that is more often used.

An all solid-state solution

Prof. Y. Shirley Meng. nanoengineering professor at UC San Diego, the corresponding author on the Science paper, and director of the Institute for Materials Discovery and Design at UC San Diego.

In addition to removing all carbon and binders from the anode, the team also removed the liquid electrolyte. Instead, they used a sulfide-based solid electrolyte. Their experiments showed this solid electrolyte is extremely stable in batteries with all-silicon anodes. 

"This new work offers a promising solution to the silicon anode problem, though there is more work to do," said professor Meng, "I see this project as a validation of our approach to battery research here at UC San Diego. We pair the most rigorous theoretical and experimental work with creativity and outside-the-box thinking. We also know how to interact with industry partners while pursuing tough fundamental challenges." 

Past efforts to commercialize silicon alloy anodes mainly focus on silicon-graphite composites, or on combining nano-structured particles with polymeric binders. But they still struggle with poor stability.

By swapping out the liquid electrolyte for a solid electrolyte, and at the same time removing the carbon and binders from the silicon anode, the researchers avoided a series of related challenges that arise when anodes become soaked in the organic liquid electrolyte as the battery functions. 

At the same time, by eliminating the carbon in the anode, the team significantly reduced the interfacial contact (and unwanted side reactions) with the solid electrolyte, avoiding continuous capacity loss that typically occurs with liquid-based electrolytes.

This two-part move allowed the researchers to fully reap the benefits of low cost, high energy and environmentally benign properties of silicon.

Impact & Spin-off Commercialization

Darren H. S. Tan. CEO and Co-founder of UNIGRID L.L.C, and lead author on the silicon all solid-state battery research work published in Science.

“The solid-state silicon approach overcomes many limitations in conventional batteries. It presents exciting opportunities for us to meet market demands for higher volumetric energy, lowered costs, and safer batteries especially for grid energy storage,” said Darren H. S. Tan, the first author on the Science paper. 

Sulfide-based solid electrolytes were often believed to be highly unstable. However, this was based on traditional thermodynamic interpretations used in liquid electrolyte systems, which did not account for the excellent kinetic stability of solid electrolytes. The team saw an opportunity to utilize this counterintuitive property to create a highly stable anode.

Tan is the CEO and cofounder of a startup, UNIGRID Battery, that has licensed the technology for these silicon all solid-state batteries.

In parallel, related fundamental work will continue at UC San Diego, including additional research collaboration with LG Energy Solution. 

“LG Energy Solution is delighted that the latest research on battery technology with UC San Diego made it onto the journal of Science, a meaningful acknowledgement,” said Myung-hwan Kim, President and Chief Procurement Officer at LG Energy Solution. “With the latest finding, LG Energy Solution is much closer to realizing all-solid-state battery techniques, which would greatly diversify our battery product lineup.” 

“As a leading battery manufacturer, LGES will continue its effort to foster state-of-the-art techniques in leading research of next-generation battery cells,” added Kim. LG Energy Solution said it plans to further expand its solid-state battery research collaboration with UC San Diego.

The study had been supported by LG Energy Solution’s open innovation, a program that actively supports battery-related research. LGES has been working with researchers around the world to foster related techniques. 

Paper title

“Carbon Free High Loading Silicon Anodes Enabled by Sulfide Solid Electrolytes,” in the Sept. 24, 2021 issue of Science.

Authors
Darren H. S. Tan, Yu-Ting Chen, Hedi Yang, Wurigumula Bao, Bhagath Sreenarayanan, Jean-Marie Doux, Weikang Li, Bingyu Lu, So-Yeon Ham, Baharak Sayahpour, Jonathan Scharf, Erik A. Wu, Grayson Deysher, Zheng Chen and Ying Shirley Meng from the Department of NanoEngineering, Program of Chemical Engineering, and Sustainable Power & Energy Center (SPEC) University of California San Diego Jacobs School of Engineering; Hyea Eun Han, Hoe Jin Hah, Hyeri Jeong, Jeong Beom Lee, from LG Energy Solution, Ltd.

Funding
This study was financially supported by the LG Energy Solution company through the Battery Innovation Contest (BIC) program. Z.C. acknowledges funding from the start-up fund support from the Jacob School of Engineering at University of California San Diego. Y.S.M. acknowledges funding support from Zable Endowed Chair Fund.


 

 

 

Decoding birds' brain signals into syllables of song

September 23, 2021 -- Researchers can predict what syllables a bird will sing—and when it will sing them—by reading electrical signals in its brain, reports a new study from the University of California San Diego.

Having the ability to predict a bird’s vocal behavior from its brain activity is an early step toward building vocal prostheses for humans who have lost the ability to speak.

“Our work sets the stage for this larger goal,” said Daril Brown, an electrical and computer engineering Ph.D. student at the UC San Diego Jacobs School of Engineering and the first author of the study, which was published Sept. 23 in PLoS Computational Biology. “We’re studying birdsong in a way that will help us get one step closer to engineering a brain machine interface for vocalization and communication.”

The study explores how brain activity in songbirds such as the zebra finch can be used to forecast the bird’s vocal behavior. Songbird vocalizations are of particular interest to researchers because of their similarities to human speech; they are both complex and learned behaviors.

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Vocal recording of a male zebra finch (top) and the corresponding neural activity (bottom). Images courtesy of PLoS Computational Biology

In this work, the researchers implanted silicon electrodes in the brains of male adult zebra finches and recorded the birds’ neural activity while they sang. The researchers studied a specific set of electrical signals called local field potentials. These signals were recorded in the part of the brain that is necessary for the learning and production of song.

What’s special about local field potentials is that they are being used to predict vocal behavior in humans. These signals have so far been heavily studied in human brains, but not in songbird brains.

UC San Diego researchers wanted to fill this gap and see if these same signals in zebra finches could similarly be used to predict vocal behavior. The project is a cross-collaborative effort between engineers and neuroscientists at UC San Diego led by Vikash Gilja, a professor of electrical and computer engineering professor, and Timothy Gentner, a professor of psychology and neurobiology.

“Our motivation for exploring local field potentials was that most of the complementary human work for speech prostheses development has focused on these types of signals,” said Gilja. “In this paper, we show that there are many similarities in this type of signaling between the zebra finch and humans, as well as other primates. With these signals we can start to decode the brain’s intent to generate speech.”

“In the longer term, we want to use the detailed knowledge we are gaining from the songbird brain to develop a communication prosthesis that can improve the quality of life for humans suffering a variety of illnesses and disorders,” said Gentner.

The researchers found that different features of the local field potentials translate into specific syllables of the bird’s song, as well as when the syllables will occur during song.

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Illustration of the experimental workflow. As a male zebra finch sings his song—which consists of the sequence, "1, 2, 3,"— he thinks about the next syllable he will sing ("4"). The bird’s neural activity is recorded and the local field potentials are extracted. The researchers then analyze features of these signals to predict what syllable the is thinking of singing next.

“Using this system, we’re able to predict with high fidelity the onset of a songbird’s vocal behavior—what sequence the bird is going to sing, and when it is going to sing it,” said Brown.

The researchers can even predict variations in the song sequence, down to the syllable. For example, say the bird’s song is built on a repeating set of syllables, “1, 2, 3, 4,” and every now and then the sequence can change to something like “1, 2, 3, 4, 5,” or “1, 2, 3.” Features in the local field potentials reveal these changes, the researchers found.

“These forms of variation are important for us to test hypothetical speech prostheses, because a human doesn’t just repeat one sentence over and over again,” said Gilja. “It’s exciting that we found parallels in the brain signals that are being recorded and documented in human physiology studies to our study in songbirds.”

Paper: “Local Field Potentials in a Pre-motor Region Predict Learned Vocal Sequences.” Co-authors include Jairo I. Chavez, Derek H. Nguyen, Adam Kadwory, Bradley Voytek and Ezequiel M. Arneodo, UC San Diego.

This work was supported by the National Institutes of Health (R01DC008358, R01DC018055, R01GM134363), the National Science Foundation (BCS-1736028), the Kavli Institute for the Brain and Mind (IRG #2016-004), the Office of Naval Research (MURI N00014-13-1-0205), and the University of California—Historically Black Colleges and Universities Initiative.

Graduate students honored as Siebel Scholars

September 23, 2021-- Five graduate students working at the interface of engineering and medicine have been honored as 2022 Siebel Scholars. They are pursuing graduate degrees in bioengineering, electrical engineering, nanoengineering, and bioinformatics, all with a focus on advancing human health. 

Their research could lead to a human speech prosthesis; understanding the impact of genetic diversity in the immune system on tumor growth; a cell membrane coating technology to better deliver drugs; understanding the pathophysiology of pelvic floor muscle dysfunction after vaginal delivery; and improved early screening for coronary artery disease.

"Wow. This year's Siebel Scholars are all working on exciting projects that truly reflect the Jacobs School's efforts to leverage engineering and computer science to advance medicine and improve human health. The Jacobs School is focused on relevant research projects that lead to positive impacts on the daily lives of people," said Albert P. Pisano, Dean of the UC San Diego Jacobs School of Engineering. “These five outstanding Siebel Scholars have demonstrated not only their academic prowess, but their commitment to sharing their skills and time in service of the next generation of researchers. I am honored to congratulate them.”

The Siebel Scholars program recognizes the most talented students in the world’s leading graduate schools of business, computer science, bioengineering and energy science. The students are selected based on outstanding academic performance and leadership, and each receive a $35,000 award toward their final year of study.

The five UC San Diego 2022 Siebel Scholars are:

 

Daril Brown

Daril Brown is an electrical and computer engineering Ph.D. student under the dual advisement of electrical engineering professor Vikash Gilja and psychology professor Timothy Gentner. His research seeks to establish songbirds as a novel animal model for the development of a human speech prosthesis. Awarded an NSF Graduate Research Fellowship and a UC-HBCU Fellowship, Brown has a unique background having earned his bachelor’s in mechanical engineering from Howard University, and a master’s in bioengineering at UC San Diego. His extensive mentorship efforts across campus, including with the STARS and Academic Connections programs, earned him induction into the Bouchet Honors Society. Many of his mentees have gone on to Ph.D. programs across the country. A three-time UC San Diego Grad Slam finalist, Brown is a strong advocate for science literacy and accessibility, and was recently featured on the KPBS Rad Scientist podcast. Brown plans to forge a career intersecting industry and academia developing translational neurotechnology.

 

 

Andrea Castro

Andrea Castro is a bioinformatics PhD candidate in Hannah Carter’s lab at the UC San Diego School of Medicine. She received her bachelor’s degree in microbiology, immunology, and molecular genetics from UCLA in 2017, and her master’s in computer science from UC San Diego in 2021. Her research involves investigating the relationship between patient genetic diversity in the immune system and tumor evolution; leveraging large-scale genomic, transcriptomic, and proteomic datasets to learn more about immune surveillance and selection on tumors. She is passionate about developing comprehensive bioinformatic methods to improve application of exciting immunotherapy treatments to patients of all tumor types. Castro enjoys mentoring and hopes to help lift up the next generation of diverse scientists.

 

 

Pamela Duran

Pamela Duran received her bachelor’s degree in bioengineering from Universidad Autónoma de Baja California (Tijuana, Mexico), graduating with Honors Distinction. She is currently a bioengineering Ph.D candidate at UC San Diego, co-advised by bioengineering professor Karen Christman and Dr. Marianna Alperin, associate professor of obstetrics, gynecology, and reproductive sciences. Her research focuses on understanding the pathophysiology of pelvic floor muscle dysfunction after vaginal delivery—the leading risk factor for pelvic floor disorders. Her thesis also includes the application of an acellular biomaterial to prevent and treat pathological alterations after birth injury. During her Ph.D, Duran has received a T32 pre-doctoral training in Translational Musculoskeletal Research and an NIH F31 diversity pre-doctoral fellowship. Besides research, she has mentored undergraduate and master’s students and summer students in the STARS program, as well as the ENLACE program, which connects students from the U.S. and Mexico through shared research experiences. Her goal is to pursue a career in academia to develop engineering solutions to advance women’s health and to increase diversity in the STEM field, especially the Hispanic community.

 

Lauren Severance

Lauren Severance is a Ph.D. candidate in the UC San Diego department of bioengineering; she received her bachelor’s in biomedical engineering at Vanderbilt University. Advised by bioengineering professor Elliot McVeigh, she aims to improve early screening for coronary artery disease. Severance’s thesis work is focused on developing novel methods for early coronary artery calcium detection on CT. She has created numerous collaborations with clinicians, geneticists, and epidemiologists, resulting in discovery of a completely novel use for consumer genetic tests in coronary disease screening.She has received an NIH F31 fellowship and recognition from the Society of Cardiovascular Computed Tomography, and her publications have garnered editorial acclaim from leading preventive cardiologists. In addition to research, Severance is passionate about scientific communication and community engagement. She has led several educational outreach projects and serves as a UC San Diego Center for Ethics in Science and Technology student representative.

 

Jiarong Zhou

Jiarong Zhou is a nanoengineering PhD candidate under the guidance of nanoengineering professor Liangfang Zhang. His research focuses on employing cell membrane coating technology to design multivalent nanovaccines against cancer, bacteria, and parasites. Zhou’s work has resulted in numerous peer-reviewed articles and conference presentations. During his time in graduate school, he received a T32 Fellowship from NIH, a scholarship from the ARCS Foundation, and the prestigious Ford Fellowship from the National Academies of Science, Engineering, and Medicine. As a Gordon Scholar, Zhou had an impressive leadership record as an undergraduate, and in his doctoral studies he served as the president of the Jacobs Graduate Student Council and VP Internal of healthcare startup incubator Blue LINC. In the lab, Zhou has mentored several junior graduate and undergraduate students outside of research; his passion and dedication for outreach is evident through his participation in mentorship programs such as JUMP, GradAMP, and Grad Pals.

 

IROS 2021 preview: robotic mapping and manipulation

Sept. 22, 2021-- Researchers at the UC San Diego Contextual Robotics Institute will present three papers at the IROS 2021 conference, which takes place Sept. 27 to Oct. 1, 2021, both online and in person in Prague. 

The papers focus on mapping and exploration for mobile robots and dexterous robotic manipulation. 

Active Exploration and Mapping via Iterative Covariance Regulation over Continuous SE(3) Trajectories

Shumon Koga, Arash Asgharivaskasi, Nikolay Atanasov

This paper develops \emph{iterative Covariance Regulation} (iCR), a novel method for active exploration and mapping for a mobile robot equipped with on-board sensors. The problem is posed as optimal control over the SE(3) pose kinematics of the robot to minimize the differential entropy of the map conditioned the potential sensor observations. Researchers introduce a differentiable field of view formulation, and derive iCR via the gradient descent method to iteratively update an open-loop control sequence in continuous space so that the covariance of the map estimate is minimized. The team demonstrates autonomous exploration and uncertainty reduction in simulated occupancy grid environments.

 https://shumon0423.github.io/IROS2021_webpage/

CORSAIR: Convolutional Object Retrieval and Symmetry-AIded Registration

Tianyu Zhao, Qiaojun Feng, Sai Jadhav, Nikolay Atanasov

This paper considers online object-level mapping using partial point-cloud observations obtained online in an unknown environment. Researchers develop an approach for fully Convolutional Object Retrieval and Symmetry-AIded Registration (CORSAIR). The model extends the Fully Convolutional Geometric Features model to learn a global object-shape embedding in addition to local point-wise features from the point-cloud observations. The global feature is used to retrieve a similar object from a category database, and the local features are used for robust pose registration between the observed and the retrieved object. The formulation also leverages symmetries, present in the object shapes, to obtain promising local-feature pairs from different symmetry classes for matching. Researchers present results from synthetic and real-world datasets with different object categories to verify the robustness of our method.

 https://acsweb.ucsd.edu/~qif007/CORSAIR/

State-Only Imitation Learning for Dexterous Manipulation

Ilija Radosavovic1, Xiaolong Wang2, Lerrel Pinto3, Jitendra Malik1

Modern model-free reinforcement learning methods have recently demonstrated impressive results on a number of problems. However, complex domains like dexterous manipulation remain a challenge due to the high sample complexity. To address this, current approaches employ expert demonstrations in the form of state-action pairs, which are difficult to obtain for real-world settings such as learning from videos. In this paper, researchers move toward a more realistic setting and explore state-only imitation learning. To tackle this setting, the team trained an inverse dynamics model and used it to predict actions for state-only demonstrations. The inverse dynamics model and the policy are trained jointly. The method performs on par with state-action approaches and considerably outperforms RL alone. By not relying on expert actions, researchers are able to learn from demonstrations with different dynamics, morphologies, and objects.

https://people.eecs.berkeley.edu/~ilija/soil/


 

Computer scientists honored for their work discovering that cars are vulnerable to hacking

Stefan Savage, a professor in the UC San Diego Department of Computer Science and Engineering, is part of a team receiving the Golden Goose Award from AAAS. 

September 22, 2021-- Many people think of cars as a series of mechanical parts that — hopefully — work together to   take us places, but that's not the whole story. 

Inside most modern cars is a network of computers, called "electronic control units," that control all the systems and communicate with each other to keep everything rolling smoothly along. 

More than 10 years ago, a team from the  University of California San Diego and University of Washington investigated whether these computing systems could be hacked and how that would affect a driver's ability to control their car. To their own surprise — and to the alarm of car manufacturers — the researchers were able to manipulate the car in many ways, including disabling the brakes and stopping the engine, from a distance. This work led to two scientific papers that opened up a new area of cybersecurity research and served as a wake-up call for the automotive industry. 

Now the team has received the Golden Goose Award from the American Association for the Advancement of Science. The Golden Goose Award recipients demonstrate how scientific advances resulting from foundational research can help respond to national and global challenges, often in unforeseen ways. The award, established in 2012, honors scientific studies or research that may have seemed obscure, sounded “funny,” or for which the results were totally unforeseen at the outset, but which ultimately led, often serendipitously, to major breakthroughs that have had significant societal impact.

"When General Motors started advertising its OnStar service, Yoshi and I had a conversation, saying, 'I bet there's something there,'" Savage said. "Moreover, vulnerabilities in traditional computers had fairly limited impacts. You might lose some data or get a password stolen. But nothing like the visceral effect of a car’s brakes suddenly failing. I think that bridging that gap between the physical world and the virtual one was something that made this exciting for us."The car cybersecurity project was led by Stefan Savage and Tadayoshi Kohno, two professors of computer science at UC San Diego and the University of Washington, respectively. Kohno is a UC San Diego Ph.D. alumnus, receiving his Ph.D. in Computer Science and Engineering in 2006. 

Tadayoshi Kohno, a professor at the University of Washington, co-led the research. 

"More than 10 years ago, we saw that devices in our world were becoming incredibly computerized, and we wanted to understand what the risks might be if they continued to evolve without thought toward security and privacy,” Kohno said. “This award shines light on the importance of being thoughtful and strategic in figuring out what problems to work on today."Savage and Kohno are both computer security researchers who often chatted about potential upcoming threats that could be good to study.

The team’s papers prompted manufacturers to rethink car safety concerns and create new standard procedures for security practices. GM ended up appointing a vice president of product security to lead a new division. The Society for Automotive Engineers (SAE), the standards body for the automotive industry, quickly issued the first automotive cybersecurity standards.  Other car companies followed along, as did the federal government. In 2012, the Defense Advanced Research Projects Agency launched a new government project geared toward creating hacking-resistant, cyber–physical systems. 

"I like to think about what would have happened if we hadn't done this work," Kohno said. "It is hard to measure, but I do feel that neighboring industries saw this work happening in the automotive space and then they acted to avoid it happening to them too. The question that I have now is, as security researchers, what should we be investigating today, such that we have the same impact in the next 10 years?" 

Steve Chekoway (with black mask) and Karl Kosher were the two Ph.D. students on the project, at UC San Diego and UW respectively. 

Discovering vulnerabilities

Savage and Kohno formed a super-team of researchers from both universities. The team purchased a pair of Chevy Impalas — one for each university — to study as a representative car. Researchers worked collaboratively and in parallel, letting curiosity guide them.

The first task was to learn the language the cars' computerized components used to communicate with each other. Then the researchers worked to inject their own voices into the conversation. 

For example, the team started sending random messages to the cars' brake controllers to try to influence them.

"We figured out ways to put the brake controller into this test mode," said Karl Koscher, a research scientist at UW, who also earned his PhD in Seattle. "And in the test mode, we found we could either leak the brake system pressure to prevent the brakes from working or keep the system fully pressurized so that it slams on the brakes."

The team published two papers in 2010 and 2011 describing the results. 

"The first paper asked what capabilities an attacker would have if they were able to compromise one of the components in the car. We connected to the cars' internal networks to examine what we could do once they were hacked," said Stephen Checkoway, an assistant professor of computer science at Oberlin College who completed this research as a UC San Diego doctoral student. "The second paper explored how someone could hack the car from afar."

In these papers, the researchers chose not to unveil that they had used Chevy Impalas, and opted to contact GM privately.

"In our conversations with GM, they were quite puzzled. They said, 'There's no way to make the brake controller turn off the brakes. That's not a thing,'" Savage said. "That Karl could remotely take over our car and make it do something the manufacturer didn't think was possible reflects one of the key issues at play here. The manufacturer was hamstrung because they knew how the system was supposed to work. But we didn't have that liability. We only knew what the car actually did." 

Daniel Anderson, Alexei Czeskis, Brian Kantor, Damon McCoy, Shwetak Patel, Franziska Roesner and Hovav Shacham filled out the rest of the team. This research was funded by the National Science Foundation, the Air Force Office of Scientific Research, a Marilyn Fries endowed regental fellowship and an Alfred P. Sloan research fellowship.

 

 

 

Other award recipients

This year’s two other Golden Goose awards went to Katalin Karikó and Drew Weissman for their role in making mRNA into a medical therapy; and to V. Craig Jordan, who is known for pioneering the scientific principles behind a class of drugs called selective estrogen receptor modulators, or SERMs.

UC San Diego researchers who received the Golden Goose award in the past include Larry Smarr, former director of the California Institute for Telecommunications and Technology and a professor in the Department of Computer Science and Engineering; and Nobel laureate Roger Tsien, a professor of pharmacology, chemistry and biochemistry, who passed away in 2016. 

 

 

 



 

Mosaic ImmunoEngineering Expands Its Modular Vaccine Platform (MVP) Through New Technology Licensing Agreement with the University of California San D

New upgrades to old wireless tech could enable real-time 3D motion capture

September 20, 2021 -- A wireless technology that is helping people find their keys and wallets could one day be used for precise and real-time 3D motion capture, thanks to upgrades developed by electrical engineers at the University of California San Diego. 

The team’s new work improves on a wireless communication technology called ultra-wideband, or UWB. The technology has been around for years, but only recently has UWB started gaining popularity as it promises greater accuracy than Wi-Fi and Bluetooth for determining the location and movement of other devices. 

It also has the potential to open up even bigger possibilities, such as indoor navigation; smart warehouses that provide precise and real-time location of inventory and personnel; and 3D motion capture that can be done wirelessly in real-time for applications such as VR and sports analytics. 

But to get there, several limitations of current UWB technology must be overcome, said Dinesh Bharadia, a professor of electrical and computer engineering and faculty member of the Center for Wireless Communications at the UC San Diego Jacobs School of Engineering. UWB systems need to work much faster than they do now, operate at extremely low power, and provide high accuracy in 3D localization, he explained.

Bharadia’s Wireless Communication Sensing and Networking group recently developed a prototype UWB system that meets these criteria. It communicates data with a latency of just one millisecond; it uses so little power that it can run continuously for more than two years on a small coin cell battery; and it can pinpoint 3D location to within three centimeters for stationary objects, and eight centimeters for moving objects. 

The researchers will present their UWB system, dubbed ULoc, at the UbiComp 2021 conference which will take place virtually from Sept. 21 to 26. 

The new system fundamentally changes the process that UWB systems use to locate an object. UWB systems typically consist of two main components: a small tracking device called a tag, which can be attached to an object, and a set of devices called anchors that are installed at various spots in the environment to detect radio signals from the tag. 

The way UWB tracking currently works is that the tag sends out signals to all the anchors, and the anchors in turn send these signals back to the tag. The system measures the times that it takes for these signals to return to the tag. It then uses this information to calculate the distances between the tag and each anchor, and the tag’s location can then be triangulated.

The problem with this process, explained Bharadia, is that it involves a lot of signal exchanges. One tag needs to send a separate signal to every anchor, and every anchor, in turn, sends a signal back to the tag. “This makes the system slow. It’s not scalable, and it does not provide 3D localization,” said Bharadia.

Person holds a chip, standing in an open room surrounded by four electronic circuit boards.
The new UWB system consists of a small electronic tag (inset shows the size of a tag compared to a U.S. penny) that transmits one signal simultaneously to four anchors.

To simplify this process, the researchers updated the software for the tag so that it only needs to send one signal total to all the anchors. This also drastically reduces the tag’s power use; it can run continuously for more than two years on a small coin cell battery, while current UWB tags can only last for a few months on this type of battery. They also built new anchors that can work with just that one signal and get a good read of the tag’s 3D location. The team developed special antenna arrays and new algorithms that enable the anchors to accurately estimate the 3D angle and direction from which the tag’s signal is arriving. The anchors are able to measure this 3D angle from multiple vantage points so they can locate the tag with precision.

In tests, the new UWB system accurately tracked the 3D location of the tag within a millisecond of latency while one of the researchers was holding it and moving it around an open office space. The researchers point out that the system performed well despite it being in a “noisy” environment—computer screens, glass windows, and metal sheets interfere with UWB signals and create noise.

The team is now working on building an end-to-end motion capture system for applications ranging from VR gaming to sports analytics and autonomous robots for healthcare. The researchers say they are looking to collaborate with industrial partners to further develop and commercialize the technology.

Paper: “ULoc: Low-Power, Scalable and cm-Accurate UWB-Tag Localization and Tracking for Indoor Applications.” Co-authors include Minghui Zhao, Tyler Chang, Aditya Arun, Roshan Ayyalasomayajula, and Chi Zhang, UC San Diego.

Grow and eat your own vaccines?

Grant enables study of plants as mRNA factories

Three Jacobs School undergraduate programs ranked in nation's top 10

Sept. 14, 2021-- Three undergraduate academic programs at the Jacobs School of Engineering were ranked in the top 10 programs for undergraduates in rankings released Sept. 13, 2021 by U.S. News and World Report. 

The biocomputing, bioinformatics and biotechnology program, a multidisciplinary undergraduate offering supported by three UC San Diego divisions, including the Jacobs School of Engineering, was ranked first in the nation. 

The mobile and web applications undergraduate program housed in the Department of Computer Science and Engineering, was ranked number 7. The bioengineering and biomedical undergraduate program was number 8 (the graduate program is ranked third in the nation, according to rankings released in spring 2021).

"These top-ten rankings for our undergraduate programs reflect a much larger trend at the UC San Diego Jacobs School of Engineering. Top-tier research from all six departments at the Jacobs School is continually vitalizing and revitalizing our undergraduate curricula," said Albert P. Pisano, dean of the UC San Diego Jacobs School of Engineering. "This is part of the magic of the Jacobs School."

UC San Diego as a whole ranks as the 8th best public university for undergraduates in the United States. The school also ranks 13th among best colleges for veterans, moving up two spots from last year. Overall, UC San Diego was ranked 34th in the complete list of over 300 private and public undergraduate universities in the nation, jumping one spot from the previous year.

In the undergraduate U.S. News national ranking, the Jacobs School was ranked as the 11th best public engineering school and 19th best overall. The school is also ranked 9th best engineering school in the nation in U.S. News graduate rankings released earlier this year. 

The bioinformatics undergraduate program climbed from second to first place this year. The program is designed to provide career opportunities for bachelor’s graduates. Students graduating from this program are in great demand at top graduate schools, medical schools, and industry. The major is offered in the departments of bioengineering, biology, chemistry and biochemistry, and computer science. The program offers a wide range of opportunities for undergraduate research in many laboratories on campus. 

Ranked 8th in the nation, the undergraduate bioengineering and biomedical program prepares students for a variety of careers in the biomedical device industry and for further education in graduate school. The program addresses the bioengineering topics of biomechanics, biotransport, bioinstrumentation, bioelectricity, biosystems, and biomaterials, and the complementary fields of systems and organ physiology. Education in these areas allows application of bioengineering and scientific principles to benefit human health by advancing methods for effective diagnosis and treatment of disease through development of medical devices and technologies. 

"We in the Department of Bioengineering have a tradition of pushing boundaries in terms of research and educational innovation. Now we have four degree programs (Bioengineering, Biotechnology, Biosystems, Bioinformatics) at the top of our rankings,” said bioengineering department chair Kun Zhang. “We owe our success to the continuous efforts by our faculty, staff and students since 1966, and the strong support by the campus leadership."

In addition to the university’s excellent academic reputation, U.S. News lauded UC San Diego as the No. 26 college in the nation for social mobility for undergraduates. The university has a strong track record of promoting upward social mobility and has committed to remaining accessible to students of all backgrounds. For fall 2021, more than one-third of first-year students and over half of transfer students admitted to UC San Diego will be the first in their family to attend a university. 

Now in its 37th year, the latest edition of the Best Colleges list assesses U.S. bachelor's degree-granting institutions based on 17 measures of academic quality. Ranking factors include graduation and retention rates, faculty resources, social mobility and undergraduate academic reputation, among other measures.

In addition to this latest ranking from U.S. News, UC San Diego is consistently recognized as a leader within various national and global university ranking lists. According to the 2021-2022 U.S. News & World Report survey, UC San Diego Health ranked first in San Diego, placing it among the nation’s best hospitals. Earlier this month, UC San Diego was also named the nation’s third best public university as part of Forbes’ 2021 ranking of top colleges. Additionally, the university ranked eighth among U.S. public universities in the 2021-22 edition of the “Global 2000 List by the Center for World University Rankings.”

To read the complete U.S. News & World Report 2022 Best Colleges rankings, visit the publication’s website. For a complete listing of UC San Diego rankings and accolades, visit the Campus Profile.

 

How a plant virus could protect and save your lungs from metastatic cancer

ALT TEXT
Nanoparticles engineered from the cowpea mosaic virus have shown efficacy in treating and greatly reducing the spread of metastatic cancers in the lungs of mice.

September 14, 2021 -- Using a virus that grows in black-eyed pea plants, nanoengineers at the University of California San Diego developed a new treatment that could keep metastatic cancers at bay from the lungs. The treatment not only slowed tumor growth in the lungs of mice with either metastatic breast cancer or melanoma, it also prevented or drastically minimized the spread of these cancers to the lungs of healthy mice that were challenged with the disease.

The research was published Sept. 14 in the journal Advanced Science.

Cancer spread to the lungs is one of the most common forms of metastasis in various cancers. Once there, it is extremely deadly and difficult to treat.

Researchers at the UC San Diego Jacobs School of Engineering developed an experimental treatment that combats this spread. It involves a bodily injection of a plant virus called the cowpea mosaic virus. The virus is harmless to animals and humans, but it still registers as a foreign invader, thus triggering an immune response that could make the body more effective at fighting cancer.

The idea is to use the plant virus to help the body’s immune system recognize and destroy cancer cells in the lungs. The virus itself is not infectious in our bodies, but it has all these danger signals that alarm immune cells to go into attack mode and search for a pathogen, said Nicole Steinmetz, professor of nanoengineering at UC San Diego and director of the university’s Center for Nano-ImmunoEngineering.

To draw this immune response to lung tumors, Steinmetz’s lab engineered nanoparticles made from the cowpea mosaic virus to target a protein in the lungs. The protein, called S100A9, is expressed and secreted by immune cells that help fight infection in the lungs. And there is another reason that motivated Steinmetz’s team to target this protein: overexpression of S100A9 has been observed to play a role in tumor growth and spread.

“For our immunotherapy to work in the setting of lung metastasis, we need to target our nanoparticles to the lung,” said Steinmetz. “Therefore, we created these plant virus nanoparticles to home in on the lungs by making use of S100A9 as the target protein. Within the lung, the nanoparticles recruit immune cells so that the tumors don’t take.”

“Because these nanoparticles tend to localize in the lungs, they can change the tumor microenvironment there to become more adept at fighting off cancer—not just established tumors, but future tumors as well,” said Eric Chung, a bioengineering Ph.D. student in Steinmetz’s lab who is one of the co-first authors on the paper.

To make the nanoparticles, the researchers grew black-eyed pea plants in the lab, infected them with cowpea mosaic virus, and harvested the virus in the form of ball-shaped nanoparticles. They then attached S100A9-targeting molecules to the surfaces of the particles.

The researchers performed both prevention and treatment studies. In the prevention studies, they first injected the plant virus nanoparticles into the bloodstreams of healthy mice, and then later injected either triple negative breast cancer or melanoma cells in these mice. Treated mice showed a dramatic reduction in the cancers spreading to their lungs compared to untreated mice.

In the treatment studies, the researchers administered the nanoparticles to mice with metastatic tumor in their lungs. These mice exhibited smaller lung tumors and survived longer than untreated mice.

What’s remarkable about these results, the researchers point out, is that they show efficacy against extremely aggressive cancer cell lines. “So any change in survival or lung metastasis is pretty striking,” said Chung. “And the fact that we get the level of prevention that we do is really, really amazing.”

Steinmetz envisions that such a treatment could be especially helpful to patients after they have had a cancerous tumor removed. “It wouldn’t be meant as an injection that’s given to everyone to prevent lung tumors. Rather, it would be given to patients who are at high risk of their tumors growing back as a metastatic disease, which often manifests in the lung. This would offer their lungs protection against cancer metastasis,” she said.

Before the new treatment can reach that stage, the researchers need to do more detailed immunotoxicity and pharmacology studies. Future studies will also explore combining this with other treatments such as chemotherapy, checkpoint drugs or radiation.

Paper: “S100A9-Targeted Cowpea Mosaic Virus as a Prophylactic and Therapeutic Immunotherapy Against Metastatic Breast Cancer and Melanoma.” In addition to Young Hun (Eric) Chung, co-first authors of the study include Jooneon Park and Hui Cai. Nicole Steinmetz serves as the corresponding author of this work.

This work was supported in part by the National Institutes of Health (R01 CA224605, R01 HL137674 and U01-CA218292).

Disclosure: Nicole Steinmetz is a co-founder of and has a financial interest in Mosaic ImmunoEngineering Inc. The other authors declare no conflict of interest.

A new dataset for better augmented and mixed reality

Developed by UC San Diego computer scientists, OpenRooms and associated tools scale up ability to simulate indoor 3D scenes with strong photorealism.

OpenRooms creates photorealistic synthetic scenes from input images or scans, with unprecedented control over shape, materials and lighting.

September 10, 2021-- Computer scientists at the University of California San Diego have released OpenRooms, an new, open source dataset with tools that will help users manipulate objects, materials, lighting and other properties in indoor 3D scenes to advance augmented reality and robotics.

“This was a huge effort, involving 11 Ph.D. and master’s students from my group and collaborators across UC San Diego and Adobe,” said Manmohan Chandraker, a professor in the UC San Diego Department of Computer Science and Engineering. “It is an important development, with great potential to impact both academia and industry in computer vision, graphics, robotics and machine learning.” 

The OpenRooms dataset and related updates are publicly available at this website, with technical details described in an associated paper presented at CVPR 2021 in May.

Applications

OpenRooms lets users realistically adjust scenes to their liking. If a family wants to visualize a kitchen remodel, they can change the countertop materials, lighting or pretty much anything in the room. 

“With OpenRooms, we can compute all the knowledge about the 3D shapes, material and lighting in the scene on a per pixel basis,” said Chandraker. “People can take a photograph of a room and insert and manipulate virtual objects. They could look at a leather chair, then change the material to a fabric chair and see which one looks better.”

OpenRooms can even show how that chair might look in the daytime under natural light from a window or under a lamp at night. It can also help solve robotics problems, such as the best route to take over floors with varying friction profiles. These capabilities are finding a lot of interest in the simulation community because, previously, the data was proprietary or not available with comparable photorealism.

“These tools are now available in a truly democratic fashion,” said Chandraker, “providing accessible assets for photorealistic augmented reality and robotics applications.”

Making Augmented Reality More Real

Chandraker’s team uses computational methods to make sense of the visual world. They are particularly focused on how shapes, materials and lighting interact to form images.

“We essentially want to understand how the world is created, and how we can act upon it,” he said. “We can insert objects into existing scenes or advance self-driving, but to do these things, we need to understand various aspects of a scene and how they interact with each other.”

This deep understanding is essential to achieve photorealism in mixed reality. Inserting an object into a scene requires reasoning about shading from various light sources, shadows cast by other objects or inter-reflections from the surrounding scene. The framework must also handle similar long-range interactions among distant parts of the scene to change materials or lighting in complex indoor scenes. 

Hollywood solves these problems with measurement-based platforms, such as shooting actor Andy Serkis inside a gantry and converting those images into Gollum in the Lord of the Rings Trilogy. The lab wants to achieve similar effects without expensive systems.

Open source toolbox

To get there, the group needed to find creative ways to represent shapes, materials and lighting. But acquiring this information can be time-consuming, data hungry and expensive, especially when dealing with complex indoor scenes featuring furniture and walls that have different shapes and materials and are illuminated by several light sources, such as windows, ceiling lights or lamps.  

“One would have to measure the lighting and material properties at every point in the room,” said Chandraker. “It’s doable but it simply does not scale.”

OpenRooms uses synthetic data to render these images, which provides an accurate and inexpensive way to provide ground truth geometry, materials and lighting. The data can be used to train powerful deep neural networks that estimate those properties in real images, allowing photorealistic object insertion and material editing. 

These possibilities were demonstrated in a CVPR 2020 oral presentation by Zhengqin Li, a fifth-year Ph.D. student advised by Chandraker, and first author on the OpenRooms paper. The software provides automated tools that allow users to take real images and convert them into photorealistic, synthetic counterparts.

“We are creating a framework where users can use their cell phones or 3D scanners for developing datasets that enable their own augmented reality applications,” said Chandraker. “They can simply use scans or sets of photographs.”

Chandraker and team were motivated, in part, by the need to create a public domain platform. Large tech companies have tremendous resources to create training data and other IP, making it difficult for small players to get a foothold.

This was recently illustrated when a Lithuanian company, called Planner 5D, sued Facebook and Princeton, claiming they unlawfully utilized its proprietary data.

“You can imagine such data is really useful for many applications,” said Chandraker. “But progress in this space has been limited to a few big players who have the capacity to do these kinds of complex measurements or work with expensive assets created by artists.”



 

UC San Diego leads a $12.25 million grant to improve epilepsy treatment

September 9, 2021 -- The National Institutes of Health has awarded a $12.25 million grant to the University of California San Diego to develop and enhance brain-sensing and brain-stimulating platform technologies to enable treatment of drug-resistant epilepsy. 

The project is led by UC San Diego electrical engineering professor Shadi Dayeh who leads the Integrated Electronics and Biointerfaces Laboratory and brings together expertise from all across UC San Diego, including the Jacobs School of Engineering and Health Sciences. The nation-wide team includes researchers and longtime collaborators of Dayeh at Massachusetts General Hospital led by Dr. Sydney Cash and Oregon Health & Sciences University led by Dr. Ahmed Raslan.

Epilepsy, a group of neurological disorders characterized by repeated seizures, affects more than 3.4 million people in the U.S. according to the Centers for Disease Control and Prevention (CDC); and nearly one-third of these individuals suffer from poor seizure control even after all current medical therapies are pursued. In these situations, clinicians try to identify the abnormal brain tissue that generates the seizures. Surgeons then target this area for surgical removal, or for implantation of an electrical pulse generator that modifies seizure generation. Current technologies to identify the specific regions in the brain that trigger epileptic seizures – called epileptic foci – are imprecise. Improved mapping of these targets will allow better surgical planning – and more generally – will enhance our understanding of brain physiology.  

Dayeh's work in brain-computer interfaces began when he realized his lab's materials science, device, and integration techniques could allow for sensor grids that offer the tantalizing possibility of providing surgeons with a much clearer picture of the spots in the brain likely initiating the seizures. One of the improvements is an 100-fold increase in the density of sensors embedded within the grids. The new NIH grant will allow the team to expand technical refinement of these higher-density grids and their testing in pigs to the point where they are ready for full-scale clinical trials in people.

"UC San Diego leads the world in neurotechnology development for less invasive brain interfaces," said UC San Diego Chancellor Pradeep K. Khosla. "This new grant affirms the UC San Diego interdisciplinary research approach in which engineers, surgeons, and clinicians and researchers of all stripes engage in sustained research collaborations."

"This grant is a significant win for the campus and the region that will have long-lasting positive impacts," said David Brenner, MD, Vice Chancellor of UC San Diego Health Sciences. "The deep collaborations between neurosurgeons and engineers at UC San Diego will shape the future of medicine for the better."

"The team is making incredible progress on these large, flexible grids of sensors with high sensor density. This combination of attributes has the potential to launch a new era of neurotechnologies for improved patient outcomes. These advances are only possible when engineers intensively collaborate with clinicians, shoulder to shoulder, in order to understand how the technologies are being used in the clinic and how they can be improved," said Albert P. Pisano, Dean of the UC San Diego Jacobs School of Engineering.

Higher resolution recording and stimulation for better diagnosis and treatment

The sensor grids the team plans to test will collect information that is 100 times higher resolution than what is collected in the grids already approved for longer-term use in humans. Both classes of sensor grids function using the same basic principle, though there are important differences. The sensors are embedded in a thin flat material that is placed directly on the surface of the brain in order to record brain activity. Each sensor in the grid records the brain waves being produced by the area of the brain near each sensor.

Illustration of the less invasive wireless sensor grid being developed at UC San Diego
 


Compared to the grids that have already been approved for longer-term use, the new UC San Diego sensor grids have many more sensors per unit of surface area, and the substrate material is more flexible and better conforms to the brain surface, which helps with signal quality. The advances in both the sensor density and the flexibility are thanks to fundamental materials science advances made in Dayeh's lab in the Department of Electrical and Computer Engineering at the UC San Diego Jacobs School of Engineering.

"Materials science and advanced technology integrations are leading to big advances in less invasive sensor technologies which rest on the surface of the brain cortex," said Dayeh. "There is so much potential for materials science to advance clinical medicine, but it needs to be done extremely carefully and the work must engage clinicians and patients as soon as possible. That's what we've been doing, and this grant will allow us to continue this important work."  

The higher density of sensors in the UC San Diego grids means the information about where specific brain activation patterns are originating is more precise. This precision is useful for identifying the spots in the brain that are triggering the seizures. The researchers also believe that the higher resolution information could uncover a much deeper understanding about the origins of epilepsy.

In addition, some of the sensors are also able to gently stimulate the surface of the brain. The new UC San Diego grids can target specific areas for electrical stimulation with greater precision, which allows smaller amounts of electrical stimulation to be used and for that electrical stimulation to be applied with greater precision.

“While we currently have advanced options for patients with epilepsy who do not respond to medication, we are always seeking better options that can improve care,” says Sharona Ben-Haim, MD, neurosurgeon at UC San Diego Health who is a co-investigator on this project. “A more powerful brain sensor may enable neurosurgeons to better identify brain tissue that is causing seizures, and remove this region with greater precision, which may translate to reduced side effects and faster recovery times for patients.”  

The team will also be testing related probes that are inserted down into the cortex, rather than resting on the surface. In some cases, information available from these kinds of "depth probes" is necessary to identify the areas triggering seizures.
 

UC San Diego electrical engineering professor Shadi Dayeh will lead the project. 

With the NIH funding, the team will do the work necessary to show that the UC San Diego sensors are capable of functioning as well, if not better than, approved versions of the sensors. In addition, the team hopes to show that the higher density of sensors and stimulators allows the team to collect new kinds of information – "emerging biomarkers" – that could help identify better ways to diagnose and treat drug-resistant epilepsy.

“This grant demonstrates the power of UC San Diego’s robust neuroscience and engineering ecosystems. Improved temporo-spatial resolution will help usher in a new era for the treatment of neurological disease and provide new insights into the music of the brain,” says co-investigator Alexander Khalessi, MD, MBA, chair of the Department of Neurological Surgery at UC San Diego Health and professor of neurological surgery, radiology and neuroscience at UC San Diego School of Medicine. “In addition to better serving our epilepsy patients, we have the opportunity to leverage materials science and computational power to decode this final frontier of nervous system function.”

A one-month window

The grant is designed to fund the efforts necessary to advance the safety and efficacy testing of the UC San Diego grids to the point where the next step is full-scale clinical trials in which the sensor grids are implanted for up to 30 days.

These grids have already been used to safely record signals from the surfaces of human brains, for short periods of time, during surgeries in which a portion of the skull was already going to be temporarily removed.

The one-month window is important because people with drug-resistant epilepsy typically need to be monitored with implanted brain sensors for at least two weeks in order to collect the best data for determining what regions in the brain are triggering the seizures.

"We've been fortunate to collaborate with neurosurgeons at UC San Diego, Massachusetts General Hospital, and Oregon Health & Sciences University in order to demonstrate that our high-density grids are safe and effective in humans for short periods of time," said Dayeh. "This NIH BRAIN Initiative grant will allow us to keep advancing this work to the point that we are ready for clinical trials where the sensor grids are implanted for much longer periods of time in people. I’m thrilled that we'll have the opportunity to do this work as a community here at UC San Diego, and with our external partners."

A broader view of brain activity at high resolution

In addition, the UC San Diego grids can be printed in formats that are significantly larger than the grids being developed elsewhere, similar in area coverage to those currently used in the clinic, but with a much higher sensor density. The team is planning to print and test grids that are about six centimeters by six centimeters offering 4,096 sensor channels plus 256 electrical-stimulation channels. This is compared to only 36 sensor channels and 36 electrical-stimulation channels in commercial grade grids – with a similar surface area – that are now being used in the clinic.

With this combination of higher resolution, broader coverage, and longer-use times the researchers hope that future generations of these sensor grids will eventually be useful in applications well beyond drug-resistant epilepsy. The high-resolution information coming from larger regions of the surface of the brain, for example, could be incorporated into future generations of brain-computer interfaces designed to help people with severe paralysis communicate and control prostheses.

Interrelated projects funded by the grant to build an advanced Epilepsy Monitoring System

The grant also includes funding for engineers at the UC San Diego Jacobs School of Engineering to lead multiple efforts needed to make the device wireless and make it clinically viable. This includes the wireless transfer of data and the energy necessary to power the implanted components of the device, and the software display of the high channel count recording.  

The grant also includes funding for sustained conversation and dialog that includes researchers from multiple fields, patients, patient advocates, and bioethicists.

In parallel, UC San Diego is planning to build up capacity for good manufacturing practice (GMP) medical device manufacturing on campus. The larger goal is to be able to manufacture sensor grids on campus that are cleared for use in clinical trials.

These efforts position UC San Diego as a national and global leader in neurotechnology for less invasive brain interface technologies.

The project, officially entitled "Thin, High-Density, High-Performance, Depth and Surface Microelectrodes for Diagnosis and Treatment of Epilepsy" is supported through the National Institutes of Health’s Brain Research Through Advancing Innovative Neurotechnologies (BRAIN) Initiative under award number UG3NS123723.

Funding is contingent on milestones and is made through the NIH's Brain Research Through Advancing Innovative Neurotechnologies (BRAIN) Initiative, part of a large effort among federal and non-federal partners to use knowledge about how the brain works to develop more effective therapies for neurological disorders.


Collaborators

UC San Diego
Eric Halgren, Departments of Radiology and Neurosciences
Gert Cauwenberghs, Department of Bioengineering
Gal Mishne, Department of Computer Science and Engineering
Peter Asbeck, Department of Electrical and Computer Engineering
Mark Stambaugh, Qualcomm Institute
Sharona Ben-Haim, Jerry Shih, David Barba, Alexander Khalessi, Department of Neurological Surgery
Xinlian Zhang, Family Med And Public Health
Michael Kalichman, Research Ethics Program

Massachusetts General Hospital
Sydney Cash, Angelique Paulk, Department of Neurology
Ziv Williams, Robert Richardson, Functional Neurosurgery

Oregon Health & Sciences University
Ahmed Raslan, Department of Neurological Surgery
Ilker Yaylali, David Spencer,  Department of Neurology

Previous Funding

Dayeh has developed early generation of the sensors with the support of a 2019 NIH Director’s New Innovator Award (1DP2EB029757-01), a 2017 NSF Scalable Nanomanufacturing Award (No. 1728497), and a 2014 NSF CAREER Award (No. 1351980). In addition, Dayeh and colleagues – including his longtime collaborator and mentor Eric Halgren – have received support from the KAVLI Institute for Brain and Mind, the Qualcomm Institute, and together with Dr. Ben-Haim, the three received support from UC San Diego's Altman Clinical and Translational Research Institute (ACTRI) and Institute of Engineering in Medicine (IEM) for a GEM award, an AIM award from the OIC, and private donors.

According to Dayeh, the team's technology integration work is at the core of the BRAIN Initiative vision “to discover how dynamic patterns of neural activity are transformed into cognition, emotion, perception, and action in health and disease” (BRAIN 2025 Report)

UC San Diego researchers make glycomics data AI-ready

With systems biology approach, researchers enable big-data glycomics that will open new paths from glycomics data sets to clinical breakthroughs and cancer diagnosis

September 8, 2021: Researchers at the University of California San Diego have created a tool that allows glycomics datasets to be analyzed using explainable Artificial Intelligence (AI) systems and other machine learning approaches. In a recent paper published in Nature Communications, the team demonstrated that glycomics data require extra care to be properly used for statistical analysis or machine learning. They also offer a new preprocessing solution to prepare glycomics data to substantially boost the power of its use with machine learning and AI. They named the approach GlyCompare. It takes a systems level perspective that accounts for shared biosynthetic pathways of glycans within and across samples.

To introduce GlyCompare, the team demonstrated their ability to enhance comparisons of glycomics datasets by shining light on the hidden relationships between glycans in several contexts, including gastric cancer tissues. Cancer is a useful example given the importance of glycan changes to cancer and its utility for early-stage diagnosis.

"We applied GlyCompare to cancer tissues and showed that while one couldn't find cancer specific glycans using standard statistical methods, novel biomarkers emerge when processed using our method," said UC San Diego professor of Bioengineering and Pediatrics Nathan Lewis, who is the corresponding author on the paper. Lewis Co-Directs the CHO Systems Biology Center, and glycoengineered CHO cell lines were used to produce diverse proteins used in the study.

In another analysis, the team showed the method substantially boosts statistical power, such that one needs half as many samples to get equivalent power to detect biomarkers. In the paper, the researchers outline how the methods behind GlyCompare will be transformative for bringing glycomics to the clinic. In fact, Lewis is part of the founding team of a new start-up that is licensing related intellectual property to commercialize this technology for high value applications, including cancer diagnostics.

One of the keys to the GlyCompare approach is that it looks at the biological steps needed to synthesize the subunits that make up glycans, rather than just looking at only the whole glycans themselves, greatly improving the accuracy of statistical analyses of glycomics data. The researchers believe this approach will enable the detection of more subtle changes in glycosylation in many applications, including early stage cancer. Moreover, GlyCompare could lead to new insights on the mechanisms behind the observed changes in glycans that are present.  

Bokan Bao and Benjamin P. Kellman, the co-first-authors on the paper, are both in the Bioinformatics and Systems Biology Graduate Program, and members of the Department of Bioengineering at the UC San Diego Jacobs School of Engineering.

Paper title
Correcting for sparsity and interdependence in glycomics by accounting for glycan biosynthesis

Funding
This work was conducted with support from the Novo Nordisk Foundation provided to the Technical University of Denmark (NNF10CC1016517, NNF20SA0066621: N.E.L.), NIGMS (R35 GM119850: N.E.L.), NICHD (R21 HD080682: L.B.), and USDA (USDA/ARS 6250-6001; M.W.H.).

GlyCompare on GitHub

Author Affiliations

Department of Pediatrics, UC San Diego Health
Bokan Bao, Benjamin P. Kellman, Austin W. T. Chiang, Yujie Zhang, James T. Sorrentino, Austin K. York, Lars Bode & Nathan E. Lewis

Bioinformatics and Systems Biology Graduate Program, UC San Diego
Bokan Bao, Benjamin P. Kellman & James T. Sorrentino

Department of Bioengineering, UC San Diego Jacobs School of Engineering Bokan Bao, Benjamin P. Kellman, James T. Sorrentino & Nathan E. Lewis

The Novo Nordisk Foundation Center for Biosustainability at UC San Diego
Austin W. T. Chiang & Nathan E. Lewis

Department of Pediatrics, Children’s Nutrition Research Center, US Department of Agriculture/Agricultural Research Service, Baylor College of Medicine, Houston, TX, USA
Mahmoud A. Mohammad & Morey W. Haymond

 



 

These fridge-free COVID-19 vaccines are grown in plants and bacteria

Two hands wearing blue gloves touch one plant in a tray of small plants.

September 7, 2021 -- Nanoengineers at the University of California San Diego have developed COVID-19 vaccine candidates that can take the heat. Their key ingredients? Viruses from plants or bacteria.

The new fridge-free COVID-19 vaccines are still in the early stage of development. In mice, the vaccine candidates triggered high production of neutralizing antibodies against SARS-CoV-2, the virus that causes COVID-19. If they prove to be safe and effective in people, the vaccines could be a big game changer for global distribution efforts, including those in rural areas or resource-poor communities.

“What’s exciting about our vaccine technology is that is thermally stable, so it could easily reach places where setting up ultra-low temperature freezers, or having trucks drive around with these freezers, is not going to be possible,” said Nicole Steinmetz, a professor of nanoengineering and the director of the Center for Nano-ImmunoEngineering at the UC San Diego Jacobs School of Engineering.

The vaccines are detailed in a paper published Sept. 7 in the Journal of the American Chemical Society.

The researchers created two COVID-19 vaccine candidates. One is made from a plant virus, called cowpea mosaic virus. The other is made from a bacterial virus, or bacteriophage, called Q beta.

Both vaccines were made using similar recipes. The researchers used cowpea plants and E. coli bacteria to grow millions of copies of the plant virus and bacteriophage, respectively, in the form of ball-shaped nanoparticles. The researchers harvested these nanoparticles and then attached a small piece of the SARS-CoV-2 spike protein to the surface. The finished products look like an infectious virus so the immune system can recognize them, but they are not infectious in animals and humans. The small piece of the spike protein attached to the surface is what stimulates the body to generate an immune response against the coronavirus.

The researchers note several advantages of using plant viruses and bacteriophages to make their vaccines. For one, they can be easy and inexpensive to produce at large scales. “Growing plants is relatively easy and involves infrastructure that’s not too sophisticated,” said Steinmetz. “And fermentation using bacteria is already an established process in the biopharmaceutical industry.”

Another big advantage is that the plant virus and bacteriophage nanoparticles are extremely stable at high temperatures. As a result, the vaccines can be stored and shipped without needing to be kept cold. They also can be put through fabrication processes that use heat. The team is using such processes to package their vaccines into polymer implants and microneedle patches. These processes involve mixing the vaccine candidates with polymers and melting them together in an oven at temperatures close to 100 degrees Celsius. Being able to directly mix the plant virus and bacteriophage nanoparticles with the polymers from the start makes it easy and straightforward to create vaccine implants and patches. 

The goal is to give people more options for getting a COVID-19 vaccine and making it more accessible. The implants, which are injected underneath the skin and slowly release vaccine over the course of a month, would only need to be administered once. And the microneedle patches, which can be worn on the arm without pain or discomfort, would allow people to self-administer the vaccine.

“Imagine if vaccine patches could be sent to the mailboxes of our most vulnerable people, rather than having them leave their homes and risk exposure,” said Jon Pokorski, a professor of nanoengineering at the UC San Diego Jacobs School of Engineering, whose team developed the technology to make the implants and microneedle patches.

“If clinics could offer a one-dose implant to those who would have a really hard time making it out for their second shot, that would offer protection for more of the population and we could have a better chance at stemming transmission,” added Pokorski, who is also a founding faculty member of the university’s Institute for Materials Discovery and Design.

In tests, the team’s COVID-19 vaccine candidates were administered to mice either via implants, microneedle patches, or as a series of two shots. All three methods produced high levels of neutralizing antibodies in the blood against SARS-CoV-2.

Potential pan-coronavirus vaccine

These same antibodies also neutralized against the SARS virus, the researchers found.

It all comes down to the piece of the coronavirus spike protein that is attached to the surface of the nanoparticles. One of these pieces that Steinmetz’s team chose, called an epitope, is almost identical between SARS-CoV-2 and the original SARS virus.

“The fact that neutralization is so profound with an epitope that’s so well conserved among another deadly coronavirus is remarkable,” said co-author Matthew Shin, a nanoengineering Ph.D. student in Steinmetz’s lab. “This gives us hope for a potential pan-coronavirus vaccine that could offer protection against future pandemics.”

Another advantage of this particular epitope is that it is not affected by any of the SARS-CoV-2 mutations that have so far been reported. That’s because this epitope comes from a region of the spike protein that does not directly bind to cells. This is different from the epitopes in the currently administered COVID-19 vaccines, which come from the spike protein’s binding region. This is a region where a lot of the mutations have occurred. And some of these mutations have made the virus more contagious.

Epitopes from a nonbinding region are less likely to undergo these mutations, explained Oscar Ortega-Rivera, a postdoctoral researcher in Steinmetz’s lab and the study’s first author. “Based on our sequence analyses, the epitope that we chose is highly conserved amongst the SARS-CoV-2 variants.”

This means that the new COVID-19 vaccines could potentially be effective against the variants of concern, said Ortega-Rivera, and tests are currently underway to see what effect they have against the Delta variant, for example.

Plug and play vaccine

Another thing that gets Steinmetz really excited about this vaccine technology is the versatility it offers to make new vaccines. “Even if this technology does not make an impact for COVID-19, it can be quickly adapted for the next threat, the next virus X,” said Steinmetz.

Making these vaccines, she says, is “plug and play:” grow plant virus or bacteriophage nanoparticles from plants or bacteria, respectively, then attach a piece of the target virus, pathogen, or biomarker to the surface.

“We use the same nanoparticles, the same polymers, the same equipment, and the same chemistry to put everything together. The only variable really is the antigen that we stick to the surface,” said Steinmetz.

The resulting vaccines do not need to be kept cold. They can be packaged into implants or microneedle patches. Or, they can be directly administered in the traditional way via shots.

Steinmetz and Pokorski’s labs have used this recipe in previous studies to make vaccine candidates for diseases like HPV and cholesterol. And now they’ve shown that it works for making COVID-19 vaccine candidates as well.

Next steps

The vaccines still have a long way to go before they make it into clinical trials. Moving forward, the team will test if the vaccines protect against infection from COVID-19, as well as its variants and other deadly coronaviruses, in vivo.

Paper: “Trivalent subunit vaccine candidates for COVID-19 and their delivery devices.” Co-authors include Angela Chen, Veronique Beiss, Miguel A. Moreno-Gonzalez, Miguel A. Lopez-Ramirez, Maria Reynoso and Joseph Wang, UC San Diego; Hong Wang and Brett L. Hurst, Utah State University.

This work was funded in part by a National Science Foundation both through a RAPID grant (CMMI-2027668) and through the UC San Diego Materials Research Science and Engineering Center (MRSEC, grant DMR-2011924).

Disclosure: Nicole Steinmetz and Jon Pokorski are co-founders of and have a financial interest in Mosaic ImmunoEngineering Inc. All other authors declare no competing interests.

UC San Diego nanoengineers receive $2.7M NSF grant to make battery manufacturing waste-free

September 1, 2021 -- A team led by nanoengineers at the University of California San Diego has been awarded a $2.7 million grant from the National Science Foundation to develop an eco-friendly and low-cost manufacturing process for sodium all-solid-state batteries. The process will be used to create large-scale energy storage systems—for buildings, electric grids, and wind and solar farms—that are more efficient, affordable and safe.

“In order for our society to shift to more renewable energy sources, we need technology that will enable rechargeable batteries with high safety, low cost, long life and high resilience to environmental changes,” said Zheng Chen, a professor of nanoengineering at the UC San Diego Jacobs School of Engineering and the project’s lead investigator.

“Today’s lithium-ion batteries can no longer meet these requirements because of the safety issues associated with flammable liquid electrolytes and scaling challenges for critical materials—cobalt, nickel and lithium—that are typically used for making them. So we are working to improve the production of a promising alternative: sodium all-solid-state batteries.”

The goal of the project is to help transform sodium all-solid-state battery manufacturing into an efficient and eco-friendly process. These batteries are of great interest to scientists because they are made using low-cost transition metals such as chromium, manganese and iron. This overcomes the critical materials limitation facing lithium-ion batteries. In addition, the all-solid-state architecture is intrinsically safer and can employ multi-layer stacking to achieve higher system-level energy densities. These features make the batteries desirable for emerging large-scale storage applications.

To improve today’s sodium all-solid-state battery manufacturing processes, Chen and colleagues will develop a dry fabrication technology that eliminates the use of caustic organic solvents. The technology will also recycle materials from used batteries to create new battery materials—specifically electrodes and solid-state electrolytes—that perform the same as the originals. The result will be a process that is closed-loop, high-precision and high-yield.

“This project assembles expertise in chemical engineering, nanoengineering, chemistry, materials science, life-cycle analysis/technoeconomic analysis, machine learning and data science, as well as collaborators in community colleges and industry to develop new fabrication processes, advanced materials and new battery protypes that can potentially be used for a wide range of large-scale storage systems,” said Chen, who is also a faculty member of the Sustainable Power and Energy Center at the UC San Diego Jacobs School of Engineering.

The research team includes UC San Diego nanoengineering professors Ying Shirley Meng, Andrea Tao and Shyue Ping Ong, who are all faculty members of the university’s Sustainable Power and Energy Center and Institute for Materials Discovery and Design, and Elsa Olivetti, a professor of materials science and engineering at MIT.

Computer science students qualify for programming World Finals

August 31, 2021--A team of UC San Diego computer science students has qualified to compete in the World Finals of the International Collegiate Programming Contest (ICPC), the world’s preeminent programming and coding competition. The students clinched a spot when they placed sixth in the ICPC North American Championship in August 2021.

Computer science PhD student Zihan Wang, master’s student Shuxin Chen, and undergraduate Haihao Sun will represent UC San Diego at the World Final, tentatively scheduled for March 2022. 

During an ICPC competition, teams of three students are given a set of 10 to 13 algorithmic programming problems. They have five hours, and one computer, to solve as many problems as they can in the shortest amount of time. 

(l-r) Computer science students Zihan Wang, Shuxin Chen and Haihao Sun will represent UC San Diego at the ICPC World Finals in March 2022.

“It really has some strategy to it,” said Wang. “We have to divide the problems amongst ourselves and find the most useful problem for each person to work on. And we need to help each other debug; some people may be even better at debugging than at other types of problems. And there’s just one computer so we also need to divide the time, since some people may need to brute force code, and others may need to use their time to debug their code, so we need to plan it out.”

Though the North American Championships were held remotely, removing some element of that strategy since all three team members had access to a computer, the students say the competitions are both exciting and nerve-racking. 

“This competition is rewarding and very exciting,” said Wang. “In our mind this kind of competitive programming is really like a sports competition. We’re very excited, our main goal is to get the highest rank we can.”

The students train together every week, allotting three to five hours to work through a sample problem set similar to what they might encounter in a competition. At UC San Diego, there is an ICPC club, where as many as 20 students will participate weekly in these practice sessions. The club holds selection contests to help students form teams, and decide which teams will get to compete at various challenges. 

While some members of the ICPC club are competitive programmers, like Wang, Chen and Sun, many others use the practice problems as a way to strengthen their programming skills for internship or job interviews. During club meetings, there are always problems at a variety of skill levels, to support both groups of participants. 

“The skills I’ve picked up in the competition have helped me learn programming and development skills very quickly,” said Sun. “As a participant in ICPC, I think I’ve learned to write code and debug more quickly than other people.”

Wang said having this student club as a resource is hugely beneficial; many schools don’t have an ICPC club, and students are left to find their own teammates, register for competitions and train on their own. Having an organized structure to facilitate these connections not only gives the students more time to actually train, but also helps foster a tighter community. 

“The community at UC San Diego really is a great community which cultivates a lot of great engineers, great problem solvers,” said Sun.

Jingbo Shang, a professor in the Department of Computer Science and Engineering and the Halicioglu Data Science Institute, joined the leadership of the campus ICPC club in 2020. Since then, he’s also begun offering a for-credit computer science course-- Introduction to Programming Contests-- to help support students wanting to improve these skills. 

“ICPC has long been regarded as a competition of the world’s smartest collegiate computer programmers,” said Shang. “The World Finals sets the stage for the world’s smartest trophy."

Studies highlight benefit of spatial visualization app in bridging critical STEM education gap

A student uses the Spatial Vis app on a tablet. Photos by David Baillot/UC San Diego.

August 30, 2021--Software developed by engineering professors at UC San Diego has improved spatial visualization—a critical skill in STEM careers—in students in high school and college courses, both in person and remotely. 

Two publications presented at the July 2021 American Society of Engineering Education Annual Conference highlighted the Spatial Vis app’s success in the remote learning environment necessitated by COVID-19, and among high school students. 

Spatial visualization, the ability to think in three dimensions, is critical in Science, Technology, Engineering, and Math (STEM) careers, from Computer-Aided-Design in engineering to using ultrasound for medical procedures. As this New York Times piece points out, this concept is often missing from K-16 curricula and as a result, the skill is underdeveloped in many students. To address this issue, two engineering faculty at the Jacobs School of Engineering at UC San Diego developed the Spatial Vis software to teach students how to sketch 2D projections and 3D shapes. The touchscreen app provides automatic grading and personalized feedback. The immediate feedback creates much higher student engagement than the traditional approach of sketching on paper and waiting days for a grade.

The app is produced by eGrove Education Inc., which was co-founded by Nathan Delson, a UC San Diego mechanical engineering teaching professor, and Lelli Van Den Einde, a fellow UC San Diego structural engineering teaching professor. 

At the ASEE conference, Van Den Einde and Delson presented findings that detail the success of the app in improving students’ spatial visualization skills. They measure this by having the students take a standardized spatial visualization test before using the Spatial Vis app, and then again after using the app. Students whose pre-test score is 70% or below are categorized as “at-risk” for low graduation rates in future STEM programs. 

In their study of two high school classes, results showed that students in this at-risk group improved their test score by 15.6% after using the Spatial Vis app. Even more significant is that 60% of all of the low-performing students moved out of the at-risk category on their post-test scores, making them more likely to persist in STEM careers. Not only did their skills improve, but so did their confidence; 42% of students reported their spatial visualization skills were “very good” or “good” before using the app, while 90% of the high school students said they felt their skills were “very good” or “good” after using the app. 

The second paper, on the Suitability of Spatial Visualization Training for Remote Learning,  compared in-person use of the Spatial Vis app before COVID-19 with the experience using it during remote learning due to the pandemic, in freshman engineering graphics courses at two universities. Among college students, there was a correlation between the measured student persistence and gains in spatial visualization ability. These gains occurred both before and during COVID, though the gains were slightly less significant during COVID.

In one course, using Spatial Vis improved student scores especially among students who were deemed at-risk based on their spatial visualization standardized test before taking the course.  In the first class, at-risk students’ test scores improved 18.9% in 2019 and 11.3% in 2020. Of those low performing students students, 48.8% in 2019 and 35.7% in 2020 moved out of the at-risk category, making them more likely to persist in STEM careers.The second class had at-risk score improvements of 22.3% in 2019 and 22.2% in 2020 with 78.4% (2019) and 69.2% (2020) of these initially low-performing students moving out of the at-risk category on their post-test scores.

While the cause of the slight decrease in score improvement during 2020 is unknown, the researchers speculate it could be attributed to overall lower engagement due to the challenging environment as courses transitioned to emergency remote instruction at the start of the pandemic. Still, the app led to marked improvements in students’ spatial visualization skills, and teachers noticed the benefits of the teaching tool, too. 

“During COVID, we had high school and middle school teachers reaching out to us to provide experiences that students could engage with remotely,” said Van Den Einde. “Now that classes are returning to in-person education the teachers are interested in continuing to use Spatial Vis since they saw how its use increased persistence and self-regulated learning among their students.”

A student and a teaching assistant use the Spatial Vis app in class.

Sketching has a long history in education, and is used for communication and creativity in many STEM fields. The physical act of freehand sketching has been shown to increase spatial visualization skills, and its benefits are supported by the NSF-funded Engage Engineering initiative. Improvement of these skills has significantly increased retention in STEM for women and other underrepresented minorities. These prior studies were based on sketching on paper, which can be laborious to grade and do not provide real time feedback to the student. Spatial Vis’ digital platform, with automatic grading and personalized feedback, aims to change that.

In 2019, this UC San Diego spinoff received a $750,000 Small Business Innovation Research (SBIR) Phase II grant from the National Science Foundation to develop the app. Van Den Einde and Delson co-founded eGrove Education, Inc. to commercialize the Spatial Vis software and make it available to educational institutions worldwide.


To learn more about Spatial Vis please visit www.egrove.education

Jacobs School welcomes 27 new faculty

      

The University of California San Diego Jacobs School of Engineering is proud to introduce the 27 new professors hired in 2020 and 2021. These professors are among the nearly 140 faculty who have joined the UC San Diego Jacobs School of Engineering in the last eight years.

These new faculty and the bold research they pursue will further the Jacobs School’s mission of leveraging engineering and computer science for the public good. 

“It’s my great honor to welcome these engineers, computer scientists, educators and researchers to the Jacobs School of Engineering community,” said Albert P. Pisano, Dean of the Jacobs School. “We are a young, powerful school because we have added cohort after cohort of energetic, imaginative, bold new faculty. I am very much looking forward to seeing the impact they will make.”

These faculty join a school on the rise; the, UC San Diego Jacobs School of Engineering jumped to the #9 spot in the influential U.S. News and World Report Rankings of Best Engineering Schools in March 2020, and twelve months later, despite the headwinds, held that position. 

2021 New Faculty PDF

Jacobs School new faculty

BIOENGINEERING

Brian Aguado, Assistant Professor

Aguado’s goal is to develop precision biomaterials that enable the evaluation of a patient's unique biology to diagnose and treat a variety of health disorders as a function of sex, age, and/or ancestry. Specifically, Aguado aims to develop sex-specific biomaterial technologies to treat cardiovascular diseases, including aortic valve disease and heart failure.

Previously: Postdoctoral Fellow, University of Colorado at Boulder

Ph.D.: Northwestern University

 

Andrew Bartko, Professor of Practice

Bartko’s goal is to inspire, nurture, and sustain vibrant collaborations between UC San Diego’s microbiome experts and industry partners in the life science, nutrition, energy, information technology, clinical and healthcare industries. Specifically, Bartko aims to focus on creating and commercializing innovative technologies to accelerate microbiome discoveries and healthcare breakthroughs across academic and industry collaborations.

Previously: Research Leader, Battelle 

Ph.D.: Georgia Institute of Technology

 

Bogdan Bintu, Assistant Professor

Bintu develops new microscopy tools that can simultaneously “see” thousands of DNA sequences, RNA molecules and proteins in individual cells. He uses these tools to understand how neurons specialize within the olfactory nervous system.

Previously: Ph.D. Candidate, Harvard University

Ph.D.: Harvard University


Benjamin Smarr, Assistant Professor

Smarr’s research focuses on time series analysis in biological systems, with an emphasis on practical information extraction for translational applications. His main project is TemPredict, which brings together wearable device data from 50K people with over 2 million daily symptom reports and is used to identify signs of COVID-19 onset, progression, and recovery.

Previously: Postdoctoral Fellow, UC Berkeley

Ph.D.: University of Washington

 

COMPUTER SCIENCE AND ENGINEERING

Mai ElSherief, Assistant Teaching Professor

ElSherief uses computational and data science problems that model online social interactions to infer and understand online misuse behaviors and psychological well-being. Her other research interests include social computing, natural language processing, machine learning, and communication.

Previously: Postdoctoral Fellow, Georgia Institute of Technology

Ph.D.: UC Santa Barbara 

 

Carlos Jensen, Associate Vice Chancellor, Educational Innovation

Jensen’s research lies at the intersection between usability and software engineering, with an emphasis on studying how Open Source communities operate and organize, and the tools and processes needed to make them more efficient. His recent work uses automated testing techniques to help developers improve the reliability of large and complex open source software.

Previously: Associate Dean, Oregon State University

Ph.D.: Georgia Institute of Technology

 

Tzu-Mao Li, Assistant Professor

Li connects classical computer graphics and image processing algorithms with modern data-driven methods to facilitate physical exploration. His work added 3D understanding to computer vision models; used data to improve camera imaging pipeline quality; and made light transport simulation faster by using information implicitly defined by rendering programs.

Previously: Postdoctoral Researcher, UC Berkeley and MIT

Ph.D.: Massachusetts Institute of Technology


Imani Munyaka, Assistant Professor

Munyaka is a human-centered computing researcher. Her research interests include public policy, information security, computer science education, educational technologies, voting technologies, cybersecurity and minorities in STEM. Her goal is to improve and alleviate the security and privacy concerns of those most vulnerable.

Previously: Ph.D. Candidate, University of Florida

Ph.D.: University of Florida

 

Kristen Vaccaro, Assistant Professor

Vaccaro focuses on how to design machine learning systems to give users a sense of agency and control. She found that some existing ways of providing control for social media can function as placebos, increasing user satisfaction even when they do not work. She will help develop systems to give users control and oversight, and ethical guidelines and policies.

Previously: Research assistant, University of Illinois at Urbana-Champaign

Ph.D.: University of Illinois at Urbana-Champaign

 

Rose Yu, Assistant Professor

The goal of Yu’s research is to advance machine learning and enable interpretable, efficient and robust large-scale spatiotemporal reasoning. Her work has been successfully applied to solve challenging domain problems in sustainability, health and physical sciences.

Previously: Assistant professor, Northeastern University

Ph.D.: University of Southern California

 

ELECTRICAL AND COMPUTER ENGINEERING

Nick Antipa, Assistant Professor

Antipa’s research aims to develop design frameworks that merge optical models with algorithms, allowing optimization of both components and enabling the development of cutting-edge imaging and display systems. By considering both the hardware and digital domains, new computational optical systems emerge that extend capability beyond what is available.

Previously: Ph.D. Candidate, UC Berkeley

Ph.D.: UC Berkeley

 

Mingu Kang, Assistant Professor

Kang researches vertically-integrated VLSI information processing for machine learning and signal processing algorithms. His research focuses on energy- and latency-efficient integrated circuits, architectures and systems by leveraging novel computing paradigms including in-memory, in-sensor and neuromorphic computing with both CMOS and emerging devices.

Previously: Research Scientist, IBM Research

Ph.D: University of Illinois at Urbana-Champaign

 

Florian Meyer, Assistant Professor

Meyer researches statistical signal processing for navigation, mapping and multiobject tracking in applications including maritime situational awareness, autonomous driving, and indoor localization. He investigates efficient and scalable high-dimensional nonlinear estimation using graphical models where the number of states to be estimated may also be unknown.

Previously: Postdoctoral Fellow and Associate, MIT

Ph.D.: Vienna University of Technology

 

Karcher Morris, Assistant Teaching Professor

Morris’s teaching aims to embed project-based learning throughout the undergraduate electrical and computer engineering curriculum, complementing theoretical foundations. By connecting students with application-oriented coursework and industry-relevant challenges, Morris promotes an early engagement between students and their research/industry goals.

Previously: Ph.D. Candidate, UC San Diego

Ph.D.: UC San Diego

 

Yuanyuan Shi, Assistant Professor

Shi's research interests are in the area of energy systems and cyber-physical systems, spanning from machine learning to optimization and control. She works on data-driven control for complex networked systems and market mechanism design under multi-agent learning dynamics.

Previously: Postdoctoral Researcher, Caltech

Ph.D: University of Washington

 

Yatish Turakhia, Assistant Professor

Turakhia develops algorithms and hardware accelerators to enable faster and cheaper progress in biology and medicine. He also develops computational methods that enable biological discoveries, such as new genotype-phenotype relationships.

Previously: Postdoctoral Researcher, UC Santa Cruz

Ph.D.: Stanford University

 

Yang Zheng, Assistant Professor

Zheng develops methods and frameworks for the optimization and control of network systems and their applications to cyber-physical systems, especially autonomous vehicles and traffic systems. His goal is to develop computationally efficient and distributed solutions for large-scale network systems by exploring and exploiting real-world system structures.

Previously: Postdoctoral Researcher, Harvard

Ph.D.: University of Oxford

 

MECHANICAL AND AEROSPACE ENGINEERING

Sylvia Herbert, Assistant Professor

Herbert focuses on developing new techniques for safety and efficiency in autonomous systems. She has developed methods for scalable safety and real-time decision making that draw from control theory, cognitive science and reinforcement learning, which are backed by both rigorous theory and physical testing on robotic platforms.

Previously: Graduate Researcher, UC Berkeley

Ph.D.: UC Berkeley

 

Patricia Hidalgo-Gonzalez, Assistant Professor

Hidalgo-Gonzalez focuses on high penetration of renewable energy using optimization, control theory and ML. She co-developed a power system expansion model for Western North America’s grid under climate change uncertainty.  She is interested in power dynamics, energy policy, electricity market redesign, and learning for dynamical systems with safety guarantees.

Previously: Ph.D. Candidate, UC Berkeley

Ph.D: UC Berkeley

 

Stephanie Lindsey, Assistant Professor

Lindsey’s work lies at the interface of fluid mechanics, numerical analysis and cardiovascular developmental biology. She seeks to determine causal-effect relationships for the creation of cardiac malformations and address important challenges in clinical treatment of congenital heart defects through a combined computational-experimental approach.

Previously: Postdoctoral Researcher, Stanford University

Ph.D.: Cornell University

 

Marko Lubarda, Assistant Teaching Professor

Lubarda is dedicated to engineering pedagogy and enriching students' learning experiences through curriculum design, teaching innovations and support of undergraduate student research. He works in the areas of computational analysis, engineering mathematics, materials science, solid mechanics, device physics, and magnetic nanotechnologies.

Previously: Assistant Professor, University of Donja Gorica, Montenegro

Ph.D.: UC San Diego

 

Lonnie Petersen, Assistant Professor

Dr. Petersen is a physician scientist specializing in space and aviation physiology and development of countermeasure devices for use in space. During the COVID-19 pandemic, she co-lead a team that developed a low-cost, easy-to-use ventilator and other ways to support critically ill COVID19 patients and mitigate the spread of disease.

Previously: Postdoctoral Researcher, UC San Diego School of Medicine

Ph.D.: University of Copenhagen

 

Lisa Poulikakos, Assistant Professor

Poulikakos harnesses nanophotonics, the study and manipulation of light on the nanoscale, to bridge engineering and biomedicine. The resulting in-vivo and ex-vivo nanophotonic probes aim to elucidate the origin and propagation of a range of diseases, leading to low-cost medical diagnostics; rapid, on-chip biochemical drug testing; or in-situ biomedical imaging.

Previously: Postdoctoral Researcher, Stanford University

Ph.D.: ETH Zurich

 

Aaron Rosengren, Assistant Professor

Rosengren conducts fundamental and applied research in astrodynamics, space situational awareness and space traffic management to define perennial, ad-hoc practices and policies to make space a sustainable resource. His contributions are in the fields of celestial mechanics and nonlinear dynamics, with a strong focus on space debris and small Solar-System bodies.

Previously: Assistant Professor, University of Arizona

Ph.D.: University of Colorado, Boulder

 

Jon Wade, Professor of Practice

Wade’s objective is to ensure that the research conducted and the curriculum developed in systems engineering has the greatest impact on addressing the critical challenges that face our global society and nation. He leads research in the area of complex, evolving systems engineering methods, processes, tools, and education.

Previously: Research Professor, Stevens Institute of Technology

Ph.D: Massachusetts Institute of Technology

 

NANOENGINEERING

Zeinab Jahed, Assistant Professor

Jahed designs electronics that integrate intelligently with biological systems at the nanoscale. She designs non-invasive and high-throughput bio-electronic tools to record and manipulate biological activities and uses AI and ML techniques to interpret the large data sets from these nano-bio-electronic tools to answer important biological questions.

Previously: Postdoctoral Researcher, Stanford University

Ph.D.: UC Berkeley

 

STRUCTURAL ENGINEERING

Georgios Tsampras, Assistant Professor

Tsampras’ research goal is to improve the seismic response and simplify the lifetime management of structures and civil infrastructures. He conducts integrated experimental and analytical research on components, connections, and systems that enhance the safety and reliability of structures and civil infrastructures against earthquakes.

Previously: Falcon Vehicle Structures Engineer, SpaceX

Ph.D.: Lehigh University

 

ANTHROPOLOGY, PERFORMANCE, and TECHNOLOGY PROGRAM

Hortense Gerardo, Director

The Anthropology, Performance, and Technology (APT) program at the Jacobs School of Engineering aims to empower a new generation of socially-engaged, culturally relevant, and artistically as well as scientifically and technically creative engineers. Gerardo, a playwright with a PhD in anthropology and performance studies, directs the program.

 Previously: Associate Professor of Anthropology and Performing Arts, Lassell College

Ph.D.: Boston University

 

This technology could bring the fastest version of 5G to your home and workplace

UC San Diego engineers developed a system that enables millimeter wave signals to overcome blockages while providing high throughput

ALT TEXT
UC San Diego electrical and computer engineering Ph.D. student Ish Jain poses with the new millimeter wave setup that he developed. The setup improves the throughput and reliability of millimeter wave signals.

August 23, 2021 -- Consumers of today’s 5G cellphones may have experienced one of the following tradeoffs: impressive download speeds with extremely limited and spotty coverage, or widespread and reliable coverage with speeds that aren’t much faster than today’s 4G networks.

A new technology developed by electrical engineers at the University of California San Diego combines the best of both worlds and could enable 5G connectivity that is ultra-fast and reliable at the same time.

The team will present their work at the ACM SIGCOMM 2021 conference which will take place online Aug. 23 to 27.

The technology presents a solution to overcome a roadblock to making high band 5G practical for the everyday user: the speedy wireless signals, known as millimeter waves, cannot travel far and are easily blocked by walls, people, trees and other obstacles.

Today’s high band 5G systems communicate data by sending one laser-like millimeter wave beam between a base station and a receiver—for example, a user’s phone. The problem is if something or someone gets in the way of that beam’s path, then the connection gets blocked completely.

“Relying on a single beam creates a single point of failure,” said Dinesh Bharadia, a professor of electrical and computer engineering at the UC San Diego Jacobs School of Engineering, who is the senior author on the ACM SIGCOMM paper.

Two beams are better than one

Bharadia and his team, who are part of the UC San Diego Center for Wireless Communications, came up with a clever solution: split the one laser-like millimeter wave beam into multiple laser-like beams, and have each beam take a different path from the base station to the receiver. The idea is to improve the chances that at least one beam reaches the receiver when an obstacle is in the way.

ALT TEXT
Experimental setup of the multi-beam millimeter wave system.

The researchers created a system capable of doing this and tested it inside an office and outside a building on campus. The system provided a high throughput connection (up to 800 Mbps) with 100% reliability, which means that the signal didn’t drop or lose strength as the user moved around obstacles like desks, walls and outdoor sculptures. In outdoor tests, the system provided connectivity up to 80 meters (262 feet) away.

To create their system, the researchers developed a set of new algorithms. One algorithm first instructs the base station to split the beam into multiple paths. Some of these paths take a direct shot from the base station and the receiver; and some paths take an indirect route, where the beams bounce off what are called reflectors—surfaces in the environment that reflect millimeter waves like glass, metal, concrete or drywall—to get to the receiver. The algorithm then learns which are the best paths in the given environment. It then optimizes the angle, phase and power of each beam so that when they arrive at the receiver, they combine constructively to create a strong, high quality and high throughput signal.

With this approach, more beams result in a stronger signal.

“You would think that splitting the beam would reduce the throughput or quality of the signal,” Bharadia said. “But with the way that we’ve designed our algorithms, it turns out mathematically that our multi-beam system gives you a higher throughput while transmitting the same amount of power overall as a single-beam system.”

The other algorithm maintains the connection when a user moves around and when another user steps in the way. When these happen, the beams get misaligned. The algorithm overcomes this issue by continuously tracking the user’s movement and realigning all the beam parameters.

ALT TEXT
Hardware of the multi-beam millimeter wave system.

The researchers implemented their algorithms on cutting-edge hardware that they developed in the lab. “You don’t need any new hardware to do this,” said Ish Jain, an electrical and computer engineering Ph.D. student in Bharadia’s lab and the first author of the paper. “Our algorithms are all compliant with current 5G protocols.”

The hardware consists of a small base station and receiver. The base station is equipped with a phased array that was developed in the lab of UC San Diego electrical and computer engineering professor Gabriel Rebeiz, who is an expert in phased arrays for 5G and 6G communications and is also a member of the university’s Center for Wireless Communications.

The team is now working on scaling their system to accommodate multiple users.

More information can be found on the project’s website: https://wcsng.ucsd.edu/mmreliable/

Paper: “Two beams are better than one: Towards Reliable and High Throughput mmWave Links.” Co-authors include Raghav Subbaraman, UC San Diego.

This work is supported by the National Science Foundation (grant 1925767).

Researchers develop first steerable catheter for brain surgery

August 18, 2021-- A team of engineers and physicians has developed a steerable catheter that for the first time will give neurosurgeons the ability to steer the device in any direction they want while navigating the brain’s arteries and blood vessels. The device was inspired by nature, specifically insect legs and flagella--tail-like structures that allow microscopic organisms such as bacteria to swim.  

The team from the University of California San Diego describes the breakthrough in the Aug. 18 issue of Science Robotics

The steerable catheter was successfully tested in pigs at the Center for the Future of Surgery at UC San Diego. 

Approximately one in 50 people in the United States has an unruptured intracranial aneurysm--a thin-walled, blister-like lesion on a cerebral artery that is prone to rupture. These kinds of lesions affect over 160 million people worldwide, half of them under the age of 50. Of patients that suffer ruptured aneurysms, more than half die. Half of the survivors experience long-term disabilities. Studies show that a quarter of cases cannot be operated on because of how difficult the aneurysms are to reach. 

“As a neurosurgeon, one of the challenges that we have is directing catheters to the delicate, deep recesses of the brain,” said Dr. Alexander Khalessi, chair of the Department of Neurological Surgery at UC San Diego Health. “Today’s results demonstrate proof of concept for a soft, easily steerable catheter that would significantly improve our ability to treat brain aneurysms and many other neurological conditions, and I look forward to advancing this innovation toward patient care.”

A view of the steerable catheter, right, and how it navigates a brain blood vessel (insert on the left). 

The current state of the art in aneurysm surgery involves neurosurgeons inserting guidewires into an artery near the groin to take catheters through the aorta and all the way up into the brain. Surgeons use curved-tip guidewires to navigate the brain's arteries and junctions. But these guidewires have to be removed before the catheter’s tip can be used to provide treatment.

 “Once the guidewire is retrieved the catheter will return to its native shape, often straight, resulting in loss of access to the pathology,” said Dr. Jessica Wen, who was instrumental in serving as a bridge between clinicians and engineers, and coordinated work with the Center for the Future of Surgery at UC San Diego.

As a result, it is extremely difficult to place and keep it in the right position to release platinum coils that block blood flow to the aneurysm and prevent a brain bleed.  

Steerable catheters are not available for neurosurgery because of how small the brain's blood vessels are. Specifically, devices need to be less than one millimeter in diameter--that’s roughly the diameter of a few human hairs--and about five feet long (160 cm). Industrial fabrication methods struggle at this scale. That’s partially because gravity, electrostatics, and the van der Waals force are all similar at this size. So once you pick something up with tweezers, you cannot drop it. If you coax it from the tweezers, it may leap into the air from opposing forces and disappear, never to be found again. 

“Unfortunately, many of the most important blood vessels we need to treat are among the most tortuous and fragile in the body,” said James Friend, a professor at the UC San Diego Jacobs School of Engineering and School of Medicine and the paper’s corresponding author. “Although robotics is rising to the need in addressing many medical problems, deformable devices at the scales required for these kinds of surgeries simply do not exist.”

Bioinspiration

To solve this problem, researchers turned to inspiration both from nature and from soft robotics.

“We were inspired by flagella and insect legs, as well as beetles mating, where microscale hydraulics and large aspect deformation are involved,” said Gopesh Tilvawala, who recently earned a Ph.D. in Friend’s research group and the paper’s first author. “This led us to developing [a] hydraulically actuated soft robotic microcatheter.”

Computer simulations and new fabrication methods

A steerable catheter allows surgeons to deliver therapies, in this case platinum coils that block blood flow to an  aneurysm, in the deepest recess of the brain. 

The team had to invent a whole new way of casting silicone in three dimensions that would work at those scales, by depositing concentric layers of silicone on top of one another with different stiffnesses. The result is a silicone rubber catheter with four holes inside its walls, each about one half the diameter of a human hair. 

The team also conducted computer simulations to determine the configuration of the catheter; how many holes it should include; where these should be placed; and the amount of hydraulic pressure needed to actuate it. To guide the catheter, the surgeon compresses a handheld controller to pass saline fluid into the tip to steer it. Saline is used to protect the patient; if the device should fail, then saline harmlessly enters the bloodstream. The catheter’s steerable tip is visible on X-rays. 

A new way of doing neurosurgery

A fluoroscopic image of the steerable catheter navigating a brain artery in a pig and deploying coils. 

The work is poised to make a significant difference in the way aneurysm surgery is conducted, physicians said. “This technology is ideal for situations when I need to make a 180 degree turn from the catheter position in the parent artery, and maintaining position and reducing kick-out is critical,” said Dr. David Santiago-Dieppa, neurosurgeon at UC San Diego Health. “This advance may ultimately allow us to treat aneurysms, other brain pathologies and even strokes that we haven’t been able to in the past.”

“This type of precision can be realized with steerable tools and the successful deployment of these tools should move us forward in permitting improved access, decreased procedural time, better capacity utilization, decreased radiation exposure and other related and expected benefits,” said Dr. Alexander Norbash, chair of the Department of Radiology at UC San Diego Health. 

The next steps include a statistically significant number of animal trials and first in human trial. 

The work was funded by the American Heart Association, the American-Australian Association Sir Keith Murdoch Scholarship, UC San Diego’s Galvanizing Engineering in Medicine program, the Chancellor's Research Excellence Scholarship, and the National Institutes of Health. 

 

Ultrasound remotely triggers immune cells to attack tumors in mice without toxic side effects

August 12, 2021 -- Bioengineers at the University of California San Diego have developed a cancer immunotherapy that pairs ultrasound with cancer-killing immune cells to destroy malignant tumors while sparing normal tissue.

The new experimental therapy significantly slowed down the growth of solid cancerous tumors in mice.

The team, led by the labs of UC San Diego bioengineering professor Peter Yingxiao Wang and bioengineering professor emeritus Shu Chien, detailed their work in a paper published Aug. 12 in Nature Biomedical Engineering.

The work addresses a longstanding problem in the field of cancer immunotherapy: how to make chimeric antigen receptor (CAR) T-cell therapy safe and effective at treating solid tumors.  

CAR T-cell therapy is a promising new approach to treat cancer. It involves collecting a patient’s T cells and genetically engineering them to express special receptors, called CAR, on their surface that recognize specific antigens on cancer cells. The resulting CAR T cells are then infused back into the patient to find and attack cells that have the cancer antigens on their surface.

This therapy has worked well for the treatment of some blood cancers and lymphoma, but not against solid tumors. That’s because many of the target antigens on these tumors are also expressed on normal tissues and organs. This can cause toxic side effects that can kills cells—these effects are known as on-target, off-tumor toxicity.

“CAR T cells are so potent that they may also attack normal tissues that are expressing the target antigens at low levels,” said first author Yiqian (Shirley) Wu, a project scientist in Wang’s lab.

“The problem with standard CAR T cells is that they are always on—they are always expressing the CAR protein, so you cannot control their activation,” explained Wu.

To combat this issue, the team took standard CAR T cells and re-engineered them so that they only express the CAR protein when ultrasound energy is applied. This allowed the researchers to choose where and when the genes of CAR T cells get switched on.

“We use ultrasound to successfully control CAR T cells directly in vivo for cancer immunotherapy,” said Wang, who is a faculty member of the Institute of Engineering in Medicine and the Center for Nano-ImmunoEngineering, both at UC San Diego. What’s exciting about the use of ultrasound, noted Wang, is that it can penetrate tens of centimeters beneath the skin, so this type of therapy has the potential to non-invasively treat tumors that are buried deep inside the body.

The team’s approach involves injecting the re-engineered CAR T cells into tumors in mice and then placing a small ultrasound transducer on an area of the skin that’s on top of the tumor to activate the CAR T cells. The transducer uses what’s called focused ultrasound beams to focus or concentrate short pulses of ultrasound energy at the tumor. This causes the tumor to heat up moderately—in this case, to a temperature of 43 degrees Celsius (109 degrees Fahrenheit)—without affecting the surrounding tissue. The CAR T cells in this study are equipped with a gene that produces the CAR protein only when exposed to heat. As a result, the CAR T cells only switch on where ultrasound is applied.

The researchers put their CAR T cells to the test against standard CAR T cells. In mice that were treated with the new CAR T cells, only the tumors that were exposed to ultrasound were attacked, while other tissues in the body were left alone. But in mice that were treated with the standard CAR T cells, all tumors and tissue expressing the target antigen were attacked.

“This shows our CAR T-cell therapy is not only effective, but also safer,” said Wu. “It has minimal on-target, off-tumor side effects.”

The work is still in the early stages. The team will be performing more preclinical tests and toxicity studies before it can reach clinical trials.

###

Paper: “Control of the activity of CAR-T cells within tumours via focused ultrasound.” Co-authors include Yahan Liu, Ziliang Huang, Xin Wang, Jiayi Li, Linshan Zhu, Molly Allen, Yijia Pan, Robert Bussell, Aaron Jacobson, Thomas Liu and Shu Chien, UC San Diego; Zhen Jin, Shanghai Jiao Tong University, China; and Praopim Limsakul, Prince of Songkla University, Thailand.

This work was supported in part by the National Institutes of Health (grants HL121365, GM125379, GM126016, CA204704 and CA209629).

Disclosure: Peter Yingxiao Wang is scientific co-founder of and has financial interest in Cell E&G Inc. and in Acoustic Cell Therapy Inc., a company that aims to license the technology for further development. These financial interests do not affect the design, conduct or reporting of this research.

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New tool enables mapping of protein interaction networks at scale

Visualization of a protein-protein interaction network identified using PROPER-seq.

August 3, 2021-- Proteins—long chains of amino acids—each play a unique role in keeping our cells and bodies functioning, from carrying out chemical reactions, to delivering messages, and protecting us from potentially harmful foreign invaders. More recent research has shown that these proteins not only serve their individual purpose, but also interact with other proteins to carry out even more numerous and complex functions through these protein-protein interactions (PPI).

Collectively, all the protein-protein interactions in a cell form a PPI network. Experimentally identifying a PPI network within human cells has required a tremendous amount of time and resources, with experiments required to identify every individual PPI, and many additional experiments to investigate these protein pairs for network-level interactions.

Now, bioengineers at the University of California San Diego have developed a technology capable of revealing the PPIs among thousands of proteins, in a single experiment. The tool, called PROPER-seq (protein-protein interaction sequencing), allows researchers to map the PPI network from their cells of interest within several weeks, without any specialized resources such as antibodies or premade gene libraries.

The researchers describe this technology in Molecular Cell on August 3. They applied PROPER-seq on human embryonic kidney cells, T lymphocytes, and endothelial cells, and identified 210,518 PPIs involving 8,635 proteins.

"PROPER-seq is capable of scanning the order of 10,000×10,000 protein pairs in one experiment," said Kara Johnson, a recent UC San Diego bioengineering Ph.D. alumna and the first author of this paper. The research was conducted in bioengineering professor Sheng Zhong’s lab.

The central idea of PROPER-seq is to label every PPI with a unique DNA sequence, and then read these DNA sequence labels through next-generation sequencing. To implement this idea, Zhong's team developed a technique called SMART-display, which attaches a unique DNA barcode to every protein. They also devised a method called "Incubation, ligation and sequencing" (INLISE) to sequence the pair of DNA barcodes that are attached to two interacting proteins. The third component of PROPER-seq is a software package called PROPERseqTools, that incorporates statistical tools to identify the PPIs from the DNA sequencing data. This trio of tools—SMART-display, INLISE, and PROPERseqTools—together is known as PROPER-seq.

A further breakdown of these three components of PROPERseq is available in this blog post.

A laboratory would start the PROPER-seq protocol with their cells of interest, and obtain the output as a list of identified PPIs. The user can also get the DNA sequence read counts and other statistics associated with every identified PPI.

Zhong's team applied PROPER-seq on human embryonic kidney cells, T lymphocytes, and endothelial cell,s and obtained 210,518 PPIs involving 8,635 proteins. The team created a public database with a web interface to download, search, and visualize these PPIs (https://genemo.ucsd.edu /proper).

A graphical abstract of the three tools that together are known as PROPER-seq.

The team validated the PROPER-seq-identified PPIs (called PROPER v1.0) with previously characterized PPIs documented in PPI databases. The team found more than 1,300 and 2,400 PPIs in PROPER v1.0 are supported by previous co-immunoprecipitation experiments and affinity purification-mass spectrometry experiments, respectively.

The team experimentally validated four PROPER-seq identified PPIs that have not been reported in the literature. These four PPIs involve PARP1, a critical protein for DNA repair and a drug target of several human cancers, and four other proteins involved in the trafficking of molecules and transcription regulation. These validations suggest mechanistic links between PARP1 and import/export of molecules to/from the nucleus as well as gene transcription.

Their results show that PROPER v1.0 overlaps with more than 17,000 computationally predicted PPIs without prior experimental validation. The experimental support offered by PROPER-seq to these previously uncharacterized PPIs suggests the solid predictive ability of protein structure-based computational models.

The team found PROPER v1.0 overlaps with one hundred synthetic lethal (SL) gene pairs. An SL gene pair can cause cell death when both genes of this gene pair are lost. This finding suggests a connection between physical interactions (PPIs) and human genetic interactions.

Looking forward, the team hopes PROPER-seq can assist researchers in screening many protein pairs and identify PPIs of interest. In addition, the PROPER-seq identified PPIs from different labs can expand the PPI networks' reference maps and illuminate cell-type-specific PPIs.  

###

Other major contributors to this work include UC San Diego bioengineering Ph.D. student Zhijie Qi, bioengineering postdoc alumna Zhangmin Yan, and bioinformatics and systems biology Ph.D. student Xingzhao Wen, who carried out protein network analysis. Professor Zhen Chen at City of Hope collaborated with Zhong’s team on validation of PROPER-seq identified PPIs.  

This work is supported by the National Institutes of Health, and the Ella Fitzgerald Charitable Foundation.

Lipomi named new Faculty Director of IDEA Engineering Student Center

Darren Lipomi, professor of nanoengineering and faculty director of the IDEA Engineering Student Center

August 2, 2021--NanoEngineering Professor Darren Lipomi has been named the new Faculty Director of the IDEA Engineering Student Center at the UC San Diego Jacobs School of Engineering. His appointment began July 1, 2021. 

The IDEA Engineering Student Center-- where IDEA stands for Inclusion, Diversity, Excellence, and Achievement--has supported thousands of UC San Diego engineering and computer science students through to graduation in the 10 years since its founding. The Center offers programs including summer prep and mentorship programs, peer-led engineering learning communities, support for student diversity organizations, community and culture-building efforts and more. 

The IDEA Engineering Student Center’s mission is to support all students on the challenging path of an engineering and computer science education at UC San Diego, with specific programs that build community, and provide academic and peer support for students traditionally underrepresented in the engineering and computer science fields including Black, Latinx and Native American students, women, first-generation college students, LGBTQ+ students, and low-income students.

“I am incredibly excited for this opportunity,” said Lipomi. "My family didn’t have a lot of money when I was growing up. My dad didn’t go to college, and I am the only scientist or engineer in my immediate or extended family. I owe a great deal to student services offices like the IDEA Center, and am especially grateful to them for the role they played in introducing me to undergraduate research.”

Lipomi has been involved with the IDEA Center in various roles since he joined UC San Diego in 2012, including organizing 36 seminars in the Graduate and Postdoc Scholarly Talk Series.

"I always derive such energy from working with our engineering students. I’m especially excited by the opportunity to engage with our students on social media, and to help in their transition to learning on campus, full time, this fall."

Olivia Graeve, professor of mechanical and aerospace engineering, and outgoing faculty director of the IDEA Center.

Lipomi will build on the momentum and achievements that the IDEA Engineering Student Center has made over the last six years under the leadership of Mechanical and Aerospace Engineering Professor Oliva Graeve. 

“I am incredibly grateful to Professor Graeve for her vision and leadership, and I am proud of the entire IDEA Engineering Student Center team,” said Albert P. Pisano, Dean of the Jacobs School of Engineering. “Their collective efforts have propelled the IDEA Center to new heights, directly benefiting our students.”

Some of the accomplishments of the IDEA Center under Graeve’s leadership are outlined on IDEA’s 10th year anniversary website and in the Center's annual reports

At the Jacobs School, Lipomi is known for his ability to create inclusive research and learning environments for his students inside and outside the lab. In 2017, he received a campus Diversity Champion award. He has extended his ability to facilitate important STEM conversations and empower young researchers across the nation and around the world through his podcast, which is called "Molecular Podcasting with Darren Lipomi." Many of his podcast episodes relate directly or indirectly to equity, diversity and inclusion. 

In terms of research, Lipomi is a world leader in thin film electronic materials, whose applications include solar energy and artificial touch. Like many high-impact engineering professors, he engages in the virtuous cycle between fundamental and applied research. He is the recipient of the Air Force Young Investigator Award, the NIH Director’s New Innovator Award, and the Presidential Early Career Award for Scientists and Engineers (PECASE).

“Together, we are working harder than ever to make the Jacobs School a place where all students, staff and faculty have the resources, support, and community connections inside and outside the classroom that empower them to succeed and thrive,” said Pisano. “Please join me in welcoming Professor Lipomi to the position of Faculty Director, and in thanking Professor Graeve for all her work and accomplishments in this role.”

NSF makes $20 Million investment in Optimization-focused AI Research Institute led by UC San Diego

The Institute will pursue foundational breakthroughs at the nexus of artificial intelligence and optimization to transform chip design, robotics, and communication networks.

The National Science Foundation (NSF) announced today an investment of $220 million to establish 11 artificial intelligence (AI) institutes, each receiving $20 million over five years. One of these, The Institute for Learning-enabled Optimization at Scale (TILOS), will be led by the University of California San Diego in partnership with the Massachusetts Institute of Technology; San Diego-based National University; the University of Pennsylvania; the University of Texas at Austin; and Yale University. TILOS is also partially supported by Intel Corporation.

“These institutes are hubs for academia, industry and government to accelerate discovery and innovation in AI," said National Science Foundation Director Sethuraman Panchanathan. "Inspiring talent and ideas everywhere in this important area will lead to new capabilities that improve our lives ... and position us in the vanguard of competitiveness and prosperity.” 

"As a global society, we can't afford to allow advances in optimization to be underutilized," said UC San Diego Chancellor Pradeep K. Khosla. "The TILOS team is made of an incredible combination of engineers, computer scientists, data scientists and educators who will tackle the hardest theoretical and applied challenges in optimization through virtuous feedback loops that ensure the advances will make a positive difference in the real world."

Learning-enabled optimization

“Optimization is a universal quest: we are driven to do better,” said Andrew Kahng, a computer science and electrical engineering professor at the UC San Diego Jacobs School of Engineering and TILOS director. “Optimization is also a hard problem, as the number of choices explodes in large-scale systems. The TILOS mission is to make today’s impossible optimizations possible, at scale and in practice. Whether for energy-efficiency, safety, robustness or other criteria, improved optimizations have the potential to bring incalculable benefits to society.”

Optimization is a fundamental component of machine learning, an important area of modern AI. Conversely, learning can help solve difficult optimization problems. Foundational research in TILOS will explore this interplay to develop optimization methods that can change the leading edge of real-world practice. In close collaboration with industry partners, institute researchers will develop learning-enabled optimization tools for application areas of strategic importance to the United States, including chip design, robotics, and communication networks.

Fundamental and applied research

"Optimization is both a science and a technology,” commented Rajesh K. Gupta, director of the Halicioglu Data Science Institute, UC San Diego’s campus hub for data science that will house TILOS. “This new AI institute will not only discover new science at the interface of AI and optimization, but also deliver it to real-world practitioners as a technology: measuring it to improve it, with benchmarking and a roadmap of progress.”

Foundational research will drive important applications. In chip design, these advances would dramatically shorten the time needed to design chips, increasing quality, productivity and innovation in the process. In robotics, optimization breakthroughs would improve the way robots learn and interact with humans and other robots in many contexts, including search and rescue, autonomous transportation, and warehouses. In communication networks, better optimization would lead to more capable and efficient power grids, mobile phones, and ecosystems within the Internet of Everything.  

Data and insights from optimization in these application areas will further inspire and challenge fundamental research efforts in AI and optimization. This virtuous cycle in TILOS will accelerate the pace of discovery and translation into the leading edge of practice.

Education and workforce development

The TILOS research will engage undergraduates, graduate students and post-doctoral researchers at every step. In addition, the TILOS team has planned a broad program for workforce development, which will identify and teach new practical skills and mindsets that emerge from fundamental and applied advances in optimization. The team is building an openly accessible program of continuing education with long-term, lifelong learning and skills renewal as its central tenet.

Broadening participation

TILOS programming will extend beyond the classroom, with embodied robot demonstrations, community art installations, and portable, adaptable “outreach in a box” modules to engage and excite a next generation of learners. These initiatives aim to grow awareness of, and access to, new career and educational opportunities -- especially among students who are traditionally underrepresented in engineering.

"Many meaningful and rewarding career opportunities will emerge at the nexus of AI, optimization, and application domains. As a team, we will pursue basic research, translate our results into industrial practice, train the future workforce, and bring awareness of the broader educational and job opportunities that result from advances in AI and optimization," said Kahng. 

 

Learn more:

TILOS website

NSF Invests $20M in UC San Diego-headquartered Artificial Intelligence (AI) Research Institute

Robotics researchers at UC San Diego key part of new NSF AI Institute

NSF Invests $20M in UC San Diego-headquartered Artificial Intelligence (AI) Research Institute

Training Computers To Transfer Music From One Style To Another

July 23, 2021

UC San Diego music and computer science professor Shlomo Dubnov (right) with co-author and high school student Conan Lu (far left), with fellow COSMOS student: mapping the architecture of a machine learning tool to transfer one sample of music from one style to another.

Can artificial intelligence enable computers to translate a musical composition between musical styles – e.g., from pop to classical or to jazz? According to a professor of music and computer science at UC San Diego and a high school student, they have developed a machine learning tool that does just that.

“People are more familiar with machine learning that can automatically convert an image in one style to another, like when you use filters on Instagram to change an image’s style,” said UC San Diego computer music professor Shlomo Dubnov, who is an affiliate faculty member in the Computer Science and Engineering department. “Past attempts to convert compositions from one musical style to another came up short because they failed to distinguish between style and content.”

To fix that problem, Dubnov and co-author Conan Lu developed ChordGAN – a conditional generative adversarial network (GAN) architecture that uses chroma sampling, which only records a 12-tones note distribution note distribution profile to separate style (musical texture) from content (i.e., tonal or chord changes).

“This explicit distinction of style from content allows the network to consistently learn style features,” noted Lu, a senior from Redmond High School in Redmond, Washington, who began developing the technology in summer 2019 as a participant in UC San Diego’s California Summer School for Mathematics and Science (COSMOS). Lu was part of the COSMOS “Music and Technology” cluster taught by Dubnov, who also directs the Qualcomm Institute’s Center for Research in Entertainment and Learning (CREL).

On July 20, Dubnov and Lu will present their findings in a paper* to the 2nd Conference on AI Music Creativity (AIMC 2021). The virtual conference – on the theme of “Performing [with] Machines” – takes place June 18-22 via Zoom. The conference is organized by the Institute of Electronic Music and Acoustics at the University of Music and Performing Arts in Graz, Austriaia from June 18-22.

After attending the COSMOS program in 2019 at UC San Diego, Lu continued to work remotely with Dubnov through the pandemic to jointly author the paper to be presented at AIMC 2021.

For their paper, Dubnov and Lu developed a data set comprised of a few hundred MIDI audio-data samples from pop, jazz and classical music styles. The MIDI files were pre-processed to turn the audio files into piano roll and chroma formats – training the network to convert a music score.

“One advantage of our tool is its flexibility to accommodate different genres of music,” explained Lu. “ChordGAN only controls the transfer of chroma features, so any tonal music can be given as input to the network to generate a piece in the style of a particular musical style.

To evaluate the tool’s success, Lu used the so-called Tonnetz distance to measure the preservation of content (e.g., chords and harmony) to ensure that converting to a different style would not result in losing content in the process.

“The Tonnetz representation displays harmonic relationships within a piece,” noted Dubnov. “Since the main goal of style transfer in this method is to retain the main harmonies and chords of a piece while changing stylistic elements, the Tonnetz distance provides a useful metric in determining the success of the transfer.”

The measure at left extracted from a pop piece and transferred into the classical network, which generated the measure at right. While harmonic structure remains constant within the measure, salient changes in note rendering are present in the classical style.

The researchers also added an independent genre classifier (to evaluate that the resulting style transfer was realistic). In testing the accuracy of their genre classifier, it functioned best on jazz clips (74 percent accuracy), and only slightly less well on pop music (68 percent) and classical (64 percent). (While the original evaluation for classical music was limited to Bach preludes, subsequent testing with classical compositions from Haydn and Mozart also proved effective.)

“Given the success of evaluating ChordGAN for style transfer under our two metrics,” said Lu, “our solution can be utilized as a tool for musicians to study compositional techniques and generate music automatically from lead sheets.”

The high school student’s earlier research on machine learning and music earned Lu a bronze grand medal at the 2021 Washington Science and Engineering Fair. That success also qualified him to compete at the Regeneron International Science and Engineering Fair (ISEF), the largest pre-collegiate science fair in the world. Lu became a finalist at ISEF and received an honorable mention from the Association for the Advancement of Artificial Intelligence.

 

*Lu, C. and Dubnov, S. ChordGAN: Symbolic Music Style Transfer with Chroma Feature ExtractionAIMC 2021, Graz, Austria.

Soft skin patch could provide early warning for strokes, heart attacks

Two fingers press down on a soft, electronic patch against the skin.
This soft, stretchy skin patch uses ultrasound to monitor blood flow to organs like the heart and brain. This image was selected as the cover image for the July 2021 issue of Nature Biomedical Engineering.

July 22, 2021 -- Engineers at the University of California San Diego developed a soft and stretchy ultrasound patch that can be worn on the skin to monitor blood flow through major arteries and veins deep inside a person’s body.

Knowing how fast and how much blood flows through a patient’s blood vessels is important because it can help clinicians diagnose various cardiovascular conditions, including blood clots; heart valve problems; poor circulation in the limbs; or blockages in the arteries that could lead to strokes or heart attacks.

The new ultrasound patch developed at UC San Diego can continuously monitor blood flow—as well as blood pressure and heart function—in real time. Wearing such a device could make it easier to identify cardiovascular problems early on.

A team led by Sheng Xu, a professor of nanoengineering at the UC San Diego Jacobs School of Engineering, reported the patch in a paper published July 16 in Nature Biomedical Engineering.

The patch can be worn on the neck or chest. What’s special about the patch is that it can sense and measure cardiovascular signals as deep as 14 centimeters inside the body in a non-invasive manner. And it can do so with high accuracy.

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Ultrasound patch worn on the neck. Images courtesy of Nature Biomedical Engineering

“This type of wearable device can give you a more comprehensive, more accurate picture of what’s going on in deep tissues and critical organs like the heart and the brain, all from the surface of the skin,” said Xu.

“Sensing signals at such depths is extremely challenging for wearable electronics. Yet, this is where the body’s most critical signals and the central organs are buried,” said Chonghe Wang, a former nanoengineering graduate student in Xu’s lab and co-first author of the study. “We engineered a wearable device that can penetrate such deep tissue depths and sense those vital signals far beneath the skin. This technology can provide new insights for the field of healthcare.”

Another innovative feature of the patch is that the ultrasound beam can be tilted at different angles and steered to areas in the body that are not directly underneath the patch.  

This is a first in the field of wearables, explained Xu, because existing wearable sensors typically only monitor areas right below them. “If you want to sense signals at a different position, you have to move the sensor to that location. With this patch, we can probe areas that are wider than the device’s footprint. This can open up a lot of opportunities.”

How it works

The patch is made up of a thin sheet of flexible, stretchable polymer that adheres to the skin. Embedded on the patch is an array of millimeter-sized ultrasound transducers. Each is individually controlled by a computer—this type of array is known as an ultrasound phased array. It is a key part of the technology because it gives the patch the ability to go deeper and wider.

The phased array offers two main modes of operation. In one mode, all the transducers can be synchronized to transmit ultrasound waves together, which produces a high-intensity ultrasound beam that focuses on one spot as deep as 14 centimeters in the body. In the other mode, the transducers can be programmed to transmit out of sync, which produces ultrasound beams that can be steered to different angles.

“With the phased array technology, we can manipulate the ultrasound beam in the way that we want,” said Muyang Lin, a nanoengineering Ph.D. student at UC San Diego who is also a co-first author of the study. “This gives our device multiple capabilities: monitoring central organs as well as blood flow, with high resolution. This would not be possible using just one transducer.”

The phased array consists of a 12 by 12 grid of ultrasound transducers. When electricity flows through the transducers, they vibrate and emit ultrasound waves that travel through the skin and deep into the body. When the ultrasound waves penetrate through a major blood vessel, they encounter movement from red blood cells flowing inside. This movement changes or shifts how the ultrasound waves echo back to the patch—an effect known as Doppler frequency shift. This shift in the reflected signals gets picked up by the patch and is used to create a visual recording of the blood flow. This same mechanism can also be used to create moving images of the heart’s walls. 

A potential game changer in the clinic

For many people, blood flow is not something that is measured during a regular visit to the physician. It is usually assessed after a patient shows some signs of cardiovascular problems, or if a patient is at high risk.

The standard blood flow exam itself can be time consuming and labor intensive. A trained technician presses a handheld ultrasound probe against a patient’s skin and moves it from one area to another until it’s directly above a major blood vessel. This may sound straightforward, but results can vary between tests and technicians.

Since the patch is simple to use, it could solve these problems, said Sai Zhou, a materials science and engineering Ph.D. student at UC San Diego and co-author of the study. “Just stick it on the skin, then read the signals. It’s not operator dependent, and it poses no extra work or burden to the technicians, clinicians or patients,” he said. “In the future, patients could wear something like this to do point of care or continuous at-home monitoring.”

In tests, the patch performed as well as a commercial ultrasound probe used in the clinic. It accurately recorded blood flow in major blood vessels such as the carotid artery, which is an artery in the neck that supplies blood to the brain. Having the ability to monitor changes in this flow could, for example, help identify if a person is at risk for stroke well before the onset of symptoms.

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Ultrasound patch wired to its full experimental setup.

The researchers point out that the patch still has a long way to go before it is ready for the clinic. Currently, it needs to be connected to a power source and benchtop machine in order to work. Xu’s team is working on integrating all the electronics on the patch to make it wireless.

Paper: “Continuous monitoring of deep-tissue haemodynamics with stretchable ultrasonic phased arrays.” Co-authors include Baiyan Qi*, Zhuorui Zhang*, Mitsutoshi Makihata, Boyu Liu, Yi-hsi Huang, Hongjie Hu, Yue Gu, Yimu Chen, Yusheng Lei, Shu Chien and Erik Kistler, UC San Diego; Taeyoon Lee, Yonsei University and Korea Institute of Science and Technology; and Kyung-In Jang, Daegu Gyeonbuk Institute of Science and Technology, Republic of Korea.

*These authors contributed equally

This work was supported by the National Institutes of Health (grant 1R21EB027303-01A1) and the Center for Wearable Sensors at the UC San Diego Jacobs School of Engineering.

UC San Diego among six U.S. institutions in new Wu Tsai Human Performance Alliance

The Joe and Clara Tsai Foundation makes a $220M commitment to create the Wu Tsai Human Performance Alliance, to advance human well-being through the study of peak performance

July 21, 2021--The University of California San Diego is one of six universities invited to participate in the Wu Tsai Human Performance Alliance, which publicly launched on July 21, 2021. 

The Wu Tsai Human Performance Alliance is a scientific collaboration that aims to transform human health on a global scale through the discovery and translation of the biological principles underlying human performance. 

The Alliance was created through a $220M philanthropic investment from the Joe and Clara Tsai Foundation after philanthropists Clara Wu Tsai and Joe Tsai identified an opportunity for broad societal impact by using new insights into the scientific principles underlying athletic performance to improve human fitness and thriving. 

“Scientific funding has traditionally been focused on the study of diseases,” said Clara Wu Tsai, founder of the Wu Tsai Human Performance Alliance. “We are taking the opposite approach and studying the human body at its healthiest and most vital, to enable the thriving of all people – from an Olympic Gold Medal-level athlete to a grandfather lacking the mobility to enjoy a full life.”

The Alliance is a public-private partnership comprised of scientists, clinicians, engineers, coaches, athletes and innovators from UC San Diego; as well as Stanford University; Boston Children’s Hospital, a Harvard Medical School Affiliate; University of Kansas; University of Oregon; and the Salk Institute for Biological Studies. 

The big-picture motivation of the Alliance extends to empowering all humans to perform at peak physical, intellectual and emotional capacity. 

"UC San Diego is one of six world-renowned institutions selected to help launch the Wu Tsai Human Performance Alliance," said UC San Diego Chancellor Pradeep K. Khosla. "We are uniquely equipped to help build upon fundamental, applied and clinical expertise to empower all people to perform at peak physical, intellectual and emotional capacity. UC San Diego brings to the Alliance dynamic, multi-scale modelling expertise as well as the capacity to generate bedrock experimental and clinical data that will drive new ‘living models’ of human performance and recovery. We look forward to continuing our tradition of collaborative research with friends and new partners."

 

The UC San Diego arm of the Alliance is led by Andrew McCulloch, a professor in the departments of Bioengineering and Medicine at UC San Diego and director of UC San Diego’s campus-wide Institute of Engineering in Medicine.

UC San Diego activities within the Alliance are organized around two grand challenges: a scientific project, the Multiscale Athlete, led by McCulloch; and an applied project, the Triton Center for Performance and Injury Science, led by Sam Ward, a professor in the departments of Orthopaedic Surgery and Radiology at UC San Diego Health. 

Multiscale Athlete 

For the Multiscale Athlete "moonshot" project, UC San Diego researchers are creating new generations of computational models of the musculoskeletal system. The new models will go well beyond representing a static picture of the muscles, bones, tendons and ligaments in the human body. The goal, instead, is to bring these mathematical models "to life" by incorporating biological processes so that a person’s whole-body athletic model can change and adapt over time to reflect things like injuries or changes in training regimens. 

The researchers are using the term "multiscale" because biological research is performed at multiple "scales." From small to large, these biological scales include the genetic, molecular, cellular, tissue, and organ systems scales. Through the Multiscale Athlete project and the Alliance’s Digital Athlete project at Stanford University, the UC San Diego researchers aim to weave new information and insights from all these different biological scales into whole-body mathematical models of athletic performance.

 

One of the big goals of these living models is to provide useful insights and predictions that are based on what is actually happening, at multiple scales, in a person’s muscles, bones, ligaments and tendons at any given time based on things like a particular exercise regime, a specific diet, an injury, or the details of an individual’s sleep patterns. 

"Our multiscale modeling teams are critical glue that will connect the other research teams across the Alliance. We are a synergistic layer that will make the Alliance much greater than the sum of the individual parts," said McCulloch. "UC San Diego is a recognized world-leader in multiscale modeling of living systems. It’s tremendously exciting to have this opportunity to apply our expertise to the important challenge of understanding the science of human performance and improving human thriving."

Triton Center for Performance and Injury Science

What makes the difference between being a good athlete and a great athlete? Can we predict when a dancer is at risk of injury? What can accelerate an athlete’s recovery? 

These are the kinds of questions that drive the UC San Diego researchers, and the larger efforts of the Alliance more generally. 

"The goal is to understand how the underlying biology behaves in many different human performance contexts," said Ward, who leads the Triton Center for Performance and Injury Science at UC San Diego, which is one of the Innovation Hubs of the Alliance.

"Our concept is to figure out how to fold dynamic models of molecular biology, cell biology and physiology into larger scale models of human movement to aid decision making related to performance, training, and recovery. You can ask questions and do experiments in models that you can’t do in humans. But to make the models useful, you need to get great experimental data and rigorous validation to make sure that the models represent what’s actually happening in the human body during and after training, performance, and recovery."

 

With a new "biobank" of tissue samples, ethically collected from athletes as well as laboratory animals, UC San Diego-led teams will generate new biological measurements that will feed into the engineering models in order to accurately represent what’s happening in the human body during and after exercise training and injury. 

"What sorts of training or rest will be most effective for a baseball pitcher near the end of a long season? How do we precisely pair a therapy to a specific individual with a specific injury? To make these kinds of mappings, you need to understand what’s happening biologically in the underlying tissues," said Ward.

It is the interaction between mechanics and biology that the UC San Diego team believes will create breakthroughs in our understanding of peak athletic performance, and peak human performance, more generally. 

"If you don’t understand what’s going on with the underlying biological ‘state’ of tissues, in the cells themselves, you can’t make a prediction about what is going to cause an injury, improve training, or accelerate healing," said Ward. 

Putting the pieces together

Through the Multiscale Athlete moonshot project and the Performance and Injury Science innovation hub, the UC San Diego teams are pulling in the same direction. 

UC San Diego researchers will use tissue samples from the biobank to run laboratory experiments looking for biological information at multiple scales that offers insights on athletic performance, or injury recovery.  

One of the likely scenarios is the following: first, researchers identify genetic, molecular or cellular information in laboratory experiments on tissue samples that point to new ideas about athletic performance or recovery after exercise or after injury. Laboratory experiments will inform and validate the team’s computer simulations, which will inspire additional experiments. 

The researchers will then be able to apply insights that emerge from this feedback loop between laboratory experiments and computational models to predict what will occur in humans, in terms of anatomy and physiology. Biomarkers in sweat, saliva or blood of human athletes; or information that can be picked up via non-invasive imaging tools, will help the research teams translate their insights to humans.   

To dive deeper into the actual experiences of elite athletes, the UC San Diego researchers are also collaborating with UC San Diego Athletics and other groups in the San Diego community. 

“In athletics, as in life, we know that injuries occur when demand exceeds capacity. The Wu Tsai Human Performance Alliance provides an excellent opportunity to understand better the success factors driving physical readiness associated with optimal performance in sport and life," said Matt Kritz, PhD, Senior Associate Athletic Director for Athletic Performance and Health at UC San Diego.

Scientific advances and successes that emerge from the Alliance will be freely accessible to everyone—to scientists, to athletes and coaches, to clinicians and health care personnel, to technology designers, and to the general public. The aim is to enable people with all kinds of bodies to thrive at every stage of life.

 

UC San Diego projects and collaborators include:

Multiscale Models of Musculoskeletal Tissue States

Andrew McCulloch, UC San Diego Departments of Bioengineering and Medicine

Systems Biology of Musculoskeletal Tissue States

Padmini Rangamani, UC San Diego Department of Mechanical and Aerospace Engineering
Pradipta Ghosh, UC San Diego School of Medicine 

Mechanobiology of Cell and Matrix interactions

Adam Engler, UC San Diego Department of Bioengineering
Stephanie Fraley, UC San Diego Department of Bioengineering 

Biomechanics of Musculoskeletal Tissues

Daniela Valdez-Jasso, UC San Diego Department of Bioengineering
Andrew McCulloch, UC San Diego Department of Bioengineering

Performance Evolution

Kimberly Cooper, UC San Diego Division of Biological Sciences 

Triton Center for Performance and Injury Science

Sam Ward, UC San Diego Health Sciences
Robert Sah, UC San Diego Department of Bioengineering
UC San Diego Athletics
Rady Children’s Hospital  

UC San Diego among six U.S. institutions in new Wu Tsai Human Performance Alliance

The Joe and Clara Tsai Foundation makes a $220M commitment to create the Wu Tsai Human Performance Alliance, to advance human well-being through the study of peak performance

July 21, 2021--The University of California San Diego is one of six universities invited to participate in the Wu Tsai Human Performance Alliance, which publicly launched on July 21, 2021. 

The Wu Tsai Human Performance Alliance is a scientific collaboration that aims to transform human health on a global scale through the discovery and translation of the biological principles underlying human performance. 

The Alliance was created through a $220M philanthropic investment from the Joe and Clara Tsai Foundation after philanthropists Clara Wu Tsai and Joe Tsai identified an opportunity for broad societal impact by using new insights into the scientific principles underlying athletic performance to improve human fitness and thriving. 

“Scientific funding has traditionally been focused on the study of diseases,” said Clara Wu Tsai, founder of the Wu Tsai Human Performance Alliance. “We are taking the opposite approach and studying the human body at its healthiest and most vital, to enable the thriving of all people – from an Olympic Gold Medal-level athlete to a grandfather lacking the mobility to enjoy a full life.”

The Alliance is a public-private partnership comprised of scientists, clinicians, engineers, coaches, athletes and innovators from UC San Diego; as well as Stanford University; Boston Children’s Hospital, a Harvard Medical School Affiliate; University of Kansas; University of Oregon; and the Salk Institute for Biological Studies. 

The big-picture motivation of the Alliance extends to empowering all humans to perform at peak physical, intellectual and emotional capacity. 

"UC San Diego is one of six world-renowned institutions selected to help launch the Wu Tsai Human Performance Alliance," said UC San Diego Chancellor Pradeep K. Khosla. "We are uniquely equipped to help build upon fundamental, applied and clinical expertise to empower all people to perform at peak physical, intellectual and emotional capacity. UC San Diego brings to the Alliance dynamic, multi-scale modelling expertise as well as the capacity to generate bedrock experimental and clinical data that will drive new ‘living models’ of human performance and recovery. We look forward to continuing our tradition of collaborative research with friends and new partners."

 

The UC San Diego arm of the Alliance is led by Andrew McCulloch, a professor in the departments of Bioengineering and Medicine at UC San Diego and director of UC San Diego’s campus-wide Institute of Engineering in Medicine.

UC San Diego activities within the Alliance are organized around two grand challenges: a scientific project, the Multiscale Athlete, led by McCulloch; and an applied project, the Triton Center for Performance and Injury Science, led by Sam Ward, a professor in the departments of Orthopaedic Surgery and Radiology at UC San Diego Health. 

Multiscale Athlete 

For the Multiscale Athlete "moonshot" project, UC San Diego researchers are creating new generations of computational models of the musculoskeletal system. The new models will go well beyond representing a static picture of the muscles, bones, tendons and ligaments in the human body. The goal, instead, is to bring these mathematical models "to life" by incorporating biological processes so that a person’s whole-body athletic model can change and adapt over time to reflect things like injuries or changes in training regimens. 

The researchers are using the term "multiscale" because biological research is performed at multiple "scales." From small to large, these biological scales include the genetic, molecular, cellular, tissue, and organ systems scales. Through the Multiscale Athlete project and the Alliance’s Digital Athlete project at Stanford University, the UC San Diego researchers aim to weave new information and insights from all these different biological scales into whole-body mathematical models of athletic performance.

 

One of the big goals of these living models is to provide useful insights and predictions that are based on what is actually happening, at multiple scales, in a person’s muscles, bones, ligaments and tendons at any given time based on things like a particular exercise regime, a specific diet, an injury, or the details of an individual’s sleep patterns. 

"Our multiscale modeling teams are critical glue that will connect the other research teams across the Alliance. We are a synergistic layer that will make the Alliance much greater than the sum of the individual parts," said McCulloch. "UC San Diego is a recognized world-leader in multiscale modeling of living systems. It’s tremendously exciting to have this opportunity to apply our expertise to the important challenge of understanding the science of human performance and improving human thriving."

Triton Center for Performance and Injury Science

What makes the difference between being a good athlete and a great athlete? Can we predict when a dancer is at risk of injury? What can accelerate an athlete’s recovery? 

These are the kinds of questions that drive the UC San Diego researchers, and the larger efforts of the Alliance more generally. 

"The goal is to understand how the underlying biology behaves in many different human performance contexts," said Ward, who leads the Triton Center for Performance and Injury Science at UC San Diego, which is one of the Innovation Hubs of the Alliance.

"Our concept is to figure out how to fold dynamic models of molecular biology, cell biology and physiology into larger scale models of human movement to aid decision making related to performance, training, and recovery. You can ask questions and do experiments in models that you can’t do in humans. But to make the models useful, you need to get great experimental data and rigorous validation to make sure that the models represent what’s actually happening in the human body during and after training, performance, and recovery."

 

With a new "biobank" of tissue samples, ethically collected from athletes as well as laboratory animals, UC San Diego-led teams will generate new biological measurements that will feed into the engineering models in order to accurately represent what’s happening in the human body during and after exercise training and injury. 

"What sorts of training or rest will be most effective for a baseball pitcher near the end of a long season? How do we precisely pair a therapy to a specific individual with a specific injury? To make these kinds of mappings, you need to understand what’s happening biologically in the underlying tissues," said Ward.

It is the interaction between mechanics and biology that the UC San Diego team believes will create breakthroughs in our understanding of peak athletic performance, and peak human performance, more generally. 

"If you don’t understand what’s going on with the underlying biological ‘state’ of tissues, in the cells themselves, you can’t make a prediction about what is going to cause an injury, improve training, or accelerate healing," said Ward. 

Putting the pieces together

Through the Multiscale Athlete moonshot project and the Performance and Injury Science innovation hub, the UC San Diego teams are pulling in the same direction. 

UC San Diego researchers will use tissue samples from the biobank to run laboratory experiments looking for biological information at multiple scales that offers insights on athletic performance, or injury recovery.  

One of the likely scenarios is the following: first, researchers identify genetic, molecular or cellular information in laboratory experiments on tissue samples that point to new ideas about athletic performance or recovery after exercise or after injury. Laboratory experiments will inform and validate the team’s computer simulations, which will inspire additional experiments. 

The researchers will then be able to apply insights that emerge from this feedback loop between laboratory experiments and computational models to predict what will occur in humans, in terms of anatomy and physiology. Biomarkers in sweat, saliva or blood of human athletes; or information that can be picked up via non-invasive imaging tools, will help the research teams translate their insights to humans.   

To dive deeper into the actual experiences of elite athletes, the UC San Diego researchers are also collaborating with UC San Diego Athletics and other groups in the San Diego community. 

“In athletics, as in life, we know that injuries occur when demand exceeds capacity. The Wu Tsai Human Performance Alliance provides an excellent opportunity to understand better the success factors driving physical readiness associated with optimal performance in sport and life," said Matt Kritz, PhD, Senior Associate Athletic Director for Athletic Performance and Health at UC San Diego.

Scientific advances and successes that emerge from the Alliance will be freely accessible to everyone—to scientists, to athletes and coaches, to clinicians and health care personnel, to technology designers, and to the general public. The aim is to enable people with all kinds of bodies to thrive at every stage of life.

 

UC San Diego projects and collaborators include:

Multiscale Models of Musculoskeletal Tissue States

Andrew McCulloch, UC San Diego Departments of Bioengineering and Medicine

Systems Biology of Musculoskeletal Tissue States

Padmini Rangamani, UC San Diego Department of Mechanical and Aerospace Engineering
Pradipta Ghosh, UC San Diego School of Medicine 

Mechanobiology of Cell and Matrix interactions

Adam Engler, UC San Diego Department of Bioengineering
Stephanie Fraley, UC San Diego Department of Bioengineering 

Biomechanics of Musculoskeletal Tissues

Daniela Valdez-Jasso, UC San Diego Department of Bioengineering
Andrew McCulloch, UC San Diego Department of Bioengineering

Performance Evolution

Kimberly Cooper, UC San Diego Division of Biological Sciences 

Triton Center for Performance and Injury Science

Sam Ward, UC San Diego Health Sciences
Robert Sah, UC San Diego Department of Bioengineering
UC San Diego Athletics
Rady Children’s Hospital  

Calling all couch potatoes: this finger wrap can let you power electronics while you sleep

ALT TEXT
This thin, flexible strip can be worn on a fingertip and generate small amounts of electricity when a person’s finger sweats or presses on it.

July 13, 2021 -- A new wearable device turns the touch of a finger into a source of power for small electronics and sensors. Engineers at the University of California San Diego developed a thin, flexible strip that can be worn on a fingertip and generate small amounts of electricity when a person’s finger sweats or presses on it.

What’s special about this sweat-fueled device is that it generates power even while the wearer is asleep or sitting still. This is potentially a big deal for the field of wearables because researchers have now figured out how to harness the energy that can be extracted from human sweat even when a person is not moving.

This type of device is the first of its kind, said co-first author Lu Yin, a nanoengineering Ph.D. student at the UC San Diego Jacobs School of Engineering. “Unlike other sweat-powered wearables, this one requires no exercise, no physical input from the wearer in order to be useful. This work is a step forward to making wearables more practical, convenient and accessible for the everyday person.”

The new wearable energy harvester is described in a paper published July 13 in Joule.

The device also generates extra power from light finger presses—so activities such as typing, texting, playing the piano or tapping in Morse code can also become sources of energy.

“We envision that this can be used in any daily activity involving touch, things that a person would normally do anyway while at work, at home, while watching TV or eating,” said Joseph Wang, a professor of nanoengineering at the UC San Diego Jacobs School of Engineering and the study’s senior author. “The goal is that this wearable will naturally work for you and you don’t even have to think about it.”

The device derives most of its power from sweat produced by the fingertips, which are 24-hour factories of perspiration. It’s a little-known fact that the fingertips are one of the sweatiest spots on the body; each one is packed with over a thousand sweat glands and can produce between 100 to 1000 times more sweat than most other areas on the body.

“The reason we feel sweatier on other parts of the body is because those spots are not well ventilated,” said Yin. “By contrast, the fingertips are always exposed to air, so the sweat evaporates as it comes out. So rather than letting it evaporate, we use our device to collect this sweat, and it can generate a significant amount of energy.”

But not just any sweat-fueled device can work on the fingertip. Collecting sweat from such a small area and making it useful required some innovative materials engineering, explained Yin. The researchers had to build different parts of the device to be super absorbent and efficient at converting the chemicals in human sweat into electrical energy.

Yin worked on this project with UC San Diego nanoengineering Ph.D. students Jong-Min Moon and Juliane Sempionatto, who are the study’s other co-first authors, as part of a team led by Wang, who is also the director of the Center for Wearable Sensors at UC San Diego. Wang and his team pioneered sweat-fueled wearables 8 years ago. Since then, they have been building on the technology to create new and better ways to power wearables using sustainable sources, such as the wearers themselves and their surroundings.

This latest energy harvesting technology is especially unique in that it could serve as a power source anytime, anywhere. It does not have the same limitations as, say, solar cells, which only work under sunlight, or thermoelectric generators, which only work when there’s a large temperature difference between the device and the surroundings.

How it works

The device is a thin, flexible strip that can be wrapped around the fingertip like a Band-Aid. A padding of carbon foam electrodes absorbs sweat and converts it into electrical energy. The electrodes are equipped with enzymes that trigger chemical reactions between lactate and oxygen molecules in sweat to generate electricity. Underneath the electrodes is a chip made of what’s called a piezoelectric material, which generates additional electrical energy when pressed.

As the wearer sweats or presses on the strip, the electrical energy gets stored in a small capacitor and is discharged to other devices when needed.

The researchers had a subject wear the device on one fingertip while doing sedentary activities. From 10 hours of sleep, the device collected almost 400 millijoules of energy—this is enough to power an electronic wristwatch for 24 hours. From one hour of casual typing and clicking on a mouse, the device collected almost 30 millijoules.

And this is just from one fingertip. Strapping devices on the rest of the fingertips would generate 10 times more energy, the researchers said.

“By using the sweat on the fingertip—which flows out naturally regardless of where you are or what you’re doing—this technology provides a net gain in energy with no effort from the user. This is what we call a maximum energy return on investment,” said Wang.

“Compare this to a device that harvests energy as you exercise,” explained Yin. “When you are running, you are investing hundreds of joules of energy only for the device to generate millijoules of energy. In that case, your energy return on investment is very low. But with this device, your return is very high. When you are sleeping, you are putting in no work. Even with a single finger press, you are only investing about half a millijoule.”

In other experiments, the researchers connected their energy harvester to an electronic system consisting of a chemical sensor connected to a small low-power display, which shows a numerical reading of the sensor’s data. Either pressing the energy harvester 10 times every 10 seconds or simply wearing it on the fingertip for two minutes was enough to power both the sensor and the display. In one experiment, the researchers hooked up their device to a vitamin C sensor that they developed in the lab. They had a subject take a vitamin C pill and then use the finger-powered system to read their vitamin C level. In another experiment, the researchers showed that their system could also be used with a lab-built sodium sensor to read the sodium ion level of a saltwater solution.

“Our goal is to make this a practical device,” said Yin. “We want to show that this is not just another cool thing that can generate a small amount of energy and then that’s it—we can actually use the energy to power useful electronics such as sensors and displays.”

To that end, the team is making further improvements to the device so that it is more efficient and durable. Future studies will include combining it with other types of energy harvesters to create a new generation of self-powered wearable systems.

Paper: “A Passive Perspiration Biofuel Cell: High Energy Return on Investment.” Co-authors include Muyang Lin, Mengzhu Cao, Alexander Trifonov, Fangyu Zhang, Zhiyuan Lou, Jae-Min Jeong, Sang-Jin Lee and Sheng Xu, UC San Diego.

This work was supported by the Center for Wearable Sensors at the UC San Diego Jacobs School of Engineering. 

Artificial Intelligence Could Be New Blueprint for Precision Drug Discovery

Mathematical approach could transform drug development by searching for disease targets, then predicting if a drug will be successful

July 12, 2021--Writing in the July 12, 2021 online issue of Nature Communications, researchers at University of California San Diego describe a new approach that uses machine learning to hunt for disease targets and then predicts whether a drug is likely to receive FDA approval. 

The study findings could measurably change how researchers sift through big data to find meaningful information with significant benefit to patients, the pharmaceutical industry and the nation’s health care systems. 

Pradipta Ghosh, MD, is senior author of the study and professor in the departments of Medicine and Cellular and Molecular Medicine at UC San Diego School of Medicine.

“Academic labs and pharmaceutical and biotech companies have access to unlimited amounts of ‘big data’ and better tools than ever to analyze such data. However, despite these incredible advances in technology, the success rates in drug discovery are lower today than in the 1970s,” said Dr. Pradipta Ghosh, senior author of the study and professor in the departments of Medicine and Cellular and Molecular Medicine at UC San Diego School of Medicine. 

“This is mostly because drugs that work perfectly in preclinical inbred models, such as laboratory mice, that are genetically or otherwise identical to each other, don’t translate to patients in the clinic, where each individual and their disease is unique. It is this variability in the clinic that is believed to be the Achilles heel for any drug discovery program.” 

In the new study, Ghosh and colleagues replaced the first and last steps in preclinical drug discovery with two novel approaches developed within the UC San Diego Institute for Network Medicine (iNetMed), which unites several research disciplines to develop new solutions to advance life sciences and technology and enhance human health. 

The researchers used the disease model for inflammatory bowel disease (IBD), which is a complex, multifaceted, relapsing autoimmune disorder characterized by inflammation of the gut lining. Because it impacts all ages and reduces the quality of life in patients, IBD is a priority disease area for drug discovery and is a challenging condition to treat because no two patients behave similarly.

“Our study shows how the likelihood of success in phase III clinical trials, for any target, can be determined with mathematical precision,” said Debashis Sahoo, PhD, co-senior author of the study who leads PreCSN and is associate professor in the departments of Pediatrics and Computer Science at UC San Diego School of Medicine and UC San Diego. 

 “Our approach could provide the predictive horsepower that will help us understand how diseases progress, assess a drug’s potential benefits and strategize how to use a combination of therapies when current treatment is failing,” Sahoo said.

The first step, called target identification, used an artificial intelligence (AI) methodology developed by The Center for Precision Computational System Network (PreCSN), the computational arm of iNetMed. The AI approach helps model a disease using a map of successive changes in gene expression at the onset and during the progression of the disease. What sets this mapping apart from other existing models is the use of mathematical precision to recognize and extract all possible fundamental rules of gene expression patterns, many of which are overlooked by current methodologies. 

Soumita Das, PhD, is co-senior author of the study, director of the HUMANOID center and an associate professor in the Department of Pathology at UC San Diego School of Medicine.

The underlying algorithms ensure that the identified gene expression patterns are ‘invariant’ regardless of different disease cohorts. In other words, PreCSN builds a map that extracts information that applies to all IBD patients. 

“In head-to-head comparisons, we demonstrated the superiority of this approach over existing methodologies to accurately predict ‘winners’ and ‘losers’ in clinical trials,” said Ghosh. 

The last step, called target validation in preclinical models, was conducted in a first-of-its-kind Phase ‘0’ clinical trial using a living biobank of organoids created from IBD patients at The HUMANOID Center of Research Excellence (CoRE), the translational arm of iNetMed. 

The Phase ‘0’ approach involves testing the efficacy of the drugs identified using the AI model on human disease organoid models—cultured human cells in a 3D environment that mimic diseases outside of the body. In this case, an IBD-afflicted gut-in-a-dish. 

“The ‘phase 0’ trial concept was developed because most drugs fail somewhere between phases I and III. Before proceeding to patients in the clinic, ‘phase 0’ tests efficacy in the human disease models, where ineffective compounds can be rejected early in the process, saving millions of dollars,” said Soumita Das, PhD, co-senior author of the study, director of the HUMANOID center and an associate professor in the Department of Pathology at UC San Diego School of Medicine.

Biopsy tissues for the study were taken during colonoscopy procedures involving IBD patients. Those biopsies were used as the source of stem cells to grow organoids. 

“There were two major surprises. First, we saw that despite being away from the immune cells in the gut wall and the trillions of microbes that are in the gut lining, these organoids from IBD patients showed the tell-tale features of a leaky gut with broken cell borders,” said Das.

“Second, the drug identified by the AI model not only repaired the broken barriers, but also protected them against the onslaught of pathogenic bacteria that we added to the gut model. These findings imply that the drug could work in both acute flares as well as for maintenance therapy for preventing such flares.”

The researchers found the computational approach had a surprisingly high level of accuracy across diverse cohorts of IBD patients, and together with the Phase ‘0’ approach, they developed a first-in-class therapy to restore and protect the leaky gut barrier in IBD. 

Debashis Sahoo, PhD, is co-senior author of the study who leads PreCSN and is associate professor in the departments of Pediatrics and Computer Science at UC San Diego School of Medicine and UC San Diego

The authors said next steps include testing if the drug that passed the human phase ‘0’ trial in a dish can pass phase III trials in clinic; and whether the same methodologies can be used with other diseases, ranging from diverse types of cancers and Alzheimer’s disease to non-alcoholic fatty liver disease. 

“Our blueprint has the potential to shatter status quo and deliver better drugs for chronic diseases that have yet to have good therapeutic solutions,” said Ghosh.

Co-authors include: Lee Swanson, Ibrahim Sayed, Gajanan Katkar, Stella-Rita Ibeawuchi, Yash Mittal, Rama Pranadinata, Courtney Tindle, Mackenzie Fuller, Dominik Stec and John Chang, all with UC San Diego. 

This study was supported in part, the National Institutes of Health (grants AI141630, DK107585, R56 AG069689, UG3TR003355, UG3TR002968, R01-AI55696, T32 DK 007202, 1TL1TR001443, 3R01DK107585-02S1), the DiaComp Pilot and Feasibility Award (R00-CA151673, R01-GM138385), Padres Pedal the Cause/C3 Collaborative Translational Cancer Research Award (#PTC2017), the Leona M. and Harry B. Helmsley Charitable Trust and The American Association of Immunologists Intersect Fellowship Program for Computational Scientists and Immunologists. 

Disclosure: Soumita Das, Debashis Sahoo and Pradipta Ghosh have a patent on the methodology.

Ishwar K. Puri named USC vice president for research

Women in Engineering --Anna Pridmore, P.E., Ph.D.

Machine learning enhances non-verbal communication in online classrooms

If concertmaster (top left) looks at her camera, it will appear to the musicians that she is looking at all of them. But gaze tracking system shows she is looking at Walter (second row center), and labels the concertmaster’s video feed with the cue “Walter” so the entire class knows intended gaze recipient. The cue updates continuously when she looks at another musician – establishing non-verbal communication with the ensemble.

June 21, 2021--Researchers in the Center for Research on Entertainment and Learning (CREL) at the University of California San Diego have developed a system to analyze and track eye movements to enhance teaching in tomorrow’s virtual classrooms – and perhaps future virtual concert halls.

UC San Diego music and computer science professor Shlomo Dubnov, an expert in computer music who directs the Qualcomm Institute-based CREL, began developing the new tool to deal with a downside of teaching music over Zoom during the COVID-19 pandemic.

“In a music classroom, non-verbal communication such as facial affect and body gestures is critical to keep students on task, coordinate musical flow and communicate improvisational ideas,” said Dubnov. “Unfortunately, this non-verbal aspect of teaching and learning is dramatically hampered in the virtual classroom where you don’t inhabit the same physical space.”

To overcome the problem, Dubnov and Ph.D. student Ross Greer recently published a conference paper on a system that uses eye tracking and machine learning to allow an educator to make ‘eye contact’ with individual students or performers in disparate locations – and lets each student know when he or she is the focus of the teacher’s attention.

The researchers built a prototype system and undertook a pilot study in a virtual music class at UC San Diego via Zoom.

“Our system uses a camera to capture the presenter’s eye movements to track where they are looking on screen,” explained Greer, an electrical and computer engineering Ph.D. student in UC San Diego’s Jacobs School of Engineering. “We divided the screen into 91 squares, and after determing the location of the teacher’s face and eyes, we came up with a ‘gaze-estimation’ algorithmm that provides the best estimate of which box – and therefore which student – the teacher is looking at.”

As the system recognizes a change in where the teacher is looking, the algorithm determines the identity of the student and tags his or her name on screen so everyone knows whom the presenter is focusing on.

In the pilot study, Dubnov and Greer found the system to be highly accurate in estimating the presenter’s gaze – managing to get within three-quarters of an inch (2cm) of the correct point on a 27.5 x 13 inches (70x39cm) screen. “In principle,” Greer told New Scientist magazine, “the system should work well on small screens, given enough quality data.”

One downside, according to Dubnov: the further the presenter is from the camera, the eyes become smaller and harder to track, resulting in less accurate gaze estimation. Yet with better training data, higher-quality camera resolution, and further advances in tracking facial and body gestures, he thinks the system could even allow the conductor to wield a baton remotely and conduct a distributed symphony orchestra -- even if every musician is located somewhere else.

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Ross Greer and Shlomo Dubnov, Eye-Tracking Software Could Make Video Calls Fee More LifelikeProceedings of CSME (2021), ISBN: 978-989-758-502-9  DOI: 10.5220/0010539806980708

Bio-inspired hydrogel protects the heart from post-op adhesions

Researchers developed a device to spray the hydrogel during surgeries. Download high resolution version of this image on Flickr.  Image credit:  UC San Diego Jacobs School of Engineering / David Baillot

June 18, 2021-- A hydrogel that forms a barrier to keep heart tissue from adhering to surrounding tissue after surgery was developed and successfully tested in rodents by a team of University of California San Diego researchers. The team of engineers, scientists and physicians also conducted a pilot study on porcine hearts, with promising results.

They describe their work in the June 18, 2021 issue of Nature Communications.

In rats, the hydrogel prevented the formation of adhesions altogether. In a small pilot study, porcine hearts treated with the hydrogel experienced less severe adhesions that were easier to remove. In addition, the hydrogel did not appear to cause chronic inflammation. 

Adhesions--organ tissue sticking to surrounding tissue--are a relatively common problem when surgeons need to operate again at the same site, which happens in 20 percent of cases every year in cardiac surgery. Re-operations are particularly common when the patients are children suffering from cardiac malformations--as the child’s heart grows, additional interventions are needed. 

Adhesions form within the first 30 days post-op and can complicate operations and increase the risk of mortality during interventions. In some cases, they can also interfere with proper heart function or completely prevent a repeat surgery. One of the paper’s senior authors, UC San Diego bioengineering professor Karen Christman, experienced this when one of her uncles couldn’t have  a heart valve repaired because of severe adhesions. 

“Our work is an engineering solution driven by a medical problem,” said Christman, who co-founded a company, Karios Technologies, to bring the hydrogel into the clinic. “And now it’s poised to significantly improve cardiac surgery, both for adults and children.”

The work brought together not only bioengineers and physicians, but also chemists and materials scientists.  

In academic medical centers such as UC San Diego, most surgeons conduct repeat operations and encounter adhesions fairly regularly. In this study, in rats, 70 percent of animals in the control group developed severe adhesions. 

Currently there are no FDA approved products marketed for preventing adhesions after heart surgery.  “This product will have a significant impact on the lives of many patients who potentially require repeat operations, either on the heart or anywhere else in the body,” said Dr. Michael M. Madani, chair of the Division of Cardiovascular and Thoracic Surgery at UC San Diego Health and one of the paper’s co-authors.

How it’s made

By contrast, the hydrogel developed by bioengineers in Christman’s lab is designed specifically to meet both the patients’ and surgeons’ needs. It’s sprayable, so easy to apply. Once sprayed onto tissue, it binds to the heart muscle and turns into a soft, elastic coating that creates a protective barrier, while still allowing for movement. The gel can be easily removed from tissue and dissolves after more than four to six weeks. 

The biggest challenge was making sure that the hydrogel attaches strongly  enough to the heart but doesn’t swell, as swelling can put dangerous pressure on the heart. Christman and team used what’s known as crosslinking chemistry, which consists of linking two molecules together with a covalent bond, to accomplish this. Masaki Fujita, the paper’s first author and a visiting scientist in the Department of Bioengineering at UC San Diego, had the idea of using a compound known as catechol, similar to what mussels use to adhere to rocks, to ensure the hydrogel stayed in place on the heart. 

Catechol contains an amino acid, L-dopa, that is a muscle binding protein. In this case, it was added to the gel base, a water soluble polymer, known as PEG. The result is a hydrogel that sticks onto the organ it is applied to, but then creates a protective barrier that lasts at least up to four weeks before dissolving. By that point, adhesions are less likely to form. To the researchers’ knowledge, it’s the first time this type of formulation has been used for preventing adhesions after surgery.

Spraying device

Left: a rodent heart treated with the hydrogel post-op shows little to no adhesions two weeks post-op. Right: a heart from the control rodent group shows severe adhesions.

Researchers also designed a device to safely and accurately spray the hydrogel inside the area where open heart surgery is being performed. The device houses the hydrogel’s two main components in two different chambers. Each component is made of PEG with different reactive groups that crosslink together to form the hydrogel. One of the solutions also includes the catechol-modified PEG to ensure it stays on the heart. The two mix as they exit the device, forming a gel. The process is akin to using two cans of spray paint, for example blue and yellow, to create a third color, green. 

Next steps and bigger picture

The next step is to do a large-scale trial in pigs to refine dosage and examine how the hydrogel binds to sutures and drains. The ultimate goal is to conduct a human pediatric study in 18 months to two years and bring the product to the FDA for approval in five years.

Karios Technologies is licensing the technology from UC San Diego.  “We want feedback from surgeons,” Gregory, CEO of Karios Technologies said. “We designed this material specifically for use on the heart and ease of use by the surgeon.”

The technology could easily translate to other organs also requiring multiple operations and susceptible to adhesions, researchers said. 

The work was funded by the National Heart, Lung and Blood Institute through the UC Center for Accelerated Innovation, and the National Center for Advancing Translational Sciences through the UC San Diego Center for Clinical and Translational Research Institute. 

Christman co-founded and holds equity interest in Karios Technologies, a startup that aims to commercialize the hydrogel technology. Dr. Madani is a consultant for the company. Christman, Fujita and Madani are inventors on patents and patent applications related to the work. 

 

Imperfections in jewels used as sensors for new quantum materials

'It Feels Like I'm Talking into a Void': How Do We Improve the Virtual Classroom?

 

A pseudonymous snapshot of a discussion-based lecture at UC San Diego. Most students are not sharing videos and all are muted except the one person who is speaking.

June 17, 2021--The COVID pandemic precipitated a major shift to virtual learning—an unplanned test of whether these technologies can scale effectively. But did they?

Researchers in the UC San Diego Department of Computer Science and Engineering wanted to look beyond the anecdotal evidence to better understand where remote education fell short and how we might improve it. In a study presented at the Association for Computing Machinery’s Conference on Human Factors in Computing Systems (CHI), the team examined faculty and student attitudes towards virtual classrooms and proposed several technological refinements that could improve their experience, such as flexible distribution of student video feeds and enhanced chat functions.

“We wanted to understand instructor and student perspectives and see how we can marry them,” said Nadir Weibel, a computer science associate professor and senior author on the paper. “How can we improve students’ experience and give better tools to instructors?”

The project was initiated and led by computer science Ph.D. student and first author Matin Yarmand. With coauthors Scott Klemmer, a professor of cognitive science and computer science, and Carnegie Mellon University Ph.D. student Jaemarie Solyst, the team interviewed seven UC San Diego faculty members to better understand their experience. Their primary fault with online learning is that many students never turn their cameras on.

“When I’m presenting the lecture content, it feels like I’m talking into a void,” said one professor. “How do I tell whether students are engaged?” asked another. “You have no sense if people are getting it or not getting it.”

The researchers then distributed student surveys. The 102 responses they showed—not surprisingly—that students resist turning on their cameras and often remain muted. Some don’t want their peers to see them; others are eating or performing unrelated tasks; some are unaware video feedback helps instructors; and a hardcore few see no need to turn their cameras on at all.

While students feel awkward asking questions on video, they overwhelmingly like chat functions, which make them more likely to participate. “I’m more comfortable asking questions in chat, since I feel less like I’m interrupting the lecture,” said one respondent. The survey also showed chat rooms drive more community among students. As a result, the authors propose that text communication could promote student engagement and community, even in in-person classrooms.

Students also have trouble connecting with instructors. Online classes lack opportunities for short conversations and questions that can happen during “hallway time” before and after live lectures.

Gathering together, virtually

The Gather lounge contains the instructor’s office in the middle and many other spaces for student collaboration. The red ellipses indicate small group interactions that are taking place before the lecture starts.

In response to these concerns, the researchers have suggested potential solutions. Technology that reads social cues, such as facial expressions or head nods, could provide invaluable feedback for instructors. Video feeds could also be refined to make instructors the center of attention, as they are in real-life classrooms, rather than one of many co-equal video boxes.

Increased chat use could improve both online and in-person classes, as some students have always been reluctant to call attention to themselves.

Weibel and colleagues have also been exploring how virtual reality environments could improve online learning. Using a tool called Gather, they have been testing an instructor lounge, in which students and faculty could meet before or even during class.

“The way Gather works is you move your avatar around in the space, and if it gets close enough to somebody, you can have a one-to-one conversation with just that person,” said Weibel. “Nobody else is part of it. People can just come and talk to me directly or chat with their friends and peers.”

The team is also working on a natural language processing bot that could make the experience more interactive. For example, if two people are struggling on the same assignment, it could connect them to improve collaboration or point to additional resources on Canvas.

The authors believe online classes, such as MOOCs, which were popular before COVID, will continue into the future. Weibel hopes this research and other efforts will refine the technology and improve the online learning experience.

“Some classes will be back in person,” he said. “Some will be only online and some will be hybrid, but I think online learning is probably here to stay.”

AI predicts how patients with viral infections, including COVID-19, will fare

This image shows specialized lung cells (resembling a beaded necklace) that may mount a cytokine storm in response to some viral infections.

June 17, 2021--Debashis Sahoo, a professor in the UC San Diego Department of Computer Science and Engineering and of pediatrics at UC San Diego School of Medicine, along with other researchers at the School of Medicine have used an artificial intelligence algorithm to sift through terabytes of gene expression data — which genes are “on” or “off” during infection — to look for shared patterns in patients with past pandemic viral infections, including SARS, MERS and swine flu.

Two telltale signatures emerged from the study, published June 11, 2021 in eBiomedicine. One, a set of 166 genes, reveals how the human immune system responds to viral infections. A second set of 20 signature genes predicts the severity of a patient’s disease. For example, the need to hospitalize or use a mechanical ventilator. The algorithm’s utility was validated using lung tissues collected at autopsies from deceased patients with COVID-19 and animal models of the infection.

Sahoo co-led the study with Dr. Pradipta Ghosh, professor of cellular and molecular medicine at UC San Diego School of Medicine and Moores Cancer Center, and Soumita Das, associate professor of pathology at UC San Diego School of Medicine.

“These viral pandemic-associated signatures tell us how a person’s immune system responds to a viral infection and how severe it might get, and that gives us a map for this and future pandemics,” said Ghosh.

During a viral infection, the immune system releases small proteins called cytokines into the blood. These proteins guide immune cells to the site of infection to help get rid of the infection. Sometimes, though, the body releases too many cytokines, creating a runaway immune system that attacks its own healthy tissue. This mishap, known as a cytokine storm, is believed to be one of the reasons some virally infected patients, including some with the common flu, succumb to the infection while others do not.

But the nature, extent and source of fatal cytokine storms, who is at greatest risk and how it might best be treated have long been unclear.

“When the COVID-19 pandemic began, I wanted to use my computer science background to find something that all viral pandemics have in common — some universal truth we could use as a guide as we try to make sense of a novel virus,” Sahoo said. “This coronavirus may be new to us, but there are only so many ways our bodies can respond to an infection.”

The data used to test and train the algorithm came from publicly available sources of patient gene expression data — all the RNA transcribed from patients’ genes and detected in tissue or blood samples. Each time a new set of data from patients with COVID-19 became available, the team tested it in their model. They saw the same signature gene expression patterns every time.

From a simple blood draw, gene expression patterns associated with pandemic viral infections could provide clinicians with a map to help define patients’ immune responses, measure disease severity, predict outcomes and test therapies.

“In other words, this was what we call a prospective study, in which participants were enrolled into the study as they developed the disease and we used the gene signatures we found to navigate the uncharted territory of a completely new disease,” Sahoo said.

By examining the source and function of those genes in the first signature gene set, the study also revealed the source of cytokine storms: the cells lining lung airways and white blood cells known as macrophages and T cells. In addition, the results illuminated the consequences of the storm: damage to those same lung airway cells and natural killer cells, a specialized immune cell that kills virus-infected cells.

“We could see and show the world that the alveolar cells in our lungs that are normally designed to allow gas exchange and oxygenation of our blood, are one of the major sources of the cytokine storm, and hence, serve as the eye of the cytokine storm,” Das said. “Next, our HUMANOID Center team is modeling human lungs in the context of COVID-19 infection in order to examine both acute and post-COVID-19 effects.”

The researchers think the information might also help guide treatment approaches for patients experiencing a cytokine storm by providing cellular targets and benchmarks to measure improvement.

To test their theory, the team pre-treated rodents with either a precursor version of Molnupiravir, a drug currently being tested in clinical trials for the treatment of COVID-19 patients, or SARS-CoV-2-neutralizing antibodies. After exposure to SARS-CoV-2, the lung cells of control-treated rodents showed the pandemic-associated 166- and 20-gene expression signatures. The treated rodents did not, suggesting that the treatments were effective in blunting cytokine storm.

“It is not a matter of if, but when the next pandemic will emerge,” said Ghosh, who is also director of the Institute for Network Medicine and executive director of the HUMANOID Center of Research Excellence at UC San Diego School of Medicine. “We are building tools that are relevant not just for today’s pandemic, but for the next one around the corner.”

Co-authors of the study include: Gajanan D. Katkar, Soni Khandelwal, Mahdi Behroozikhah, Amanraj Claire, Vanessa Castillo, Courtney Tindle, MacKenzie Fuller, Sahar Taheri, Stephen A. Rawlings, Victor Pretorius, David M. Smith, Jason Duran, UC San Diego; Thomas F. Rogers, Scripps Research and UC San Diego; Nathan Beutler, Dennis R. Burton, Scripps Research; Sydney I. Ramirez, La Jolla Institute for Immunology; Laura E. Crotty Alexander, VA San Diego Healthcare System and UC San Diego; Shane Crotty, Jennifer M. Dan, La Jolla Institute for Immunology and UC San Diego.

Funding for this research came, in part, from the National Institutes for Health (grants R00-CA151673, R01-GM138385, R01-AI141630, CA100768, CA160911, R01DK107585, R01-AI155696, R00RG2628, R00RG2642 and U19-AI142742), UC San Diego Sanford Stem Cell Clinical Center, La Jolla Institute for Immunology Institutional Funds, and VA San Diego Healthcare System.

Researchers translate a bird's brain activity into song

Study demonstrates the possibilities of a future speech prosthesis for humans

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Zebra finch. Photo by iStock_thawats

June 16, 2021 -- It is possible to re-create a bird’s song by reading only its brain activity, shows a first proof-of-concept study from the University of California San Diego. The researchers were able to reproduce the songbird’s complex vocalizations down to the pitch, volume and timbre of the original.

Published June 16 in Current Biology, the study lays the foundation for building vocal prostheses for individuals who have lost the ability to speak.

“The current state of the art in communication prosthetics is implantable devices that allow you to generate textual output, writing up to 20 words per minute,” said senior author Timothy Gentner, a professor of psychology and neurobiology at UC San Diego. “Now imagine a vocal prosthesis that enables you to communicate naturally with speech, saying out loud what you’re thinking nearly as you’re thinking it. That is our ultimate goal, and it is the next frontier in functional recovery.”

The approach that Gentner and colleagues are using involves songbirds such as the zebra finch. The connection to vocal prostheses for humans might not be obvious, but in fact, a songbird’s vocalizations are similar to human speech in various ways. They are complex, and they are learned behaviors.

“In many people’s minds, going from a songbird model to a system that will eventually go into humans is a pretty big evolutionary jump,” said Vikash Gilja, a professor of electrical and computer engineering at UC San Diego who is a co-author on the study. “But it’s a model that gives us a complex behavior that we don’t have access to in typical primate models that are commonly used for neural prosthesis research.”

The research is a cross-collaborative effort between engineers and neuroscientists at UC San Diego, with the Gilja and Gentner labs working together to develop neural recording technologies and neural decoding strategies that leverage both teams’ expertise in neurobiological and behavioral experiments.

The team implanted silicon electrodes in male adult zebra finches and monitored the birds’ neural activity while they sang. Specifically, they recorded the electrical activity of multiple populations of neurons in the sensorimotor part of the brain that ultimately controls the muscles responsible for singing.

The researchers fed the neural recordings into machine learning algorithms. The idea was that these algorithms would be able to make computer-generated copies of actual zebra finch songs just based on the birds’ neural activity. But translating patterns of neural activity into patterns of sounds is no easy task.

“There are just too many neural patterns and too many sound patterns to ever find a single solution for how to directly map one signal onto the other,” said Gentner.

To accomplish this feat, the team used simple representations of the birds’ vocalization patterns. These are essentially mathematical equations modeling the physical changes—that is, changes in pressure and tension—that happen in the finches’ vocal organ, called a syrinx, when they sing. The researchers then trained their algorithms to map neural activity directly to these representations.


Bird song sample: number of a bird in the study, followed by its own natural recorded song and then the reproduced, biomechanical version of the same song.

This approach, the researchers said, is more efficient than having to map neural activity to the actual songs themselves.

“If you need to model every little nuance, every little detail of the underlying sound, then the mapping problem becomes a lot more challenging,” said Gilja. “By having this simple representation of the songbirds’ complex vocal behavior, our system can learn mappings that are more robust and more generalizable to a wider range of conditions and behaviors.”

The team’s next step is to demonstrate that their system can reconstruct birdsong from neural activity in real time.

Part of the challenge is that songbirds’ vocal production, like humans’, involves not just output of the sound but a constant monitoring of the environment and constant monitoring of the feedback. If you put headphones on humans, for example, and delay when they hear their own voice, disrupting just the temporal feedback, they’ll start to stutter. Birds do the same thing. They’re listening to their own song.  They make adjustments based on what they just heard themselves singing and what they hope to sing next, Gentner explained. A successful vocal prosthesis will ultimately need to work on a timescale that is similarly fast and also intricate enough to accommodate the entire feedback loop, including making adjustments for errors.

“With our collaboration,” said Gentner, “we are leveraging 40 years of research in birds to build a speech prosthesis for humans—a device that would not simply convert a person’s brain signals into a rudimentary set of whole words but give them the ability to make any sound, and so any word, they can imagine, freeing them to communicate whatever they wish.”

Paper: “Neurally driven synthesis of learned, complex vocalizations.” Co-authors include Ezequiel M. Arneodo, Shukai Chen and Daril E. Brown, all at UC San Diego.

This work was supported by the National Institutes of Health (grant R01DC018446), the Kavli Institute for the Brain and Mind (IRG no. 2016-004), the Office of Naval Research (MURI N00014-13-1-0205) and a Pew Latin American Fellowship in the Biomedical Sciences.

Declaration of interests: Vikash Gilja is a compensated consultant of Paradromics, Inc., a brain-computer interface company.

Genetically engineered nanoparticle delivers dexamethasone directly to inflamed lungs

June 16, 2021--Nanoengineers at the University of California San Diego have developed immune cell-mimicking nanoparticles that target inflammation in the lungs and deliver drugs directly where they’re needed. As a proof of concept, the researchers filled the nanoparticles with the drug dexamethasone and administered them to mice with inflamed lung tissue. Inflammation was completely treated in mice given the nanoparticles, at a drug concentration where standard delivery methods did not have any efficacy. 

The researchers reported their findings in Science Advances on June 16.

Schematic of a genetically engineered cell membrane-coated nanoparticle designed to deliver dexamethasone to inflamed lungs. Credit: Zhang Lab

What’s special about these nanoparticles is that they are coated in a cell membrane that’s been genetically engineered to look for and bind to inflamed lung cells. They are the latest in the line of so-called cell membrane-coated nanoparticles that have been developed by the lab of UC San Diego nanoengineering professor Liangfang Zhang. His lab has previously used cell membrane-coated nanoparticles to absorb toxins produced by MRSA; treat sepsis; and train the immune system to fight cancer. But while these previous cell membranes were naturally derived from the body’s cells, the cell membranes used to coat this dexamethasone-filled nanoparticle were not.

Liangfang Zhang, a professor of nanoengineering at UC San Diego, has been developing cell membrane-coated nanoparticles for over a decade.

“In this paper, we used a genetic engineering approach to edit the surface proteins on the cells before we collected the membranes. This significantly advanced our technology by allowing us to precisely overexpress certain functional proteins on the membranes or knockout some undesirable proteins,” said Zhang, who is a senior author of the paper. 

Joon Ho Park, a graduate student in Zhang’s lab and first author of the paper, said the researchers noticed that when endothelial cells become inflamed, they overexpress a protein called VCAM1, whose purpose is to attract immune cells to the site of inflammation. In response, the immune cells express a protein called VLA4, which seeks out and binds to VCAM1. 

“We engineered cell membranes to express the full version of VLA4 all the time,” said Park. “These membranes constantly overexpress VLA4 in order to seek out VCAM1 and the site of inflammation. These engineered cell membranes allow the nanoparticle to find the inflamed sites, and then release the drug that’s inside the nanoparticle to treat the specific area of inflammation.”

While the nanoparticle won’t directly enhance the efficacy of the drug—dexamethasone in this case—concentrating it at the site of interest may mean a lower dosage is required. This study showed that the dexamethasone accumulated at the site of interest at higher levels, and faster, than standard drug delivery approaches. 

“We’re delivering the exact same drug used in the clinic, but the difference is we’re concentrating the drugs to the point of interest,” said Park. “By having these nanoparticles target the inflammation site, it means a larger portion of the medicine will wind up where it’s needed, and not be cleared out by the body before it can accumulate and be effective.”

The researchers note that this genetically engineered cell membrane approach is a platform technology that in theory can be used to target not only inflammation in other areas of the body— VCAM1 is a universal signal of inflammation—but much broader use cases as well.

“This is a versatile platform, not just for lung inflammation but any type of inflammation that upregulates VCAM1,” said Park. “This technology can be generalized; this engineered cell membrane-coated nanoparticle doesn’t have to overexpress VLA4, it could be swapped out to another protein that can target other areas of the body or accomplish other goals.”

Nanoengineering graduate student Joon Ho Park is first author of the study.
 

To engineer the cell membranes to overexpress the VLA4 protein, Park and the team start with packaging VLA4 genes into a viral vector. They then insert this reprogrammed viral vector into lab-grown host cells derived from mice. The cells incorporate the genes that the viral vector is carrying into their own genome and as a result, produce membranes that constantly overexpress VLA4. 

The researchers’ next step is to study the process using human cell membranes, instead of mice cell membranes, that are engineered to express the human version of VLA4. There are still many steps needed before the technology could be tested in human clinical trials, but the researchers say that these early results from the platform technology are encouraging. 

“By leveraging the established gene editing techniques, this study advances the cell membrane-coated nanoparticles to a new level and opens up new opportunities for targeted drug delivery and other medical applications”, concluded by Zhang.  

Paper: “Genetically engineered cell membrane–coated nanoparticles for targeted delivery of dexamethasone to inflamed lungs.” Co-authors include Yao Jiang, Jiarong Zhou, Hua Gong, Animesh Mohapatra, Jiyoung Heo, Weiwei Gao, and Ronnie H. Fang.

This work was supported by the National Institutes of Health (R01CA200574) and the Defense Threat Reduction Agency Joint Science and Technology Office for Chemical and Biological Defense (HDTRA1-18-1-0014).

Titans of industry, academia team up to advance engineering in medicine

Generosity of Shu and K.C. Chien and Peter Farrell to be recognized through named research collaboratory in Franklin Antonio Hall

June 10, 2021--When renowned UC San Diego bioengineer Shu Chien completed medical school in 1953, he wanted to find ways to make technological advancements in healthcare that would improve human lives. To do so, he had to find an engineer to collaborate with, since physicians and engineers were largely siloed professions at the time.

Peter Farrell, founder of sleep-disordered breathing medical device company ResMed, experienced something similar when completing his bioengineering Ph.D. research into treatments with the artificial kidney, working under the guidance of two advisors: one a nephrologist, and the other an engineer.

“Many years ago, if you talked to leaders in medical school about engineering, they’d say ‘Oh we’re not very interested in that,” said Chien. “But today, almost every major medical school leadership would like to have an engineering presence, and conversely leadership in engineering would like to have biomedical engineering complementation.”

Chien went on to earn a Ph.D. in physiology, and helped to create the engineering-meets-medicine world he was looking for as a young physician. The great success of his efforts are reflected in advances made by former students and colleagues around the world and right here at UC San Diego where the Bioengineering Department is ranked No. 3 in the nation according to U.S. News & World Report and No.1 according to the National Research Council of the U.S. National Academies.

Chien's research includes work critical to our understanding of how blood flows in the cardiovascular system. He is one of only a handful of individuals to be awarded the U.S. National Medal of Science and to be voted into all three National Academies (Science, Medicine and Engineering).

As founder of ResMed, Peter Farrell’s development of a machine that helps people with sleep apnea breathe better while asleep has transformed lives and led to greater understanding of the link between sleep-disordered breathing and chronic illnesses such as diabetes and hypertension. The concept of nasal CPAP (continuous positive airway pressure) was pioneered by Dr. Colin Sullivan at the University of Sydney Medical School to treat obstructive sleep apnea. Farrell came to the interface of engineering and medicine as an engineer. He is an elected member of the National Academy of Engineering, and served as founding director of biomedical engineering at the University of New South Wales, Sydney before becoming vice president of research and development at Baxter Healthcare, Japan.

Farrell was research and development vice president at Baxter for five years before founding ResMed, where he remains Chairman of the Board. ResMed sells 360,000 medical devices a month and 1.2 million masks of various types in more than 140 countries to treat sleep apnea, COPD and other respiratory conditions. ResMed is listed on the New York Stock Exchange (RMD) and employs 7,500 people.

Chien and Farrell agree that while the silos that once kept engineering and medicine as distinctly separate from one another have been breaking down, there is still room for improvement.

“Without engineering, medicine is just not going to advance at the level that it should,” said Farrell. “The participation of both fields is not only here to stay, it’s vital for healthcare in general. Engineers and physicians, pharmaceutical scientists and biologists all need to be working together, as a team. In the good programs, like UC San Diego, the silos have virtually disappeared.”

The UC San Diego Institute for Engineering in Medicine, which Chien founded, with Farrell sitting on the advisory board, is a prime example of how engineering and medicine have converged on campus. The Institute facilitates the integration of engineering principles and novel technologies with biomedical and translational research.

KC and Shu Chien

As the silos between engineering and medicine continue to dissolve, there is a growing need on campus for facilities where engineers, physicians and medical researchers can work in the same physical research ecosystems. Shu Chien and his wife, KC, recently joined forces with Peter Farrell to support this vision.

The Chiens and Farrell each recently donated $1.5 million to support programmatic expansion of engineering and medicine on campus. A large collaborative research facility for engineering and medicine in the Jacobs School’s newest building, Franklin Antonio Hall, will be named in recognition of their generosity.

The named Chien-Farrell Institute for Engineering in Medicine Collaboratory will serve as a hub for research at the interface of engineering and medicine. This collaborative research facility is one of 13 such "collaboratories" within the Jacobs School's newest building, Franklin Antonio Hall.

The Chien-Farrell Collaboratory will bring faculty, students, researchers and industry partners from different fields together in the same space, to facilitate the types of truly interdisciplinary, collaborative research required to solve society’s greatest challenges in medicine and healthcare.

“Today, one young person can get trained and have knowledge in all of these fields,” said Chien. “Nevertheless, one person cannot do as much as people collaborating together—we’re limited beings, so we still need a group to work together. That’s the beauty of interdisciplinary research: different people with different expertise mutually beneficial to each other. When we work together like this, the total of our efforts is much greater than the sum of each individual’s work.”

The Chien-Farrell Collaboratory in particular and Franklin Antonio Hall more generally will focus not only on collaborations among researchers from disparate fields, but among academic teams and industry partners as well.

“Entrepreneurship is not about risk taking, it’s about opportunity seeking,” said Farrell “Industry and academia all need to be part of the same ecosystem with the same goals. They support each other in a loop where the best ideas are fed into the marketplace to generate revenue, where a portion of the profit flows back to academia in research support coupled with potential equity. This new Collaboratory and Franklin Antonio Hall accelerate that loop, delivering good ideas which solve problems into the marketplace. Everybody benefits: it can help the campus, the students, society as a whole.”

“I'm really very honored to share the naming of the building with Peter,” said Chien. “He and his company Resmed have made tremendous contributions to the science and engineering of respiratory and sleep problems. I myself am a beneficiary of their product with sleep apnea, so I personally am grateful for that.”

“Shu is a pleasure to work with and a good guy to be involved with,” said Farrell. “He gets it. I have a lot of respect for him.”

Franklin Antonio Hall

In addition to the Chien-Farrell Collaboratory, 12 more of these large research facilities make up the heart of Franklin Antonio Hall. Each collaboratory will house a collection of professor-led research groups from different but related disciplines. Together, these complementary research teams will pursue grand-challenge research in areas like renewable energy technologies, smart cities and smart transportation, wearable and robotics innovations, and digital privacy and security. The building is designed to maximize the circulation and collaboration of UC San Diego faculty, students, professional research staff, and industry partners.

Franklin Antonio Hall will also serve as an important new facility for undergraduate and graduate-student learning, both inside and outside the classroom. The building will provide critical workspace for Jacobs School undergraduate student organizations that are participating in national design competitions. Teams of students will design, build and test their projects in this new collaborative environment. Teams will cycle through the space annually to best serve the growing number of nationally ranked student teams.

Franklin Antonio Hall is named after UC San Diego alumnus Franklin Antonio in recognition of his incredible $30 million gift to the UC San Diego Jacobs School of Engineering. The approximately 186,000 square foot university building is projected to be completed in early 2022.

Philanthropic gifts, like the gift from Shu and K.C. Chien and Peter Farrell, contribute to the Campaign for UC San Diego—a university-wide comprehensive fundraising effort concluding in 2022. Alongside UC San Diego’s philanthropic partners, the university is continuing its nontraditional path toward revolutionary ideas, unexpected answers, lifesaving discoveries and planet-changing impact. Visit the Campaign for UC San Diego website to learn more.

World's largest outdoor earthquake simulator undergoes major upgrade

June 9, 2021-- A major upgrade to the world’s largest outdoor earthquake simulator reached a milestone mid-April when the facility’s floor--all 300,000 lbs of it--was put back into place. When completed this fall, the simulator will have the ability to reproduce multi-dimensional earthquake motions with unprecedented accuracy to make structures and their residents safer during strong shakes.

The simulator, or shake table,  will be able to test the world’s heaviest and tallest structures to gauge how well they would withstand various types of earthquakes. The shake table will be equipped with the ability to reproduce all the six possible movements of the ground, known as six degrees of freedom. The first test following the upgrade will feature a full-scale, 10-story, cross-laminated timber building. 

The shake table's platen, or floor, is put back into place by two cranes at the Englekirk Structural Engineering Center. 

“This facility will save a large number of human lives by making the places we live and work in safer during earthquakes,” said Joel Conte, the shake table’s principal investigator and a professor of structural engineering at the University of California San Diego. Conte and colleagues lay out the details of the upgrade in a paper published in January 2021 in Frontiers in Built Environment

In the paper, researchers also detail the impact that the shake table has had on building and design codes since it opened in 2004. 

In  San Francisco, approximately 6,000 “soft-story” wood-frame buildings are being retrofitted to make them safer in strong earthquakes. Full-scale testing of retrofit systems for these soft-story wood-frame buildings was performed on the UC San Diego shake table in 2013. Professor John van de Lindt from Colorado State University, who led this project, played a key role in writing the guidelines for the retrofit of these buildings.

In 2008, a test led by Professors Robert Fleischman of the University of Arizona and Jose Restrepo of UC San Diego led to new recommendations on how precast concrete floors, known as diaphragms, should be built into parking garage structures to improve their seismic behavior.

In 2011 and 2012, during a series of landmark tests, a team tested elevators and stairs inside a full-size, six-story building. The findings led to new, better guidelines for the way these components should be connected to buildings’ structural frames so they don’t detach during a quake.

How it works
 

Principal investigator Joel Conte (right), who is also a professor of structural engineering at UC San Diego, and Koorosh Lotfizadeh, the table's operations manager, inspect the platen. 

The principle behind the table is relatively simple: various structures are built on top of the facility’s floor, or platen, which is connected to a series of horizontal and vertical actuators, or pistons, that move back and forth, simulating earthquake motions. The movements follow precise earthquake records that researchers have gathered from around the world.

The facility is transitioning from one degree of freedom--the ability to move structures backwards and forwards--to six degrees of freedom, adding the ability to move up and down, left to right, as well as pitch, roll and yaw motions. To understand these last three, think of an airplane in flight: pitch is when the nose of the airplane goes up and its tail goes down; roll is when one wing dips and the other lifts; and yaw is when the plane’s whole body slides from left to right. 

Two additional horizontal actuators were added to two existing ones in a new configuration in order to move the table horizontally forwards and backwards; left to right; and to make a yaw motion. The six existing actuators that move the table up and down were hooked up to a new, stronger hydraulic power source. 

Why do six degrees of freedom matter? 

Tests on a soft-story structure helped design guidelines to retrofit these buildings. 

Reproducing earthquake motions in six degrees of freedom is key because during a temblor, the ground might move in more than one direction. For example, during the 1994 Northridge earthquake in the Los Angeles area, bridge columns punched through bridge decks, hinting at a strong vertical ground motion component. Similarly, during the 1971 San Fernando earthquake, the buildings twisted and swayed, hinting that the ground was probably rotating.

Principal investigator Conte says he believes results of prior tests would have revealed additional ways to make buildings safer if they had been done in six degrees of freedom rather than one.

More power, better sensors

The upgrade will also add a new, state-of-the-art sensing and data collection system with a total of 768 channels to carry information coming from a wide range of sensors, including high-definition cameras, strain gauges, accelerometers and more. The software controlling the shake table also will be upgraded. 

In addition, the mechanism that powers the shake table also been expanded and connected to a hydraulic power system whose capacity has quadrupled. 
 

Students thrive in program focused on diversifying undergraduate engineering at UC San Diego

First cohort of ACES Scholars graduate after completing NSF-funded program supporting students from backgrounds traditionally underrepresented in engineering

Xavier Perez, Yoon Jung Choi and Armando Godoy-Velasquez are members of the first cohort of ACES Scholars.

June 9, 2021--Among the more than 1,400 undergraduate engineering and computer science students earning bachelor’s degrees from the University of California San Diego Jacobs School of Engineering this year, are Xavier Perez, Yoon Jung Choi, and Armando Godoy-Velasquez, who are all members of the first cohort of ACES Scholars. Students in the National Science Foundation-funded Academic Community for Engineering Success (ACES) Scholars program are highly motivated students from economically and educationally underserved backgrounds; nearly all are Pell grant eligible, many are the first in their family to attend college, and many are women or from underrepresented groups in engineering. 

Perez, Choi and Godoy-Velasquez say their participation in the ACES Scholars program was crucial in not only helping them make it to graduation, but to leave their undergraduate years with research experience, internships, and involvement in student organizations under their belts, and offers to attend graduate school and industry careers in hand.

ACES Scholars Program

UC San Diego is one of six universities in the NSF-funded Redshirt in Engineering Consortium, which aims to support low income students through an engineering degree by intervening in the crucial first two years on campus. The program was formed in 2016, and UC San Diego’s Redshirt-funded ACES Scholars program started in the fall of 2017. The Consortium takes its name from the practice of redshirting in college athletics, with the idea of providing extra support to help promising engineering students complete a bachelor’s degree.

“This NSF funding has boosted our ability to provide comprehensive support and improve undergraduate student success here at the Jacobs School," said Pamela Cosman, the UC San Diego PI for the NSF award and a professor in the Department of Electrical and Computer Engineering. Cosman served as Associate Dean for Students of the Jacobs School of Engineering from September 2013 to December 2016. "This NSF investment has allowed us to reach more students, and to engage with them on multiple levels, through programs administered through our IDEA Engineering Student Center."

Summer Engineering Institute at the Jacobs School

ACES Scholars receive a scholarship to participate in the IDEA Engineering Student Center's five-week Summer Engineering Institute before the fall quarter of their first year even begins. The goal of this summer program for incoming Jacobs School undergraduates is to strengthen students' technical preparation and study skills while also offering community building activities to help the students develop a supportive peer network and a familiarity with campus life. As part of the program, students take an academic enrichment course such as ENG 15 "Engineer your Success" as well as a foundational technical engineering course. 

"The Summer Engineering Institute is about building community, making friends, and focusing on the skills and strategies that set our students up for academic and personal success at the Jacobs School of Engineering," said Mechanical and Aerospace Engineering professor Olivia Graeve, who is wrapping up her service as Faculty Director of the IDEA Engineering Student Center this summer. "It's quite gratifying to see so many incoming Jacobs School students coming together through the Summer Engineering Institute. I wish this program had existed when I was an engineering undergraduate here at UC San Diego."

Faculty and Peer Mentorship

Another key component of the ACES program is mentorship. ACES Scholars are paired with a faculty mentor and peer mentor to help answer questions, direct the students to useful contacts, and provide another layer to the support network. ACES Scholars also attend weekly discussions with ACES Program advisor Jessica Baldis and their whole cohort during fall quarter, and monthly or quarterly meetings for the rest of the program.

ACES Scholars have access to professional and technical development workshops, including resume preparation help, which is particularly important because the internship cycle in engineering starts early in the year and many students have never gone through the steps needed to land an engineering internship. ACES Scholars also have access to many additional resources provided by the IDEA Center, including coding workshops, guest speakers, and scholarships. 

Below are snapshots of how the three students have thrived at the Jacobs School thanks in part to the ACES Program. 

"In different ways, each of these students made the most of, and benefited greatly from, early access to community building; research; and peer, staff and faculty mentorship," said UC San Diego nanoengineering professor Darren Lipiomi, the incoming Faculty Director of the IDEA Engineering Student Center. "The ACES Scholars program is a powerful example of how a little extra support and guidance to students at the start of their undergraduate careers can transform careers and lives."

Xavier Perez

Electrical engineering student Xavier Perez has been involved in so much on and off campus it’s hard to keep track of it all. He’s been active in groups ranging from the Society of Hispanic Professional Engineers to intramural soccer; was selected as one of five UC San Diego students for the UC LEADS research program; and conducted award-winning research in Professor Vikash Gilja’s Translational Neuroengineering Lab. He credits his willingness to make these connections and seek out these opportunities to the ACES Scholars program, which helped him get his footing before school even started. 

“The Summer Engineering Institute was amazing,” Perez said. “It opened all these doors as they introduced me to the world of engineering at UC San Diego. With the two classes we got the chance to take--I took ECE5 as well as ENG10--I met the professor I have done research with up until today.”

After meeting Gilja through ECE5, Perez jumped at the opportunity to do research in his lab through the STARS and UC LEADS programs. After fielding offers from Columbia University and UC Irvine, Perez chose to pursue his PhD at UC San Diego, in none other than Gilja’s lab. He’ll be earning his doctorate in electrical engineering with a focus on medical devices and systems. 

His current research has contributed to a neurally-driven speech prosthesis, based on studying the neural activities of song birds. Perez designed a custom recording studio to record the birds’ songs that is 10 times less expensive than the existing professional installation system being used.

Aside from the SEI and meetings with his faculty mentor, Perez said the friends he made through ACES were crucial to his success.

“That’s the other part -- the ACES Scholar community helped me come to UC San Diego with a  group of friends already, which was very helpful. I still talk to all my ACES friends; I even lived with two of them off campus. Another part of the ACES program I really enjoyed was the cohort meetings we had. That was impactful in the sense that it brought us all together once a month or once a quarter such that we could see everyone all together.”
 

Yoon Jung Choi

For chemical engineering student Yoon Jung Choi, the ACES Scholars program was all about making connections. For example, her peer mentor when she first arrived at UC San Diego was an active member of Engineers for a Sustainable World. This introduction to the group and a couple of its members convinced the sustainability-focused Choi to get involved as well. She was an active member of ESW all four years, and served in leadership roles. 

Similarly, her ACES faculty mentors gave her the encouragement and know-how to reach out to her professors. She has been conducting research for the last two years in Professor Ping Liu’s lab, focused on developing new battery technologies.

“I worked on multiple research projects and I also got my name on two publications from that. From this research group I got exposure to the fundamentals of lithium ion batteries, and different experimental techniques to make them and characterize them.”

Choi also appreciated the ACES Scholars regular cohort meetings and discussions. 

“That was very helpful because it provides space for people to mingle and form a community. They also allow people to help each other, clarify concepts in classes, and just hang out with your peers. I think the Jacobs School of Engineering does a great job of forming community; ACES is a great example of that.”

Choi will intern at the NASA Glenn Research Center this summer, before heading to UC Berkeley to earn her master’s degree.

Armando Godoy-Velasquez

Armando Godoy-Velasquez was introduced to structural engineering in a rather unusual way.

“I heard about structural engineering when I was watching a Netflix show called Prison Break,’ he said. “The main character is a structural engineer so I looked it up and started researching about structural engineering, and it really interested me. I liked building things and designing things, and a couple of my family members work in construction so it’s always intrigued me.”

After learning that UC San Diego is the only school in the nation with an undergraduate structural engineering degree, his mind was made up.

It’s all come full circle for Godoy-Velasquez, who accepted a full time position as a field engineer with Turner Construction, after having interned for the company for the past year.  His current project involves, you guessed it, renovating and upgrading the electrical, mechanical, and plumbing systems in a local prison. He’s also worked on commercial office renovations, and may get the opportunity to work on the new San Diego Airport terminal.

Godoy-Velasquez is more than qualified for the job. Thanks to his ACES faculty mentor, he started conducting research in the Powell Laboratory during his first year on campus.

“I worked on a project for the California Earthquake Agency, researching how homes built before the 1980s were prone to more damage during earthquakes,” Godoy-Velasquez said. “So we built walls inside the Powell Lab, then tested them against earthquakes and studied their performance. Then we rebuilt them reinforced with plywood sheeting and compared the differences in performance with reinforcement and without reinforcement.”

During his time at UC San Diego, Godoy-Velasquez played on the men’s club soccer team, was a member of the Tau Kappa Epsilon fraternity, was a member of SHPE, and also joined the Associated Schools of Construction Design-Build project team. Their project was sponsored by Clarke Construction company, which was building the new Sixth College at UC San Diego, so a lot of their homework was based off those real, current, plans. 

In addition to his ACES faculty mentor providing an early research opportunity, Godoy-Velasquez said the Summer Engineering Institute was also critical to his success. 

“SEI was a really crucial program for me. I’m still friends with everyone I met in SEI; that’s pretty much been my main study group in college. When I started off my first quarter after SEI, I felt like I wasn’t a freshman. That was thanks to SEI, all the workshops we had, I felt like I’d been there for a year already.”

He had such a positive experience that he returned the following year as a peer facilitator to help incoming students get the same jump start that he did. 

“The peer mentors during my SEI year were really cool, and I still keep in touch with them. They helped me out even after SEI. Being able to give that back to incoming students was really great.”

Super productive 3D bioprinter could help speed up drug development

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The high-throughput 3D bioprinting setup performing prints on a standard 96-well plate. Images adapted from Biofabrication

June 8, 2021 -- A 3D printer that rapidly produces large batches of custom biological tissues could help make drug development faster and less costly. Nanoengineers at the University of California San Diego developed the high-throughput bioprinting technology, which 3D prints with record speed—it can produce a 96-well array of living human tissue samples within 30 minutes. Having the ability to rapidly produce such samples could accelerate high-throughput preclinical drug screening and disease modeling, the researchers said.

The process for a pharmaceutical company to develop a new drug can take up to 15 years and cost up to $2.6 billion. It generally begins with screening tens of thousands of drug candidates in test tubes. Successful candidates then get tested in animals, and any that pass this stage move on to clinical trials. With any luck, one of these candidates will make it into the market as an FDA approved drug.

The high-throughput 3D bioprinting technology developed at UC San Diego could accelerate the first steps of this process. It would enable drug developers to rapidly build up large quantities of human tissues on which they could test and weed out drug candidates much earlier.

“With human tissues, you can get better data—real human data—on how a drug will work,” said Shaochen Chen, a professor of nanoengineering at the UC San Diego Jacobs School of Engineering. “Our technology can create these tissues with high-throughput capability, high reproducibility and high precision. This could really help the pharmaceutical industry quickly identify and focus on the most promising drugs.”

The work was published in the journal Biofabrication.

The researchers note that while their technology might not eliminate animal testing, it could minimize failures encountered during that stage.

“What we are developing here are complex 3D cell culture systems that will more closely mimic actual human tissues, and that can hopefully improve the success rate of drug development,” said Shangting You, a postdoctoral researcher in Chen’s lab and co-first author of the study.

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Examples of the geometries that the high-throughput 3D bioprinter can rapidly produce.

 

The technology rivals other 3D bioprinting methods not only in terms of resolution—it prints lifelike structures with intricate, microscopic features, such as human liver cancer tissues containing blood vessel networks—but also speed. Printing one of these tissue samples takes about 10 seconds with Chen’s technology; printing the same sample would take hours with traditional methods. Also, it has the added benefit of automatically printing samples directly in industrial well plates. This means that samples no longer have to be manually transferred one at a time from the printing platform to the well plates for screening.

“When you’re scaling this up to a 96-well plate, you’re talking about a world of difference in time savings—at least 96 hours using a traditional method plus sample transfer time, versus around 30 minutes total with our technology,” said Chen.

Reproducibility is another key feature of this work. The tissues that Chen’s technology produces are highly organized structures, so they can be easily replicated for industrial scale screening. It’s a different approach than growing organoids for drug screening, explained Chen. “With organoids, you’re mixing different types of cells and letting them to self-organize to form a 3D structure that is not well controlled and can vary from one experiment to another. Thus, they are not reproducible for the same property, structure and function. But with our 3D bioprinting approach, we can specify exactly where to print different cell types, the amounts and the micro-architecture.”

How it works

To print their tissue samples, the researchers first design 3D models of biological structures on a computer. These designs can even come from medical scans, so they can be personalized for a patient’s tissues. The computer then slices the model into 2D snapshots and transfers them to millions of microscopic-sized mirrors. Each mirror is digitally controlled to project patterns of violet light—405 nanometers in wavelength, which is safe for cells—in the form of these snapshots. The light patterns are shined onto a solution containing live cell cultures and light-sensitive polymers that solidify upon exposure to light. The structure is rapidly printed one layer at a time in a continuous fashion, creating a 3D solid polymer scaffold encapsulating live cells that will grow and become biological tissue.

The digitally controlled micromirror array is key to the printer’s high speed. Because it projects entire 2D patterns onto the substrate as it prints layer by layer, it produces 3D structures much faster than other printing methods, which scans each layer line by line using either a nozzle or laser.

“An analogy would be comparing the difference between drawing a shape using a pencil versus a stamp,” said Henry Hwang, a nanoengineering Ph.D. student in Chen’s lab who is also co-first author of the study. “With a pencil, you’d have to draw every single line until you complete the shape. But with a stamp, you mark that entire shape all at once. That’s what the digital micromirror device does in our technology. It’s orders of magnitude difference in speed.”

This recent work builds on the 3D bioprinting technology that Chen’s team invented in 2013. It started out as a platform for creating living biological tissues for regenerative medicine. Past projects include 3D printing liver tissues, blood vessel networks, heart tissues and spinal cord implants, to name a few. In recent years, Chen’s lab has expanded the use of their technology to print coral-inspired structures that marine scientists can use for studying algae growth and for aiding coral reef restoration projects.

Now, the researchers have automated the technology in order to do high-throughput tissue printing. Allegro 3D, Inc., a UC San Diego spin-off company co-founded by Chen and a nanoengineering Ph.D. alumnus from his lab, Wei Zhu, has licensed the technology and recently launched a commercial product.

Paper: “High throughput direct 3D bioprinting in multiwell plates.” Co-authors include Xuanyi Ma, Leilani Kwe, Grace Victorine, Natalie Lawrence, Xueyi Wan, Haixu Shen and Wei Zhu.

This work was supported in part by the National Institutes of Health (R01EB021857, R21AR074763, R21HD100132, R33HD090662) and the National Science Foundation (1903933, 1937653).

Class of 2021 students honored at Ring Ceremony

The recipients of the 2021 Jacobs School of Engineering Awards of Excellence

June 8, 2021-- In addition to UC San Diego’s commencement ceremonies, the Jacobs School of Engineering will honor the class of 2021 at its annual Ring Ceremony on Saturday, June 12. During the Ceremony, graduating engineering and computer science students will receive their class ring, and recite together the Jacobs School of Engineering oath, vowing to practice engineering with integrity and high ethical standards. 

Six students who have made significant contributions to their department and the Jacobs School community, will also be honored with Awards of Excellence. 

Watch the Ring Ceremony live here: https://jacobsschool.ucsd.edu/idea/programs/ring-ceremony  And learn more about these impressive graduates below. 


Bioengineering: Aoife O’Farrell

 Aoife O’Farrell was drawn to bioengineering because of the excitement of the field; there is still so much to discover about how our bodies work, and how we can treat disease. She wanted to find ways to transfer medical discoveries from the lab to patients that need them, and had the opportunity to do so as an undergraduate researcher at the UC San Diego Moores Cancer Center.

“I am most excited by the opportunities in the field of immunoengineering - designing novel therapeutics to modulate the immune system to treat cancer and autoimmune disease. I currently work at the Moores Cancer Center, studying how immune checkpoint blockade inhibitors can best be used to treat certain types of cancer, and hope to continue similar work in the future to aid patients currently unresponsive to standard of care.”

After graduating, she’s pursuing a PhD in bioengineering at the University of Pennsylvania, with funding from the NSF Graduate Research Fellowship Program. She plans to continue her immunoengineering and immo-oncology research, and hopes to eventually become a professor at a public university. 

Aside from coursework and hands-on research with Dr. Robert Saddawi-Konefka in the Gutkind Lab at Moores, O’Farrell was involved in several organizations that helped shape her time on campus: she worked as a Campus Ambassador (tour guide) for three years; and served as an officer in both Engineers without Borders and the Biomedical Engineering Society (BMES).

As the project lead for Engineers Without Borders’  Project FogCatchers, O'Farrell led a team of 15 students to develop technology to aid those without access to clear water, and authored two successful research grants to fund this work. As BMES’ Vice President External, she helped run Bioengineering Day in 2020, including a quick pivot to a virtual event, and planned the Bioengineering Career Fair in 2021. 

Her advice to students is to be willing to try things that make you uncomfortable.

“It sounds cliche, but I think the best advice I can give is to say “yes” to things,” O’Farrell said. “There were a lot of times where I felt uncomfortable about jumping into something (like leading an engineering-based project team, or writing a research grant to ask for funding) but being willing to try anyways opened so many doors that I never would have experienced otherwise. There’s a lot of support on campus at UC San Diego to help with  whatever it is you want to learn.”

 

Computer Science and Engineering: Priyal Suneja

Priyal Suneja’s favorite class was always math, until a basic programming class in high school got her curious about how the words she was typing could make the computer perform certain functions. 

“In order to learn exactly how that pipeline worked, I decided to pursue CS as a major,” Suneja said.

After graduating with the Department’s Award of Excellence, Suneja is heading to the University of Washington, Seattle, for a PhD in Systems and Networking. 

While at UC San Diego, she served as a computer science tutor, conducted research in operating systems, and was involved in the Women in Computing student organization, serving as president this year.

“I started out as a member of WIC and then proceeded to serve as a board member. I had the privilege to serve as WIC’s president over this last year.”

Her advice for students is to get to know your peers and professors.

“My journey at UC San Diego would have been starkly different had I not met the friends and mentors that I met. They made me realize the importance of enjoying what I do, and helped me believe that I could do anything that I set my mind to. I owe all the fun parts of my four years at UC San Diego to the people that I met here.”

 

Electrical and Computer Engineering: Geeling Chau

To computer engineering student Geeling Chau, electrical and computer engineering is magic. 

“Electrical engineering is the magic that has enabled the life changing technological advancements we've seen in the past few decades. Through doing robotics in high school and taking a hands-on interactive device design course, I was fortunate to see first hand the utility of studying this field and gain the confidence that I could take a step into understanding this magic.”

At UC San Diego, she’s applied this magic to brain computer interface work, through research in Professor Vikash Gilja’s Translational Neuroengineering Lab. She specifically worked on a project trying to detect emotional signals from a user playing video games. Chau also conducted research in the Voytek Lab on a data science project on parameterizing power spectral features on working memory neural signals, and with the de Sa Lab on building real-time BCIs for detecting focus levels.

In addition to research, Chau has been involved in the IEEE Honor Society, Eta Kappa Nu (HKN), serving as an officer for three years. While president of HKN, she co-founded the NeuroTech club, which has grown to span more than seven departments at UC San Diego. As a computer engineering student, she also worked as a tutor in the Computer Science and Engineering Department. 

After graduating with the ECE Award for Excellence, Chau is heading to CalTech to pursue a PhD in Computation and Neural Systems. She hopes to contribute to the field of neural engineering, and the next generation of brain computer interface technologies.

Her advice to students?

“There's a lot you can do as an engineering student at UC San Diego - be strategic in what opportunities you choose, and remember why you chose it -- this really helped me get through times that felt tough. You will be pushed to your limits, but remember that being in that uncomfortable state is how you will grow the fastest.”

 

Mechanical and Aerospace Engineering: Luca Scotzniovsky

Luca Scotzniovsky was amazed by planes as a child, and was intrigued by how an object so large and heavy could even get off the ground. This translated into a serious interest in physics in high school, and eventually to aerospace engineering. After being involved in aerospace engineering organizations and conducting research in two different labs at the Jacobs School, he found his calling.

“Upon working in the Large-Scale Design Optimization Lab, I found the path I wanted to follow once I finished my undergraduate career,” Scotzniovsky said.

He will return to UC San Diego next year to pursue a Ph.D. in mechanical and aerospace engineering, working in Professor John Hwang’s Large-Scale Design Optimization Lab, conducting fluid mechanics-based optimization and modeling for urban air mobility vehicles.

During his undergraduate years, Scotzniovsky played on the Men’s Club Soccer Team, including two years as president and captain. He was also a member of Design-Build-Fly, and conducted research in Hwang’s lab, as well in Professor David Saintillan’s lab, where he focused on data analysis of a DNA Loop Extrusion model. 

Scotzniovsky makes no bones about it--engineering is challenging. But focusing on the basics and having a support network will make the journey possible, and enjoyable.

“You can ask anyone in the Jacobs School of Engineering and they will agree that engineering is plain hard, and everyone has had a tough time with it at some point. My experiences have shown me that you really get out what you put into it and that the basic concepts are crucial to really understand the more complex subtopics within engineering. Another thing, which I wish I knew earlier, is that the experience of joining major-related organizations is not only interesting but just as important when it comes to learning and gaining relevant expertise. The one thing that shouldn't stop you from applying for a club, lab, or internship is your course-related experience, especially since the opportunity will provide the proper tools to succeed.”

 

Nanoengineering: Zoe Li

Chemical engineering student Zoe Li came to campus with a career plan in place: she wanted to be a teacher. Working as a teaching assistant in the nanoengineering and math departments, as well as working as a physics tutor in the PATHS program, helped her decide she would specialize in science and STEM education.

 After graduating with the Department of Nanoengineering’s Award of Excellence, Li, who double majored in psychology with a minor in education, will return to UC San Diego for the one-year master’s of education plus teaching credential program, before shaping the next generation of scientists and engineers as a secondary science teacher. 

“I’ve had a lot of jobs in education; I’ve taught pretty much everything from theater when I was younger, and writing, and now I’m teaching more of the STEM subjects like math, science and computer science,” she said. “So it’s been a shift for me. I thought I was going to be an English teacher when I was in high school, but now I’m like ‘Science is cool too’!”

In addition to these teaching roles, on campus Li also worked as a Resident Assistant for three years in Marshall and Revelle colleges, and is an EcoNaut for Housing, Dining and Hospitality, educating students on their latest sustainability goals and calls to action. This year, that included educating students about HDH’s new reusable to-go containers. 

Her advice for students is to find a group of friends you can commiserate with--which can include professors! 

“What got me through these years was having a good group of friends in all my classes. Every time I felt like I could just drop out of chemical engineering and just be a psychology major, my friends would say ‘No, we need to take these classes together!’ In chemical engineering we take almost all our classes with the same cohort so you get to know thm super well. That’s what got me through it, getting to know friends. My other advice is be friends with your professors. They get you through it too.”
 

Structural Engineering: Janelle Coleen Dela Cueva

In high school, Janelle Coleen Dela Cueva was involved in extracurriculars including auto mechanics and woodshop, where she got to work on cars and build birdhouses. 

“ I had so much fun working on these projects that I felt pursuing a degree in structural engineering would allow me to continue designing and creating throughout my entire life. When it comes to coursework, I found that solving problems with a practical application of theory solidified my love for engineering.”

After graduating with the Award of Excellence, Dela Cueva will return to UC San Diego to pursue a PhD in structural engineering, researching advanced aerospace composites.

As an undergraduate, Dela Cueva was involved with the Society of Civil and Structural Engineers (SCSE), serving as Social Chair and VP Internal, and also conducted research as a UC Leadership Excellence through Advanced Degrees (UC LEADS) undergraduate fellowship, having the opportunity to be first author on a paper characterizing fracture in carbon fiber composites. 

Through her roles with SCSE, Dela Cueva had a particular focus on outreach to younger students, and creating a supportive environment for all students at UC San Diego. 

“I found that plan and action go hand in hand to push forward solutions for issues affecting students of color.  In my many roles, I led a team of 5 students to create and promote professional development opportunities for students in my department. Transforming ideas into many initiatives, I created opportunities for young engineers through general body meetings, scientific writing workshops, and industry panels. Through SCSE, I started out teaching local middle schoolers about seismic engineering with our Seismic Outreach initiative and moved onto building houses in Tijuana. I experienced firsthand the integral role engineering plays in impacting the community and I wanted to continue being a part of that throughout my career.”

Her advice to students is to take advantage of every opportunity available, but not at the expense of your own well-being. 

“Over the four years that I have spent studying at UC San Diego, I learned that taking the time to rest will really let your work shine. I also believe that it’s important to not be disheartened by failures, but rather take the chance to learn from them. There will inevitably be times that you don’t succeed at first, but with great effort and support from the people around you things will always work out in the end.”

Doing this allowed her to not only survive her undergraduate years, but enjoy the process too.

“I had a lot of fun. The Jacobs School of Engineering has one the most diverse set of opportunities to grow in engineering. The hands-on experience and education that I received on advanced aerospace composite manufacturing was a rare opportunity that is seldom found at other schools. I feel genuinely lucky and grateful to be able to complete my undergraduate at this institution."

Stabilizing gassy electrolytes could make ultra-low temperature batteries safer

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Artistic rendering of a battery separator that condenses gas electrolytes into liquid at a much lower pressure. The new separator improves battery performance in the extreme cold by keeping more electrolyte, as well as lithium ions, flowing in the battery. Credit: Chen group

 

June 7, 2021 -- A new technology could dramatically improve the safety of lithium-ion batteries that operate with gas electrolytes at ultra-low temperatures. Nanoengineers at the University of California San Diego developed a separator—the part of the battery that serves as a barrier between the anode and cathode—that keeps the gas-based electrolytes in these batteries from vaporizing. This new separator could, in turn, help prevent the buildup of pressure inside the battery that leads to swelling and explosions.

“By trapping gas molecules, this separator can function as a stabilizer for volatile electrolytes,” said Zheng Chen, a professor of nanoengineering at the UC San Diego Jacobs School of Engineering who led the study.

The new separator also boosted battery performance at ultra-low temperatures. Battery cells built with the new separator operated with a high capacity of 500 milliamp-hours per gram at -40 C, whereas those built with a commercial separator exhibited almost no capacity. The battery cells still exhibited high capacity even after sitting unused for two months—a promising sign that the new separator could also prolong shelf life, the researchers said.

The team published their findings June 7 in Nature Communications.

The advance brings researchers a step closer to building lithium-ion batteries that can power vehicles in the extreme cold, such as spacecraft, satellites and deep-sea vessels.

This work builds on a previous study published in Science by the lab of UC San Diego nanoengineering professor Ying Shirley Meng, which was the first to report the development of lithium-ion batteries that perform well at temperatures as low as -60 C. What makes these batteries especially cold hardy is that they use a special type of electrolyte called a liquefied gas electrolyte, which is a gas that is liquefied by applying pressure. It is far more resistant to freezing than a conventional liquid electrolyte.

But there’s a downside. Liquefied gas electrolytes have a high tendency to go from liquid to gas. “This is the biggest safety issue with these electrolytes,” said Chen. In order to use them, a lot of pressure must be applied to condense the gas molecules and keep the electrolyte in liquid form.

To combat this issue, Chen’s lab teamed up with Meng and UC San Diego nanoengineering professor Tod Pascal to develop a way to liquefy these gassy electrolytes easily without having to apply so much pressure. The advance was made possible by combining the expertise of computational experts like Pascal with experimentalists like Chen and Meng, who are all part of the UC San Diego Materials Research Science and Engineering Center (MRSEC).

Their approach makes use of a physical phenomenon in which gas molecules spontaneously condense when trapped inside tiny, nanometer-sized spaces. This phenomenon, known as capillary condensation, enables a gas to become liquid at a much lower pressure.

The team leveraged this phenomenon to build a battery separator that would stabilize the electrolyte in their ultra-low temperature battery—a liquefied gas electrolyte made of fluoromethane gas. The researchers built the separator out of a porous, crystalline material called a metal-organic framework (MOF). What’s special about the MOF is that it is filled with tiny pores that are able to trap fluoromethane gas molecules and condense them at relatively low pressures. For example, fluoromethane typically condenses under a pressure of 118 psi at -30 C; but with the MOF, it condenses at just 11 psi at the same temperature.

“This MOF significantly reduces the pressure needed to make the electrolyte work,” said Chen. “As a result, our battery cells deliver a significant amount of capacity at low temperature and show no degradation.”

The researchers tested the MOF-based separator in lithium-ion battery cells—built with a carbon fluoride cathode and lithium metal anode—filled with fluoromethane gas electrolyte under an internal pressure of 70 psi, which is well below the pressure needed to liquefy fluoromethane. The cells retained 57% of their room temperature capacity at -40 C. By contrast, cells with a commercial separator exhibited almost no capacity with fluoromethane gas electrolyte at the same temperature and pressure.

The tiny pores of the MOF-based separator are key because they keep more electrolyte flowing in the battery, even under reduced pressure. The commercial separator, on the other hand, has large pores and cannot retain the gas electrolyte molecules under reduced pressure.

But tiny pores are not the only reason the separator works so well in these conditions. The researchers engineered the separator so that the pores form continuous paths from one end to the other. This ensures that lithium ions can still flow freely through the separator. In tests, battery cells with the new separator had 10 times higher ionic conductivity at -40 C than cells with the commercial separator.

Chen’s team is now testing the MOF-based separator on other electrolytes. “We are seeing similar effects. We can use this MOF as a stabilizer to adsorb various kinds of electrolyte molecules and improve the safety even in traditional lithium batteries, which also have volatile electrolytes.”

Paper: “Sub-Nanometer Confinement Enables Facile Condensation of Gas Electrolyte for Low-Temperature Batteries.” Co-authors include Guorui Cai*, Yijie Yin*, Dawei Xia*, Amanda A. Chen, John Holoubek, Jonathan Scharf, Yangyuchen Yang, Ki Kwan Koh, Mingqian Li, Daniel M. Davies and Matthew Mayer, UC San Diego; and Tae Hee Han, Hanyang University, Seoul, Korea.

*These authors contributed equally to this work

This work was supported by NASA’s Space Technology Research Grants Program (ECF 80NSSC18K1512), the National Science Foundation through the UC San Diego Materials Research Science and Engineering Center (MRSEC, grant DMR-2011924) and startup funds from the Jacobs School of Engineering at UC San Diego. This work was performed in part at the San Diego Nanotechnology Infrastructure (SDNI) at UC San Diego, a member of the National Nanotechnology Coordinated Infrastructure, which is supported by the National Science Foundation (grant ECCS-1542148). This research used resources of the National

Energy Research Scientific Computing Center, a DOE Office of Science User Facility supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. This work also used the Extreme Science and Engineering Discovery Environment (XSEDE), and the Comet and Expanse supercomputers at the San Diego Supercomputing Center, which is supported by National Science Foundation (grant ACI-1548562).

NASA's Perseverance inspires UC San Diego's Yonder Dynamics

Several members of the Yonder Dynamics team, with their rover Apathy

By Melissa Hernandez

June 3, 2021--NASA’s latest feat, the landing of its rover Perseverance on Mars this past February, inspired the nation and world, as people were able to watch in near real-time as the autonomous robot touched down on Mars. Perseverance has an important job: gathering soil samples and other intel on the red planet to answer the age-old question: Is there life on Mars? This accomplishment was particularly exciting for the Yonder Dynamics student robotics team at the Jacobs School of Engineering at UC San Diego, which builds a Mars rover of their own each year in a bid to compete in the international University Rover Challenge (URC) hosted by The Mars Society.

 Rovers that are accepted to the competition are tasked with tackling challenges similar to what Perseverance faces, including autonomously collecting soil samples, traversing difficult terrain to deliver a payload, repairing broken equipment on a mock lander, and autonomously navigating to a set site. Though the in-person URC competition was cancelled in 2020 and 2021 due to COVID-19, the Yonder Dynamics team and their rover, Apathy, were one of 36 teams from around the world that qualified for a pared down remote competition in June 2021, with teams competing at their own campuses. Watch footage of their rover here.

Fourth-year biophysics student and Yonder Dynamics Project Manager and Science Team Lead Luke Piszkin, said watching the Perseverance’s landing was inspirational. 

“The NASA rovers have been a huge inspiration for us at Yonder, especially the students on the science sub-team. The goal of the science team is to develop ways for our rover to look for signs of life in the environment to find out if there is life on other planets,” Piszkin said. “We’ve mimicked the Perseverance’s way of detecting life on our rover by using a high-powered spectroscopy laser to use light scattering to detect organic molecules in the soil, which would give us clues of past life."

Yonder’s 2020 rover, Apathy, was one of 36 from around the world that qualified for the University Rover Challenge competition before it was cancelled due to COVID-19 restrictions. This wasn’t the only setback the team would face in 2020. Yonder Dynamics also had to make changes to the way they functioned as a robotics team, as the pandemic forced them into a fully remote workflow, which is especially challenging for a team building a physical robot. Despite not having access to their rover or being able to work in-person, the team was able to not only complete a submission to the virtual 2021 competition, but they were even able to make improvements to Apathy, including a complete revamp of the electronics of the rover, an improvement to the code underpinning its autonomous tasks, and mechanical improvements to Apathy’s robotic arm.

Electrical team lead and second-year electrical engineering student Karl Johnson, notes the changes the electrical team has been able to make. 

“We changed a lot of the wiring on our rover from a breadboard, which is not optimal and very complicated. This year we decided to learn more about printed circuit board design, and we’ve designed and printed our own PCBs to put on the rover,” Johnson said. “Even without access to the rover we can design the boards to then replace the existing breadboards once we have physical access to the rover. It provides an opportunity for all the electronics team members to contribute to the rover.”

 The country-wide shutdown not only affected the Yonder team in terms of the way they work on the rover, but it affected their approach to planning their future as an organization on campus. Their entire recruitment process was completed online.

Fourth-year computer science student and Software co-lead Cyrus Cowley explained that the software team was able to create a simulated version of Apathy, which allowed them to work on the autonomous tasks, without accessing the actual robot.

“Because of COVID-19, we have been focusing a lot on simulation. We’ve gone through and taken our entire software stack and simulated it. It can run on any member of the software team’s computer,” Cowley said. “We can launch the simulation with just two commands. We rethought our approach to our autonomous traversal task entirely, and things have gone pretty well.”

On the mechanical side of things, Johnson highlighted that not having physical access to their hardware was a blow to the mechanical team. To deal with this, they created CAD replicas of the mechanics of the robot, using these simulated versions of their hardware to test out changes and new additions. Through this form of remote designing, the mechanics team has been able to visualize the future physical changes that will be done to the rover. 

 “We have been able to improve a lot of aspects that have been flaws in our design through our CAD models,” Johnson said. “When we get back to physically working on it, these  will help us improve the mechanics of our rover.”

“We promoted recruitment events normally as we would before and much like we would’ve done in person we had a general body meeting for potential new members,” Johnson said. “This year we had a pretty good turnout for interviews, fortunately, but with things being virtual it is difficult to keep retention with new members.”

The new robotic arm that the Yonder team designed for Apathy.

Despite the circumstances, the Yonder Team was able to submit the System Acceptance Review documents required to earn a spot in the University Rover Challenge; these consist of a five-minute video and a seven-page report detailing the ins and outs of their rover. Their hard work paid off when they found out that Apathy was one of only 36 from around the world to score highly enough to qualify for the pared down version of the competition being held remotely in 2021. Unfortunately, since each competing team needs to setup their own course on their own campus this year due to COVID considerations, the Yonder Dynamics team made the tough decision to not compete.

“Unfortunately, we will not be participating in the virtual competition this year because we do not have the time or resources to set up the courses for ourselves,” said Piszkin. “But seeing Apathy score so well was a really great feeling, knowing that all the time and effort we put in during the last year made a difference. Although we have to miss this year's virtual competition, we are looking forward to competing for the presumably in-person URC 2022.”

The team first qualified for the competition in 2017, and has since qualified in 2018 and 2020. Their latest rover, Apathy, is a nod to the team’s culture.

“We just thought it was funny,” said Piszkin. “It sort of represents the style of Yonder: we don't take ourselves too seriously.”

Light-shrinking material lets ordinary microscope see in super resolution

Square, semi-transparent material held against light.
This light-shrinking material turns a conventional light microscope into a super-resolution microscope. Credit: Junxiang Zhao

June 1, 2021 -- Electrical engineers at the University of California San Diego developed a technology that improves the resolution of an ordinary light microscope so that it can be used to directly observe finer structures and details in living cells.

The technology turns a conventional light microscope into what’s called a super-resolution microscope. It involves a specially engineered material that shortens the wavelength of light as it illuminates the sample—this shrunken light is what essentially enables the microscope to image in higher resolution.

“This material converts low resolution light to high resolution light,” said Zhaowei Liu, a professor of electrical and computer engineering at UC San Diego.

Closeup of a microscope stage.
The material mounted on the stage of an inverted microscope. Credit: Junxiang Zhao

“It’s very simple and easy to use. Just place a sample on the material, then put the whole thing under a normal microscope—no fancy modification needed.”

The work, which was published in Nature Communications, overcomes a big limitation of conventional light microscopes: low resolution. Light microscopes are useful for imaging live cells, but they cannot be used to see anything smaller. Conventional light microscopes have a resolution limit of 200 nanometers, meaning that any objects closer than this distance will not be observed as separate objects. And while there are more powerful tools out there such as electron microscopes, which have the resolution to see subcellular structures, they cannot be used to image living cells because the samples need to be placed inside a vacuum chamber.

“The major challenge is finding one technology that has very high resolution and is also safe for live cells,” said Liu.

The technology that Liu’s team developed combines both features. With it, a conventional light microscope can be used to image live subcellular structures with a resolution of up to 40 nanometers.

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Artistic rendering of the new super resolution microscopy technology. Animal cells (red) are mounted on a slide coated with the multilayer hyperbolic metamaterial. Nanoscale structured light (blue) is generated by the metamaterial and then illuminates the animal cells. Image credit: Yeon Ui Lee

 

The technology consists of a microscope slide that’s coated with a type of light-shrinking material called a hyperbolic metamaterial. It is made up of nanometers-thin alternating layers of silver and silica glass. As light passes through, its wavelengths shorten and scatter to generate a series of random high-resolution speckled patterns. When a sample is mounted on the slide, it gets illuminated in different ways by this series of speckled light patterns. This creates a series of low resolution images, which are all captured and then pieced together by a reconstruction algorithm to produce a high resolution image.

Microscope images displayed in orange against a black background.
Comparison of images taken by a light microscope without the hyperbolic metamaterial (left column) and with the hyperbolic metamaterial (right column): two close fluorescent beads (top row), quantum dots (middle row), and actin filaments in Cos-7 cells (bottom row). Adapted from Nature Communications

The researchers tested their technology with a commercial inverted microscope. They were able to image fine features, such as actin filaments, in fluorescently labeled Cos-7 cells—features that are not clearly discernible using just the microscope itself. The technology also enabled the researchers to clearly distinguish tiny fluorescent beads and quantum dots that were spaced 40 to 80 nanometers apart.

The super resolution technology has great potential for high speed operation, the researchers said.  Their goal is to incorporate high speed, super resolution and low phototoxicity in one system for live cell imaging.

Liu’s team is now expanding the technology to do high resolution imaging in three-dimensional space. This current paper shows that the technology can produce high resolution images in a two-dimensional plane. Liu’s team previously published a paper showing that this technology is also capable of imaging with ultra-high axial resolution (about 2 nanometers). They are now working on combining the two together.

Paper title: “Metamaterial assisted illumination nanoscopy via random super-resolution speckles.” Co-authors include: Yeon Ui Lee*, Junxiang Zhao*, Qian Ma*, Larousse Khosravi Khorashad, Clara Posner, Guangru Li, G. Bimananda M. Wisna, Zachary Burns and Jin Zhang, UC San Diego.

*These authors contributed equally to this work

This work was supported by the Gordon and Betty Moore Foundation and the National Institutes of Health (R35 CA197622). This work was performed in part at the San Diego Nanotechnology Infrastructure (SDNI) at UC San Diego, a member of the National Nanotechnology Coordinated Infrastructure, which is supported by the National Science Foundation (grant ECCS-1542148).

A 'self-stirring' pill enhances drug bioavailability

Self-propelling microparticles enhance the dissolution of drugs in the stomach, achieving better bioavailability without the side effects of high dosing.

May 28, 2021 -- The majority of drugs we take are administered orally, and while this route is easy for patients, safe, and effective, there are many hurdles to overcome before a drug molecule can be delivered to a desired organ or location in the body. This is not always a bad thing and your body does a fairly good job at keeping foreign molecules and parasites out. However, ensuring drugs are absorbed at levels high enough to elicit a desired therapeutic outcome can be challenging.

One of the main parameters to assess drug performance is bioavailability, which is defined as the fraction of dosed drug that reaches systemic circulation. Achieving high bioavailability depends strongly on drug solubility, stability in the stomach, and its absorption in the GI tract, among other factors. One way around this is high dosing, but this can be dangerous and result in undesired side effects. Needless to say, efficient absorption through this route is often difficult to achieve.

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Top row: Images of aspirin-loaded static (white) and microstirring pills (black). Bottom row: The tube used to perform the pill administration by oral gavage. Images courtesy of Advanced Science

From modifying the structure of drug molecules to developing sophisticated formulation systems, researchers are exploring new and innovative ways to safely enhance drug bioavailability. In a recent study published in Advanced Science, researchers at the University of California San Diego report the development of a microstirring pill platform with built-in mixing capability to enhance drug uptake and bioavailability.

“For over a decade we have been working on using micromotor-based active transport to improve the delivery of drugs,” said Joseph Wang, a professor of nanoengineering at UC San Diego and co-corresponding author of the study. “Our recent efforts have been aimed at bridging the field of microrobots with the pharmaceutical industry. Our goal has been to greatly increase the bioavailability of oral drugs by incorporating a built-in stirring capability into traditional drug tablets.”

To accomplish this, Wang, an expert in the field of microrobotics, reached out to UC San Diego nanoengineering professor Liangfang Zhang, who is himself an expert in drug design and delivery and the study's other corresponding author. They hypothesize that including chemically-powered microstirrers into a pharmaceutical pill could enhance the drug dissolution and dispersion in the stomach, leading to faster absorption and increased bioavailability.

The researchers note that their “smart pill” platform is safe. “Similar to conventional oral pills, the self-stirring pills cause no damage to the stomach,” said Wang.

Zhang and Wang’s pill contains embedded “microengines” called Janus microparticles made from magnesium microparticles that are partially coated with a thin layer of titanium dioxide. The fabrication process leaves a small opening in the particle’s structure through which microbubbles generated via an internal chemical reaction can exit and shoot the microparticle around.

“Embedding microscopic stirrers into a pill matrix offers significantly faster pill disintegration and dissolution,” explained Wang. “Since the encapsulated drugs and microstirrers are decoupled, the drug loading is not affected or compromised by the microstirrer.”

In vivo studies using animal models demonstrated that the enhanced pills greatly improved the absorption and bioavailability of aspirin, both immediately post administration and at longer time scales. “Considering [these] encouraging results, we anticipate a high likelihood of clinical translation of the microstirring pill technology,” said Wang.

“In principal, the microstirrer pill can be broadly applicable for numerous types of oral drugs. The concept thus has a very high translation potential: adding only one excipient material (the synthetic microstirrers) into the pill formulation without changing anything else.”

Source: Advanced Science News

Thin, large-area device converts infrared light into images

May 27, 2021 -- Seeing through smog and fog. Mapping out a person’s blood vessels while monitoring heart rate at the same time—without touching the person’s skin. Seeing through silicon wafers to inspect the quality and composition of electronic boards. These are just some of the capabilities of a new infrared imager developed by a team of researchers led by electrical engineers at the University of California San Diego.

The imager detects a part of the infrared spectrum called shortwave infrared light (wavelengths from 1000 to 1400 nanometers), which is right outside of the visible spectrum (400 to 700 nanometers). Shortwave infrared imaging is not to be confused with thermal imaging, which detects much longer infrared wavelengths given off by the body.

The imager works by shining shortwave infrared light on an object or area of interest, and then converting the low energy infrared light that’s reflected back to the device into shorter, higher-energy wavelengths that the human eye can see.

“It makes invisible light visible,” said Tina Ng, a professor of electrical and computer engineering at the UC San Diego Jacobs School of Engineering.

While infrared imaging technology has been around for decades, most systems are expensive, bulky and complex, often requiring a separate camera and display. They are also typically made using inorganic semiconductors, which are costly, rigid and consist of toxic elements such as arsenic and lead.

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The new infrared imager is thin and compact with a large-area display. Credit: Ning Li

The infrared imager that Ng’s team developed overcomes these issues. It combines the sensors and the display into one thin device, making it compact and simple. It is built using organic semiconductors, so it is low cost, flexible and safe to use in biomedical applications. It also provides better image resolution than some of its inorganic counterparts.

The new imager, published recently in Advanced Functional Materials, offers additional advantages. It sees more of the shortwave infrared spectrum, from 1000 to 1400 nanometers—existing similar systems often only see below 1200 nanometers. It also has one of the largest display sizes of infrared imagers to date: 2 square centimeters in area. And because the imager is fabricated using thin film processes, it is easy and inexpensive to scale up to make even larger displays.

Energizing infrared photons to visible photons

The imager is made up of multiple semiconducting layers, each hundreds of nanometers thin, stacked on top of one another. Three of these layers, each made of a different organic polymer, are the imager’s key players: a photodetector layer, an organic light-emitting diode (OLED) display layer, and an electron-blocking layer in between.

The photodetector layer absorbs shortwave infrared light (low energy photons) and then generates an electric current. This current flows to the OLED display layer, where it gets converted into a visible image (high energy photons). An intermediate layer, called the electron-blocking layer, keeps the OLED display layer from losing any current. This is what enables the device to produce a clearer image.

This process of converting low energy photons to higher energy photos is known as upconversion. What’s special here is that the upconversion process is electronic. “The advantage of this is it allows direct infrared-to-visible conversion in one thin and compact system,” said first author Ning Li, a postdoctoral researcher in Ng’s lab. “In a typical IR imaging system where upconversion is not electronic, you need a detector array to collect data, a computer to process that data, and a separate screen to display that data. This is why most existing systems are bulky and expensive.”

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The imager sees the word "EXIT" concealed by smog (left). An image of the setup without smog (right). Courtesy of Ning Li/Advanced Functional Materials 

Another special feature is that the imager is efficient at providing both optical and electronic readouts. “This makes it multifunctional,” said Li. For example, when the researchers shined infrared light on the back of a subject’s hand, the imager provided a clear picture of the subject’s blood vessels while recording the subject’s heart rate.

The researchers also used their infrared imager to see through smog and a silicon wafer. In one demonstration, they placed a photomask patterned with “EXIT” in a small chamber filled with smog. In another, they placed a photomask patterned with “UCSD” behind a silicon wafer. Infrared light penetrates through both smog and silicon, making it possible for the imager to see the letters in these demonstrations. This would be useful for applications such as helping autonomous cars see in bad weather and inspecting silicon chips for defects.

The researchers are now working on improving the imager’s efficiency.

Paper title: “Organic Upconversion Imager with Dual Electronic and Optical Readouts for Shortwave Infrared Light Detection.” Co-authors include Naresh Eedugurala and Jason D. Azoulay, University of Southern Mississippi; and Dong-Seok Leem, Samsung Electronics Co., Ltd.

This work was supported by the National Science Foundation (ECCS-1839361) and Samsung Advanced Institute of Technology. The work was performed in part at the San Diego Nanotechnology Infrastructure (SDNI) at UC San Diego, a member of the National Nanotechnology Coordinated Infrastructure, which is supported by the National Science Foundation (grant ECCS-1542148). 

Sustainable method to 3D print steel wins big at Triton Innovation Challenge

May 26, 2021--Engineers, physicians, biologists and business students at UC San Diego showcased their environmentally focused technologies at the ninth annual Triton Innovation Challenge business competition. A startup developing a 3D printing technique that can manufacture steel cheaper than existing methods, with no carbon emissions and minimal wasted scrap metal, earned the $7,000 Grand Prize.

The Triton Innovation Challenge is a business competition focused on fostering creativity and bringing to the spotlight commercially promising, environmentally focused technologies generated by students, staff and faculty from across UC San Diego. The competition is hosted by the Jacobs School of Engineering, Rady School of Management and Scripps Institution of Oceanography, and showcases startups or technologies that come from, are inspired by, or directly impact nature. The competition is funded by the William and Kathryn Scripps Family Foundation.

Jacobs School of Engineering materials science Ph.D. students Andy Zhao and Olivia Dippo are the founders of Green Steel Printing, which won Grand Prize at the Triton Innovation Challenge.

On May 21, five teams presented their ventures virtually to a panel of five judges and an audience, with $12,500 worth of prizes on the line: a Grand Prize of $7,000; Runner Up earning $4,000; and an Audience Choice award of $1,500. All the competing teams participated in a pitch-prep workshop and received other training and networking opportunities as part of the Challenge program. 

Green Steel Printing, a venture founded by Jacobs School of Engineering materials science Ph.D. students Olivia Dippo and Andy Zhao, earned the Grand Prize for their solution to reducing carbon emissions and metal waste in the steel manufacturing industry. Current steel manufacturing processes take iron oxide ore, and burn coal or natural gas to reduce the ore into iron, which is then converted to steel. This accounts for 7 percent of global carbon dioxide emissions. 

“For every ton of steel produced, 1.8 tons of carbon dioxide is emitted,” said Zhao. “There’s an inherent carbon price you have to pay to produce steel; there are fossil fuels embedded in the steel supply chain.” 

The traditional process of manufacturing steel parts is subtractive, meaning companies purchase large blocks of steel, and then remove material until they reach the desired shape and size of the part they’re building, resulting in a lot of scrap metal waste.

Green Steel aims to solve both of these problems by combining metal 3D printing, with green hydrogen technology, to generate steel with no carbon emissions, and significantly less scrap metal waste. Their patent pending 3D printing process is also projected to be cheaper than existing methods.

“Inspired by metal 3D printing and inspired by using green hydrogen as a replacement for fossil fuels, we have come up with our Green Steel printer,” said Dippo. “The two inputs are iron oxide ore—which is how the material comes out of the earth—and green hydrogen. These two things are mixed together in a reaction zone that forms iron powder. We can add additional alloying elements such as carbon in order to make steel, and at the very bottom of the machine we have our print head, where we can print the desired shapes.”

In the future, they plan to partner with aerospace or automotive companies to produce steel parts.

Dippo and Zhao are securing additional funding and lab space to further develop their steel 3D printing machine, and hope to have a prototype complete in about a year. 

The judges selected Lichen Lab as the Triton Innovation Challenge Runner Up. Lichen Lab, founded by biology alumnus Will Landry, developed and sells an alarm to help lab users keep their fume hoods closed, not only improving lab safety, but reducing energy consumption and saving money as well. When these fume hoods are left open when not in use, they waste upwards of $1,000 in energy per hood annually.

The Audience Choice award went to SynBioEnergy, founded by bioengineering PhD student Tyler Myers. SynBioEnergy uses a bioreactor to treat wastewater and desalinate water, using the components filtered out of the water as a biofuel to power the device. They plan to market the small-scale device to wineries and agricultural industries needing to meet state wastewater treatment regulations. 

Other Triton Innovation Challenge finalists include Algeon Materials, founded by Rady School of Management students, which leverages ocean derived materials like kelp to create plastic alternatives, initially in the retail space for items like hangers; and Kryos Cooling, led by a UC San Diego physician and faculty in the School of Public Health, which is developing a cooling vest for the increasing number of people living in hot climates, or who work outside in the summer. 

In addition to the Triton Innovation Challenge, Scripps Oceanography and Rady School of Management are now launching another innovation program, startBlue, on campus this fall. The startBlue accelerator program is currently accepting applications from San Diego-based innovators, engineers, and scientists who are working to solve ocean-related challenges. The deadline to apply for the fall cohort is July 2, 2021. Visit the startBlue website to learn more.

Improved maps for self-driving vehicles win Research Expo 2021

May 25, 2021-- From monitoring the structural integrity of airplane wings, to improving lithographic 3D printing processes, to creating better maps for self-driving cars, this year’s Research Expo symposium showcased the depth and breadth of work done by graduate engineering and computer science students at the University of California San Diego Jacobs School of Engineering.

Computer science Ph.D. students David Paz-Ruiz and Hengyuan Zhang took the top prize, the Lea Rudee Outstanding Poster Award, in addition to the Best Poster Award for the Department of Computer Science and Engineering. Their work focuses on improving the maps that self-driving vehicles use to navigate the world. They worked under the direction of Henrik Christensen, director of UC San Diego’s Contextual Robotics Institute and a professor in the computer science department.

David Paz-Ruiz Hengyuan Zhang

Paz-Ruiz and Zhang are tackling a problem that makes it hard for self-driving cars to scale up: most rely on high-definition (HD) maps, with resolution as small as one centimeter, which are manually labeled.

The computer scientists instead created what is known as semantic maps--2D data based on camera images overlapping with point cloud maps. The maps contain information about drivable areas, crosswalks, sidewalks, and lane markings. 

“Unlike HD maps, our maps do not include centimeter level annotations for the trajectories that the vehicle can follow,” Paz-Ruiz said. “Instead, we seek to generate these in real time.” 

“Our semantic maps are generated without human labeling effort and can be continuously updated if the environment was to change in the future,” Zhang added. 

Researchers can build a semantic map of campus in just a few hours. By contrast, an HD map would take weeks. In addition, the researchers’ maps can be used across different robots and different vehicles. 

“At UCSD we are studying how smart vehicles can be used in urban areas such the university campus or a parking lot at the airport to assist people with daily tasks” adds Prof. Christensen 

This year, the 39th annual Research Expo event was held virtually, with students submitting video presentations ahead of time, and answering questions about their work during the live event from judges, alumni and industry representatives. In all, 250 people attended the event. 

In addition to Paz-Ruiz and Zhang, one research project from each of the Jacobs School’s six departments was recognized. They are listed below, with links to their video presentations: 

Bioengineering

Sandhya Sihra

"A Heart-to-Heart Worth Having"

Computer Science and Engineering

David Paz and Hengyuan Zhang

"Towards Autonomous Vehicle Navigation without HD Maps"

Electrical and Computer Engineering

Ross Greer

“Trajectory Prediction in Autonomous Driving with a Lane Heading Auxiliary Loss”

Mechanical and Aerospace Engineering

Jessica Medrado

"Fundamentals of water-evaporation processes for renewable energy application"

NanoEngineering

David Wirth and Justin Hochberg

"A Highly Expandable Foam for Lithographic 3D Printing"

Structural Engineering

Adrielly Hokama Razzini

"Structural Health Monitoring of an Airplane’s Wings Using Gaussian Process Regressors"


 

Zexiang Xu wins Chancellor's Dissertation Medal

Undergraduate researchers earn Goldwater Scholarship

May 13, 2021-- Three UC San Diego undergraduate students with impressive academic and research credentials were selected to receive the Goldwater Scholarship, designed to foster and encourage outstanding students to pursue research careers in the fields of the natural sciences, engineering and mathematics. The Goldwater Scholarship, which provides students up to $7,500 toward tuition, books and fees, is the preeminent undergraduate award of its type in these fields.

The scholarship is named in honor of Senator Barry Goldwater, and this year was administered in partnership with the Department of Defense National Defense Education Programs.

Bioengineering students Aditi Gnanasekar and Claire Zhang, and physics student Mara Casebeer, received the scholarship in recognition of their research contributions and plans to pursue careers in research.

Aditi Gnanasekar

Aditi Gnanasekar was interested in biology, computer science and technology from an early age, but was not sure how to combine all three fields until she discovered the Bioengineering: Biotechnology major at UC San Diego.

“There is definitely a lot of computation within the biotech track, but it also has a focus on chemical engineering concepts and biomolecular techniques as well, so it’s the perfect blend of those disciplines,” said Gnanasekar.

She has applied her bioengineering know-how as an undergraduate researcher in the lab of Professor Weg Ongkeko at the UC San Diego School of Medicine, analyzing RNA sequences to extract information on immune cell expression, ultimately working toward characterizing cancers on the molecular level.

“Recently, I’ve been working on research into the intratumor microbiome, and specific microbes that are characterized in specific tumors,” Gnanasekar said. “We think it’s pretty interesting that there are microbes that are only present in certain tumors, and think they could play a critical role in determining the clinical outcome of cancer.”

After earning her bachelor’s degree, Gnanasekar plans to pursue an M.D./Ph.D., enabling her to continue this type of research while also working hands-on with patients.

In addition to earning the Goldwater Scholarship, Gnanasekar is also one of just 11 Jacobs School of Engineering students in the class of 2022 to receive the prestigious Jacobs School Scholar award, supported by school namesakes Dr. Irwin and Joan Jacobs. Jacobs Scholars are selected for demonstrated academic achievement, leadership, commitment to community, and innovative potential, and become a close community of scholars during their undergraduate years.

Outside of the classroom, Gnanasekar played intramural sports, sung in a capella groups, and volunteered with UC San Diego StRIVE, assisting adults with disabilities. But research was her main passion.

“My lab is really important—they’re like a second family to me.”

She advises students interested in research to stick with it, even when the going gets tough.

“One of the biggest lessons I’ve learned from doing scientific research and being part of a lab is being really patient,” she said. “Research is hard and you need to be persistent—you can't expect to get published right away or for your experiments to work out your way. A lot of times experiments will fail; that's totally expected and fine. And even if they do fail, that doesn't mean the research was useless or you didn't get anything out of it. That information is still very important.”

Claire Zhang 

As a young student, Claire Zhang was intrigued by both patient-facing clinical medicine and the technical innovations required to better manage disease. An early hands-on introduction to biomedical research solidified her desire to do both, and helped her see a path to do so.

Now a bioengineering student at UC San Diego, Zhang plans to earn an M.D./Ph.D. after graduation, with a goal of improving computational precision medicine by unifying molecular, cellular and physiological data as a physician scientist. She got a taste for what this can look like as an undergraduate researcher in the lab of Dr. Kevin King, from the Departments of Medicine and Bioengineering. Zhang used tools like single-cell RNA sequencing to study diseases in which the immune system becomes activated even though there is no infection, including heart attacks.

“Dr. King has been an incredible role model and crucial source of support and mentorship over the past two years, and inspired my interest in pursuing a physician-scientist career myself,” said Zhang.

She hopes to put the medical and computational skills she’s learning to use to synthesize all the various data points we can learn about an individual‒ from genetics to heart rate to sleep habits‒into actionable information.

“We’ve gotten quite good at drawing conclusions from each of these types of data on their own, but synthesizing information from all of these diverse sources to make holistic personalized predictions about one’s risk for disease, or what drugs will be most effective for someone, could truly revolutionize clinical medicine.”

Like Gnanasekar, Zhang is also a Jacobs School Scholar, one of the 11 Jacobs School of Engineering students in the class of 2022 to receive the prestigious full-ride scholarship award that is supported by school namesakes Dr. Irwin and Joan Jacobs.

In addition to the Jacobs Scholars community and her research, Zhang is involved in the International Health Collective, a student-run nonprofit that operates a monthly free clinic in Tijuana, Mexico, and is a member of the Theta Tau professional engineering fraternity.

Her advice for current and future students?

“Take advantage of opportunities to grow, even (and sometimes especially) if they make you uncomfortable. Apply to that internship that you don’t think you’ll get into, email that professor whose research sounded interesting, try out a few student orgs!”

Mara Casebeer

Mara Casebeer, a biological physics student with a minor in chemistry, has been captivated by the power of physics since high school.

“My junior year of high school I had an amazing physics teacher who showed me everything that physics could do,” she said. “We had one lab where we had to calculate the angle we needed to release a ball in order to get it to land in a basket. On the first try, based off our calculations, we got it right in the basket, nothing but net. And that blew my mind, that simple physics equations can predict what’s happening in the natural world so easily.”

As an undergraduate researcher at the Scripps Institution of Oceanography, Casebeer now harnesses the power of physics to study how radio frequency cell-to-cell communications and high-frequency electromagnetic waves interact with biological systems. She models how DNA behaves and changes in these high-frequency environments.

After graduating in 2022, Casebeer plans to earn a doctorate in biological physics, and continue conducting research in experimental and computational biophysics. At UC San Diego, Casebeer is also a supplemental physics instructor through the Teaching and Learning Commons, an experience which has affirmed her goal of becoming a professor one day, combining her love of research and teaching.

Outside of research, coursework and teaching, Casebeer is also co-president of the Warren Honor Society, plays intramural soccer and clarinet in the chamber ensemble and is part of the Undergraduate Women in Physics organization.

Her advice to current and future students?

“Don’t be afraid to put yourself out there in terms of research‒it can never hurt to talk to a professor after class about their research, or email them. It can be really intimidating but if it’s something you’re passionate about it’ll be worth it.”

Bioengineering student earns Strauss Scholarship

May 13, 2021--UC San Diego bioengineering undergraduate Zina Patel was selected to receive the $15,000 Strauss Scholarship, awarded to outstanding students developing social change or public service projects. Patel is one of only 14 students to receive the scholarship, which aims to prepare future leaders by encouraging them to undertake a high-impact venture and providing the funds to get started.

Patel’s project, called This Able, is a free online platform that connects college students with disabilities interested in joining the workforce, to mentors with disabilities already in the workforce. The goal is to not only provide mentorship, but to also provide these students with tailored expertise to bolster their job applications by assisting with resumes, interview preparation and more.

“The goal of this effort is to guide the next generation of those with disabilities and empower them by providing mentorship and networking opportunities,” said Patel. “I hope that This Able will serve as an avenue to increase employment rates for the special needs community and help cultivate a diverse and inclusive workforce, setting a precedent for the post-COVID world. My long-term and ultimate goal is to hand This Able off to web developers with disabilities who can run the platform, making it uniquely for those with disabilities by those with disabilities.”

Patel was inspired to create This Able as a volunteer at TRACE Alternative School in San Diego, where she witnessed talented job applicants being passed over for jobs they seemed to be qualified for. According to the Bureau of Labor and Statistics, only 18 percent of people with disabilities were employed in 2020. 

“As a volunteer at TRACE, I have heard countless stories from students about unsuccessful job applications,” Patel said. “ More often than not, it’s because of their disability and stigmas/stereotypes surrounding that. They are often seen as a liability rather than an asset, who will bring a fresh perspective to the table. And I wanted to do something about this because I personally knew those students who were the faces behind the rejection letters. I knew their potential that many companies didn’t recognize. That’s my motivation for This Able — to help the students I’ve worked with and others like them secure a job and secure their independence.”

Patel said her engineering courses have prepared her well for not only the technical skills required to build out a platform like This Able, but also in the critical thinking and problem solving skills necessary for undertaking a project of this scale. 

“Another key component that I really love about engineering and entrepreneurship is customer development — going out in the community to talk to the people who will be using the technologies I create and getting their perspectives to drive the development of my projects,” she said.

Patel is doing that now for This Able, working with the UC San Diego Office for Students with Disabilities to conduct user testing. She hopes to launch the platform in the fall. 

On campus, Patel has been active in the Student-run Intercommunicative and Vocational Education (StRIVE) group, which aims to assist adults with disabilities in the critical age range of 18-22 with their transition to independent living; that’s how she taught and interacted with young adults with disabilities at TRACE, and is also part of the reason she’s studying engineering. Patel entered UC San Diego as a molecular and cellular biology student, but an experience during her freshman year convinced her that bioengineering was a better fit. 

“While volunteering at an autism center in India during my freshman year, I noticed that many of the students had no access to or could not afford assistive technology,” she said. “In fact, the school itself did not have an elevator for those in wheelchairs. Back in the US, I was a volunteer for an alternative school where all students had at least one form of assistive technology. Seeing the gap between students with disabilities and assistive technology in the country my ancestors come from, I decided to pursue a career in bioengineering to better understand the creation of medical devices so that I could one day give back to those students in need.”

Personalized sweat sensor reliably monitors blood glucose without finger pricks

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A handheld device combined with a touch sweat sensor (strip at right) measures glucose in sweat, while a personalized algorithm converts that data into a blood glucose level. Image courtesy of ACS Sensors

May 10, 2021 -- Many people with diabetes endure multiple, painful finger pricks each day to measure their blood glucose. Now, engineers at the University of California San Diego have developed a device that can measure glucose in sweat with the touch of a fingertip, and then a personalized algorithm provides an accurate estimate of blood glucose levels.

The work was published recently in ACS Sensors.

According to the American Diabetes Association, more than 34 million children and adults in the U.S. have diabetes. Although self-monitoring of blood glucose is a critical part of diabetes management, the pain and inconvenience caused by finger-stick blood sampling can keep people from testing as often as they should. And while scientists have developed ways to measure glucose in sweat, levels of the sugar are much lower than in blood, and they can vary with a person’s sweat rate and skin properties. As a result, the glucose level in sweat usually doesn’t accurately reflect the value in blood.

To obtain a more reliable estimate of blood sugar from sweat, a team led by UC San Diego nanoengineering professor Joseph Wang and Juliane Sempionatto, a nanoengineering Ph.D. student in Wang’s lab, devised a system that could collect sweat from a fingertip, measure glucose and then correct for individual variability.

The researchers made a touch-based sweat glucose sensor with a polyvinyl alcohol hydrogel on top of an electrochemical sensor, which was screen-printed onto a flexible plastic strip. When volunteers placed their fingertip on the sensor surface for one minute, the hydrogel absorbed tiny amounts of sweat. Inside the sensor, glucose in the sweat underwent an enzymatic reaction that resulted in a small electrical current that was detected by a handheld device.

The researchers also measured the volunteers’ blood sugar through a standard finger prick test, and they developed a personalized algorithm that could translate each person’s sweat glucose to their blood glucose levels. In tests, the algorithm was more than 95% accurate in predicting blood glucose levels before and after meals. To calibrate the device, a person with diabetes would need a finger prick only once or twice per month. But before the sweat diagnostic can be used to manage diabetes, a large-scale study must be conducted, the researchers say.

The work was supported by the UC San Diego Center for Wearable Sensors and the National Research Foundation of Korea.

Paper title: “Touch-Based Fingertip Blood-Free Reliable Glucose Monitoring: Personalized Data Processing for Predicting Blood Glucose Concentrations.”

This system helps robots better navigate emergency rooms

May 10, 2021-- Computer scientists at the University of California San Diego have developed a more accurate navigation system that will allow robots to better negotiate busy clinical environments in general and emergency departments more specifically.  The researchers have also developed a dataset of open source videos to help train robotic navigation systems in the future. 

The team, led by Professor Laurel Riek and Ph.D. student Angelique Taylor, detail their findings in a paper for the International Conference on Robotics and Automation taking place May 30 to June 5 in Xi’an, China.  

The project stemmed from conversations with clinicians over several years. The consensus was that robots would best help physicians, nurses and staff in the emergency department by delivering supplies and materials. But this means robots have to know how to avoid situations where clinicians are busy tending to a patient in critical or serious condition. 

“To perform these tasks, robots must understand the context of complex hospital environments and the people working around them,” said Riek, who holds appointments both in computer science and emergency medicine at UC San Diego. 

Taylor and colleagues built the navigation system, the Safety Critical Deep Q-Network (SafeDQN), around an algorithm that takes into account how many people are clustered together in a space and how quickly and abruptly these people are moving. This is based on observations of clinicians’ behavior in the emergency department. When a patient’s condition worsens, a team immediately gathers around them to render aid. Clinicians’ movements are quick, alert and precise. The navigation system directs the robots to move around these clustered groups of people, staying out of the way.

“Our system was designed to deal with the worst case scenarios that can happen in the ED,” said Taylor, who is part of Riek’s Healthcare Robotics lab at the UC San Diego Department of Computer Science and Engineering. 

The team trained the algorithm on videos from YouTube, mostly coming from documentaries and reality shows, such as “Trauma: Life in the ER” and “Boston EMS.”  The set of more than 700 videos is available for other research teams to train other algorithms and robots.

Researchers tested their algorithm in a simulation environment, and compared its performance to other state-of-the-art robotic navigation systems. The SafeDQN system generated the most efficient and safest paths in all cases. 

Next steps include testing the system on a physical robot in a realistic environment. Riek and colleagues plan to partner with UC San Diego Health researchers who operate the campus’ healthcare training and simulation center. 

The algorithms could also be used outside of the emergency department, for example during search and rescue missions. 

Ph.D. student Sachiko Matsumoto and undergraduate student Wesley Xiao also contributed to the paper. 

Social Navigation for Mobile Robots in the Emergency Department

Angelique M. Taylor, Sachiko Mastumoto, Wesley Xiao and Laurel Riek, University of California San Diego
http://cseweb.ucsd.edu/~lriek/papers/taylor-icra-2021.pdf


 

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May 8, 2021

Programs help Jacobs School undergraduates make the most of research experiences

GEAR and ERSP set engineering and computer science students up for success as researchers

May 6, 2021 -- As a first year bioengineering major at UC San Diego, Kanksha Patel had heard that there were opportunities to do research in professors’ labs as an undergraduate, but she didn't know how to get started or what lab to join.

Emily Tang liked physics but, as a first year, wasn't clear what her nanoengineering major was all about or if it was really for her. 

These two University of California San Diego engineering undergraduates broadened their understanding of what it means to study engineering -- and transformed their college experiences -- by getting involved in engineering research through a Jacobs School of Engineering program called GEAR

GEAR stands for Guided Engineering Apprenticeship in Research, and it's run by the IDEA Engineering Student Center here at the UC San Diego Jacobs School of Engineering. The program is modeled off a similar program for computer science undergraduates at the Jacobs School of Engineering called the Early Research Scholars Program (ERSP)

ERSP was launched by Christine Alvarado, who is a professor in the Department of Computer Science and Engineering and also Associate Dean for Students for the Jacobs School of Engineering. 

Both GEAR and ERSP bring second-year undergraduates into university research labs where they work on team projects that contribute to the actual research mission of the lab. In both programs, in addition to mentorship from people within the research lab, students get outside guidance, mentorship and community building opportunities. Students with no previous research experience and students from traditionally underrepresented groups in engineering and computer science are particularly encouraged to apply. Applications are due in the spring, and the programs run from fall through the spring of the following academic year. 

One of the unique aspects of these programs is that the students are systematically required to discover and truly understand the big picture "Why" of the research lab they have joined. 

"Challenging undergraduate students to understand the big picture 'Why' of the research laboratory they are working in gives them the ability to understand why their contribution matters, why the intermediate step they are responsible for is important," said Ekaterina (Katya) Evdokimenko, Ph.D.

Evdokimenko teaches the two-credit ENG 20 "Introduction to Engineering Research" course which all GEAR students take during the first-quarter of their three-quarter GEAR experience. The students cover a lot of ground in ENG 20, all of it tied to making the most of their first research experience in a lab and building on the experience in order to open more opportunities and eventually a fulfilling career. 

The final ENG 20 project is a customized research proposal which the students use as a roadmap for their research project which continues for the next two quarters. 

"Each week you log something different," said Patel, the bioengineering major who was embedded in Karsten Zengler's microbiology lab which is part of the Center for Microbiome Innovation at UC San Diego. The students learn how to communicate effectively within a research lab environment, including teasing out the big-picture goals of the lab and learning how to communicate with the professor who leads the lab as well as graduate students, research scientists and other lab group members to keep them updated.

Emily Tang felt intimidated by the prospect of joining nanoengineering professor Zheng Chen's battery lab, but she found a supportive environment and developed a research project to test the efficiency of lithium ion batteries with varying electrolyte concentrations. 

"GEAR gave me more direction in what nanoengineering even is," said Tang. "I'm a nanoengineering major with an environmental studies minor. Renewable energy is something that bridges these interests."

Building on the momentum from her research experience, Tang enrolled in a graduate-level nano-scale energy course taught by world-renowned battery pioneer and nanoengineering professor Shiley Meng

GEAR and ERSP are specifically designed for undergraduates who have never worked in a professor's research lab and aim to give all students, no matter their past experiences, the tools and support necessary for success. 

"The biggest thing about the GEAR program for me is that it's introductory. I didn't know what research was like," said Tang. 

Patel learned about herself through the experience. "I wasn't sure if I would like research and the lab environment." After going through GEAR, she said, "I decided I really like research. I want to pursue research after graduation."

Both Patel and Tang were in the first cohort of GEAR students during the 2019-2020 school year. They both thrived and went on to serve as tutors for the Fall 2020 GEAR class, ENG 20, taught by Evdokimenko. 

"I think the GEAR experience helps students understand if they WANT to be an engineer or if they WANT to be in an engineering research lab," said Evdokimenko. "Students need to understand what it means to be an engineer."

"I think the GEAR experience helps students to understand what it means to be an engineer, what exactly engineers do, and what the word 'research' implies," said Evdokimenko. 

The ERSP and GEAR programs give Jacobs School of Engineering students opportunities to answer these questions. 

"This idea of engaging sophomores in research is a little bit out there," said Alvarado in a video showcasing ERSP. "People take time to warm up to the idea that sophomores can do something meaningful in a research project." 

In addition to inspiring the Jacobs-School-wide program, ERSP has also inspired similar programs at a handful of universities including UC Santa Barbara. 

ERSP was originally supported with funding from the National Science Foundation and is currently funded through the Department of Computer Science and Engineering here at UC San Diego. GEAR is supported through the Jacobs School of Engineering, and the pilot year was partially funded through support from the Office for Equity, Diversity, and Inclusion (EDI) at UC San Diego.

UC San Diego runs a wide range of programs that help undergraduate students get involved in research. There is a Student Research portal on TritonLink and also a campus-wide Undergraduate Research website.

We need to build more EV fast-charging stations, researchers say

The campus is home to one of the largest, most diverse range of electric vehicle charging stations at any university in the world.

May 5, 2021-- A team of engineers recommends expanding fast-charging stations for electric vehicles as campuses and businesses start planning for a post-pandemic world. 

The recommendation is based on a study of charging patterns for electric vehicles on the University of California San Diego campus from early January to late May of 2020, after the university moved most of its operations online. Researchers say the findings can be applied to a broader range of settings. 

“Workplace charging is a critical enabler of carbon-free transportation as the electrons consumed primarily come from solar power plants, as opposed to at-home charging, which occurs at night and relies more on fossil fuel power plants,” said Jan Kleissl, the paper’s senior author and a professor of environmental engineering at UC San Diego.

It’s the first time that a research team gathered information on workplace charging patterns for electric vehicles during the COVID-19 pandemic. As expected, charging declined dramatically once most campus operations became remote. Also as expected, charging at the campus’ medical center was less impacted as medical facilities continued most in-person operations and healthcare workers and patients kept using those charging stations. 

This reflects nationwide trends. Vehicle travel in the United States declined by about 40 percent from mid-March to mid-April 2020, according to the National Bureau of Economic Research.

But DC fast chargers that provide a full charge in about half an hour were less affected than what is known as Level 2 chargers, which provide a full charge over eight hours. Energy dispatched at Level 2 chargers on the main UC San Diego campus decreased by 84 percent. DC fast charging initially dropped by 67 percent. These stations quickly returned to near-normal usage in a short period of time, unlike Level 2 charging stations. 

“This finding reinforces ongoing efforts to deploy at least an additional 20 DCFCs primarily on the perimeter of campus in order to serve both UC San Diego commuters as well as the general public in need of recharging,” said Byron Washom, the UC San Diego director of strategic energy initiatives and one of the paper’s coauthors.

The team details their findings in the March 23 issue of the Journal of Renewable and Sustainable Energy. 

Only four out of 100 stations in the study were fast-charging. More broadly, in the United States, only a tiny fraction of charging stations are fast-charging, and most of those only serve Tesla vehicles. For example, California has about 31,800 EV charging stations. Of those, almost 3000 are Tesla supercharging stations, only available to Tesla vehicles. An additional 470 are DCFC stations managed by California-based Chargepoint. 

The study looked at 100 charging stations in 28 parking structures. Specifically, researchers found that from March 11 to May 20, 2020: 

  • Charging on the main campus dropped by 84 percent from pre-pandemic levels
  • Charging dropped by 50 percent at the parking structures at the UC San Diego medical center locations
  • Charging at DC fast charging stations initally dropped by 67 percent before going back up to near pre-pandemic levels 

Charging will likely not resume back to normal even  after the pandemic ends, researchers say. 

“Commuting patterns based on five days a week in the office are unlikely to  resume, however, as employers may allow more telecommuting even after the end of the pandemic,” Kleissl said. . 

That may be good news as the anticipated dramatic increase in EV adoption over the coming years would otherwise strain the existing charging infrastructure, he  added.

Impact of the Coronavirus Pandemic on Electric Vehicle Workplace Charging

Graham McClone, Jan Kleissl, Byron Washom, Sushil Silwal, University of California San Diego


 

The Wave Beneath Their Wings

The intricate dance between waves, wind, and gliding pelicans is worked out for the first time

April 21, 2021-- It’s a common sight: pelicans gliding along the waves, right by the shore. These birds make this kind of surfing look effortless, but actually the physics involved that give them a big boost are not simple. 

Researchers at the University of California San Diego have recently developed a theoretical model that describes how the ocean, the wind and the birds in flight interact in a recent paper in Movement Ecology.

This cartoon illustrates the equation that describes the physics of wave slope-soaring. 

UC San Diego mechanical engineering PhD student Ian Stokes and adviser Professor Drew Lucas of UC San Diego’s Department of Mechanical and Aerospace Engineering and Scripps Institution of Oceanography found that pelicans can completely offset the energy they expend in flight by exploiting wind updrafts generated by waves through what is known as wave-slope soaring. In short, by practicing this behavior, seabirds take advantage of winds generated by breaking waves to stay aloft.

The model could be used to develop better algorithms to control drones that need to fly over water for long periods of time, the researchers said. Potential uses do not stop there.

“There’s a community of biologists and ornithologists that studies the metabolic cost of flight in birds that can use this and see how their research connects to our estimates from theory. Likewise, our model generates a basic prediction for the winds generated by passing swell, which is important to physicists who study how the ocean and atmosphere interact in order to improve weather forecasting,” Stokes said. 

“This is an interesting project because it shows how the waves are actually moving the air around, making wind. If you're a savvy bird, you can optimize how you move to track waves and to take advantage of these updrafts. Since seabirds travel long distances to find food, the benefits may be significant,” Lucas said. 

Stokes and Lucas are, of course, not the first scientists to study the physics of the atmosphere that pelicans and other birds are hardwired to intuit so they can conserve energy for other activities. For centuries, humans have been inspired by the sight of birds harnessing the power and patterns of the winds for soaring flight.

That’s how it started with Stokes, who is now in the second year of his PhD at UC San Diego. As a UC Santa Barbara undergraduate, Stokes, a surfer and windsurfer in his off hours, needed a project for his senior physics class and thought of the birds that would accompany him on the waves. When he looked closer, he appreciated the connection between their flight dynamics and the study of environmental fluid dynamics, a speciality of scientists at UC San Diego. The project ultimately turned into a master’s thesis with Lucas, drawing inspiration from oceanographers at Scripps who seek to understand the interactions between the ocean and atmosphere.

Wave-slope soaring is just one of the many behaviors in seabirds that take advantage of the energy in their environment. By tapping into these predictable patterns, the birds are able to forage, travel, and find mates more effectively. 

“As we appreciate their mastery of the fluid, ever-changing ocean environment, we gain insight into the fundamental physics that shape our world,” said Lucas.

Pelicans glide above the waves, a behavior known as wave-slope soaring.
Photo: Simone Staff

 

Computer Scientists Discover Vulnerability Affecting Computers Globally

From left, clockwise: Dean Tullsen, professor, and Ph.D. student Mohammadkazen Taram at UC San Diego, teamed up with UC San Diego alumnus and UVA professor Ashish Venkat. 

April 30, 2021--Computer scientists at the University of California San Diego with researchrs at the University of Virginia School of Engineering to uncover a line of attack that breaks current defenses against Spectre, a devastating hardware flaw in computers eqwuipped with Intel and AMD processors. This means that billions of computers and other devices across the globe are just as vulnerable today as they were when Spectre was first announced.

The team reported its discovery to international chip makers in April and will present the new challenge at a worldwide computing architecture conference, the International Symposium on Computer Architecture, or ISCA, in June.

Led by Ashish Venkat, a UVA professor and UC San Diego alumni, with Dean Tullsen, a professor in the Department of Computer Science and Engineering at UC San Diego, the researchers found a new way for hackers to exploit something called a “micro-op cache,” which speeds up computing by storing simple commands and allowing the processor to fetch them quickly and early in the speculative execution process. Micro-op caches have been built into Intel computers manufactured since 2011.

The UC San Diego/UVA team reverse-engineered certain undocumented features in Intel and AMD processors. They have detailed the findings in their paper: “I See Dead µops: Leaking Secrets via Intel/AMD Micro-Op Caches.”

These two UC San Diego and UVA teams have collaborated before, including on a paper UC San Diego Ph.D. student Mohammadkazem Taram presented at the ACM International Conference on Architectural Support for Programming Languages and Operating Systems in April 2019. The paper, “Context-Sensitive Fencing: Securing Speculative Execution via Microcode Customization,” which introduced one of just a handful more targeted microcode-based defenses developed to stop Spectre in its tracks, was recently selected as a Top Pick in Hardware and Embedded Security among papers published in the six-year period between 2014 and 2019.

Read the full story from UVA about their research and its impact here.

CAREER awards for three researchers at UC San Diego Contextual Robotics Institute

May 15, 2021--Three researchers at the Contextual Robotics Institute at UC San Diego have received CAREER awards from the National Science Foundation in 2021. Their work ranges from robot mapping, to invertebrate locomotion, to autonomous robotic surgery. 

The projects’ descriptions are below.

Nikolai Atanasov

Atanasov’s project, “Active Bayesian Inference for Collaborative Robot Mapping" is an integrated research and education career development effort. It aims to design motion planning algorithms that enable robots to actively reduce uncertainty about their environment. Theoretically, this is an active Bayesian inference problem, aiming to achieve optimal control of a sensing and probabilistic estimation process. Practically, this is the goal of reproducing the curiosity that humans and animals exhibit when exploring an unknown environment on a robot system. The project considers collaboration among multiple robots to collaboratively explore and build a map of their environment. Applications include environmental monitoring, disaster response, and security and surveillance.
https://www.nsf.gov/awardsearch/showAward?AWD_ID=2045945

Nicholas Gravish

Gravish's NSF CAREER award is entitled "The exceptional biomechanics of legged locomotion in the microcosmos". When viewed in relative terms, the fastest legged animals on the planet are the smallest of invertebrates.  These remarkable feats of movement are enabled by strong limbs, robust foot attachment mechanics, and resilient exoskeleton structures and these feats are unmatched in current insect-scale robotics. In this proposal we will study the legged movement performance in small invertebrates to reveal a set of radically different locomotor constraints and opportunities, enabled by favorable geometric and dynamic scaling laws. By elucidating principles of legged movement in small animals we seek to extrapolate these concepts to the insect-scale robots built in the Gravish lab. Overall the goal of this proposal is to better understand the rules of mobility and locomotion for scientific and engineering gain. 
https://www.nsf.gov/awardsearch/showAward?AWD_ID=2048235&HistoricalAwards=false

 Michael Yip

Yip's NSF CAREER award, entitled "Contextually Informed Autonomous Robotic Surgery", will investigate how doctors use an understanding of the geometry and mechanics of human anatomy to guide their actions in surgery, and imbue surgical robots with this knowledge. By defining anatomical context for surgical robots, robots will be able to evaluate and optimize safe plans and trajectories in autonomous procedures, particularly those that involve stabilizing patients during first response. Yip's NIH Trailblazer award, entitled "Robotically controlled intraluminal instruments for flexible endoscopic intervention", investigates the design of handheld robotic catheters that may be used with flexible bronchoscopes for biopsying lung cancer. The work hypothesizes that handheld robotics may potentially offer a low-cost and more accessible solution today's expensive robot-assisted surgical diagnoses and interventional procedures and a potentially more complete diagnosis than with passive, manually controlled instruments.
https://www.nsf.gov/awardsearch/showAward?AWD_ID=2045803&HistoricalAwards=false


 

Building a voice assistant for older adults

April 28, 2021-- Computer scientists at the University of California San Diego received an Amazon Research Award to develop a voice assistant to better communicate with older adults. Their initial goal is to create a system capable of understanding and answering the medical questions of adults over age 65.

The way the elderly sometimes struggle to use voice assistants like Alexa or Siri may often be joked about, but the problem is real: data show that adults over 65—a demographic expected to double between 2010 and 2050—tend to give up on using these tools after several unsuccessful attempts at getting their questions answered. 

The problem is that existing natural language processing (NLP) systems—the artificial intelligence models used to train computers to understand spoken and written human language—are trained to understand short, formal questions. This is fine for people who grew up with computer technology and know how to phrase their questions to be understood by the device. But older adults are used to speaking to people, not machines, and often struggle to pare down longer or conversational  questions to a sentence the artificial intelligence underpinning the voice assistants can understand.   

“Our job is to bridge that gap,” said Khalil Mrini, the UC San Diego computer science PhD student who will be supported by the Amazon Research Award to work on the project. “We’re working on technology that will flip the burden: instead of having older adults change or reformulate their question, we want the AI to be able to learn and understand the older adult.”

Computer science PhD student Khalil Mrini is working to make human language technology accessible to more populations.

To accomplish this, Mrini, a graduate student in UC San Diego computer science Professor Ndapa Nakashole’s lab, is working to create an end-to-end question answering system that can: 1) shorten the user’s question down to its key components, 2) match the shortened medical question to a frequently asked question from a database of 17,000 medical questions sourced from the National Institutes of Health; and 3) select the relevant portions of the corresponding longer answer to share with the user. 

Mrini has already completed the first step—training the AI to summarize a long question into a shorter one—which he did by training the NLP model jointly on summarizing questions and a classification task called question entailment, in which the model learns to tell if by answering a short question, the initial longer question has been addressed. 

“We found that if you’re training on both summarization—which is basically feeding longer user questions and the model learns to generate the short question—and at the same time training on question entailment, that classification task, then you’re able to generate better results,” said Mrini.

This question summarization AI model can be implemented as a standalone feature into existing voice assistants like Alexa, or integrated as a first step into any question answering system, where it can shorten user questions.

The team is still working on getting the tool to match the question with one in a pool of FAQs—in this case provided by the NIH—and then have the AI select the relevant pieces of a longer answer to read back to the user. 

Computer science Professor Ndapa Nakashole’s research focuses on developing algorithms that enable computers to understand and generate human language.

"The potential impact of this work is substantial because it aims to broaden the population of people who can benefit from conversational agents, by targeting an important segment of the population, older adults,” said Nakashole.

Making AI more inclusive

Why did this segment of the population need an add-on feature after the fact? Why were their user needs not considered in initial voice assistant testing? It’s a problem Mrini says is pervasive in AI systems and training, and one that he and researchers in the VOLI team are trying to rectify.

“Among users of existing question answering systems, older adults are underrepresented,” he said. “It stems from a lack of representation among internet users, which escalates into not having a lot of data about this particular demographic and so on. You have a problem that escalates into a lack of data, and if there’s no data, you can’t train an algorithm to meet their specific needs.”

Mrini is intimately familiar with this problem. As a native of Morocco, he noticed that virtually no AI models worked for his native language, Darija, a form of Arabic spoken in Morocco. 

“I realized there were—and still are—close to no NLP models or AI models that work well for my native language. So my first ever project was making data so that AI can be trained for my native language,” Mrini said.

He’s interned at Adobe Research and the Alexa group at Amazon, working to make AI models that can predict the syntax of a sentence in an interpretable way, and summarize the important takeaways of longer articles, respectively. 

“The global goal of my research is to make human language technology more interpretable and more accessible to wider audiences,” Mrini said. “Now I’m mainly working on English-language technology, but to make it more accessible for marginalized or underrepresented audiences, so older adults in this case.”

This project is part of the larger VOLI effort, (Voice Assistant for Quality of Life and Healthcare Improvement in Aging Populations) led by natural language processing researchers including Nakashole, along with geriatric physicians, and human computer interaction researchers at UC San Diego. One of the key goals of this NIH-funded project is to develop a personalized and context-aware voice-based digital assistant to improve the quality of life and the healthcare of older adults. Ultimately, the researchers hope the device will enable older adults to remain independent and optimize interactions with healthcare and service providers.

The principal investigators on the NIH grant are:
Qualcomm Institute Research Scientist Emilia Farcas; computer science Professors Ndapa Nakashole and Nadir Weibel; geriatric physician Dr. Alison Moore; and internal medicine physician and biomedical informatician Dr. Michael Hogarth.

UC San Diego joins Bytecode alliance to build safer software foundations for the Internet

The nonprofit is focused on building an ecosystem to advance the unique advantages of WebAssembly

April 28, 2021 -- The University of California San Diego has joined The Bytecode Alliance, a nonprofit organization dedicated to creating new software foundations and building on standards such as WebAssembly and WebAssembly System Interface (WASI). UC San Diego is part of a cross-industry collaboration alongside other new members Arm, DFINITY Foundation, Embark Studios, Google and Shopify to support the alliance, which was incorporated by Fastly, Intel, Mozilla and Microsoft.  

These organizations share a vision of a WebAssembly ecosystem that fixes cracks in today’s software foundations that are holding the industry and its software supply chains back from a secure, performant, cross-platform and cross-device future. 

Computer science professor Deian Stefan says, "they will contribute tools and techniques for a more secure software ecosystem"

“WebAssembly is quickly becoming the de facto intermediate representation for building secure systems. WebAssembly takes a principled approach to security and gives us just the right building blocks to build the next generation secure and high-assurance systems,” said Deian Stefan, an assistant professor in the Department of Computer Science and Engineering at the UC San Diego Jacobs School of Engineering. “It’s a core part of the sandboxing and high-assurance security toolkits we are developing at UC San Diego.”  

UC San Diego researchers and collaborators have developed the RLBox framework that uses WebAssembly to sandbox libraries, the CT-Wasm language extension for writing secure crypto code in WebAssembly, the Swivel compiler that mitigates Spectre attacks and the VeriWasm tool that verifies the safety of native compiled WebAssembly.

 “As members of the Bytecode Alliance we hope to help shape the direction of WebAssembly and contribute tools and techniques that will amplify the alliance’s vision towards a more secure software ecosystem,” Stefan said.

The Bytecode Alliance, founded in 2019, has helped bring attention to the inherent weaknesses in predominant models for building software, which rely heavily on composing up to thousands of third-party modules without security boundaries between them. These weaknesses in the software supply chain have historically been instrumental in breaching government systems, critical infrastructure services, and a large number of companies, as well as in stealing personal information of hundreds of millions, perhaps even billions of people. 

Neural implant monitors multiple brain areas at once, provides new neuroscience insights

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SEM images of the neural implant’s microelectrode array. Images courtesy of Nature Neuroscience

April 27, 2021 -- How do different parts of the brain communicate with each other during learning and memory formation? A new study by researchers at the University of California San Diego takes a first step at answering this fundamental neuroscience question.

The study was made possible by developing a neural implant that monitors the activity of different parts of the brain at the same time, from the surface to deep structures—a first in the field. Using this new technology, the researchers show that diverse patterns of two-way communication occur between two brain regions known to play a role in learning and memory formation—the hippocampus and the cerebral cortex. The researchers also show that these different patterns of communication are tied to events called sharp-wave ripples, which occur in the hippocampus during sleep and rest.

The researchers published their findings Apr. 19 in Nature Neuroscience.

“This technology has been developed particularly for studying interactions and communications between different brain regions simultaneously,” said co-corresponding author Duygu Kuzum, a professor of electrical and computer engineering at the UC San Diego Jacobs School of Engineering. “Our neural implant is versatile; it can be applied to any area of the brain and can enable study of other cortical and subcortical brain regions, not just the hippocampus and cerebral cortex.”

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The neural implant connected to a customized printed circuit board.

“Little is known about how various brain regions work together to generate cognition and behavior,” said Takaki Komiyama, a professor of neurobiology and neurosciences at UC San Diego School of Medicine and Division of Biological Sciences, who is the study’s other co-corresponding author. “In contrast to the traditional approach of studying one brain area at a time, the new technology introduced in this study will begin to allow us to learn how the brain as a whole works to control behaviors and how the process might be compromised in neurological disorders.”

The neural implant is made up of a thin, transparent, flexible polymer strip fabricated with an array of micrometer-sized gold electrodes, onto which platinum nanoparticles have been deposited. Each electrode is connected by a micrometers-thin wire to a custom-printed circuit board. Kuzum’s lab developed the implant. They worked with Komiyama’s lab to perform brain imaging studies in transgenic mice.

Engineering a multi-use neural probe

What makes this neural implant unique is that it can be used to monitor activity in multiple brain regions at the same time. It can record electrical signals from single neurons deep inside the brain, like in the hippocampus, while imaging large areas like the cerebral cortex.

“Our probe enables us to combine these modalities in the same experiment seamlessly. This cannot be done with current technologies,” said Xin Liu, an electrical and computer engineering Ph.D. student in Kuzum’s lab. Liu is a co-first author of the study along with Chi Ren, a recent UC San Diego biological sciences Ph.D. graduate who is now a postdoctoral researcher in Komiyama’s lab, and Yichen Lu, an electrical and computer engineering Ph.D. student in Kuzum’s lab.

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The flexible neural probe allows the working distance of the microscope to be close to the surface (top), while a conventional probe with rigid parts makes the working distance (red arrows) much farther (bottom).

Several design features make multi-region monitoring possible. One is that this probe is flexible. When it is inserted deep into the brain to monitor a region like the hippocampus, the part that sticks out of the brain can be bent down and make room for a microscope to be lowered close to the surface to do imaging of the cerebral cortex at the same time. Conventional neural probes are rigid, so they get in the microscope’s way; as a result, they cannot be used to monitor deep brain structures while imaging the brain’s surface. And even though the UC San Diego team’s neural probe is soft and flexible, it is engineered to withstand buckling under pressure during insertion.

Another important feature is that this probe is transparent, so it gives the microscope a clear field of view. It also does not generate any shadows or additional noise during imaging.

Exploring fundamental neuroscience questions

The motivation for this study was getting to the root of how different cognitive processes, such as learning and memory formation, occur in the brain. Such processes involve communication between the hippocampus and cerebral cortex. But how exactly does this communication happen? And which brain region initiates this communication: the hippocampus or the cerebral cortex? These types of questions have been left unanswered because it is very difficult to study these two brain regions simultaneously, said Kuzum.

“We were interested in investigating the nature of cortical-hippocampal interactions, so we built a technology to explore this neuroscience problem,” she said.

The researchers used their probe to monitor the activity of the hippocampus and the cerebral cortex in transgenic mice. Specifically, they monitored activity before, during and after oscillations that occur in the hippocampus called sharp-wave ripples.

Their experiments revealed that communication between the hippocampus and cerebral cortex is two-sided: sometimes the cortex initiates communication, other times it’s the hippocampus. This is an important first clue for understanding inter-region communication in the brain, the researchers said.

ALT TEXT
L-R: Co-first authors Xin Liu, Chi Ren and Yichen Lu.

“The hippocampal-cortical interaction is important in memory consolidation and retrieval,” said Ren. “The two-sided communication we reported here is different from the conventional notion that the cortex passively receives the information from the hippocampus. Instead, the cortex is actively involved in encoding information into the brain and may play an instructive role during memory consolidation and retrieval.”

“We can now begin new studies to unlock how processes like learning and memory happen,” said Kuzum. “For example, when the brain acquires new information, how does the hippocampus transfer the memory to the cortex for storage, or does the cortex send a cue to transfer the memory? Our findings show that communication can be initiated by either, but to go beyond that we’d need to do behavioral studies.”

ALT TEXT
Examples of different cortical activity patterns during sharp-wave ripples.

This study also reveals that there are diverse and distinct modes of communication between the hippocampus and the cerebral cortex. The researchers found that the hippocampus communicates with at least eight different parts of the cerebral cortex every time sharp-wave ripples occur. Further, each of these eight cortical activity patterns is tied to a different population of neurons in the hippocampus.

“These findings suggest that the interactions between brain regions, not only between cortex and hippocampus, can be fundamentally diverse and flexible. Therefore, multiple brain regions can efficiently work together to generate cognition and behavior that rapidly adapt to changing environments,” said Ren.

Paper title: “Multimodal neural recordings with Neuro-FITM uncover diverse patterns of cortical-hippocampal interactions.” Co-authors of the study include Yixiu Liu, Jeong-Hoon Kim and Stefan Leutgeb, all at UC San Diego.

This research was supported by the Office of Naval Research (N000142012405 and N00014162531), the National Science Foundation (ECCS-2024776, ECCS-1752241 and ECCS-1734940), and the National Institutes of Health (R21 EY029466, R21 EB026180, DP2 EB030992, R01 NS091010A, R01 EY025349, R01 DC014690, R21 NS109722 and P30 EY022589).

From self-driving cars, to drones, to healthcare robotics: UC San Diego at ICRA 2021 preview

April 26, 2021-- A record number of papers from robotics faculty at the University of California San Diego were accepted to the 2021 International Conference on Robotics and Automation taking place in Xi’an.China, May 30 to June 5. 

From helping robots navigate the ER, to making it easier for autonomous drones to fly around obstacles, to teaching robots how to suture wounds, the papers demonstrate the breath and depths of robotics research taking place at the UC San Diego Contextual Robotics Institute. 

“It is encouraging to see the strong growth in submissions in all areas of robotics research,” said Henrik Christensen, director of the robotics institute, which includes more than 50 faculty and more than 100 graduate students. “In spite of COVID-19 and all the challenges it presents, our research work continues in full force.”

Below is a list of papers accepted to the conference, in alphabetical order by department, with summaries and links. 

Department of Computer Science and Engineering

Looking Farther in Parametric Scene Parsing with Ground and Aerial Imagery

 

Raghava Modhugu, Harish Rithish Sethuram, Manmohan Chandraker, C.V. Jawahar

In this paper, researchers demonstrate the effectiveness of using aerial imagery as an additional modality to overcome challenges in road scene understanding. We propose a novel architecture, Unified, that combines features from both aerial and ground imagery to infer scene attributes. 

http://cdn.iiit.ac.in/cdn/cvit.iiit.ac.in/images/ConferencePapers/2021/Scene_attributes___ICRA_2021.pdf

Auto-calibration Method Using Stop Signs for Urban Autonomous Driving Applications

 

Yunhai Han, Yuhan Liu, David Paz, Henrik Christensen
Researchers developed an approach to calibrate sensors for self-driving cars using recognition of traffic signs, such as stop signs. The approach is based on detection, geometry estimation, calibration, and recursive updating. Results from natural environments are presented that clearly show convergence and improved performance.

https://arxiv.org/abs/2010.07441

Social Navigation for Mobile Robots in the Emergency Department

 

Angelique Taylor, Sachiko Mastumoto, Wesley Xiao, and Laurel D. Riek
In this paper, we introduce the Safety-Critical Deep Q-Network (SafeDQN) system, a new acuity-aware navigation system for mobile robots.

http://cseweb.ucsd.edu/~lriek/papers/taylor-icra-2021.pdf

Temporal Anticipation and Adaptation Methods for Fluent Human-Robot Teaming

 

Tariq Iqbal and Laurel D. Riek
In this paper, we introduce TANDEM: Temporal Anticipa- tion and Adaptation for Machines, a series of neurobiologically- inspired algorithms that enable robots to fluently coordinate with people. TANDEM leverages a human-like understanding of external and internal temporal changes to facilitate coordination.

http://cseweb.ucsd.edu/~lriek/papers/iqbal-riek-icra-2021.pdf

 

Department of Electrical and Computer Engineering

Mesh Reconstruction from Aerial Images for Outdoor Terrain Mapping Using Joint 2D-3D Learning

 

Q. Feng, N. Atanasov
This paper develops a joint 2D-3D learning approach to reconstruct local meshes at each camera keyframe, which can be assembled into a global environment model. Each local mesh is initialized from sparse depth measurements.
https://arxiv.org/abs/2101.01844

Coding for Distributed Multi-Agent Reinforcement Learning

 

B. Wang, J. Xie, N. Atanasov
We propose a coded distributed learning framework, which speeds up the training of MARL algorithms in the presence of stragglers, while maintaining the same accuracy as the centralized approach. As an illustration, a coded distributed version of the multi-agent deep deterministic policy gradient(MADDPG) algorithm is developed and evaluated
https://arxiv.org/abs/2101.02308

Non-Monotone Energy-Aware Information Gathering for Heterogeneous Robot Teams

X. Cai, B. Schlotfeldt, K. Khosoussi, N. Atanasov, G. J. Pappas, J. How
This work proposes a distributed planning approach based on local search, and shows how to reduce its computation and communication requirements without sacrificing algorithm performance.
https://arxiv.org/abs/2101.11093

Active Bayesian Multi-class Mapping from Range and Semantic Segmentation Observations

 

A. Asgharivaskasi, N. Atanasov
This work develops a Bayesian multi-class mapping algorithm utilizing range-category measurements. We derive a closed-form efficiently computable lower bound for the Shannon mutual information between the multi-class map and the measurements.
https://arxiv.org/abs/2101.01831

Learning Barrier Functions with Memory for Robust Safe Navigation

 

K. Long, C. Qian, J. Cortes, N. Atanasov
This paper investigates safe navigation in unknown environments, using onboard range sensing to construct control barrier functions online. To represent different objects in the environment, we use the distance measurements to train neural network approximations of the signed distance functions incrementally with replay memory. This allows us to formulate a novel robust control barrier safety constraint which takes into account the error in the estimated distance fields and its gradient.
https://arxiv.org/abs/2011.01899

Generalization in reinforcement learning by soft data augmentation

 

Nicklas Hansen, Xiaolong Wang
Instead of learning policies directly from augmented data, we propose SOft Data Augmentation (SODA), a method that decouples augmentation from policy learning. Specifically, SODA imposes a soft constraint on the encoder that aims to maximize the mutual information between latent representations of augmented and non-augmented data, while the RL optimization process uses strictly non-augmented data.
https://nicklashansen.github.io/SODA/

Bimanual Regrasping for Suture Needles using Reinforcement Learning for Rapid Motion Planning

 

Z.Y. Chiu, F. Richter, E.K. Funk, R.K. Orosco, M.C. Yip
In this work, we present rapid trajectory generation for bimanual needle regrasping via reinforcement learning (RL). Demonstrations from a sampling-based motion planning algorithm is incorporated to speed up the learning. In addition, we propose the ego-centric state and action spaces for this bimanual planning problem, where the reference frames are on the end-effectors instead of some fixed frame.
https://arxiv.org/pdf/2011.04813.pdf

Real-to-Sim Registration of Deformable Soft-Tissue with Position-Based Dynamics for Surgical Robot Autonomy

 

F. Liu, Z. Li, Y. Han, J. Lu, F. Richter, M.C. Yip
In this work, we propose an online, continuous, real-to-sim registration method to bridge from 3D visual perception to position-based dynamics(PBD) modeling of tissues. The PBD method is employed to simulate soft tissue dynamics as well as rigid tool interactions for model-based control.
https://arxiv.org/abs/2011.00800

Model-Predictive Control of Blood Suction for Surgical Hemostasis using Differentiable Fluid Simulations

 

J. Huang*, F. Liu*, F. Richter, M.C. Yip
We investigate the integration of differentiable fluid dynamics to optimizing a suction tool's trajectory to clear the surgical field from blood as fast as possible. The fully differentiable fluid dynamics is integrated with a novel suction model for effective model predictive control of the tool.
https://arxiv.org/abs/2102.01436

SuPer Deep: A Surgical Perception Framework for Robotic Tissue Manipulation using Deep Learning for Feature Extraction

 

J. Lu, A. Jayakumari, F. Richter, Y. Li, M.C. Yip
In this work, we overcome the challenge by exploiting deep learning methods for surgical perception. We integrated deep neural networks, capable of efficient feature extraction, into the tissue reconstruction and instrument pose estimation processes.
https://arxiv.org/pdf/2003.03472.pdf

Data-driven Actuator Selection for Artificial Muscle-Powered Robots

 

T. Henderson, Y. Zhi, A. Liu, M.C. Yip
To accelerate the development of artificial muscle applications, researchers developed a data driven approach for robot muscle actuator selection using Support Vector Machines (SVM). This first-of-its-kind method gives users insight into which actuators fit their specific needs and actuation performance criteria, making it possible for researchers and engineers with little to no prior knowledge of artificial muscles to focus on application design. It also provides a platform to benchmark existing, new, or yet-to-be-discovered artificial muscle technologies.
https://arxiv.org/abs/2104.07168

Optimal Multi-Manipulator Arm Placement for Maximal Dexterity during Robotics Surgery

 

J. Di, M. Xu, N. Das, M.C. Yip
Engineers created a method to generate the optimal manipulator base positions for the multi-port da Vinci surgical system that minimizes self-collision and environment-collision, and maximizes the surgeon's reachability inside the patient. The metrics and optimization strategy are generalizable to other surgical robotic platforms so that patient-side manipulator positioning may be optimized and solved.
J. Di, M. Xu, N. Das, M.C. Yip
https://arxiv.org/abs/2104.06348

MPC-MPNet: Model-Predictive Motion Planning Networks for Fast, Near-Optimal Planning under Kinodynamic Constraints

 

L. Li, Y.L. Miao, A.H. Qureshi, M.C. Yip
We present a scalable, imitation learning-based, Model-Predictive Motion Planning Networks framework that quickly finds near-optimal path solutions with worst-case theoretical guarantees under kinodynamic constraints for practical underactuated systems. Our framework introduces two algorithms built on a neural generator, discriminator, and a parallelizable Model Predictive Controller (MPC).
https://arxiv.org/pdf/2101.06798.pdf

Autonomous Robotic Suction to Clear the Surgical Field for Hemostasis using Image-based Blood Flow Detection

 

F. Richter, S. Shen, F. Liu, J. Huang, E.K. Funk, R.K. Orosco, M.C. Yip
In this work, we present the first, automated solution for hemostasis through development of a novel probabilistic blood flow detection algorithm and a trajectory generation technique that guides autonomous suction tools towards pooling blood. The blood flow detection algorithm is tested in both simulated scenes and in a real-life trauma scenario involving a hemorrhage that occurred during thyroidectomy.
https://arxiv.org/abs/2010.08441

Department of Mechanical and Aerospace Engineering

Scalable Learning of Safety Guarantees for Autonomous Systems using Hamilton-Jacobi Reachability

 

Sylvia Herbert, Jason J. Choi, Suvansh Qazi, Marsalis Gibson, Koushil Sreenath, Claire J. Tomlin
In this paper we synthesize several techniques to speed up computation: decomposition, warm-starting, and adaptive grids. Using this new framework we can update safe sets by one or more orders of magnitude faster than prior work, making this technique practical for many realistic systems.
https://arxiv.org/abs/2101.05916

Planning under non-rational perception of uncertain spatial costs

 

Aamodh Suresh and Sonia Martinez
This work investigates the design of risk- perception-aware motion-planning strategies that incorporate non-rational perception of risks associated with uncertain spatial costs. Our proposed method employs the Cumulative Prospect Theory (CPT) to generate a perceived risk map over a given environment.
https://arxiv.org/pdf/1904.02851.pdf


 

Three from UC San Diego Elected to American Academy of Arts and Sciences

From left: Ananda Goldrath, Eileen Myles and Stefan Savage

April 23, 2021, San Diego, CA -- Three members of the University of California San Diego community, including two professors and one professor emeritus, have been elected to the American Academy of Arts and Sciences—one of the oldest and most esteemed honorary societies in the nation.

Ananda Goldrath, Eileen Myles and Stefan Savage are among the Academy’s 2021 class of 252 members. They join fellow 2021 classmates who are artists, scholars, scientists and leaders in the public, non-profit and private sectors, including: civil rights lawyer and scholar Kimberlé Crenshaw; computer scientist Fei-Fei Li; composer, songwriter, and performer Robbie Robertson; and media entrepreneur and philanthropist Oprah Winfrey. 

The American Academy of Arts and Sciences has honored exceptionally accomplished individuals and engaged them in advancing the public good for more than 240 years. Professor Walter Munk was the first UC San Diego faculty member elected to the Academy. Since then, more than 80 faculty from disciplines that span the entire campus have received this prestigious honor. 

"This year, our faculty are being recognized for three vastly different fields of study: immunology, literature, and cybersecurity,” said UC San Diego Chancellor Pradeep K. Khosla. “Having the oldest and most distinguished American national academy honor the career accomplishments of these prestigious faculty both honors their individual successes and spotlights the breadth of expertise and influence of our Triton faculty. UC San Diego’s well-established prowess in science, technology and art offers a truly well-rounded experience for our students, our researchers and our collaborative faculty.”

In the statement announcing this year's new Academy members, David Oxtoby, President of the American Academy said, “The past year has been replete with evidence of how things can get worse; this is an opportunity to illuminate the importance of art, ideas, knowledge, and leadership that can make a better world.”

Following is more information about each of UC San Diego’s newest Academy members:

Ananda Goldrath
Goldrath is a Tata Chancellor’s Professor in the Division of Biological Sciences and former chair of the Molecular Biology Section. Her work as an immunologist has contributed to the understanding of transcriptional networks that govern the formation and maintenance of long-lived protective immunity. Goldrath’s research explores the mechanistic basis underlying memory T cell differentiation as a strategy to program the immune system to meet pathogens or malignancies in the tissues where they first pose a threat. This information has made it possible to beneficially manipulate the immune system to eliminate infection and malignancies. Goldrath is a Pew Scholar and Leukemia and Lymphoma Society Fellow and a member of the Immunological Genome Project, the Leadership Council of the Program in Immunology and Scientific Advisory Committee of the San Diego Center for Precision Immunotherapy at UC San Diego.

Eileen Myles
Myles, professor emeritus of fiction writing in the Department of Literature, began their career in New York City in 1974 as a poet, novelist, public talker and art journalist. While at UC San Diego from 2002 to 2007, they taught courses in poetry writing, short fiction, writing between genres and the libretto, among others. Also during this time, they wrote the libretto for the opera “Hell,” composed by Michael Webster with productions in 2004 and 2006. Myles is the recipient of a Guggenheim Fellowship, a Creative Capital/Andy Warhol Foundation Arts Writers grant, four Lambda Literary Awards, the Shelley Award from the Poetry Society of America, and a 2014 artist grant from the Foundation for Contemporary Arts. In 2016 they received a Creative Capital grant and the Clark Prize for Excellence in Art Writing and, in 2019, a poetry award from the American Academy of Arts and Letters. The Publishing Triangle honored Myles with the Bill Whitehead Award for Lifetime Achievement in 2020, recognizing writers in the LGBT community. Their 22 books include “For Now” (2020), “evolution” (2018), “Afterglow” (2017), “I Must Be Living Twice/new & selected poems” (2015) and “Chelsea Girls” (1994).

Stefan Savage
Savage is a cybersecurity researcher who holds an expansive view of the field. He and colleagues bring together computer science and the social sciences in their work by taking into account economics, policy and regulations, not just technology. His team has been instrumental in pointing out security vulnerabilities in cars, which have been addressed by the automotive industry’s regulatory bodies and manufacturers. They have tracked the financial transactions responsible for funding email spam campaigns and botnets around the world. The data has been used by government agencies and credit card companies to block these transactions. Savage and colleagues also have designed ways to measure and pinpoint the source of attacks that cripple the internet and large websites, known as distributed denial of service attacks. Savage has received numerous awards for his work, including a McArthur fellowship in 2017, the ACM Prize in Computing in 2015, and three test of time awards from leading academic computer security organizations. He holds the Irwin and Joan Jacobs Chair at the Jacobs School of Engineering and is a professor in the UC San Diego Department of Computer Science and Engineering.

In addition to these three faculty members, alumna Angela Davis is also part of this year’s class of fellows. A well known activist who is now on faculty at the University of California Santa Cruz, Davis earned a master’s degree from the Department of Philosophy at UC San Diego in 1969. She worked closely with philosopher Herbert Marcuse. Her likeness is now part of the Price Center’s Black Legacy Mural, and she is also portrayed on the walls of the Che Cafe. 

The American Academy of Arts & Sciences was founded in 1780 by John Adams, John Hancock and others who believed the new republic should honor exceptionally accomplished individuals and engage them in advancing the public good. The 2021 members join the company of those elected before them, including Benjamin Franklin and Alexander Hamilton in the eighteenth century; Ralph Waldo Emerson and Maria Mitchell in the nineteenth; Robert Frost, Martha Graham, Margaret Mead, Milton Friedman and Martin Luther King, Jr. in the twentieth; and more recently Joan C. Baez, Judy Woodruff, John Lithgow, and Bryan Stevenson. International Honorary Members include Charles Darwin, Albert Einstein, Winston Churchill, Laurence Olivier, Mary Leakey, John Maynard Keynes, Akira Kurosawa and Nelson Mandela.

Combining nanomaterials in 3D to build next-generation imaging devices

Man wearing a labcoat.
Oscar Vazquez-Mena. Photos by Erik Jepsen/University Communications

April 12, 2021 -- For years, two-dimensional nanomaterials just one or a few atoms thick have been all the rage in the world of materials science. Take graphene, for example. This one-layer sheet of carbon atoms yields a material that is hundreds of times stronger than steel, highly conductive and super-flexible.

Oscar Vazquez-Mena, a professor of nanoengineering at the UC San Diego Jacobs School of Engineering, is taking these types of materials to the next dimension. His research focuses on integrating different nanoscale materials together in 3D to create an entirely new generation of devices for environmental monitoring, energy harvesting and biomedical applications.

“It opens up so many more possibilities for what we could do with our nanoengineering tools,” said Vazquez-Mena, who recently received a five-year, $500,000 CAREER Award through the National Science Foundation for one such project.

The project involves combining graphene with semiconducting nanoparticles called quantum dots to create devices that can “see” a broad range of different wavelengths of light, such as infrared and ultraviolet, that are invisible to the human eye. These devices, called multi-spectrum photodetectors, could enable cameras to take pictures of infections, poisonous gases and harmful radiation; check for food quality or contamination; and monitor air and water quality. They could also aid vision at night and when it’s foggy.

Closeup of an electronic chip.
Chips integrating graphene and quantum dots.

Vazquez-Mena’s approach would make these devices ultra-thin. “Because we are working with nanomaterials, we can in principle engineer very thin photodetectors on the order of one micrometer, which could easily be integrated into smartphones and other mobile devices for convenient deployment outside of the lab,” he said.

An aspect of this project that is near and dear to Vazquez-Mena is mentoring and training the next generation of nanoengineers. He will be developing hands-on nanoengineering fabrication workshops for pre-college students, particularly underrepresented students at schools that may have limited resources and laboratory equipment.

This builds on Vazquez-Mena’s ongoing work promoting STEM education and research among migrant communities and children of deported parents, as well as UC San Diego transfer students. In recognition of his outreach work, Vazquez-Mena has been named an Emerging Scholar in 2020 by Diverse: Issues in Higher Education magazine. He was also recently named an Outstanding Engineering Educator by San Diego County Engineering Council.

“In my career, I had plenty of support and opportunities, so for me it is very important to provide these two things to students who come from underserved communities and have a strong desire to make discoveries and contribute to our society through science and technology,” said Vazquez-Mena.

At the start of 2020, Vazquez-Mena started a pilot program to help new Latinx/Chicanx transfer students at UC San Diego get involved in research activities. The program, called Research Paths for LatinX Students, is supported by the university’s Latinx/Chicanx Academic Excellence Initiative. Students attend Saturday sessions where they learn about the importance of research, different research opportunities on campus and strategies to join a lab. During the pandemic, the program shifted to offering virtual workshops on Coding, Arduino controllers and Machine Learning for students to continue learning at home.

Imaging the brain with ultrasound

In another project, Vazquez-Mena is stacking nanostructures to build 3D arrays that can allow ultrasound to go through the skull and do non-invasive imaging and stimulation of the human brain. Such technology would be useful for treating brain disease and trauma without having to open the skull or insert wires and implants in the brain. It could also allow physicians to rapidly diagnose brain trauma in patients without having to perform costly MRI scans.

Getting ultrasound through the skull and into the brain is no easy task. The human skull is relatively thick and dense, so it either reflects or absorbs ultrasound waves before they can make it to the brain.

To get past this barrier, Vazquez-Mena is engineering a special kind of material—called a metamaterial—composed of nanostructures that can cancel the reflections created by the skull and essentially redirect ultrasound waves to go through it. The metamaterial is made of nanometers-thin membranes of silicon nitride and microscale acoustic cavities. Both components are arranged together in a 3D array that can enable the material to manipulate sound waves in ways that cannot be done with conventional materials.

“This is another example of building 3D constructions based on nanomaterials that achieve new and exciting properties,” said Vazquez-Mena.

This project is funded by a prestigious Director’s Fellowship awarded to Vazquez-Mena by the Defense Advanced Research Projects Agency (DARPA). The multidisciplinary work involves collaboration with UC San Diego mechanical and aerospace engineering professors James Friend and Nicholas Boechler, who are experts in ultrasound acoustics, and with UC San Diego rheumatology professor Monica Guma.

In 2018, Vazquez-Mena received a DARPA Young Faculty award (YFA) to pursue this project. The DARPA YFA recognizes rising stars in junior research positions who are pursuing basic science research and provides $500,000 of funding for a two-year period. As one of the program’s top-performing awardees, Vazquez-Mena was selected for the highly competitive DARPA Director’s Fellowship, which provides up to $500,000 of additional funding and support.

UC San Diego researchers developing COVID-19 vaccine technology -- no refrigeration or second dose needed

Understudied Mutations Have Big Impact on Gene Expression

Variable number tandem repeats modulate genes associated with Alzheimer's disease, obesity, cancer and other conditions

Vineet Bafna, a professor in the UC San Diego Department of Computer Science and Engineering and senior author on the paper

April 9, 2021-- An international team of researchers led by computer scientists at the University of California San Diego have identified 163 variable number tandem repeats (VNTRs) that actively regulate gene expression. In a paper published in Nature Communications this week, the researchers provide new insights into this understudied mechanism, how it may drive disease and other traits and could ultimately impact patient care.

VNTRs are common genomic variations that appear as repeated DNA sequences longer than six base pairs.

“VNTRs have been difficult to identify through sequencing information, particularly short reads,” said Vineet Bafna, a professor in the UC San Diego Department of Computer Science and Engineering and senior author on the paper. “We developed a fast computational method to identify these variations, which gave us a new lens to observe their potential impact on gene expression and disease.”

While VNTRs are one of the most common genetic variations, detecting them has been both challenging and expensive. As a result, genome-wide association studies have mostly ignored VNTRs, excluding a potentially rich repository of disease-causing mutations.

Using the new method they developed, researchers found more than 10,000 VNTRs in a group of 652 people. Of those, 163 changed the way genes were expressed in 46 different tissue types. Nearly half had a particularly strong impact on Alzheimer’s disease, familial cancers, diabetes and other conditions.

“We looked closely at these 163 VNTRs to understand their impact,” said UC San Diego computer science Ph.D. student Mehrdad Bakhtiari. “One was affecting expression levels of a gene called AS3MT, which has been implicated in schizophrenia. The tandem repeat controls gene expression and the expression affects the disease.”

A new neural-network based method

The new computational method,  called adVNTR-NN, rapidly finds VNTRs  in short read genomic sequencing data. Short read technology breaks up DNA samples into relatively small pieces and uses sophisticated algorithms to piece together complete sequences. Popularized by Illumina, short reads are the most common, and least expensive, form of next-generation sequencing.

“Our computational method runs quite fast and it works in the most cost-effective sequencing technologies,” said Bakhtiari, the first author on the paper. “So, it should be easy to scale and easy to use for people outside of research settings, for example, hospitals.”

Next steps

The authors have high confidence in these results, as 91% of the initial findings were validated in two other cohorts. However, there is still more work to do. The researchers want to better quantify the impact VNTRs have on specific genes, as well as determining whether there is indeed a causal link between certain VNTRs and the diseases they have been linked to.

“We’re learning more about the importance of complex and repetitive regions of the genome and the roles they play in human traits,” said Melissa Gymrek, assistant professor in the Computer Science and Engineering department and the School of Medicine and coauthor on the paper. “VNTRs  have been almost impossible to look at in most available sequencing datasets on a large scale.”

The team also wants to study specific conditions, such as autism spectrum disorder, to better understand patients’ VNTR profiles and how those influence their conditions.

“These findings open a whole new window to study the role VNTRs play in gene expression,” said Bafna. “Given that these sequences are physically larger than single nucleotide polymorphisms and are also quite prevalent, these efforts could eventually have a major impact on patient care.”

In addition to Bafna, Bakhtiari, and Gymrek, paper coauthors include Jonghun Park of the Computer Science and Engineering Department, Yuan-Chun Ding and Susan L. Neuhausen of the Beckman Research Institute of City of Hope, Sharona Shleizer-Burko of UC San Diego Department of Medicine, and Bjarni V. Halldórsson and Kári Stefánssonde of CODE Genetics, Reykjavik, Iceland.

 

 

testing

April 9, 2021

Diversifying the ranks of engineering faculty

UC San Diego Jacobs School of Engineering joins program to diversify engineering faculty

The University of California San Diego Jacobs School of Engineering has partnered with University of Michigan to strengthen a program that addresses the lack of diversity in the engineering academia. 

The program, NextProf Pathfinder, is a two-day program developed at Michigan Engineering and aimed at first and second-year PhD students, as well as students in masters programs, in an effort to keep them pursuing careers in academia.

It’s the newest program in a larger effort that began in 2012 as NextProf. To date, more than 144 women and people from underrepresented groups who attended its workshops have achieved tenure-track faculty positions. And UC San Diego Jacobs School of Engineering is the third institution to partner with Michigan Engineering on a NextProf program.

At workshops, participants hear from top faculty and deans from around the U.S. to gain a better understanding of academic life and how to achieve a position in it. They learn best practices in applying and networking for positions, how to set up a lab and what kind of work/life balance they can expect, for example. NextProf Pathfinder, designed for earlier-stage students, teaches participants what types of experiences they should seek out to best position themselves. The NextProf workshops for later-stage students and postdocs focus more on how to leverage those experiences and communicate about them.

The two schools will partner on the NextProf Pathfinder program going forward, with the institutions swapping hosting duties each year. This year, the program will be in Ann Arbor, from October 17-19. The conference will be in San Diego in 2022.

“One of the reasons I’m particularly excited about this partnership is that, given UCSD’s location and the demographics of that region of the country, it will make our workshops more accessible to Latinx graduate students,” said Lola Eniola-Adefoso, a U-M professor of chemical engineering and a University Diversity and Social Transformation Professor. “Latinx faculty members are dramatically underrepresented in academia and this is an important step toward changing that.”

For UC San Diego Jacobs School of Engineering, NextProf Pathfinder represents an important move forward in its broader efforts to create learning and research environments where all engineering and computer science students, staff and faculty thrive.
 

Karen L. Christman, Associate Dean for Faculty, Professor of Bioengineering, UC San Diego Jacobs School of Engineering 

“NextProf Pathfinder is one concrete step in a larger effort to create a broader academic culture where all students—and in particular students who are traditionally underrepresented in engineering—are empowered with the knowledge the networks, the role models and the momentum needed to establish fulfilling and meaningful careers,” said Karen Christman, associate dean for faculty and professor of bioengineering at UC San Diego Jacobs School of Engineering. “Critical to this project is ensuring that students who are traditionally underrepresented in engineering have all that they need to make the jump from graduate student to engineering professor and head of an independent lab. That’s what NextProf Pathfinder is designed to do.”

Engineering is a field which, despite efforts going back decades, remains stubbornly white and male. The number of female faculty members is trending upward in recent years, but only slowly. And the percentage of people from underrepresented groups in faculty positions has been flat for roughly two decades.

Such a monolithic engineering culture has repercussions for society-at-large, as we’ve seen illustrated recently by facial recognition technologies that aren’t accurate for Black faces, for example. Increasing the diversity of academic engineering researchers and educators is seen as an essential step in advancing technologies that don’t exacerbate inequities.

But the current lack of diversity in professor roles can make non-white and non-male candidates feel unwelcome or devalued, Eniola-Adefoso says. Each one that opts for something outside academia, in favor of a career where they feel more at home, can perpetuate the cycle.

NextProf Pathfinder is the newest part of the larger NextProf effort co-founded in 2012 by Alec D. Gallimore, the Robert J. Vlasic Dean of Engineering, the Richard F. and Eleanor A. Towner Professor, an Arthur F. Thurnau Professor, and a professor of aerospace engineering.

NextProf began as a program for third- to fifth-year PhD students and recent doctoral graduates from anywhere in the nation. Since that time it has expanded to three workshops:

  • NextProf Engineering, founded in 2015, is held every spring at U-M and is open to all engineering students and postdocs at U-M.
  • NextProf Pathfinder, founded in 2018, is open to first- and second-year PhD students and master’s students considering a PhD. Before a COVID-19 hiatus in 2020, it had welcomed 73 participants from 32 institutions in its first two years.
  • NextProf Nexus, an expansion of the original NextProf workshop, began in 2018 when the University of California, Berkeley joined as a partner and sponsoring institution. Georgia Tech joined the following year. Now, the three partner universities take turns hosting it.


Katherine Adler is a fifth-year PhD candidate in civil and environmental engineering at Cornell University. She was once a participant in both the NextProf Nexus and Pathfinder programs.

“The Nexus program provided more concrete tools to which I refer as I refine my faculty application materials,” Adler said. “After attending these workshops, I can better visualize my path to becoming a successful research faculty member and better understand the high expectations for faculty candidates.”

Testing

April 3, 2021

Test

UC San Diego Engineering Ranks #9 in U.S. News and World Report Best Engineering Schools Rankings

March 30, 2021 - For the second year in a row, the University of California San Diego Jacobs School of Engineering has ranked #9 in the nation in the influential U.S. News & World Report Rankings of Best Engineering Schools. 

This #9 ranking is up from #11 two years ago, #12 three years ago, #13 four years ago, and #17 five years ago.  

“The Jacobs School of Engineering has earned its ninth place among the nation’s most innovative, distinctive and prestigious engineering schools,” said UC San Diego Chancellor Pradeep K. Khosla. “UC San Diego’s engineers and computer scientists regularly collaborate with students, faculty and staff across our $1.4 billion dollar research enterprise. This unique cooperative, cross-discipline connectivity sparks discoveries and drives innovations that garner national and global recognition."

The Jacobs School of Engineering at UC San Diego leverages engineering and computer science for the public good through education, research and transfer of innovation to society. The #9 ranking brings welcome attention to the Jacobs School's work to create and strengthen interrelated education, research and innovation ecosystems.

“Ranking ninth in the nation is a tribute to the hard work, grit and excellence of our students, staff, faculty, industry partners, collaborators and friends," said Albert P. Pisano, Dean of the UC San Diego Jacobs School of Engineering. "I look at rankings as recognition rather than definition. It's wonderful to be recognized for some of the ways we are strengthening and growing as a school and as a community."

Research relevance

The UC San Diego Jacobs School of Engineering has launched 14 Agile Research Centers and Institutes since 2014. This effort has driven deeper collaborations within the Jacobs School and across the UC San Diego campus. It has also driven deeper interactions between Jacobs School research teams and collaborators in industry and government labs. The goal is to tackle fundamental, relevant challenges that no individual research lab or company is likely to solve alone. This process of taking on difficult, interdisciplinary challenges involving academia, industry and government provides engaging training and learning environments for Jacobs School of Engineering students. These students go on to graduate as an empowered innovation workforce. 

The most recent institute is a cross-campus collaboration, co-launched with the UC San Diego Division of Physical Sciences, called the UC San Diego Institute for Materials Discovery and Design. Researchers deeply involved in this Institute recently won a prestigious National Science Foundation (NSF) Materials Research Science and Engineering Center (MRSEC)

A few recent research results that have emerged from cross-disciplinary research projects tied to agile research centers and institutes include: a skin patch bringing us closer to wearable, all-in-one health monitor; a robot that doesn't need electronics; and a nano-scale particle for better COVID-19 tests.

San Diego regional innovation ecosystems

The fact that the UC San Diego Jacobs School of Engineering has established itself as a top-nine engineering school adds to San Diego's momentum as a world-class, well-rounded hub for technology and innovation. 

In addition to its #9 ranking, the Jacobs School of Engineering at UC San Diego is the largest engineering school on the U.S. West Coast, according to the latest enrollment data from ASEE. In Fall 2020, the Jacobs School enrolled 9,174 students. The Jacobs School has awarded nearly 15,000 degrees over the last 6 years. 

"The UC San Diego Jacobs School of Engineering is educating the innovation workforce the nation needs," said Pisano. "And more than ever, as a region, we are employing this innovation workforce here in San Diego."

Creating more and better environments for training this innovation workforce is one of the motivations behind Franklin Antonio Hall, which is UC San Diego's new engineering building. It is on schedule to open in Spring 2022.

Students from all across campus will take classes in Franklin Antonio Hall, which will serve as a national model for how to build innovation ecosystems with physical roots and virtual collaboration infrastructure with national and international impact. This is how engineering for the public good will get done in the future.

Bioengineering climbs to #3

In the same US News & World Report Rankings, the Department of Bioengineering at the UC San Diego Jacobs School of Engineering ranked #3 in the nation. This is up from #4 last year in the same ranking. Bioengineering at UC San Diego has ranked among the top four programs in the nation every year for more than a decade.

"The UC San Diego Department of Bioengineering has been inventing and re-inventing the field of bioengineering for more than 50 years, and it continues to take the field in new and exciting directions. I'm thrilled that we have moved up to #3 in the nation," said UC San Diego professor and chair of bioengineering Kun Zhang. "Some of the most influential work that helped launch the field of bioengineering happened here at UC San Diego. Today, our campus remains an incredibly open and vibrant environment. This enables us to recruit some of the most talented young investigators, and continue exploring the next frontiers and embracing non-traditional research directions in the realm of bioengineering."

Bioengineers from UC San Diego recently made headlines around the world for newly published work advancing an effort to develop a gene therapy for chronic pain that could offer a safer, non-addictive alternative to opioids

One of the newest bioengineering faculty at UC San Diego is Lingyan Shi, who is developing new methods and systems for recording what is happening within live cells

Jacobs School rankings

Highly ranked doctoral programs in engineering at the Jacobs School: bioengineering (3); computer engineering (14); electrical engineering (16); aerospace engineering (17); mechanical engineering (17); civil engineering (20).

The full listing of Jacobs School rankings:
2022 US News & World Report Rankings of Best Engineering Schools are here

 

New ways of looking inside living cells

From developing new imaging platforms, to asking new biological questions, and developing new disease diagnostics, UC San Diego bioengineering professor Lingyan Shi is pushing the boundaries of what's possible when we look inside living cells.

UC San Diego bioengineering professor Lingyan Shi

By Becky Ham

March 29, 2021-- Energy from an exquisitely targeted photon can vibrate the chemical bond of molecules like a pluck on a guitar string. Instead of music, these vibrational frequencies allow University of California San Diego bioengineering professor Lingyan Shi to see specific molecules within a living cell.

The cutting-edge imaging technologies used by Shi, who leads the Laboratory of Optical Bioimaging and Spectroscopy at UC San Diego, are a mouthful: stimulated Raman scattering (SRS) microscopy, multiphoton fluorescence microscopy (MPF), and resonance Raman microscopy (RRS). However, they all use light of specific wavelengths to probe chemical vibrational bonds in biological tissues.   

Different molecules such as fats, proteins, and DNA have distinct vibrational modes, and produce a subtle, yet distinct photo-spectral output. This allows researchers to identify these molecules with high chemical and spatial resolution. The powerful techniques don’t disturb living tissues, so they can be used across a variety of applications. For instance, SRS microscopy can generate a digital histological image of a biopsy in mere minutes, without the use of any chemical dyes and minimal sample preparation. Digital histology, which can mimic the staining seen in traditional histology  techniques (see figure 2), may make its way into the operating room as an intraoperative technique that saves time and improves surgical performance. Another application of Raman-based technologies includes the probing of metabolic dynamics and compositions. Various tissues and even diseases like cancer are marked by distinct metabolic changes. Understanding these dynamics will aid in early detection and better understanding of such diseases and nutrition. 

As one of the world’s leading experts in ultrafast optical imaging, the new Assistant Professor of Bioengineering at the UC San Diego Jacobs School of Engineering has no shortage of ideas about the potential of Raman-based technologies. “When we are developing a new technology, a new tool,” she says, “it will definitely inspire us to ask new biological questions.” 

Seeing without Disturbing

One of those questions is: how can we observe very small molecules in the body, without disturbing their natural functions? For her doctoral research, Shi had been tagging very small drug molecules with fluorescent probes to watch how they passed through the blood-brain barrier. But on the molecular scale, “if we consider size of the drug as a ping-pong ball, but the attached fluorescent particle was like another ping-pong ball or even bigger,” she explained. The bulky fluorescent label on the drugs was likely perturbing the drug’s behavior (such as its permeability and diffusion coefficient) in the body.

A 2014 seminar by her postdoctoral mentor Wei Min at Columbia University illustrated how stimulated Raman scattering microscopy could solve this problem. “At the time, I was very biological problem-oriented, and this was just a great tool for my research,” Shi says. “But when I got to know more and more about the technology, I realized that biological questions and imaging technology are mutually inspirational. It’s not unidirectional.”

Today, no single imaging technique reigns supreme in Shi’s lab. She and her students work with a variety of platforms, depending on the biological question at hand. Some techniques are better at seeing deep into living tissue, Shi explains, while others can probe a broader range of chemical bonds. She has also pioneered new ways of using heavy water to tag molecules with an isotope of hydrogen called deuterium (Fig. 3), to follow the metabolic activities under different physiological or pathological conditions. 

As mentioned, a powerful application centers on detecting metabolic changes that occur during tumor formation, when energy-hungry cancer cells metabolize differently than healthy cells. Shi recently led a study that combined several techniques to detect early metabolic changes that distinguish triple-negative breast cancer from less aggressive cancer types.

Triple-negative breast cancer predominantly affects Black and Latina women, and is difficult to detect early in the disease. “But the optical imaging technology we’re developing can tell you a lot about metabolic changes at a very early stage,” says Shi. “Early-stage diagnosis is critical to increase the survival rate among these women and reduce their cost of treatment.

“Homebuilt” Lab

Many of the imaging systems Shi and her students use are not commercially available yet, and they combine instrumentation and probes to fit their needs. “It’s like a homebuilt microscopy platform in my lab,” Shi says.

The researchers are always tinkering with the platforms to improve the image resolution and sensitivity to the optical signal. Shi holds 6 patents as a co-inventor related to optical imaging and is interested in commercializing or licensing some of these technologies.

“The application of these technologies is still in the infant stage,” she explains. “I think we need to do more educational presentations to show what kinds of information we can achieve, and to demonstrate how useful it is.”

Shi is excited to welcome research collaborators at UC San Diego, from biological scientists to genetics experts, and she is eager to mentor passionate students from underrepresented minorities in her lab, at every level from undergraduate to postdoc. 

“We’re very motivated here at UCSD, and the atmosphere is great. I enjoy seeing students become aware of something they didn’t know about before,” she says. “It’s a very happy moment.”

Shi joined the UC San Diego faculty in October 2019, and she says COVID-19 has made setting up a lab more difficult in some ways. At first it was challenging to source supplies, but lately she’s been more worried that the pandemic will keep her from throwing lab dinner parties and birthday celebrations that usually “bring us all together and make it feel like a family.”

“But I try to think positively about it,” Shi says. “This has also given me more time to think about the future research directions we want to explore.”

Research Expo 2021

Robot, heal thyself

Nanoengineers develop self-repairing microbots

March 17, 2021--Living tissue can heal itself from many injuries, but giving similar abilities to artificial systems, such as robots, has been extremely challenging. Now, researchers at the University of California San Diego reporting in Nano Letters have developed small, swimming robots that can magnetically heal themselves on-the-fly after breaking into two or three pieces. The strategy could someday be used to make hardier devices for environmental or industrial clean up, the researchers say. Watch a video of the self-healing swimmers here.

Scientists have developed small robots that can “swim” through fluids and carry out useful functions, such as cleaning up the environment, delivering drugs and performing surgery. Although most experiments have been done in the lab, eventually these tiny machines would be released into harsh environments, where they could become damaged.

Swimming robots are often made of brittle polymers or soft hydrogels, which can easily crack or tear. Senior author and UC San Diego nanoengineering professor Joseph Wang and colleagues wanted to design swimmers that could heal themselves while in motion, without help from humans or other external triggers.

The researchers made swimmers that were 2 cm long (a little less than an inch) in the shape of a fish that contained a conductive bottom layer; a rigid, hydrophobic middle layer; and an upper strip of aligned, strongly magnetic microparticles. The team added platinum to the tail, which reacted with hydrogen peroxide fuel to form oxygen bubbles that propelled the robot.

When the researchers placed a swimmer in a petri dish filled with a weak hydrogen peroxide solution, it moved around the edge of the dish. Then, they cut the swimmer with a blade, and the tail kept traveling around until it approached the rest of the body, reforming the fish shape through a strong magnetic interaction.

The robots could also heal themselves when cut into three pieces, or when the magnetic strip was placed in different configurations. The versatile, fast and simple self-healing strategy could be an important step toward on-the-fly repair for small-scale swimmers and robots, the researchers say.

Coronavirus circulated undetected months before first COVID-19 cases in Wuhan, China

Study dates emergence as early as October 2019; simulations suggest in zoonotic viruses in most cases die out naturally before causing a pandemic.

The SARS-CoV-2 virus under a microscope. Photo credit: National Institute of Allergy and Infectious Diseases

March 24, 2021--Using molecular dating tools and epidemiological simulations, bioinformaticians and computer scientists at the University of California San Diego, with colleagues at the University of Arizona and Illumina, Inc., estimate that the SARS-CoV-2 virus was likely circulating undetected for at most two months before the first human cases of COVID-19 were described in Wuhan, China, in late-December 2019.

Writing in the March 18, 2021 online issue of Science, they also note that their simulations suggest that the mutating virus dies out naturally more than three-quarters of the time without causing an epidemic.

“Our study was designed to answer the question of how long could SARS-CoV-2 have circulated in China before it was discovered,” said senior author Joel O. Wertheim, associate professor in the Division of Infectious Diseases and Global Public Health at the UC San Diego School of Medicine.

“To answer this question, we combined three important pieces of information: a detailed understanding of how SARS-CoV-2 spread in Wuhan before the lockdown, the genetic diversity of the virus in China, and reports of the earliest cases of COVID-19 in China. By combining these disparate lines of evidence, we were able to put an upper limit of mid-October 2019 for when SARS-CoV-2 started circulating in Hubei province.”

The epidemiological models were designed and run by Ph.D. student Jonathan Pekar, in the UC San Diego bioinformatics program, who is also part of Wertheim’s research group. 

Niema Moshiri, an assistant teaching professor in computer science at the Jacobs School, coded the simulations used in this Science paper. 

Niema Moshiri, an assistant teaching professor in the UC San Diego Department of Computer Science and Engineering, created all the code behind the epidemiological simulations, which can be found here and here on GitHub. The simulations are based on a robust framework for the simultaneous simulation of a transmission network and viral evolution, as well as simulation of sampling imperfections of the transmission network and of the sequencing process. 

Cases of COVID-19 were first reported in late December 2019 in Wuhan, located in the Hubei province of central China. The virus quickly spread beyond Hubei. Chinese authorities cordoned off the region and implemented mitigation measures nationwide. By April 2020, local transmission of the virus was under control but, by then, COVID-19 was pandemic with more than 100 countries reporting cases.

SARS-CoV-2 is a zoonotic coronavirus, believed to have jumped from an unknown animal host to humans. Numerous efforts have been made to identify when the virus first began spreading among humans, based on investigations of early-diagnosed cases of COVID-19. The first cluster of cases — and the earliest sequenced SARS-CoV-2 genomes — were associated with the Huanan Seafood Wholesale Market, but study authors say the market cluster is unlikely to have marked the beginning of the pandemic because the earliest documented COVID-19 cases had no connection to the market.

Regional newspaper reports suggest COVID-19 diagnoses in Hubei date back to at least Nov. 17, 2019, suggesting the virus was already actively circulating when Chinese authorities enacted public health measures.

In the new study, researchers coupled epidemiological simulations with molecular clock evolutionary analyses to try to home in on when the first, or index, case of SARS-CoV-2 occurred. “Molecular clock” is a term for a technique that uses the mutation rate of genes to deduce when two or more life forms diverged — in this case, when the common ancestor of all variants of SARS-CoV-2 existed, estimated in this study to as early as mid-November 2019.

Molecular dating of the most recent common ancestor is often taken to be synonymous with the index case of an emerging disease. However, said co-author Michael Worobey, professor of ecology and evolutionary biology at University of Arizona: “The index case can conceivably predate the common ancestor — the actual first case of this outbreak may have occurred days, weeks or even many months before the estimated common ancestor. Determining the length of that ‘phylogenetic fuse’ was at the heart of our investigation.”

Based on this work, the researchers estimate that the median number of persons infected with SARS-CoV-2 in China was less than one until Nov. 4, 2019. Thirteen days later, it was four individuals, and just nine on December 1, 2019. The first hospitalizations in Wuhan with a condition later identified as COVID-19 occurred in mid December.

Study authors used a variety of analytical tools to model how the SARS-CoV-2 virus may have behaved during the initial outbreak and early days of the pandemic when it was largely an unknown entity and the scope of the public health threat not yet fully realized.

These tools included epidemic simulations based on the virus’s known biology, such as its transmissibility and other factors. In just 29.7 percent of these simulations was the virus able to create self-sustaining epidemics. In the other 70.3 percent, the virus infected relatively few persons before dying out. The average failed epidemic ended just eight days after the index case.

“Typically, scientists use the viral genetic diversity to get the timing of when a virus started to spread,” said Wertheim. “Our study added a crucial layer on top of this approach by modeling how long the virus could have circulated before giving rise to the observed genetic diversity.”

“Our approach yielded some surprising results. We saw that over two-thirds of the epidemics we attempted to simulate went extinct. That means that if we could go back in time and repeat 2019 one hundred times, two out of three times, COVID-19 would have fizzled out on its own without igniting a pandemic. This finding supports the notion that humans are constantly being bombarded with zoonotic pathogens.”

Wertheim noted that even as SARS-CoV-2 was circulating in China in the fall of 2019, the researchers’ model suggests it was doing so at low levels until at least December of that year.

“Given that, it’s hard to reconcile these low levels of virus in China with claims of infections in Europe and the U.S. at the same time,” Wertheim said. “I am quite skeptical of claims of COVID-19 outside China at that time.”

The original strain of SARS-CoV-2 became epidemic, the authors write, because it was widely dispersed, which favors persistence, and because it thrived in urban areas where transmission was easier. In simulated epidemics involving less dense rural communities, epidemics went extinct 94.5 to 99.6 percent of the time.

The virus has since mutated multiple times, with a number of variants becoming more transmissible.

“Pandemic surveillance wasn’t prepared for a virus like SARS-CoV-2,” Wertheim said. “We were looking for the next SARS or MERS, something that killed people at a high rate, but in hindsight, we see how a highly transmissible virus with a modest mortality rate can also lay the world low.”

Konrad Scheffler, Illumina, Inc. was also a co-author.

Funding for this research came, in part, from the National Institutes of Health (grants AI135992, AI136056, T15LM011271), the Google Cloud COVID-19 Research Credits Program, the David and Lucile Packard Foundation, the University of Arizona and the National Science Foundation (grant 2028040).


 

Welcome to the Jacobs School, Class of 2025

Why Commercialization of Carbon Capture and Sequestration has Failed and How it Can Work

Credibility of incentives - a function of policy and politics - is a key, researchers say

Despite extensive support, 80 percent of projects that seek to commercialize carbon capture and sequestration technology have ended in failure. Credit: Coatesy/iStock

March 22, 2021 - There are 12 essential attributes that explain why commercial carbon capture and sequestration projects succeed or fail in the U.S., University of California San Diego researchers say in a recent study published in Environmental Research Letters

The paper was coauthored by Jacobs School alumnus Ryan Hanna, now an assistant research scientist at UC San Diego. 

Carbon capture and sequestration (CCS) has become increasingly important in addressing climate change. The Intergovernmental Panel on Climate Change (IPCC) relies greatly on the technology to reach zero carbon at low cost. Additionallyit is among the few low-carbon technologies in President Joseph R. Biden’s proposed $400 billion clean energy plan that earns bipartisan support. 

In the last two decades, private industry and government have invested tens of billions of dollars to capture CO2 from dozens of industrial and power plant sources. Despite the extensive support, these projects have largely failed. In fact, 80 percent of projects that seek to commercialize carbon capture and sequestration technology have ended in failure. 

“Instead of relying on case studies, we decided that we needed to develop new methods to systematically explain the variation in project outcome of why do so many projects fail,” said  lead author Ahmed Y. Abdulla, research fellow with UC San Diego’s Deep Decarbonization Initiative and assistant professor of mechanical and aerospace engineering at Carleton University. “Knowing which features of CCS projects have been most responsible for past successes and failures allows developers to not only avoid past mistakes, but also identify clusters of existing, near-term CCS projects that are more likely to succeed.”

He added, “By considering the largest sample of U.S. CCS projects ever studied, and with extensive support from people who managed these projects in the past, we essentially created a checklist of attributes that matter and gauged the extent to which each does.”

Credibility of incentives and revenues is key

The researchers found that the credibility of revenues and incentives—functions of policy and politics—are among the most important attributes, along with capital cost and technological readiness, which have been studied extensively in the past.

“Policy design is essential to help commercialize the industry because CCS projects require a huge amount of capital up front,” the authors, comprised of an international team of researchers, note. 

The authors point to existing credible policies that act as incentives, such as the 2018 expansion of the 45Q tax credit. It provides companies with a guaranteed revenue stream if they sequester CO2 in deep geologic repositories.

The only major incentive companies have had thus far to recoup their investments in carbon capture is by selling the CO2 to oil and gas companies, who then inject it into oil fields to enhance the rate of extraction—a process referred to as enhanced oil recovery.

The 45Q tax credit also incentivizes enhanced oil recovery, but at a lower price per CO2 unit, compared to dedicated geologic CO2 storage.   

Beyond selling to oil and gas companies, CO2 is not exactly a valuable commodity, so few viable business cases exist to sustain a CCS industry on the scale that is necessary or envisioned to stabilize the climate.

“If designed explicitly to address credibility, public policy could have a huge impact on the success of projects,” said David Victor, co-lead of the Deep Decarbonization Initiative and professor of industrial innovation at UC San Diego’s School of Global Policy and Strategy.

Results with expert advice from project managers with real-world experience

While technological readiness has been studied extensively and is essential to reducing the cost and risk of CCS, the researchers looked beyond the engineering and engineering economics to determine why CCS continues to be such a risky investment. Over the course of two years, the researchers analyzed publicly available records of 39 U.S. projects and sought expertise from CCS project managers with extensive, real-world experience. 

They identified 12 possible determinants of project outcomes, which are technological readiness, credibility of incentives, financial credibility, cost, regulatory challenges, burden of CO2 removal, industrial stakeholder opposition, public opposition, population proximity, employment impact, plant location, and the host state’s appetite for fossil infrastructure development.

To evaluate the relative influence of the 12 factors in explaining project outcomes, the researchers built two statistical models and complemented their empirical analysis with a model derived through expert assessment.

The experts only underscored the importance of credibility of revenues and incentives; the vast majority of successful projects arranged in advance to sell their captured CO2 for enhanced oil recovery. They secured unconditional incentives upfront, boosting perceptions that they were resting on secure financial footing.

The authors conclude models in the study—especially when augmented with the structured elicitation of expert judgment—can likely improve representations of CCS deployment across energy systems. 

“Assessments like ours empower both developers and policymakers,” the authors write. “With data to identify near-term CCS projects that are more likely to succeed, these projects will become the seeds from which a new CCS industry sprouts.”

Co-authors include Jacobs School alumnus Ryan Hanna, assistant research scientist at UC San Diego; Kristen R Schell, assistant professor at Carleton University; and Oytun Babacan, research fellow at Imperial College London. 

Artificial neuron device could shrink energy use and size of neural network hardware

Goto Flickr
SEM image of the artificial neuron device. Images courtesy of Nature Nanotechnology

March 18, 2021 -- Training neural networks to perform tasks, such as recognizing images or navigating self-driving cars, could one day require less computing power and hardware thanks to a new artificial neuron device developed by researchers at the University of California San Diego. The device can run neural network computations using 100 to 1000 times less energy and area than existing CMOS-based hardware.

Researchers report their work in a paper published Mar. 18 in Nature Nanotechnology.

Neural networks are a series of connected layers of artificial neurons, where the output of one layer provides the input to the next. Generating that input is done by applying a mathematical calculation called a non-linear activation function. This is a critical part of running a neural network. But applying this function requires a lot of computing power and circuitry because it involves transferring data back and forth between two separate units—the memory and an external processor.

Now, UC San Diego researchers have developed a nanometer-sized device that can efficiently carry out the activation function.

“Neural network computations in hardware get increasingly inefficient as the neural network models get larger and more complex,” said corresponding author Duygu Kuzum, a professor of electrical and computer engineering at the UC San Diego Jacobs School of Engineering. “We developed a single nanoscale artificial neuron device that implements these computations in hardware in a very area- and energy-efficient way.”

The new study was performed as a collaboration between UC San Diego researchers from the Department of Electrical and Computer Engineering (led by Kuzum, who is part of the university's Center for Machine-Integrated Computing and Security) and a DOE Energy Frontier Research Center (EFRC led by physics professor Ivan Schuller), which focuses on developing hardware implementations of energy-efficient artificial neural networks.

The device implements one of the most commonly used activation functions in neural network training called a rectified linear unit. What’s particular about this function is that it needs hardware that can undergo a gradual change in resistance in order to work. And that’s exactly what the UC San Diego researchers engineered their device to do—it can gradually switch from an insulating to a conducting state, and it does so with the help of a little bit of heat.

This switch is what’s called a Mott transition. It takes place in a nanometers-thin layer of vanadium dioxide. Above this layer is a nanowire heater made of titanium and gold. When current flows through the nanowire, the vanadium dioxide layer slowly heats up, causing a slow, controlled switch from insulating to conducting.

Chips on a circuit board
Left: Closeups of the synaptic device array (top) and the activation, or neuron, device array (bottom). Right: A custom printed circuit board built with the two arrays.

“This device architecture is very interesting and innovative,” said first author Sangheon Oh, an electrical and computer engineering Ph.D. student in Kuzum's lab. Typically, materials in a Mott transition experience an abrupt switch from insulating to conducting because the current flows directly through the material, he explained. “In this case, we flow current through a nanowire on top of the material to heat it and induce a very gradual resistance change.”

To implement the device, the researchers first fabricated an array of these so-called activation (or neuron) devices, along with a synaptic device array. Then they integrated the two arrays on a custom printed circuit board and connected them together to create a hardware version of a neural network.

The researchers used the network to process an image—in this case, a picture of Geisel Library at UC San Diego. The network performed a type of image processing called edge detection, which identifies the outlines or edges of objects in an image. This experiment demonstrated that the integrated hardware system can perform convolution operations that are essential for many types of deep neural networks.

A building shaped like an upside-down pyramid
Image of Geisel Library used for edge detection (left). Output of the convolution operations for the lateral filter (center) and vertical filter (right).

The researchers say the technology could be further scaled up to do more complex tasks such as facial and object recognition in self-driving cars. With interest and collaboration from industry, this could happen, noted Kuzum.

“Right now, this is a proof of concept,” Kuzum said. “It’s a tiny system in which we only stacked one synapse layer with one activation layer. By stacking more of these together, you could make a more complex system for different applications.”

Paper: “Energy Efficient Mott Activation Neuron for Full Hardware Implementation of Neural Networks.”

This work was supported by the Office of Naval Research, Samsung Electronics, the National Science Foundation, the National Institutes of Health, a Qualcomm Fellowship and the U.S. Department of Energy, Office of Science through an Energy Frontier Research Center.

How to speed up muscle repair

Drawing of muscle fiber
Illustration of skeletal muscle fiber. Credit: Kavitha Mukund

March 17, 2021 -- A study led by researchers at the University of California San Diego Jacobs School of Engineering provides new insights for developing therapies for muscle disease, injury and atrophy. By studying how different pluripotent stem cell lines build muscle, researchers have for the first time discovered how epigenetic mechanisms can be triggered to accelerate muscle cell growth at different stages of stem cell differentiation.

The findings were published Mar. 17 in Science Advances.

“Stem cell-based approaches that have the potential to aid muscle regeneration and growth would improve the quality of life for many people, from children who are born with congenital muscle disease to people who are losing muscle mass and strength due to aging,” said Shankar Subramaniam, distinguished professor of bioengineering, computer science and engineering, and cellular and molecular medicine at UC San Diego and lead corresponding author on the study. “Here, we have discovered that specific factors and mechanisms can be triggered by external means to favor rapid growth.”

The researchers used three different human induced pluripotent stem cell lines and studied how they differentiate into muscle cells. Out of the three, one cell line grew into muscle the fastest. The researchers looked at what factors made this line different from the rest, and then induced these factors in the other lines to see if they could accelerate muscle growth.

They found that triggering several epigenetic mechanisms at different time points sped up muscle growth in the “slower” pluripotent stem cell lines. These include inhibiting a gene called ZIC3 at the outset of differentiation, followed by adding proteins called beta-catenin transcriptional cofactors later on in the growth process.

“A key takeaway here is that all pluripotent stem cells do not have the same capacity to regenerate,” Subramaniam said. “Identifying factors that will prime these cells for specific regeneration will go a long way in regenerative medicine.”

Next, the team will explore therapeutic intervention, such as drugs, that can stimulate and accelerate muscle growth at different stages of differentiation in human induced pluripotent stem cells. They will also see whether implanting specific pluripotent stem cells in dystrophic muscle can stimulate new muscle growth in animals. Ultimately, they would like to see if such a stem cell-based approach could regenerate muscle in aging humans.

Paper: “Temporal mechanisms of myogenic specification in human induced pluripotent stem cells.” Co-authors of the study include Priya Nayak, UC San Diego; Alexandre Colas, Sanford Burnham Prebys Medical Discovery Institute; Mark Mercola, Stanford University; and Shyni Varghese, Duke University.

Defending human-robot teams against adversaries goal of computer science grant

Computer science professor Kamalika Chaudhuri is part of a MURI grant going to multiple institutions. Her work is on Cohesive and Robust Human-Bot Cybersecurity Teams.  

March 16, 2021-- UC San Diego computer science professor Kamalika Chaudhuri is part of a multi-university team that has won a prestigious US Department of Defense Multidisciplinary University Research Initiative (MURI) Award to develop rigorous methods for robust human-machine collaboration against adversaries. 

Chaudhuri will receive $750,000 to fund her research on the project titled Cohesive and Robust Human-Bot Cybersecurity Teams, which aims to develop rigorous parameters for Human-Bot Cybersecurity teams with the goal of developing a cohesive team that is not vulnerable to active human and machine learning (ML) adversaries. 

“We now know how to develop machine learning methods that are robust to adversaries, yet in many applications, humans work in coordination with machine learning software, and adversaries can still disrupt the process,” said Chaudhuri, whose research interests lie in the foundations of trustworthy machine learning. “This project will investigate in detail how that can happen, and how we can design algorithms and tools to be robust to these adversaries."

Cybersecurity is the most challenging task that the Department of Defense (DoD) faces today. A typical human analyst in a cybersecurity task has to deal with a plethora of information, such as intrusion logs, network flows, executables, and provenance information for files. Real cybersecurity scenarios are even more challenging: an active adversarial environment, with large amounts of information and techniques that neither humans nor machines can handle alone. 

In addition to human analysts, machine learning (ML) bots have become part of these cybersecurity teams. ML bots reduce the burden on human analysts by filtering information, thus freeing up cognitive resources for tasks related to the high-level mission.

The team will first focus on ways to build trust within the HBCT by investigating techniques to produce explanations for the human analysts of how the ML bots work. These explanations will be presented in an appropriate vocabulary for the analysts and will be specific to the task of the HBCT, providing valuable insight for the human analysts so they will trust the ML model and reduce manual effort.

The group will also research how analysts integrate information to arrive at decisions, as well as their mental models of how bots operate. This will allow them to take a step towards automating the decision-making process. Moreover, the mental model can help design robust ML models that are more specific to the task of the HBCT.

Adaptability will be key as well. Human-bot team dynamics change as new adversaries with different capabilities arise, and adversaries adapt in response to new team strategies. Adversaries interactive learning must be taken into account to develop methods for the entire team to adaptto adversaries in an interactive manner.

Chaudhuri and her research group will develop methods that can improve generalization capabilities of current machine learning methods to rare inputs, bolster the quality of explanations provided by them and design principled solutions for adversarial robustness. 

“This will build on some of our prior and current work in the area of interactive learning, as well as principled methods for defending against adversaries,” she said. 

Since its inception in 1985, the tri-Service MURI program has convened teams of investigators with the hope that collective insights drawn from research across multiple disciplines could facilitate the advancement of newly emerging technologies and address the Department’s unique problem sets. Complementing the Department’s single-investigator basic research grants, the highly competitive MURI program has made immense contributions to both national defense and society at large. Innovative technological advances from the MURI program help drive and accelerate current and future military capabilities and find multiple applications in the commercial sector.

Seven universities comprise the research team, which is led by Somesh Jha at the University of Wisconsin-Madison: Carnegie Mellon University, University of California San Diego, Pennsylvania State University, University of Melbourne, Macquarie University, and University of Newcastle. Benjamin Rubinstein of the University of Melbourne will lead the Australian team, or AUSMURI, funded by the Australian Government. The team brings together diverse expertise spanning computer security, machine learning, psychology, decision sciences, and human-computer interaction

 


 

Researchers at UC San Diego Unveil New Interactive Web Tool for Visualizing Large-Scale Phylogenetic Trees

March 17, 2021

The proliferation of sequencing technologies and an ever-increasing focus on ‘omic studies over the past several years have spawned massive quantities of data and many tools to process and analyze the results. As these tools have evolved, so has the need for even greater scale and the ability to visualize complex data sets in more efficient ways.

Born of these needs for advancement, a team of researchers with the Center for Microbiome Innovation (CMI) at the University of California San Diego (UC San Diego), led by Kalen Cantrell and Marcus W. Fedarko, unveiled EMPress, a new interactive visualization tool, in an article published in mSystems on March 16, 2021. The paper, entitled “EMPress Enables Tree-Guided, Interactive, and Exploratory Analyses of Multi-omic Data Sets,” showcases the tool’s functionality, versatility, and scalability, and explores some of the potential applications in visualization and data analysis.

"Although there are many excellent existing tools for visualizing trees, we wanted to create a tool that could be used within a web browser and could scale to really large trees," Fedarko remarked when discussing the development process. "Another motivation was that there were many custom features that no existing tool, to our knowledge, supported - for example, the ability to interactively link samples in an ordination with a phylogenetic tree, showing the sequences contained within each sample, or going the opposite way, the samples containing a given sequence."

Aside from interactively integrating ordinations with trees, EMPress also introduces the ability to animate a tree’s changes over time. While other tools have included a temporal dimension to trees, the ability to animate the tree alongside an ordination is a novel feature that the team believes will enhance the exploratory analysis of ‘omic data sets.

What began as an undergraduate project at UC San Diego’s Early Research Scholars Program has since grown into a collaboration that spans both academia and industry. The team at CMI has worked closely with IBM Research’s Artificial Intelligence for Healthy Living Center throughout the process, as well as researchers at the Simons Foundation, Cornell University, and Justus Liebig University.

Developing a tool that was not only web-based but capable of storing, processing, and visualizing such large phylogenetic trees presented numerous challenges. As the scale of microbiome and other ‘omic studies has continued to grow, so too has the technical complexity required to accommodate and analyze the large, complex data sets those studies produce.

FIG 1 Earth Microbiome Project paired phylogenetic tree (including 756,377 nodes) and unweighted UniFrac ordination (including 26,035 samples). (a) Graphical depiction of EMPress’ unified interface with fragment insertion tree (left) and unweighted UniFrac sample ordination (right). Tips are colored by their phylum-level taxonomic assignment; the barplot layer is a stacked barplot describing the proportions of samples containing each tip summarized by level 1 of the EMP ontology. Inset shows summarized sample information for a selected feature. The ordination highlights the two samples containing the tip selected in the tree enlarged to show their location. (b) Subset of EMP samples with pH information: the inner barplot ring shows the phylum-level taxonomic assignment, and the outer barplot ring represents the mean pH of all the samples where each tip was observed. (c) pH distributions summarized by phylum-level assignment with median pH indicated by dotted lines. Interactive figures can be accessed at https://github.com/knightlab-analyses/empress-analyses.

"We resolved some of these issues by creating our own custom WebGL, shaders which are capable of visualizing millions of points, and implementing high-performance data structures such as the balanced parentheses tree that helped drastically reduce the memory footprint of EMPress," according to Cantrell. As the code has been refined and optimized through several phases of development, it has enabled the analysis of larger and larger data sets, including a tree with over 750,000 nodes. 

While the article in mSystems represents the tool’s formal unveiling, it has already seen use in several studies and applications. Researchers at the CMI utilized EMPress in their recently published analysis of the composition and microbial load of the human oral microbiome. Additionally, epidemiologists with UC San Diego’s Return to Learn program have been using the tool to help manage the university’s response to the COVID-19 pandemic. These applications have provided critical feedback and facilitated improvements to continue streamlining the analyses for which EMPress is designed.

As development continues, there are several planned features, including the ability to explore time-series data, potential anomaly detection, implementing support for annotating various types of data, and further improving performance to allow for larger data sets. The tool’s source code is available on GitHub, and the team is eager to see how their peers expand upon their work.

“Just as EMPress builds on the many existing tree visualization tools in the literature (iTOL, PHYLOViZ, Anvi'o, SigTree, FigTree, ggtree, TopiaryExplorer, MicroReact, Archaeopteryx, etc.), we're sure that other tools will pop up soon enough that build on the concepts used in EMPress -- we look forward to seeing how the landscape of these tools changes in the future,” Fedarko added.

 

FIG 2 EMPress is a versatile exploratory analysis tool adaptable to various ‘omics data types. (a) RoDEO differential abundance of microbial functions from metatranscriptomic sequencing of COVID-19 patients (n = 8) versus community-acquired pneumonia patients (n = 25) and versus healthy control subjects (n = 20). The tree represents the four-level hierarchy of the KEGG enzyme codes. The barplot depicts significantly differentially abundant features (P , 0.05) in COVID-19 patients. Clicking on a tip produces a pop-up insert tabulating the name of the feature, its hierarchical ranks, and any feature annotations. (b) Global FoodOmics Project LC-MS data. Stacked barplots indicate the proportions of samples (n = 70) (stratified by food) containing the tips in an LC-MS Qemistree of food-associated compounds, with tip nodes colored by their chemical superclass. (c) De novo tree constructed from 16S rRNA sequencing data from 32 oral microbiome samples. Samples were taken before (n = 16) and after (n = 16) subjects (n = 10) brushed their teeth; each barplot layer represents a different differential abundance method’s measure of change between before- and after-brushing samples. The innermost layer shows estimated log-fold changes produced by Songbird, the middle layer shows effect sizes produced by ALDEx2, and the outermost layer shows the W-statistic values produced by ANCOM (see Materials and Methods). The tree is colored by tip nodes’ phylum-level taxonomic classifications. Interactive figures can be accessed at https://github.com/knightlab-analyses/empress-analyses.

 

Additional co-authors include Gibraan Rahman, Daniel McDonald, Yimeng Yang, Thant Zaw, Antonio Gonzalez, Mehrbod Estaki, Qiyun Zhu, Erfan Sayyari, George Armstrong, Anupriya Tripathi, Julia M. Gauglitz, Clarisse Marotz, Nathaniel L. Matteson, Cameron Martino, Se Jin Song, Austin D. Swafford, Pieter C. Dorrestein, Kristian G. Andersen, Yoshiki Vázquez-Baeza, and Rob Knight, all at UC San Diego; Stefan Janssen at Justus Liebig University; Niina Haiminen and Laxmi Parida at the IBM Thomas J. Watson Research Center; Kristen L. Beck and Ho-Cheol Kim at the IBM Almaden Research Center; James T. Morton at the Simons Foundation; Jon G. Sanders at Cornell University; and Anna Paola Carrieri at IBM Research Europe.

This piece was written by CMI’s contributing editor Cassidy Symons

Writing a New Chapter on Innovation

UC San Diego establishes local chapter of National Academy of Inventors

 

March 17, 2021 - The University of California San Diego is the first University of California campus to establish a chapter of the National Academy of Inventors (NAI), a move that will help the campus build and sustain a more robust innovation ecosystem. This designation provides tools and resources to help UC San Diego raise the profile of its inventions and technologies, encourage innovations on campus and educate student entrepreneurs.

“Invention is in our DNA,” said Chancellor Pradeep K. Khosla, an NAI fellow who was recognized for his work in enhancing cybersecurity. “Since 2014, UC San Diego has seen a 153% increase in licensed startups, a 120% increase in industry funding, and a 78% increase in licenses. Just last year, our research program generated more than 500 new invention disclosures, including over 200 new patents. Establishing a local NAI chapter will help further develop our students, create stronger connections to the region’s flourishing community of inventors, and showcase UC San Diego’s growing research prowess.”

An NAI chapter designation gives the UC San Diego community access to networks and tools that can facilitate inventorship and entrepreneurism in students, faculty and staff. Chapter members will be able to participate in annual meetings, network with inventors around the world and meet participants from organizations like the U.S. Patent and Trademark Office. They’ll also be able to submit articles to NAI’s journal Technology and Innovation.

The chapter will have a faculty advisory board to discuss metrics for success and programming opportunities, as well as strategic priorities for the coming year. The inaugural board includes faculty from across campus, including Health Sciences, the Rady School of Management and the Jacobs School of Engineering to ensure representation across UC San Diego’s innovation ecosystem.

Innovation programming helps faculty and students potentially turn research into products, such as this wearable patch that can heat or cool the skin. (cr: David Baillot/UC San Diego Jacobs School of Engineering)

“Students, staff and faculty from all parts of campus will be most welcome in the new chapter," said Albert P. Pisano, dean of the UC San Diego Jacobs School of Engineering. "Speaking as an engineer, educator and inventor, I know firsthand that we get the best solutions when we look at challenges from all directions. We need everyone at the innovation and invention table.” 

Pisano was inducted into the National Academy of Inventors in 2019  based on the impact of medical devices that treat arterial diseases, currently being commercialized via a startup company.

While NAI fellows are inducted into the academy through a formal nomination process, chapter members will apply locally through UC San Diego’s Office of Innovation and Commercialization. Students will have the unique opportunity to become honorary members and have access to mentorship and professional development resources.

TODAY’S INNOVATION FOR TOMORROW’S WORLD

Student entrepreneurs are supported by programs like The Basement and will be able to join the NAI chapter as honorary members. (cr: Erik Jepsen/UC San Diego)

The university’s commitment to innovation and entrepreneurship runs deep and goes beyond the campus borders. While programs like Institute for the Global EntrepreneurThe Basement and StartR at the Rady School of Management support students and faculty in their startup endeavors, capital projects like the Design and Innovation Building and Downtown Park & Market “The U” promise to strengthen the connection between the campus and industry partners, government entities and community members.

“UC San Diego prioritizes innovation, technology transfer and entrepreneurship for the sustained economic prosperity of the region,” said Associate Vice Chancellor for Innovation and Commercialization Paul Roben. “Our recent designation as an NAI Chapter will allow us to connect with world-renowned inventors, while nurturing and mentoring innovators, business owners and the workforce of tomorrow.” 

Upcoming events supporting and celebrating campus innovation include the grand opening of the Design and Innovation Building, a Student Inventor and Startup Showcase focused on “Enriching Human Life and Society,” and the NAI Investor Awards.

“Launching an official NAI Chapter is an amazing step at creating a united innovation ecosystem on campus and within your community to celebrate and share the importance of academic innovation and invention,” said NAI Director Jayde Stewart. “The NAI is honored and proud to have you as members and look forward to celebrating the successes of your students and faculty innovators through your local Chapter.”

The National Academy of Inventors was founded in 2010 to recognize and encourage inventors, enhance the visibility of academic technology, and educate and mentor innovation-minded students. NAI boasts over 1,000 fellows and 250 institutions worldwide. In total, the fellows have formed more than 9,000 companies and generated over $190 billion from nearly 11,000 licensed inventions. UC San Diego is home to 13 NAI fellows, including current and emeritus faculty.

Writing a New Chapter on Innovation

UC San Diego establishes local chapter of National Academy of Inventors

March 17, 2021--The University of California San Diego is the first University of California campus to establish a chapter of the National Academy of Inventors (NAI), a move that will help the campus build and sustain a more robust innovation ecosystem. This designation provides tools and resources to help UC San Diego raise the profile of its inventions and technologies, encourage innovations on campus and educate student entrepreneurs.

“Invention is in our DNA,” said Chancellor Pradeep K. Khosla, an NAI fellow who was recognized for his work in enhancing cybersecurity. “Since 2014, UC San Diego has seen a 153% increase in licensed startups, a 120% increase in industry funding, and a 78% increase in licenses. Just last year, our research program generated more than 500 new invention disclosures, including over 200 new patents. Establishing a local NAI chapter will help further develop our students, create stronger connections to the region’s flourishing community of inventors, and showcase UC San Diego’s growing research prowess.”

An NAI chapter designation gives the UC San Diego community access to networks and tools that can facilitate inventorship and entrepreneurism in students, faculty and staff. Chapter members will be able to participate in annual meetings, network with inventors around the world and meet participants from organizations like the U.S. Patent and Trademark Office. They’ll also be able to submit articles to NAI’s journal Technology and Innovation.

The chapter will have a faculty advisory board to discuss metrics for success and programming opportunities, as well as strategic priorities for the coming year. The inaugural board includes faculty from across campus, including Health Sciences, the Rady School of Management and the Jacobs School of Engineering to ensure representation across UC San Diego’s innovation ecosystem.

Innovation programming helps faculty and students potentially turn research into products, such as this wearable patch that can heat or cool the skin. (cr: David Baillot/UC San Diego Jacobs School of Engineering)

“Students, staff and faculty from all parts of campus will be most welcome in the new chapter," said Albert P. Pisano, dean of the UC San Diego Jacobs School of Engineering. "Speaking as an engineer, educator and inventor, I know firsthand that we get the best solutions when we look at challenges from all directions. We need everyone at the innovation and invention table.” 

Pisano was inducted into the National Academy of Inventors in 2019  based on the impact of medical devices that treat arterial diseases, currently being commercialized via a startup company.

While NAI fellows are inducted into the academy through a formal nomination process, chapter members will apply locally through UC San Diego’s Office of Innovation and Commercialization. Students will have the unique opportunity to become honorary members and have access to mentorship and professional development resources.

TODAY’S INNOVATION FOR TOMORROW’S WORLD

 

The university’s commitment to innovation and entrepreneurship runs deep and goes beyond the campus borders. While programs like Institute for the Global EntrepreneurThe Basement and StartR at the Rady School of Management support students and faculty in their startup endeavors, capital projects like the Design and Innovation Building and Downtown Park & Market “The U” promise to strengthen the connection between the campus and industry partners, government entities and community members.

“UC San Diego prioritizes innovation, technology transfer and entrepreneurship for the sustained economic prosperity of the region,” said Associate Vice Chancellor for Innovation and Commercialization Paul Roben. “Our recent designation as an NAI Chapter will allow us to connect with world-renowned inventors, while nurturing and mentoring innovators, business owners and the workforce of tomorrow.” 

Upcoming events supporting and celebrating campus innovation include the grand opening of the Design and Innovation Building, and a Student Inventor and Startup Showcase focused on “Enriching Human Life and Society.”

Student entrepreneurs are supported by programs like The Basement and will be able to join the NAI chapter as honorary members. (cr: Erik Jepsen/UC San Diego)

“Launching an official NAI Chapter is an amazing step at creating a united innovation ecosystem on campus and within your community to celebrate and share the importance of academic innovation and invention,” said NAI Director Jayde Stewart. “The NAI is honored and proud to have you as members and look forward to celebrating the successes of your students and faculty innovators through your local Chapter.”

The National Academy of Inventors was founded in 2010 to recognize and encourage inventors, enhance the visibility of academic technology, and educate and mentor innovation-minded students. NAI boasts over 1,000 fellows and 250 institutions worldwide. In total, the fellows have formed more than 9,000 companies and generated over $190 billion from nearly 11,000 licensed inventions. UC San Diego is home to 13 NAI fellows, including current and emeritus faculty.

Swift Sewage-Sifting System Boosts Efforts to Forecast and Mitigate the Spread of COVID-19

March 11, 2021- 

As the COVID-19 pandemic proliferated in early 2020, tracking the spread of a frequently asymptomatic virus presented a novel challenge for public health officials. Diagnostic testing was often unavailable and not fast enough to act as a useful forecasting tool.

While symptoms can take several days to appear, the virus immediately begins replicating in the gastrointestinal tract, and traces of it end up in the infected individuals’ stool. Researchers at the University of California San Diego (UC San Diego) quickly determined that testing sewage for viral markers would allow for earlier detection of infections and potential outbreaks.

The wastewater sampling initiative began as a pilot program on the UC San Diego campus in the summer of 2020 with only six collection sites but quickly grew as they determined that environmental testing was a key to preventing the spread of COVID-19. However, the manual work involved in concentrating samples was a roadblock to scaling the surveillance program beyond the university.

“Viral concentration is typically the biggest bottleneck in wastewater analyses since it's laborious and very time-consuming. Here, we optimized that step via automation with liquid-handling robots,” said Smruthi Karthikeyan, a postdoctoral researcher at UC San Diego School of Medicine. The automated system not only increases the number of samples that can be processed concurrently - 24 in 40 minutes - it also removes the potential for human error and accelerates the timeline from the collection of samples to viral detection, enabling a more rapid response to positive results.

This project marked the first collaboration between the Center for Microbiome Innovation (CMI) and the Center for Machine-Integrated Computing & Security (CMICS), both research centers are part of UC San Diego Jacobs School of Engineering. The system is described in a new paper entitled “High-Throughput Wastewater SARS-CoV-2 Detection Enables Forecasting of Community Infection Dynamics in San Diego County”, published March 2, 2021, in mSystems.

As a result of the increased scale at which wastewater samples were tested, the team could track viral detection patterns from a far higher-level perspective than before. “In this paper, we observed strong correlations and forecasting potential between viral content in daily wastewater samples from the Point Loma wastewater treatment plant and positive COVID-19 cases reported for San Diego county when modeled with temporal information,” according to Nancy Ronquillo, a graduate student researcher with the CMICS.

While the system is already enabling health officials to forecast the spread of COVID-19 with greater speed and accuracy, efforts continue to expand what data can be extracted from wastewater. Karthikeyan noted that performing viral genome sequencing of the samples could help track the prevalence of different variants of SARS-CoV-2 and model the impact they’re having on viral spread throughout the community. On a more granular level, the team is studying the dynamics of viral shedding and transmission at UC San Diego, which will ultimately aid the university in safely reopening the campus under the Return to Learn program.

"The Center for Microbiome Innovation and Center for Machine-Integrated Computing & Security collaboration accelerated the trace viral pathogen detection modeling in large-scale wastewater sampling throughout San Diego," remarked Andrew Bartko, executive director of the CMI. "We're grateful to contribute to this interdisciplinary team and generate impactful developments in the fight against COVID-19. We look forward to leveraging our complementary technologies and expertise in the future."

Additional co-authors include Pedro Belda-Ferre, Destiny Alvarado, Tara Javidi, Christopher A. Longhurst, and Rob Knight, all at UC San Diego.


 

Tracking infection dynamics in San Diego County. (A) Map showing the San Diego sewer mains (depicted in purple) that feed into the influent stream at the primary wastewater treatment plant (WWTP) at Point Loma. Overlaid are the cumulative cases recorded from the different zip codes in the county during the course of the study. The caseload was counted by cases per zip code from areas draining into the WWTP. The sizes of the circles are proportional to the diagnostic cases reported from each zone, and the color gradient shows the number of cases per 100,000 residents. (B) Daily new cases reported by the county of San Diego. (C) SARS-CoV-2 viral gene copies detected per liter of raw sewage determined from N1 Cq values corrected for PMMoV (pepper mild mottle virus) concentration. All viral concentration estimates were derived from the processing of two sample replicates and two PCR replicates for each sample (error bars show the standard deviations [SD]).

 

This piece was written by CMI’s contributing editor Cassidy Symons

 

Structural engineers get hands-on experience with composite materials

Students test the performance of the blades they designed and built using composite materials.

March 11, 2021-- Structural engineering students at the Jacobs School got hands-on experience designing, manufacturing and analyzing structures made from composite materials through the Design of Composite Structures course, held in-person thanks to UC San Diego’s Return to Learn policies.

“This is actually a pretty unique class that I don't think you find in engineering departments across the country in terms of the subject matter, and also that it’s taught at the undergrad level,” said Hyonny Kim, a professor of structural engineering at UC San Diego. “Composite materials are high performance materials used to make aerospace structures and space structures. They’re extremely light, strong, and stiff. The class is about how we design them, manufacture them, and quantitatively analyze them.”

The course, held in the fall quarter, started off in a reduced-capacity setting indoors, with half of the students completing a lab project one week, and the other half the following week. When county COVID-19 requirements shifted to outdoor only-education, Kim and his team of dedicated graduate teaching assistants moved the course outside. 

“I felt and observed that the students really enjoyed this,” said Kim. “I think they got a lot out of it, coming to campus, having some direct interaction with instructors. There was a lot of good learning as well as just the psychological benefits of feeling engaged with school, being able to have some social interaction with their teammates. I think it was all around really good for all the students.”

Kim and the TAs prepared individual lab kits for each student taking the course remotely.

In order to make this lab course work for the 26 students in-person as well as the 17 students taking the course remotely, Kim and the TAs created individual kits for each of the three lab projects, that students picked up or had shipped to them.

For the labs, students first made a flat plate with carbon fiber/epoxy composite to get accustomed to the process of using composite materials. They then made a carbon fiber structural channel beam with a different type of composite that is what’s called pre-impregnated (prepreg), where the epoxy is already combined with the fibers; this prepreg material is what most high-end aerospace structures are made with. For the third lab, students made beams out of fiberglass with a foam core. 

They put this understanding of composites to use for the final project: a competition to see which team could build the most efficient wind turbine blades using a glass fiber/epoxy composite. The student teams had to figure out what angle and configuration to set the blades; build them as light and aerodynamic as possible; and have them generate the most power from a controlled fixed-speed wind source. 

Students working on lab assignments outside.

Each team of five students included two who were completely remote, and were responsible for designing the 3D-printed part that was used to position their team’s blades in the wind turbine. 

“We really tried to give everyone, including the remote students, as close to a hands-on role as possible,” Kim said, noting that after months of quarantining and being isolated from friends, instructors and the campus, students seemed to really appreciate the opportunity to meet safely in person. 

Students made carbon fiber structural channel beams with prepreg material.

“The class seemed to work really well,” said Kim “I really emphasized the right culture to the students: a no blame, no shame culture where if they, lets say, got sick or were exposed or had concerns because of X, Y or Z, they didn’t need to justify telling me they couldn’t or shouldn’t come to class that week. I broadcast that message really clearly, and I thought the students were fantastic. They were excellent and very responsible about that.”

Many of these students are now in the structural engineering capstone design course this quarter, co-taught by Kim, who is also teaching a Repair of Aerospace Structures class that also conducts labs outside. 

Computer science student brings Black beauty products to UC San Diego

Jaida Day, a math-computer science student, started Black Beauty Near You to make beauty products more accessible for UC San Diego students. Photos courtesy of Jaida Day.

March 11, 2021--When Jaida Day arrived at UC San Diego to begin her undergraduate studies, she found a welcoming campus environment, peers and faculty to push her academically, beautiful beaches and opportunities to get involved in student organizations. But she also found there was something missing.

“I grew up in Los Angeles where I could go down the street and find the products I need for my hair and my skin, things of that sort, because there are other people who look like me in that area,” said Day. “But coming to La Jolla, I realized the beauty supply stores, the CVS, even the markets on campus, they don't have what I need for my hair and skin.”

Her options? Drive 30 minutes to the closest beauty supply that carried the items she needed; order her hygiene necessities online and have them shipped; or stock up at home during breaks and bring the products back to campus with her. With no car and only a few trips home each year, she recognized she wasn’t the only student facing this dilemma, and decided to take action.

“I was talking to my mom about it and she said ‘Well, you should come up with something to fix that.’ So that’s pretty much how Black Beauty Near You came about.”

The mathematics-computer science student put her web development skills to use, and launched her Black Beauty Near You business with a goal of making Black hair and skin care products more accessible to UC San Diego students. Through her website, people can order brushes, combs, bobby pins, braid charms, scalp oil, edge control, durags, makeup and other items they need.

For a time, Black Beauty Near You had a physical setup in the Black Resource Center’s The Shop, but with COVID-19 restrictions, sales are now all online. Day delivers the items to students on campus, and frequently changes up her inventory to reflect student requests.

To Day, this is just the first step, a stopgap measure until more permanent solutions are put in place. The UC San Diego Black Student Union—of which Day is co-publicity manager—is working with university administration to try and get more of these products that Black students need in markets on campus.

“My mind goes far. I know this isn't the only school where there's not Black beauty products on campus, and it would be nice if there could be better access to these items at more universities. It doesn’t have to be through Black Beauty Near You, but perhaps in the future I’ll find a way to help universities get these products on their campus, because I think it’s just a disconnect of knowing what is needed.”

In addition to working towards her math-computer science major—a combination of the mathematical theory and methods used in computer science, along with computer programming, structure, and algorithms—Day is also the web development chair of the Women in Computing undergraduate student organization, and was an intern for the Black Resource Center (BRC). She has a knack for finding ways to use her technical skills to empower her communities.

Day selling her products at the Black Resource Center's The Shop. With COVID-19 restrictions, sales are now all online.

As a BRC intern, Day organized an event called Engineering Orgs Near You, bringing engineering student organizations to the Black Resource Center to recruit new members and share what they do. For her internship final project, she created a website called Magnifying San Diego, where people new to campus can find information on local places to hang out, get their hair or nails done, eat, or find a therapist, with a focus on the Black community.

“Jaida is a brilliant, motivated, and self-less scholar and person. She was an exemplar as an intern at the BRC, but she has also continued to be a dedicated and active member of the Black community at UC San Diego,” said Porsia Curry, director of the Black Resource Center. “Her yearlong project not only blew us away, but continues to be a tremendous resource for Black students. Our center and community are better because of her contributions.”

As WiC’s web development chair, she led the development of the group’s new website, developed entirely from scratch.

“I had never done that before, I had always used templates to develop a website, but never from scratch,” said Day. “So, I was nervous. But WiC is the best community ever; they’re so welcoming, so supportive, so helpful. Myself and some of our other board members got together virtually every week over the summer to work on the website, and we got it done.”

Her advice to students is to branch out and try new things.

“If I had never gone to that first WiC meeting, I would have never had this supportive community in my actual major. Because it’s one thing to hang around with people I identify with as my race, but it’s another to be with people who get the struggle of being a computer science student. So definitely try to find your community or communities on campus. Go to those different org meetings, you never know what you’ll find.”

Always thinking big picture, Day also had advice for increasing underrepresented groups in the computer science field as a whole, and here at UC San Diego.

For starters, more computer science camps and coding programs like Kode with Klossy, where Day got her first introduction to computer science, are needed, particularly in underserved areas.

“The summer after my junior year I did a two-week coding boot camp program through Kode with Klossy, and I thought OK that’s what I want to do; I know I’m good at math and think I like computer science, so why not do both,” said Day. “More of those programs and classes in schools or even like the coding camp I did would be a good start, just so students can have the option to see if they like it. Because if I hadn’t done that coding camp, I would not be a computer science student. I couldn't even tell you what I’d be doing.”

Looking closer to campus, Day said she knows the UC San Diego admissions team is researching ways to reach more diverse groups of students and encourage them to attend UC San Diego, but emphasized the importance of this work.

“I probably only know one Black woman computer science student in each grade level,” she said. “We have to do better at bringing in more Black CS students. It’s isolating in class, and while I’ve gotten over it, it can be really isolating as a first year student when you come in and don’t see anyone that looks like you. We definitely have to do better with that.”

In October 2020, the Jacobs School of Engineering launched a Student and Faculty Racial Equity Task Force to assess and improve its efforts to create equitable learning and working environments, as one piece of UC San Diego’s larger efforts to address this issue. Learn more through the Office of Equity, Diversity and Inclusion. The Department of Computer Science and Engineering and the Division of Physical Sciences (which administers the Math-Computer Science major) are also actively engaged in addressing diversity issues.

With gene therapy, scientists develop opioid-free solution for chronic pain

March 10, 2021 -- A gene therapy for chronic pain could offer a safer, non-addictive alternative to opioids. Researchers at the University of California San Diego developed the new therapy, which works by temporarily repressing a gene involved in sensing pain. It increased pain tolerance in mice, lowered their sensitivity to pain and provided months of pain relief without causing numbness.

The researchers report their findings in a paper published Mar. 10 in Science Translational Medicine.

The gene therapy could be used to treat a broad range of chronic pain conditions, from lower back pain to rare neuropathic pain disorders—conditions for which opioid painkillers are the current standard of care.

woman in business attire
Ana Moreno, UC San Diego bioengineering alumna and CEO and co-founder of Navega Therapeutics

“What we have right now does not work,” said first author Ana Moreno, a bioengineering alumna from the UC San Diego Jacobs School of Engineering. Opioids can make people more sensitive to pain over time, leading them to rely on increasingly higher doses. “There’s a desperate need for a treatment that’s effective, long-lasting and non-addictive.”

The idea for such a treatment emerged when Moreno was a Ph.D. student in UC San Diego bioengineering professor Prashant Mali’s lab. Mali had been investigating the possibility of applying CRISPR-based gene therapy approaches to rare as well as common human diseases. Moreno’s project focused on exploring potential therapeutic avenues. One day, she came across a paper about a genetic mutation that causes humans to feel no pain. This mutation inactivates a protein in pain-transmitting neurons in the spinal cord, called NaV1.7. In individuals lacking functional NaV1.7, sensations like touching something hot or sharp do not register as pain. On the other hand, a gene mutation that leads to overexpression of NaV1.7 causes individuals to feel more pain.

When Moreno read this, it clicked. “By targeting this gene, we could alter the pain phenotype,” she said. “What’s also cool is that this gene is only involved in pain. There aren’t any severe side effects observed with this mutation.”

Non-permanent gene therapy

Moreno had been working on gene repression using the CRISPR gene editing tool as part of her dissertation. Specifically, she was working with a version of CRISPR that uses what’s called “dead” Cas9, which lacks the ability to cut DNA. Instead, it sticks to a gene target and blocks its expression.

Moreno saw an opportunity to use this approach to repress the gene that codes for NaV1.7. She points out an appeal of this approach: “It’s not cutting out any genes, so there are no permanent changes to the genome. You wouldn’t want to permanently lose the ability to feel pain,” she said. “One of the biggest concerns with CRISPR gene editing is off-target effects. Once you cut DNA, that’s it. You can’t go back. With dead Cas9, we’re not doing something irreversible.”

Mali, who is a co-senior author of the study, says that this use of dead Cas9 opens the door to using gene therapy to target common diseases and chronic ailments.

“In some common diseases, the issue is that a gene is being misexpressed. You don’t want to completely shut it down,” he said. “But if you could turn down the dose of that gene, you could bring it to a level where it is not pathogenic. That is what we are doing here. We don’t completely take away the pain phenotype, we dampen it.”

Moreno and Mali co-founded the spinoff company Navega Therapeutics to work on translating this gene therapy approach, which they developed at UC San Diego, into the clinic. They teamed up with Tony Yaksh, an expert in pain systems and a professor of anesthesiology and pharmacology at UC San Diego School of Medicine. Yaksh is a scientific advisor to Navega and co-senior author of the study.

Early lab studies

The researchers engineered a CRISPR/dead Cas9 system to target and repress the gene that codes for NaV1.7. They administered spinal injections of their system to mice with inflammatory and chemotherapy-induced pain. These mice displayed higher pain thresholds than mice that did not receive the gene therapy; they were slower to withdraw a paw from painful stimuli (heat, cold or pressure) and spent less time licking or shaking it after being hurt.

The treatment was tested at various timepoints. It was still effective after 44 weeks in the mice with inflammatory pain and 15 weeks in those with chemotherapy-induced pain. The length of duration is still being tested, researchers said, and is expected to be long-lasting. Moreover, the treated mice did not lose sensitivity or display any changes in normal motor function.

To validate their results, the researchers performed the same tests using another gene editing tool called zinc finger proteins. It’s an older technique than CRISPR, but it does the same job. Here, the researchers designed zinc fingers that similarly bind to the gene target and block expression of NaV1.7. Spinal injections of the zinc fingers in mice produced the same results as the CRISPR-dead Cas9 system.

“We were excited that both approaches worked,” Mali said. “The beauty about zinc finger proteins is that they are built on the scaffold of a human protein. The CRISPR system is a foreign protein that comes from bacteria, so it could cause an immune response. That’s why we explored zinc fingers as well, so we have an option that might be more translatable to the clinic.”

The researchers say this solution could work for a large number of chronic pain conditions arising from increased expression of NaV1.7, including diabetic polyneuropathy, erythromelalgia, sciatica and osteoarthritis. It could also provide relief for patients undergoing chemotherapy.

And due to its non-permanent effects, this therapeutic platform could address a poorly met need for a large population of patients with long-lasting (weeks to months) but reversible pain conditions, Yaksh said.

“Think of the young athlete or wounded war fighter in which the pain may resolve with wound healing,” he said. “We would not want to permanently remove the ability to sense pain in these people, especially if they have a long life expectancy. This CRISPR/dead Cas9 approach offers this population an alternative therapeutic intervention—that’s a major step in the field of pain management.”  

Researchers at UC San Diego and Navega will next work on optimizing both approaches (CRISPR and zinc fingers) for targeting the human gene that codes for NaV1.7. Trials in non-human primates to test for efficacy and toxicity will follow. Researchers expect to file for an IND and to commence human clinical trials in a couple years.

Paper title: “Long-lasting Analgesia via Targeted in situ Repression of NaV1.7.” Co-authors include Fernando Alemán, Glaucilene F. Catroli, Matthew Hunt, Michael Hu, Amir Dailamy, Andrew Pla, Sarah A. Woller, Nathan Palmer, Udit Parekh, Daniella McDonald, Amanda J. Robers, Vanessa Goodwill, Ian Dryden, Robert F. Hevner, Lauriane Delay and Gilson Gonçalves dos Santos.

This work was supported by UC San Diego Institutional Funds and the National Institutes of Health (grants R01HG009285, RO1CA222826, RO1GM123313, R43CA239940, R43NS112088, R01NS102432, R01NS099338).

Disclosure: Ana Moreno, Fernando Alemán, Prashant Mali and Tony Yaksh have a financial interest in Navega Therapeutics. The terms of these arrangements have been reviewed and approved by the University of California San Diego in accordance with its conflict of interest policies.

'Wearable microgrid' uses the human body to sustainably power small gadgets

March 9, 2021 -- Nanoengineers at the University of California San Diego have developed a “wearable microgrid” that harvests and stores energy from the human body to power small electronics. It consists of three main parts: sweat-powered biofuel cells, motion-powered devices called triboelectric generators, and energy-storing supercapacitors. All parts are flexible, washable and can be screen printed onto clothing.

The technology, reported in a paper published Mar. 9 in Nature Communications, draws inspiration from community microgrids.

“We’re applying the concept of the microgrid to create wearable systems that are powered sustainably, reliably and independently,” said co-first author Lu Yin, a nanoengineering Ph.D. student at the UC San Diego Jacobs School of Engineering. “Just like a city microgrid integrates a variety of local, renewable power sources like wind and solar, a wearable microgrid integrates devices that locally harvest energy from different parts of the body, like sweat and movement, while containing energy storage.” 

Stretchable electronics on a white long sleeved shirt
The wearable microgrid uses energy from human sweat and movement to power an LCD wristwatch and electrochromic device. Photos by Lu Yin

The wearable microgrid is built from a combination of flexible electronic parts that were developed by the Nanobioelectronics team of UC San Diego nanoengineering professor Joseph Wang, who is the director of the Center for Wearable Sensors at UC San Diego and corresponding author on the current study. Each part is screen printed onto a shirt and placed in a way that optimizes the amount of energy collected.

Biofuel cells that harvest energy from sweat are located inside the shirt at the chest. Devices that convert energy from movement into electricity, called triboelectric generators, are positioned outside the shirt on the forearms and sides of the torso near the waist. They harvest energy from the swinging movement of the arms against the torso while walking or running. Supercapacitors outside the shirt on the chest temporarily store energy from both devices and then discharge it to power small electronics.

Harvesting energy from both movement and sweat enables the wearable microgrid to power devices quickly and continuously. The triboelectric generators provide power right away as soon as the user starts moving, before breaking a sweat. Once the user starts sweating, the biofuel cells start providing power and continue to do so after the user stops moving.

“When you add these two together, they make up for each other’s shortcomings,” Yin said. “They are complementary and synergistic to enable fast startup and continuous power.” The entire system boots two times faster than having just the biofuel cells alone, and lasts three times longer than the triboelectric generators alone.

The wearable microgrid was tested on a subject during 30-minute sessions that consisted of 10 minutes of either exercising on a cycling machine or running, followed by 20 minutes of resting. The system was able to power either an LCD wristwatch or a small electrochromic display—a device that changes color in response to an applied voltage—throughout each 30-minute session.

Greater than the sum of its parts

Stretchable electronics on a white shirt
Biofuel cells harvest energy from sweat.

The biofuel cells are equipped with enzymes that trigger a swapping of electrons between lactate and oxygen molecules in human sweat to generate electricity. Wang’s team first reported these sweat-harvesting wearables in a paper published in 2013. Working with colleagues at the UC San Diego Center for Wearable Sensors, they later updated the technology to be stretchable and powerful enough to run small electronics.

The triboelectric generators are made of a negatively charged material, placed on the forearms, and a positively charged material, placed on the sides of the torso. As the arms swing against the torso while walking or running, the oppositely charged materials rub against each and generate electricity.

Stretchable electronics on a white shirt
Triboelectric generator harvests energy from movement.

Each wearable provides a different type of power. The biofuel cells provide continuous low voltage, while the triboelectric generators provide pulses of high voltage. In order for the system to power devices, these different voltages need to be combined and regulated into one stable voltage. That’s where the supercapacitors come in; they act as a reservoir that temporarily stores the energy from both power sources and can discharge it as needed.

Yin compared the setup to a water supply system.

“Imagine the biofuel cells are like a slow flowing faucet and the triboelectric generators are like a hose that shoots out jets of water,” he said. “The supercapacitors are the tank that they both feed into, and you can draw from that tank however you need to.”

Stretchable electronics on a white shirt
Supercapacitors store energy and discharge it to other electronic devices that the user is wearing.

All of the parts are connected with flexible silver interconnections that are also printed on the shirt and insulated by waterproof coating. The performance of each part is not affected by  repeated bending, folding and crumpling, or washing in water—as long as no detergent is used.

The main innovation of this work is not the wearable devices themselves, Yin said, but the systematic and efficient integration of all the devices.

“We’re not just adding A and B together and calling it a system. We chose parts that all have compatible form factors (everything here is printable, flexible and stretchable); matching performance; and complementary functionality, meaning they are all useful for the same scenario (in this case, rigorous movement),” he said.

Other applications

This particular system is useful for athletics and other cases where the user is exercising. But this is just one example of how the wearable microgrid can be used. “We are not limiting ourselves to this design. We can adapt the system by selecting different types of energy harvesters for different scenarios,” Yin said.

The researchers are working on other designs that can harvest energy while the user is sitting inside an office, for example, or moving slowly outside.

Paper: “A Self-Sustainable Wearable Multi-Modular E-Textile Bioenergy Microgrid System.” Co-authors include Kyeong Nam Kim*, Jian Lv*, Farshad Tehrani, Muyang Lin, Zuzeng Lin, Jong-Min Moon, Jessica Ma, Jialu Yu and Sheng Xu.

*These authors contributed equally to this work.

This work was supported by the UC San Diego Center for Wearable Sensors and the National Research Foundation of Korea.

Adhesion, contractility enable metastatic cells to go against the grain

Schematic of cells migrating over a step gradient. For durotactic cells, higher tractions and longer bond lifetimes on the stiff side drive adhesion maturation and net migration toward the stiffer substrate. For adurotactic cells, tractions balance across the boundary due to longer bond lifetimes on the soft side of the step gradient.

March 9, 2021--Bioengineers at the University of California San Diego and San Diego State University have discovered a key feature that allows cancer cells to break from typical cell behavior and migrate away from the stiffer tissue in a tumor, shedding light on the process of metastasis and offering possible new targets for cancer therapies. 

It has been well documented that cells typically migrate away from softer tissue to stiffer regions within the extracellular matrix—a process called durotaxis. Metastatic cancer cells are the rare exception to this rule, moving away from the stiffer tumor tissue to softer tissue, and spreading the cancer as they migrate. What enables these cells to display this atypical behavior, called adurotaxis, and migrate away from the stiffer tumor hasn’t been well understood.

Building off previous research led by bioengineers in UC San Diego Professor Adam Engler’s lab, which found that weakly adherent, or less sticky, cells migrated and invaded other tissues more than strongly adherent cells, the team has now shown that the contractility of these weakly adherent cells is what enables them to move to less stiff tissue. By chemically reducing the contractility of weakly adherent cells, they become durotactic, migrating toward stiffer tissue; increasing the contractility of strongly adherent cells makes them migrate down the stiffness gradient. The researchers reported their findings on March 9 in Cell Reports. 

“The main takeaway here is that the less adherent, more contractile cells are the ones that don’t exhibit typical durotactic behavior,” said Benjamin Yeoman, a bioengineering PhD student in the joint program at UC San Diego and SDSU, and first author of the study. “But beyond that, we see this in several different types of cancer, which opens up the possibility that maybe there’s this commonality between different types of carcinomas that could potentially be a target for a more universal treatment.”

To find out what enables this atypical behavior, Yeoman first used computational models developed in bioengineer Parag Katira’s lab in the SDSU Department of Mechanical Engineering, to try and pinpoint what was different about the cells that were able to move against the stiffness gradient. The models showed that changing a cell’s contractile force could modulate the cell’s adhesion strength in an environment of a certain stiffness, which would change their ability to be durotactic. To confirm the computational results, Yeoman used a microfluidic flow chamber device designed for previous research on cell adherence in Engler’s lab, to experiment with the contractility of real cancer cells from breast cancer, prostate cancer and lung cancer cell lines. 

“It worked perfectly,” said Katira, co-corresponding author of the paper. “It was really an ideal collaboration, where you have experimental results that show something is different; then you have a computational model that predicts it and explains why something is happening; and then you go back and do experiments to actually test if that’s going on. All of these blocks fell into place to bring this interesting result.”

The microfluidic cell-sorting device developed in Engler’s lab allowed the researchers to isolate cells based on adhesion strength. Credit: Benjamin Yeoman

The parallel plate flow chamber device used to test the computational theory was designed by engineers in Engler’s lab studying the effect of adherence on cell metastasis and cancer recurrence, and first described in Cancer Research in February 2020. Using this patent pending device, the researchers now isolated cells based on adhesion strength, and seeded them onto photopatterned hydrogels with alternating soft and stiff profiles. The researchers used time-lapse video microscopy to watch how the cells moved, and found that strongly adherent cells would durotax, moving to stiffer sections, while weakly adherent cells would migrate to softer tissue. 

After investigating several potential mechanisms within the cell enabling this behavior, the team focused on contractility as a key marker of its ability to adurotax. By modulating the number of active myosin motors within the cell— a marker of contractile ability—they were able to get previously durotactic cells to migrate away from stiffer tissue, and previously adurotactic, weakly adherent cells to migrate up the stiffness gradient.

The researchers hope that this work, and the further development of the microfluidic cell sorting device, will enable better assessments of disease prognosis in the future. Their ultimate aim is to be able to use the parallel plate flow chamber as a way to measure the metastatic potential of a patient’s cells, and use that as a predictor for cancer recurrence to drive more effective treatments and outcomes. 

“Understanding the mechanisms that govern invasion of many different tumor types enables us to better use this device to sort and count cells with weak adhesion and their percentage in a tumor, which may correlate with poor patient outcomes,” said Adam Engler, professor of bioengineering at UC San Diego and co-corresponding author of the paper. 

The researchers cautioned that this discovery doesn’t preclude other mechanisms from playing a role in the metastasis of cells. It does, however, highlight the important role that adherence and contractility do play, which needs to be studied further.

“The point is not to say that nothing else can drive cells away from a tumor,” said Katira. “There could be other drivers for metastasis, but this is clearly an important mechanism, and the fact that cells can do this across lung, breast and pancreatic cancer cells tells us this is generalizable.”

Going forward, the engineers plan to study other parameters that may contribute to adurotaxis; investigate the effect of different types of tumor environments on a cell’s ability to adurotax; and move from the individual cell scale to the population scale, to see how adhesion and contractility function and can be modulated when there is a mixed population of cells with unique mechanical properties.

This project was funded by grants from the National Science Foundation, National Institutes of Health and the Army Research Office. 

Three-layered masks most effective against large respiratory droplets

The droplet impacting on the mask surface is recorded at 20,000 frames per second. These time sequence images of droplet impingement on a single-, double-, and triple-layer masks show the total number count of atomized droplets is significantly higher for the single-layer mask in comparison with the double-layer mask, while only a single droplet penetrates through the triple-layer mask. Credit: Basu et al, Science Advances, March 5 2021

March 5, 2021-- If you are going to buy a face mask to protect yourself and others from COVID-19, make sure it’s a three-layered mask. You might have already heard this recommendation, but researchers have now found an additional reason why three-layered masks are safer than single or double-layered alternatives. 

While this advice was originally based on studies that showed three layers prevented small particles from passing through the mask pores, researchers have now shown that three-layered surgical masks are also most effective at stopping large droplets from a cough or sneeze from getting atomized into smaller droplets. These large cough droplets can penetrate through the single- and double-layer masks and atomize to much smaller droplets, which is particularly crucial since these smaller droplets (often called aerosols) are able to linger in the air for longer periods of time. Researchers studied surgical masks with one, two and three layers to demonstrate this behavior. 

The researchers reported their results in Science Advances on March 5

The team notes that single and double-layer masks do provide protection in blocking some of the liquid volume of the original droplet and are significantly better than wearing no mask at all. They hope their findings on ideal mask pore size, material thickness, and layering could be used by manufacturers to produce the most effective masks designs.

Using a droplet generator and a high-speed time-lapse camera, the team of engineers from the University of California San Diego, Indian Institute of Science and University of Toronto found that, counterintuitively, large respiratory droplets containing virus emulating particles (VEPs) actually get atomized when they hit a single-layer mask, and many of these VEPs pass through that layer. Think of it like a water droplet breaking into smaller droplets as it’s being squeezed through a sieve. For a 620 micron droplet—the size of a large droplet from a cough or sneeze—a single-layer surgical mask only restricts about 30 percent of the droplet volume; a double-layer mask performs better, restricting about 91 percent of the droplet volume; while a three layer mask has negligible, nearly zero droplet ejection. This video illustrates the research as well.

“While it is expected that large solid particles in the 500–600-micron range should be stopped by a single-layer mask with average pore size of 30 micron, we are showing that this is not the case for liquid droplets,” said Abhishek Saha, professor of mechanical and aerospace engineering at UC San Diego and a co-author of the paper. “If these larger respiratory droplets have enough velocity, which happens for coughs or sneezes, when they land on a single-layer of this material it gets dispersed and squeezed through the smaller pores in the mask.” 

Schematic diagram of viral load getting trapped inside the mask layer. Droplets and virus are not drawn to scale. Basu et al, Science Advances, March 5 2021

This is a problem. Droplet physics models have shown that while these large droplets are expected to fall to the ground very quickly due to gravity, these now smaller, 50-80 micron-sized droplets coming through the first and second layer of a mask will linger in the air, where they can spread to people at larger distances. 

The team of engineers— which also includes Professors Swetaprovo Chaudhuri from University of Toronto, and Saptarshi Basu of the Indian Institute of Science— were well-versed in this type of experiment and analysis, though they were used to studying the aerodynamics and physics of droplets for applications including propulsion systems, combustion, or thermal sprays. They turned their attention to respiratory droplet physics last year when the COVID-19 pandemic broke out, and since then, have been studying the transport of these respiratory droplets and their roles in transmission of Covid-19 type diseases

“We do droplet impact experiments a lot in our labs,” said Saha. “For this study, a special generator was used to produce a relatively fast-moving droplet. The droplet was then allowed to land on a piece of mask material—that could be a single layer, double, or triple layer, depending on which we’re testing. Simultaneously, we use a high-speed camera to see what happens to the droplet.”

Using the droplet generator, they’re able to alter the size and speed of the droplet to see how that affects the flow of the particle. 

Going forward, the team plans to investigate the role of different mask materials, as well as the effect of damp or wet masks, on particle attrition. 

Coronavirus-like particles could ensure reliability of simpler, faster COVID-19 tests

Series of test tubes containing yellow and pink liquid
RT-LAMP test samples showing positive (yellow) and negative (pink) results. Image credit: Soo Khim Chan

March 2, 2021 -- Rapid COVID-19 tests are on the rise to deliver results faster to more people, and scientists need an easy, foolproof way to know that these tests work correctly and the results can be trusted. Nanoparticles that pass detection as the novel coronavirus could be just the ticket.

Such coronavirus-like nanoparticles, developed by nanoengineers at the University of California San Diego, would serve as something called a positive control for COVID-19 tests. Positive controls are samples that always test positive. They are run and analyzed right alongside patient samples to verify that COVID-19 tests are working consistently and as intended.

The positive controls developed at UC San Diego offer several advantages over the ones currently used in COVID-19 testing: they do not need to be kept cold; they are easy to manufacture; they can be included in the entire testing process from start to finish, just like a patient sample; and because they are not actual virus samples from COVID-19 patients, they do not pose a risk of infection to the people running the tests.

Researchers led by Nicole Steinmetz, a professor of nanoengineering at UC San Diego, published their work in the journal Biomacromolecules.

This work builds on an earlier version of the positive controls that Steinmetz’s lab developed for the RT-PCR test, which is the gold standard for COVID-19 testing. The positive controls in the new study can be used not only for the RT-PCR test, but also for a cheaper, simpler and faster test called the RT-LAMP test, which can be done on the spot and provide results in about an hour.

Having a hardy tool to ensure these tests are running accurately—especially for low-tech diagnostic assays like the RT-LAMP—is critical, Steinmetz said. It could help enable rapid, mass testing of COVID-19 in low-resource, underserved areas and other places that do not have access to sophisticated testing equipment, specialized reagents and trained professionals.

Upgraded positive controls

Goto Flickr
Coronavirus-like nanoparticles, made from plant viruses and bacteriophage, could serve as positive controls for the RT-LAMP test. Image credit: Soo Khim Chan

The new positive controls are essentially tiny virus shells—made of either