News Release

These energy-packed batteries work well in extreme cold and heat

Study first author Guorui Cai, a nanoengineering postdoctoral researcher at UC San Diego, prepares a battery pouch cell for testing at subfreezing temperature. Photos by David Baillot/UC San Diego Jacobs School of Engineering

July 4, 2022 -- Engineers at the University of California San Diego have developed lithium-ion batteries that perform well at freezing cold and scorching hot temperatures, while packing a lot of energy. The researchers accomplished this feat by developing an electrolyte that is not only versatile and robust throughout a wide temperature range, but also compatible with a high energy anode and cathode.

The temperature-resilient batteries are described in a paper published the week of July 4 in Proceedings of the National Academy of Sciences (PNAS).

Such batteries could allow electric vehicles in cold climates to travel farther on a single charge; they could also reduce the need for cooling systems to keep the vehicles’ battery packs from overheating in hot climates, said Zheng Chen, a professor of nanoengineering at the UC San Diego Jacobs School of Engineering and senior author of the study.

“You need high temperature operation in areas where the ambient temperature can reach the triple digits and the roads get even hotter. In electric vehicles, the battery packs are typically under the floor, close to these hot roads,” explained Chen, who is also a faculty member of the UC San Diego Sustainable Power and Energy Center. “Also, batteries warm up just from having a current run through during operation. If the batteries cannot tolerate this warmup at high temperature, their performance will quickly degrade.”

In tests, the proof-of-concept batteries retained 87.5% and 115.9% of their energy capacity at -40 and 50 C (-40 and 122 F), respectively. They also had high Coulombic efficiencies of 98.2% and 98.7% at these temperatures, respectively, which means the batteries can undergo more charge and discharge cycles before they stop working.

High temperature performance of battery pouch cells being tested in an oven heated to 50 C.

The batteries that Chen and colleagues developed are both cold and heat tolerant thanks to their electrolyte. It is made of a liquid solution of dibutyl ether mixed with a lithium salt. A special feature about dibutyl ether is that its molecules bind weakly to lithium ions. In other words, the electrolyte molecules can easily let go of lithium ions as the battery runs. This weak molecular interaction, the researchers had discovered in a previous study, improves battery performance at sub-zero temperatures. Plus, dibutyl ether can easily take the heat because it stays liquid at high temperatures (it has a boiling point of 141 C, or 286 F).

Stabilizing lithium-sulfur chemistries

What’s also special about this electrolyte is that it is compatible with a lithium-sulfur battery, which is a type of rechargeable battery that has an anode made of lithium metal and a cathode made of sulfur. Lithium-sulfur batteries are an essential part of next-generation battery technologies because they promise higher energy densities and lower costs. They can store up to two times more energy per kilogram than today’s lithium-ion batteries—this could double the range of electric vehicles without any increase in the weight of the battery pack. Also, sulfur is more abundant and less problematic to source than the cobalt used in traditional lithium-ion battery cathodes.

But there are problems with lithium-sulfur batteries. Both the cathode and anode are super reactive. Sulfur cathodes are so reactive that they dissolve during battery operation. This issue gets worse at high temperatures. And lithium metal anodes are prone to forming needle-like structures called dendrites that can pierce parts of the battery, causing it to short-circuit. As a result, lithium-sulfur batteries only last up to tens of cycles.

Zheng Chen, professor of nanoengineering at UC San Diego.

“If you want a battery with high energy density, you typically need to use very harsh, complicated chemistry,” said Chen. “High energy means more reactions are happening, which means less stability, more degradation. Making a high-energy battery that is stable is a difficult task itself—trying to do this through a wide temperature range is even more challenging.”

The dibutyl ether electrolyte developed by the UC San Diego team prevents these issues, even at high and low temperatures. The batteries they tested had much longer cycling lives than a typical lithium-sulfur battery. “Our electrolyte helps improve both the cathode side and anode side while providing high conductivity and interfacial stability,” said Chen.

The team also engineered the sulfur cathode to be more stable by grafting it to a polymer. This prevents more sulfur from dissolving into the electrolyte.

Next steps include scaling up the battery chemistry, optimizing it to work at even higher temperatures and further extending cycle life.

Paper: “Solvent selection criteria for temperature-resilient lithium-sulfur batteries.” Co-authors include Guorui Cai, John Holoubek, Mingqian Li, Hongpeng Gao, Yijie Yin, Sicen Yu, Haodong Liu, Tod A. Pascal and Ping Liu, all at UC San Diego.

This work was supported by an Early Career Faculty grant from 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 the Office of Vehicle Technologies of the U.S. Department of Energy through the Advanced Battery Materials Research Program (Battery500 Consortium, contract DE-EE0007764). 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).

US and Czech scientists collaborate to explore gamma-ray production with high power lasers

July 1, 2022 -- The U.S. National Science Foundation (NSF) and the Czech Science Foundation (GACR) are funding a new collaborative project of scientists from the University of California San Diego in the U.S. and ELI Beamlines (Institute of Physics of the Czech Academy of Sciences) in the Czech Republic which aims to leverage the capabilities of the ELI Beamlines multi-petawatt laser facility. Researchers hope these experiments can achieve a breakthrough by demonstrating efficient generation of dense gamma-ray beams.

Stellar objects like pulsars can create matter and antimatter directly from light because of their extreme energies. In fact, the magnetic field, or “magnetosphere,” of a pulsar is filled with electrons and positrons that are created by colliding photons.

Reproducing the same phenomena in a laboratory on Earth is extremely challenging. It requires a dense cloud of photons with energies that are millions of times higher than visible light, an achievement that has so far eluded the scientists working in this field. However, theories suggest that high-power lasers ought to be able to produce such a photon cloud.

As the first international laser research infrastructure dedicated to the application of high-power and high-intensity lasers, the Extreme Light Infrastructure (ELI ERIC) facilities will enable such research possibilities. The ELI ERIC is a multi-site research infrastructure based on specialized and complementary facilities ELI Beamlines (Czech Republic) and ELI ALPS (Hungary). The new capabilities at ELI will create the necessary conditions to test the theories in a laboratory.

Super computer simulation of energetic gamma-ray emission (yellow arrows) by a dense plasma (green) irradiated by a high-intensity laser beam (red and blue). The laser propagates from left to right, with the emitted photons flying in the same direction. The smooth blue and red regions represent a strong magnetic field generated by the plasma, whereas the oscillation region corresponds to the laser magnetic field.

This project combines theoretical expertise from the University of California San Diego (U.S.), experimental expertise from ELI Beamlines, as well as target fabrication and engineering expertise from General Atomics (U.S.). The roughly $1,000,000 project, jointly funded by NSF and GACR, will be led by Prof. Alexey Arefiev at UC San Diego. Target development for rep-rated deployment will take place at General Atomics, led by Dr. Mario Manuel, while the primary experiments will be conducted at ELI Beamlines by a team led by Dr. Florian Condamine and Dr. Stefan Weber.

The concept for the project was developed by Arefiev’s research group at UC San Diego, which specializes in supercomputer simulations of intense light-matter interactions. The approach for this project leverages an effect that occurs when electrons in a plasma are accelerated to near light speeds by a high-powered laser. This effect is called “relativistic transparency” because it causes a previously opaque dense plasma to become transparent to laser light.

In this regime, extremely strong magnetic fields are generated as the laser propagates through the plasma. During this process, the relativistic electrons oscillate in the magnetic field, which in turn causes the emission of gamma-rays, predominantly in the direction of the laser.

“It is very exciting that we are in a position to generate the sort of magnetic fields that previously only existed in extreme astrophysical objects, such as neutron stars,” says Arefiev. “The ability of the ELI Beamlines lasers to reach very high on-target intensity is the key to achieving this regime.”

These experiments will provide the first statistically relevant study of gamma-ray generation using high-powered lasers. Researchers hope the work will open the way for secondary high-energy photon sources that can be used not only for fundamental physics studies, but also for a range of important industrial applications such as material science, nuclear waste imaging, nuclear fuel assay, security, high-resolution deep-penetration radiography, etc.  Such “extreme imaging” requires robust, reproducible, and well-controlled gamma-ray sources. The present proposal aims exactly at the development of such unprecedented sources.

The experiments will be greatly assisted by another technological advance. Until recently, high-power laser facilities could execute about one shot every hour, which limited the amount of data that could be collected. However, new facilities like ELI Beamlines are capable of multiple shots per second. These capabilities allow for statistical studies of laser-target interactions in ways that were impossible only a few years ago. That means a shift in the way such experiments are designed and executed is necessary to take full advantage of the possibilities.

“The P3 installation at ELI Beamlines is a unique and versatile experimental infrastructure for sophisticated high-field experiments and perfectly adapted to the planned program,” comments Condamine. Weber notes, “This collaboration between San Diego and ELI Beamlines is expected to be a major step forward to bring together the US community and the ELI-team for joint experiments.”

Thus, a major part of this project is training the next generation of scientists at ELI Beamlines to develop techniques that can fully leverage its rep-rated capabilities. UC San Diego students and postdoctoral researchers will also train on rep-rated target deployment and data acquisition on General Atomics’ new GALADRIEL laser facility to help improve the efficiency of the experiments conducted at ELI Beamlines.

The P3 (Plasma Physics Platform)-installation at ELI Beamlines where the experiments will take place.N

“This is the first project funded by the Czech Science Foundation and the US National Science Foundation. I believe that the new collaboration between the agencies will lead to a number of successful projects and collaborating scientific teams from the Czech Republic and the USA will benefit from it,” says GACR president Dr. Petr Baldrian.

“We are thrilled to be working with our counterparts in the Czech Republic to further expand international scientific cooperation in artificial intelligence, nanotechnology, and plasma science research. I am optimistic this will be the first of many collaborative projects between NSF and GACR,” says the Director of NSF, Dr. Sethuraman Panchanathan.

UC San Diego Center for Visual Computing celebrates a strong showing at SIGGRAPH 2022

June 23, 2022 

UC San Diego faculty and research teams affiliated with the UC San Diego Center for Visual Computing are well represented, yet again, at SIGGRAPH 2022, which is the top academic venue for the computer graphics field. 

"By my count, UC San Diego researchers are on more papers and presentations at SIGGRAPH 2022 than any other school. It's great to be recognized for our world-class research," said Ravi Ramamoorthi, the UC San Diego computer science professor who leads the Center for Visual Computing.  Besides Ramamoorthi, UC San Diego faculty with papers at SIGGRAPH include assistant professors Hao Su, Albert Chern and Tzu-Mao Li, all of whom have been hired in the past 5 years, as part of the Center for Visual Computing’s rapid growth. Their research covers a broad range of topics, including physical simulation, realistic image synthesis or rendering, geometry processing, differentiable programming and computational photography.  

SIGGRAPH 2022 papers and presentations with UC San Diego / Center for Visual Computing / Department of Computers Science and Engineering affiliations are listed below. 

1. Approximate Convex Decomposition for 3D Meshes With Collision-aware Concavity and Tree Search

Project description: Approximate convex decomposition enables efficient geometry processing algorithms specifically designed for convex shapes (e.g., collision detection). We propose a method that is better to preserve collision conditions of the input shape with fewer components. It thus supports delicate and efficient object interaction in downstream applications.

 

2. Covector Fluids

Project description: We simulate Euler equations for inviscid fluids by using a novel formulation based on covectors. This new formulation is an entirely velocity-based method in the vein of advection-projection methods while emulating vortex methods. This allows for capturing more intricate vortex dynamics and reducing dissipation of energy with low computational overhead.

 

3. Designing Perceptual Puzzles by Differentiating Probabilistic Programs

Project description: We design new examples of visual illusions like "The Dress" by finding "adversarial examples" for principled models of human perception — specifically probabilistic models, which treat vision as Bayesian inference. To perform this search efficiently, we design a differentiable probabilistic programming language, exposing MCMC inference as a first-class differentiable function.

 

4. Filament Based Plasma

Project description: We assemble a computational pipeline for procedurally generating the visual appearance of our sun. Using Lagrangian elements, the features of the solar atmosphere are reconstructed at a high level of detail.
 

5. Neural Jacobian Fields: Learning Intrinsic Mappings of Arbitrary Meshes

Project description: We introduce a framework for deep learning of deformations of meshes. The trained network is highly accurate and produces realistic results and can be applied to meshes of arbitrary triangulations and not a fixed one. We show various experiments such as UV mapping, elastic deformations, and learning to repose humans.

 

6. Photon-driven Neural Reconstruction for Path Guiding

Project description: We present a path-guiding approach that can reconstruct high-quality sampling distributions using an offline trained neural network. We leverage photons traced from light sources for sampling density reconstruction, which is effective for challenging scenes with global illumination. We further partition the scene space into an adaptive hierarchical grid.

 

7. Rendering Neural Materials on Curved Surfaces

Project description: Neural material representations address some limitations of traditional analytic BRDFs. However, they still approximate the material on an infinite plane, which prevents them from correctly handling silhouette and parallax effects. This paper proposes neural materials capable of correctly handling such silhouette effects by taking into account the curvature information.

 

8. Searching for Fast Demosaicking Algorithms

Project description: We present a method to automatically synthesize a Pareto frontier of efficient, high-quality e-mosaicking algorithms across a range of computational budgets. It performs a multi-objective, discrete-continuous optimization which simultaneously solves for the program structure and parameters that best trade off computational cost and image quality.

 

9. SofGAN: A Portrait Image Generator With Dynamic Styling

Project description: SofGAN is a portrait generator that allows for high-quality rendering with attribute controlling over camera pose, geometry, and texture styles.

10. A Unified Newton Barrier Method for Multibody Dynamics

Project description: We present a simulation framework for multibody dynamics with optimization time integration. Our method naturally supports mixed rigid-deformables and mixed codimensional geometries while providing guaranteed robustness and accurate resolution of frictional contact and a wide range of articulation constraints, including restitution.

UC San Diego Center for Visual Computing celebrates a strong showing at SIGGRAPH 2022

June 23, 2022: UC San Diego faculty and research teams affiliated with the UC San Diego Center for Visual Computing are well represented, yet again, at SIGGRAPH 2022, which is the top academic venue for the computer graphics field. 

Images related to three of the ten UC San Diego projects being presented at SIGGRAPH 2022.

"By my count, UC San Diego researchers are on more papers and presentations at SIGGRAPH 2022 than any other school. It's great to be recognized for our world-class research," said Ravi Ramamoorthi, the UC San Diego computer science professor who leads the Center for Visual Computing. Besides Ramamoorthi, UC San Diego faculty with papers at SIGGRAPH include assistant professors Hao Su, Albert Chern and Tzu-Mao Li, all of whom have been hired in the past 5 years, as part of the Center for Visual Computing’s rapid growth. Their research covers a broad range of topics, including physical simulation, realistic image synthesis or rendering, geometry processing, differentiable programming and computational photography.  

SIGGRAPH 2022 papers and presentations with UC San Diego / Center for Visual Computing / Department of Computers Science and Engineering affiliations are listed below. 

1. Approximate Convex Decomposition for 3D Meshes With Collision-aware Concavity and Tree Search
Project description: Approximate convex decomposition enables efficient geometry processing algorithms specifically designed for convex shapes (e.g., collision detection). We propose a method that is better to preserve collision conditions of the input shape with fewer components. It thus supports delicate and efficient object interaction in downstream applications.

2. Covector Fluids
Project description: We simulate Euler equations for inviscid fluids by using a novel formulation based on covectors. This new formulation is an entirely velocity-based method in the vein of advection-projection methods while emulating vortex methods. This allows for capturing more intricate vortex dynamics and reducing dissipation of energy with low computational overhead.

3. Designing Perceptual Puzzles by Differentiating Probabilistic Programs
Project description: We design new examples of visual illusions like "The Dress" by finding "adversarial examples" for principled models of human perception — specifically probabilistic models, which treat vision as Bayesian inference. To perform this search efficiently, we design a differentiable probabilistic programming language, exposing MCMC inference as a first-class differentiable function.

4. Filament Based Plasma
Project description: We assemble a computational pipeline for procedurally generating the visual appearance of our sun. Using Lagrangian elements, the features of the solar atmosphere are reconstructed at a high level of detail.

5. Neural Jacobian Fields: Learning Intrinsic Mappings of Arbitrary Meshes
Project description: We introduce a framework for deep learning of deformations of meshes. The trained network is highly accurate and produces realistic results and can be applied to meshes of arbitrary triangulations and not a fixed one. We show various experiments such as UV mapping, elastic deformations, and learning to repose humans.

6. Photon-driven Neural Reconstruction for Path Guiding
Project description: We present a path-guiding approach that can reconstruct high-quality sampling distributions using an offline trained neural network. We leverage photons traced from light sources for sampling density reconstruction, which is effective for challenging scenes with global illumination. We further partition the scene space into an adaptive hierarchical grid.

7. Rendering Neural Materials on Curved Surfaces
Project description: Neural material representations address some limitations of traditional analytic BRDFs. However, they still approximate the material on an infinite plane, which prevents them from correctly handling silhouette and parallax effects. This paper proposes neural materials capable of correctly handling such silhouette effects by taking into account the curvature information.

8. Searching for Fast Demosaicking Algorithms
Project description: We present a method to automatically synthesize a Pareto frontier of efficient, high-quality e-mosaicking algorithms across a range of computational budgets. It performs a multi-objective, discrete-continuous optimization which simultaneously solves for the program structure and parameters that best trade off computational cost and image quality.

9. SofGAN: A Portrait Image Generator With Dynamic Styling
Project description: SofGAN is a portrait generator that allows for high-quality rendering with attribute controlling over camera pose, geometry, and texture styles.

10. A Unified Newton Barrier Method for Multibody Dynamics
Project description: We present a simulation framework for multibody dynamics with optimization time integration. Our method naturally supports mixed rigid-deformables and mixed codimensional geometries while providing guaranteed robustness and accurate resolution of frictional contact and a wide range of articulation constraints, including restitution.

Students earn top marks in Mars rover competition

June 22, 2022--The UC San Diego Yonder Dynamics student team made a triumphant return to the first in-person University Rover Challenge since 2019, claiming 1st place in the science portion of the Mars rover robotics competition, and 8th place overall out of 26 teams from around the world.

Their rover, named Complacency in jest, was put to the test in the rough, rocky terrain of Hanksville, Utah. The University Rover Challenge (URC), hosted by the Mars Society, has four mission challenges that the rovers must complete: testing for signs of life, traversing difficult terrain to deliver a payload, repairing broken equipment on a mock lander, and autonomously navigating to a set location.

Complacency crushed the science portion of the mission, where teams must use tools and sensors onboard their rover to collect soil and rock samples to search for signs of life and analyze the composition of the rocks. The Yonder team used a powerful camera on the Complacency to photograph the rocks to determine their composition, and used Raman spectroscopy to test for beta carotene, a molecule that helps protect bacteria from UV light and can be used to detect signs of extinct life. To detect extant, or still existing life, they used a turbidity testing approach to detect how high levels of bacteria are in the soil. 

While this earned the team first place in this portion of the competition, Nupoor Patil, a biochemistry and cognitive science double major who served as the Science team lead within Yonder Dynamics, said the team already has plans to improve for next year’s competition. 

“We think there are better ways to test for extant life than our approach this year, so something that we will probably be doing for next year is protein or lipid testing, maybe even some carbohydrate testing,” Patil said. “ And then more environmental testing, so measures including pH, pressure, temperature, and things like that will also give us a better idea of whether there is life and bacteria in the soil or not.”

Karl Johnson, an electrical engineering student and the Yonder Dynamics project manager, said the science portion of the rover isn’t the only thing the team hopes to update in the upcoming year. 

“One of the things we're working on is we're going to be in contact with some of the microwave engineering and antenna professors at UC San Diego to figure out the best approach for the wireless communication aspect of the competition, for a hopefully more efficient approach than the high frequency but directional antenna we used this year,” Johnson said. “This year we kept our chassis from our previous rover Apathy and upgraded the electronics and sensors on it, but next year we’re planning to upgrade that part as well so we’ll have a brand new chassis.”

Johnson and Patil are two of the roughly 30 students from across UC San Diego who spent long hours perfecting the autonomy, mechanics, communication and on-board sensors of the rover. They came away not only with a sense of camaraderie, but also tangible skills for what they hope to pursue after graduation.

“I’m interested in astrobiology, which is the field that I’ve been working in with Yonder, and that is something that I will be looking into for graduate school because there’s a lot out there in terms of looking for life on other planets,” said Patil. 

Johnson plans to parlay his optics expertise within electrical engineering to a space-related field, be it telescopes, internet for satellites, or something at NASA’s Jet Propulsion Lab. 

“It's really cool to work on a team where even though my focus on this team is very robotics-heavy and electronics related, the ideas and the overall field is so exciting to me,” he said.

Yonder Dynamics is recruiting new students to join them as they build their 2023 rover and work to top their 8th place finish next year. Learn more at their website. 

New phylogenetic tool can handle the SARS-CoV-2 data load

By Kiran Kumar and Katherine Connor

June 22, 2022--Researchers at UC San Diego, in collaboration with UC Santa Cruz, have developed a new software tool for tracing and mapping the evolution of the SARS-CoV-2 virus, that is capable of handling the unprecedented amount of genetic data being generated by the quickly evolving pathogen. The software is used to efficiently and accurately track new variants of this virus on what’s known as a phylogenetic tree: a visual history or map of an organism’s genetic changes and variations over time and geography. Using this new optimization tool, called matOptimize, researchers are now able to more accurately track the viral genome of SARS-CoV-2,  mapping new variants onto the phylogenetic tree as they develop, and tracking the evolutionary and transmission dynamics of the virus. 

The tool was described in the journal Bioinformatics, with UC San Diego undergraduate computer engineering student Cheng Ye as first author. Hear more about Ye’s journey to research as an undergraduate, and his experience working on such a timely project, in this Q&A. 

“With over 10 million SARS-CoV-2 genome sequences now available, maintaining an accurate, comprehensive phylogenetic tree of all available SARS-CoV-2 sequences is becoming computationally infeasible with existing software, but is essential for getting a detailed picture of the virus’ evolution and transmission,” the researchers, under the direction of UC San Diego Electrical and Computer Engineering Professor Yatish Turakhia, write in the paper. 

An example phylogenetic tree (left) and its corresponding index tree.

Currently, the program used for  SARS-CoV-2 phylogeny is called UShER: Ultrafast Sample placement on Existing tRee. UShER was developed by Turakhia as a postdoctoral researcher at UC Santa Cruz, and is used by UC Santa Cruz to maintain the SARS-CoV-2 phylogeny. It is publicly viewable at - https://taxonium.org/?backend=https://api.cov2tree.org.

A few months into the pandemic, UShER faced a challenge with adding new genetic sequences onto the tree; the team would add sequences step-wise, one at a time, but when the genetic sequence input was incorrect or ambiguous, the system would lose accuracy. 

 “UShER would make a guess: an educated guess, but still a guess,” said Turakhia. 

Thus, these sequences would occasionally be sub-optimally placed on the tree, producing false mutations. In order to refine these placements, a tree optimizing method was needed. However, existing tree optimizers were unable to keep up with the amount of  SARS-CoV-2 genetic data being generated, with currently 10 million sequences mapped and up to 100,000 sequences added daily.

That’s when Turakhia worked with Ye and other students in his lab on the challenge of creating a better tree optimizer. Ye had joined Turakhia’s lab through the Electrical and Computer Engineering Summer Research Internship Program (SRIP) in January 2021. When it became clear to Turakhia that Ye's fundamentals in data structures, parallel algorithms, programming, and bioinformatics were quite strong, he entrusted him with taking a leading role on this task.

Cheng Ye, left, was awarded the Electrical and Computer Engineering Best Undergraduate Research Award for his work on matOptimize. His advisor, Professor Yatish Turakhia, is pictured at right.

 "I was initially assigned to work on accelerating sequence alignment on graphic processing units, but I thought the SARS-COV-2 phylogeny project might be more exciting, and it indeed was," said Ye. 

“In those days [Cheng] became an expert in tree-optimization,” said Turakhia.

 Many of the existing tree optimizers were closed source, so Ye was forced to work with what was available in the literature to devise a solution to the data challenge. After a few months of research, Ye developed matOptimize, currently the only tool capable of keeping up with the amount of rapidly evolving SARS-CoV-2 genetic data.

In order to achieve this, Ye created a true parallel software, with processing  distributed over several CPUs, and a significantly lower memory requirement. This allows it to be scaled to the level of data required in the SARS-CoV-2 phylogeny. 

Today, UShER as the phylogenetic tree software and matOptimize as the tree optimization method, are being used together to characterize the SARS-CoV-2 phylogeny. There is now an entire catalog of genetic sequences which, from phylogenetic inferences, are highlighted as more dangerous or transmissible sequences which UC San Diego and UC Santa Cruz scientists continue to track.

Moving forward, Turakhia’s team is using this information to study the recombination of SARS-CoV-2, a phenomenon that may lead to newer, dangerous variants.

 "In collaboration with Professor Russell Corbett-Detig's group at UC Santa Cruz, Cheng and I developed a software called RIPPLES, that can sensitively detect recombinants in 1000x larger datasets,” said Turakhia. “This software will help monitor the emergence of new SARS-CoV-2 recombinants and is likely to be applied to other pathogens as well in the future.”

UC San Diego researchers part of $25M project to build artificial coral reefs for coastal protection

June 21, 2022 -- A team of researchers involving the University of California San Diego has received a $25 million award from the U.S. Department of Defense’s Defense Advanced Research Projects Agency (DARPA) to build artificial coral reefs to protect coastal areas in Hawai’i against flooding, erosion and storm damage.

The artificial reefs will be designed to work with local ecology to create a living, growing and self-healing system. The reefs will provide a natural defense that can keep pace with sea-level rise over time and slow down waves, dissipating their energy before they reach land. A big benefit of artificial reefs is that they can be rapidly deployed to provide immediate protection while promoting the growth of reef-supporting organisms. Natural reefs take decades to mature, but the artificial versions can reach full functionality in a matter of months to years.

The project is an academic-industry partnership led by the University of Hawai’i, with other partners including UC San Diego, Florida Atlantic University and Makai Ocean Engineering.

Coral larvae crawling over a bioactive coating to look for a settlement habitat. Such a bioactive material can be rapidly fabricated via 3D printing. Images by Daniel Wangpraseurt

The UC San Diego team is working on two methods for attracting both corals and beneficial reef fish to the artificial structures. First, researchers at the UC San Diego Department of NanoEngineering will 3D print biomaterials that will be coated onto the artificial reefs. The biomaterials will be designed with special microstructures to enhance coral recruitment, the process in which tiny drifting coral larvae attach and establish themselves on a reef.  The microstructures also aim to inhibit algal and bacterial fouling on the artificial reefs.   

Scientists at UC San Diego’s Scripps Institution of Oceanography will also test “acoustic enrichment,” a process where sounds from other healthy reef environments are broadcast to attract both algae-eating fish and coral larvae to the structures.  Scripps Oceanography scientists will also conduct passive acoustic monitoring of the reef structure to help monitor what and how many organisms settle on the structure over time.

Daniel Wangpraseurt, an assistant project scientist at the UC San Diego Jacobs School of Engineering, will lead the effort with co-investigators Shaochen Chen, professor and chair of nanoengineering at the UC San Diego Jacobs School of Engineering, and Aaron Thode, a research scientist at Scripps Oceanography. The UC San Diego effort will be funded with $4 million of the DARPA award.

“This is an exciting opportunity for radical innovation, with the potential to be a game changer for the engineering of artificial coral reefs,” said Wangpraseurt. “Our team will develop new biomaterials that will kick-start the living reef by applying state-of-the-art medical tissue engineering approaches."

3D printed skeletal microarchitecture that can be used as inspiration for new reef-like materials.

To create the biomaterials, the UC San Diego team will use a rapid, 3D bioprinting technology developed in Chen’s lab. The technology can reproduce detailed microscale structures in mere seconds, mimicking the complex designs and functions of living tissues. Wangpraseurt and Chen have collaborated in recent years to 3D print coral-inspired microscale structures that are capable of growing dense populations of microscopic algae. The new DARPA-funded project takes their work to the next level, expanding their efforts to help create hybrid biological and engineered reef-mimicking structures for coastal defenses suited to a changing environment.

“We are now scaling up our rapid bioprinting platform, which will be critical to manufacture biomaterials for large scale coral reef engineering,” said Chen.

Thode, who recently participated in another recent DARPA-funded project on coral reef acoustics, will be adapting underwater sound playback technology initially developed to attract sperm whales away from fishing vessels to prevent the 70-foot animals from taking fish from their haul. 

“In addition to developing methods to encourage rapid ecosystem development on artificial reefs, I’m hoping in the future this research could also help accelerate efforts to recover degraded or dying natural reefs,” said Thode.

Plant virus plus immune cell-activating antibody clear colon cancer in mice, prevent recurrence

June 21, 2022 -- A new combination therapy to combat cancer could one day consist of a plant virus and an antibody that activates the immune system’s “natural killer” cells, shows a study by researchers at the University of California San Diego.

In mouse models of colon cancer, the combination therapy eliminated all tumors and prevented their recurrence, which in turn resulted in 100% survival. The therapy also increased survival in mouse models of melanoma.

The work is reported in a paper published June 17 in Nano Letters.

The proof-of-concept therapy enhances the activity of cancer killing immune cells known as natural killer cells, which naturally reside in the body and in tumors. The job of natural killer cells is to target and destroy cancer cells—in doing so, they release molecules called antigens that the immune system can recognize and produce antibodies against.

The problem is that there are not enough natural killer cells in or near cancerous tumors to be effective. And those that are in the tumors cannot do their job because cancer cells can secrete molecules that bind to natural killer cells and suppress them.

The therapy overcomes these problems using two key ingredients: cowpea mosaic virus, which is a plant virus that infects legumes but is harmless to animals and humans, and an antibody called anti-4-1BB. Cowpea mosaic virus has a special ability to attract natural killer cells to the tumor microenvironment, while anti-4-1BB binds to receptors on these cells to snap them out of their immunosuppressed state. By joining forces, the plant virus and antibody not only draw a large enough crowd of natural killer cells to the tumors, but also fire them up for attack.

“With a combination therapy, we significantly improve cancer response,” said study senior author Nicole Steinmetz, professor of nanoengineering and director of the Center for NanoImmunoEngineering at the UC San Diego Jacobs School of Engineering. “Cancers work by manipulating the body through multiple pathways. When we hit on multiple pathways by combining different therapeutic agents (cowpea mosaic virus and anti-4-1BB), we get better results.”

“Nowadays, cancer is not treated with just one medication—it requires a multi-pronged approach. Our work takes advantage of different strategies to activate the innate immune system and destroy tumors. This can then initiate an adaptive immune response to help prevent tumor recurrence,” said first author Edward (Ted) Koellhoffer, a resident physician in radiology at UC San Diego Health who is a clinician-scientist in Steinmetz’s lab.

The researchers first tested their combination therapy on mouse models of colon cancer. The treatment regimen consisted of one weekly injection of cowpea mosaic virus and two weekly injections of anti-4-1BB. The injections were administered into the abdominal cavities of the mice for three weeks. All mice that were given the combination therapy experienced complete tumor elimination and survived for at least 90 days. When these mice were later rechallenged with colon cancer, any new tumors were also eliminated, and the mice all survived. The researchers also tested cowpea mosaic virus as a solo therapy and while it exhibited potency, the combination therapy demonstrated synergy and outperformed any controls.

“What’s remarkable is that the treated mice gain an immunological memory, meaning that their immune systems remember the tumor cells and can attack them on their own when the cancer reappears,” said Koellhoffer.

The researchers tested the same treatment regimen on mouse models of melanoma. Again, the combination therapy reduced tumor growth and protected the surviving mice from recurrence of the disease when rechallenged with melanoma.

“While the combination therapy was most impressive in the colon cancer model, improvement was also seen in the melanoma model,” said Steinmetz. “Based on the data, more research is needed to understand whether this therapy is effective against a broad range of cancers, or whether the real potential is for intraperitoneal disseminated disease.”

Steinmetz’s team plans to explore that further. The researchers hope that their combination therapy will lay the groundwork for an in situ cancer vaccine.

Paper: “Cowpea mosaic virus and Natural Killer Cell Agonism for In Situ Cancer Vaccination.”

This work was supported by the National Institutes of Health (R01 CA224605, R01 CA253615, U01 CA218292 and T32EB005970) and the Shaughnessy Family Fund for Nano-ImmunoEngineering at UC San Diego.

UC San Diego Computer Scientist Plays Major Role in $25M Cancer Grand Challenges Project

Vineet Bafna will join a team of international researchers investigating extrachromosomal DNA, a major driver of tumor evolution

Vineet Bafna, a professor in the UC San Diego Department of Computer Science and Engineering, is a key player on the $25M Cancer Grand Challenge Project.

June 16, 2022-- University of California San Diego computer scientist Vineet Bafna is part of a team of world-class researchers that has been awarded a five-year, $25 million Cancer Grand Challenges grant to learn how the destructive genetic lesion extrachromosomal DNA (ecDNA) influences numerous cancers and to identify possible therapies.

Cancer Grand Challenges is a global research funding program created by the United States National Cancer Institute (part of the National Institutes of Health) and Cancer Research UK. The group funds multidisciplinary research teams to solve some of medical science’s thorniest challenges – in this case, ecDNA, a major driver of tumor evolution. As part of a $500 million initiative, Cancer Grand Challenges announced four teams, including the ecDNA group (called eDyNAmiC), on June 16.

The team will investigate the mechanisms that drive ecDNA—small, circular pieces of genetic information that allow cancer cells to rapidly evolve and become resistant to even the most potent anti-cancer treatments. These genetic anomalies appear in about a third of cancers, promote aggressive tumor behavior and generate poor patient outcomes.

“In many cancers, DNA replication and repair machinery is so dysregulated that we begin to see gross abnormalities in the genome; it is no longer a stable molecule,” said Bafna, a professor in UC San Diego’s Department of Computer Science and Engineering and a faculty member in the university’s HalıcıoÄŸlu Data Science Institute. “Fragments of genetic material break away from their native locations on chromosomes, forming small, circular molecules that are capable of independent regulation. 

“These breakaway fragments can duplicate tumor-promoting oncogenes, making 20, 50, maybe 100 copies, helping cancers become more aggressive and resist treatments. While their existence has been known for nearly 80 years, their prevalence in cancer was not fully appreciated until recently,” Bafna said. 

The research team

Extra-chromosomal DNA, or ecDNA, (indicated by orange and blue arros), are small, circular pieces of genetic information that allow cancer cells to rapidly evolve and become resistant to even the most potent anti-cancer treatments.

Bafna will be part of a research all-star team led by Paul Mischel, MD, professor of pathology, Stanford Medicine. The group combines expertise in cancer genomics, yeast genetics, epigenomics, patient tracking, machine learning and mathematical modeling, immunobiology, chemistry and other disciplines to interrogate ecDNA’s role in cancer and develop new therapeutic options against it.

“We’re poised to transform the collective understanding of many aggressive forms of cancer and provide new insight into how to diagnose, monitor and treat patients for whom current therapies do not work,” said Mischel. 

For this project, Bafna will help spearhead the computational genomics analyses. He has been working for years with Mischel and others to develop mathematical and computational techniques to identify ecDNA and other structural changes in chromosomes.

For example, his group maps short (150 base pair) ecDNA fragments to a reference genome to look for duplications, as well as evidence of rearrangements linked to tumor genomes. Using optical mapping technology, they seek to clarify the complex interrelationships between these rogue DNA elements and remaining chromosomes. In a complementary approach, Bafn’s lab has pioneered deep learning methods to detect and quantify ecDNA in cellular images. 

“If a region is sampled about 30 times in a normal genome, and 300 times in the cancer genome, you know it has been amplified by a factor of ten,” said Bafna. “However, understanding the architecture of the rearranged genome is more fundamental; it explains how the regulatory circuit is rewired in ecDNA, and if new enhancer elements have been hijacked to further dysregulate oncogene expression.”

This work is becoming increasingly important because ecDNAs are, unfortunately, quite common. Bafna and colleagues have found them in lung and kidney cancers, melanomas and glioblastomas. Duplications were particularly high in glioblastomas, the deadliest type of brain cancer. So far, they’ve found ecDNA in 40% of the tumors they’ve investigated.

“These structural variations are both incredibly important and understudied,” said Bafna. “Now, we can begin to fill in the knowledge gap on ecDNA origin, function and evolution and find ways to counteract it.” 

The eDyNAmiC team brings together researchers from 11 institutions across the US, UK and Germany: Stanford University and Sarafan ChEM-H; University of California San Diego; New York University Langone Health; University of Texas Southwestern Medical Center; Scripps Research; Queen Mary University London; University College London; Max Delbrück Center for Molecular Medicine and Charité Berlin; Fred Hutchinson Cancer Research Center; University of Cambridge; Jackson Laboratory for Genomic Medicine.

 

One step closer to fire safe, recyclable lithium-metal batteries

Netflix-style algorithm builds blueprint of cancer genomes

June 15, 2022 -- The science behind predicting your viewing habits on Netflix could one day be used to guide doctors in managing some of the hardest-to-treat cancers, shows a study led by the University of California San Diego and University College London.

The researchers used artificial intelligence to analyze and categorize the size and scale of DNA changes across the genome when cancer starts and grows. By analyzing genomes from 9,873 patients with 33 types of cancer, the scientists found 21 categories of common changes to the structure and number of chromosomes in the genetic material of tumors.

These categories of common DNA changes, known as copy number signatures, could be used to build a blueprint to predict how a cancer is likely to progress and design the most effective treatments for it. The findings are reported in a paper published June 15 in Nature.

“Cancer is a complex disease, but we’ve demonstrated that there are remarkable similarities in the changes that happen in chromosomes when different cancers start and grow,” said Ludmil Alexandrov, a professor of bioengineering and cellular and molecular medicine at UC San Diego, who is a co-lead author of the study.

When cancer starts, mutations in the DNA can cause large-scale faults to occur across their whole genome. These faults can result in too few or too many chromosomes compared to normal cells. Tumors can also develop faults in the mechanisms designed to repair their DNA, which in turn leads to further faults in the structure of DNA within chromosomes, as well as errors when the DNA tries to make copies of itself.

The researchers were interested in studying these large-scale genomic faults across different types of cancer. Enter a suite of AI tools developed by Alexandrov’s lab, called SigProfiler, which scans sequencing data from cancer patients and identifies common patterns in chromosome changes in different types of cancer.

“Based on these changes that the genome has previously experienced, our algorithm can predict how your cancer is likely to behave—similar to how Netflix can predict which series you’ll choose to binge watch next based on your previous viewing activities,” said Alexandrov.

This algorithm was key in identifying the 21 copy number signatures found in this study. This also enabled the researchers to predict how some of the hardest-to-treat cancers will behave.

One the copy number signatures created by the algorithm is attributed to an event known as chromothripsis, where chromosomes in tumors fragment and rearrange. This copy number signature was associated with the worst survival outcomes, the researchers found. Take patients with a lethal, fast-growing brain cancer called glioblastoma, for example. On average, glioblastoma patients whose tumors did not undergo chromothripsis were found survive six months longer than those whose tumors did. 

“Mutations are the key drivers of cancer, but a lot of our understanding is focused on changes to individual genes in cancer. We’ve been missing the bigger picture of how vast swathes of genes can be copied, moved around or deleted without catastrophic consequences for the tumor,” said Nischalan Pillay, a professor of sarcoma and genomics at University College London and co-lead author of the study. “Understanding how these large-scale genomic events arise will help us regain an advantage over cancer.”

The researchers have made SigProfiler and other software tools used in the study feely available to other scientists, so that they use the tools to build their own Netflix-style libraries of chromosome changes in DNA based on data obtained from sequencing tumors.

“As it becomes faster and cheaper to read an individual’s genetic code in full, we hope that our blueprint will be widely used to navigate that code and help doctors offer better and more personalized cancer treatment,” said Alexandrov.

As part of their next steps, the researchers are exploring some of the identified categories of copy-number changes as clinical biomarkers for predicting response to anti-cancer therapies.

Paper: “Signatures of copy number alterations in human cancer.”

This work was supported by a Cancer Grand Challenge award from Cancer Research UK.

An Zheng Awarded Chancellor's Dissertation Medal

Graeve appointed director of the Graduate Program in Materials Science and Engineering

June 9, 2022-- Olivia A. Graeve, a professor in the Department of Mechanical and Aerospace Engineering, has been appointed Director of the Graduate Program in Materials Science and Engineering at UC San Diego. This university-wide program includes nearly 100 faculty from across campus. It offers both Master's and Ph.D. degrees and serves more than 200 students per year. It is the largest graduate program of its kind in the UC System and one of the largest in the nation.

Professor Olivia Graeve has been appointed Director of the Graduate Program in Materials Science

The Graduate Program in Materials Science and Engineering at UC San Diego is truly interdisciplinary, with faculty from the Jacobs School of Engineering's Department of Bioengineering, Department of Electrical and Computer Engineering, Department of Mechanical and Aerospace Engineering, Department of NanoEngineering, and Department of Structural Engineering; from the School of Biological Sciences; from the School of Physical Sciences' Department of Chemistry and Biochemistry, and Department of Physics; from the Scripps Institution of Oceanography; and from UC San Diego Health.

The Graduate Program in Materials Science is managed through the Department of Mechanical and Aerospace Engineering in the UC San Diego Jacobs School of Engineering. As Director, Graeve will coordinate faculty participation, oversee curricula, and manage the budget and staff.

Graeve is Director of the CaliBaja Center for Resilient Materials and Systems at UC San Diego. She is a Fellow of the American Association for the Advancement of Science (AAAS) and the American Ceramic Society. She is a member of the Academy of Sciences of Latin America, the Mexican Academy of Sciences, and the Mexican Academy of Engineering. She is editor of the journal, Materials Letters. She recently completed six years of successful and high impact leadership of the IDEA Engineering Student Center at the UC San Diego Jacobs School of Engineering.

We would like to thank Mechanical and Aerospace Engineering Professor Prabhakar Bandaru for his outstanding service as Director of the Graduate Program in Materials Science and Engineering over the last six years. He strengthened, expanded, and raised the profile of this graduate program in numerous ways.

The Graduate Program in Materials Science and Engineering is an important part of the larger, collaborative, world-class materials science ecosystem at UC San Diego. This ecosystem includes the campus-wide Institute for Materials Discovery and Design (IMDD), the UC San Diego Materials Research Science and Engineering Center (UC San Diego MRSEC), and a wide range of related programs, centers and initiatives across campus. Michael Sailor, Professor of Chemistry and Biochemistry, recently took on the role of Director of the Institute for Materials Discovery and Design (IMDD). He is also the founding director of the UC San Diego MRSEC.

 

 

Ultra-thin, flexible probe provides neural interface that's minimally invasive and long-lasting

June 9, 2022 -- Researchers at the University of California San Diego and the Salk Institute for Biological Studies have developed a tiny neural probe that can be implanted for longer time periods to record and stimulate neural activity, while minimizing injury to the surrounding tissue.

Photograph of a small capsule supporting the neural probe, with a closeup of the microfiber tip. Credit: Spencer Ward

The new neural probe, detailed in a paper published June 7 in Nature Communications, is extremely thin—about one-fifth the width of a human hair—and flexible. The team says that this type of neural probe would be ideal for studying small and dynamic areas of the nervous system like peripheral nerves or the spinal cord.

“This is where you’d need a really small, flexible probe that can fit in between vertebrae to interface with neurons and can bend as the spinal cord moves,” said Axel Nimmerjahn, associate professor at the Salk Institute and co-senior author of the study.

These features also make it more compatible with biological tissue and less prone to triggering an immune response, which in turn make it suitable for long-term use.

“For chronic neural interfacing, you want a probe that’s stealthy, something that the body doesn’t even know is there but can still communicate with neurons,” said study co-senior author Donald Sirbuly, professor of nanoengineering at the UC San Diego Jacobs School of Engineering.

While there are other ultra-thin, flexible probes out there, what sets this small probe apart is that it can both record the electrical activity of neurons and stimulate specific sets of neurons using light.

“Having this dual modality—electrical recording and optical stimulation—in such a small footprint is a unique combination,” said Sirbuly.

The probe consists of an electrical channel and an optical channel. The electrical channel contains an ultra-thin polymer electrode. The optical channel contains an optical fiber that is also ultra-thin. Putting these two channels together required some clever engineering. The researchers needed to figure out how to insulate the channels to keep them from interfering with each other and have them both fit into a tiny probe measuring just 8 to 14 micrometers in diameter, all while making sure that the device was mechanically flexible, robust, biocompatible and able to perform on par with state-of-the-art neural probes. This involved finding the right combination of materials to build the probe and optimizing the fabrication of the electrical channel.

The team implanted the probes in the brains of live mice for up to one month. The probes caused hardly any inflammation in the brain tissue after prolonged implantation. As the mice moved about in a controlled environment, the probes were able to record electrical activity from neurons with high sensitivity. The probes were also used to target specific neuron types to produce certain physical responses. Using the probes’ optical channels, the researchers stimulated neurons in the cortex of the mice to move their whiskers.

These tests in brain tissue were done as a proof of concept. The team hopes to perform future studies in the spinal cord using their probe.

“Currently, we know relatively little about how the spinal cord works, how it processes information, and how its neural activity might be disrupted or impaired in certain disease conditions,” said Nimmerjahn. “It has been a technical challenge to record from this dynamic and tiny structure, and we think that our probes and future probe arrays have the unique potential to help us study the spinal cord—not just understand it on a fundamental level, but also have the ability to modulate its activity.”

UC San Diego and the Salk Institute have submitted a patent application on the neural probe technology described in this work.

Paper: “Electro-optical mechanically flexible coaxial microprobes for minimally invasive interfacing with intrinsic neural circuits.”

This work was supported by the Defense Advanced Research Projects Agency (DARPA) Biological Technologies Office Electrical Prescriptions program (HR0011-16-2-0027), the UC San Diego Kavli Institute for Brain and Mind (2018-1492) and the National Institutes of Health (R01 NS108034, U19 NS112959, U01 NS103522, and P30 CA014195). 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).

ACM Dissertation Honorable Mention

Bluetooth signals can be used to identify and track smartphones

It's the first time researchers have demonstrated it's feasible to track individuals using Bluetooth

June 8, 2022-- A team of engineers at the University of California San Diego has demonstrated for the first time that the Bluetooth signals emitted constantly by our mobile phones have a unique fingerprint that can be used to track individuals’ movements.

Mobile devices, including phones, smartwatches and fitness trackers, constantly transmit signals, known as Bluetooth beacons, at the rate of roughly 500 beacons per minute.These beacons enable features like Apple’s “Find My” lost device tracking service; COVID-19 tracing apps; and connect smartphones to other devices such as wireless earphones.

Prior research has shown that wireless fingerprinting exists in WiFi and other wireless technologies. The critical insight of the UC San Diego team was that this form of tracking can also be done with Bluetooth, in a highly accurate way. 

“This is important because in today’s world Bluetooth poses a more significant threat as it is a frequent and constant wireless signal emitted from all our personal mobile devices,” said Nishant Bhaskar, a Ph.D. student in the UC San Diego Department of Computer Science and Engineering and one of the paper’s lead authors. 

The team, which includes researchers from the Departments of Computer Science and Engineering and Electrical and Computer Engineering, presented its findings at the IEEE Security & Privacy conference in Oakland, Calif., on May 24, 2022.

Researchers tested their method to track Bluetooth fingerprints on campus. They use an off-the-shelf device to track and identify devices.

All wireless devices have small manufacturing imperfections in the hardware that are unique to each device. These fingerprints are an accidental byproduct of the manufacturing process. These imperfections in Bluetooth hardware result in unique distortions, which can be used as a fingerprint to track a specific device. For Bluetooth, this would allow an attacker to circumvent anti-tracking techniques such as constantly changing the address a mobile device uses to connect to Internet networks. 

Tracking individual devices via Bluetooth is not straightforward. Prior fingerprinting techniques built for WiFi rely on the fact that WiFi signals include a long known sequence, called the preamble. But preambles for Bluetooth beacon signals are extremely short.  

“The short duration gives an inaccurate fingerprint, making prior techniques not useful for Bluetooth tracking,” said Hadi Givehchian, also a UC San Diego computer science Ph.D. student and a lead author on the paper. 

Instead, the researchers designed a new method that doesn’t rely on the preamble but looks at the whole Bluetooth signal. They developed an algorithm that estimates two different values found in Bluetooth signals. These values vary based on the defects in the Bluetooth hardware, giving researchers the device’s unique fingerprint. 

Real-world experiments

The researchers evaluated their tracking method through several real-world experiments. In the first experiment, they found 40% of 162 mobile devices seen in public areas, for example coffee shops, were uniquely identifiable. Next, they scaled up the experiment and observed 647 mobile devices in a public hallway across two days. The team found that 47% of these devices had unique fingerprints. Finally, the researchers demonstrated an actual tracking attack by fingerprinting and following a mobile device owned by a study volunteer as they walked in and out of their house.

Challenges

Researcher were able to detect unique fingerprints for 47% of 647 devices.

Although their finding is concerning, the researchers also discovered several challenges that an attacker will face in practice. Changes in ambient temperature for example, can alter the Bluetooth fingerprint. Certain devices also send Bluetooth signals with different degrees of power, and this affects the distance at which these devices can be tracked.

Researchers also note that their method requires an attacker to have a high degree of expertise, so it is unlikely to be a widespread threat to the public today.

Despite the challenges, the researchers found that Bluetooth tracking is likely feasible for a large number of devices. It also does not require sophisticated equipment: the attack can be performed with equipment that costs less than $200. 

Solutions and next steps

So how can the problem be fixed? Fundamentally, Bluetooth hardware would have to be redesigned and replaced. But the researchers believe that other, easier solutions can be found. The team is currently working on a way to hide the Bluetooth fingerprints via digital signal processing in the Bluetooth device firmware.

Researchers are also exploring whether the method they developed could be applied to other types of devices. “Every form of communication today is wireless, and at risk,” said Dinesh Bharadia, a professor in the UC San Diego Department of Electrical and Computer Engineering and one of the paper’s senior authors. “We are working to build hardware-level defenses to potential attacks.” 

Researchers noticed that just disabling Bluetooth may not necessarily stop all phones from emitting Bluetooth beacons. For example, beacons are still emitted when turning off Bluetooth from the control center on the home screen of some Apple devices. “As far as we know, the only thing that definitely stops Bluetooth beacons is turning off your phone,” Bhaskar said. 

Researchers are careful to say that even though they can track individual devices, they are not able to obtain any information about the devices’ owners. The study was reviewed by the campus’ Internal Review Board and campus counsel.

“It’s really the devices that are under scrutiny,” said Aaron Schulman, a UC San Diego computer science professor and one of the paper’s senior authors. 

Evaluating Physical-Layer BLE Location Tracking Attacks on Mobile Devices

Dinesh Bharadia, UC San Diego Department of Electrical and Computer Engineering

Nishant Bhaskar, Hadi Givehchian, Aaron Schulman, UC San Diego Department of Computer Science and Engineering

Christian Dameff, UC San Diego Department of Emergency Medicine

Eliana Rodriguez Herrera Hector Rodrigo Lopez Soto, UC San Diego ENLACE Program

 

UC San Diego researchers working to trace roots of triple negative breast cancer

Shankar Subramaniam

June 7, 2022 -- Researchers at the University of California San Diego, in collaboration with researchers at City of Hope Hospital, have launched a new project to uncover the mechanisms that lead to triple negative breast cancer in human breast tissues.

The UC San Diego project is funded by Wellcome Leap’s Delta Tissue (ΔT) program, which aims to develop a platform to measure and model key cell and tissue states that drive infectious diseases and aggressive, hard-to-treat cancers.

Among these cancers is triple negative breast cancer (TNBC). What makes TNBC so aggressive and hard to treat is that the cancer cells in TNBC lack three things found in many other breast cancers: an estrogen receptor, a progesterone receptor, and extra receptors for a protein called HER2. As a result, the cancer does not respond to breast cancer treatments that target these receptors. TNBC accounts for about 10 to 15 percent of all breast cancers.

The team, led by UC San Diego bioengineering professor Shankar Subramaniam, will perform fundamental studies to decipher the precise pathways involved in TNBC initiation, progression and metastasis. The researchers will use innovative experimental approaches, multi-omics strategies and data analytics to delineate these pathways and develop robust models of TNBC. Their work could potentially help identify stage and etiology-specific next generation therapeutics for TNBC.

Class of 2022 honored with Awards of Excellence

June 7, 2022-- The Jacobs School of Engineering will honor the undergraduate class of 2022 at its annual Ring Ceremony on Saturday, June 11, after the campus convocation. 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/current-undergraduates/ring-ceremony  and learn more about these impressive graduates below.

Bioengineering Award of Excellence: Kendra Worthington

Kendra Worthington chose to study bioengineering because of its diversity, both in terms of the research she could pursue, and in the community of scientists conducting this research. After years of leadership in the Biomedical Engineering Society and hands-on research experience in Professor Karen Christman’s lab as an undergraduate, Worthington will be pursuing a PhD in biological engineering at the University of Colorado Boulder next year, with funding from the NSF Graduate Research Fellowship Program. She plans to continue her research in biomaterials, and hopes to become a researcher working to bring next-generation therapeutics to those who need them most. Read the full Q&A with Kendra Worthington.

 

 

Computer Science and Engineering Award of Excellence: Eman Sherif

Eman Sherif was drawn to computer science for its flexibility. “With a computer science degree, I knew I could enter basically any field whether it is education, government, healthcare, etc,” she said. After experiencing computer science research thanks to the Early Research Scholars Program, Sherif plans to earn a PhD in computer science at the University of Washington, Seattle, focusing on computer science education. In addition to ERSP, Sherif was active in the National Society of Black Engineers at UC San Diego. Read the full Q&A with Eman Sherif.

 

 

 

Electrical and Computer Engineering Award of Excellence: Raini Wu

Raini Wu decided to pursue electrical engineering when he realized how few people truly understood how the electronic tools that are ubiquitous today really worked, and wanted to be one of the few who did. Through his coursework, conducting research in the Wireless Communications Sensing and Networking Group (WCSNG), and participation in HKN, the electrical engineering honor society, he’s developed a pretty thorough understanding of how these electronic devices work. Next year, Wu will be earning his master’s degree through the Department of Electrical and Computer Engineering’s BS/MS program, focusing on communication theory and systems. Read the full Q&A with Raini Wu.

 

 

Mechanical and Aerospace Engineering Award of Excellence: Rachel Luu

First-generation student Rachel Luu applied to engineering on a whim, not knowing exactly what the field entailed. After conducting research on bio-inspired materials as an undergraduate and participating in IDEA Engineering Student Center programming as an ACES Scholar, she’s now on her way to a PhD program in materials science at MIT, as an MIT Rosenblith Presidential Fellow and NSF Graduate Research Fellow. She plans to pursue a career leading her own research lab with a goal of creating bioinspired sustainable materials. Read the full Q&A with Rachel Luu.

 

 

 

 

 

NanoEngineering Award of Excellence: Meghan Shen

The idea of gaining perspective by seeing things most people don’t get to see drew Meghan Shen to study nanoengineering. After conducting research in the Lab for Energy Storage and Conversion, being involved in the Tau Beta Pi engineering honor society, and working in the Teaching and Learning Commons, Shen decided to pursue a PhD in materials science at UC Berkeley.

“I hope to leverage my experience working in the lab to plan thoughtful experiments regarding materials characterization,” she said. “In my career, I want to be a mentor that encourages students to believe in themselves. I also want to fight for educational equity and make sure everyone gets to learn what they love.”

Read the full Q&A with Meghan Shen

 

Structural Engineering Award of Excellence: Ramtin Azarbad

Ramtin Azarbad was fascinated by the tangible applications of structural engineering; you can walk by buildings you helped design! At UC San Diego, he served as co-president of the Society of Civil and Structural Engineers, helping host the Pacific Southwest Symposium that drew 850 students from around the region to campus. He also held leadership position in the campus chapter of Circle K International. After earning a master’s degree in structural design and analysis here at UC San Diego, he plans to get an industry position as a structural designer.

Read the full Q&A with Ramtin Azarbad.

UC San Diego students win 2nd place in nation-wide autonomous, electric go-kart race

UC San Diego students with their autonomous go-kart at the evGrandPrix competition.

June 6, 2022-- A team of engineering and data science students from UC San Diego came in 2nd place at the  second annual autonomous, electric (EV) GrandPrix go-kart race hosted at Purdue University in May. Teams of students from around the country came together to race the autonomous electric go-karts they built over the year. These are not ordinary go-karts. Each electric vehicle sports  autonomous perception, navigation, and control systems optimized for the race setting: a roughly one-third of a mile lap on the race track in the fastest time, all on its own. 

The team also included several students from the University of Hawaii, and UC Berkeley. At UC San Diego, the force behind this project is the TritonAI student organization.

UC San Diego students qualified for the final round in 2021, the first year of the competition, and wound up taking third place. This year, the students made it back to the competition and won  second place. 

Electrical engineering student Chaztine Embucado was on this year's evGrandPrix team.

Chaztine Embucado, an electrical engineering student at the UC San Diego Jacobs School of Engineering, was part of this year’s team. She shares how she got involved, and what the experience was like, in this Q&A:

How did you get involved with the autonomous evGrandPrix competition?

I study electrical engineering with a power engineering depth, and one of my major requirements is to do a senior design capstone class. In this class, we rank the available projects based on preference. Based on this ranking, our experience, and interest, we are assigned a project and I’m glad to have been placed in the one for this autonomous electric go-kart. So via this class I worked within the TritonAI team. 

What was your role?

At the very beginning, it was to work with the MAE capstone team to choose a brushless DC motor for the go-kart. We were choosing between three different ones. The two requirements were that it can be controlled using the specific motor controller that we already had, and that it fit on the existing mount for the kart.

After conducting testing and choosing a motor, I was a little bit of a floater, soldering connectors and pins for backup components, making the cart look professional, basically cable and wire management to minimize clutter and maximize ease in future troubleshooting. The power distribution network was pretty much centralized at the back of the kart, but there were sensors, cameras, the GPS, etc. at the front of the kart so we needed wires that brought power from the back of the cart and brought it up to the front.. 

Had you been involved in similar projects before? 

I was part of SEDS, and worked on the rocket engine test stand called Colossus. Through that I learned a lot about the power distribution system; being able to understand the organization of  a system that has worked before, I think helped me in this case. It was exciting to be a part of the team to re-assemble the electronics panel and turn it on for the first time in a while. Leading up to that point I practiced a lot of practical skills and used tools I never have before, so I’m grateful for my time there.

I was also on the electrical team for Triton Racing and assisted in the wiring harness for the car. Making sure that the wires were long enough, twisting them correctly, and separating the branches appropriately for the sensors all around the car was tedious, but it was a good experience. I learned more about how much work goes into the details of power distribution and applied practical concepts of electronics, which was refreshing.

What was the competition itself like?

It was pretty exciting. It was cool to be in Indiana in general – even restaurants had racing flags put up outside, or an Indy 500 special for the next weekend. Even though it’s a competition, the environment with the other teams was so welcoming. One night when the track closed but everyone wanted to keep working, there was a specific library that allowed teams to bring their karts and test there. Kennesaw State University, who actually won, were so nice to us and said “You can work here right next to us, and you can use our lights.” Especially at the track, being able to see other teams’ karts and talk to them about their design choices and issues made it more of a transfer of knowledge than a cut-throat competition. 

Any idea what you’ll do with your degree and this experience once you graduate?

I’m really interested in applying electrical engineering to motor sports, and I’m currently an intern at Honda Performance Development. I’ve been working with them on solar simulations to enable more solar power, since they’re working towards being carbon neutral. I’ve also been able to look into their power consumption and power generation. 

Then in July, I have a one-year internship in the UK. Once I’ve done that I’ll have to finish some general education requirements before graduating.

Advice for current students?

I know it's hard, but try to not compare yourself to others. I think that was one of the things that pressured me a lot, because by the time I was a junior I hadn’t done an internship, and was just barely joining a student org. Sophomore year I was in the Air Force ROTC (Reserve Officer’s Training Corps) thinking that I would be set for the rest of college and after, but that didn’t work out. So even if something like that happens, or you find yourself in that kind of situation, it’s important to just keep moving forward and be confident in the steps that you are taking.

And also to the women engineers, or the women who are in STEM: you belong. Don’t let anyone say or make you feel that you don’t deserve your space. You do, and the peers who support you are worth leaning on because this is difficult. It’s not expected that you go through everything alone.

At the competition, we were the team with the most diversity and with the most women, and I think that gave me a lot of hope and confidence in this place I’m currently at. It was kind of the culmination of being a senior, and having to go through a lot of classes where there weren’t a lot of women, so it was a positive and full-circle experience to have such diversity on this team.  

 

The TritonAI team’s sponsors include Honda Performance Development, DeepRacer, RoboSense, BrainCorp, Livox, the Jacobs School of Engineering Triton Engineering Student Council, and Viasat. Full list of sponsors: https://tritonai.org/sponsors/

 

ISEI Founder Jimmy Anklesaria receives 2022 J. Shipman Gold Medal Award

June 2, 2022: Jimmy Anklesaria, the founder of the UC San Diego Institute for Supply Chain Excellence and Innovation (ISEI), has been named the 2022 J. Shipman Gold Medal Award winner by the Institute for Supply Management. The award is in recognition of Anklesaria's distinguished service in the supply management profession.

Jimmy Anklesaria

Anklesaria founded the Institute for Supply Chain Excellence and Innovation (ISEI) at UC San Diego in 2017. This Institute is in the process of moving to its new home in the UC San Diego Jacobs School of Engineering. The Rady School of Management, the Institute's original UC San Diego home, will remain actively involved in the Institute going forward.

"While 'systems-level thinking' is now a buzzword, Jimmy Anklesaria has been demonstrating the value of understanding the system, and the on-the-ground facts within the system, for decades. I look forward to the good we can do by getting more involved in the excellent work that Jimmy Anklesaria and the entire Institute for Supply Chain Excellence and Innovation are pursuing," said Albert P. Pisano, Dean of the UC San Diego Jacobs School of Engineering. "I'd like to add my personal congratulations to Jimmy: the inspiration and support you provide to students and others interested in learning to solve supply chain challenges is inspiring!"

The J. Shipman Gold Medal Award is the Institute for Supply Management's most esteemed honor. It is presented annually to an individual who personally contributes to the advancements of purchasing and supply management while providing assistance and guidance to other professionals.

“Jimmy, like many Shipman Medalists, has profoundly influenced many generations of supply management leaders. Even while he advised some of the world’s most iconic companies, such as Hewlett-Packard and IBM, he has assiduously mentored and cultivated succeeding generations,” said Institute for Supply Management chief executive officer Tom Derry.

“I’m so humbled and honored to receive the Shipman Award and join 90 other awardees, many of whom I know and have worked with over the past three decades,” said Anklesaria. “I’ve learned so much from the supply chain community and hope to spend the rest of my career sharing experiences and ideas with the emerging leaders of our profession.”

In celebration of this new award, Anklesaria was interviewed on Manufacturing Talk Radio.

Anklesaria joins an elite group of J. Shipman Gold Medal Award winners, including three board members of the Institute for Supply Chain Excellence and Innovation (ISEI) at UC San Diego: Sue Spence in 2020; Tom Linton in 2019; and Bob Monczka in 2008.

Anklesaria is a fellow member of the Institute of Chartered Accountants and holds a law degree from University Law College, Bangalore and an MBA from University of San Diego. Anklesaria is the author of Supply Chain Cost Management: The AIM & DRIVE® Process for Achieving Extraordinary Results and is co-author of Zero-Base Pricing™: Achieving World-Class Competitiveness Through Reduced All-In-Cost with David N. Burt and Warren E. Norquist.
 

A quarter of world's Internet users rely on infrastructure that is susceptible to attack

Fraction of each country's IP addresses that are exposed to observation or selective tampering by companies that connect Internet service providers to the global Internet. Countries are shaded in progressive shades of blue, with wost exposed countries in the darkest blue. Countries in gray excluded from the study.

May 25, 2022-- About a quarter of the world’s Internet users live in countries that are more susceptible than previously thought to targeted attacks on their Internet infrastructure. Many of the at-risk countries are located in the Global South. 

That’s the conclusion of a sweeping, large-scale study conducted by computer scientists at the University of California San Diego. The researchers surveyed 75 countries. 

“We wanted to study the topology of the Internet to find weak links that, if compromised, would expose an entire nation’s traffic,” said Alexander Gamero-Garrido, the paper’s first author, who earned his Ph.D. in computer science at UC San Diego. 

The structure of the Internet can differ dramatically in different parts of the world. In many developed countries, like the United States, a large number of Internet providers compete to provide services for a large number of users. These networks are directly connected to one another and exchange content, a process known as direct peering. All the providers can also plug directly into the world’s Internet infrastructure.

“But a large portion of the Internet doesn’t function with peering agreements for network connectivity,” Gamero-Garrido pointed out. 

In other nations, many of them still developing countries, most users rely on a handful of providers for Internet access, and one of these providers serves an overwhelming majority of users. Not only that, but those providers rely on a limited number of companies called transit autonomous systems to get access to the global Internet and traffic from other countries. Researchers found that often these transit autonomous system providers are state owned. 

This, of course, makes countries with this type of Internet infrastructure particularly vulnerable to attacks because all that is needed is to cripple a small number of transit autonomous systems. These countries, of course, are also vulnerable if a main Internet provider experiences outages. 

In the worst case scenario, one transit autonomous system serves all users. Cuba and Sierra Leone are close to this state of affairs. By contrast, Bangladesh went from only two to over 30 system providers, after the government opened that sector of the economy to private enterprise. 

This underlines the importance of government regulation when it comes to the number of Internet providers and transit autonomous systems available in a country. For example, researchers were surprised to find that many operators of submarine Internet cables are state-owned rather than privately operated.

Researchers also found traces of colonialism in the topology of the Internet in the Global South. For example, French company Orange has a strong presence in some African countries. 

Researchers relied on Border Gateway Protocol data, which tracks exchanges of routing and reachability information among autonomous systems on the Internet. They are aware that the data can be incomplete, introducing potential inaccuracies, though these are mitigated by the study’s methodology and validation with real, in-country Internet operators. 

Next steps include looking at how critical facilities, such as hospitals, are connected to the Internet and how vulnerable they are. 

Quantifying Nations’ Exposure to Traffic Observation and Selective Tampering (PDF)

 Alberto Dainotti (now at Georgia Institute of Technology),  Alexander Gamero-Garrido (now at Northeastern University), Bradley Huffaker and Alex C. Snoeren, University of California San Diego Esteban Carisimo, Northwestern University 
Shuai Hao, Old Dominion University 

 

Alumni Q&A: David Loo, serial entrepreneur on his journey and inviting luck into your professional life

Jacobs School alumnus David Loo worked his way up from software engineer to founding developer of ServiceNow and CEO of Perspectium Pictures courtesy of David Loo

May 24, 2022 -- David Loo graduated from UC San Diego in 1991 with a degree in computer engineering. During his 35-year career, he worked his way up from software engineer to founding developer of ServiceNow and CEO of Perspectium, the company he cofounded after leaving ServiceNow. In this Q&A, Loo talks about his journey and gives some advice about how to invite luck into your professional life.

What brought you to UC San Diego? 

I am a first-generation immigrant born in Malaysia and came to the US for my undergraduate education.   I was motivated by my older brother who came to the US  before me. At first I attended Pasadena City College, as did my brother who eventually continued on to UCLA–the decision was a cost saving one.I had been an admirer of the UCSD Pascal programming language and the computer science work at UCSD since high school and as I made friends who were also planning to attend UCSD, the choice was easy.  After a year, my brother packed up his Honda Civic with all of my belongings in the back and we drove to San Diego.

How was your experience at UC San Diego?

Going to UC San Diego wasn’t what I was expecting. It was better.

I was thrown into an open collaborative environment and allowed to fail. That experience set me up for the rest of my life. 

I had a great first year because I already had a group of friends that also transferred from Pasadena City College and were in the same situation.  They became my roommates off campus eventually.

My first impression of the campus was how large and spread out it was. I remember being surrounded by trees and there was an ocean view. Also there were apartments right on the edge of it. I loved the distance between classrooms because it introduced a different pace for the day. To go from class to class, you actually had to sprint or bike from one place to the other, forcing the students to get out and move. When I had to get to class, I would sprint or jump on my bicycle; it was much more refreshing than going from one class to another in the same building. It’s the first time I saw eucalyptus trees. I love the singing tree. There are so many of these little gems that survived time and change. I also loved the traditions, like the annual watermelon drop and the Sun God festival.

ServiceNow group pic at Solana Beach. (Loo is in shorts, holdong the surfboard)

I appreciated the multiple little nooks and crannies that are there if you just want some quiet time to study. The main library (Geisel) was an engineering marvel and a frequent hideout for me. I sat right to the edge of the “mushroom building” and would gaze down. It gave me a free floating sensation and then soon I would doze off.  A highly recommended stress relieving experience during finals cram.

I really appreciate the hands-on approach that UCSD facilitated. The professors were there to guide you on what you need to do, and provided freedom to attain your outcomes and goals. It was really clear  that it was up to you to succeed.  I remember at the time, especially with labs, you had to rely on your creativity, resourcefulness, and tenacity to complete assignments in time. The teacher’s assistants (TA) were of great help.

I had a great time learning, and not just subject matters, but more importantly how to work with and among my peers, and how to negotiate. I learned to be self-sufficient and at the same time to be part of a larger collaborative team, in a short amount of time.

Were there any professors that you remember, who taught you more perhaps? 

TC Hu, an emeritus professor in the Department of Computer Science and Engineering

I took a class with TC Hu (now an emeritus professor in the Department of Computer Science and Engineering). In his class, I was exposed to code optimizing strategies that resulted in execution speed improvements at scale.  I learned that even the little things mattered with Professor Hu. However, at some point, hardware engineers had achieved nano-circuit improvements that rendered code optimization insignificant. This led me to a realization that in science and engineering, we must always be broad and accepting of all solutions to achieve our  goal. At the same time, we must all be cautious not to fall into an obsessive and myopic approach for the sake of being perfect while disregarding the sometimes simple and obvious solution.  I learned to pick my battles and where best to spend energy and time.

What was your greatest challenge as a student and what advice would you have for current students who want to make the most of their experience at UC San Diego?

I would tell them to spend more time in class and less time working, if they can. I worked at least 20 hours a week through most of my four years at UCSD, and in retrospect, missed out on a lot of important social and collaborative activities as well as just being too tired most of the time. I had little choice as I was putting myself partly through school. If I had the chance to go through it again full time, without working, I would choose that. However, with the time gained from not working, don't party all the time and play computer games in your dorm room! Make use of your environment, meet people and participate to further your goals as much as you can. Friendships and relationships you make at this time will last a lifetime.

Do your best not because graduating is the goal (it’s one goal), but because the journey to get there is just as valuable.

A lot of happiness comes from struggle and the ability to overcome struggle. It’s not a bad idea to put yourself in a spot where you are challenged, but only for the right goals and reasons, do so with intention. In school, don't take the easy class but challenge yourself with a class that benefits you the most after graduating.  Struggle with purpose and intent, but also have the wisdom to know when you're not going to win that battle.

What advice do you have for students who want to become entrepreneurs? 

Make serendipity happen. These are the three ways I know: 

1. Take your time: the longer you persevere, the more chances of being lucky. However this requires you to be aware when it’s time to open that door opportunity has presented to you.
2. Be smart: you can’t roll a rock uphill all the time. You must know when it’s worthwhile to struggle, or when it’s not. Have the wisdom to pick the right battle and persevere.
3. Get resources: find people that can help you, and who you can support in return. Surround yourself with people who are smarter than you. Every successful person I know has a mentor or two along the way that helped them along. Find your mentor.

One more thing:

Starting is the hardest. If you don’t start, you won’t finish.

Make a good life for everyone around you and create opportunities for other people. Have lunch with people, talk to them, offer your support, find your mentor but also be a mentor to someone else. Always keep a lookout for opportunities that present themselves. 

Tell us about your professional journey? 

Perspectium team picture

My professional journey actually started before I graduated UCSD. As stated previously I’ve always worked half time through school, I mainly worked 20 hours a week–sometimes more–at the UCSD Cancer Center, as a database administrator. I was named as a contributor in a clinical trial paper, that was a proud moment for me. However, the experience caused me to delay my graduation till spring.

After UCSD, I decided to seek off campus experience and found a job at First American CredCo as a database administrator and 4GL programmer. It was 1991, the economy was really bad, unemployment at an all-time high, so I was happy to have found a job. I was blessed to have found a mentor there who guided my career and gave me opportunities. I remember going beyond my work requirements as I got into creating reusable software components for the rest of the team. I also participated in a pattern matching algorithm for credit scoring that resulted in a patent being granted.  The company later sponsored me for permanent residence and that’s the greatest opportunity I was given. 

I jumped into my first startup company after a couple of years. An early software startup in Carlsbad was hiring quality assurance engineers to validate an X Windows based application development platform.  This was my chance to move away from 4GL and into mainstream software engineering and so I dove in headfirst.  The pay was horrible and the hours even more so, but it didn’t matter because this was the struggle I was looking for.  As it turned out, the company didn’t make it. After a month working there, the worst happened. I was let go without pay as they closed the company doors.

Some would think this is the worst that could have happened but in retrospect it was the beginning of my journey to always move, challenge myself, adapt and push forward.

I was hooked on the “startup” life in that short time and was lucky to find my next one soon after.  A couple of engineers that left the previous company

A group picture of Perspectium employees on Zoom.

started another company, Triteal Corporation, and asked me to join them. I got my first taste of traveling for work at this company and perfected my startup life – work long hours, customer is first, and do whatever it takes. This was also my first experience of a company initial public offering (IPO). Bad luck struck again as the company declared bankruptcy soon after and I left.

I needed some stability at that time as I was planning to get married. I found a job as a Product Architect for Peregrine Systems, in Del Mar. It was a public company. I got married and we were saving up for a house.  This formative experience allowed me to grow as a software engineer in an enterprise computing environment. I traveled all over the world helping Global 1000 companies achieve their enterprise service management goals.  At this company is also where I discovered my life changing mentor, Fred Luddy, CTO of Peregrine Systems. At some point, I was helping the office of the CTO in mergers and acquisition technical validations, a turning point in my career. 

How did you become the cofounder of ServiceNow?

After Fred quit Peregrine, we kept in touch. He had been a great mentor to me, and I wanted to continue the relationship. We kept each other updated about the latest Java and Web technologies at that time. One day, almost a year later, we had lunch at CPK in Del Mar and he showed me a couple of printouts. It was a web-driven platform for creating applications. That became the base for ServiceNow. I asked Fred to hire me at that point and that’s how I started at ServiceNow as the first employee. I spent 8 years building automation and an integration system for ServiceNow, and towards the end created a developer bootcamp program to train engineers. The bootcamp program eventually became the ServiceNow Developer Community. I trained and got to know around 120 of these early engineers in the company.

Eventually ServiceNow became a public company and grew too large for me. I was still longing for the rapid pace of startup life, so I left in 2013.

Within a month of leaving, I started my own company, Perspectium Corp. I was still actively involved in the ServiceNow community and as the CEO and Chief Engineer of Perspectium, created value for its customers. Another 8 years went by as I grew Perspectium into a global enterprise with Global 1000 customers and about 80 employees, I finally sold the company.

At this time, I am incubating a technology that might turn into another startup. 

How did you juggle career and family? 

If I hadn’t had a supportive spouse, I wouldn’t have been able to do what I do today. Startups do not guarantee stable pay and so we had to rely on savings in the beginning. We had been married 2  years at the time I joined ServiceNow, and we had an 8-month-old daughter. I was jumping ship from a stable, good-paying job to build a startup from scratch with a mentor. We checked our savings and decided that we could risk living without income for about 6 months, and so with my wife’s blessing I jumped right in. I took a big pay cut, but we never missed a paycheck from ServiceNow.

We had moved to our second home by then, and we had a hefty mortgage payment. So eventually my wife had to take a job to supplement our income when our daughter was old enough. That fueled my crazy late nights and my traveling. Looking back, that was a life changing event for our family.
 

Mission Critical: How Humans and Robots Can Team up in Uncertain Environments

UC San Diego roboticist leads $7.5M grant on human-robot teaming

Laurel Riek is one of two UC San Diego lead researchers on a $7.5M grant on human-robot teaming.

May 20, 2022-- In the midst of a medical emergency or disaster response, how can humans and robots work together more effectively? 

That’s the question University of California San Diego roboticist Laurel Riek and a team of researchers are seeking to answer with a new $7.5 million Department of Defense Multidisciplinary University Research Initiative (MURI) award. 

Riek, an associate professor in the Department of Computer Science and Engineering in the Jacobs School of Engineering and the director of the Healthcare Robotics Lab at UC San Diego, will lead the project that seeks to advance research in robotics and autonomy, with the goal of aiding human teams working in critical environments.

She is one of two UC San Diego researchers to lead a MURI project in this year’s round of funding. Three other teams of which UC San Diego researchers are a part also received MURI awards.  (Read more about UC San Diego FY22 MURI awards.) 

“It is important that robots can understand the goals, activities, and intentions of human teams, and their context, to be useful teammates,” she said.  The trans-disciplinary team joins the fields of robotics, artificial intelligence (AI), cognitive science, and human factors to investigate the science of human-agent teaming (HAT).

Riek’s MURI project will explore how teams reason, coordinate and trust, particularly regarding how teams change over time. It will address key questions in HAT, including: 

• Modeling and operationalizing team mental models, for example, looking at how human and robotic teammates can collaboratively achieve a shared understanding of knowledge of tasks and the environment. 
• Understanding how team dynamics change over time,  including when robots take actions to calibrate and maintain their trust in one another, when they jointly act together, and when they engage in shared decision making. Researchers will study teaming temporally, both in real time and over time. 
• Exploring how two key mediators, coordination and team cognition, affect team performance. Both are understudied in HAT research, yet very important to team outcomes. 

“By creating new methods that model team evolution both dynamically and over time and by scientifically establishing how autonomy affects human teammates, this work will yield new insights for HAT in uncertain environments,” said Riek, who has been studying human robot teaming in safety-critical environments for over a decade.

Ultimately, this project will create innovative, cognitively-informed conceptual frameworks and computational models of teaming; establish core elements of a new interdisciplinary science of human-agent teams; accelerate the advancement of HAT in mission critical environments; and pioneer rapid prototyping and rigorous field testing of new guidelines and interventions for HAT design.

Other researchers on the project include Susan Simkins, Penn State University; Ericka Rovira, U.S. Military Academy; Thomas Griffiths, Princeton University; Angela Yu, UC San Diego; Francesco Bullo, UC Santa Barbara; Vaibhav Srivastva, Michigan State University; and Vijay Gupta, University of Notre Dame.

 

Using everyday WiFi to help robots see and navigate better indoors

May 20, 2022 -- Engineers at the University of California San Diego have developed a low cost, low power technology to help robots accurately map their way indoors, even in poor lighting and without recognizable landmarks or features.

The technology consists of sensors that use WiFi signals to help the robot map where it’s going. It’s a new approach to indoor robot navigation. Most systems rely on optical light sensors such as cameras and LiDARs. In this case, the so-called “WiFi sensors” use radio frequency signals rather than light or visual cues to see, so they can work in conditions where cameras and LiDARs struggle—in low light, changing light, and repetitive environments such as long corridors and warehouses. 

And by using WiFi, the technology could offer an economical alternative to expensive and power hungry LiDARs, the researchers noted. 

A team of researchers from the Wireless Communication Sensing and Networking Group, led by UC San Diego electrical and computer engineering professor Dinesh Bharadia, will present their work at the 2022 International Conference on Robotics and Automation (ICRA), which will take place from May 23 to 27 in Philadelphia.

“We are surrounded by wireless signals almost everywhere we go. The beauty of this work is that we can use these everyday signals to do indoor localization and mapping with robots,” said Bharadia.

“Using WiFi, we have built a new kind of sensing modality that fills in the gaps left behind by today’s light-based sensors, and it can enable robots to navigate in scenarios where they currently cannot,” added Aditya Arun, who is an electrical and computer engineering Ph.D. student in Bharadia’s lab and the first author of the study.

The researchers built their prototype system using off-the-shelf hardware. The system consists of a robot that has been equipped with the WiFi sensors, which are built from commercially available WiFi transceivers. These devices transmit and receive wireless signals to and from WiFi access points in the environment. What makes these WiFi sensors special is that they use this constant back and forth communication with the WiFi access points to map the robot’s location and direction of movement. 

“This two-way communication is already happening between mobile devices like your phone and WiFi access points all the time—it’s just not telling you where you are,” said Roshan Ayyalasomayajula, who is also an electrical and computer engineering Ph.D. student in Bharadia’s lab and a co-author on the study. “Our technology piggybacks on that communication to do localization and mapping in an unknown environment.” 

Here's how it works. At the start, the WiFi sensors are unaware of the robot’s location and where any of the WiFi access points are in the environment. Figuring that out is like playing a game of Marco Polo—as the robot moves, the sensors call out to the access points and listen for their replies, using them as landmarks. The key here is that every incoming and outgoing wireless signal carries its own unique physical information—an angle of arrival and direct path length to (or from) an access point—that can be used to figure out where the robot and access points are in relation to each other. Algorithms developed by Bharadia’s team enable the WiFi sensors to extract this information and make these calculations. As the call and response continues, the sensors pick up more information and can accurately locate where the robot is going.

The researchers tested their technology on a floor of an office building. They placed several access points around the space and equipped a robot with the WiFi sensors, as well as a camera and a LiDAR to perform measurements for comparison. The team controlled their robot to travel several times around the floor, turning corners, going down long and narrow corridors, and passing through both bright and dimly lit spaces. 

In these tests, the accuracy of localization and mapping provided by the WiFi sensors was on par with that of the commercial camera and LiDAR sensors. 

“We can use WiFi signals, which are essentially free, to do robust and reliable sensing in visually challenging environments,” said Arun. “WiFi sensing could potentially replace expensive LiDARs and complement other low cost sensors such as cameras in these scenarios.”

That’s what the team is now exploring. The researchers will be combining WiFi sensors (which provide accuracy and reliability) with cameras (which provide visual and contextual information about the environment) to develop a more complete, yet inexpensive, mapping technology.

Paper title: “P2SLAM: Bearing Based WiFi SLAM for Indoor Robots.” Co-authors include William Hunter, UC San Diego.

Student startup LIMBER makes 3D-printed prostheses affordable and accessible

Joshua Pelz, a Ph.D. student in the Department of Structural Engineering, co-founded LIMBER Prosthetics, which develops custom bioinspired, 3D-printed prostheses. Photo by Erik Jepsen/University Communications.

May 19, 2022-- Every quarter, UC San Diego engineers Joshua Pelz and Luca De Vivo, as well as prosthetics specialist Herb Barrack, travel to Ensenada, Mexico, where they work with amputees to provide free, 3D-printed, custom-made prostheses. 

The team takes scans of the amputees’ residual limbs with smartphones, which they then bring back to the UC San Diego campus. They use the scans to build a digital model of the amputated limb and a compatible prosthesis. Then, using a 3D printer the team developed, the prosthesis is printed in just 12 hours.  

LIMBER designs and 3D-prints custom prosthesis made from cutting-edge materials. Photo by Erik Jepsen/University Communications.

After the prosthesis is 3D-printed, the team returns to Mexico, where they fine-tune the fit. The project is supported by the Rotary Foundation and is looking for other funding sources as well. Information on how to make a donation is available on the project’s website.

The World Health Organization estimates that there are 40 million amputees in developing countries, 95% of whom have to make do without a prosthetic limb. This is because prosthetic limbs are expensive and time-consuming to manufacture. Patients have to undergo repeated visits to doctor’s offices and need to have access to specialists. 

Using this combination of personalized scans as well as digital designs and 3D-printing on a large scale could reduce the cost of a prosthesis by anywhere from 50% to 90% and deliver prosthetics much faster to those who need them. Pelz, De Vivo and Barrack have formed a startup, LIMBER Prosthetics & Orthotics, Inc., to commercialize the technology. 

LIMBER’s business plan is two-fold. The company plans to sell its personalized prostheses in developed countries while providing its services for developing countries at discounted prices or for free. 

The company will revolutionize access to prostheses for amputees, said Diana Zambrano, a San Diego resident who is herself an amputee and has helped the team test the devices. 

An amputee tests a LIMBER prosthesis at a clinic in Ensenada, Mexico. Photo courtesy of LIMBER.

“Mobility is a necessity,” Zambrano said. “LIMBER can print out a leg in a day, and right away, you have a leg to walk on. It’s amazing.”

LIMBER’s methods will also make prostheses much more affordable–costs currently can run upwards of $20,000, Zambrano said. “It’s going to be wonderful to have prosthetics that are affordable for everyone,” she added. 

The LIMBER devices are comfortable, she said. They are also made from water-proof materials, in contrast to traditional prosthetics made of carbon fiber and metal. Materials for prosthetics have improved dramatically over the last 35 years, from wood all the way to space-age materials and materials that can be 3D-printed, said Barrack, who is a certified prosthetist and orthotist. 

LIMBER has conducted many tests to see what kinds of loads 3D materials could bear and design their prosthetics accordingly, Barrack said. They also are conducting testing to make sure the prosthetics are safe. “Patient safety comes first,” he said. 

UC San Diego roots

LIMBER has deep roots at UC San Diego: it is currently part of the medical technology accelerator in the Institute for the Global Entrepreneur (IGE) at the UC San Diego Jacobs School of Engineering. LIMBER is also part of UC San Diego’s Basement startup accelerator. The company will soon start raising a seed round of funding. They connected with mentors through IGE, including medical device executive Michael Collins. 

The project started in 2016 in the research group of Falko Kuester, a professor in the Department of Structural Engineering. Dubbed the Limber Integrative Imaging Modeling Manufacturing for Bold Exoskeleton Research project, or LIMBER, the project’s goal was to bring together imagining, modeling, simulation testing and 3D-printing to create low-cost, one-piece prosthetics that can be tailor specifically to match user needs. Preliminary, proof-of-concept studies with lower-limb amputees have shown the potential of this approach. The project was housed in the Qualcomm Institute here on campus. 

LIMBER cofounder Luca De Vivo, a postdoctoral student in the Department of Structural Engineering (left), talks to two members of the Calafia Rotary Club in Ensenada, Mexico. LIMBER has partnered with the Rotary Club to provide prostheses for local amputees. Photo courtesy of LIMBER.

“It is truly inspiring to work with enthusiastic and innovative students in the classroom and the lab and see their ideas and careers take flight,” Kuester said.

De Vivo and Pelz both took Engineering Frontiers, a graduate-level class taught by Kuester, and later served as teaching assistants and mentors in the class. They made the work part of their doctoral research and launched their startup at the same time. They also connected with Barrack thanks to Kuester. Pelz and De Vivo started going on Rotary Foundation trips to Ensenada to help amputees.

“I found my passion for this project when we visited a clinic in Mexico and saw the huge impact our technology can have,” Pelz said. 

De Vivo became interested in the connection between natural structures and materials science as an undergraduate student in structural engineering at UC San Diego. He decided to deepen his understanding as a doctoral student. 

Democratizing prosthesis

The structure of the LIMBER prostheses are inspired by the structure of the cholla cactus. Photo courtesy of LIMBER.

Traditionally, a model of the residual limb is carved by hand by a specialist; a time-consuming process that is expensive and can’t be replicated. “They are like sculptors,” De Vivo said. “And there are not enough of them.” Specialists then build the prosthesis to fit around this model. 

Instead, LIMBER uses digital tools to democratize access. The team is using an off-the-shelf app on their phones to scan the amputated limb. They upload the data to a computer-aided design program to build a digital twin of the patient’s residual limb. They then build a model of the prosthesis to complement the digital twin. This allows the researchers to save a lot of time, as they don’t have to do several fittings to get the shape of the prosthetic right. 

Researchers also decreased the weight of the prosthetic by using cutting edge 3D-printing materials. Most of their new prosthetics are made from a combination of nylon and nylon filled with chopped carbon fiber. By 3D-printing with the two materials, the team can vary the stiffness of the limb, making the foot more flexible, for example. Researchers also built a custom 3D printer from the ground up. 

Bioinspiration and next steps

The prostheses are manufactured using a printer that the LIMBER team designed and built from scratch. Photo courtesy of LIMBER.

The design of the prosthetics is inspired by the structure of the Cholla cactus, which De Vivo studied both as an undergraduate and graduate student. The cacti’s wooden skeleton needs to withstand difficult desert conditions and hurricane force winds. It does this thanks to its skeleton: a cylinder of wooden fibers that criss-cross at a 45 degree angle, with oval empty spaces in between them, a little like a chain link fence. This open space allows the cacti skeleton to bend or rotate in windy conditions. 

Pelz and De Vivo are still working to perfect their process. They are now conducting materials testing. This summer, they will start a human subject study to evaluate the prosthetics’ performance. They also plan to incorporate sensors within the prosthesis for better performance. Their work will be documented in several scientific articles set to appear this year. 

“Digital twin technology combined with 3D-printing holds tremendous promise to change the way prosthetics are manufactured–and made accessible,” Kuester, the structural engineering professor, said. 

 

Center faculty member Thomas A. DeFanti named to IEEE Virtual Reality Academy

Induction into the academy is a highly prestigious honor in the impactful field of virtual reality

Multi-tasking wearable continuously monitors glucose, alcohol, and lactate

The device can be worn on the upper arm while the wearer goes about their day. Photos by Laboratory for Nanobioelectronics / UC San Diego

May 9, 2022 -- Imagine being able to measure your blood sugar levels, know if you’ve had too much to drink, and track your muscle fatigue during a workout, all in one small device worn on your skin. Engineers at the University of California San Diego have developed a prototype of such a wearable that can continuously monitor several health stats—glucose, alcohol, and lactate levels—simultaneously in real-time.

The device is about the size of a stack of six quarters. It is applied to the skin through a Velcro-like patch of microscopic needles, or microneedles, that are each about one-fifth the width of a human hair. Wearing the device is not painful—the microneedles barely penetrate the surface of the skin to sense biomolecules in interstitial fluid, which is the fluid surrounding the cells beneath the skin. The device can be worn on the upper arm and sends data wirelessly to a custom smartphone app.

Researchers at the UC San Diego Center for Wearable Sensors describe their device in a paper published May 9 in Nature Biomedical Engineering.

“This is like a complete lab on the skin,” said center director Joseph Wang, a professor of nanoengineering at UC San Diego and co-corresponding author of the paper. “It is capable of continuously measuring multiple biomarkers at the same time, allowing users to monitor their health and wellness as they perform their daily activities.”

Most commercial health monitors, such as continuous glucose monitors for patients with diabetes, only measure one signal. The problem with that, the researchers said, is that it leaves out information that could help people with diabetes, for example, manage their disease more effectively. Monitoring alcohol levels is useful because drinking alcohol can lower glucose levels. Knowing both levels can help people with diabetes prevent their blood sugar from dropping too low after having a drink. Combining information about lactate, which can be monitored during exercise as a biomarker for muscle fatigue, is also useful because physical activity influences the body’s ability to regulate glucose.

“With our wearable, people can see the interplay between their glucose spikes or dips with their diet, exercise and drinking of alcoholic beverages. That could add to their quality of life as well,” said Farshad Tehrani, a nanoengineering Ph.D. student in Wang’s lab and one of the co-first authors of the study.

Microneedles merged with electronics

The disposable microneedle patch detaches from the reusable electronic case.

The wearable consists of a microneedle patch connected to a case of electronics. Different enzymes on the tips of the microneedles react with glucose, alcohol and lactate in interstitial fluid. These reactions generate small electric currents, which are analyzed by electronic sensors and communicated wirelessly to an app that the researchers developed. The results are displayed in real time on a smartphone.

An advantage of using microneedles is that they directly sample the interstitial fluid, and research has shown that biochemical levels measured in that fluid correlate well with levels in blood.

“We’re starting at a really good place with this technology in terms of clinical validity and relevance,” said Patrick Mercier, a professor of electrical and computer engineering at UC San Diego and co-corresponding author of the paper. “That lowers the barriers to clinical translation.”

The device can be recharged on an off-the-shelf wireless charging pad.

The microneedle patch, which is disposable, can be detached from the electronic case for easy replacement. The electronic case, which is reusable, houses the battery, electronic sensors, wireless transmitter and other electronic components. The device can be recharged on any wireless charging pad used for phones and smartwatches.

Integrating all these components together into one small, wireless wearable was one of the team’s biggest challenges. It also required some clever design and engineering to combine the reusable electronics, which must stay dry, with the microneedle patch, which gets exposed to biological fluid.

“The beauty of this is that it is a fully integrated system that someone can wear without being tethered to benchtop equipment,” said Mercier, who is also the co-director of the UC San Diego Center for Wearable Sensors.

Testing

The wearable was tested on five volunteers, who wore the device on their upper arm, while exercising, eating a meal, and drinking a glass of wine. The device was used to continuously monitor the volunteers’ glucose levels simultaneously with either their alcohol or lactate levels. The glucose, alcohol and lactate measurements taken by the device closely matched the measurements taken respectively by a commercial blood glucose monitor, Breathalyzer, and blood lactate measurements performed in the lab.

Next steps

Farshad Tehrani and fellow co-first author Hazhir Teymourian, who is a former postdoctoral researcher in Wang’s lab, co-founded a startup company called AquilX to further develop the technology for commercialization. Next steps include testing and improving upon how long the microneedle patch can last before being replaced. The company is also excited about the possibility of adding more sensors to the device to monitor medication levels in patients and other health signals.

Paper: “An integrated wearable microneedle array for the continuous monitoring of multiple biomarkers in interstitial fluid.” Co-authors include Brian Wuerstle*, Jonathan Kavner*, Ravi Patel, Allison Furmidge, Reza Aghavali, Hamed Hosseini-Toudeshki, Christopher Brown, Fangyu Zhang, Kuldeep Mahato, Zhengxing Li, Abbas Barfidokht, Lu Yin, Paul Warren, Nickey Huang and Zina Patel, all at UC San Diego.

*These authors contributed equally

This work is supported by the Center for Wearable Sensors at UC San Diego and the National Institutes of Health National Institute of Neurological Disorders and Stroke (grant R21 NS114764 – 01A1).

Breaking through to the brain

Engineering nanomaterials to diagnose and treat traumatic brain injuries

Ester Kwon, a professor of bioengineering at the Jacobs School of Engineering, is developing nanomaterials to diagnose and treat traumatic brain injuries. Photos by Erik Jepsen/UC San Diego

May 5, 2022--Traumatic brain injuries might have faded from the headlines since the NFL reached a $765 million settlement for concussion-related brain injuries, but professional football players aren’t the only ones impacted by these injuries. Each year, between 2 million and 3 million Americans suffer from traumatic brain injuries—from elderly people who fall and hit their head, to adolescents playing sports or falling out of trees, to people in motor vehicle accidents.

There are currently no treatments to stop the long-term effects of a traumatic brain injury (TBI), and accurate diagnosis requires a visit to a medical center for a CT scan or MRI, both of which involve large, expensive equipment.

Kwon works at the crux of two burgeoning fields: biological nanomaterials and neuroscience.

UC San Diego bioengineering Professor Ester Kwon, who leads the Nanoscale Bioengineering research lab at the Jacobs School of Engineering, aims to change that. Kwon’s team is developing nanomaterials—materials with dimensions on the nanometer scale—that could be used to diagnose traumatic brain injury on the spot, be it a sports field, the scene of a car accident, or a clinical setting. They’re also engineering nanoparticles that could target the portion of the patient’s brain that was injured, delivering specific therapeutics to treat the injury and improve the patient’s long-term quality of life.

“It’s really a dire state for these patients, and TBI is unfortunately quite prevalent,” said Kwon.

“Patients with a traumatic brain injury will often experience changes in their motor function, their cognitive abilities and psychosocial behavior, such as depression.”

Overcoming the blood-brain barrier

Diagnosing and treating brain injuries has stymied scientists and physicians for so long for several reasons, the first of which is the blood-brain barrier. The barrier is a semipermeable layer of cells meant to keep potentially harmful toxins that circulate in the blood from entering the brain. This barrier makes it difficult to get diagnostic or therapeutic particles into the brain.

To overcome the challenge of bypassing the blood-brain barrier, Kwon’s lab is taking advantage of a recent insight from the realm of cancer research.

“Nanomedicine has historically been applied to the field of cancer,” said Kwon. “My lab has been thinking about how there are some parallels in disease physiology between brain injuries and cancer. For example, there are changes to the vasculature in a cancer patient—the blood vessels in a tumor aren't normal, they have holes—and people have exploited that to get nanomaterials into the tumor through these holes. Similarly, in TBI, there are holes in the vasculature created by the injury that can be exploited to get nanomaterials into the brain.”

Diagnosing TBI

Rebecca Kandell, a bioengineering PhD student in Kwon's lab, is also a Sloan Scholar.

Kwon’s research group aims to diagnose TBI using biomarkers from a simple urine or blood sample. While scientists have known for decades that a class of enzymes called proteases show increased activity in the injured parts of the brain, getting a sensor into the brain to measure the activity of these proteases remained elusive. Taking advantage of the vascular holes caused by TBI, Kwon’s team was able to develop a nanomaterial that can detect this protease activity, and release a fluorescent signal in the exact location where activity is increased. Their studies, published in February 2020 and December 2021, were the first demonstration of a sensor that could detect protease activity to identify and locate TBI in mice.

Follow-on studies in mice showed that levels of this protease activity picked up by their nanosensors, which were delivered intravenously, could be measured in blood and urine samples.

While researchers still need to perfect the measurement of these protease signals from urine or blood samples before the TBI diagnostic tool could be used by humans, promising advances from a similar concept used for liver fibrosis are encouraging.

“A very similar type of material has already been used in humans to detect liver disease, which is exciting for us in terms of the approach being established as safe,” said Kwon.

Treating TBI

In addition to diagnosing TBI, Kwon’s lab is working to engineer nanoparticles that could be designed to reach the specific part of the brain that was impacted, carrying a therapeutic payload to reduce inflammation, or deliver pro-regenerative therapeutics. These two components would work in tandem, with the diagnostic tool generating information on the exact type and location of the injury, to inform what specific therapeutics would work best and where they need to be delivered.

“Our big dream is to create a precision medicine approach,” said Kwon. “Which is basically to understand the molecular basis for the disease, and apply a therapeutic that’s specific to that molecular underpinning. Because the patient population is heterogeneous, if we know more precisely what’s happening molecularly, we can potentially match therapeutics to their condition and hopefully mitigate any side effects.”

The nanoparticles her lab develops are about the size of a virus. They are made up of a polymer core which carries the desired payload, coated in an outer layer of peptides which give it a location to travel to, like a GPS.

RNA-loaded nanoparticle

In addition to filling the core of these nanoparticles with therapeutic drugs, Kwon’s lab is also working to engineer a nanoparticle that could be used to carry RNA material to the brain for a variety of purposes, from reducing inflammation, to encouraging damaged cell growth. These particular nanoparticles are made from lipids that protect the RNA cargo, and ensure it can be released and activated where needed. This type of lipid nanoparticle carrying RNA cargo is similar to what is used in the mRNA vaccines for COVID-19.

Kwon's lab is also working to engineer a nanoparticle that could be used to carry RNA material to the brain.

To date, there haven’t been any targeted lipid nanoparticles that can reach specific cell types in humans, which would be necessary for use in the brain. Engineering these particles to target specific cell types in the brain is a main focus area of Kwon’s research.

For Kwon, all of the possibilities and experimentation are part of the excitement of working at the crux of the two burgeoning fields of biological nanomaterials and neuroscience.

“In general, the field of nanomaterials for the brain is a few decades behind our sisters and brothers in cancer therapy,” she said. “There has been a lot of rapid development in neuroscience—our knowledge of the basic biology of the brain—which has only happened in the last decade or so. And that sets the table for engineers to start understanding how to design materials to interact with the brain in more sophisticated ways.”

Unveiling the genes linked to the synthesis of many complex Human Milk Oligosaccharides (HMOs)

Arrhythmia mapping technology demonstrates positive clinical results

May 4, 2022--Bioengineers and cardiologists from the University of California San Diego invented a technology that can accurately and noninvasively map atrial and ventricular heart arrhythmias in a matter of minutes. The technology, developed by Vektor Medical Inc., a company co-founded by UC San Diego faculty, demonstrated 97.3 percent accuracy in a clinical validation study, and recently received FDA clearance.

The vMap technology localizes the source of arrhythmia using only data from a noninvasive 12-lead ECG.

Instead of sending a catheter into a patient’s heart to localize the source of the arrhythmia, the new vMap technology requires only data from a standard noninvasive 12-lead electrocardiogram (ECG) – performed in most clinical and ambulatory settings – to create a three-dimensional interactive map of arrhythmia source locations in all four chambers of the heart.

The researchers used computational modeling to create over one million simulations of different heart arrhythmias. The patient’s ECG recordings are compared to this simulation database to accurately locate the source of the arrhythmia.

vMap was invented by bioengineers and cardiologists from UC San Diego, and has been developed by Vektor Medical, a startup co-founded by Professor of Bioengineering, Andrew McCulloch; Professor of Medicine and electrophysiologist, Dr. David Krummen; Assistant Professor of Medicine, electrophysiologist, and bioengineering alumnus, Dr. Gordon Ho; and bioengineering alumnus Dr. Christopher Villongco, Vektor’s chief technology officer. The Vektor Medical team presented their clinical trial results at the Heart Rhythm Society meeting in San Francisco.

Pinpointing an electrical fault

David Krummen, MD, cardiac electrophysiologist at UC San Diego Health and professor of medicine at UC San Diego School of Medicine, is a co-inventor of vMap.

The current standard of care for treating heart arrhythmias – any type of irregular heartbeat that is too fast, too slow, or mistimed due to an electrical signal misfiring – is to carefully burn or freeze the exact spot in the heart where the electrical misfiring is coming from. This procedure, called an ablation, resets the electrical signals and heartbeat. Hundreds of thousands of ablations are performed in the United States every year. But before an electrophysiologist can perform an ablation, they need to know precisely where in the heart the arrhythmia is coming from.

“Mapping is critical to planning and performing ablation. The current process of arrhythmia localization relies upon invasive catheter mapping” said Dr. David Krummen. “It generally works well, but the process can be time consuming, increasing fluoroscopy and anesthesia exposure for the patient. Moreover, occasionally the catheter-based process may "bump" the arrhythmia source and suppress the clinical arrhythmia, preventing further mapping.”

“We wanted to find a way to pinpoint the arrhythmia source location using data from the 12-lead ECG,” he added. “The 12-lead ECG is used in a variety of clinical settings outside the electrophysiology laboratory including the emergency department, the intensive care unit, and the outpatient clinic. One of the major goals of the system is to leverage arrhythmia data from these ECGs to potentially allow arrhythmia source mapping prior to arrival in electrophysiology lab.”

The computational solution

That’s where bioengineering Professor Andrew McCulloch and Christopher Villongco, a PhD student in McCulloch’s lab at the time and now Vektor’s CTO, came in. McCulloch has spent the last 35 years at UC San Diego making models of the heart, from the biochemistry and physiology of its cells and the mechanics of its muscle fibers to the electrical rhythms of the whole heart. His cardiac computational modeling software, Continuity, allows researchers to accurately simulate the heart down to the cellular level. Villongco and McCulloch originally set out to develop personalized computational models to help patients and physicians predict the outcome of certain heart procedures, but soon hit a stumbling block: how to translate computational modeling from academic use to real-time, actionable clinical use?

“Developing detailed, personalized models for individual patients was appropriate for our research at the time, but the process of creating a single model requires a lot of high-quality clinical data, computational power, time, and modeling expertise,” said Villongco. “We learned from collaborating with Drs. Krummen and Ho that the actual clinical demands were quite the opposite: minimal data, limited computational power, rapid analysis, and ease of use in the existing clinical workflow.”

Andrew McCulloch, a professor of bioengineering and Shu Chien Chancellor’s Endowed Chair in Engineering and Medicine, has spent the last 35 years at UC San Diego modeling the heart.

Learning from the collaboration, the team realized they needed to create a massive library of computational models of arrhythmias.

Then the challenge became how to create a model library, when it took a powerful computer cluster several days to create just one model? Combining computationally efficient modeling methods with modern-day computing architectures and resources, a library of over one million arrhythmia simulations was created in just under one year, a vast improvement from the tens of thousands of years it would have otherwise taken. The clinical product was then designed and implemented according to the needs and experiences of electrophysiologists.

The initial research was funded by grants from the NIH, a Jacobs School of Engineering entrepreneurship program, and the Galvanizing Engineering in Medicine program. Then, thanks to funding from the NIH-backed Center for Accelerated Innovation – intended to help transfer technologies from the lab to the clinic – the researchers and Vektor team were able to further hone the tool, expand its capabilities, and test its accuracy. A multicenter, blinded clinical trial showed that in 255 arrhythmia episodes from 225 patients, the vMap tool had a regional accuracy of 96.9%, with a spatial accuracy of 15mm. The median time to complete the mapping process was 48 seconds.

“It’s one thing to make fancy simulations, but it’s altogether another to make something that can be used in the pressure of a clinic, in a matter of minutes, that’s reliable,” said McCulloch. “And we’ve shown that vMap meets all these needs.” McCulloch is also the director of the UC San Diego Institute for Engineering in Medicine, and the Shu Chien Chancellor’s Endowed Chair in Engineering and Medicine.

vMap is a tool for physicians to better understand seven important and often dangerous arrhythmias – ventricular tachycardia; premature ventricular complex; ventricular fibrillation; focal atrial tachycardia; premature atrial complex; orthodromic atrioventricular reentrant tachycardia; and atrial fibrillation.  The information vMap provides is intended to increase the success rate for patients undergoing these ablation procedures.

vMap is currently in use by physicians at UC San Diego Health with the intent to reduce ablation procedure times and increase ablation success rates for patients with these seven arrhythmias. 

Disclosure: Andrew McCulloch, Ph.D. is a professor of bioengineering at UC San Diego Jacobs School of Engineering. Dr. McCulloch is an inventor of vMap and has equity as a co-founder and Scientific Advisory Board member to Vektor Medical, Inc.

David Krummen, MD, is a cardiac electrophysiologist at UC San Diego Health and professor of medicine at UC San Diego School of Medicine. Dr. Krummen is inventor of vMap and has equity as a co-founder and clinical advisor to Vektor Medical, Inc. 

Study of promising Alzheimer's marker in blood prompts warning about brain-boosting supplements

May 3, 2022 -- Elevated levels of an enzyme called PHGDH in the blood of older adults could be an early warning sign of Alzheimer’s disease, and a study led by the University of California San Diego provides new evidence to support this claim. In analyzing brain tissue, researchers observed a trend consistent with their previous findings in blood samples: expression levels of the gene coding for PHGDH were consistently higher in adults with different stages of Alzheimer’s disease, even the early stages before cognitive symptoms manifested.

The findings also prompt caution against the use of dietary supplements that contain the amino acid serine as a remedy for Alzheimer’s disease. Because PHGDH is a key enzyme in the production of serine, the increased PHGDH expression found in Alzheimer’s patients suggests that the rate of serine production in the brain is also increased, and thus, taking additional serine may not be beneficial, the researchers warned.  

Researchers led by Sheng Zhong, a professor of bioengineering at the UC San Diego Jacobs School of Engineering, and Xu Chen, a professor of neurosciences at UC San Diego School of Medicine, published their findings May 3 in Cell Metabolism.

The new study builds on earlier work by Zhong and colleagues that first identified PHGDH as a potential blood biomarker for Alzheimer’s disease. The researchers had analyzed blood samples of older adults and found a steep increase in PHGDH gene expression in Alzheimer’s patients, as well as in healthy individuals approximately two years before they were diagnosed with the disease.

The results were promising, and the researchers were curious if this increase could be linked back to the brain. In their new study, they show that this indeed is the case.

“It’s exciting that our previous discovery of a blood biomarker is now corroborated with brain data,” said Zhong. “Now we have strong evidence that the changes we see in human blood are directly correlated to changes in the brain in Alzheimer’s disease.”

The researchers analyzed genetic data collected from post-mortem human brains from subjects in four different research cohorts, each made up of 40 to 50 individuals 50 years and older. The subjects consisted of Alzheimer’s patients, so-called “asymptomatic” individuals (people without cognitive problems and without an Alzheimer’s diagnosis, but whose post-mortem brain analyses showed early signs of Alzheimer’s-related changes), and healthy controls.

The results showed a consistent increase in PHGDH expression among Alzheimer’s patients and asymptomatic individuals in all four cohorts compared to the healthy controls. Moreover, expression levels were higher the more advanced the disease. This trend was also observed in two different mouse models of Alzheimer’s disease.

The researchers also compared the subjects’ PHGDH expression levels with their scores on two different clinical assessments: the Dementia Rating Scale, which rates a person’s memory and cognitive ability, and Braak staging, which rates the severity of Alzheimer’s disease based on the brain’s pathology. The results showed that the worse the scores, the higher the expression of PHGDH in the brain.

“The fact that this gene’s expression level directly correlates with both a person’s cognitive ability and disease pathology is remarkable,” said Zhong. “Being able to quantify both of these complex metrics with a single molecular measurement could potentially make diagnosis and monitoring progression of Alzheimer’s disease much simpler.”

The case against serine

The findings come with implications for serine supplements, which are advertised to improve memory and cognitive function. The key player responsible for making serine in the body is PHGDH. Some researchers have proposed that PHGDH expression is reduced in Alzheimer’s disease, and that boosting serine intake could help with treatment and prevention. Clinical trials are already underway to test serine treatments in older adults experiencing cognitive decline.

But with their data consistently showing increased PHGDH expression in Alzheimer’s, the researchers posit that serine production may likely be increased in this disease, contrary to what some other groups claim.

“Anyone looking to recommend or take serine to mitigate Alzheimer’s symptoms should exercise caution,” said co-first author Riccardo Calandrelli, who is a research associate in Zhong’s lab.

Next steps

The researchers are looking to study how changing PHGDH gene expression will affect disease outcomes. The approach could lead to new therapeutics for Alzheimer’s.

A San Diego-based biotechnology startup co-founded by Zhong, called Genemo, is working to develop a PHGDH blood test for early detection of Alzheimer’s disease.

Paper: “PHGDH expression increases with progression of Alzheimer’s disease pathology and symptoms.” Co-authors include John Girardini, Zhangming Yan and Annie Hiniker, UC San Diego; and Zhiqun Tan and Xiangmin Xu, UC Irvine.

This work is partially funded by the National Institutes of Health (grant UG3CA256960) and a Kruger Research Award. The authors thank the University of California Alzheimer’s Disease Research Centers at UC Irvine (funded by NIH grant P50AG16573) and UC San Diego (funded by NIH grant P30AG062429) for providing postmortem tissue samples.

Researchers transform an amorphous solid into a new lithium-ion battery material

Researchers at UC San Diego and Boise State University have developed a new approach to making novel lithium-ion battery materials. The approach transforms a non-crystalline material into a crystalline anode material with exceptional battery properties—by cycling it with lithium. Credit: Xiong lab

May 2, 2022 -- Researchers at the University of California San Diego and Boise State University have developed a new approach to making novel lithium-ion battery materials. The approach transforms a non-crystalline material into a crystalline one—by cycling it with lithium.

Using this approach, the team transformed a non-crystalline (amorphous) material called niobium oxide into a novel crystalline Nb₂O₅ anode with exceptional lithium storage and fast cycling. This process can potentially be used to make other lithium-ion battery materials that cannot be easily made via traditional means.

The study, jointly led by researchers in the labs of Shyue Ping Ong, a professor of nanoengineering at the University of California San Diego, and Hui (Claire) Xiong, a professor of materials science and engineering at Boise State University, was published May 2 in Nature Materials.

The discovery of new materials for lithium-ion batteries has taken on a renewed urgency. Fueled by rising gas prices, there has been a surge in demand for electric vehicles (EVs), and with it, for the lithium-ion batteries that power them. However, today’s lithium-ion batteries are still too expensive and charge too slowly.

“Lithium-ion batteries are the leading technology for the rechargeable battery market, but there's also an increase in the demand for the battery to have high energy, and faster charging times,” said Pete Barnes, a Ph.D. alumnus of Xiong’s group and the lead author of the work. “If you want to charge your EV for 15 minutes and then get on the road for the next 200 or 300 miles, you need new battery electrodes that can be charged at a very fast rate without much loss in performance.”

Among one of the biggest bottlenecks to charging in today’s lithium-ion batteries is the anode. The most common anode is made of graphite, which is very energy dense, but cannot be charged too quickly due to the risk of fire and explosions from a process known as lithium metal plating. Intercalation metal oxides, like the rock salt Nb₂O₅ material discovered by the team, are promising anode alternatives due to the reduced risk of lithium plating at low voltages.

To create the new anode material, Xiong’s group developed an innovative technique called electrochemically-induced amorphous-to-crystalline transformation. The new electrode can achieve high lithium storage of 269 mAh/g at a charging rate of 20 mA/g, and more importantly, continues to retain a high capacity of 191 mAh/g at a high charging rate of 1 A/g.

“The most exciting aspect of this work is the discovery of a completely new approach to create novel lithium-ion battery electrodes,” said Xiong. “The trick is to start from a higher energy phase, such as an amorphous material. Just cycling the material with lithium allows us to create new crystalline arrangements that exhibit improved properties beyond those made via traditional means such as solid-state reactions.”

The exceptional rate performance of the anode is due to its disordered rock salt (DRX), which is like ordinary kitchen table salt but with the Li and Nb atoms arranged in a random fashion. While DRX cathode materials are well-known, DRX anodes are relatively rare.

Using computational techniques, Yunxing Zuo, a Ph.D. alumnus of Ong’s Materials Virtual Lab at UC San Diego, showed that the process of inserting Li into amorphous Nb₂O₅ allows materials scientists to access metastable materials. The team also developed a metric to identify other metal oxides that can potentially be synthesized in a similar fashion. The computations also show that the DRX structure contains paths for fast lithium diffusion, resulting in high rate performance.

“We believe this work to be merely the beginning of a completely new way of thinking about materials synthesis,” said Ong. “Atoms like to arrange themselves in certain ways. When we make materials the traditional way, we usually get the same arrangements again and again. This new approach opens up a promising avenue for creating other unconventional metal oxides.”

The team’s collaborators on this work include Sungsik Lee, Justin Connell, Hua Zhou and Yuzi Liu at Argonne National Laboratory; Paul Davis, Paul Simmonds, and Darin Schwartz at Boise State; and Yingge Du and Zihua Zhu at Pacific Northwest National Laboratory.

'Eye-catching' smartphone app could make it easy to screen for neurological disease at home

A smartphone user can image the eye using the RGB selfie camera and the front-facing near-infrared camera included for facial recognition. Measurements from this imaging could be used to assess the user’s cognitive condition. Credit: Digital Health Lab

April 29, 2022 -- Researchers at the University of California San Diego have developed a smartphone app that could allow people to screen for Alzheimer’s disease, ADHD and other neurological diseases and disorders—by recording closeups of their eye.

The app uses a near-infrared camera, which is built into newer smartphones for facial recognition, along with a regular selfie camera to track how a person’s pupil changes in size. These pupil measurements could be used to assess a person’s cognitive condition.  

The technology is described in a paper that will be presented at the ACM Computer Human Interaction Conference on Human Factors in Computing Systems (CHI 2022), which will take place from April 30 to May 5 in New Orleans as a hybrid-onsite event.

“While there is still a lot of work to be done, I am excited about the potential for using this technology to bring neurological screening out of clinical lab settings and into homes,” said Colin Barry, an electrical and computer engineering Ph.D. student at UC San Diego and the first author of the paper, which received an Honorable Mention for Best Paper award. “We hope that this opens the door to novel explorations of using smartphones to detect and monitor potential health problems earlier on.”

Pupil size can provide information about a person’s neurological functions, recent research has shown. For example, pupil size increases when a person performs a difficult cognitive task or hears an unexpected sound.

Measuring the changes in pupil diameter is done by performing what’s called a pupil response test. The test could offer a simple and easy way to diagnose and monitor various neurological diseases and disorders. However, it currently requires specialized and costly equipment, making it impractical to perform outside the lab or clinic.

Engineers in the Digital Health Lab, led by UC San Diego electrical and computer engineering professor Edward Wang, collaborated with researchers at the UC San Diego Center for Mental Health Technology (MHTech Center) to develop a more affordable and accessible solution.

“A scalable smartphone assessment tool that can be used for large-scale community screenings could facilitate the development of pupil response tests as minimally-invasive and inexpensive tests to aid in the detection and understanding of diseases like Alzheimer’s disease.  This could have a huge public health impact,” said Eric Granholm, a psychiatry professor at UC San Diego School of Medicine and director of the MHTech Center.

A diagram of the flow from data acquisition to the final data. A user self administers a pupil response test, then the data are collected off-device to compute the distance and pupil diameter. The final result is shown on the far right. Credit: Digital Health Lab

 

The app developed by the UC San Diego team uses a smartphone’s near-infrared camera to detect a person’s pupil. In the near-infrared spectrum, the pupil can be easily differentiated from the iris, even in eyes with darker iris colors. This enables the app to calculate pupil size with sub-millimeter accuracy across various eye colors. The app also uses a color picture taken by the smartphone’s selfie camera to capture the stereoscopic distance between the smartphone and the user. The app then uses this distance to convert the pupil size from the near-infrared image into millimeter units. 

The app’s measurements were comparable to those taken by a device called a pupillometer, which is the gold standard for measuring pupil size.

The researchers also included various features in their app to make it more user friendly for older adults. 

“For us, one of the most important factors in technology development is to ensure that these solutions are ultimately usable for anyone. This includes individuals like older adults who might not be accustomed to using smartphones,” said Barry. 

The researchers worked with older adult participants to design a simple app interface that allows users to self administer pupil response tests. This interface included voice commands, image-based instructions, and a cheap, plastic scope to direct the user to place their eye within the view of the smartphone camera.

“By testing directly with older adults, we learned about ways to improve our system’s overall usability and even helped us innovate older adult specific solutions that make it easier for those with different physical limits to still use our system successfully,” said Wang, who is also a faculty member in the UC San Diego Design Lab. “When developing technologies, we must look beyond function as the only metric of success, but understand how our solutions will be utilized by end-users who are very diverse.”

The Digital Health Lab is continuing this work in a project to enable similar pupillometry function on any smartphone rather than just the newer smartphones. Future studies will also involve working with older adults to evaluate home use of the technology. The team will work with older individuals with mild cognitive impairment to test the app as a risk screening tool for early stage Alzheimer's disease.

This work was funded by the National Institute of Aging.

To learn more about this project and other works by the UCSD Digital Health Lab, see their webpage at https://digihealth.eng.ucsd.edu/.

Paper: “At-Home Pupillometry using Smartphone Facial Identification Cameras.”

Researchers shed light on why a certain plant virus is so powerful at fighting cancer

April 27, 2022 -- A plant virus that infects legumes, called cowpea mosaic virus, has a special power that you may not have known about: when injected into a tumor, it triggers the immune system to treat the cancer—even metastatic cancer—and prevents it from recurring.

For the past seven years, researchers at the University of California San Diego and Dartmouth College have been studying and testing cowpea mosaic virus—in the form of nanoparticles—as a cancer immunotherapy and have reported promising results in lab mice and companion dog patients. Its performance has been unmatched by other cancer-fighting strategies the team has tested. But the exact reasons for its success have remained a mystery.

In a new study published in the journal Molecular Pharmaceutics, the researchers uncover details that explain why cowpea mosaic virus in particular is exceptionally effective against cancer.

The work was led by Nicole Steinmetz, a professor of nanoengineering at the UC San Diego Jacobs School of Engineering, and Steven Fiering, a professor of microbiology and immunology at the Geisel School of Medicine at Dartmouth. Steinmetz and Fiering are co-founders of a biotechnology startup, called Mosaic ImmunoEngineering Inc., which has licensed the cowpea mosaic virus nanotechnology and is working to translate it into the clinic as a cancer immunotherapy.

“This study helps validate the cowpea mosaic plant virus nanoparticle as our lead cancer immunotherapy candidate,” said Steinmetz, who also serves as the director of the Center for NanoImmunoEngineering at UC San Diego. “Now we have mechanistic data to explain why it is the most potent candidate, which further de-risks it for clinical translation.”

Up until now, Steinmetz, Fiering and their teams had a general idea of how their lead candidate worked. The cowpea mosaic virus nanoparticles, which are infectious in plants but not in mammals, are injected directly inside a tumor to serve as immune system bait. The body’s immune cells recognize the virus nanoparticles as foreign agents and get fired up to attack. When the immune cells see that the virus nanoparticles are inside a tumor, they go after the cancerous cells.

The beauty of this approach, noted Steinmetz, is that it not only takes care of that one tumor, but it also launches a systemic immune response against any metastatic and future tumors. The researchers have seen it work in mouse models of melanoma, ovarian cancer, breast cancer, colon cancer and glioma. They’ve also had success using it to treat canine patients with melanoma, breast cancer and sarcoma.

What’s also interesting is that cowpea mosaic virus has worked the best at triggering an anti-cancer immune response compared to other plant viruses or virus-like particles the researchers have studied. “We’ve shown that it works, and now we need to show what makes it so special that it can induce this kind of response,” said first author Veronique Beiss, a former postdoctoral researcher in Steinmetz’s lab. “That’s the knowledge gap we’re looking to fill.”

To get answers, the researchers compared cowpea mosaic virus with two other plant viruses from the same family that have the same shape and size. One virus, cowpea severe mosaic virus, shares a similar RNA sequence and protein composition. The other, tobacco ring spot virus, is similar only in structure. “We thought these would be great comparisons to see if this potent anti-tumor efficacy runs in this particular family of plant viruses,” said Steinmetz. “And we can dig deeper by comparing to relatives with and without sequence homology.”

The researchers created plant virus-based nanoparticle immunotherapies and injected them into the melanoma tumors of mice. Each immunotherapy candidate was administered in three doses given 7 days apart. Mice given the cowpea mosaic virus nanoparticles had the highest survival rate and the smallest tumors, with tumor growth essentially stalling four days after the second dose.

The researchers then extracted immune cells from the spleen and lymph nodes from the treated mice and analyzed them. They found that the plant viruses all have a protein shell that activates receptors, called toll-like receptors, that are on the surface of immune cells. But what’s unique about cowpea mosaic virus is that it activates an additional toll-like receptor through its RNA. Activating this additional receptor triggers more types of pro-inflammatory proteins called cytokines, which help boost the immune system’s anti-cancer response. In other words, triggering a stronger inflammatory response makes the immune system work harder to look for and get rid of tumors, explained Beiss.

The team’s analysis also found another unique way that the cowpea mosaic virus boosts the immune response. Four days after the second dose, the researchers measured high levels of cytokines. And these levels stayed high over a long period of time. “We don’t see this with the other two plant viruses. The cytokine levels peak quickly, then go down and are gone,” said Beiss. “This prolonged immune response is another key difference that sets cowpea mosaic virus apart.”

While this sheds light on cowpea mosaic virus’s superior potency and efficacy, Steinmetz acknowledges that there is more work to do. “The answers we’ve discovered here have opened up more questions,” she said. “How does this virus nanoparticle get processed in the cell? What happens to its RNA and proteins? Why is the RNA of cowpea mosaic virus recognized but not the RNA of other plant viruses? Understanding the detailed journey of this particle through the cell and how it compares to other particles will help us nail down what makes cowpea mosaic virus uniquely effective against cancer.”

Paper: “Cowpea Mosaic Virus Outperforms Other Members of the Secoviridae as In Situ Vaccine for Cancer Immunotherapy.” Co-authors include Chenkai Mao, Dartmouth College.

This work was funded by the National Institutes of Health (grants U01-CA218292, R01-CA224605 and R01 CA253615) and the Department of Defense, Congressionally Directed Medical Research Program (W81XWH2010742).

Conflict of interest statement: Nicole Steinmetz and Steven Fiering are co-founders of, have equity in, and have a financial interest with Mosaic ImmunoEngineering Inc. Steinmetz serves as Director, Board Member, and Acting Chief Scientific Officer, and paid consultant to Mosaic. Fiering serves as scientific advisor and paid consultant to Mosaic. The other authors declare no potential conflicts of interest.

Study Reveals Genetic Diversity of a Particularly Problematic Pathogen

Clostridioides difficile is a bacterial bane within health care, typically infecting patients rendered vulnerable by antibiotic use

April 27, 2022

An illustration of a Clostridoides difficile bacillus, a common cause of antibiotic-associated intestinal illness. Photo credit: Centers for Disease Control and Prevention

Researchers at University of California San Diego School of Medicine and Jacobs School of Engineering, with colleagues at Baylor College of Medicine, have used a systems biology approach to parse the genetic diversity of Clostridioides difficile, a particularly problematic pathogen in health care settings.

The Centers for Disease Control estimates that the bacterium causes approximately 500,000 infections in the United States annually, with severe diarrhea and colitis (inflammation of the colon) as characteristic symptoms.

The researchers’ findings are published in the April 27, 2022 online issue of PNAS.

C. difficile is the most dominant cause of hospital-associated infections, in part from the use of antibiotics, which can kill enough healthy bacteria to allow C. difficile to grow unchecked. Infections are particularly dangerous in older persons. One in 11 people over the age of 65 who are diagnosed with a hospital-associated case of C. difficile die within one month, reports the CDC.

“C. diff is persistent and pervasive,” said senior author Jonathan M. Monk, PhD, a research scientist in the Systems Biology Research Group at UC San Diego, directed by Bernhard O. Palsson, PhD, professor of bioengineering and an adjunct professor in the UC San Diego School of Medicine. “It doesn’t cause typical diarrhea. Most people do recover, but some become seriously ill, require hospitalization and some die from complications like kidney failure or sepsis.”

To better understand the genetic features of C. difficile — and thus develop models that can identify and predict its complex and constant evolution — researchers used whole-genome sequencing, high-throughput phenotypic screening and metabolic modeling of 451 bacterial strains.

This data was used to construct a “pangenome” or entire set of genes representative of all known C. difficile strains, from which they identified 9,924 distinct gene clusters, of which 2,899 were considered to be core (found in all strains) while 7,025 were “accessory” (present in some strains but missing in others).

Using a new typing method, they categorized 176 genetically distinct groups of strains.

“Typing by accessory genome allows for the discovery of newly acquired genes in genomes of pathogens that may otherwise go unnoticed with standard typing methods,” said co-author Jennifer K. Spinler, PhD, an instructor in pathology and immunology at the Baylor College of Medicine. “This could be critical in understanding what drives an outbreak and how to fight its spread.”

Thirty-five strains representing the overall set were experimentally profiled with 95 different nutrient sources, revealing 26 distinct growth profiles. The team then built 451 strain-specific genome scale models of metabolism to computationally produce phenotype diversity in 28,864 unique conditions. The models were able to correctly predict growth in 76 percent of measured cases.

“One of the strengths of the presented work is the cohesion of distinct biological data types into comprehensive systems biology frameworks that enable analysis at scale,” said first author Charles J. Norsigian, PhD, a data scientist in the Systems Biology Research Group. “By interpreting strains of C. difficile in a population context, we were able to bring to light pertinent strain features regarding nutrient niche, virulence factors, and antimicrobial resistance determinants that might have otherwise gone undetected.”

Co-authors include: Bernhard O. Palsson, UC San Diego; Heather A. Danhof, Colleen K. Brand, Firas S. Midani, Robert A. Britton and Tor C. Savidge, Baylor College of Medicine; and Jared T. Broddrick and Jennifer K. Spinier, NASA Ames Research Center.

Funding for this research came, in part, from the National Institutes of Health (grants P30-DK56338, U01-AI124290, R01AI12378, F32AI136404 AND 1-U01-AI124316).

Opioid treatment tracking startup celebrates string of successes

April 27, 2022--When the creme de la creme of the San Diego startup and innovation space take over Petco Park for San Diego Innovation Day on April 28, CARI Health, a startup supported by the UC San Diego innovation ecosystem, will be among the “Cool Companies” showcased to venture capitalists. Inclusion in local startup hub Connect’s Cool Companies list isn’t the only recent bright spot for CARI Health; the startup, which is developing a wearable opioid medication monitor, also won the $300,000 grand prize at the San Diego Angel Conference in March, and is now looking to close out a seed round of funding. 

Patrik Schmidle, CEO of CARI Health (center) holds the $300,000 grand prize check at the San Diego Angel Conference.

“Nearly 200 people a day die from opioid drug overdoses; it’s a huge problem, and the only way out of this is to get more people into treatment, and then to keep them there,” said Patrik Schmidle, CEO and founder of CARI Health, which offers a solution to this problem.

The startup is developing a wireless, wearable medication monitor that allows clinicians and  patients to track information about medication levels in the patient’s body. Initially, the company plans to use the wearable to help opioid addiction patients in recovery track their treatment medication compliance.  

The device works much the same way a continuous glucose monitor does for diabetics; the patient sticks the device– which has tiny, painless needless on the bottom– on their arm. The needles connect with interstitial fluid, detecting levels of specified medications to ensure the patient is complying with their treatment regimen. This information can be shared with the patient’s doctors or even family members, to help ensure the patient is taking their medication as prescribed. The patient replaces the wearable every seven to 10 days.

This stands in stark contrast to existing options for opioid addiction treatment, where patients often need to physically show up to a clinic to be given their prescribed medication and ensure it’s taken. 

“What our device is intended to do is to remove some of the challenges that opioid addiction patients in recovery face, associated with getting their medication,” Schmidle said. “In some cases that means right now they have to physically go to the clinic to get their medication. By wearing this monitor they wouldn’t have to do that anymore, and that’s life changing.” 

While the initial goal is to track treatment compliance to ensure better outcomes for addiction patients, Schmidle says data from the tool could have much broader implications. The CARI Health device is unique in that it’s able to detect and track multiple medications at the same time. 

“Today clinicians really don’t know how each patient metabolizes medications, so it’s sort of a one size fits all in terms of dosing and titration,” he said “This will give us unique insights to enable clinicians to customize the dosing and the titration for each patient, depending on their metabolism and the drug’s therapeutic range.”

CARI Health has a working prototype and plans to start clinical trials later this year. 

A deconstructed view of CARI Health’s wearable medication monitor.

UC San Diego Innovation Ecosystem

CARI Health got its start in the UC San Diego Qualcomm Institute Innovation Space, where it was housed from 2015 to 2020. Initially, Schmidle was working on an implantable device to detect opioids, with the hope of helping patients in recovery by alerting their medical team or select family members if they had a relapse. The company pivoted in early 2021 from an implantable to a wearable that can detect the medications that are used to treat opioid addiction.

Research from the lab of Drew Hall, a professor of electrical and computer engineering at the Jacobs School of Engineering at UC San Diego, was crucial to the CARI Health device’s feasibility. Hall’s Biosensors and Bioelectronics Laboratory pioneered techniques to enable ultra-low-power devices such as this wearable, which is expected to last for up to 10 days without charging required. His work on miniaturizing the electronics required to power such a device was also critical. Hall now serves as a technical advisor to CARI Health. 

Dr. Carla Marienfeld, a clinical professor and an addiction psychiatrist at UC San Diego Health who is the medical director for the Substance Treatment and Recovery (STAR) Program for people with substance use disorders, has been another critical supporter, serving as a research collaborator and clinical advisor to CARI Health since 2016. Marienfeld advises the company on patient care, clinical utility, and what’s required of such a device from the patient and clinician perspectives. 

Though it now has its own office and lab space in UTC, Schmidle says the UC San Diego innovation ecosystem is still crucial to the startup’s success. CARI Health has been part of the UC San Diego Institute for the Global Entrepreneur’s (IGE) MedTech Accelerator for close to two years, drawing guidance and support from one-on-one mentoring with successful entrepreneurs and business leaders, as well as from larger group check-ins and workshops. 

“The support has just been game-changing,” he said. “Not just the weekly coaching and mentoring, but also the larger group interactions we had with the full group of IGE mentors that would provide feedback. It’s really important to get that feedback from people that have launched businesses and commercialized solutions and have been in the space; it really helps you understand where the biggest risks are, what are the things you have to work on most, what do you prioritize, how do you need to change your messaging. It’s helped us iterate and improve.” 

Startup cofounded by UC San Diego bioengineer wins angel investment competition

Karios Technologies commercializes a hydrogel to prevent adhesions during heart surgeries

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

April 19, 2022--Karios Technologies, a company cofounded by UC San Diego bioengineering professor Karen Christman, won the inaugural Apis Health Angel Conference, a Seattle-based event that connects investors and health-related startups. 

Karios took $155,000 home. More than 50 companies were part of the event’s first round, and only six made it to the finals, which took place in late March 2022. 

The company is commercializing a hydrogel that forms a barrier to keep heart tissue from adhering to surrounding tissue after surgery. The hydrogel was 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.

Karios Technologies is licensing the technology from UC San Diego.  “We are excited to be working to address this large unmet need in cardiac surgery–and other surgeries,”  said Gregory Grover, CEO, Co-Inventor, and Co-Founder of Karios Technologies. "Innovation is needed in this space and would have a significant and positive impact on patients, specifically the lives of young children with cardiac anomalies who require multiple life saving surgeries.”

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. UC San Diego bioengineering professor 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. “And now it’s poised to significantly improve cardiac surgery, both for adults and children.”

 

Cleaning up Online Bots' Act-- and Speech

Researchers develop a method to keep bots from using toxic language

April 20, 2022-- Researchers at the University of California San Diego have developed algorithms to rid speech generated by online bots of offensive language, on social media and elsewhere. 

Chatbots using toxic language is an ongoing issue. But perhaps the most famous example is Tay, a Twitter chatbot unveiled by Microsoft in March 2016. In less than 24 hours, Tay, which was learning from conversations happening on Twitter, started repeating some of the most offensive utterances tweeted at the bot, including racist and misogynist statements. 

The issue is that chatbots are often trained to repeat their interlocutors’ statements during a conversation. In addition, the bots are trained on huge amounts of text, which often contain toxic language and tend to be biased; certain groups of people are overrepresented in the training set and the bot learns language representative of that group only. An example is a bot producing negative statements about a country, propagating bias because it’s learning from a training set where people have a negative view of that country.

“Industry is trying to push the limits of language models,” said UC San Diego computer science Ph.D. student Canwen Xu, the paper’s first author. “As researchers, we are comprehensively considering the social impact of language models and addressing concerns.”

Researchers and industry professionals have tried several approaches to clean up bots’ speech–all with little success. Creating a list of toxic words misses words that when used in isolation are not toxic, but become offensive when used in combination with others. Trying to remove toxic speech from training data is time consuming and far from foolproof. Developing a neural network that would identify toxic speech has similar issues.

Instead, the UC San Diego team of computer scientists first fed toxic prompts to a pre-trained language model to get it to generate toxic content. Researchers then trained the model to predict the likelihood that content would be toxic. They call this their “evil model.” They then trained a “good model,” which was taught to avoid all the content highly ranked by the “evil model.” 

They verified that their good model did as well as state-of-the-art methods–detoxifying speech by as much as 23 percent. 

They presented their work at the AAAI Conference on Artificial Intelligence held online in March 2022. 

Researchers were able to develop this solution because their work spans a wide range of expertise, said Julian McAuley, a professor in the UC San Diego Department of Computer Science and Engineering and the paper’s senior author. 

“Our lab has expertise in algorithmic language, in natural language processing and in algorithmic de-biasing,” he said. “This problem and our solution lie at the intersection of all these topics.” 

However, this language model still has shortcomings. For example, the bot now shies away from discussions of under-represented groups, because the topic is often associated with hate speech and toxic content. Researchers plan to focus on this problem in future work. 

“We want to make a language model that is friendlier to different groups of people,” said computer science Ph.D. student Zexue He, one of the paper’s co-authors. 

The work has applications in areas other than chatbots, said computer science Ph.D. student and paper co-author Zhankui He. It could, for example, also be useful in diversifying and detoxifying recommendation systems. 

 Leashing the Inner Demons: Self-Detoxification for Language Models

Canwen Xu, Zexue He, Zhankui He and Julian McAuley, Department of Computer Science and Engineering, University of California San Diego

https://arxiv.org/pdf/2203.03072.pdf

 

 

 

Tara Javidi awarded $1M NSF grant to make wireless networks more resilient

Sun and solar panels shine at 40th Research Expo

Tala Sidawi receives her best poster award from Dean Albert P. Pisano at Research Expo 2022. It was the 40th anniversary of the event. Photos by Erik Jepsen/UC San Diego

 

April 19, 2022 -- Nanoengineering master’s student Tala Sidawi had her time in the sun at the 2022 edition of Research Expo. Sidawi took home the grand prize for her work to model how solar panels “breathe” water in real time. Such a model could help researchers design solar panels that last longer and perform better in humid environments, and also cost less to build.

“My goal was to emphasize a big problem that the solar panel industry is experiencing and how my research can provide a solution,” said Sidawi. “I had a great time presenting and seeing people understand and ask thoughtful questions about my research, some of which sparked ideas for future work. Winning the grand prize was surreal and a confidence booster for my communication skills—and it validated all the effort I’ve put into my work. Now I’m more excited than ever to enter industry, especially since communication in R&D is such a sought-after skill.”

For the 40th anniversary of Research Expo, the sun showed up for everyone, as more than 100 students set up their posters in the engineering courtyard, around the giant bear statue made out of rocks that is part of the Stuart Collection here on campus. The Expo was held outside for the first time in the event’s history and the weather obligingly cooperated, as Jacobs School Dean Albert P. Pisano pointed out. Research Expo helps students acquire key skills, Dean Pisano added. 

“It’s crucial that you take time to understand your research in the larger context of your field,” he said. “And it’s crucial to have the skill to explain your work and its context to someone far outside of your field. That is how you will be successful in the world.”

This year, in addition to a $750 cash prize, all department winners received a $1000 gift certificate to UC San Diego Extension classes. 

Ph.D. candidate April Aralar, winner of the People's Choice award at Research Expo 2022, poses with Sam Knight, director of the UC San Diego Alumni Board.

Also new this year, participants could vote for a “people’s choice” winning poster. Bioengineering Ph.D. candidate April Aralar, from the research group of associate professor Stephanie Fraley, won the award for her poster titled “Toward an improved method for neonatal sepsis diagnosis.” 

Best poster winner

Sidawi, who is a researcher in the lab of UC San Diego nanoengineering professor David Fenning, received the Lea Rudee Outstanding Poster Award, which came with a $1500 cash prize, as well as the Best Poster Award for the Department of NanoEngineering.

Her research aims to address a problem with solar panels—their performance and longevity suffer when they are exposed to moisture. Water entering a solar panel and staying inside can cause different types of damage such as corrosion, yellowing, and weakening of adhesive bonds between materials inside the panel. 

By modeling the behavior of water in solar panels, Sidawi is helping lay the groundwork for researchers to design and build solar panels that can better withstand or repel moisture.

“The idea is that we can use these simulations to predict optimal designs for solar panels in different moisture conditions,” said Sidawi. “Researchers in academia and industry could potentially plug into this simulation and figure out the best combination of materials and the best architecture for their solar panels.”

To create her model, Sidawi first took a prototype solar panel and subjected it to thousands of hours of high temperature and humidity. These experiments were meant to simulate the degradation the solar panel would experience over 20 years. She then used noninvasive infrared imaging techniques developed in Fenning’s lab to analyze the water inside the solar panel. She used this information and coupled it with a year’s worth of weather data collected from various cities, including San Diego, Phoenix and Miami, to model the behavior and movement of water in the solar panel throughout the year.

“To expand the reach of solar power and lower its cost, we need to be able to optimize solar panels for their location,” said Sidawi. A solar panel built for Phoenix, for example, won’t necessarily work in Miami, she explained. “Although both locations get a lot of sun, the solar panels will be exposed to different levels of humidity, and thus, experience different reactions to water and experience different types of degradation.”

Sidawi hopes that her work can help improve the reliability, performance and cost of solar power in more cities.

“With the work that we’ve done here, maybe we’ll be able to make solar panels that last just as long in Miami as they do in Phoenix,” she said.

Sponsors

Extension is one of the event’s key sponsors this year, along with ASML, Viasat, and Qualcomm. 

“We are here because these students’ creativity, innovation and energy gives us the inspiration to go back to our work and think about the problems we are tackling in a new way,” said Nikolai Devereaux, ViaSat engineering director, who earned both a bachelor’s degree and a master of advanced studies at the Jacobs School. 

All winning posters

The student winners’ short video presentations are linked below.

Overall winner

Moisture ingress and distribution in bifacial silicon photovoltaics
Student: Tala Sidawi
Faculty: David Fenning, Associate Professor 

Department Winners:

Bioengineering–Shu and K.C. Chien Best Poster

Toward a genetic therapy for Duchenne Muscular Dystrophy by RNA end-joining
Student Ryan Hsu
Faculty: Sam Pfaff, a professor at the Salk Institute for Biological Studies and UC San Diego bioengineering affiliate

Computer Science and Engineering

IC Obfuscation through sequential history to combat reverse engineering and fault injection attacks
Student: Leon Li
Faculty: Alex Orailoglu, Professor

Electrical and Computer Engineering

A 0.66 W/MM2 power density, 92.4% peak efficiency hybrid converter with nH-scale inductors for 12V system
Student: Tianshi Xie
Faculty: Hanh-Phuc Le, Assistant Professor

Katie Osterday Best Poster in the Department of Mechanical and Aerospace Engineering

Microscale Concert Hall Acoustics for Sonogenetics
Student: Aditya Vasan
Faculty: James Friend, Professor

NanoEngineering

Moisture ingress and distribution in bifacial silicon photovoltaics
Student: Tala Sidawi
Faculty: David Fenning, Associate Professor 

Structural Engineering

Seismic response of rail embankments
Student: Axel Yarahuaman Chamorro
Faculty: John McCartney, Professor

Two teaching professors recognized with integrity awards

The 12th annual Integrity Awards celebrate substantial contributions to academic, research and professional integrity

Niema Moshiri is an assistant teaching professor at the Jacobs School of Engineering, and received an Integrity Award.

April 15, 2022-- Efforts to ensure the integrity of remote learning developed by Niema Moshiri, an assistant teaching professor in UC San Diego’s Department of Computer Science and Engineering, and Janine Tiefenbruck, a lecturer in the Halicioglu Data Science Institute, were recognized at UC San Diego’s 12th annual Integrity Awards. Tiefenbruck started as a lecturer in the Computer Science and Engineering department before joining the Halicioglu Data Science Institute.

The Integrity Awards are an annual campus tradition organized by the Academic Integrity Office in collaboration with the Executive Vice Chancellor's Office and celebrated each Spring quarter. The awards acknowledge the contributions of community members unafraid to live by their principles and manifest one of the university’s most important core values: integrity.

Moshiri and Tiefenbruck devised data-driven frameworks to prevent cheating in emergency remote learning initiatives. They were honored during a virtual ceremony April 13.

“Integrity is essential to our ongoing success at UC San Diego, as a university, a campus, and a community,” said Tricia Bertram Gallant, director of the Academic Integrity Office. “In the modern world, maintaining our integrity is easier said than done, which is why models for ethical behavior are so important. This year’s remarkable honorees embody integrity at its best, and their work is an example for us all.”

During the COVID-19 pandemic, educators around the world have been forced to adapt quickly to a radically different educational landscape. While many remote learning initiatives have been successful, others have given rise to controversies around mercenary external proctoring companies and incentives for students to cheat. With their desire to create more reliable and productive alternatives, Tiefenbruck and Moshiri developed data-driven frameworks that help keep students honest and unlock new opportunities for true learning to take place.

Moshiri and Tiefenbruck each developed similar data-driven approaches to detecting exam collaboration, drawing heavily on the material they teach their own students.

“In an attempt to maintain academic rigor during remote exams, many courses have imposed various forms of surveillance, often in the form of remote proctoring services in which students are monitored by strangers and are sometimes even recorded, which has eroded trust,” Moshiri said. “Importantly, the tool is open-source and utilizes many computer science principles my students use in their own coursework, so I demonstrate the tool to them as a teaching moment as well as an exercise to solidify their trust in the process.”

Tiefenbruck noted the importance of integrity in remote teaching.

“Integrity is important to me because of the many students I see working tirelessly in their classes. I want their hard work to be rewarded and their grades to be a reflection of what they’ve learned, which is impossible unless everyone is doing their part to present an honest picture of what they know. The collaboration tools we’ve created help ensure that the work each student submits is their own.”

 

NSF funds UC San Diego computer science graduate student developing view synthesis techniques

Alexander Trevithick, a UC San Diego computer science graduate student affiliated with the UC San Diego Center for Visual Computing, has been awarded a prestigious National Science Foundation (NSF) Graduate Student Research Fellowship.

Alex Trevithick is advised by Professor Ravi Ramamoorthi in the Department of Computer Science and Engineering at the UC San Diego Jacobs School of Engineering. Ramamoorthi also Directs the UC San Diego Center for Visual Computing.

Trevithick's research is focused on developing techniques for synthesizing novel views of scenes from a single input view. Combining the cutting-edge method Neural Radiance Fields for View Synthesis (NeRF) with a learned discrete representation of the 3D world, his proposed method will be able to reason about the color and geometry of unseen regions while preserving global and multiview consistency. The project will have many important downstream applications in areas such as robotic locomotion and artificial / virtual reality.
 

Image from the seminal Neural Radiance Fields for View Synthesis (NeRF) paper, on which UC San Diego computer science professor Ravi Ramamoorthi is an author.

What excites Trevithick most about the project is its inherent 'magic': “that we can take a single input view and envision what the rest of the world looks like, far away from the input camera, yet consistent with this input, is a truly magical ability,” said Trevithick. He believes that such tasks embody true intelligence, and he is excited to advance visual intelligence in such a challenging and exciting setting.

The NSF Graduate Student Research Fellowship recognizes and supports outstanding graduate students in NSF-supported STEM disciplines who are pursuing research-based master’s and doctoral degrees at accredited US institutions.

 

 

 

 

Bioengineers Visualize Fat Storage in Fruit Flies

April 14, 2022

Lingyan Shi is a bioengineering professor at the UC San Diego Jacobs School of Engineering

For the first time, researchers have visually monitored, in high resolution, the timing and location of fat storage within the intact cells of fruit flies. The new optical imaging tool from the lab of bioengineering professor Lingyan Shi at the University of California San Diego is already being used to untangle often discussed, yet mysterious, links between diet and things like obesity, diabetes and aging. The work from bioengineers at the UC San Diego Jacobs School of Engineering is published in the journal Aging Cell.

The optical microscopy platform developed by the UC San Diego bioengineers is unique. It allows the researchers to visually track, in high resolution within fat cells, how specific dietary changes affect the way flies turn the energy from their food into fat. The tool also allows the researchers to monitor the reverse process of changing fat back into energy. In addition, the researchers can now visually monitor changes in size in individual fat-storage "containers" within the class of fruit fly cells that is analogous to mammalian fat (adipose) cells.

In the new paper in Aging Cell, the researchers demonstrated the ability to visually track changes in fat (lipid) metabolism in flies after they were put on a wide range of different diets. The diets included calorie-restricted diets, high protein diets, and diets with twice, four-times, and ten-times the sugar of a standard diet.

"With our new optical microscopy system, we can see both where and when fats are being put into storage and taken out of storage," said Shi, the bioengineering professor at UC San Diego who is the corresponding senior author on the new paper. "This is the first imaging technology that can visualize fat metabolism at high resolution in both space and time within individual fat cells. We have demonstrated that we can see both where and when lipid metabolism changes within individual fruit fly fat body cells in response to dietary changes."

"Interest in optimizing the human diet is intense," Shi continued. "People want answers to questions like, 'What are the best diets to slow aging? What are the best diets for losing weight? What are the best diets for extending health span?' I don't yet have answers to these questions, but in my lab, we develop new technologies that are getting us closer to answering some of the big dietary questions out there."

In the new work in Aging Cell, for example, the researchers report a new way to answer questions like:

How much does a specific diet, such as a high-protein diet, or a high-sugar diet, or a calorie-restricted diet, alter a fruit fly's process of turning energy from food into fat? And how much do these same diets affect a fruit fly's process of turning fat back into energy?

"We developed this tool to help us untangle the relationships between diet and phenomena like obesity, diabetes, aging, and longevity," said Shi.

Tracking the size of fat droplets within intact fruit fly cells is one example of what's possible with the new visualization platform.

These images were captured by the technology developed in Lingyan Shi's bioengineering lab at UC San Diego. The technology allows researchers to collect high-resolution information, in both time and space, from within individual fat cells of fruit flies. The images in the lower row are zoomed-in portions of the images in the upper row. Together, these images tell a visual story of fat (lipid) metabolism in fruit flies that were fed different diets. The higher the color-coded value, the higher the rate of fat metabolism. Older visualization platforms do not allow researchers to see these kinds of changes in lipid metabolism within individual fat cells.

"Droplet size is a way to track how much of the stored fat is 'turning over' or getting converted back into energy. This is an important aspect of lipid metabolism, and we now have a tool that allows us to track changes in the size of specific lipid droplets within individual cells of fruit flies," said Yajuan Li, MD. PhD, who is a postdoctoral researcher in the Shi lab at UC San Diego and the first author on the paper in Aging Cell.

Heavy water

The new visualization platform builds on some of Shi's earlier work using a variation on regular water, called heavy water or (D2O). Heavy water is, literally, heavier than regular water. Heavy water molecules contain one oxygen atom like regular water. But in place of the pair of hydrogen atoms—the "H2" in "H20"—heavy water contains a pair of heavier deuterium atoms.

Like "regular" water, heavy water is freely incorporated into cells in living organisms. So when the researchers provide heavy water to a fruit fly, and then that fruit fly begins to convert energy from its food into fat molecules to be stored, some of those fat molecules contain deuterium. In this way, the prevalence of deuterium atoms in lipids stored within the fat cells of fruit flies provides a way to measure how much fat that fly has stored.

By changing a fly's diet at the same time that you introduce heavy water, you have a way to monitor how the diet changes lipid turnover. More details on how the system works are in this 2021 profile, in which Shi said, “When we are developing a new technology, a new tool, it will definitely inspire us to ask new biological questions.”

When it comes to understanding the connections between diet composition and lipid metabolism, the new biological questions are bringing researchers back to some of the oldest and most intriguing questions about links between diet and obesity, diabetes, aging and longevity.

---

Paper title: "DO-SRS imaging of diet regulated metabolic activities in Drosophila during aging processes" in the journal Aging Cell on March 7, 2022. Authors: Yajuan Li, Wenxu Zhang, Anthony A. Fung, and Lingyan Shi from the Department of Bioengineering at the University of California San Diego Jacobs School of Engineering. Funding: NIH, Grant/Award Number: U54 pilot grant 2U54CA132378; Jacobs School of Engineering, University of California San Diego; Hellman Fellow Award from UC San Diego.

ASCE Pacific Southwest Student Symposium draws students from 14 universities across California and Hawaii to San Diego to compete in civil engineering

Researchers map lung development after birth into late childhood for the first time

Map of human lung cell types that were profiled via single-cell sequencing methods. Images adapted from Cell Genomics

April 12, 2022 -- How do the lungs develop after taking their first breaths outside the womb? What cellular events and changes early in life give rise to lung malfunction and disease? To help answer these questions, scientists have constructed the first single-cell atlas of postnatal lung development in humans and mice.

The research could help provide a more detailed understanding—at the level of individual cells—of which genetic and epigenetic factors affect lung health across the human lifespan, starting from birth. 

The work, recently published in Cell Genomics, was led by a team of researchers at the University of California San Diego and the University of North Carolina at Chapel Hill.

By analyzing lung tissue samples from newborn and young humans and mice, the researchers were able to gain insights on how certain cell types in the lung originate and change during childhood.

“These are unique samples that we’ve collected information on during a time in lung development that has not been well studied,” said first author Thu Elizabeth Duong, a physician-scientist in pediatric respiratory medicine at UC San Diego School of Medicine and pulmonologist at Rady Children’s Hospital-San Diego. “What’s exciting is being able to see, at single-cell resolution, what the lung cells are doing at this stage in development.”

The goal is to build a so-called “reference map” of the human lungs. Such a map would serve as a foundation to understand the cellular differences between healthy and diseased lungs. This work represents a small step toward building a reference for the pediatric population.

“Your respiratory health gets shaped by what happens during your early years of life. So when things go wrong, we can refer back to these early years to identify potential causes of disease,” said Duong.

“In cases of lung abnormality or disease, we can zoom in and examine what specific types of cells are different from their counterparts in the healthy references and what are the molecular pathways underlying these changes,” said Kun Zhang, professor and chair of bioengineering at UC San Diego who is a senior author of the study. “Diagnosis and treatment could then be developed based on differences from the reference map.”

The lungs are an important barrier in the body. They let in and maintain the balance of vital substances such as oxygen, while removing wastes such as carbon dioxide. And they filter the air that we breathe. The researchers hope that their findings here will lay the groundwork for more in-depth studies of how environmental factors such as exposure to air pollution and smoking influence lung health and disease throughout different stages of life.

To construct their map, the researchers analyzed post-mortem human lung tissues that were collected at different time points, starting from day one and up to 9 years after birth. The researchers also collected lung tissue samples from mice at matching time points between one day and nearly one month after birth.

The researchers used next-generation single-cell sequencing technologies developed in Zhang’s lab to analyze individual nuclei of more than 80,000 human and mouse lung cells combined.

Immunofluorescence image of alveolar epithelial cell states in a human lung.

With this analysis, the researchers could start to map developmental pathways for different lung cell types including alveolar epithelial type 1 cells. These cells are vital for the exchange of oxygen and carbon dioxide gases. The researchers gained clues as to how alveolar type 1 cells communicate with other cells such as myofibroblasts, and how this communication could play a role in alveolar cell development.

The study also revealed a unique population of fibroblast cells in the human lung that was not observed in mice. These fibroblasts are cells in connective tissue that play a role in how the lungs stretch. The researchers also found cell states in the human lung that are present in early life at birth but disappear by 9 years of age.

“These data are helping us piece together how key cell types in the lung come into existence,” said Duong. “We hope this will serve as a valuable resource for lung researchers moving forward.”

Paper: “A single-cell regulatory map of postnatal lung alveologenesis in humans and mice.” Co-authors include Yan Wu, Brandon Chin Sos, Weixiu Dong and Siddharth Limaye, UC San Diego; Lauraine H. Rivier, Greg Myers and James S. Hagood, University of North Carolina at Chapel Hill.

UC San Diego Computer Scientist Honored for Debugging Work

Yuanyuan (YY) Zhou garners most influential paper for helping debug software for multicore processors

YY Zhou is a professor in the UC San Diego Department of Computer Science and Engineering.

In 2008, multicore processors, in which two or more processing units are embedded into an integrated circuit, were exploding in popularity. However, multicores spawned their own unique programming challenges.

University of California San Diego computer scientist Yuanyuan (YY) Zhou realized the enormous task in front of researchers: writing software to take advantage of those multiple CPUs could have a lot of bugs.

A professor in the Department of Computer Science and Engineering and the Qualcomm Endowed Chair, Zhou has now been honored with an Architectural Support for Programming Languages and Operating Systems (ASPLOS) 2022 most influential paper for her 2008 study: Learning from mistakes: a comprehensive study on real world concurrency bug characteristics.

“To take advantage of the multiple CPUs, we needed to make our software with multiple threads running in parallel,” said Zhou. “But when you write that kind of program, they can have a lot of bugs, which really concerned people at the time.”

One of the main issues was concurrency bugs, which happen when two programs are run simultaneously. In the study, Zhou and her team catalogued the types of bugs people were experiencing. They found that around a third of these problems were not adequately addressed by existing debugging tools. In addition, many of the potential fixes for these bugs did not always work.

Concurrency issues were proving to be a huge drag on programming efficiency in multicore processors. So many bugs to fix and so few effective mechanisms to fix them.

Practical Fixes 

The paper provided a path forward for programmers at Microsoft and many other companies to write code more effectively for multicore processors, but it almost didn’t happen. Zhou was presenting some other work to Intel when they recommended that she publish the findings of their empirical studies on real-world concurrency bugs.

“The Intel people told us that would be more interesting, both in the academic world and to companies like Intel and Microsoft,” said Zhou. “We realized they were right and this study would be more relevant and would address an important problem. So, it was really almost accidental that we did this paper at all.”

The paper continues to be important, as mobile apps also use multiple threads, necessitating robust tools to help detect and root out concurrency bugs. Still, despite its ongoing relevance, Zhou was surprised the paper was selected this year as most influential.

“I know it's one of the top cited papers at ASPLOS, but I didn't expect them to select it,” said Zhou. “Initially, I didn’t even intend to write it. So, this was really nice and a surprise.”

ICRA 2022 preview: from robots inspired by insects to helping robots navigate and interact

April 11, 2022-- From algorithms that help robots better navigate and interact with the world and humans, to robots inspired by insects, researchers at the University of California San Diego are making significant contributions to the field of robotics at the 2022 International Conference on Robotics and Automation taking place from May 23 to 27, 2022  in Philadelphia.

The conference brings together the world's top researchers and most important companies to share ideas and advances in the field. This year’s theme is “the future of work”. 

Henrik Christensen, director of the UC San Diego Contextual Robotics Institute, is the ICRA 2022 chair of forums for the conference and organized six forums: The future of work, Industry, Venture Capital, National Programs National Research Strategies and an entrepreneurship event.

“ICRA is the premier robotics conference and after two years of being virtual the objective is to be back to in-person presentations and networking. It is encouraging to see such a diverse set of strong contributions from UCSD from new mechanisms over medical systems to next generation transportation” says Henrik Christensen. 

Nikolay Atanasov, a professor in the Department of Electrical and Computer Engineering, is the conference’s chair of workshops, overseeing 51 events. He is also giving a talk titled “Signed Directional Distance Functions” at the Robotic Perception and Mapping workshop, May 23, 2022. 

Laurel Riek, a professor in the Department of Computer Science and Engineering, will be speaking at a workshop on "Shared Autonomy in Physical Human-Robot Interaction: Adaptability and Trust.” The working title of her talk is "Proximate Human Robot Teaming: Fluent and Trustworthy Interaction".  

Sylvia Herbert is one of the organizers of the Debates on the Future of Robotics workshop, which tackles topics such as the state of robotics as an academic discipline, its relationship with other fields in computer science and engineering, and its broader social and economic impacts. 

 

Below are abstracts for the UC San Diego papers accepted to the conference. 

P2SLAM: Bearing Based WiFi SLAM for Indoor Robots

Aditya Arun, Roshan Ayyalasomayajula, William Hunter and Dinesh Bharadia, Department of Electrical and Computer Engineering, UC San Diego

Autonomous Actuation of Flapping Wing Robots Inspired by Asynchronous Insect Muscle

James Lynch and Nick Gravish, Department of Mechanical and Aerospace Engineering, UC San Diego
Jeff Gau and Simon Sponberg, School of Physics, Georgia Institute of Technology

In most instances, flapping wing robots have emulated the “synchronous” actuation of insects, in which the wingbeat timing is generated from a time-dependent, rhythmic signal. An understudied area in flapping wing robotics is that of “asynchronous” actuation in which the wingbeat is self-excited through state-dependent feedback. The internal dynamics of asynchronous insect flight muscle enable high-frequency, adaptive wingbeats with minimal direct neural control. In this paper, we investigate how the delayed stretch-activation (dSA) response of asynchronous insect flight muscle can be transformed into a feedback control law for flapping wing robots that results in stable limit cycle wingbeats. We first demonstrate in theory and simulation the mechanism by which asynchronous wingbeats self-excite. Then, we implement the feedback law on a dynamically-scaled robophysical model as well as on an insect-scale robotic flapping wing. Experiments on the large- and small-scale robots demonstrate good agreement with the theory results and highlight how dSA parameters govern wingbeat amplitude and frequency. Lastly, we demonstrate that asynchronous actuation has several advantages over synchronous actuation schemes, including the ability to rapidly adapt or halt wingbeats in response to external loads or collisions through low-level feedback control.

TridentNetV2: Lightweight Graphical Global Plan Representations for Dynamic Trajectory Generation

David Paz, Hao Xiang, Andrew Liang, and Henrik I. Christensen, Department of Computer Science and Engineering, UC San Diego

A framework for dynamic trajectory generation for autonomous navigation, which does not rely on HD maps as the underlying representation is presented. High Defi- nition (HD) maps have become a key component in most autonomous driving frameworks, which include complete road network information annotated at a centimeter-level that include traversable waypoints, lane information, and traffic signals. Instead, the presented approach models the distributions of feasible ego-centric trajectories in real-time given a nominal graph-based global plan and a lightweight scene representation. By embedding contextual information, such as crosswalks, stop signs, and traffic signals, the new  approach achieves low errors across multiple urban navigation datasets that include diverse intersection maneuvers, while maintaining real-time performance and reducing network complexity. Underlying datasets introduced are available online.

Combining suction and friction to stabilize a soft gripper to shear and normal forces, for manipulation of soft objects in wet environments

Jessica Sandoval, Iman Adibnazari, Michael T. Tolley, Department of Mechanical and Aerospace Engineering, UC San Diego
Thomas Xu, Dimitri D. Deheyn,  Scripps Institution of Oceanography, UC San Diego

Soft robotic gripping in wet environments is generally limited by the presence of a liquid that lubricates the interface between the gripper and an object being manipulated. The use of soft grippers is particularly beneficial for manipulating soft, delicate objects, yet is further limited by low grip strengths. We propose the use of suction, a form of adhesion that functions well in wet environments, to enhance soft robotic grippers. We stabilized the suction against shear disturbances using soft actuated fingers decorated with fluid-channeling patterns to enhance friction, counteracting the interfacial lubrication experienced in wet environments. We therefore combined the uses of attachment via suction and shear stability via friction to create an adhesive soft gripper. We evaluated the contributions to attachment of each component to help stabilize it against dislodgement forces that act in parallel and normal to an object that it aimed to manipulate. By identifying these contributions, we envision that such an adhesive gripper can be used to benefit soft robotic manipulation in a variety of wet environments, from surgical to subsea applications.

Look Closer: Bridging Egocentric and Third-person Views with Transformers for Robotic Manipulation

Rishabh Jangir, Nicklas Hansen, Sambaran Ghosal, Mohit Jain and Xiaolong Wang
Department of Electrical and Computer Engineering, UC San Diego

Learning to solve precision-based manipulation tasks from visual feedback using Reinforcement Learning (RL) could drastically reduce the engineering efforts required by traditional robot systems. However, performing fine-grained motor control from visual inputs alone is challenging, especially with a static third-person camera as often used in previous work. We propose a setting for robotic manipulation in which the agent receives visual feedback from both a third-person camera and an egocentric camera mounted on the robot's wrist. While the third-person camera is static, the egocentric camera enables the robot to actively control its vision to aid in precise manipulation. To fuse visual information from both cameras effectively, we additionally propose to use Transformers with a cross-view attention mechanism that models spatial attention from one view to another (and vice-versa), and use the learned features as input to an RL policy. Our method improves learning over strong single-view and multi-view baselines, and successfully transfers to a set of challenging manipulation tasks on a real robot with uncalibrated cameras, no access to state information, and a high degree of task variability. In a hammer manipulation task, our method succeeds in 75% of trials versus 38% and 13% for multi-view and single-view baselines, respectively.

CRANE: a 10 Degree-of-Freedom, Tele-surgical System for Dexterous Manipulation within Imaging Bores

Dimitri Schreiber, Zhaowei Yu, Hanpeng Jiang, Taylor Henderson, Guosong Li1, Renjie Zhu,  and Michael C. Yip, Department of Electrical and Computer Engineering, UC San Diego
Alexander M. Norbash, Department of Radiology, UC San diego
Julie Yu, Department of Mechanical and Aerospace Engineering, UC San Diego

Physicians perform minimally invasive percuta- neous procedures under Computed Tomography (CT) image guidance both for the diagnosis and treatment of numerous diseases. For these procedures performed within Computed Tomography Scanners, robots can enable physicians to more accurately target sub-dermal lesions while increasing safety. However, existing robots for this application have limited dexterity, workspace, or accuracy. This paper describes the design, manufacture, and performance of a highly dexterous, low-profile, 8+2 Degree-of-Freedom (DoF) robotic arm for CT guided percutaneous needle biopsy. In this article, we propose CRANE: CT Robot and Needle Emplacer. The design focuses on system dexterity with high accuracy: extending physicians’ ability to manipulate and insert needles within the scanner bore while providing the high accuracy possible with a robot. We also propose and validate a system architecture and control scheme for low profile and highly accurate image-guided robotics, that meets the clinical requirements for target accuracy during an in- situ evaluation. The accuracy is additionally evaluated through a trajectory tracking evaluation resulting in <0.2mm and <0.71â—¦ tracking error. Finally, we present a novel needle driving and grasping mechanism with controlling electronics that provides simple manufacturing, sterilization, and adaptability to accom- modate different sizes and types of needles.

Configuration Space Decomposition for Scalable Proxy Collision Checking in Robot Planning and Control

Mrinal Verghese, Nikhil Das, Yuheng Zhi, and Michael Yip
Department of Electrical and Computer Engineering, UC San Diego

Real-time robot motion planning in complex high-dimensional environments remains an open problem. Motion planning algorithms, and their underlying collision checkers, are crucial to any robot control stack. Collision checking takes up a large portion of the computational time in robot motion planning. Existing collision checkers make trade-offs between speed and accuracy and scale poorly to high-dimensional, complex environments. We present a novel space decomposition method using K-Means clustering in the Forward Kinematics space to accelerate proxy collision checking. We train individual configuration space models using Fastron, a kernel perceptron algorithm, on these decomposed subspaces, yielding compact yet highly accurate models that can be queried rapidly and scale better to more complex environments. We demonstrate this new method, called Decomposed Fast Perceptron (D-Fastron), on the 7-DOF Baxter robot producing on average 29× faster collision checks and up to 9.8× faster motion planning compared to state-of-the-art geometric collision checkers.

Robotic Tool Tracking under Partially Visible Kinematic Chain: A Unified Approach

Florian Richter, Jingpei Lu, and Michael C. Yip, Department of Electrical and Computer Engineering, UC San Diego
Ryan K. Orosco, Department of Surgery, Division of Head and Neck Surgery, UC San Diego

Anytime a robot manipulator is controlled via visual feedback, the transformation between the robot and camera frame must be known. However, in the case where cameras can only capture a portion of the robot manipulator in order to better perceive the environment being interacted with, there is greater sensitivity to errors in calibration of the base-to- camera transform. A secondary source of uncertainty during robotic control are inaccuracies in joint angle measurements, which can be caused by biases in positioning and complex transmission effects such as backlash and cable stretch. In this work, we bring together these two sets of unknown parameters into a unified problem formulation when the kinematic chain is partially visible in the camera view. We prove that these parameters are non-identifiable implying that explicit estimation of them is infeasible. To overcome this, we derive a smaller set of parameters we call Lumped Error since it lumps together the errors of calibration and joint angle measurements. A particle filter method is presented and tested in simulation and on two real world robots to estimate the Lumped Error and show the efficiency of this parameter reduction.

Pose Estimation for Robot Manipulators via Keypoint Optimization and Sim-to-Real Transfer

Jingpei Lu, Florian Richter and Michael C. Yip, Department of Electrical and Computer Engineering, UC San Diego

Keypoint detection is an essential building block for many robotic applications like motion capture and pose estimation. Historically, keypoints are detected using uniquely engineered markers such as checkerboards or fiducials. More recently, deep learning methods have been explored as they have the ability to detect user-defined keypoints in a marker-less manner. However, different manually selected keypoints can have uneven performance when it comes to detection and localization. An example of this can be found on symmetric robotic tools where DNN detectors cannot solve the correspondence problem correctly. In this work, we propose a new and autonomous way to define the keypoint locations that overcomes these challenges. The approach involves finding the optimal set of keypoints on robotic manipulators for robust visual detection and localization. Using a robotic simulator as a medium, our algorithm utilizes synthetic data for DNN training, and the proposed algorithm is used to optimize the selection of keypoints through an iterative approach. The results show that when using the optimized keypoints, the detection performance of the DNNs improved significantly. We further use the optimized keypoints for real robotic applications by using domain randomization to bridge the reality gap between the simulator and the physical world. The physical world experiments show how the proposed method can be applied to the wide-breadth of robotic applications that require visual feedback, such as camera-to-robot calibration, robotic tool tracking, and end-effector pose estimation. As a way to encourage further research in this topic, we establish the “Robot Pose” dataset, comprising calibration and tracking problems and ground truth data, available online†.

 

Concrete Canoes, Steel Bridges test students' structural engineering savvy

UC San Diego hosts 850+ students for civil engineering symposium

Students from the University of Hawai'i at Manoa's Concrete Canoe team paddle in the co-ed sprint races in Mission Bay. Photo by Erik Jepsen/University Communications.

April 7, 2022--For the first time in 15 years, UC San Diego structural engineering students hosted the American Society of Civil Engineers’ Pacific Southwest Symposium from March 31 - April 2, drawing 850 students from 14 universities in Southern California and Hawaii to campus for civil and structural engineering challenges including the Concrete Canoe and Steel Bridge competitions. In addition to hosting the regional conference, the UC San Diego Steel Bridge team won first place, clenching a spot at the national competition in May.

“It’s very exciting because the last time we hosted was in 2007, and this year is special because it’s the first in-person conference in two years,” said Raymond Chu, a structural engineering student and symposium planning chair. “The goal is to create a welcoming and uplifting environment for our community of civil and structural engineers to come out and meet each other, participate in technical competitions where we demonstrate all we’ve learned in classes, and meet and socialize with students from across the region.”

The three-day symposium, organized by the UC San Diego student chapter of the Society of Civil and Structural Engineers, includes the flagship Concrete Canoe and Steel Bridge competitions, as well as transportation design, sustainability, surveying, Trimber-Strong two-story wood structure building, and GeoWall retaining wall-building competitions. There’s also social activities like tug-of-war, can jam, ultimate frisbee, a scavenger hunt, and more opportunities for students from across the region to get to know one another.

“I know over the last two years a lot of us have felt a disconnect to school, classmates, and the college experience because we’ve been remote all the time or partially, so it's just really nice to have everyone together again,” said Chu. “This conference is a great opportunity for students to get a sense of the community and camaraderie we have in structural and civil engineering.”

The UC San Diego Steel Bridge team poses with their 1st-place-winning bridge, lovingly named Bridget. Photo by Diane Zelman.

That camaraderie was on display at the Steel Bridge competition, where teams of students race to put together the lightest, strongest and stiffest 21-foot bridge made of steel in the shortest amount of time, while meeting a list of stringent design requirements. The UC San Diego team put together their bridge, lovingly named Bridget, in a blazing 10 minutes and 40 seconds. Weighing in at 138 pounds and dipping just half an inch under a 2,500 pound load– the weight of a Toyota Corolla– was enough to earn the team first place at this regional contest, and a spot at nationals, held at Virginia Tech May 27-28. More on the team’s journey to nationals: https://jacobsschool.ucsd.edu/news/release/3419

“We are so proud of this win because of the challenges this team has overcome coming out of a 2-year pandemic hiatus,” said Saul Chaplin, a structural engineering student and Steel Bridge co-project manager. “Six months ago, no-one knew how to weld, we were still looking for a space to fabricate, and no one on the team had ever built a bridge before. Through brutal and brutally fun 40-hour weeks of bridging as well as incredible mentorship, we have now trained 15 welders, we have built Bridget, our 21-foot pink-colored monster of a bridge, and we have developed hands-on engineering and metalworking skills that will last our lifetimes. The trip to Virginia is the cherry on top and a dream-come-true for me.”

Steel Bridge team members have spent the last year planning their design, analyzing computer models of their bridge to test how it will perform, conducting destructive tests on steel prototype connections, and eventually fabricating the dozens of steel stringers, connections, beams, and columns that make up their bridge. On competition day, they race to assemble all these parts into their final bridge, careful to avoid certain areas of the construction zone that mimic a river where students can’t stand. Team members enjoy the experience as much for the community they build as the skills they’re able to sharpen. 

“The nice thing about working here is everyone gets to do a little bit of everything; everyone gets the chance to weld, grind, use the chop saw. I’ve done as much as I want to do really,” said structural engineering student and team welding lead Becca Bauman. ”The community is great too, everyone is super positive and encouraging.”

The UC San Diego concrete canoe team also experienced the importance of camaraderie, when they supported each other to the finish line even though their canoe suffered a catastrophic crack during de-molding. The teams are tasked with building a 20-foot long reinforced canoe made of concrete that can hold four paddlers, and this year racing them in slalom and sprint courses on Mission Bay.

The UC San Diego Concrete Canoe team rallied after their canoe suffered a catastrophic crack, and used a canoe from a previous competition to still participate in the races. Photo by Lan Yao/University Communications.

“Our team experienced one of the tragic parts of this project,” said Huyson Tran, structural engineering student and project manager for this year’s Concrete Canoe team. “Our canoe actually did crack in half, but being able to keep persevering and learn from that was what it’s all about. We were lucky enough to have one of our canoes from past years to race and have fun, cheering on all the teams, and our teammates paddling. It’s invigorating.”

Several other teams also experienced some cracks, leaks and misadventures during the races, which is par for the course. Considering that this is the first year any team has built a physical canoe in two years, and that the vast majority of symposium participants were attending for the first time, made the technical accomplishments even more impressive. 

“2019 was the last in-person conference, and I was there myself as a freshman,” said symposium chair Chu. “Because of the amazing experience I had as a first year, I really wanted to make that possible for students this year, since anyone who isn’t a senior hasn’t been to this conference before. Everybody is learning as we go, figuring things out on the fly. In the end, it really worked out.”

It took the students years of planning– during a pandemic that forced constant changes to these plans— to finalize the logistics of hosting such a large event. 

“The Department of Structural Engineering could not be more proud of our SCSE student leadership team who have worked tirelessly for the past two years to put on such a great in-person symposium,” said Lelli Van Den Einde, a teaching professor of structural engineering at UC San Diego and the SCSE faculty advisor. “The PSWS gives students an opportunity to apply the knowledge and skills they learn in their classes through real world design-build competitions. We are thrilled with the success of the Steel Bridge team and are excited to see them represent UC San Diego at nationals.”

Research Expo enters its 4th decade

April 1, 2022-- Connected systems take center stage at the UC San Diego Jacobs School of Engineering’s 40th annual Research Expo on Thursday, April 14, 2022. Join us to hear from more than 100 graduate students from all six Jacobs School of Engineering departments, as they present their groundbreaking engineering and computer science research.

In addition to seeing what technologies are in development by graduate students at our Top 10 engineering school, Research Expo features faculty lightning talks, this year centered on connected systems: from computational modeling for systems medicine, to sustainable supply chain systems to wireless and materials systems.

Register to reserve your spot at the 40th anniversary of this flagship event. 

Faculty Lightning Talks

Padmini Rangamani

Mechanical and aerospace engineering Professor Padmini Rangamani will share her lab’s work on Computational Modeling for Systems Medicine and Human Health. Rangamani's research is focused on understanding the design principles of biological systems. Her long-term research goal is  to understand the  control of  cell shape  by  analyzing biological membranes and their interaction with proteins and the cytoskeleton using principles from transport phenomena. This is a unifying framework that brings together mechanics of the membrane, membrane-bound proteins, and their coupled interactions. Rangamani is part of the Wu Tsai Human Performance Alliance at UC San Diego, aiming to transform human health on a global scale through the discovery and translation of the biological principles underlying human performance.

 

John Wade

John Wade, a professor of practice in the Department of Mechanical and Aerospace Engineering, is working 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. He will speak about Ethical Sustainability in the realm of systems and supply chain.

 

 

Sujit Dey

Electrical engineering Professor Sujit Dey directs the UC San Diego Center for Wireless Communications, and is faculty director of the Institute for the Global Entrepreneur. His recent work includes using wireless wearable systems to provide personalized healthcare recommendations to patients, and a DARPA program to increase the security of our nation’s semiconductor supply chain that wireless communications depend upon.

 

 

Andrea Tao

Nanoengineering Professor Andrea Tao co-leads the Predictive Assembly thrust of the UC San Diego Materials Research Science and Center (MRSEC) funded by the NSF. The Predictive Assembly research team is working to bring the computational and predictive tools that the pharmaceutical industry has used successfully to design "small molecule" drugs with particular properties and behaviors into the realm of materials science. Tao, who is also a member of the Sustainable Power and Energy Center, also applies her nanoscale assembly skills to materials development for waste-free batteries. She will talk about Multiscale Materials Design.

 

 

 

An array of brain sensors that can record electrical signals directly from the surface of the human brain in record-breaking detail.

Curious what’s depicted in this year’s Research Expo image? It’s a close-up shot of an array of brain sensors that 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. 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. The work was led by electrical engineering Professor Shadi Dayeh. 

 

Computer Science and Engineering Researchers Assemble the First Complete Human Genome

March 31, 2022

Two decades after the Human Genome Project produced a draft sequence, an international research team, including University of California San Diego computer scientists, has published the first complete genome. The work was done by the Telomere to Telomere (T2T) consortium, and six papers describing the project will be published April 1 in a special edition of Science.

The team from UC San Diego’s Department of Computer Science and Engineering contributed to two of the papers: Complete genomic and epigenetic maps of human centromeres and The complete sequence of a human genome. The second pulls together the many strands of research that went into completing the project.

“This is a major milestone,” said Pavel Pevzner, Ronald R. Taylor Distinguished Professor of Computer Science at the UC San Diego Jacobs School of Engineering. “Around 8% of the human genome had gone unsequenced for decades. By filling these gaps, we gain a better understanding of human biology and can now identify formerly hidden genetic anomalies that may lead to disease.”

The T2T researchers found the 8% gap contains repetitive DNA, numerous genes and almost as much genetic information as an entire chromosome. Most of the newly sequenced DNA was near chromosomal telomeres (long chromosome caps) and centromeres (dense middle sections).

The now-complete genome sequence illuminates more than two million additional variants, providing new information on 622 medically relevant genes. This complete sequence will also boost our understanding of chromosomes, opening new lines of research into how they segregate and divide. 

“Generating a truly complete human genome sequence represents an incredible scientific achievement, providing the first comprehensive view of our DNA blueprint,” said Eric Green, M.D., Ph.D., director of the National Human Genome Research Institute, which helped fund the project. “This foundational information will strengthen the many ongoing efforts to understand all the functional nuances of the human genome, which in turn will empower genetic studies of human disease.”

Centromeres are found in the middle of chromosomes, where the various arms meet, and help pull them apart during cell division. These structures make up around 6.2% of the entire human genome and have been virtually impossible to assemble because they contain so many repeating DNA sequences.

“Centromeres are where cell division is initiated, so it’s important to know what’s going on there,” said Andrey Bzikadze, a computer science Ph.D. student at UC San Diego in Pevzner’s lab and co-author on both papers. “But these repeating sequences are incredibly difficult to assemble because there’s almost no variation. It’s like doing a jigsaw puzzle that only shows blue sky.”

In addition to determining the centromere sequences, the UC San Diego team also helped validate the entire genome assembly.

“Our tool was the only one that was able to look into the most complicated regions of the genome, including the centromeres,” said Bzikadze. “We were really dedicated to finding the problems in these assemblies in difficult, complex regions.”

While the majority of genome sequences are currently conducted on short read instruments, which chop DNA into small snippets (around 300 nucleotides) before reassembling it, this technology proved incapable of filling the gaps in the human genome. However, in the past few years, long read machines (greater than 10,000 nucleotides) have shown tremendously improved accuracy, making this complete human genome sequence possible.

“Long reads were essential to accomplish this,” said Bzikadze. “Without the long reads, this would not have been possible.”

Story by Josh Baxt.

UC San Diego engineering ranks #10 in U.S. News and World Report best engineering schools rankings

The University of California San Diego Jacobs School of Engineering has ranked #10 in the nation in the influential U.S. News & World Report Rankings of Best Engineering Schools. This #10 ranking is up from #17 six years ago, and it's the third year in a row the Jacobs School of Engineering ranked within the top ten. 

"Our top-ten ranking 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, and this world-class ranking is well deserved recognition of the excellence, hard work, and creativity of our entire community."

The newest venue for this community of innovators is Franklin Antonio Hall, which is opening now, in Spring 2022. Franklin Antonio Hall has been designed to facilitate innovation. The research facilities are organized around 13 collaborative research facilities called "collaboratories." Each collaboratory is home to multiple professor-led research groups working in complementary areas of relevant research. This design allows students from different labs to work in the same shared laboratories, increasing opportunities for cross-disciplinary collaborations and innovations to emerge.

Franklin Antonio Hall's research collaboratories will include researchers from across the UC San Diego campus and the Torrey Pines Mesa. This is yet another way that engineers and computer scientists at the UC San Diego Jacobs School of Engineering bring their expertise and creativity to UC San Diego's $1.54 billion dollar research enterprise.

Jacobs School rankings

In the same US News & World Report Rankings, the Department of Bioengineering at the UC San Diego Jacobs School of Engineering ranked #4 in the nation. Bioengineering at UC San Diego has ranked among the top four programs in the nation every year for more than a decade.

We are especially pleased to note our highly ranked doctoral programs in engineering and computer science at the UC San Diego Jacobs School of Engineering: 

Bioengineering #4
Computer Science, Systems: #8
Computer Science #11
Computer Science, Programming Languages: #11 
Computer Science, Artificial Intelligence: #11
Computer Science, Theory: #12   
Computer Engineering #13
Electrical Engineering #14 
Aerospace Engineering #17 
Civil Engineering #17
Mechanical Engineering #23  

The full listing of Jacobs School rankings are here.

2023 US News & World Report Rankings of Best Engineering Schools are here.

We have the keys to Franklin Antonio Hall

The Power of Bugs

New research from computer scientists shows how bacteria can fuel low-power sensors

March 28, 2022

Soil power? A new study by UC San Diego computer scientists is showing how microbes can be used to fuel low-power sensors

Computer scientists at the University of California San Diego are showing how soil microbes can be harnessed to fuel low-power sensors. This opens new possibilities for microbial fuel cells (MFCs), which can power soil hydration sensors and other devices.

Led by Department of Computer Science and Engineering (CSE) Assistant Professor Pat Pannuto and Gabriel Marcano, a PhD student working with Pannuto, this research was presented today at the first Association for Computer Machinery (ACM) Workshop on No Power and Low Power Internet of Things.

“Our most immediate applications are in agricultural settings, trying to create closed-loop controls. First for watering, but eventually for fertilization and treatment: sensing nitrates, nitrogen, phosphorous, potassium. This could help us understand how to limit run off and other effects,” said Pannuto, senior author on the study titled "Soil Power? Can Microbial FuelCells Power Non-Trivial Sensors?"

Current sensors are often powered by batteries or small solar or wind generators, but that creates other problems. Batteries must be changed periodically and above-ground generators are easily damaged by plows or other machinery.

MFCs are self-contained, eliminate the need for above-ground infrastructure and periodic maintenance and can be buried with the sensors below till lines. Ultimately, biodegradable fuel cells and associated circuity could just melt away, alleviating the need to retrieve dead sensors.

“In some cases, we’re dropping these sensors in ecologically sensitive habitats to monitor the environment,” said Pannuto. “We don’t want to make the problem worse by leaving a bunch behind.”

*Watch a video recapping this research here.

Powering the Internet of Everything

Pannuto joined the Computer Science and Engineering faculty in 2019 and specializes in embedded systems and how computing can be deployed in the physical world.

“A lot of my research looks at energy scavenging, which is where this paper comes in, and long-range and low-power communications,” said Pannuto. “How are we going to support the eventual internet of everything?”

While all microbes produce energy – and can be found in virtually any random handful of dirt – the researchers are particularly interested in a family of anerobic bacteria called geobacter.

“These have been used to reduce uranium and heavy metal toxicity in soil,” said Marcano. “Recent studies have shown they are quite prolific at electricity generation.”

While the current paper was done in house in the Department of Computer Science andEngineering at the UC San Diego Jacobs School of Engineering, it is part of larger project with Colleen Josephson at UC Santa Cruz and Josiah Hester, Weitao Shuai and George Wells at Northwestern.

In addition to farm monitoring, the researchers are also working with wetland protection groups. The unifying theme is supporting long-term measurement in areas that lack supporting infrastructure.

And while MFCs won’t be powering anything that requires a lot of energy, they do offer tremendous potential to support passive monitoring systems and provide enhanced data for farms and wetlands.

“We’re not going to run a cell phone off soil anytime soon, but we can harvest enough energy to kick out a data packet a couple of times a day,” said Pannuto. “We can develop monitoring infrastructure just using the available energy in dirt.”

CARI Health Takes Top Prize at SDAC

IGE MedTech Startup Wins Big

March 24, 2022

San Diego Angel Conference awarded $300,000 to San Diego-based CARI Health – an IGE MedTech Startup company developing a device to monitor medications used in treating opioid addiction. CARI Health produces a wearable monitor that measures levels of addiction medication for dosing and addiction medication adherence. 

 

CARI Health Takes Top Prize at SDAC

Concert hall acoustics for non-invasive ultrasound brain treatments

A team led by engineers at the University of California San Diego has developed a device that is a first step to enabling noninvasive, ultrasound-based therapies for the brain. For example, ultrasound waves are currently being used in clinical trials to treat epilepsy.

Current approaches are focusing ultrasound waves to reach their specific target in the brain. But this has proven difficult, as ultrasound tends to bounce around within the skull, which leads to some areas of the brain being over-exposed while others are not exposed enough. In worst-case scenarios, this can cause hemorrhage and overheating in brain tissue.

“We can’t modify the inside of the skull,” said senior author Professor James Friend, in the Department of Mechanical and Aerospace Engineering at the University of California San Diego. “The only thing we could do was to change how the device that produces the sound works.”

Researchers tried a different approach: diffusing ultrasound waves instead of focusing them. They accomplished this by placing a microscale diffuser on the transducer that produces the ultrasound waves. The device is built based on the Schroeder diffuser–the best sound diffuser mathematical models can provide. This is the same math that is used to design concert halls so that every audience member can hear music perfectly.

The team details their research in the Feb. 16, 2022 issue of Advanced NanoBiomed Research.

The ultrasound waves are applied to cells that have been engineered to be more responsive to ultrasound stimuli by researchers at the Salk Institute. The cells are exposed to an adenovirus that causes them to form an ion channel called TRPA1 that is sensitive to ultrasound.

“By using a targeted approach for this delivery, we can use uniformly distributed ultrasound instead of focused ultrasound,” Friend said. 

A close-up of the device Photo gallery on Flickr

Researchers showed that the device worked as intended first in a Petri dish with human embryonic kidney cells and neuron cells. The cells showed twice as high an activation in the TRPA1 channel with the diffuser than without. In addition, researchers used the diffuser with an ultrasound wave generator on mice. They found that the diffuser creates a uniform acoustic field in the skull cavity, ensuring that only the brain regions engineered to be sensitive to ultrasound were stimulated.

“The idea behind sonogenetics is to engineer cells to be more responsive to ultrasound stimuli,” said Aditya Vasan, a PhD student in Friend’s lab and the paper’s first author. “We do this by screening for proteins that respond to ultrasound stimulation at specific pressures and frequencies; and by genetically engineering specific brain regions to express these proteins."

The diffuser is built with tiny pits that modulate how the ultrasound waves are emitted. Specifically, the diffuser ensures the waves are emitted in a staggered manner, which helps prevent the creation of echoes. The depths of the pits are calculated with the Schroeder diffuser model. Next steps include better understanding the way ultrasound waves stimulate cells and conducting broader in vivo studies.

“One of the goals with sonogenetics is to control which cells respond: think of it as a knob that controls lights that you have accurate control over,” Vasan said. “Ultimately, we want to show that sonogenetics work in people.”

Microscale concert hall acoustics to produce uniform ultrasound stimulation for targeted sonogenetics in hsTRPA1-transfected cells

Aditya Vasan, James Friend, Medically Advanced Devices Laboratory, Department of Mechanical and Aerospace Engineering, Jacobs School of Engineering and Department of Surgery, School of Medicine, University of California San Diego

Uri Magaram, Neurosciences Graduate Program, UC San Diego Florian Allein, Nicholas Boechler, Department of Mechanical and Aerospace Engineering, UC San Diego Marc Duque, Sreekanth H. Chalasani, The Salk Institute for Biological Studies

Lighter, stiffer, faster, stronger

Steel Bridge team to compete at Pacific Southwest Symposium, hosted by UC San Diego

March 21, 2022--On April 2, student teams from Southern California and Hawaii will gather on the UC San Diego campus to put together the strongest, lightest bridge made of steel in the shortest amount of time. The Steel Bridge competition is a highlight of the American Society of Civil Engineers’ Pacific Southwest Symposium, being hosted by UC San Diego for the first time in 15 years. 

The student teams have spent a year designing and building their bridge, and will aim to put the dozens of pieces that go into the 21-foot long bridges together in under five minutes. Then, they’ll put 2500 pounds– the weight of a Toyota Corolla– on top of each bridge, which they hope will bend less than an inch under the weight. 

In addition to Steel Bridge, the three-day symposium includes Concrete Canoe races in Mission Bay, other structural engineering competitions, community building games, and an awards banquet at the San Diego Air and Space Museum. For more information and to participate, visit:https://scse.ucsd.edu/psws.html

Structural engineering student and Steel Bridge co-project manager Saul Chaplin said he got interested in bridges when he realized that they might look simple from afar, but a lot of intricate details below the surface are responsible for that. 

“For example the Golden Gate Bridge, on the surface level you have swoopy curves and two towers. If you zoom in you can see there’s secondary cables that support the deck. And on the deck you can see this intricate truss structure. And if you look even closer you can see seismic isolators that absorb the motion of the earth. What you see on the surface is so simplistic. I love how the closer I look, the more I find to learn about,” said Chaplin.

The team of roughly 20 UC San Diego students, many of them structural engineers, spend the first part of the year designing a bridge that meets that year’s requirements. These requirements change each year, including where the bridge can touch the ground, and certain design elements it must include. 

The team's 2022 bridge, measuring in at 21 feet long and 2.5 feet tall.

Then they move from the chalkboard to the computer, and make a 3D fully functioning model of the bridge and all of its components– stringers, connections, beams, columns– and test the model to see how their design would respond to the 2,500 pound load. After analyzing their design, they get to building. The team, which is part of UC San Diego’s Society of Civil and Structural Engineers, works out of the High Bay Physics Laboratory, using saws, grinders, and welding equipment to transform raw steel into their bridge.

“We have a steel design class, but this is a lot of learning as you go too,” said Richard Tang, co-project manager and structural engineering student. “You use theory, but you have to get in there and actually do it. We had a lot of connections that looked fine on paper and then we tested it and had to make changes.”

Learning as they go has actually been a bright spot for students wanting hands-on experiences during the COVID-19 pandemic when many classes were virtual.

“I’m taking a statics class right now and we were learning about bridges and trusses,” said Jenny Ruiz, a structural engineering student on the team. “I found it fascinating but it was really hard since with online school it’s hard to visualize what’s going on. So I thought why not come here and see how it actually works. On my first day I learned how to weld, which was very interesting. They were so welcoming and taught me how to use all of this equipment.”

For this year’s competition, the student teams are graded on deflection– how much the bridge bends under 2,500 pounds of weight– constructability–how fast they construct it– and weight. Historically, the UC San Diego team has done well, routinely placing in the top 10 and even top three. While they hope to earn a spot on the podium again this year, the students also value the opportunity to learn by doing, and the community they’ve formed through the organization. 

Some members of the Steel Bridge team working in the High Bay Physics Lab space.

“I’ve been able to do everything,” said structural engineering student and team welding lead Becca Bauman. “The nice thing about working here is everyone gets to do a little bit of everything; everyone gets the chance to weld, grind, use the chop saw. I’ve done as much as I want to do really; it’s really cool. The community is great too, everyone is super positive and encouraging. We’ve got a tight deadline so it’s great seeing everyone come together and work hard to get it done.”

While the team is excited to be hosting this year’s conference, it does come with high stakes. 

“The exciting part about us hosting the conference this year, and the scary thing about that, is we’ll invite all our professors and friends out, my family is coming down; I want to make sure this bridge is completely functional like three times over so when it’s competition day nothing bad will happen,” Chaplin said.

UC San Diego bioengineers inducted into prestigious biomedical institution

March 16, 2022 -- Two bioengineers at the University of California San Diego will be inducted into the College of Fellows of the American Institute for Medical and Biological Engineering (AIMBE). Professors Stephanie Fraley and Prashant Mali are among the 153 new AIMBE Fellows who will be recognized at a ceremony during AIMBE’s 2022 Annual Event on March 25.

The College of Fellows is comprised of the top two percent of medical and biological engineers in the country, including the most accomplished and distinguished engineering and medical school chairs, research directors, professors, innovators and successful entrepreneurs.

Stephanie Fraley

As many cancers are caused by infectious diseases, Fraley’s team works on developing diagnostic technologies to achieve simple yet comprehensive infectious disease screening and identification. In clinical samples, detecting pathogens can be a needle in a haystack problem. By integrating mechanical, electrical and biomolecular engineering approaches along with imaging and machine learning techniques, Fraley and her team have developed innovative technologies that will not only advance patient care, but also generate new insights into research on heterogeneous microbial populations. 

Fraley’s work also aims to understand how living cells migrate in reliable and orchestrated ways. Cell migration is a complex behavior that emerges from the interactions of tens of thousands of molecular pieces. Today, most of the knowledge of cell migration is confined to artificial 2D environments. Fraley and her team develop quantitative microscopy and imaging techniques, engineer 3D matrices and engage in molecular engineering to bring cell migration research into the third dimension. Applications include therapies for metastatic cancer cells.   

Prashant Mali

Mali is being recognized for his pioneering contributions to genome editing and enabling gene and cell based human therapeutics. He has helped develop CRISPRs and ADARs as powerful tools for DNA and RNA editing, respectively. Recently, Mali’s lab developed a new RNA editing technology that could make it simpler to repair disease-causing mutations in RNA without compromising precision or efficiency. The technology is the first proof-of-concept in vivo RNA editing for treating genetic diseases using ADARs that are native to cells. His lab has also developed a CRISPR-based gene therapy for chronic pain, which could offer a safer and non-addictive alternative to opioids. The Mali lab has a strong translational focus with several gene therapy technologies licensed to and being further developed by startup companies including Navega Therapeutics and Shape Therapeutics, both co-founded by Mali.

“We are very excited to learn that Drs. Fraley and Mali’s outstanding contributions to our field have been recognized by their peers,” said Adam Engler, professor and chair of bioengineering at the UC San Diego Jacobs School of Engineering. “They are a testament to the passion that faculty in our bioengineering department have for scholarship, training and research—to date, 28 bioengineering faculty members at UC San Diego have been named AIMBE fellows.”

AIMBE’s mission is to recognize excellence in, and advocate for, the fields of medical and biological engineering to advance society. Since 1991, AIMBE’s College of Fellows has led the way for technological growth and advancement in the fields of medical and biological engineering. Fellows have helped revolutionize medicine and related fields to enhance and extend the lives of people all over the world. They have successfully advocated for public policies that have enabled researchers and business-makers to further the interests of engineers, teachers, scientists, clinical practitioners, and ultimately, patients.

For more information about the AIMBE Annual Event, visit www.aimbe.org

Renowned controls researcher receives new award for transformational contributions to the field

Miroslav Krstic, a UC San Diego professor and research administrator, is the inaugural recipient of the A.V. “Bal” Balakrishnan Research Award for Scientific Excellence in Research in the Mathematics of Systems.

March 14, 2022-- Professor Miroslav Krstic at the University of California San Diego is the inaugural recipient of the A.V. “Bal” Balakrishnan Research Award for Scientific Excellence in Research in the Mathematics of Systems. 

The award was established by the Viterbi School of Engineering at the University of Southern California through a gift from Sophia Balakrishnan, honoring the memory of her late husband. He was a distinguished researcher and pioneer in distributed parameter systems and aeroelasticity. The award is open to nominations from the control systems, communications, signal processing, mechanics, and mathematical areas of aerospace engineering. 

Krstic serves as senior associate vice chancellor for research for UC San Diego, in addition to his role as professor in the Department of Mechanical and Aerospace Engineering, where he holds the Daniel L. Alspach Endowed Chair in Dynamic Systems and Control. 

Krstic was chosen as the inaugural recipient of this award, in a competitive nomination pool, for his transformational contributions to partial differential equations control, nonlinear delay systems, extremum seeking, adaptive control, stochastic nonlinear stabilization, and their industrial applications – including everything from stabilizing stop-and-go motion in congested traffic to estimating the state of health of batteries for electric vehicles and mobile phones. 

Krstic opened up a whole new area of research in control theory by reviving what are known as extremum seeking algorithms. His advances made it possible to better conduct chemical analysis of rocks on the Mars rover Curiosity. They also have helped achieve a 200-fold increase in area density in the microchips that run smartphones, resulting in a multi-billion dollar impact for the semiconductor photolithography industry.

He is an expert in controls who has received several lifetime achievement recognitions. In 2021, he received the Richard E. Bellman Control Heritage Award; in 2019, the Reid Prize from the Society for Industrial Mathematics and the Nonlinear Control Systems Award from the International Federation for Automatic Control; and in 2017 the Oldenburger Medal of the American Society of Mechanical Engineers. 

Krstic also is Fellow of the Institute of Electrical and Electronics Engineers, the American Society of Mechanical Engineers, the Society for Industrial and Applied Mathematics, the International Federation of Automatic Control, the American Association for the Advancement of Science, and the UK’s Institution of Engineering and Technology, as well as associate fellow of American Institute of Aeronautics and Astronautics.

“Control systems arise both in  engineering systems, such as maximizing the power output of wind turbines, and in biological systems, in which feedback ensures survival, from cells to organisms, in addition to governing the slow dynamics of evolution,” Krstic said. 

In the Office of Research Affairs, Krstic oversees the Organized Research Units, the proposal development services, the academic review of research scientists, relationships with national labs, and initiatives with several federal research agencies.

The Balakrishnan Award comes with a $10,000 honorarium. Krstic will receive the prize and present a lecture at the USC Viterbi School of Engineering in Fall 2022. 

 

A new brain-computer interface with a flexible backing

The flexible backing allows arrays of micro-scale needles to conform to the contours of the brain, which improves high-resolution brain recording

March 14, 2022: Engineering researchers have invented an advanced brain-computer interface with a flexible and moldable backing and penetrating microneedles. Adding a flexible backing to this kind of brain-computer interface allows the device to more evenly conform to the brain’s complex curved surface and to more uniformly distribute the microneedles that pierce the cortex. The microneedles, which are 10 times thinner than the human hair, protrude from the flexible backing, penetrate the surface of the brain tissue without piercing surface venules, and record signals from nearby nerve cells evenly across a wide area of the cortex.   

This novel brain-computer interface has thus far been tested in rodents. The details were published online on February 25 in the journal Advanced Functional Materials. This work is led by a team in the lab of electrical engineering professor Shadi Dayeh at the University of California San Diego, together with researchers at Boston University led by biomedical engineering professor Anna Devor. 

Artist rendition of the flexible, conformable, transparent backing of the new brain-computer interface with penetrating microneedles developed by a team led by engineers at the University of California San Diego in the laboratory of electrical engineering professor Shadi Dayeh. The inset image on the left shows an illustration of hard-backed Utah Arrays, as a comparison.  Image credit: Shadi Dayeh / UC San Diego / SayoStudio

This new brain-computer interface is on par with and outperforms the “Utah Array,” which is the existing gold standard for brain-computer interfaces with penetrating microneedles. The Utah Array has been demonstrated to help stroke victims and people with spinal cord injury. People with implanted Utah Arrays are able to use their thoughts to control robotic limbs and other devices in order to restore some everyday activities such as moving objects.

The backing of the new brain-computer interface is flexible, conformable, and reconfigurable, while the Utah Array has a hard and inflexible backing. The flexibility and conformability of the backing of the novel microneedle-array favors closer contact between the brain and the electrodes, which allows for better and more uniform recording of the brain-activity signals. Working with rodents as model species, the researchers have demonstrated stable broadband recordings producing robust signals for the duration of the implant which lasted 196 days. 

In addition, the way the soft-backed brain-computer interfaces are manufactured allows for larger sensing surfaces, which means that a significantly larger area of the brain surface can be monitored simultaneously. In the Advanced Functional Materials paper, the researchers demonstrate that a penetrating microneedle array with 1,024 microneedles successfully recorded signals triggered by precise stimuli from the brains of rats. This represents ten times more microneedles and ten times the area of brain coverage, compared to current technologies.

Thinner and transparent backings

These soft-backed brain-computer interfaces are thinner and lighter than the traditional, glass backings of these kinds of brain-computer interfaces. The researchers note in their Advanced Functional Materials paper that light, flexible backings may reduce irritation of the brain tissue that contacts the arrays of sensors. 

The flexible backings are also transparent. In the new paper, the researchers demonstrate that this transparency can be leveraged to perform fundamental neuroscience research involving animal models that would not be possible otherwise. The team, for example, demonstrated simultaneous electrical recording from arrays of penetrating micro-needles as well as optogenetic photostimulation.

Two-sided lithographic manufacturing

The flexibility, larger microneedle array footprints, reconfigurability and transparency of the backings of the new brain sensors are all thanks to the double-sided lithography approach the researchers used. 

Conceptually, starting from a rigid silicon wafer, the team's manufacturing process allows them to build microscopic circuits and devices on both sides of the rigid silicon wafer. On one side, a flexible, transparent film is added on top of the silicon wafer. Within this film, a bilayer of titanium and gold traces is embedded so that the traces line up with where the needles will be manufactured on the other side of the silicon wafer. 

Working from the other side, after the flexible film has been added, all the silicon is etched away, except for free-standing, thin, pointed columns of silicon. These pointed columns of silicon are, in fact, the microneedles, and their bases align with the titanium-gold traces within the flexible layer that remains after the silicon has been etched away. These titanium-gold traces are patterned via standard and scalable microfabrication techniques, allowing scalable production with minimal manual labor. The manufacturing process offers the possibility of flexible array design and scalability to tens of thousands of microneedles.  

Toward closed-loop systems

Looking to the future, penetrating microneedle arrays with large spatial coverage will be needed to improve brain-machine interfaces to the point that they can be used in "closed-loop systems” that can help individuals with severely limited mobility. For example, this kind of closed-loop system might offer a person using a robotic hand real-time tactical feedback on the objects the robotic hand is grasping.  

Tactile sensors on the robotic hand would sense the hardness, texture, and weight of an object. This information recorded by the sensors would be translated into electrical stimulation patterns which travel through wires outside the body to the brain-computer interface with penetrating microneedles. These electrical signals would provide information directly to the person's brain about the hardness, texture, and weight of the object. In turn, the person would adjust their grasp strength based on sensed information directly from the robotic arm. 

This is just one example of the kind of closed-loop system that could be possible once penetrating microneedle arrays can be made larger to conform to the brain and coordinate activity across the "command" and "feedback" centers of the brain.

Previously, the Dayeh laboratory invented and demonstrated the kinds of tactile sensors that would be needed for this kind of application, as highlighted in this video.

Pathway to commercialization

The advanced dual-side lithographic microfabrication processes described in this paper are patented (US 10856764). Dayeh co-founded Precision Neurotek Inc. to translate technologies innovated in his laboratory to advance state of the art in clinical practice and to advance the fields of neuroscience and neurophysiology.

Paper title: "Scalable Thousand Channel Penetrating Microneedle Arrays on Flex for Multimodal and Large Area Coverage BrainMachine Interfaces," in Advanced Functional Materials

 Authors
S. H. Lee, K. Lee, D. R. Cleary, K. J. Tonsfeldt, H. Oh, F. Azzazy, Y. Tchoe, A. M. Bourhis, L. Hossain, Y. G. Ro, A. Tanaka, S. A. Dayeh are affiliated with the Integrated Electronics and Biointerfaces Laboratory in the Department of Electrical and Computer Engineering at the University of California San Diego Jacobs School of Engineering.

D. R. Cleary has a primary appointment in the Department of Neurological Surgery at UC San Diego Health.

M. Thunemann, K. Kılıç, and A. Devor are affiliated with the Biomedical Engineering Department at Boston University.

Corresponding author
Shadi Dayeh
Electrical and Computer Engineering Department
UC San Diego Jacobs School of Engineering
Email: sdayeh@eng.ucsd.edu

Funding
This work was supported by the National Institutes of Health Awards NIBIB DP2-EB029757, the NIH BRAIN Initiative R01NS123655-01,UG3NS123723-01 to S.A.D., 1R01DA050159-01, R01 MH111359-05 to A.D., and F32 MH120886-01 to D.R.C.; National Science Foundation Award No. 1728497 and CAREER No. 1351980; and by the KAVLI Institute for Brain and Mind to S.A.D.. Technical support from the Nano3 cleanroom facilities at UC San Diego’s Qualcomm Institute. This work was performed in part at the San Diego Nanotechnology Infrastructure (SDNI) of UC San Diego, a member of the National Nanotechnology Coordinated Infrastructure, which was supported by the National Science Foundation (Grant No. ECCS1542148).

New, Highly Accurate Algorithm Scales Ability to Assemble Complete Genomes

March 10, 2022-- An international team led by researchers at University of California San Diego’s Department of Computer Science and Engineering has shown that a new genome assembly algorithm, called the La Jolla Assembler (LJA), vastly improves large genomes reconstruction, the process by which DNA snippets are arranged into complete genomes, which is an essential aspect of genomic sequencing. 

In addition, LJA significantly reduces error rates and boosts the ability to scale complete human genome assembly. This will make it easier to conduct large populations studies, in which thousands or millions of people are sequenced and their genomes compared to better understand the genetic factors that contribute to disease. The study was published this week in the journal Nature Biotechnology.

“We used LJA to completely reconstruct almost half of the chromosomes in the human genome in a completely automatic fashion,” said Pavel Pevzner, the Ronald R. Taylor Distinguished Professor of Computer Science and senior author on the paper. “This reduced assembly errors five-fold compared to other assembly algorithms utilizing long, high-fidelity (HiFi) reads. The accuracy of this approach will bring important benefits, particularly for large population studies of complex and poorly studied regions of the human genome, such as centromeres or antibody-generating loci.”

Genome assemblers are computational tools that reconstruct genomes based on a collection of shorter sequences (reads). For many years, researchers relied almost exclusively on short read technologies, which generate reads up to 300 nucleotides. These provided crucial genomic information but left gaps in genomic sequences – many in biomedically important regions. As a result, the Human Genome Project, completed two decades ago, left thousands of unassembled regions – unexplored DNA that could have clinical and scientific significance.

“This incomplete human genome assembly produced a revolution in biology and medicine 20 years ago,” said Anton Bankevich, a postdoctoral researcher in the Department of Computer Science and Engineering and first author on the paper. “However, the missing pieces of the genome may hold many more secrets.” 

More recently, scientists have begun adopting long, HiFi reads (greater than 10,000 nucleotides), which have helped them sequence complete human and other genomes. The first complete human genome, generated by the Telomere-to-Telomere (T2T) consortium last year, was an important milestone. However, this feat required intensive manual work and would be virtually impossible to scale to hundreds, let alone millions, of genomes. 

To automate the process and increase speed and accuracy, Pevzner’s team adopted a computational approach called de Bruijn graphs, which helped them assemble millions of reads into complete genomes. Originally an obscure mathematical approach invented by Dutch mathematician Nicolaas de Bruijn, this technique has become a sequencing workhorse, modeling a genome as a complex road network that connects various cities (short genomic fragments) and finding ways to traverse the network while using each road. In a way, this was history repeating itself. More than 20 years ago, Pevzner and colleagues used de Bruijn graphs to make sense of short reads. 

“Although it looks like simply applying this 20-year old technique to HiFi reads would lead to excellent human genome assemblies, all previously developed algorithmic ideas fall apart when faced with constructing the enormously complex de Bruijn graph of the human genome,” said Andrey Bzikadze, a graduate student in the Bioinformatics and Systems Biology Program at UC San Diego and co-author on the paper. “Reusing old methods would require a prohibitive amount of computer memory, making them impossible to implement.” 

LJA solves this problem, reducing the data footprint as well as assembly errors. It sets the stage for improved speed and accuracy in large population studies, in which scientists will need to assemble millions of genomes to identify the gene sequences that confer good health or cause disease.

“Assembling a single genome is not enough to drive biological discovery,” said Pevzner. “It is by comparing different genomes that scientists can understand their functions and associations with diseases. That is why we need to scale genome assembly efforts and create algorithms that produce the same quality of genome assembly as the T2T human genome but can do it automatically.”

Other authors include Mikhail Kolmogorov at National Cancer Institute and Dmitry Antipov at St. Petersburg University.

 

Applications are open for Galvanizing Engineering in Medicine awards

Engineering Students to Compete in International Maritime Robot Competition

For the past three months, a team of engineering students at UC San Diego has been adding cameras, LiDAR systems, a hydrophone, and even a drone to a 16-foot seagoing vessel. Their goal? To compete in the Maritime RobotX Challenge in Australia in November 2022. In order to get there, they’ll have to turn the vessel into a completely autonomous system, capable of navigating to specific buoys, launching objects at a target, and working with a drone to map out the sea space, entirely on its own.

They are under no illusions: it’s a difficult task. But it’s a welcomed challenge that, for several of the students, has been more than 10 years in the making, thanks to the FIRST (For Inspiration and Recognition of Science and Technology) robotics outreach program, and RoboNation, the nonprofit organization behind RobotX.

“Way back in third grade, our FIRST Robotics coach wanted us to work toward underwater robotics; we started with land vehicles for the first eight years, then transitioned to underwater vehicles, initially with an 18-inch cubed underwater submersible for the RoboSub competition. The next progression of RoboSub is RobotX, which is the university-level competition, and we’re finally getting to participate this year,” said Colin Szeto, a first-year mechanical engineering student at the Jacobs School of Engineering.

When Szeto and several other RoboNation participants arrived at UC San Diego last fall, they knew they wanted to compete in the RobotX challenge. Working with Jack Silberman, a longtime FIRST Robotics coach for Team Inspiration and a lecturer for the UC San Diego Contextual Robotics Institute, as well as fellow engineering students and several former Team Inspiration teammates still in high school, the students developed and submitted their project proposal. When they found out their proposal had been accepted, they got to work, turning the wave adaptive modular vehicle (WAM-V) that all participating teams are sent as a standard starting platform, into an autonomous maritime system.

“This is an autonomous competition, so we need different sensors to maneuver around the water and determine where we are on the field,” said Daniel Scuba, also a mechanical engineering freshman, who participated in FIRST Robotics in high school and is on the team. “Some of the sensors we’ll be adding to the WAM-V include a LiDAR sensor to locate buoys in the water; as well as a hyperspectral imaging camera on the drone, and more cameras to help with way-finding. We also use a hydrophonic sensor to determine the underwater pinging frequency from a modem.”

Typically, about 15 teams from around the world compete in this weeklong biennial competition; so far, the UC San Diego team is the only competitor from California, and one of only a handful from the United States. Points are scored by completing one of several tasks, including: navigating to a certain colored buoy; maneuvering around a series of gates; launching an object at a target; working in collaboration with a drone to identify another colored marker and navigating to it; avoiding staged, fake wildlife encounters; and docking at a specific bay.

Once the competition is complete, the team plans to transition the WAM-V to scientists at UC San Diego for use in maritime field work. With this in mind, the students are configuring the mechanical systems to accommodate extra payloads, and configuring the electronic system with open ports to interface with any sensors that researchers may want to add.

The platform on top of the WAM-V will serve as home base for the autonomous drone the students are developing.

For Szeto, this is one of the neatest parts of the challenge: being exposed to the maritime domain, and learning how robotics and autonomy can intersect with earth sciences.

“I think it’s cool to be exposed to a different field of robotics,” said Szeto. “The maritime domain is not something I grew up with, but it’s super exciting to see different scientists and students be so passionate about saving the ocean, and being able to help humanity by taking care of our environment. And the system here is a vehicle for us to learn more about the oceans as well as learn more about different technology for the future.”

For Scuba, he’s most enjoying learning about the roles of the different sensors they’re using, and how to integrate them all together.

“I’m not as knowledgeable about the sensors since I come from more of a mechanical background in robotics, so I’m not used to integrating all these different types of sensors from an industrial standard; I’m more used to smaller sensors that integrate more easily. So, it’s interesting to learn how to adapt to an industry standard, and these industry level materials like motors and propulsion systems, to integrate them all together.”

With the competition still 10 months away, the team has a lot of work ahead of them.

“My FIRST Robotics Team Inspiration co-coach Alex Szeto, a systems engineer at Northrop Grumman, and I are excited that these students have this unique opportunity to learn new technical skills as they work toward the international competition,” said Silberman. “The team is open to any UC San Diego students who want to participate and expand their skills while advancing our STEM outreach efforts.”

To learn more about the team and get involved in this project or their ongoing STEM outreach efforts, visit the FIRST website.

'Project in a Box' helping kids find their passion at San Diego Library

Bioengineering alumnus on COVID-19 antiviral pill development team

Bioengineering alumnus Britton Boras

February 24, 2022-- Jacobs School of Engineering alumnus Britton Boras earned a Ph.D. in bioengineering in 2015, conducting research with Professor Andrew McCulloch on multi-scale modeling of biological systems. Now a Senior Principal Scientist at Pfizer, Boras uses the modeling skills he honed at UC San Diego to predict the most effective dosage of new therapies in development. Most recently, Boras was part of the team at Pfizer that developed the Paxlovid COVID-19 antiviral pill, the first oral antiviral treatment for COVID-19 to receive FDA emergency use authorization.

Boras shared what led him to UC San Diego, how his graduate degree prepared him for his career, and what it was like to work on such a timely and highly anticipated drug, in this Q&A.

Q: You earned a Ph.D. in bioengineering with a focus on multi-scale modeling; how and why did you choose this topic, and why at UC San Diego?

A: Between undergraduate and graduate school, I worked for several years at a small biotech company. During that time, I gained experience with computational modeling of biological systems. I really liked the ability to use mathematics and models to explain experimental results that at first seem counter-intuitive. When I applied to graduate schools, I was looking for a program that could help me expand that interest. I did a rotation in Dr. McCulloch’s lab and found a mentor and lab that balanced the experimental and the modeling sides of biology in a way that appealed to me.

Q: Where has your professional career taken you since completing your PhD?

A: After I graduated, I joined the Translational Modeling and Simulations group at Pfizer, where I have been for more than six years.

Q: Can you describe what your role at Pfizer, and on the Paxlovid team, is?

A: As the translational modeling and simulation representative on the team, my job is to use preclinical experiments (in vitro and in vivo) to try to predict what doses we should target clinically to be efficacious. We drew upon our expertise from prior Pfizer antiviral programs, in addition to HIV and HCV protease inhibitor literature and our knowledge of the SARS-CoV-2 viral PI structure to help define a target for the team.

Q: Were there any particular skills that you learned or honed during graduate school that you use regularly in your role at Pfizer?

A: Certainly, thermodynamics and mathematics skills are very useful in model construction; however, more than any particular class, the critical thinking skills that were woven throughout the entire curriculum are essential to being a good modeler. How to problem solve when you have incomplete information is one of the most valuable skills I learned. Furthermore, being able to critically evaluate your model and results or rethink the problem from a different perspective to challenge your initial assumptions is an invaluable skill that Dr. McCulloch, and the Bioengineering department as a whole, helped me learn.

Boras was co-author of a Science paper describing the antiviral pill.

Q: Whatwas it like, on a personal level, to be developing a drug with such immediate and widespread need?

A: It’s humbling. Much of my work at Pfizer has been focused on Oncology, where the road from drug discovery to observed, scalable impact on patients’ lives can take years or even a decade from when we started. To see this compound go from a molecule that showed some initially promising properties to now an authorized treatment with the potential to impact so many people around the world is inspiring. I think of all the choices the team made along the way where we could have gone in different directions that may have not led to this treatment being in the hands of patients today. It’s amazing. It’s what so many of us who go into drug development hope we can one day contribute to. I just feel so blessed to be a part of it.

Q: When you were at UC San Diego, were you involved in any organizations or groups that were meaningful to you? Or any resources that you took advantage of?

A: I was a part of the BEGS (Bioengineering graduate student) Council. I served 1 year as the Co-outreach chair. We did outreach programs like Science day at Padres Stadium, and we talked to middle school classes about science experiments. I think it’s vital to get the next generation enthusiastic about science so that they can tackle the problems they will face.

I also did intramural sports with some other bioengineering graduate students who are now some of my best friends and colleagues across bioengineering companies in San Diego. Especially given the uncertainty of the ongoing COVID-19 pandemic, these friendships have helped keep me going.

Q: What advice would you share with current students hoping to one day make an impact the way you have?

A: Find a mentor whose science appeals to you and who is interested in helping you grow and explore the area. Don’t be afraid to have conversations with professors outside the department. Some of the most interesting areas of my PhD grew out of discussions with professors outside of Bioengineering and realizing we were facing the same problem from different angles.

Finally, going back to the beginning, hone your critical thinking skills. When you generate data or a model that you are sure says one thing, take a moment to think—are there any other conclusions from the model or assumptions that would give similar results? It can help you break out of only seeing what you expect to see.

Q: Anything we didn't ask about that's important to note?

A: I was one member of a very large team aiming to meet the critical unmet need posed by COVID-19, and our work could not have advanced without our research collaborators and the clinical trial participants who bravely volunteered to be part of these studies. Communication across disciplines with chemists, biologist, pharmacologist, clinicians, and many more was essential to discovering the molecule, profiling it, and clinically testing it so that we could help people fighting this devastating disease today. I am incredibly grateful to each and every one of them.

Engineering students to compete in international maritime robot competition

February 17, 2022--For the past three months, a team of engineering students at UC San Diego has been adding cameras, LiDAR systems, a hydrophone, and even a drone to a 16-foot seagoing vessel. Their goal? To compete in the Maritime RobotX Challenge in Australia in November 2022. In order to get there, they’ll have to turn the vessel into a completely autonomous system, capable of navigating to specific buoys, launching objects at a target, and working with a drone to map out the sea space, entirely on its own.

All teams participating in the Maritime RobotX Challenge start with the same wave adaptive modular vessel (WAM-V); their challenge is to add a suite of sensors and software that will allow it to function autonomously. Photos and video by Daniel Sosa-Cobo.

They are under no illusions: it’s a difficult task. But it’s a welcomed challenge that, for several of the students, has been more than 10 years in the making, thanks to the FIRST (For Inspiration and Recognition of Science and Technology) robotics outreach program, and RoboNation, the nonprofit organization behind RobotX.

“Way back in third grade, our FIRST Robotics coach wanted us to work toward underwater robotics; we started with land vehicles for the first eight years, then transitioned to underwater vehicles, initially with an 18-inch cubed underwater submersible for the RoboSub competition. The next progression of RoboSub is RobotX, which is the university-level competition, and we’re finally getting to participate this year,” said Colin Szeto, a first-year mechanical engineering student at the Jacobs School of Engineering.

When Szeto and several other RoboNation participants arrived at UC San Diego last fall, they knew they wanted to compete in the RobotX challenge. Working with Jack Silberman, a longtime FIRST Robotics coach for Team Inspiration and a lecturer for the UC San Diego Contextual Robotics Institute, as well as fellow engineering students and several former Team Inspiration teammates still in high school, the students developed and submitted their project proposal. When they found out their proposal had been accepted, they got to work, turning the wave adaptive modular vehicle (WAM-V) that all participating teams are sent as a standard starting platform, into an autonomous maritime system.

“This is an autonomous competition, so we need different sensors to maneuver around the water and determine where we are on the field,” said Daniel Scuba, also a mechanical engineering freshman, who participated in FIRST Robotics in high school and is on the team. “Some of the sensors we’ll be adding to the WAM-V include a LiDAR sensor to locate buoys in the water; as well as a hyperspectral imaging camera on the drone, and more cameras to help with way-finding. We also use a hydrophonic sensor to determine the underwater pinging frequency from a modem.”

Typically, about 15 teams from around the world compete in this weeklong biennial competition; so far, the UC San Diego team is the only competitor from California, and one of only a handful from the United States. Points are scored by completing one of several tasks, including: navigating to a certain colored buoy; maneuvering around a series of gates; launching an object at a target; working in collaboration with a drone to identify another colored marker and navigating to it; avoiding staged, fake wildlife encounters; and docking at a specific bay.

Once the competition is complete, the team plans to transition the WAM-V to scientists at UC San Diego for use in maritime field work. With this in mind, the students are configuring the mechanical systems to accommodate extra payloads, and configuring the electronic system with open ports to interface with any sensors that researchers may want to add.

For Szeto, this is one of the neatest parts of the challenge: being exposed to the maritime domain, and learning how robotics and autonomy can intersect with earth sciences.

“I think it’s cool to be exposed to a different field of robotics,” said Szeto. “The maritime domain is not something I grew up with, but it’s super exciting to see different scientists and students be so passionate about saving the ocean, and being able to help humanity by taking care of our environment. And the system here is a vehicle for us to learn more about the oceans as well as learn more about different technology for the future.”

For Scuba, he’s most enjoying learning about the roles of the different sensors they’re using, and how to integrate them all together.

“I’m not as knowledgeable about the sensors since I come from more of a mechanical background in robotics, so I’m not used to integrating all these different types of sensors from an industrial standard; I’m more used to smaller sensors that integrate more easily. So, it’s interesting to learn how to adapt to an industry standard, and these industry level materials like motors and propulsion systems, to integrate them all together.”

With the competition still 10 months away, the team has a lot of work ahead of them.

“My FIRST Robotics Team Inspiration co-coach Alex Szeto, a systems engineer at Northrop Grumman, and I are excited that these students have this unique opportunity to learn new technical skills as they work toward the international competition,” said Silberman. “The team is open to any UC San Diego students who want to participate and expand their skills while advancing our STEM outreach efforts.”

To learn more about the team and get involved in this project or their ongoing STEM outreach efforts, visit the FIRST website.

Educating the next generation of data scientists, virtually

UC San Diego's new Master of Data Science Online program will help working professionals fill a critical need

February 16, 2022-- The University of California San Diego is launching its first online graduate degree program this fall to help meet the demand for data scientists as companies across all sectors seek to leverage vast amounts of data into meaningful insights. Applications for the new Master of Data Science Online program are now open. 

Jointly offered by UC San Diego’s renowned Halicioglu Data Science Institute (HDSI) and the Department of Computer Science and Engineering, the Master of Data Science Online degree will be a rigorous academic program targeted to working professionals. The program has been designed to make data science accessible to students drawn from diverse academic backgrounds, including those with non-technical backgrounds.

Students who want to fulfill the need for data analysis will be able to take advantage of the internationally recognized expertise of computer scientists at HDSI and in the computer science department, as courses will be taught by the same tenured or tenure-track faculty in both. 

“We are proud to offer this unique program taught by our world-class instructors,” said Rajesh K. Gupta, the founding director of HDSI and a computer science professor. “We want to ensure our graduates are robustly equipped for success in performing data-driven tasks and will be even greater assets to their current or future employers.”

Computer science Chair Sorin Lerner said: “The interdisciplinary nature of data science creates the perfect stage for our professional master’s degree. This program is exciting because it  allows students from diverse backgrounds the opportunity to earn a place.

Demand for data scientists

Data scientist has been called the “hottest job in America” by Bloomberg.  According to a recent report by Dice, the demand for data scientists increased by about 50% across healthcare, telecommunications, media/entertainment, and the financial services sectors during the pandemic as a shifting online workforce needed the help of big data, cloud computing, machine learning, and more advanced Artificial Intelligence applications. 

In addition, the Bureau of Labor Statistics sees strong growth in the data science field in its prediction that the data science field will grow about 28% through 2026, adding roughly 11.5 million new jobs.

The need for their expertise has been growing rapidly as companies across all sectors are trying to leverage the data they collect by distilling it into actionable information. Until recently, few undergraduate or graduate programs specific to data science existed. Working professionals who bring a wealth of knowledge and experience from fields where Data Science and Artificial Intelligence have a strong role are in need of formalized and advanced training for today’s roles.

“Data Science and Machine Learning are having an impact on many aspects of society, including e-commerce, financial industries, technology companies, health care, and academia. There are few aspects of society that will not be affected by Data Science,” said Lerner. 

The UC San Diego Master of Data Science Online program combines concepts from statistics, computer science and applications where data is at the forefront. 

The program begins with an introduction to data science that is approachable even for students who do not come into the program from a computer science or engineering background. However, the academic rigor, depth and breadth of the program meet the same expectations of a graduate degree in a technical field from UC San Diego. 

“Our online program allows professionals who already have an undergraduate degree to gain skills in data science and make themselves more marketable, both within their own company, or to other companies,” said Gupta. 

A UC San Diego degree, from anywhere

The two-year program will allow students to learn on their own schedule, within a flexible time frame, to accommodate students in different time zones and with varying work schedules. Courses will use video mini-lectures to teach course content in smaller modules, which provides flexibility for the students.

“Our goal is to make this online degree highly accessible to working professionals across the globe, individuals unable to attend an on-campus program or unable to obtain visas for study in the U.S, said Karen Flammer, the director of Digital Learning at UC San Diego. “The online Master of Data Science will provide tremendous value to traditional and non-traditional students, to the disciple of data science and to our university,” she said.

Applications for admission are now open. For more information on the new Master of Data Science Online program and to apply, please visit omds.ucsd.edu.

Computer Scientist Deian Stefan Receives Prestigious Sloan Research Fellowship

Stefan's research focuses on developing secure systems, especially for web browsers

Deian Stefan, an assistant professor in the Department of Computer Science and Engineering, is one of this year's Sloan Fellows.

February 15, 2022-- UC San Diego computer scientist Deian Stefan has been honored with an Alfred P. Sloan Research Fellowship. Stefan, who is an assistant professor in the Department of Computer Science and Engineering, will receive $75,000 during the two-year fellowship to advance his work on browser security.

The fellowship supports young scientists pursuing fundamental research with great potential to impact their fields. Code developed by Stefan and his team to make browsing safer is part of the newest releases of browsers Firefox and Brave. 

“This is a true honor,” said Stefan. “The researchers in my field who have gotten a Sloan Fellowship are an impressive bunch, and just being part of this is really rewarding.”

Two other UC San Diego researchers also have been recognized this year, in the Divisions of Physical Sciences and Biological Sciences. 

Stefan is being recognized for his work on secure systems. Programmers can inadvertently introduce bugs that allow hackers to steal information or hold systems for ransom. He believes a new generation of compilers–programs that turn instructions into code a machine can understand–can help solve this problem.

The key is creating secure compilers that will give programmers end-to-end guarantees that the security of their source code is preserved down to the machine code level. Stefan plans to design these compilers by building on WebAssembly, a relatively new computer language designed to enhance safety.

“By building secure compilers from high-level languages to WebAssembly, and secure compilers of WebAssembly to different hardware, we can make it easier for developers to build secure systems that have formal security guarantees,” said Stefan. With his collaborators, Stefan has been applying these ideas to make browsers safer.

Web browsers use third-party libraries–code resource repositories–to implement different features – such as rendering images, spell checking text and processing XML documents. These libraries are typically written in unsafe but fast languages, such as C, and often have unreported bugs that can be exploited by hackers to take control over computers.

To prevent attackers from exploiting these vulnerabilities, Stefan and others are modifying WebAssembly to sandbox these libraries into their own isolated worlds. This ensures the libraries cannot be used as vectors for attack.

“We’re trying to sandbox libraries so that users can browse the web safely without worrying about potentially compromised libraries harming their machines,” said Stefan. “We’re also starting to tackle this problem on the server side. We want to make it impossible for attackers to, say, upload an image and compromise servers and all the user data stored on those servers.”

Stefan has worked closely with Firefox, which has already incorporated some of his group's sandboxing work into its browser. He sees wide applications to other browsers, including Chrome and Brave, serverless cloud platforms, machine learning as service platforms and embedded systems.

The $75,000 award will give Stefan extra firepower from students and other researchers to accelerate this project and create these extra defenses. As always with computer security, it’s essential to get these new safeguards up and running quickly.

“There have been a bunch of recent, high-profile attacks on real people that could have been prevented if we had sandboxed libraries early,” said Stefan. “They have far more privileges than they need to perform their assigned tasks, and that is largely an artifact of how we build software. As we showed in Firefox, we can fundamentally shift system design towards security and eliminate this whole class of attacks.”

 

 

Simplifying RNA editing for treating genetic diseases

February 10, 2022 -- New research led by bioengineers at the University of California San Diego could make it much simpler to repair disease-causing mutations in RNA without compromising precision or efficiency.

The new RNA editing technology holds promise as a gene therapy for treating genetic diseases. In a proof of concept, UC San Diego researchers showed that the technology can treat a mouse model of Hurler syndrome, a rare genetic disease, by correcting its disease-causing mutation in RNA. The findings are published Feb. 10 in Nature Biotechnology.

What’s special about the technology is that it makes efficient use of RNA editing enzymes that naturally occur in the body’s cells. These enzymes are called adenosine deaminases acting on RNA (ADARs). They bind to RNA and convert some of the adenosine (A) bases to inosine (I), which is read by the cell’s translation machinery as guanosine (G).

Researchers have been exploring RNA editing approaches with ADARs to correct the G-to-A mutation behind genetic disorders such as cystic fibrosis, Rett syndrome and Hurler syndrome. A big advantage of RNA editing—over DNA editing, for example—is that changes to RNA are only temporary, since RNA has a short lifespan. So even if off-target edits occur, they wouldn’t be there to stay.

To make a targeted A-to-I (or essentially, an A-to-G) edit on RNA using ADARs, a short accessory strand of RNA—called a guide RNA—is needed to guide ADARs to the target and make the desired change there.

A big challenge with this approach is that traditional guide RNAs are not efficient at using native ADARs in the cell, so they require external ADARs to be brought into the cell to work, explained Prashant Mali, a bioengineering professor at the UC San Diego Jacobs School of Engineering. “But the problem with that,” he added, “is that it makes delivery complicated. And it can result in more off targets.”

To overcome these issues, Mali and colleagues engineered a new kind of guide RNA—one that is extremely effective at recruiting the cell’s own ADARs to make edits at a precise target RNA region.

“We can simply deliver just a small piece of RNA inside the cell and repair mutations in vivo. We don’t have to provide any extra enzymes,” said Mali.

The team designed the guide RNAs to target the single G-to-A mutation that causes Hurler syndrome. This mutation prevents the body from producing an enzyme that is necessary for breaking down complex sugars. Buildup of these sugars causes severe tissue damage, skeletal abnormalities, cognitive impairment, and other serious health problems. Systemic injection of the guide RNAs into diseased mice resulted in correction of 7 to 17% of the mutant RNAs after two weeks, as well as a 33% decrease in the buildup of complex sugars.

One aspect that makes the new guide RNAs effective is that they are longer than traditional guide RNAs. “This basically makes them stickier for ADARs already present in the cell to come and bind to them,” said Mali. Other unique design features make them more stable and precise than traditional guide RNAs. They can last for days and stay on the target RNA region for longer periods of time, whereas RNA in general gets quickly destroyed by the cell. That’s because these guide RNAs are built as circular rather than linear molecules; being circular makes them resistant to the cell’s RNA-degrading enzymes. In terms of precision, these guide RNAs only allow changes at the target A and not at any other As nearby. They do this by folding into loop structures at predetermined spots along the target RNA region, which prevents off-target As from getting edited.

The research is still at an early stage, said Mali, “and it remains to be seen how this RNA editing technology will work in primates.” Immediate next steps for the team will focus on improving delivery of the guide RNAs into cells.

“I’m hopeful that this work opens the door even more for RNA editing as another gene therapy tool,” said Mali.

A Seattle-based biotechnology startup co-founded by Mali, called Shape Therapeutics, is working to translate this and several other RNA editing technologies developed in Mali’s lab into the clinic.

Paper: “Robust in vitro and in vivo RNA editing via recruitment of endogenous ADARs using circular guide RNAs.” Co-authors include Dhruva Katrekar, James Yen, Yichen Xiang, Anushka Saha and Dario Meluzzi, UC San Diego; and Yiannis Savva, Shape Therapeutics.

This work was supported by UC San Diego Institutional Funds and the National Institutes of Health (R01HG009285, R01CA222826, R01GM123313, 1K01DK119687).

Mapping mutation 'hotspots' in cancer reveals new drivers and biomarkers

This artistic rendering illustrates the diversity of mutational processes that generate clustered mutations in human cancer. Depicted here are kyklonas, which are molecular cyclones that cause mutations on circular extrachromosomal DNA (ecDNA), and omikli, which is a molecular fog that causes mutations on linear chromosomal DNA. Credit: Catherine Eng

February 9, 2022 -- Researchers led by bioengineers at the University of California San Diego have identified and characterized a previously unrecognized key player in cancer evolution: clusters of mutations occurring at certain regions of the genome. The researchers found that these mutation clusters contribute to the progression of about 10% of human cancers and can be used to predict patient survival.

The findings are reported in a paper published Feb. 9 in Nature.

The work sheds light on a class of mutations called clustered somatic mutations—clustered meaning they group together at specific areas in a cell’s genome, and somatic meaning they are not inherited, but caused by internal and external factors such as aging or exposure to UV radiation, for example.

Clustered somatic mutations have so far been an understudied area in cancer development. But researchers in the lab of Ludmil Alexandrov, a professor of bioengineering and cellular and molecular medicine at UC San Diego, saw something highly unusual about these mutations that warranted further study.

“We typically see somatic mutations occurring randomly across the genome. But when we looked closer at some of these mutations, we saw that they were occurring in these hotspots. It’s like throwing balls on the floor and then suddenly seeing them cluster in a single space,” said Alexandrov. “So we couldn’t help but wonder: What is happening here? Why are there hotspots? Are they clinically relevant? Do they tell us something about how cancer has developed?”

“Clustered mutations have largely been ignored because they only make up a very small percentage of all mutations,” said Erik Bergstrom, a bioengineering PhD student in Alexandrov’s lab and the first author of the study. “But by diving deeper, we found that they play an important role in the etiology of human cancer.”

The team’s discoveries were enabled by creating the most comprehensive and detailed map of known clustered somatic mutations. They started by mapping all the mutations (clustered and non-clustered) across the genomes of more than 2500 cancer patients—an effort that in total encompassed 30 different cancer types. The researchers created their map using next-generation artificial intelligence approaches developed in the Alexandrov lab. The team used these algorithms to detect clustered mutations within individual patients and elucidate the underlying mutational processes that give rise to such events. This led to their finding that clustered somatic mutations contribute to cancer evolution in approximately 10% of human cancers.

Taking it a step further, the researchers also found that some of the cancer-driving clusters—specifically those found in known cancer driver genes—can be used to predict the overall survival of a patient. For example, the presence of clustered mutations in the BRAF gene—the most widely observed driver gene in melanoma—results in better overall patient survival compared to individuals with non-clustered mutations. Meanwhile, the presence of clustered mutations in the EGFR gene—the most widely observed driver gene in lung cancer—results in decreased patient survival.

“What’s interesting is that we see differential survival in terms of just having clustered mutations detected within these genes, and this is detectable with existing platforms that are commonly used in the clinic. So this acts as a very simple and precise biomarker for patient survival,” said Bergstrom.

“This elegant work emphasizes the importance of developing AI approaches to elucidate tumor biology, and for biomarker discovery and rapid development using standard platforms with direct line of sight translation to the clinic,” said Scott Lippman, director of Moores Cancer Center and associate vice chancellor for cancer research and care at UC San Diego. “This highlights UC San Diego’s strength in combining engineering approaches in artificial intelligence for solving current problems in cancer medicine.”  

A new mode of cancer evolution

In this study, the researchers also identified various factors that cause clustered somatic mutations. These factors include UV radiation, alcohol consumption, tobacco smoking, and most notably, the activity of a set of antiviral enzymes called APOBEC3.

APOBEC3 enzymes are typically found inside cells as part of their internal immune response. Their main job is to chop up any viruses that enter the cell. But in cancer cells, the researchers think that the APOBEC3 enzymes may be doing more harm than good.

The researchers found that cancer cells—which are often rife with circular rings of extrachromosomal DNA (ecDNA) that harbor known cancer driver genes—have clusters of mutations occurring across individual ecDNA molecules. The researchers attribute these mutations to the activity of APOBEC3 enzymes. They hypothesize that APOBEC3 enzymes are mistaking the circular rings of ecDNA as foreign viruses and attempt to restrict and chop them up. In doing so, the APOBEC3 enzymes cause clusters of mutations to form within individual ecDNA molecules. This in turn plays a key role in accelerating cancer evolution and likely leads to drug resistance. The researchers named these rings of clustered mutations kyklonas, which is the Greek word for cyclones. 

“This is a completely novel mode of oncogenesis,” said Alexandrov. Along with the team’s other findings, he explained, “this lays the foundation for new therapeutic approaches, where clinicians can consider restricting the activity of APOBEC3 enzymes and/or targeting extrachromosomal DNA for cancer treatment.”

Paper: “Mapping clustered mutations in cancer reveals APOBEC3 mutagenesis of ecDNA.”

This work was supported by a Cancer Grand Challenge award from Cancer Research UK as well as funding from the U.S. National Institutes of Health, Alfred P. Sloan Foundation, and Packard Foundation.

In a first for sonogenetics, researchers control mammalian cells with ultrasound

Researchers pinpoint a sound-sensitive mammalian protein that lets them activate brain, heart or other cells with ultrasound

February 9, 2022-- Scientists at the Salk Institute of Biological Studies and UC San Diego have engineered mammalian cells to be activated using ultrasound. The method, which the team used to activate human cells in a dish and brain cells inside living mice, paves the way toward non-invasive versions of deep brain stimulation, pacemakers and insulin pumps. The findings were published in Nature Communications on Feb. 9, 2022. 

“Going wireless is the future for just about everything,” says senior author Sreekanth Chalasani, an associate professor in Salk’s Molecular Neurobiology Laboratory. “We already know that ultrasound is safe, and that it can go through bone, muscle and other tissues, making it the ultimate tool for manipulating cells deep in the body.”

About a decade ago, Chalasani pioneered the idea of using ultrasonic waves to stimulate specific groups of genetically marked cells, and coined the term “sonogenetics” to describe it. In 2015, his group showed that, in the roundworm Caenorhabditis elegans, a protein called TRP-4 makes cells sensitive to low-frequency ultrasound. When the researchers added TRP-4 to C. elegans neurons that didn’t usually have it, they could activate these cells with a burst of ultrasound—the same sound waves used in medical sonograms. 

When the researchers tried adding TRP-4 to mammalian cells, however, the protein was not able to make the cells respond to ultrasound. A few mammalian proteins were reported to be ultrasound-sensitive, but none seemed ideal for clinical use. So Chalasani and his colleagues, including James Friend, a professor in the Department of Mechanical and Aerospace Engineering at UC San Diego, set out to search for a new mammalian protein that made cells highly ultrasound sensitive at 7 MHz, considered an optimal and safe frequency. 

“Our approach was different than previous screens because we set out to look for ultrasound-sensitive channels in a comprehensive way,” says Yusuf Tufail, a former project scientist at Salk and a co-first author of the new paper. 

The researchers added hundreds of different proteins, one at a time, to a common human research cell line (HEK), which does not usually respond to ultrasound. Then, they put each cell culture under a setup that let them monitor changes to the cells upon ultrasound stimulation. 

After screening proteins for more than a year, and working their way through nearly 300 candidates, the scientists finally found one that made the HEK cells sensitive to the 7 MHz ultrasound frequency. TRPA1, a channel protein, was known to let cells respond to the presence of noxious compounds and to activate a range of cells in the human body, including brain and heart cells. 

But the team discovered that the channel also opened in response to ultrasound in HEK cells. 

“We were really surprised,” says co-first author of the paper Marc Duque, a Salk exchange student. “TRPA1 has been well-studied in the literature but hasn’t been described as a classical mechanosensitive protein that you’d expect to respond to ultrasound.”

To test whether the channel could activate other cell types in response to ultrasound, the team used a gene therapy approach to add the genes for human TRPA1 to a specific group of neurons in the brains of living mice. When they then administered ultrasound to the mice, only the neurons with the TRPA1 genes were activated. 

Clinicians treating conditions including Parkinson’s disease and epilepsy currently use deep brain stimulation, which involves surgically implanting electrodes in the brain, to activate certain subsets of neurons. Chalasani says that sonogenetics could one day replace this approach—the next step would be developing a gene therapy delivery method that can cross the blood-brain barrier, something that is already being studied. 

Perhaps sooner, he says, sonogenetics could be used to activate cells in the heart, as a kind of pacemaker that requires no implantation. “Gene delivery techniques already exist for getting a new gene—such as TRPA1—into the human heart,” Chalasani says. “If we can then use an external ultrasound device to activate those cells, that could really revolutionize pacemakers.”

For now, the team is carrying out more basic work on exactly how TRPA1 senses ultrasound. “In order to make this finding more useful for future research and clinical applications, we hope to determine exactly what parts of TRPA1 contribute to its ultrasound sensitivity and tweak them to enhance this sensitivity,” says Corinne Lee-Kubli, a co-first author of the paper and former postdoctoral fellow at Salk.  

They also plan to carry out another screen for ultrasound sensitive proteins—this time looking for proteins that can inhibit, or shut off, a cell’s activity in response to ultrasound. 

The other authors of the paper were Uri Magaram, Janki Patel, Ahana Chakraborty, Jose Mendoza Lopez, Eric Edsinger, Rani Shiao and Connor Weiss of Salk; and Aditya Vasan and James Friend of UC San Diego. 

The work was supported by the National Institutes of Health (R01MH111534, R01NS115591), Brain Research Foundation, Kavli Institute of Brain and Mind, Life Sciences Research Foundation, W.M. Keck Foundation (SERF), and the Waitt Advanced Biophotonics and GT3 Cores (which receive funding through NCI CCSG P30014195 and NINDSR24).

Salk Communications press@salk.edu (858) 453-4100

 

A Mega Achievement: Two UC San Diego Students Named 2022 Meta PhD Research Fellows

February 4, 2022-- The University of California San Diego boasts two of this year’s 2022 Meta PhD Research Fellows—a class of 37 scholars selected from a pool of 2,300 applicants worldwide. 

As fellows, UC Diego Department of Computer Science and Engineering PhD students Stewart Grant and Kabir Nagrecha will be able to present their own research; learn about current research at Meta; as well as receive tuition and fees for up to two years and a $42,000 stipend. 

 

Stewart Grant

Stewart Grant is a fourth-year PhD student working with computer science professor Alex Snoeren as part of the SysNets Group. His research interests are at the intersection of distributed systems, networking and operating systems. He is currently focused on finding practical solutions for resource disaggregation using commodity programmable network devices. This work explores techniques for accelerating one-sided RDMA on passive banks of memory. 

“If research was not fun I’d likely not be doing it, so I'm very grateful that my environment lets me play and work at the same time. This fellowship has made me consider more deeply the practicality of my work, who may benefit from it, and what path I should consider going forward. It’s all been very… meta,” said Grant. 

Kabir Nagrecha

Kabir Nagrecha is a first year PhD student in the Databases Lab, where he is advised by Associate Professor Arun Kumar. He received competitive PhD fellowships from both the UC San Diego Department of Computer Science and Engineering and the  HalıcıoÄŸlu Data Science Institute (HDSI). His research focuses on developing systems to enable the building and deployment of scalable and efficient deep learning models. He aims to amplify the impact of machine learning and enable new applications by creating the infrastructure to support large-scale operations.

“I’m glad to have been honored with such a selective and prestigious award. But more than that, what excites me are the opportunities for the future. The fellowship gives me a great channel through which I can collaborate with researchers at Meta,” he said. “I’m hoping to use the fellowship to explore industry-relevant applications of my work as well as connect with experts in my domain who can help provide insight and guidance as my research career progresses.” 

In addition, three other UC San Diego PhD students were finalists: Ariana Mirian and Yu-Ying Yeh in the Department of Computer Science and Engineering, as well as Lauren Gilbert in the Department of Political Science. 
 

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.

Let There be Light

Alumnus earns Echoing Green Fellowship for bringing community-driven change to his native Myanmar

Lin Thu Hein (left) training Hein Htet Aung (right), Atutu Fellow for Project Sunbird, on the latest design of their solar home system before the first installation in Myanmar. Photo courtesy of Atutu.

January 27, 2022-- UC San Diego alumnus Lin Thu Hein has come full circle; after arriving in the United States from Myanmar at age 13, he is now using his degree in electrical engineering to bring solar-powered lighting to people off the grid and displaced by the recent unrest in his home state of Kachin in Myanmar.

UC San Diego electrical engineering alumnus and Echoing Green Fellow Lin Thu Hein.

Hein and the non-governmental organization (NGO) he co-founded, called Atutu, have a unique approach to this work. Through their Grassroots Design method, the NGO partners with local communities to co-create solutions to the challenge they’re working to solve: this puts the communities they work with in the driver’s seat of development efforts, instead of being beneficiaries. The approach earned Hein a coveted Echoing Green Fellowship, awarded to transformational leaders in the social sector; past Fellows include Michelle Obama, Van Jones, and Wendy Kopp, the founder of Teach for America.

Much of Hein’s formative thinking about community-driven social change stems from his years in the Global Ties program at UC San Diego. Global Ties partners interdisciplinary teams of students with nonprofits and NGOs to co-create solutions to socially urgent problems in San Diego and the developing world. Hein was part of the One Village Philippines project team, which partnered with nonprofit Gawad Kalinga in the Philippines to bring affordable solar-powered lanterns, and a source of income, to their partner village.

Through the project, Hein was able to travel to the Philippines three times over the course of four years to work hand-in-hand with the partner organization on this joint venture, a transformational experience not just for him, but for many of the students who went with him and have since decided to volunteer their time to the Atutu mission.

UC San Diego Global Ties students on the One Village Philippines team visited their partner organization in the Philippines in the summer of 2018. This was one of three trips to the Philippines Hein went on through Global Ties. Photo courtesy of Hein.

“Our experiences on those trips, talking about group dynamics, talking about the balance of power, talking about the way being on the ground changed our perspective and how we would do it differently or how we would communicate that differently, those were instrumental experiences,” said Hein. “In training our next group of volunteers and designers for Atutu, those trips helped us come up with the guide rails so that we don't have any Western designers or Western engineers taking over the conversation at the collaboration stage.”

Mandy Bratton, director of the Global Ties program, said she’s not surprised to see Hein earning this level of national recognition for his work, but is heartened that so many fellow Global Ties alumni have chosen to participate in Atutu as well.

“I knew from the moment I met Lin that he was going to go far and do this kind of important work, but the fact that he has brought along so many Global Ties alumni—almost 50% of the people he's working with at Atutu were part of the program—I think that's one of the neatest parts of the story, it’s amazing.”

Alexis Tam, a chemical engineering alumna who co-founded Atutu with Hein in 2018, is one of those alums who is still actively involved as a volunteer with the organization. She and Hein met working on the One Village Philippines project together.

Atutu Fellows (left to right: Tsaw Htoi, Jar Li Gam, Hein Htet Aung, Mung Dan Aung) unpacking and inspecting light fixtures. Photo courtesy of Atutu.

“Atutu is a unique experience because we choose to prioritize self-efficacy in the communities that we work with,” said Tam, who volunteers as the organization’s Director of Operations, managing the portfolio of emerging projects and research and development initiatives. “This upcoming year, we are setting up the infrastructure to build solar home systems for off-grid communities in Myanmar. We have done this all while working fully remote in an online community the past few years, with members all over the world. I've also made some long-lasting friendships through this organization.”

Bringing light to Myanmar

While Atutu leads humanitarian innovation projects across a variety of sectors, from developing education centers to implementing water pump systems in off-grid communities, the Echoing Green Fellowship supports one of Atutu’s projects in particular: Sunbird Solar Technologies. The goal of the Sunbird project is to partner with community members on the ground in Myanmar, called Atutu Fellows, to manufacture and install a solar light system in homes, starting in Kachin state.

“The Sunbird project in particular aligned with my professional experience and my academic experience,” said Hein, who worked at a solar microgrid startup company after graduating in 2019 with a degree in electrical engineering with a focus on renewable energy and power systems. The Echoing Green Fellowship enabled him to devote himself full-time to Atutu starting in late 2021. “My focus on renewable energy and power systems at UC San Diego, plus growing up in a community with very limited energy access, made it a good fit for me to work on the energy access aspect of our development mission.”

Hein and the Atutu team of volunteers in the United States– many of them UC San Diego alumni–and Fellows in Myanmar, were able to install about 70 of these home lighting systems before the turmoil of COVID, and later a coup in Myanmar in February 2021, forced the team to pause. Instead of stopping their efforts, the Atutu team saw a new need, as thousands of people were forced to leave their homes and move into makeshift camps for internally displaced people. The Sunbird Solar team is now partnering with Myanmarese fellows to manufacture and install these lights in the temporary settlements for the internally displaced.

The core goal of the mission remains unchanged.

Atutu Fellows (left to right: Tsaw Htoi, Jar Li Gam, Hein Htet Aung, Mung Dan Aung) unpacking and inspecting light fixtures. Photo courtesy of Atutu.

“We’re trying to empower the community that we're partnering with to have a voice, and be in the driver's seat of their own development journey,” said Hein. “Our goal is to work with a group of Atutu fellows, community members on the ground, who are interested in working on energy access but are facing some sort of systemic barriers toward that goal” said Hein. “We'll try to unblock those barriers with the access and the tools and the resources that we have.”

A journey there and back

Hein grew up in Kachin state in Myanmar. While his mom worked abroad in Thailand for several years to provide opportunities and a new pathway for him, he was raised by a team of aunties and extended family. When he was 13, his mom had an opportunity to move to the San Francisco Bay area and bring her son with her. Hein attended high school in the Bay Area before earning his degree at the Jacobs School of Engineering at UC San Diego.

“I think throughout that time there's always been this lingering desire to do good for my community and to do good for Myanmar,” he said. “I had this feeling that nothing was going to be done unless I did something; now I've got access to people who could do something about making these changes, while the people who have wanted to do something didn’t have access to these resources that I do now.”

Current Atutu members from Global Ties include Alexis Tam, Jacob Hohn, Hao-In Choi, Ayush Sapra and Anuka Zandanshatar.

Atutu Fellows in Myanmar include Mung Dan Aung, Zaw Htoi Aung, Myo Win Aung, Zaw Latt Aung, Hein Htet Aung, Chi Oo Maung, Tsaw Htoi, Gum Lawt Aung and Jar Li Gam.

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 runs ENLACE, summer research program at UC San Diego aims to encourage the participation of high school students, university students, and researchers/teachers, in research in the sciences and engineering, while promoting cross-border friendships between Latin America and the United States. Graeve 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. 24, 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, 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.

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 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 Diego

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 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

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. 

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

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.”

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.

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.

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 peninsula, Ice 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.

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. 

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.

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.

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

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.

 

How the Pandemic Lockdown Impacted UC San Diego Undergrad Internet Use

Initial spikes followed by return to pre-pandemic levels

From left: PhD student Alisa Ukani, Professor Alex Snoeren and PhD student Ariana Mirian, the paper's three co-authors in the UC San Diego Department of Computer Science and Engineering.

November 30, 2021-- University of California San Diego computer scientists recently investigated how the COVID-19 pandemic influenced internet browsing during the lockdown. Armed with de-identified internet use data from UC San Diego dorm Wi-Fi, the researchers examined how online school and leisure activities shifted – for both American and international students. The study was presented at the ACM Internet Measurement Conference 2021.

The research focused on several thousand students in single-occupancy housing and how they responded to isolation between February and May 2020. The group found, not surprisingly, that students increased their internet usage by 58 percent from February to April 2020. However, in May those numbers began coming down. This was true of general usage and, more specifically, social media.

“We found that domestic students increased their social media usage early in the lockdown, but then that usage fell,” said Department of Computer Science and Engineering Ph.D. student Alisha Ukani who is the first author on the study. “That was a common effect – per capita usage intensified in the early months of the lockdown and then fell, returning to pre-pandemic levels in May, which was a bit of a surprise.”

The research team, which was led by UC San Diego Department of Computer Science and Engineering Professor Alex Snoeren and included Ph.D. student Ariana Mirian, also studied the the browsing distinctions between international and U.S. students. Though they did not know who owned specific devices, they devised a rubric to differentiate these groups based on their browsing behaviors. For example, international students would be more likely to visit offshore sites.

“We came up with a very conservative classification system, where we looked at all the websites each person was visiting and found the geographic coordinates of that site,” said Ukani.

Graph showing the number of devices on campus, indicating the large number of students who left campus.

This ability to separate these populations, rather than treating them as a single monolith, enhanced the information they could extract from the user data. Because international students were often unable to find flights home, they were likely disproportionately represented among the students remaining in the dorms after lockdown.

The team primarily focused on three categories: Zoom, social media and gaming. Zoom activity increased on weekdays – class time – but also showed small increases on weekend afternoons, which might have represented calls with friends and family.

For social media, domestic use of Instagram and Facebook remained stable, declining in May. The platforms were more popular for Americans than international students, though the latter increased their use in May.

Both domestic and international students increased using the Steam gaming platform early in the pandemic, but those numbers went down by May. A similar pattern was observed with Nintendo Switches.

This study provides useful information about internet habits during the lockdown. But even more importantly, it polishes data gathering techniques for future efforts.

“The techniques we developed in our analysis can be used in any internet usage measurement study,” said Ukani. “People can use our methods to classify international students or detect individual applications in any other context. We believe these techniques can be used by researchers outside of UC San Diego for their own measurement research.”

 

Locked-in during lock-down: undergradaute life on the Internet in a pandemic
Alisha Ukani, Ariana Mirian and Alex C. Snoeren
 

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

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.

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

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.” 

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 WiFi 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 WiFi—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 Evolution, which 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.

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.

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 WiFi 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.

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

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.

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

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

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.

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.

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.

Maha Achour named to Forbes 50 Over 50 list

Bioengineering alumnus' sustainable chemical company raises $118M

Alumna Chuah delivers 2021 CFK Memorial Lecture to Institution of Engineers, Malaysia

Titomic acquires alumni-led Tri-D Dynamics

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 Extraction, AIMC 2021, Graz, Austria.

Soft skin patch could provide early warning for strokes, heart attacks

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.

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.

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

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