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News Release

How well do wet masks contain droplets?

Study shows damp masks still stop respiratory droplet penetration

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

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

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

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

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

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

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

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

Primary components of the experimental setup, not to scale.

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

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

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

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

 

This tool protects your private data while you browse

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

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

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

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

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

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

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

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

How SugarCoat changes the game

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

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

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

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

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

 

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

 

Michael Smith and Deian Stefan, University of California San Diego

Benjamin Livshits, Imperial College of London

Peter Snyder, Brave Software

 

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

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

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

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

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

Plateau’s Problem

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

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

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

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

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

AI-powered personalized recommendation system helps lower blood pressure

Clinical trial data show tailored recommendations improve health outcomes

An example of a personalized recommendation provided to a patient.

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

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

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

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

Early results demonstrate the power of personalized recommendations in healthcare.

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

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

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

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

The platform and research challenges 

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

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

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

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

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

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

Connected Health

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

 

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

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

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

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

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

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

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

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

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

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

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

Want to throw off your chatbot? Use figurative language

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Another example of literalized text  

Investigating Robustness of Dialog Models to Popular Figurative Language Constructs

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

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

 




 

 

ROSE YU HEADS MAJOR SCIENTIFIC MACHINE LEARNING PROJECT

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

November 5, 2021

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

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

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

Big, Big Data

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

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

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

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

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

The Physical World

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

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

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

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

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

$6M IARPA grant to secure wireless data communication

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

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

ALT TEXT
Dinesh Bharadia

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

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

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

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

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

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

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

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

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

Making Voice Assistants Accessible for Older Patients

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

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

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

Technological Barriers

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

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

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

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

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

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

New Designs, New Devices

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

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

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

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

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






 

 


 

Making Space Travel Inclusive for All

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

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

By Kiran Kumar

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Cars, Start Your Engines!

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

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

 

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

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

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

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

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

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

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

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

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

A neuro-symbolic AI approach

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

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

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

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

An autonomous vehicle pipeline

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

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

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

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

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

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

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

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

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

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

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

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

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

Jennifer Chien, GradWIC’s president

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

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

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

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

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

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

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

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

UC adopts recommendations for the responsible use of artificial intelligence

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

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

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

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

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

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

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

Using ultrasound to activate ion channels in brain cells

 

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

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

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

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

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

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

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

A unique system

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

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

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

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

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




 

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Pressure-tailored lithium deposition and dissolution in lithium metal batteries

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

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

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

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




 

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

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

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

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

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

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

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

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

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

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

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

Computer scientists part of NSF grant to make browsers safer

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

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

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

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

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

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

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

 

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

 

Low-performing computer science students face wide array of struggles

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

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

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

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

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

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

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

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

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

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

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

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

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

New Research Center Brings Genomic Medicine to Individuals of Admixed Ancestry

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

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

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

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

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

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

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

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

“To bring the CEGS program to our campus is a huge honor, and a national recognition of UC San Diego as a major player in genomics,” said Lucila Ohno-Machado, MD, PhD, Distinguished Professor of Medicine at UC San Diego School of Medicine, chair of the Department of Biomedical Informatics at UC San Diego Health, and founding faculty of the HalıcıoÄŸlu 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.

ALT TEXT
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.

ALT TEXT
Illustration of the experimental workflow. As a male zebra finch sings his song—which consists of the sequence, "1, 2, 3,"— he thinks about the next syllable he will sing ("4"). The bird’s neural activity is recorded and the local field potentials are extracted. The researchers then analyze features of these signals to predict what syllable the is thinking of singing next.

“Using this system, we’re able to predict with high fidelity the onset of a songbird’s vocal behavior—what sequence the bird is going to sing, and when it is going to sing it,” said Brown.

The researchers can even predict variations in the song sequence, down to the syllable. For example, say the bird’s song is built on a repeating set of syllables, “1, 2, 3, 4,” and every now and then the sequence can change to something like “1, 2, 3, 4, 5,” or “1, 2, 3.” Features in the local field potentials reveal these changes, the researchers found.

“These forms of variation are important for us to test hypothetical speech prostheses, because a human doesn’t just repeat one sentence over and over again,” said Gilja. “It’s exciting that we found parallels in the brain signals that are being recorded and documented in human physiology studies to our study in songbirds.”

Paper: “Local Field Potentials in a Pre-motor Region Predict Learned Vocal Sequences.” Co-authors include Jairo I. Chavez, Derek H. Nguyen, Adam Kadwory, Bradley Voytek and Ezequiel M. Arneodo, UC San Diego.

This work was supported by the National Institutes of Health (R01DC008358, R01DC018055, R01GM134363), the National Science Foundation (BCS-1736028), the Kavli Institute for the Brain and Mind (IRG #2016-004), the Office of Naval Research (MURI N00014-13-1-0205), and the University of California—Historically Black Colleges and Universities Initiative.

Graduate students honored as Siebel Scholars

September 23, 2021-- Five graduate students working at the interface of engineering and medicine have been honored as 2022 Siebel Scholars. They are pursuing graduate degrees in bioengineering, electrical engineering, nanoengineering, and bioinformatics, all with a focus on advancing human health. 

Their research could lead to a human speech prosthesis; understanding the impact of genetic diversity in the immune system on tumor growth; a cell membrane coating technology to better deliver drugs; understanding the pathophysiology of pelvic floor muscle dysfunction after vaginal delivery; and improved early screening for coronary artery disease.

"Wow. This year's Siebel Scholars are all working on exciting projects that truly reflect the Jacobs School's efforts to leverage engineering and computer science to advance medicine and improve human health. The Jacobs School is focused on relevant research projects that lead to positive impacts on the daily lives of people," said Albert P. Pisano, Dean of the UC San Diego Jacobs School of Engineering. “These five outstanding Siebel Scholars have demonstrated not only their academic prowess, but their commitment to sharing their skills and time in service of the next generation of researchers. I am honored to congratulate them.”

The Siebel Scholars program recognizes the most talented students in the world’s leading graduate schools of business, computer science, bioengineering and energy science. The students are selected based on outstanding academic performance and leadership, and each receive a $35,000 award toward their final year of study.

The five UC San Diego 2022 Siebel Scholars are:

 

Daril Brown

Daril Brown is an electrical and computer engineering Ph.D. student under the dual advisement of electrical engineering professor Vikash Gilja and psychology professor Timothy Gentner. His research seeks to establish songbirds as a novel animal model for the development of a human speech prosthesis. Awarded an NSF Graduate Research Fellowship and a UC-HBCU Fellowship, Brown has a unique background having earned his bachelor’s in mechanical engineering from Howard University, and a master’s in bioengineering at UC San Diego. His extensive mentorship efforts across campus, including with the STARS and Academic Connections programs, earned him induction into the Bouchet Honors Society. Many of his mentees have gone on to Ph.D. programs across the country. A three-time UC San Diego Grad Slam finalist, Brown is a strong advocate for science literacy and accessibility, and was recently featured on the KPBS Rad Scientist podcast. Brown plans to forge a career intersecting industry and academia developing translational neurotechnology.

 

 

Andrea Castro

Andrea Castro is a bioinformatics PhD candidate in Hannah Carter’s lab at the UC San Diego School of Medicine. She received her bachelor’s degree in microbiology, immunology, and molecular genetics from UCLA in 2017, and her master’s in computer science from UC San Diego in 2021. Her research involves investigating the relationship between patient genetic diversity in the immune system and tumor evolution; leveraging large-scale genomic, transcriptomic, and proteomic datasets to learn more about immune surveillance and selection on tumors. She is passionate about developing comprehensive bioinformatic methods to improve application of exciting immunotherapy treatments to patients of all tumor types. Castro enjoys mentoring and hopes to help lift up the next generation of diverse scientists.

 

 

Pamela Duran

Pamela Duran received her bachelor’s degree in bioengineering from Universidad Autónoma de Baja California (Tijuana, Mexico), graduating with Honors Distinction. She is currently a bioengineering Ph.D candidate at UC San Diego, co-advised by bioengineering professor Karen Christman and Dr. Marianna Alperin, associate professor of obstetrics, gynecology, and reproductive sciences. Her research focuses on understanding the pathophysiology of pelvic floor muscle dysfunction after vaginal delivery—the leading risk factor for pelvic floor disorders. Her thesis also includes the application of an acellular biomaterial to prevent and treat pathological alterations after birth injury. During her Ph.D, Duran has received a T32 pre-doctoral training in Translational Musculoskeletal Research and an NIH F31 diversity pre-doctoral fellowship. Besides research, she has mentored undergraduate and master’s students and summer students in the STARS program, as well as the ENLACE program, which connects students from the U.S. and Mexico through shared research experiences. Her goal is to pursue a career in academia to develop engineering solutions to advance women’s health and to increase diversity in the STEM field, especially the Hispanic community.

 

Lauren Severance

Lauren Severance is a Ph.D. candidate in the UC San Diego department of bioengineering; she received her bachelor’s in biomedical engineering at Vanderbilt University. Advised by bioengineering professor Elliot McVeigh, she aims to improve early screening for coronary artery disease. Severance’s thesis work is focused on developing novel methods for early coronary artery calcium detection on CT. She has created numerous collaborations with clinicians, geneticists, and epidemiologists, resulting in discovery of a completely novel use for consumer genetic tests in coronary disease screening.She has received an NIH F31 fellowship and recognition from the Society of Cardiovascular Computed Tomography, and her publications have garnered editorial acclaim from leading preventive cardiologists. In addition to research, Severance is passionate about scientific communication and community engagement. She has led several educational outreach projects and serves as a UC San Diego Center for Ethics in Science and Technology student representative.

 

Jiarong Zhou

Jiarong Zhou is a nanoengineering PhD candidate under the guidance of nanoengineering professor Liangfang Zhang. His research focuses on employing cell membrane coating technology to design multivalent nanovaccines against cancer, bacteria, and parasites. Zhou’s work has resulted in numerous peer-reviewed articles and conference presentations. During his time in graduate school, he received a T32 Fellowship from NIH, a scholarship from the ARCS Foundation, and the prestigious Ford Fellowship from the National Academies of Science, Engineering, and Medicine. As a Gordon Scholar, Zhou had an impressive leadership record as an undergraduate, and in his doctoral studies he served as the president of the Jacobs Graduate Student Council and VP Internal of healthcare startup incubator Blue LINC. In the lab, Zhou has mentored several junior graduate and undergraduate students outside of research; his passion and dedication for outreach is evident through his participation in mentorship programs such as JUMP, GradAMP, and Grad Pals.

 

IROS 2021 preview: robotic mapping and manipulation

Sept. 22, 2021-- Researchers at the UC San Diego Contextual Robotics Institute will present three papers at the IROS 2021 conference, which takes place Sept. 27 to Oct. 1, 2021, both online and in person in Prague. 

The papers focus on mapping and exploration for mobile robots and dexterous robotic manipulation. 

Active Exploration and Mapping via Iterative Covariance Regulation over Continuous SE(3) Trajectories

Shumon Koga, Arash Asgharivaskasi, Nikolay Atanasov

This paper develops \emph{iterative Covariance Regulation} (iCR), a novel method for active exploration and mapping for a mobile robot equipped with on-board sensors. The problem is posed as optimal control over the SE(3) pose kinematics of the robot to minimize the differential entropy of the map conditioned the potential sensor observations. Researchers introduce a differentiable field of view formulation, and derive iCR via the gradient descent method to iteratively update an open-loop control sequence in continuous space so that the covariance of the map estimate is minimized. The team demonstrates autonomous exploration and uncertainty reduction in simulated occupancy grid environments.

 https://shumon0423.github.io/IROS2021_webpage/

CORSAIR: Convolutional Object Retrieval and Symmetry-AIded Registration

Tianyu Zhao, Qiaojun Feng, Sai Jadhav, Nikolay Atanasov

This paper considers online object-level mapping using partial point-cloud observations obtained online in an unknown environment. Researchers develop an approach for fully Convolutional Object Retrieval and Symmetry-AIded Registration (CORSAIR). The model extends the Fully Convolutional Geometric Features model to learn a global object-shape embedding in addition to local point-wise features from the point-cloud observations. The global feature is used to retrieve a similar object from a category database, and the local features are used for robust pose registration between the observed and the retrieved object. The formulation also leverages symmetries, present in the object shapes, to obtain promising local-feature pairs from different symmetry classes for matching. Researchers present results from synthetic and real-world datasets with different object categories to verify the robustness of our method.

 https://acsweb.ucsd.edu/~qif007/CORSAIR/

State-Only Imitation Learning for Dexterous Manipulation

Ilija Radosavovic1, Xiaolong Wang2, Lerrel Pinto3, Jitendra Malik1

Modern model-free reinforcement learning methods have recently demonstrated impressive results on a number of problems. However, complex domains like dexterous manipulation remain a challenge due to the high sample complexity. To address this, current approaches employ expert demonstrations in the form of state-action pairs, which are difficult to obtain for real-world settings such as learning from videos. In this paper, researchers move toward a more realistic setting and explore state-only imitation learning. To tackle this setting, the team trained an inverse dynamics model and used it to predict actions for state-only demonstrations. The inverse dynamics model and the policy are trained jointly. The method performs on par with state-action approaches and considerably outperforms RL alone. By not relying on expert actions, researchers are able to learn from demonstrations with different dynamics, morphologies, and objects.

https://people.eecs.berkeley.edu/~ilija/soil/


 

Computer scientists honored for their work discovering that cars are vulnerable to hacking

Stefan Savage, a professor in the UC San Diego Department of Computer Science and Engineering, is part of a team receiving the Golden Goose Award from AAAS. 

September 22, 2021-- Many people think of cars as a series of mechanical parts that — hopefully — work together to   take us places, but that's not the whole story. 

Inside most modern cars is a network of computers, called "electronic control units," that control all the systems and communicate with each other to keep everything rolling smoothly along. 

More than 10 years ago, a team from the  University of California San Diego and University of Washington investigated whether these computing systems could be hacked and how that would affect a driver's ability to control their car. To their own surprise — and to the alarm of car manufacturers — the researchers were able to manipulate the car in many ways, including disabling the brakes and stopping the engine, from a distance. This work led to two scientific papers that opened up a new area of cybersecurity research and served as a wake-up call for the automotive industry. 

Now the team has received the Golden Goose Award from the American Association for the Advancement of Science. The Golden Goose Award recipients demonstrate how scientific advances resulting from foundational research can help respond to national and global challenges, often in unforeseen ways. The award, established in 2012, honors scientific studies or research that may have seemed obscure, sounded “funny,” or for which the results were totally unforeseen at the outset, but which ultimately led, often serendipitously, to major breakthroughs that have had significant societal impact.

"When General Motors started advertising its OnStar service, Yoshi and I had a conversation, saying, 'I bet there's something there,'" Savage said. "Moreover, vulnerabilities in traditional computers had fairly limited impacts. You might lose some data or get a password stolen. But nothing like the visceral effect of a car’s brakes suddenly failing. I think that bridging that gap between the physical world and the virtual one was something that made this exciting for us."The car cybersecurity project was led by Stefan Savage and Tadayoshi Kohno, two professors of computer science at UC San Diego and the University of Washington, respectively. Kohno is a UC San Diego Ph.D. alumnus, receiving his Ph.D. in Computer Science and Engineering in 2006. 

Tadayoshi Kohno, a professor at the University of Washington, co-led the research. 

"More than 10 years ago, we saw that devices in our world were becoming incredibly computerized, and we wanted to understand what the risks might be if they continued to evolve without thought toward security and privacy,” Kohno said. “This award shines light on the importance of being thoughtful and strategic in figuring out what problems to work on today."Savage and Kohno are both computer security researchers who often chatted about potential upcoming threats that could be good to study.

The team’s papers prompted manufacturers to rethink car safety concerns and create new standard procedures for security practices. GM ended up appointing a vice president of product security to lead a new division. The Society for Automotive Engineers (SAE), the standards body for the automotive industry, quickly issued the first automotive cybersecurity standards.  Other car companies followed along, as did the federal government. In 2012, the Defense Advanced Research Projects Agency launched a new government project geared toward creating hacking-resistant, cyber–physical systems. 

"I like to think about what would have happened if we hadn't done this work," Kohno said. "It is hard to measure, but I do feel that neighboring industries saw this work happening in the automotive space and then they acted to avoid it happening to them too. The question that I have now is, as security researchers, what should we be investigating today, such that we have the same impact in the next 10 years?" 

Steve Chekoway (with black mask) and Karl Kosher were the two Ph.D. students on the project, at UC San Diego and UW respectively. 

Discovering vulnerabilities

Savage and Kohno formed a super-team of researchers from both universities. The team purchased a pair of Chevy Impalas — one for each university — to study as a representative car. Researchers worked collaboratively and in parallel, letting curiosity guide them.

The first task was to learn the language the cars' computerized components used to communicate with each other. Then the researchers worked to inject their own voices into the conversation. 

For example, the team started sending random messages to the cars' brake controllers to try to influence them.

"We figured out ways to put the brake controller into this test mode," said Karl Koscher, a research scientist at UW, who also earned his PhD in Seattle. "And in the test mode, we found we could either leak the brake system pressure to prevent the brakes from working or keep the system fully pressurized so that it slams on the brakes."

The team published two papers in 2010 and 2011 describing the results. 

"The first paper asked what capabilities an attacker would have if they were able to compromise one of the components in the car. We connected to the cars' internal networks to examine what we could do once they were hacked," said Stephen Checkoway, an assistant professor of computer science at Oberlin College who completed this research as a UC San Diego doctoral student. "The second paper explored how someone could hack the car from afar."

In these papers, the researchers chose not to unveil that they had used Chevy Impalas, and opted to contact GM privately.

"In our conversations with GM, they were quite puzzled. They said, 'There's no way to make the brake controller turn off the brakes. That's not a thing,'" Savage said. "That Karl could remotely take over our car and make it do something the manufacturer didn't think was possible reflects one of the key issues at play here. The manufacturer was hamstrung because they knew how the system was supposed to work. But we didn't have that liability. We only knew what the car actually did." 

Daniel Anderson, Alexei Czeskis, Brian Kantor, Damon McCoy, Shwetak Patel, Franziska Roesner and Hovav Shacham filled out the rest of the team. This research was funded by the National Science Foundation, the Air Force Office of Scientific Research, a Marilyn Fries endowed regental fellowship and an Alfred P. Sloan research fellowship.

 

 

 

Other award recipients

This year’s two other Golden Goose awards went to Katalin Karikó and Drew Weissman for their role in making mRNA into a medical therapy; and to V. Craig Jordan, who is known for pioneering the scientific principles behind a class of drugs called selective estrogen receptor modulators, or SERMs.

UC San Diego researchers who received the Golden Goose award in the past include Larry Smarr, former director of the California Institute for Telecommunications and Technology and a professor in the Department of Computer Science and Engineering; and Nobel laureate Roger Tsien, a professor of pharmacology, chemistry and biochemistry, who passed away in 2016. 

 

 

 



 

Mosaic ImmunoEngineering Expands Its Modular Vaccine Platform (MVP) Through New Technology Licensing Agreement with the University of California San D

New upgrades to old wireless tech could enable real-time 3D motion capture

September 20, 2021 -- A wireless technology that is helping people find their keys and wallets could one day be used for precise and real-time 3D motion capture, thanks to upgrades developed by electrical engineers at the University of California San Diego. 

The team’s new work improves on a wireless communication technology called ultra-wideband, or UWB. The technology has been around for years, but only recently has UWB started gaining popularity as it promises greater accuracy than Wi-Fi and Bluetooth for determining the location and movement of other devices. 

It also has the potential to open up even bigger possibilities, such as indoor navigation; smart warehouses that provide precise and real-time location of inventory and personnel; and 3D motion capture that can be done wirelessly in real-time for applications such as VR and sports analytics. 

But to get there, several limitations of current UWB technology must be overcome, said Dinesh Bharadia, a professor of electrical and computer engineering and faculty member of the Center for Wireless Communications at the UC San Diego Jacobs School of Engineering. UWB systems need to work much faster than they do now, operate at extremely low power, and provide high accuracy in 3D localization, he explained.

Bharadia’s Wireless Communication Sensing and Networking group recently developed a prototype UWB system that meets these criteria. It communicates data with a latency of just one millisecond; it uses so little power that it can run continuously for more than two years on a small coin cell battery; and it can pinpoint 3D location to within three centimeters for stationary objects, and eight centimeters for moving objects. 

The researchers will present their UWB system, dubbed ULoc, at the UbiComp 2021 conference which will take place virtually from Sept. 21 to 26. 

The new system fundamentally changes the process that UWB systems use to locate an object. UWB systems typically consist of two main components: a small tracking device called a tag, which can be attached to an object, and a set of devices called anchors that are installed at various spots in the environment to detect radio signals from the tag. 

The way UWB tracking currently works is that the tag sends out signals to all the anchors, and the anchors in turn send these signals back to the tag. The system measures the times that it takes for these signals to return to the tag. It then uses this information to calculate the distances between the tag and each anchor, and the tag’s location can then be triangulated.

The problem with this process, explained Bharadia, is that it involves a lot of signal exchanges. One tag needs to send a separate signal to every anchor, and every anchor, in turn, sends a signal back to the tag. “This makes the system slow. It’s not scalable, and it does not provide 3D localization,” said Bharadia.

Person holds a chip, standing in an open room surrounded by four electronic circuit boards.
The new UWB system consists of a small electronic tag (inset shows the size of a tag compared to a U.S. penny) that transmits one signal simultaneously to four anchors.

To simplify this process, the researchers updated the software for the tag so that it only needs to send one signal total to all the anchors. This also drastically reduces the tag’s power use; it can run continuously for more than two years on a small coin cell battery, while current UWB tags can only last for a few months on this type of battery. They also built new anchors that can work with just that one signal and get a good read of the tag’s 3D location. The team developed special antenna arrays and new algorithms that enable the anchors to accurately estimate the 3D angle and direction from which the tag’s signal is arriving. The anchors are able to measure this 3D angle from multiple vantage points so they can locate the tag with precision.

In tests, the new UWB system accurately tracked the 3D location of the tag within a millisecond of latency while one of the researchers was holding it and moving it around an open office space. The researchers point out that the system performed well despite it being in a “noisy” environment—computer screens, glass windows, and metal sheets interfere with UWB signals and create noise.

The team is now working on building an end-to-end motion capture system for applications ranging from VR gaming to sports analytics and autonomous robots for healthcare. The researchers say they are looking to collaborate with industrial partners to further develop and commercialize the technology.

Paper: “ULoc: Low-Power, Scalable and cm-Accurate UWB-Tag Localization and Tracking for Indoor Applications.” Co-authors include Minghui Zhao, Tyler Chang, Aditya Arun, Roshan Ayyalasomayajula, and Chi Zhang, UC San Diego.

Grow and eat your own vaccines?

Grant enables study of plants as mRNA factories

Three Jacobs School undergraduate programs ranked in nation's top 10

Sept. 14, 2021-- Three undergraduate academic programs at the Jacobs School of Engineering were ranked in the top 10 programs for undergraduates in rankings released Sept. 13, 2021 by U.S. News and World Report. 

The biocomputing, bioinformatics and biotechnology program, a multidisciplinary undergraduate offering supported by three UC San Diego divisions, including the Jacobs School of Engineering, was ranked first in the nation. 

The mobile and web applications undergraduate program housed in the Department of Computer Science and Engineering, was ranked number 7. The bioengineering and biomedical undergraduate program was number 8 (the graduate program is ranked third in the nation, according to rankings released in spring 2021).

"These top-ten rankings for our undergraduate programs reflect a much larger trend at the UC San Diego Jacobs School of Engineering. Top-tier research from all six departments at the Jacobs School is continually vitalizing and revitalizing our undergraduate curricula," said Albert P. Pisano, dean of the UC San Diego Jacobs School of Engineering. "This is part of the magic of the Jacobs School."

UC San Diego as a whole ranks as the 8th best public university for undergraduates in the United States. The school also ranks 13th among best colleges for veterans, moving up two spots from last year. Overall, UC San Diego was ranked 34th in the complete list of over 300 private and public undergraduate universities in the nation, jumping one spot from the previous year.

In the undergraduate U.S. News national ranking, the Jacobs School was ranked as the 11th best public engineering school and 19th best overall. The school is also ranked 9th best engineering school in the nation in U.S. News graduate rankings released earlier this year. 

The bioinformatics undergraduate program climbed from second to first place this year. The program is designed to provide career opportunities for bachelor’s graduates. Students graduating from this program are in great demand at top graduate schools, medical schools, and industry. The major is offered in the departments of bioengineering, biology, chemistry and biochemistry, and computer science. The program offers a wide range of opportunities for undergraduate research in many laboratories on campus. 

Ranked 8th in the nation, the undergraduate bioengineering and biomedical program prepares students for a variety of careers in the biomedical device industry and for further education in graduate school. The program addresses the bioengineering topics of biomechanics, biotransport, bioinstrumentation, bioelectricity, biosystems, and biomaterials, and the complementary fields of systems and organ physiology. Education in these areas allows application of bioengineering and scientific principles to benefit human health by advancing methods for effective diagnosis and treatment of disease through development of medical devices and technologies. 

"We in the Department of Bioengineering have a tradition of pushing boundaries in terms of research and educational innovation. Now we have four degree programs (Bioengineering, Biotechnology, Biosystems, Bioinformatics) at the top of our rankings,” said bioengineering department chair Kun Zhang. “We owe our success to the continuous efforts by our faculty, staff and students since 1966, and the strong support by the campus leadership."

In addition to the university’s excellent academic reputation, U.S. News lauded UC San Diego as the No. 26 college in the nation for social mobility for undergraduates. The university has a strong track record of promoting upward social mobility and has committed to remaining accessible to students of all backgrounds. For fall 2021, more than one-third of first-year students and over half of transfer students admitted to UC San Diego will be the first in their family to attend a university. 

Now in its 37th year, the latest edition of the Best Colleges list assesses U.S. bachelor's degree-granting institutions based on 17 measures of academic quality. Ranking factors include graduation and retention rates, faculty resources, social mobility and undergraduate academic reputation, among other measures.

In addition to this latest ranking from U.S. News, UC San Diego is consistently recognized as a leader within various national and global university ranking lists. According to the 2021-2022 U.S. News & World Report survey, UC San Diego Health ranked first in San Diego, placing it among the nation’s best hospitals. Earlier this month, UC San Diego was also named the nation’s third best public university as part of Forbes’ 2021 ranking of top colleges. Additionally, the university ranked eighth among U.S. public universities in the 2021-22 edition of the “Global 2000 List by the Center for World University Rankings.”

To read the complete U.S. News & World Report 2022 Best Colleges rankings, visit the publication’s website. For a complete listing of UC San Diego rankings and accolades, visit the Campus Profile.

 

How a plant virus could protect and save your lungs from metastatic cancer

ALT TEXT
Nanoparticles engineered from the cowpea mosaic virus have shown efficacy in treating and greatly reducing the spread of metastatic cancers in the lungs of mice.

September 14, 2021 -- Using a virus that grows in black-eyed pea plants, nanoengineers at the University of California San Diego developed a new treatment that could keep metastatic cancers at bay from the lungs. The treatment not only slowed tumor growth in the lungs of mice with either metastatic breast cancer or melanoma, it also prevented or drastically minimized the spread of these cancers to the lungs of healthy mice that were challenged with the disease.

The research was published Sept. 14 in the journal Advanced Science.

Cancer spread to the lungs is one of the most common forms of metastasis in various cancers. Once there, it is extremely deadly and difficult to treat.

Researchers at the UC San Diego Jacobs School of Engineering developed an experimental treatment that combats this spread. It involves a bodily injection of a plant virus called the cowpea mosaic virus. The virus is harmless to animals and humans, but it still registers as a foreign invader, thus triggering an immune response that could make the body more effective at fighting cancer.

The idea is to use the plant virus to help the body’s immune system recognize and destroy cancer cells in the lungs. The virus itself is not infectious in our bodies, but it has all these danger signals that alarm immune cells to go into attack mode and search for a pathogen, said Nicole Steinmetz, professor of nanoengineering at UC San Diego and director of the university’s Center for Nano-ImmunoEngineering.

To draw this immune response to lung tumors, Steinmetz’s lab engineered nanoparticles made from the cowpea mosaic virus to target a protein in the lungs. The protein, called S100A9, is expressed and secreted by immune cells that help fight infection in the lungs. And there is another reason that motivated Steinmetz’s team to target this protein: overexpression of S100A9 has been observed to play a role in tumor growth and spread.

“For our immunotherapy to work in the setting of lung metastasis, we need to target our nanoparticles to the lung,” said Steinmetz. “Therefore, we created these plant virus nanoparticles to home in on the lungs by making use of S100A9 as the target protein. Within the lung, the nanoparticles recruit immune cells so that the tumors don’t take.”

“Because these nanoparticles tend to localize in the lungs, they can change the tumor microenvironment there to become more adept at fighting off cancer—not just established tumors, but future tumors as well,” said Eric Chung, a bioengineering Ph.D. student in Steinmetz’s lab who is one of the co-first authors on the paper.

To make the nanoparticles, the researchers grew black-eyed pea plants in the lab, infected them with cowpea mosaic virus, and harvested the virus in the form of ball-shaped nanoparticles. They then attached S100A9-targeting molecules to the surfaces of the particles.

The researchers performed both prevention and treatment studies. In the prevention studies, they first injected the plant virus nanoparticles into the bloodstreams of healthy mice, and then later injected either triple negative breast cancer or melanoma cells in these mice. Treated mice showed a dramatic reduction in the cancers spreading to their lungs compared to untreated mice.

In the treatment studies, the researchers administered the nanoparticles to mice with metastatic tumor in their lungs. These mice exhibited smaller lung tumors and survived longer than untreated mice.

What’s remarkable about these results, the researchers point out, is that they show efficacy against extremely aggressive cancer cell lines. “So any change in survival or lung metastasis is pretty striking,” said Chung. “And the fact that we get the level of prevention that we do is really, really amazing.”

Steinmetz envisions that such a treatment could be especially helpful to patients after they have had a cancerous tumor removed. “It wouldn’t be meant as an injection that’s given to everyone to prevent lung tumors. Rather, it would be given to patients who are at high risk of their tumors growing back as a metastatic disease, which often manifests in the lung. This would offer their lungs protection against cancer metastasis,” she said.

Before the new treatment can reach that stage, the researchers need to do more detailed immunotoxicity and pharmacology studies. Future studies will also explore combining this with other treatments such as chemotherapy, checkpoint drugs or radiation.

Paper: “S100A9-Targeted Cowpea Mosaic Virus as a Prophylactic and Therapeutic Immunotherapy Against Metastatic Breast Cancer and Melanoma.” In addition to Young Hun (Eric) Chung, co-first authors of the study include Jooneon Park and Hui Cai. Nicole Steinmetz serves as the corresponding author of this work.

This work was supported in part by the National Institutes of Health (R01 CA224605, R01 HL137674 and U01-CA218292).

Disclosure: Nicole Steinmetz is a co-founder of and has a financial interest in Mosaic ImmunoEngineering Inc. The other authors declare no conflict of interest.

A new dataset for better augmented and mixed reality

Developed by UC San Diego computer scientists, OpenRooms and associated tools scale up ability to simulate indoor 3D scenes with strong photorealism.

OpenRooms creates photorealistic synthetic scenes from input images or scans, with unprecedented control over shape, materials and lighting.

September 10, 2021-- Computer scientists at the University of California San Diego have released OpenRooms, an new, open source dataset with tools that will help users manipulate objects, materials, lighting and other properties in indoor 3D scenes to advance augmented reality and robotics.

“This was a huge effort, involving 11 Ph.D. and master’s students from my group and collaborators across UC San Diego and Adobe,” said Manmohan Chandraker, a professor in the UC San Diego Department of Computer Science and Engineering. “It is an important development, with great potential to impact both academia and industry in computer vision, graphics, robotics and machine learning.” 

The OpenRooms dataset and related updates are publicly available at this website, with technical details described in an associated paper presented at CVPR 2021 in May.

Applications

OpenRooms lets users realistically adjust scenes to their liking. If a family wants to visualize a kitchen remodel, they can change the countertop materials, lighting or pretty much anything in the room. 

“With OpenRooms, we can compute all the knowledge about the 3D shapes, material and lighting in the scene on a per pixel basis,” said Chandraker. “People can take a photograph of a room and insert and manipulate virtual objects. They could look at a leather chair, then change the material to a fabric chair and see which one looks better.”

OpenRooms can even show how that chair might look in the daytime under natural light from a window or under a lamp at night. It can also help solve robotics problems, such as the best route to take over floors with varying friction profiles. These capabilities are finding a lot of interest in the simulation community because, previously, the data was proprietary or not available with comparable photorealism.

“These tools are now available in a truly democratic fashion,” said Chandraker, “providing accessible assets for photorealistic augmented reality and robotics applications.”

Making Augmented Reality More Real

Chandraker’s team uses computational methods to make sense of the visual world. They are particularly focused on how shapes, materials and lighting interact to form images.

“We essentially want to understand how the world is created, and how we can act upon it,” he said. “We can insert objects into existing scenes or advance self-driving, but to do these things, we need to understand various aspects of a scene and how they interact with each other.”

This deep understanding is essential to achieve photorealism in mixed reality. Inserting an object into a scene requires reasoning about shading from various light sources, shadows cast by other objects or inter-reflections from the surrounding scene. The framework must also handle similar long-range interactions among distant parts of the scene to change materials or lighting in complex indoor scenes. 

Hollywood solves these problems with measurement-based platforms, such as shooting actor Andy Serkis inside a gantry and converting those images into Gollum in the Lord of the Rings Trilogy. The lab wants to achieve similar effects without expensive systems.

Open source toolbox

To get there, the group needed to find creative ways to represent shapes, materials and lighting. But acquiring this information can be time-consuming, data hungry and expensive, especially when dealing with complex indoor scenes featuring furniture and walls that have different shapes and materials and are illuminated by several light sources, such as windows, ceiling lights or lamps.  

“One would have to measure the lighting and material properties at every point in the room,” said Chandraker. “It’s doable but it simply does not scale.”

OpenRooms uses synthetic data to render these images, which provides an accurate and inexpensive way to provide ground truth geometry, materials and lighting. The data can be used to train powerful deep neural networks that estimate those properties in real images, allowing photorealistic object insertion and material editing. 

These possibilities were demonstrated in a CVPR 2020 oral presentation by Zhengqin Li, a fifth-year Ph.D. student advised by Chandraker, and first author on the OpenRooms paper. The software provides automated tools that allow users to take real images and convert them into photorealistic, synthetic counterparts.

“We are creating a framework where users can use their cell phones or 3D scanners for developing datasets that enable their own augmented reality applications,” said Chandraker. “They can simply use scans or sets of photographs.”

Chandraker and team were motivated, in part, by the need to create a public domain platform. Large tech companies have tremendous resources to create training data and other IP, making it difficult for small players to get a foothold.

This was recently illustrated when a Lithuanian company, called Planner 5D, sued Facebook and Princeton, claiming they unlawfully utilized its proprietary data.

“You can imagine such data is really useful for many applications,” said Chandraker. “But progress in this space has been limited to a few big players who have the capacity to do these kinds of complex measurements or work with expensive assets created by artists.”



 

UC San Diego leads a $12.25 million grant to improve epilepsy treatment

September 9, 2021 -- The National Institutes of Health has awarded a $12.25 million grant to the University of California San Diego to develop and enhance brain-sensing and brain-stimulating platform technologies to enable treatment of drug-resistant epilepsy. 

The project is led by UC San Diego electrical engineering professor Shadi Dayeh who leads the Integrated Electronics and Biointerfaces Laboratory and brings together expertise from all across UC San Diego, including the Jacobs School of Engineering and Health Sciences. The nation-wide team includes researchers and longtime collaborators of Dayeh at Massachusetts General Hospital led by Dr. Sydney Cash and Oregon Health & Sciences University led by Dr. Ahmed Raslan.

Epilepsy, a group of neurological disorders characterized by repeated seizures, affects more than 3.4 million people in the U.S. according to the Centers for Disease Control and Prevention (CDC); and nearly one-third of these individuals suffer from poor seizure control even after all current medical therapies are pursued. In these situations, clinicians try to identify the abnormal brain tissue that generates the seizures. Surgeons then target this area for surgical removal, or for implantation of an electrical pulse generator that modifies seizure generation. Current technologies to identify the specific regions in the brain that trigger epileptic seizures – called epileptic foci – are imprecise. Improved mapping of these targets will allow better surgical planning – and more generally – will enhance our understanding of brain physiology.  

Dayeh's work in brain-computer interfaces began when he realized his lab's materials science, device, and integration techniques could allow for sensor grids that offer the tantalizing possibility of providing surgeons with a much clearer picture of the spots in the brain likely initiating the seizures. One of the improvements is an 100-fold increase in the density of sensors embedded within the grids. The new NIH grant will allow the team to expand technical refinement of these higher-density grids and their testing in pigs to the point where they are ready for full-scale clinical trials in people.

"UC San Diego leads the world in neurotechnology development for less invasive brain interfaces," said UC San Diego Chancellor Pradeep K. Khosla. "This new grant affirms the UC San Diego interdisciplinary research approach in which engineers, surgeons, and clinicians and researchers of all stripes engage in sustained research collaborations."

"This grant is a significant win for the campus and the region that will have long-lasting positive impacts," said David Brenner, MD, Vice Chancellor of UC San Diego Health Sciences. "The deep collaborations between neurosurgeons and engineers at UC San Diego will shape the future of medicine for the better."

"The team is making incredible progress on these large, flexible grids of sensors with high sensor density. This combination of attributes has the potential to launch a new era of neurotechnologies for improved patient outcomes. These advances are only possible when engineers intensively collaborate with clinicians, shoulder to shoulder, in order to understand how the technologies are being used in the clinic and how they can be improved," said Albert P. Pisano, Dean of the UC San Diego Jacobs School of Engineering.

Higher resolution recording and stimulation for better diagnosis and treatment

The sensor grids the team plans to test will collect information that is 100 times higher resolution than what is collected in the grids already approved for longer-term use in humans. Both classes of sensor grids function using the same basic principle, though there are important differences. The sensors are embedded in a thin flat material that is placed directly on the surface of the brain in order to record brain activity. Each sensor in the grid records the brain waves being produced by the area of the brain near each sensor.

Illustration of the less invasive wireless sensor grid being developed at UC San Diego
 


Compared to the grids that have already been approved for longer-term use, the new UC San Diego sensor grids have many more sensors per unit of surface area, and the substrate material is more flexible and better conforms to the brain surface, which helps with signal quality. The advances in both the sensor density and the flexibility are thanks to fundamental materials science advances made in Dayeh's lab in the Department of Electrical and Computer Engineering at the UC San Diego Jacobs School of Engineering.

"Materials science and advanced technology integrations are leading to big advances in less invasive sensor technologies which rest on the surface of the brain cortex," said Dayeh. "There is so much potential for materials science to advance clinical medicine, but it needs to be done extremely carefully and the work must engage clinicians and patients as soon as possible. That's what we've been doing, and this grant will allow us to continue this important work."  

The higher density of sensors in the UC San Diego grids means the information about where specific brain activation patterns are originating is more precise. This precision is useful for identifying the spots in the brain that are triggering the seizures. The researchers also believe that the higher resolution information could uncover a much deeper understanding about the origins of epilepsy.

In addition, some of the sensors are also able to gently stimulate the surface of the brain. The new UC San Diego grids can target specific areas for electrical stimulation with greater precision, which allows smaller amounts of electrical stimulation to be used and for that electrical stimulation to be applied with greater precision.

“While we currently have advanced options for patients with epilepsy who do not respond to medication, we are always seeking better options that can improve care,” says Sharona Ben-Haim, MD, neurosurgeon at UC San Diego Health who is a co-investigator on this project. “A more powerful brain sensor may enable neurosurgeons to better identify brain tissue that is causing seizures, and remove this region with greater precision, which may translate to reduced side effects and faster recovery times for patients.”  

The team will also be testing related probes that are inserted down into the cortex, rather than resting on the surface. In some cases, information available from these kinds of "depth probes" is necessary to identify the areas triggering seizures.
 

UC San Diego electrical engineering professor Shadi Dayeh will lead the project. 

With the NIH funding, the team will do the work necessary to show that the UC San Diego sensors are capable of functioning as well, if not better than, approved versions of the sensors. In addition, the team hopes to show that the higher density of sensors and stimulators allows the team to collect new kinds of information – "emerging biomarkers" – that could help identify better ways to diagnose and treat drug-resistant epilepsy.

“This grant demonstrates the power of UC San Diego’s robust neuroscience and engineering ecosystems. Improved temporo-spatial resolution will help usher in a new era for the treatment of neurological disease and provide new insights into the music of the brain,” says co-investigator Alexander Khalessi, MD, MBA, chair of the Department of Neurological Surgery at UC San Diego Health and professor of neurological surgery, radiology and neuroscience at UC San Diego School of Medicine. “In addition to better serving our epilepsy patients, we have the opportunity to leverage materials science and computational power to decode this final frontier of nervous system function.”

A one-month window

The grant is designed to fund the efforts necessary to advance the safety and efficacy testing of the UC San Diego grids to the point where the next step is full-scale clinical trials in which the sensor grids are implanted for up to 30 days.

These grids have already been used to safely record signals from the surfaces of human brains, for short periods of time, during surgeries in which a portion of the skull was already going to be temporarily removed.

The one-month window is important because people with drug-resistant epilepsy typically need to be monitored with implanted brain sensors for at least two weeks in order to collect the best data for determining what regions in the brain are triggering the seizures.

"We've been fortunate to collaborate with neurosurgeons at UC San Diego, Massachusetts General Hospital, and Oregon Health & Sciences University in order to demonstrate that our high-density grids are safe and effective in humans for short periods of time," said Dayeh. "This NIH BRAIN Initiative grant will allow us to keep advancing this work to the point that we are ready for clinical trials where the sensor grids are implanted for much longer periods of time in people. I’m thrilled that we'll have the opportunity to do this work as a community here at UC San Diego, and with our external partners."

A broader view of brain activity at high resolution

In addition, the UC San Diego grids can be printed in formats that are significantly larger than the grids being developed elsewhere, similar in area coverage to those currently used in the clinic, but with a much higher sensor density. The team is planning to print and test grids that are about six centimeters by six centimeters offering 4,096 sensor channels plus 256 electrical-stimulation channels. This is compared to only 36 sensor channels and 36 electrical-stimulation channels in commercial grade grids – with a similar surface area – that are now being used in the clinic.

With this combination of higher resolution, broader coverage, and longer-use times the researchers hope that future generations of these sensor grids will eventually be useful in applications well beyond drug-resistant epilepsy. The high-resolution information coming from larger regions of the surface of the brain, for example, could be incorporated into future generations of brain-computer interfaces designed to help people with severe paralysis communicate and control prostheses.

Interrelated projects funded by the grant to build an advanced Epilepsy Monitoring System

The grant also includes funding for engineers at the UC San Diego Jacobs School of Engineering to lead multiple efforts needed to make the device wireless and make it clinically viable. This includes the wireless transfer of data and the energy necessary to power the implanted components of the device, and the software display of the high channel count recording.  

The grant also includes funding for sustained conversation and dialog that includes researchers from multiple fields, patients, patient advocates, and bioethicists.

In parallel, UC San Diego is planning to build up capacity for good manufacturing practice (GMP) medical device manufacturing on campus. The larger goal is to be able to manufacture sensor grids on campus that are cleared for use in clinical trials.

These efforts position UC San Diego as a national and global leader in neurotechnology for less invasive brain interface technologies.

The project, officially entitled "Thin, High-Density, High-Performance, Depth and Surface Microelectrodes for Diagnosis and Treatment of Epilepsy" is supported through the National Institutes of Health’s Brain Research Through Advancing Innovative Neurotechnologies (BRAIN) Initiative under award number UG3NS123723.

Funding is contingent on milestones and is made through the NIH's Brain Research Through Advancing Innovative Neurotechnologies (BRAIN) Initiative, part of a large effort among federal and non-federal partners to use knowledge about how the brain works to develop more effective therapies for neurological disorders.


Collaborators

UC San Diego
Eric Halgren, Departments of Radiology and Neurosciences
Gert Cauwenberghs, Department of Bioengineering
Gal Mishne, Department of Computer Science and Engineering
Peter Asbeck, Department of Electrical and Computer Engineering
Mark Stambaugh, Qualcomm Institute
Sharona Ben-Haim, Jerry Shih, David Barba, Alexander Khalessi, Department of Neurological Surgery
Xinlian Zhang, Family Med And Public Health
Michael Kalichman, Research Ethics Program

Massachusetts General Hospital
Sydney Cash, Angelique Paulk, Department of Neurology
Ziv Williams, Robert Richardson, Functional Neurosurgery

Oregon Health & Sciences University
Ahmed Raslan, Department of Neurological Surgery
Ilker Yaylali, David Spencer,  Department of Neurology

Previous Funding

Dayeh has developed early generation of the sensors with the support of a 2019 NIH Director’s New Innovator Award (1DP2EB029757-01), a 2017 NSF Scalable Nanomanufacturing Award (No. 1728497), and a 2014 NSF CAREER Award (No. 1351980). In addition, Dayeh and colleagues – including his longtime collaborator and mentor Eric Halgren – have received support from the KAVLI Institute for Brain and Mind, the Qualcomm Institute, and together with Dr. Ben-Haim, the three received support from UC San Diego's Altman Clinical and Translational Research Institute (ACTRI) and Institute of Engineering in Medicine (IEM) for a GEM award, an AIM award from the OIC, and private donors.

According to Dayeh, the team's technology integration work is at the core of the BRAIN Initiative vision “to discover how dynamic patterns of neural activity are transformed into cognition, emotion, perception, and action in health and disease” (BRAIN 2025 Report)

UC San Diego researchers make glycomics data AI-ready

With systems biology approach, researchers enable big-data glycomics that will open new paths from glycomics data sets to clinical breakthroughs and cancer diagnosis

September 8, 2021: Researchers at the University of California San Diego have created a tool that allows glycomics datasets to be analyzed using explainable Artificial Intelligence (AI) systems and other machine learning approaches. In a recent paper published in Nature Communications, the team demonstrated that glycomics data require extra care to be properly used for statistical analysis or machine learning. They also offer a new preprocessing solution to prepare glycomics data to substantially boost the power of its use with machine learning and AI. They named the approach GlyCompare. It takes a systems level perspective that accounts for shared biosynthetic pathways of glycans within and across samples.

To introduce GlyCompare, the team demonstrated their ability to enhance comparisons of glycomics datasets by shining light on the hidden relationships between glycans in several contexts, including gastric cancer tissues. Cancer is a useful example given the importance of glycan changes to cancer and its utility for early-stage diagnosis.

"We applied GlyCompare to cancer tissues and showed that while one couldn't find cancer specific glycans using standard statistical methods, novel biomarkers emerge when processed using our method," said UC San Diego professor of Bioengineering and Pediatrics Nathan Lewis, who is the corresponding author on the paper. Lewis Co-Directs the CHO Systems Biology Center, and glycoengineered CHO cell lines were used to produce diverse proteins used in the study.

In another analysis, the team showed the method substantially boosts statistical power, such that one needs half as many samples to get equivalent power to detect biomarkers. In the paper, the researchers outline how the methods behind GlyCompare will be transformative for bringing glycomics to the clinic. In fact, Lewis is part of the founding team of a new start-up that is licensing related intellectual property to commercialize this technology for high value applications, including cancer diagnostics.

One of the keys to the GlyCompare approach is that it looks at the biological steps needed to synthesize the subunits that make up glycans, rather than just looking at only the whole glycans themselves, greatly improving the accuracy of statistical analyses of glycomics data. The researchers believe this approach will enable the detection of more subtle changes in glycosylation in many applications, including early stage cancer. Moreover, GlyCompare could lead to new insights on the mechanisms behind the observed changes in glycans that are present.  

Bokan Bao and Benjamin P. Kellman, the co-first-authors on the paper, are both in the Bioinformatics and Systems Biology Graduate Program, and members of the Department of Bioengineering at the UC San Diego Jacobs School of Engineering.

Paper title
Correcting for sparsity and interdependence in glycomics by accounting for glycan biosynthesis

Funding
This work was conducted with support from the Novo Nordisk Foundation provided to the Technical University of Denmark (NNF10CC1016517, NNF20SA0066621: N.E.L.), NIGMS (R35 GM119850: N.E.L.), NICHD (R21 HD080682: L.B.), and USDA (USDA/ARS 6250-6001; M.W.H.).

GlyCompare on GitHub

Author Affiliations

Department of Pediatrics, UC San Diego Health
Bokan Bao, Benjamin P. Kellman, Austin W. T. Chiang, Yujie Zhang, James T. Sorrentino, Austin K. York, Lars Bode & Nathan E. Lewis

Bioinformatics and Systems Biology Graduate Program, UC San Diego
Bokan Bao, Benjamin P. Kellman & James T. Sorrentino

Department of Bioengineering, UC San Diego Jacobs School of Engineering Bokan Bao, Benjamin P. Kellman, James T. Sorrentino & Nathan E. Lewis

The Novo Nordisk Foundation Center for Biosustainability at UC San Diego
Austin W. T. Chiang & Nathan E. Lewis

Department of Pediatrics, Children’s Nutrition Research Center, US Department of Agriculture/Agricultural Research Service, Baylor College of Medicine, Houston, TX, USA
Mahmoud A. Mohammad & Morey W. Haymond

 



 

These fridge-free COVID-19 vaccines are grown in plants and bacteria

Two hands wearing blue gloves touch one plant in a tray of small plants.

September 7, 2021 -- Nanoengineers at the University of California San Diego have developed COVID-19 vaccine candidates that can take the heat. Their key ingredients? Viruses from plants or bacteria.

The new fridge-free COVID-19 vaccines are still in the early stage of development. In mice, the vaccine candidates triggered high production of neutralizing antibodies against SARS-CoV-2, the virus that causes COVID-19. If they prove to be safe and effective in people, the vaccines could be a big game changer for global distribution efforts, including those in rural areas or resource-poor communities.

“What’s exciting about our vaccine technology is that is thermally stable, so it could easily reach places where setting up ultra-low temperature freezers, or having trucks drive around with these freezers, is not going to be possible,” said Nicole Steinmetz, a professor of nanoengineering and the director of the Center for Nano-ImmunoEngineering at the UC San Diego Jacobs School of Engineering.

The vaccines are detailed in a paper published Sept. 7 in the Journal of the American Chemical Society.

The researchers created two COVID-19 vaccine candidates. One is made from a plant virus, called cowpea mosaic virus. The other is made from a bacterial virus, or bacteriophage, called Q beta.

Both vaccines were made using similar recipes. The researchers used cowpea plants and E. coli bacteria to grow millions of copies of the plant virus and bacteriophage, respectively, in the form of ball-shaped nanoparticles. The researchers harvested these nanoparticles and then attached a small piece of the SARS-CoV-2 spike protein to the surface. The finished products look like an infectious virus so the immune system can recognize them, but they are not infectious in animals and humans. The small piece of the spike protein attached to the surface is what stimulates the body to generate an immune response against the coronavirus.

The researchers note several advantages of using plant viruses and bacteriophages to make their vaccines. For one, they can be easy and inexpensive to produce at large scales. “Growing plants is relatively easy and involves infrastructure that’s not too sophisticated,” said Steinmetz. “And fermentation using bacteria is already an established process in the biopharmaceutical industry.”

Another big advantage is that the plant virus and bacteriophage nanoparticles are extremely stable at high temperatures. As a result, the vaccines can be stored and shipped without needing to be kept cold. They also can be put through fabrication processes that use heat. The team is using such processes to package their vaccines into polymer implants and microneedle patches. These processes involve mixing the vaccine candidates with polymers and melting them together in an oven at temperatures close to 100 degrees Celsius. Being able to directly mix the plant virus and bacteriophage nanoparticles with the polymers from the start makes it easy and straightforward to create vaccine implants and patches. 

The goal is to give people more options for getting a COVID-19 vaccine and making it more accessible. The implants, which are injected underneath the skin and slowly release vaccine over the course of a month, would only need to be administered once. And the microneedle patches, which can be worn on the arm without pain or discomfort, would allow people to self-administer the vaccine.

“Imagine if vaccine patches could be sent to the mailboxes of our most vulnerable people, rather than having them leave their homes and risk exposure,” said Jon Pokorski, a professor of nanoengineering at the UC San Diego Jacobs School of Engineering, whose team developed the technology to make the implants and microneedle patches.

“If clinics could offer a one-dose implant to those who would have a really hard time making it out for their second shot, that would offer protection for more of the population and we could have a better chance at stemming transmission,” added Pokorski, who is also a founding faculty member of the university’s Institute for Materials Discovery and Design.

In tests, the team’s COVID-19 vaccine candidates were administered to mice either via implants, microneedle patches, or as a series of two shots. All three methods produced high levels of neutralizing antibodies in the blood against SARS-CoV-2.

Potential pan-coronavirus vaccine

These same antibodies also neutralized against the SARS virus, the researchers found.

It all comes down to the piece of the coronavirus spike protein that is attached to the surface of the nanoparticles. One of these pieces that Steinmetz’s team chose, called an epitope, is almost identical between SARS-CoV-2 and the original SARS virus.

“The fact that neutralization is so profound with an epitope that’s so well conserved among another deadly coronavirus is remarkable,” said co-author Matthew Shin, a nanoengineering Ph.D. student in Steinmetz’s lab. “This gives us hope for a potential pan-coronavirus vaccine that could offer protection against future pandemics.”

Another advantage of this particular epitope is that it is not affected by any of the SARS-CoV-2 mutations that have so far been reported. That’s because this epitope comes from a region of the spike protein that does not directly bind to cells. This is different from the epitopes in the currently administered COVID-19 vaccines, which come from the spike protein’s binding region. This is a region where a lot of the mutations have occurred. And some of these mutations have made the virus more contagious.

Epitopes from a nonbinding region are less likely to undergo these mutations, explained Oscar Ortega-Rivera, a postdoctoral researcher in Steinmetz’s lab and the study’s first author. “Based on our sequence analyses, the epitope that we chose is highly conserved amongst the SARS-CoV-2 variants.”

This means that the new COVID-19 vaccines could potentially be effective against the variants of concern, said Ortega-Rivera, and tests are currently underway to see what effect they have against the Delta variant, for example.

Plug and play vaccine

Another thing that gets Steinmetz really excited about this vaccine technology is the versatility it offers to make new vaccines. “Even if this technology does not make an impact for COVID-19, it can be quickly adapted for the next threat, the next virus X,” said Steinmetz.

Making these vaccines, she says, is “plug and play:” grow plant virus or bacteriophage nanoparticles from plants or bacteria, respectively, then attach a piece of the target virus, pathogen, or biomarker to the surface.

“We use the same nanoparticles, the same polymers, the same equipment, and the same chemistry to put everything together. The only variable really is the antigen that we stick to the surface,” said Steinmetz.

The resulting vaccines do not need to be kept cold. They can be packaged into implants or microneedle patches. Or, they can be directly administered in the traditional way via shots.

Steinmetz and Pokorski’s labs have used this recipe in previous studies to make vaccine candidates for diseases like HPV and cholesterol. And now they’ve shown that it works for making COVID-19 vaccine candidates as well.

Next steps

The vaccines still have a long way to go before they make it into clinical trials. Moving forward, the team will test if the vaccines protect against infection from COVID-19, as well as its variants and other deadly coronaviruses, in vivo.

Paper: “Trivalent subunit vaccine candidates for COVID-19 and their delivery devices.” Co-authors include Angela Chen, Veronique Beiss, Miguel A. Moreno-Gonzalez, Miguel A. Lopez-Ramirez, Maria Reynoso and Joseph Wang, UC San Diego; Hong Wang and Brett L. Hurst, Utah State University.

This work was funded in part by a National Science Foundation both through a RAPID grant (CMMI-2027668) and through the UC San Diego Materials Research Science and Engineering Center (MRSEC, grant DMR-2011924).

Disclosure: Nicole Steinmetz and Jon Pokorski are co-founders of and have a financial interest in Mosaic ImmunoEngineering Inc. All other authors declare no competing interests.

UC San Diego nanoengineers receive $2.7M NSF grant to make battery manufacturing waste-free

September 1, 2021 -- A team led by nanoengineers at the University of California San Diego has been awarded a $2.7 million grant from the National Science Foundation to develop an eco-friendly and low-cost manufacturing process for sodium all-solid-state batteries. The process will be used to create large-scale energy storage systems—for buildings, electric grids, and wind and solar farms—that are more efficient, affordable and safe.

“In order for our society to shift to more renewable energy sources, we need technology that will enable rechargeable batteries with high safety, low cost, long life and high resilience to environmental changes,” said Zheng Chen, a professor of nanoengineering at the UC San Diego Jacobs School of Engineering and the project’s lead investigator.

“Today’s lithium-ion batteries can no longer meet these requirements because of the safety issues associated with flammable liquid electrolytes and scaling challenges for critical materials—cobalt, nickel and lithium—that are typically used for making them. So we are working to improve the production of a promising alternative: sodium all-solid-state batteries.”

The goal of the project is to help transform sodium all-solid-state battery manufacturing into an efficient and eco-friendly process. These batteries are of great interest to scientists because they are made using low-cost transition metals such as chromium, manganese and iron. This overcomes the critical materials limitation facing lithium-ion batteries. In addition, the all-solid-state architecture is intrinsically safer and can employ multi-layer stacking to achieve higher system-level energy densities. These features make the batteries desirable for emerging large-scale storage applications.

To improve today’s sodium all-solid-state battery manufacturing processes, Chen and colleagues will develop a dry fabrication technology that eliminates the use of caustic organic solvents. The technology will also recycle materials from used batteries to create new battery materials—specifically electrodes and solid-state electrolytes—that perform the same as the originals. The result will be a process that is closed-loop, high-precision and high-yield.

“This project assembles expertise in chemical engineering, nanoengineering, chemistry, materials science, life-cycle analysis/technoeconomic analysis, machine learning and data science, as well as collaborators in community colleges and industry to develop new fabrication processes, advanced materials and new battery protypes that can potentially be used for a wide range of large-scale storage systems,” said Chen, who is also a faculty member of the Sustainable Power and Energy Center at the UC San Diego Jacobs School of Engineering.

The research team includes UC San Diego nanoengineering professors Ying Shirley Meng, Andrea Tao and Shyue Ping Ong, who are all faculty members of the university’s Sustainable Power and Energy Center and Institute for Materials Discovery and Design, and Elsa Olivetti, a professor of materials science and engineering at MIT.

Computer science students qualify for programming World Finals

August 31, 2021--A team of UC San Diego computer science students has qualified to compete in the World Finals of the International Collegiate Programming Contest (ICPC), the world’s preeminent programming and coding competition. The students clinched a spot when they placed sixth in the ICPC North American Championship in August 2021.

Computer science PhD student Zihan Wang, master’s student Shuxin Chen, and undergraduate Haihao Sun will represent UC San Diego at the World Final, tentatively scheduled for March 2022. 

During an ICPC competition, teams of three students are given a set of 10 to 13 algorithmic programming problems. They have five hours, and one computer, to solve as many problems as they can in the shortest amount of time. 

(l-r) Computer science students Zihan Wang, Shuxin Chen and Haihao Sun will represent UC San Diego at the ICPC World Finals in March 2022.

“It really has some strategy to it,” said Wang. “We have to divide the problems amongst ourselves and find the most useful problem for each person to work on. And we need to help each other debug; some people may be even better at debugging than at other types of problems. And there’s just one computer so we also need to divide the time, since some people may need to brute force code, and others may need to use their time to debug their code, so we need to plan it out.”

Though the North American Championships were held remotely, removing some element of that strategy since all three team members had access to a computer, the students say the competitions are both exciting and nerve-racking. 

“This competition is rewarding and very exciting,” said Wang. “In our mind this kind of competitive programming is really like a sports competition. We’re very excited, our main goal is to get the highest rank we can.”

The students train together every week, allotting three to five hours to work through a sample problem set similar to what they might encounter in a competition. At UC San Diego, there is an ICPC club, where as many as 20 students will participate weekly in these practice sessions. The club holds selection contests to help students form teams, and decide which teams will get to compete at various challenges. 

While some members of the ICPC club are competitive programmers, like Wang, Chen and Sun, many others use the practice problems as a way to strengthen their programming skills for internship or job interviews. During club meetings, there are always problems at a variety of skill levels, to support both groups of participants. 

“The skills I’ve picked up in the competition have helped me learn programming and development skills very quickly,” said Sun. “As a participant in ICPC, I think I’ve learned to write code and debug more quickly than other people.”

Wang said having this student club as a resource is hugely beneficial; many schools don’t have an ICPC club, and students are left to find their own teammates, register for competitions and train on their own. Having an organized structure to facilitate these connections not only gives the students more time to actually train, but also helps foster a tighter community. 

“The community at UC San Diego really is a great community which cultivates a lot of great engineers, great problem solvers,” said Sun.

Jingbo Shang, a professor in the Department of Computer Science and Engineering and the Halicioglu Data Science Institute, joined the leadership of the campus ICPC club in 2020. Since then, he’s also begun offering a for-credit computer science course-- Introduction to Programming Contests-- to help support students wanting to improve these skills. 

“ICPC has long been regarded as a competition of the world’s smartest collegiate computer programmers,” said Shang. “The World Finals sets the stage for the world’s smartest trophy."

Studies highlight benefit of spatial visualization app in bridging critical STEM education gap

A student uses the Spatial Vis app on a tablet. Photos by David Baillot/UC San Diego.

August 30, 2021--Software developed by engineering professors at UC San Diego has improved spatial visualization—a critical skill in STEM careers—in students in high school and college courses, both in person and remotely. 

Two publications presented at the July 2021 American Society of Engineering Education Annual Conference highlighted the Spatial Vis app’s success in the remote learning environment necessitated by COVID-19, and among high school students. 

Spatial visualization, the ability to think in three dimensions, is critical in Science, Technology, Engineering, and Math (STEM) careers, from Computer-Aided-Design in engineering to using ultrasound for medical procedures. As this New York Times piece points out, this concept is often missing from K-16 curricula and as a result, the skill is underdeveloped in many students. To address this issue, two engineering faculty at the Jacobs School of Engineering at UC San Diego developed the Spatial Vis software to teach students how to sketch 2D projections and 3D shapes. The touchscreen app provides automatic grading and personalized feedback. The immediate feedback creates much higher student engagement than the traditional approach of sketching on paper and waiting days for a grade.

The app is produced by eGrove Education Inc., which was co-founded by Nathan Delson, a UC San Diego mechanical engineering teaching professor, and Lelli Van Den Einde, a fellow UC San Diego structural engineering teaching professor. 

At the ASEE conference, Van Den Einde and Delson presented findings that detail the success of the app in improving students’ spatial visualization skills. They measure this by having the students take a standardized spatial visualization test before using the Spatial Vis app, and then again after using the app. Students whose pre-test score is 70% or below are categorized as “at-risk” for low graduation rates in future STEM programs. 

In their study of two high school classes, results showed that students in this at-risk group improved their test score by 15.6% after using the Spatial Vis app. Even more significant is that 60% of all of the low-performing students moved out of the at-risk category on their post-test scores, making them more likely to persist in STEM careers. Not only did their skills improve, but so did their confidence; 42% of students reported their spatial visualization skills were “very good” or “good” before using the app, while 90% of the high school students said they felt their skills were “very good” or “good” after using the app. 

The second paper, on the Suitability of Spatial Visualization Training for Remote Learning,  compared in-person use of the Spatial Vis app before COVID-19 with the experience using it during remote learning due to the pandemic, in freshman engineering graphics courses at two universities. Among college students, there was a correlation between the measured student persistence and gains in spatial visualization ability. These gains occurred both before and during COVID, though the gains were slightly less significant during COVID.

In one course, using Spatial Vis improved student scores especially among students who were deemed at-risk based on their spatial visualization standardized test before taking the course.  In the first class, at-risk students’ test scores improved 18.9% in 2019 and 11.3% in 2020. Of those low performing students students, 48.8% in 2019 and 35.7% in 2020 moved out of the at-risk category, making them more likely to persist in STEM careers.The second class had at-risk score improvements of 22.3% in 2019 and 22.2% in 2020 with 78.4% (2019) and 69.2% (2020) of these initially low-performing students moving out of the at-risk category on their post-test scores.

While the cause of the slight decrease in score improvement during 2020 is unknown, the researchers speculate it could be attributed to overall lower engagement due to the challenging environment as courses transitioned to emergency remote instruction at the start of the pandemic. Still, the app led to marked improvements in students’ spatial visualization skills, and teachers noticed the benefits of the teaching tool, too. 

“During COVID, we had high school and middle school teachers reaching out to us to provide experiences that students could engage with remotely,” said Van Den Einde. “Now that classes are returning to in-person education the teachers are interested in continuing to use Spatial Vis since they saw how its use increased persistence and self-regulated learning among their students.”

A student and a teaching assistant use the Spatial Vis app in class.

Sketching has a long history in education, and is used for communication and creativity in many STEM fields. The physical act of freehand sketching has been shown to increase spatial visualization skills, and its benefits are supported by the NSF-funded Engage Engineering initiative. Improvement of these skills has significantly increased retention in STEM for women and other underrepresented minorities. These prior studies were based on sketching on paper, which can be laborious to grade and do not provide real time feedback to the student. Spatial Vis’ digital platform, with automatic grading and personalized feedback, aims to change that.

In 2019, this UC San Diego spinoff received a $750,000 Small Business Innovation Research (SBIR) Phase II grant from the National Science Foundation to develop the app. Van Den Einde and Delson co-founded eGrove Education, Inc. to commercialize the Spatial Vis software and make it available to educational institutions worldwide.


To learn more about Spatial Vis please visit www.egrove.education

Jacobs School welcomes 27 new faculty

      

The University of California San Diego Jacobs School of Engineering is proud to introduce the 27 new professors hired in 2020 and 2021. These professors are among the nearly 140 faculty who have joined the UC San Diego Jacobs School of Engineering in the last eight years.

These new faculty and the bold research they pursue will further the Jacobs School’s mission of leveraging engineering and computer science for the public good. 

“It’s my great honor to welcome these engineers, computer scientists, educators and researchers to the Jacobs School of Engineering community,” said Albert P. Pisano, Dean of the Jacobs School. “We are a young, powerful school because we have added cohort after cohort of energetic, imaginative, bold new faculty. I am very much looking forward to seeing the impact they will make.”

These faculty join a school on the rise; the, UC San Diego Jacobs School of Engineering jumped to the #9 spot in the influential U.S. News and World Report Rankings of Best Engineering Schools in March 2020, and twelve months later, despite the headwinds, held that position. 

2021 New Faculty PDF

Jacobs School new faculty

BIOENGINEERING

Brian Aguado, Assistant Professor

Aguado’s goal is to develop precision biomaterials that enable the evaluation of a patient's unique biology to diagnose and treat a variety of health disorders as a function of sex, age, and/or ancestry. Specifically, Aguado aims to develop sex-specific biomaterial technologies to treat cardiovascular diseases, including aortic valve disease and heart failure.

Previously: Postdoctoral Fellow, University of Colorado at Boulder

Ph.D.: Northwestern University

 

Andrew Bartko, Professor of Practice

Bartko’s goal is to inspire, nurture, and sustain vibrant collaborations between UC San Diego’s microbiome experts and industry partners in the life science, nutrition, energy, information technology, clinical and healthcare industries. Specifically, Bartko aims to focus on creating and commercializing innovative technologies to accelerate microbiome discoveries and healthcare breakthroughs across academic and industry collaborations.

Previously: Research Leader, Battelle 

Ph.D.: Georgia Institute of Technology

 

Bogdan Bintu, Assistant Professor

Bintu develops new microscopy tools that can simultaneously “see” thousands of DNA sequences, RNA molecules and proteins in individual cells. He uses these tools to understand how neurons specialize within the olfactory nervous system.

Previously: Ph.D. Candidate, Harvard University

Ph.D.: Harvard University


Benjamin Smarr, Assistant Professor

Smarr’s research focuses on time series analysis in biological systems, with an emphasis on practical information extraction for translational applications. His main project is TemPredict, which brings together wearable device data from 50K people with over 2 million daily symptom reports and is used to identify signs of COVID-19 onset, progression, and recovery.

Previously: Postdoctoral Fellow, UC Berkeley

Ph.D.: University of Washington

 

COMPUTER SCIENCE AND ENGINEERING

Mai ElSherief, Assistant Teaching Professor

ElSherief uses computational and data science problems that model online social interactions to infer and understand online misuse behaviors and psychological well-being. Her other research interests include social computing, natural language processing, machine learning, and communication.

Previously: Postdoctoral Fellow, Georgia Institute of Technology

Ph.D.: UC Santa Barbara 

 

Carlos Jensen, Associate Vice Chancellor, Educational Innovation

Jensen’s research lies at the intersection between usability and software engineering, with an emphasis on studying how Open Source communities operate and organize, and the tools and processes needed to make them more efficient. His recent work uses automated testing techniques to help developers improve the reliability of large and complex open source software.

Previously: Associate Dean, Oregon State University

Ph.D.: Georgia Institute of Technology

 

Tzu-Mao Li, Assistant Professor

Li connects classical computer graphics and image processing algorithms with modern data-driven methods to facilitate physical exploration. His work added 3D understanding to computer vision models; used data to improve camera imaging pipeline quality; and made light transport simulation faster by using information implicitly defined by rendering programs.

Previously: Postdoctoral Researcher, UC Berkeley and MIT

Ph.D.: Massachusetts Institute of Technology


Imani Munyaka, Assistant Professor

Munyaka is a human-centered computing researcher. Her research interests include public policy, information security, computer science education, educational technologies, voting technologies, cybersecurity and minorities in STEM. Her goal is to improve and alleviate the security and privacy concerns of those most vulnerable.

Previously: Ph.D. Candidate, University of Florida

Ph.D.: University of Florida

 

Kristen Vaccaro, Assistant Professor

Vaccaro focuses on how to design machine learning systems to give users a sense of agency and control. She found that some existing ways of providing control for social media can function as placebos, increasing user satisfaction even when they do not work. She will help develop systems to give users control and oversight, and ethical guidelines and policies.

Previously: Research assistant, University of Illinois at Urbana-Champaign

Ph.D.: University of Illinois at Urbana-Champaign

 

Rose Yu, Assistant Professor

The goal of Yu’s research is to advance machine learning and enable interpretable, efficient and robust large-scale spatiotemporal reasoning. Her work has been successfully applied to solve challenging domain problems in sustainability, health and physical sciences.

Previously: Assistant professor, Northeastern University

Ph.D.: University of Southern California

 

ELECTRICAL AND COMPUTER ENGINEERING

Nick Antipa, Assistant Professor

Antipa’s research aims to develop design frameworks that merge optical models with algorithms, allowing optimization of both components and enabling the development of cutting-edge imaging and display systems. By considering both the hardware and digital domains, new computational optical systems emerge that extend capability beyond what is available.

Previously: Ph.D. Candidate, UC Berkeley

Ph.D.: UC Berkeley

 

Mingu Kang, Assistant Professor

Kang researches vertically-integrated VLSI information processing for machine learning and signal processing algorithms. His research focuses on energy- and latency-efficient integrated circuits, architectures and systems by leveraging novel computing paradigms including in-memory, in-sensor and neuromorphic computing with both CMOS and emerging devices.

Previously: Research Scientist, IBM Research

Ph.D: University of Illinois at Urbana-Champaign

 

Florian Meyer, Assistant Professor

Meyer researches statistical signal processing for navigation, mapping and multiobject tracking in applications including maritime situational awareness, autonomous driving, and indoor localization. He investigates efficient and scalable high-dimensional nonlinear estimation using graphical models where the number of states to be estimated may also be unknown.

Previously: Postdoctoral Fellow and Associate, MIT

Ph.D.: Vienna University of Technology

 

Karcher Morris, Assistant Teaching Professor

Morris’s teaching aims to embed project-based learning throughout the undergraduate electrical and computer engineering curriculum, complementing theoretical foundations. By connecting students with application-oriented coursework and industry-relevant challenges, Morris promotes an early engagement between students and their research/industry goals.

Previously: Ph.D. Candidate, UC San Diego

Ph.D.: UC San Diego

 

Yuanyuan Shi, Assistant Professor

Shi's research interests are in the area of energy systems and cyber-physical systems, spanning from machine learning to optimization and control. She works on data-driven control for complex networked systems and market mechanism design under multi-agent learning dynamics.

Previously: Postdoctoral Researcher, Caltech

Ph.D: University of Washington

 

Yatish Turakhia, Assistant Professor

Turakhia develops algorithms and hardware accelerators to enable faster and cheaper progress in biology and medicine. He also develops computational methods that enable biological discoveries, such as new genotype-phenotype relationships.

Previously: Postdoctoral Researcher, UC Santa Cruz

Ph.D.: Stanford University

 

Yang Zheng, Assistant Professor

Zheng develops methods and frameworks for the optimization and control of network systems and their applications to cyber-physical systems, especially autonomous vehicles and traffic systems. His goal is to develop computationally efficient and distributed solutions for large-scale network systems by exploring and exploiting real-world system structures.

Previously: Postdoctoral Researcher, Harvard

Ph.D.: University of Oxford

 

MECHANICAL AND AEROSPACE ENGINEERING

Sylvia Herbert, Assistant Professor

Herbert focuses on developing new techniques for safety and efficiency in autonomous systems. She has developed methods for scalable safety and real-time decision making that draw from control theory, cognitive science and reinforcement learning, which are backed by both rigorous theory and physical testing on robotic platforms.

Previously: Graduate Researcher, UC Berkeley

Ph.D.: UC Berkeley

 

Patricia Hidalgo-Gonzalez, Assistant Professor

Hidalgo-Gonzalez focuses on high penetration of renewable energy using optimization, control theory and ML. She co-developed a power system expansion model for Western North America’s grid under climate change uncertainty.  She is interested in power dynamics, energy policy, electricity market redesign, and learning for dynamical systems with safety guarantees.

Previously: Ph.D. Candidate, UC Berkeley

Ph.D: UC Berkeley

 

Stephanie Lindsey, Assistant Professor

Lindsey’s work lies at the interface of fluid mechanics, numerical analysis and cardiovascular developmental biology. She seeks to determine causal-effect relationships for the creation of cardiac malformations and address important challenges in clinical treatment of congenital heart defects through a combined computational-experimental approach.

Previously: Postdoctoral Researcher, Stanford University

Ph.D.: Cornell University

 

Marko Lubarda, Assistant Teaching Professor

Lubarda is dedicated to engineering pedagogy and enriching students' learning experiences through curriculum design, teaching innovations and support of undergraduate student research. He works in the areas of computational analysis, engineering mathematics, materials science, solid mechanics, device physics, and magnetic nanotechnologies.

Previously: Assistant Professor, University of Donja Gorica, Montenegro

Ph.D.: UC San Diego

 

Lonnie Petersen, Assistant Professor

Dr. Petersen is a physician scientist specializing in space and aviation physiology and development of countermeasure devices for use in space. During the COVID-19 pandemic, she co-lead a team that developed a low-cost, easy-to-use ventilator and other ways to support critically ill COVID19 patients and mitigate the spread of disease.

Previously: Postdoctoral Researcher, UC San Diego School of Medicine

Ph.D.: University of Copenhagen

 

Lisa Poulikakos, Assistant Professor

Poulikakos harnesses nanophotonics, the study and manipulation of light on the nanoscale, to bridge engineering and biomedicine. The resulting in-vivo and ex-vivo nanophotonic probes aim to elucidate the origin and propagation of a range of diseases, leading to low-cost medical diagnostics; rapid, on-chip biochemical drug testing; or in-situ biomedical imaging.

Previously: Postdoctoral Researcher, Stanford University

Ph.D.: ETH Zurich

 

Aaron Rosengren, Assistant Professor

Rosengren conducts fundamental and applied research in astrodynamics, space situational awareness and space traffic management to define perennial, ad-hoc practices and policies to make space a sustainable resource. His contributions are in the fields of celestial mechanics and nonlinear dynamics, with a strong focus on space debris and small Solar-System bodies.

Previously: Assistant Professor, University of Arizona

Ph.D.: University of Colorado, Boulder

 

Jon Wade, Professor of Practice

Wade’s objective is to ensure that the research conducted and the curriculum developed in systems engineering has the greatest impact on addressing the critical challenges that face our global society and nation. He leads research in the area of complex, evolving systems engineering methods, processes, tools, and education.

Previously: Research Professor, Stevens Institute of Technology

Ph.D: Massachusetts Institute of Technology

 

NANOENGINEERING

Zeinab Jahed, Assistant Professor

Jahed designs electronics that integrate intelligently with biological systems at the nanoscale. She designs non-invasive and high-throughput bio-electronic tools to record and manipulate biological activities and uses AI and ML techniques to interpret the large data sets from these nano-bio-electronic tools to answer important biological questions.

Previously: Postdoctoral Researcher, Stanford University

Ph.D.: UC Berkeley

 

STRUCTURAL ENGINEERING

Georgios Tsampras, Assistant Professor

Tsampras’ research goal is to improve the seismic response and simplify the lifetime management of structures and civil infrastructures. He conducts integrated experimental and analytical research on components, connections, and systems that enhance the safety and reliability of structures and civil infrastructures against earthquakes.

Previously: Falcon Vehicle Structures Engineer, SpaceX

Ph.D.: Lehigh University

 

ANTHROPOLOGY, PERFORMANCE, and TECHNOLOGY PROGRAM

Hortense Gerardo, Director

The Anthropology, Performance, and Technology (APT) program at the Jacobs School of Engineering aims to empower a new generation of socially-engaged, culturally relevant, and artistically as well as scientifically and technically creative engineers. Gerardo, a playwright with a PhD in anthropology and performance studies, directs the program.

 Previously: Associate Professor of Anthropology and Performing Arts, Lassell College

Ph.D.: Boston University

 

This technology could bring the fastest version of 5G to your home and workplace

UC San Diego engineers developed a system that enables millimeter wave signals to overcome blockages while providing high throughput

ALT TEXT
UC San Diego electrical and computer engineering Ph.D. student Ish Jain poses with the new millimeter wave setup that he developed. The setup improves the throughput and reliability of millimeter wave signals.

August 23, 2021 -- Consumers of today’s 5G cellphones may have experienced one of the following tradeoffs: impressive download speeds with extremely limited and spotty coverage, or widespread and reliable coverage with speeds that aren’t much faster than today’s 4G networks.

A new technology developed by electrical engineers at the University of California San Diego combines the best of both worlds and could enable 5G connectivity that is ultra-fast and reliable at the same time.

The team will present their work at the ACM SIGCOMM 2021 conference which will take place online Aug. 23 to 27.

The technology presents a solution to overcome a roadblock to making high band 5G practical for the everyday user: the speedy wireless signals, known as millimeter waves, cannot travel far and are easily blocked by walls, people, trees and other obstacles.

Today’s high band 5G systems communicate data by sending one laser-like millimeter wave beam between a base station and a receiver—for example, a user’s phone. The problem is if something or someone gets in the way of that beam’s path, then the connection gets blocked completely.

“Relying on a single beam creates a single point of failure,” said Dinesh Bharadia, a professor of electrical and computer engineering at the UC San Diego Jacobs School of Engineering, who is the senior author on the ACM SIGCOMM paper.

Two beams are better than one

Bharadia and his team, who are part of the UC San Diego Center for Wireless Communications, came up with a clever solution: split the one laser-like millimeter wave beam into multiple laser-like beams, and have each beam take a different path from the base station to the receiver. The idea is to improve the chances that at least one beam reaches the receiver when an obstacle is in the way.

ALT TEXT
Experimental setup of the multi-beam millimeter wave system.

The researchers created a system capable of doing this and tested it inside an office and outside a building on campus. The system provided a high throughput connection (up to 800 Mbps) with 100% reliability, which means that the signal didn’t drop or lose strength as the user moved around obstacles like desks, walls and outdoor sculptures. In outdoor tests, the system provided connectivity up to 80 meters (262 feet) away.

To create their system, the researchers developed a set of new algorithms. One algorithm first instructs the base station to split the beam into multiple paths. Some of these paths take a direct shot from the base station and the receiver; and some paths take an indirect route, where the beams bounce off what are called reflectors—surfaces in the environment that reflect millimeter waves like glass, metal, concrete or drywall—to get to the receiver. The algorithm then learns which are the best paths in the given environment. It then optimizes the angle, phase and power of each beam so that when they arrive at the receiver, they combine constructively to create a strong, high quality and high throughput signal.

With this approach, more beams result in a stronger signal.

“You would think that splitting the beam would reduce the throughput or quality of the signal,” Bharadia said. “But with the way that we’ve designed our algorithms, it turns out mathematically that our multi-beam system gives you a higher throughput while transmitting the same amount of power overall as a single-beam system.”

The other algorithm maintains the connection when a user moves around and when another user steps in the way. When these happen, the beams get misaligned. The algorithm overcomes this issue by continuously tracking the user’s movement and realigning all the beam parameters.

ALT TEXT
Hardware of the multi-beam millimeter wave system.

The researchers implemented their algorithms on cutting-edge hardware that they developed in the lab. “You don’t need any new hardware to do this,” said Ish Jain, an electrical and computer engineering Ph.D. student in Bharadia’s lab and the first author of the paper. “Our algorithms are all compliant with current 5G protocols.”

The hardware consists of a small base station and receiver. The base station is equipped with a phased array that was developed in the lab of UC San Diego electrical and computer engineering professor Gabriel Rebeiz, who is an expert in phased arrays for 5G and 6G communications and is also a member of the university’s Center for Wireless Communications.

The team is now working on scaling their system to accommodate multiple users.

More information can be found on the project’s website: https://wcsng.ucsd.edu/mmreliable/

Paper: “Two beams are better than one: Towards Reliable and High Throughput mmWave Links.” Co-authors include Raghav Subbaraman, UC San Diego.

This work is supported by the National Science Foundation (grant 1925767).

Researchers develop first steerable catheter for brain surgery

August 18, 2021-- A team of engineers and physicians has developed a steerable catheter that for the first time will give neurosurgeons the ability to steer the device in any direction they want while navigating the brain’s arteries and blood vessels. The device was inspired by nature, specifically insect legs and flagella--tail-like structures that allow microscopic organisms such as bacteria to swim.  

The team from the University of California San Diego describes the breakthrough in the Aug. 18 issue of Science Robotics

The steerable catheter was successfully tested in pigs at the Center for the Future of Surgery at UC San Diego. 

Approximately one in 50 people in the United States has an unruptured intracranial aneurysm--a thin-walled, blister-like lesion on a cerebral artery that is prone to rupture. These kinds of lesions affect over 160 million people worldwide, half of them under the age of 50. Of patients that suffer ruptured aneurysms, more than half die. Half of the survivors experience long-term disabilities. Studies show that a quarter of cases cannot be operated on because of how difficult the aneurysms are to reach. 

“As a neurosurgeon, one of the challenges that we have is directing catheters to the delicate, deep recesses of the brain,” said Dr. Alexander Khalessi, chair of the Department of Neurological Surgery at UC San Diego Health. “Today’s results demonstrate proof of concept for a soft, easily steerable catheter that would significantly improve our ability to treat brain aneurysms and many other neurological conditions, and I look forward to advancing this innovation toward patient care.”

A view of the steerable catheter, right, and how it navigates a brain blood vessel (insert on the left). 

The current state of the art in aneurysm surgery involves neurosurgeons inserting guidewires into an artery near the groin to take catheters through the aorta and all the way up into the brain. Surgeons use curved-tip guidewires to navigate the brain's arteries and junctions. But these guidewires have to be removed before the catheter’s tip can be used to provide treatment.

 “Once the guidewire is retrieved the catheter will return to its native shape, often straight, resulting in loss of access to the pathology,” said Dr. Jessica Wen, who was instrumental in serving as a bridge between clinicians and engineers, and coordinated work with the Center for the Future of Surgery at UC San Diego.

As a result, it is extremely difficult to place and keep it in the right position to release platinum coils that block blood flow to the aneurysm and prevent a brain bleed.  

Steerable catheters are not available for neurosurgery because of how small the brain's blood vessels are. Specifically, devices need to be less than one millimeter in diameter--that’s roughly the diameter of a few human hairs--and about five feet long (160 cm). Industrial fabrication methods struggle at this scale. That’s partially because gravity, electrostatics, and the van der Waals force are all similar at this size. So once you pick something up with tweezers, you cannot drop it. If you coax it from the tweezers, it may leap into the air from opposing forces and disappear, never to be found again. 

“Unfortunately, many of the most important blood vessels we need to treat are among the most tortuous and fragile in the body,” said James Friend, a professor at the UC San Diego Jacobs School of Engineering and School of Medicine and the paper’s corresponding author. “Although robotics is rising to the need in addressing many medical problems, deformable devices at the scales required for these kinds of surgeries simply do not exist.”

Bioinspiration

To solve this problem, researchers turned to inspiration both from nature and from soft robotics.

“We were inspired by flagella and insect legs, as well as beetles mating, where microscale hydraulics and large aspect deformation are involved,” said Gopesh Tilvawala, who recently earned a Ph.D. in Friend’s research group and the paper’s first author. “This led us to developing [a] hydraulically actuated soft robotic microcatheter.”

Computer simulations and new fabrication methods

A steerable catheter allows surgeons to deliver therapies, in this case platinum coils that block blood flow to an  aneurysm, in the deepest recess of the brain. 

The team had to invent a whole new way of casting silicone in three dimensions that would work at those scales, by depositing concentric layers of silicone on top of one another with different stiffnesses. The result is a silicone rubber catheter with four holes inside its walls, each about one half the diameter of a human hair. 

The team also conducted computer simulations to determine the configuration of the catheter; how many holes it should include; where these should be placed; and the amount of hydraulic pressure needed to actuate it. To guide the catheter, the surgeon compresses a handheld controller to pass saline fluid into the tip to steer it. Saline is used to protect the patient; if the device should fail, then saline harmlessly enters the bloodstream. The catheter’s steerable tip is visible on X-rays. 

A new way of doing neurosurgery

A fluoroscopic image of the steerable catheter navigating a brain artery in a pig and deploying coils. 

The work is poised to make a significant difference in the way aneurysm surgery is conducted, physicians said. “This technology is ideal for situations when I need to make a 180 degree turn from the catheter position in the parent artery, and maintaining position and reducing kick-out is critical,” said Dr. David Santiago-Dieppa, neurosurgeon at UC San Diego Health. “This advance may ultimately allow us to treat aneurysms, other brain pathologies and even strokes that we haven’t been able to in the past.”

“This type of precision can be realized with steerable tools and the successful deployment of these tools should move us forward in permitting improved access, decreased procedural time, better capacity utilization, decreased radiation exposure and other related and expected benefits,” said Dr. Alexander Norbash, chair of the Department of Radiology at UC San Diego Health. 

The next steps include a statistically significant number of animal trials and first in human trial. 

The work was funded by the American Heart Association, the American-Australian Association Sir Keith Murdoch Scholarship, UC San Diego’s Galvanizing Engineering in Medicine program, the Chancellor's Research Excellence Scholarship, and the National Institutes of Health. 

 

Ultrasound remotely triggers immune cells to attack tumors in mice without toxic side effects

August 12, 2021 -- Bioengineers at the University of California San Diego have developed a cancer immunotherapy that pairs ultrasound with cancer-killing immune cells to destroy malignant tumors while sparing normal tissue.

The new experimental therapy significantly slowed down the growth of solid cancerous tumors in mice.

The team, led by the labs of UC San Diego bioengineering professor Peter Yingxiao Wang and bioengineering professor emeritus Shu Chien, detailed their work in a paper published Aug. 12 in Nature Biomedical Engineering.

The work addresses a longstanding problem in the field of cancer immunotherapy: how to make chimeric antigen receptor (CAR) T-cell therapy safe and effective at treating solid tumors.  

CAR T-cell therapy is a promising new approach to treat cancer. It involves collecting a patient’s T cells and genetically engineering them to express special receptors, called CAR, on their surface that recognize specific antigens on cancer cells. The resulting CAR T cells are then infused back into the patient to find and attack cells that have the cancer antigens on their surface.

This therapy has worked well for the treatment of some blood cancers and lymphoma, but not against solid tumors. That’s because many of the target antigens on these tumors are also expressed on normal tissues and organs. This can cause toxic side effects that can kills cells—these effects are known as on-target, off-tumor toxicity.

“CAR T cells are so potent that they may also attack normal tissues that are expressing the target antigens at low levels,” said first author Yiqian (Shirley) Wu, a project scientist in Wang’s lab.

“The problem with standard CAR T cells is that they are always on—they are always expressing the CAR protein, so you cannot control their activation,” explained Wu.

To combat this issue, the team took standard CAR T cells and re-engineered them so that they only express the CAR protein when ultrasound energy is applied. This allowed the researchers to choose where and when the genes of CAR T cells get switched on.

“We use ultrasound to successfully control CAR T cells directly in vivo for cancer immunotherapy,” said Wang, who is a faculty member of the Institute of Engineering in Medicine and the Center for Nano-ImmunoEngineering, both at UC San Diego. What’s exciting about the use of ultrasound, noted Wang, is that it can penetrate tens of centimeters beneath the skin, so this type of therapy has the potential to non-invasively treat tumors that are buried deep inside the body.

The team’s approach involves injecting the re-engineered CAR T cells into tumors in mice and then placing a small ultrasound transducer on an area of the skin that’s on top of the tumor to activate the CAR T cells. The transducer uses what’s called focused ultrasound beams to focus or concentrate short pulses of ultrasound energy at the tumor. This causes the tumor to heat up moderately—in this case, to a temperature of 43 degrees Celsius (109 degrees Fahrenheit)—without affecting the surrounding tissue. The CAR T cells in this study are equipped with a gene that produces the CAR protein only when exposed to heat. As a result, the CAR T cells only switch on where ultrasound is applied.

The researchers put their CAR T cells to the test against standard CAR T cells. In mice that were treated with the new CAR T cells, only the tumors that were exposed to ultrasound were attacked, while other tissues in the body were left alone. But in mice that were treated with the standard CAR T cells, all tumors and tissue expressing the target antigen were attacked.

“This shows our CAR T-cell therapy is not only effective, but also safer,” said Wu. “It has minimal on-target, off-tumor side effects.”

The work is still in the early stages. The team will be performing more preclinical tests and toxicity studies before it can reach clinical trials.

###

Paper: “Control of the activity of CAR-T cells within tumours via focused ultrasound.” Co-authors include Yahan Liu, Ziliang Huang, Xin Wang, Jiayi Li, Linshan Zhu, Molly Allen, Yijia Pan, Robert Bussell, Aaron Jacobson, Thomas Liu and Shu Chien, UC San Diego; Zhen Jin, Shanghai Jiao Tong University, China; and Praopim Limsakul, Prince of Songkla University, Thailand.

This work was supported in part by the National Institutes of Health (grants HL121365, GM125379, GM126016, CA204704 and CA209629).

Disclosure: Peter Yingxiao Wang is scientific co-founder of and has financial interest in Cell E&G Inc. and in Acoustic Cell Therapy Inc., a company that aims to license the technology for further development. These financial interests do not affect the design, conduct or reporting of this research.

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New tool enables mapping of protein interaction networks at scale

Visualization of a protein-protein interaction network identified using PROPER-seq.

August 3, 2021-- Proteins—long chains of amino acids—each play a unique role in keeping our cells and bodies functioning, from carrying out chemical reactions, to delivering messages, and protecting us from potentially harmful foreign invaders. More recent research has shown that these proteins not only serve their individual purpose, but also interact with other proteins to carry out even more numerous and complex functions through these protein-protein interactions (PPI).

Collectively, all the protein-protein interactions in a cell form a PPI network. Experimentally identifying a PPI network within human cells has required a tremendous amount of time and resources, with experiments required to identify every individual PPI, and many additional experiments to investigate these protein pairs for network-level interactions.

Now, bioengineers at the University of California San Diego have developed a technology capable of revealing the PPIs among thousands of proteins, in a single experiment. The tool, called PROPER-seq (protein-protein interaction sequencing), allows researchers to map the PPI network from their cells of interest within several weeks, without any specialized resources such as antibodies or premade gene libraries.

The researchers describe this technology in Molecular Cell on August 3. They applied PROPER-seq on human embryonic kidney cells, T lymphocytes, and endothelial cells, and identified 210,518 PPIs involving 8,635 proteins.

"PROPER-seq is capable of scanning the order of 10,000×10,000 protein pairs in one experiment," said Kara Johnson, a recent UC San Diego bioengineering Ph.D. alumna and the first author of this paper. The research was conducted in bioengineering professor Sheng Zhong’s lab.

The central idea of PROPER-seq is to label every PPI with a unique DNA sequence, and then read these DNA sequence labels through next-generation sequencing. To implement this idea, Zhong's team developed a technique called SMART-display, which attaches a unique DNA barcode to every protein. They also devised a method called "Incubation, ligation and sequencing" (INLISE) to sequence the pair of DNA barcodes that are attached to two interacting proteins. The third component of PROPER-seq is a software package called PROPERseqTools, that incorporates statistical tools to identify the PPIs from the DNA sequencing data. This trio of tools—SMART-display, INLISE, and PROPERseqTools—together is known as PROPER-seq.

A further breakdown of these three components of PROPERseq is available in this blog post.

A laboratory would start the PROPER-seq protocol with their cells of interest, and obtain the output as a list of identified PPIs. The user can also get the DNA sequence read counts and other statistics associated with every identified PPI.

Zhong's team applied PROPER-seq on human embryonic kidney cells, T lymphocytes, and endothelial cell,s and obtained 210,518 PPIs involving 8,635 proteins. The team created a public database with a web interface to download, search, and visualize these PPIs (https://genemo.ucsd.edu /proper).

A graphical abstract of the three tools that together are known as PROPER-seq.

The team validated the PROPER-seq-identified PPIs (called PROPER v1.0) with previously characterized PPIs documented in PPI databases. The team found more than 1,300 and 2,400 PPIs in PROPER v1.0 are supported by previous co-immunoprecipitation experiments and affinity purification-mass spectrometry experiments, respectively.

The team experimentally validated four PROPER-seq identified PPIs that have not been reported in the literature. These four PPIs involve PARP1, a critical protein for DNA repair and a drug target of several human cancers, and four other proteins involved in the trafficking of molecules and transcription regulation. These validations suggest mechanistic links between PARP1 and import/export of molecules to/from the nucleus as well as gene transcription.

Their results show that PROPER v1.0 overlaps with more than 17,000 computationally predicted PPIs without prior experimental validation. The experimental support offered by PROPER-seq to these previously uncharacterized PPIs suggests the solid predictive ability of protein structure-based computational models.

The team found PROPER v1.0 overlaps with one hundred synthetic lethal (SL) gene pairs. An SL gene pair can cause cell death when both genes of this gene pair are lost. This finding suggests a connection between physical interactions (PPIs) and human genetic interactions.

Looking forward, the team hopes PROPER-seq can assist researchers in screening many protein pairs and identify PPIs of interest. In addition, the PROPER-seq identified PPIs from different labs can expand the PPI networks' reference maps and illuminate cell-type-specific PPIs.  

###

Other major contributors to this work include UC San Diego bioengineering Ph.D. student Zhijie Qi, bioengineering postdoc alumna Zhangmin Yan, and bioinformatics and systems biology Ph.D. student Xingzhao Wen, who carried out protein network analysis. Professor Zhen Chen at City of Hope collaborated with Zhong’s team on validation of PROPER-seq identified PPIs.  

This work is supported by the National Institutes of Health, and the Ella Fitzgerald Charitable Foundation.

Lipomi named new Faculty Director of IDEA Engineering Student Center

Darren Lipomi, professor of nanoengineering and faculty director of the IDEA Engineering Student Center

August 2, 2021--NanoEngineering Professor Darren Lipomi has been named the new Faculty Director of the IDEA Engineering Student Center at the UC San Diego Jacobs School of Engineering. His appointment began July 1, 2021. 

The IDEA Engineering Student Center-- where IDEA stands for Inclusion, Diversity, Excellence, and Achievement--has supported thousands of UC San Diego engineering and computer science students through to graduation in the 10 years since its founding. The Center offers programs including summer prep and mentorship programs, peer-led engineering learning communities, support for student diversity organizations, community and culture-building efforts and more. 

The IDEA Engineering Student Center’s mission is to support all students on the challenging path of an engineering and computer science education at UC San Diego, with specific programs that build community, and provide academic and peer support for students traditionally underrepresented in the engineering and computer science fields including Black, Latinx and Native American students, women, first-generation college students, LGBTQ+ students, and low-income students.

“I am incredibly excited for this opportunity,” said Lipomi. "My family didn’t have a lot of money when I was growing up. My dad didn’t go to college, and I am the only scientist or engineer in my immediate or extended family. I owe a great deal to student services offices like the IDEA Center, and am especially grateful to them for the role they played in introducing me to undergraduate research.”

Lipomi has been involved with the IDEA Center in various roles since he joined UC San Diego in 2012, including organizing 36 seminars in the Graduate and Postdoc Scholarly Talk Series.

"I always derive such energy from working with our engineering students. I’m especially excited by the opportunity to engage with our students on social media, and to help in their transition to learning on campus, full time, this fall."

Olivia Graeve, professor of mechanical and aerospace engineering, and outgoing faculty director of the IDEA Center.

Lipomi will build on the momentum and achievements that the IDEA Engineering Student Center has made over the last six years under the leadership of Mechanical and Aerospace Engineering Professor Oliva Graeve. 

“I am incredibly grateful to Professor Graeve for her vision and leadership, and I am proud of the entire IDEA Engineering Student Center team,” said Albert P. Pisano, Dean of the Jacobs School of Engineering. “Their collective efforts have propelled the IDEA Center to new heights, directly benefiting our students.”

Some of the accomplishments of the IDEA Center under Graeve’s leadership are outlined on IDEA’s 10th year anniversary website and in the Center's annual reports

At the Jacobs School, Lipomi is known for his ability to create inclusive research and learning environments for his students inside and outside the lab. In 2017, he received a campus Diversity Champion award. He has extended his ability to facilitate important STEM conversations and empower young researchers across the nation and around the world through his podcast, which is called "Molecular Podcasting with Darren Lipomi." Many of his podcast episodes relate directly or indirectly to equity, diversity and inclusion. 

In terms of research, Lipomi is a world leader in thin film electronic materials, whose applications include solar energy and artificial touch. Like many high-impact engineering professors, he engages in the virtuous cycle between fundamental and applied research. He is the recipient of the Air Force Young Investigator Award, the NIH Director’s New Innovator Award, and the Presidential Early Career Award for Scientists and Engineers (PECASE).

“Together, we are working harder than ever to make the Jacobs School a place where all students, staff and faculty have the resources, support, and community connections inside and outside the classroom that empower them to succeed and thrive,” said Pisano. “Please join me in welcoming Professor Lipomi to the position of Faculty Director, and in thanking Professor Graeve for all her work and accomplishments in this role.”

NSF makes $20 Million investment in Optimization-focused AI Research Institute led by UC San Diego

The Institute will pursue foundational breakthroughs at the nexus of artificial intelligence and optimization to transform chip design, robotics, and communication networks.

The National Science Foundation (NSF) announced today an investment of $220 million to establish 11 artificial intelligence (AI) institutes, each receiving $20 million over five years. One of these, The Institute for Learning-enabled Optimization at Scale (TILOS), will be led by the University of California San Diego in partnership with the Massachusetts Institute of Technology; San Diego-based National University; the University of Pennsylvania; the University of Texas at Austin; and Yale University. TILOS is also partially supported by Intel Corporation.

“These institutes are hubs for academia, industry and government to accelerate discovery and innovation in AI," said National Science Foundation Director Sethuraman Panchanathan. "Inspiring talent and ideas everywhere in this important area will lead to new capabilities that improve our lives ... and position us in the vanguard of competitiveness and prosperity.” 

"As a global society, we can't afford to allow advances in optimization to be underutilized," said UC San Diego Chancellor Pradeep K. Khosla. "The TILOS team is made of an incredible combination of engineers, computer scientists, data scientists and educators who will tackle the hardest theoretical and applied challenges in optimization through virtuous feedback loops that ensure the advances will make a positive difference in the real world."

Learning-enabled optimization

“Optimization is a universal quest: we are driven to do better,” said Andrew Kahng, a computer science and electrical engineering professor at the UC San Diego Jacobs School of Engineering and TILOS director. “Optimization is also a hard problem, as the number of choices explodes in large-scale systems. The TILOS mission is to make today’s impossible optimizations possible, at scale and in practice. Whether for energy-efficiency, safety, robustness or other criteria, improved optimizations have the potential to bring incalculable benefits to society.”

Optimization is a fundamental component of machine learning, an important area of modern AI. Conversely, learning can help solve difficult optimization problems. Foundational research in TILOS will explore this interplay to develop optimization methods that can change the leading edge of real-world practice. In close collaboration with industry partners, institute researchers will develop learning-enabled optimization tools for application areas of strategic importance to the United States, including chip design, robotics, and communication networks.

Fundamental and applied research

"Optimization is both a science and a technology,” commented Rajesh K. Gupta, director of the Halicioglu Data Science Institute, UC San Diego’s campus hub for data science that will house TILOS. “This new AI institute will not only discover new science at the interface of AI and optimization, but also deliver it to real-world practitioners as a technology: measuring it to improve it, with benchmarking and a roadmap of progress.”

Foundational research will drive important applications. In chip design, these advances would dramatically shorten the time needed to design chips, increasing quality, productivity and innovation in the process. In robotics, optimization breakthroughs would improve the way robots learn and interact with humans and other robots in many contexts, including search and rescue, autonomous transportation, and warehouses. In communication networks, better optimization would lead to more capable and efficient power grids, mobile phones, and ecosystems within the Internet of Everything.  

Data and insights from optimization in these application areas will further inspire and challenge fundamental research efforts in AI and optimization. This virtuous cycle in TILOS will accelerate the pace of discovery and translation into the leading edge of practice.

Education and workforce development

The TILOS research will engage undergraduates, graduate students and post-doctoral researchers at every step. In addition, the TILOS team has planned a broad program for workforce development, which will identify and teach new practical skills and mindsets that emerge from fundamental and applied advances in optimization. The team is building an openly accessible program of continuing education with long-term, lifelong learning and skills renewal as its central tenet.

Broadening participation

TILOS programming will extend beyond the classroom, with embodied robot demonstrations, community art installations, and portable, adaptable “outreach in a box” modules to engage and excite a next generation of learners. These initiatives aim to grow awareness of, and access to, new career and educational opportunities -- especially among students who are traditionally underrepresented in engineering.

"Many meaningful and rewarding career opportunities will emerge at the nexus of AI, optimization, and application domains. As a team, we will pursue basic research, translate our results into industrial practice, train the future workforce, and bring awareness of the broader educational and job opportunities that result from advances in AI and optimization," said Kahng. 

 

Learn more:

TILOS website

NSF Invests $20M in UC San Diego-headquartered Artificial Intelligence (AI) Research Institute

Robotics researchers at UC San Diego key part of new NSF AI Institute

NSF Invests $20M in UC San Diego-headquartered Artificial Intelligence (AI) Research Institute

Training Computers To Transfer Music From One Style To Another

July 23, 2021

UC San Diego music and computer science professor Shlomo Dubnov (right) with co-author and high school student Conan Lu (far left), with fellow COSMOS student: mapping the architecture of a machine learning tool to transfer one sample of music from one style to another.

Can artificial intelligence enable computers to translate a musical composition between musical styles – e.g., from pop to classical or to jazz? According to a professor of music and computer science at UC San Diego and a high school student, they have developed a machine learning tool that does just that.

“People are more familiar with machine learning that can automatically convert an image in one style to another, like when you use filters on Instagram to change an image’s style,” said UC San Diego computer music professor Shlomo Dubnov, who is an affiliate faculty member in the Computer Science and Engineering department. “Past attempts to convert compositions from one musical style to another came up short because they failed to distinguish between style and content.”

To fix that problem, Dubnov and co-author Conan Lu developed ChordGAN – a conditional generative adversarial network (GAN) architecture that uses chroma sampling, which only records a 12-tones note distribution note distribution profile to separate style (musical texture) from content (i.e., tonal or chord changes).

“This explicit distinction of style from content allows the network to consistently learn style features,” noted Lu, a senior from Redmond High School in Redmond, Washington, who began developing the technology in summer 2019 as a participant in UC San Diego’s California Summer School for Mathematics and Science (COSMOS). Lu was part of the COSMOS “Music and Technology” cluster taught by Dubnov, who also directs the Qualcomm Institute’s Center for Research in Entertainment and Learning (CREL).

On July 20, Dubnov and Lu will present their findings in a paper* to the 2nd Conference on AI Music Creativity (AIMC 2021). The virtual conference – on the theme of “Performing [with] Machines” – takes place June 18-22 via Zoom. The conference is organized by the Institute of Electronic Music and Acoustics at the University of Music and Performing Arts in Graz, Austriaia from June 18-22.

After attending the COSMOS program in 2019 at UC San Diego, Lu continued to work remotely with Dubnov through the pandemic to jointly author the paper to be presented at AIMC 2021.

For their paper, Dubnov and Lu developed a data set comprised of a few hundred MIDI audio-data samples from pop, jazz and classical music styles. The MIDI files were pre-processed to turn the audio files into piano roll and chroma formats – training the network to convert a music score.

“One advantage of our tool is its flexibility to accommodate different genres of music,” explained Lu. “ChordGAN only controls the transfer of chroma features, so any tonal music can be given as input to the network to generate a piece in the style of a particular musical style.

To evaluate the tool’s success, Lu used the so-called Tonnetz distance to measure the preservation of content (e.g., chords and harmony) to ensure that converting to a different style would not result in losing content in the process.

“The Tonnetz representation displays harmonic relationships within a piece,” noted Dubnov. “Since the main goal of style transfer in this method is to retain the main harmonies and chords of a piece while changing stylistic elements, the Tonnetz distance provides a useful metric in determining the success of the transfer.”

The measure at left extracted from a pop piece and transferred into the classical network, which generated the measure at right. While harmonic structure remains constant within the measure, salient changes in note rendering are present in the classical style.

The researchers also added an independent genre classifier (to evaluate that the resulting style transfer was realistic). In testing the accuracy of their genre classifier, it functioned best on jazz clips (74 percent accuracy), and only slightly less well on pop music (68 percent) and classical (64 percent). (While the original evaluation for classical music was limited to Bach preludes, subsequent testing with classical compositions from Haydn and Mozart also proved effective.)

“Given the success of evaluating ChordGAN for style transfer under our two metrics,” said Lu, “our solution can be utilized as a tool for musicians to study compositional techniques and generate music automatically from lead sheets.”

The high school student’s earlier research on machine learning and music earned Lu a bronze grand medal at the 2021 Washington Science and Engineering Fair. That success also qualified him to compete at the Regeneron International Science and Engineering Fair (ISEF), the largest pre-collegiate science fair in the world. Lu became a finalist at ISEF and received an honorable mention from the Association for the Advancement of Artificial Intelligence.

 

*Lu, C. and Dubnov, S. ChordGAN: Symbolic Music Style Transfer with Chroma Feature ExtractionAIMC 2021, Graz, Austria.

Soft skin patch could provide early warning for strokes, heart attacks

Two fingers press down on a soft, electronic patch against the skin.
This soft, stretchy skin patch uses ultrasound to monitor blood flow to organs like the heart and brain. This image was selected as the cover image for the July 2021 issue of Nature Biomedical Engineering.

July 22, 2021 -- Engineers at the University of California San Diego developed a soft and stretchy ultrasound patch that can be worn on the skin to monitor blood flow through major arteries and veins deep inside a person’s body.

Knowing how fast and how much blood flows through a patient’s blood vessels is important because it can help clinicians diagnose various cardiovascular conditions, including blood clots; heart valve problems; poor circulation in the limbs; or blockages in the arteries that could lead to strokes or heart attacks.

The new ultrasound patch developed at UC San Diego can continuously monitor blood flow—as well as blood pressure and heart function—in real time. Wearing such a device could make it easier to identify cardiovascular problems early on.

A team led by Sheng Xu, a professor of nanoengineering at the UC San Diego Jacobs School of Engineering, reported the patch in a paper published July 16 in Nature Biomedical Engineering.

The patch can be worn on the neck or chest. What’s special about the patch is that it can sense and measure cardiovascular signals as deep as 14 centimeters inside the body in a non-invasive manner. And it can do so with high accuracy.

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Ultrasound patch worn on the neck. Images courtesy of Nature Biomedical Engineering

“This type of wearable device can give you a more comprehensive, more accurate picture of what’s going on in deep tissues and critical organs like the heart and the brain, all from the surface of the skin,” said Xu.

“Sensing signals at such depths is extremely challenging for wearable electronics. Yet, this is where the body’s most critical signals and the central organs are buried,” said Chonghe Wang, a former nanoengineering graduate student in Xu’s lab and co-first author of the study. “We engineered a wearable device that can penetrate such deep tissue depths and sense those vital signals far beneath the skin. This technology can provide new insights for the field of healthcare.”

Another innovative feature of the patch is that the ultrasound beam can be tilted at different angles and steered to areas in the body that are not directly underneath the patch.  

This is a first in the field of wearables, explained Xu, because existing wearable sensors typically only monitor areas right below them. “If you want to sense signals at a different position, you have to move the sensor to that location. With this patch, we can probe areas that are wider than the device’s footprint. This can open up a lot of opportunities.”

How it works

The patch is made up of a thin sheet of flexible, stretchable polymer that adheres to the skin. Embedded on the patch is an array of millimeter-sized ultrasound transducers. Each is individually controlled by a computer—this type of array is known as an ultrasound phased array. It is a key part of the technology because it gives the patch the ability to go deeper and wider.

The phased array offers two main modes of operation. In one mode, all the transducers can be synchronized to transmit ultrasound waves together, which produces a high-intensity ultrasound beam that focuses on one spot as deep as 14 centimeters in the body. In the other mode, the transducers can be programmed to transmit out of sync, which produces ultrasound beams that can be steered to different angles.

“With the phased array technology, we can manipulate the ultrasound beam in the way that we want,” said Muyang Lin, a nanoengineering Ph.D. student at UC San Diego who is also a co-first author of the study. “This gives our device multiple capabilities: monitoring central organs as well as blood flow, with high resolution. This would not be possible using just one transducer.”

The phased array consists of a 12 by 12 grid of ultrasound transducers. When electricity flows through the transducers, they vibrate and emit ultrasound waves that travel through the skin and deep into the body. When the ultrasound waves penetrate through a major blood vessel, they encounter movement from red blood cells flowing inside. This movement changes or shifts how the ultrasound waves echo back to the patch—an effect known as Doppler frequency shift. This shift in the reflected signals gets picked up by the patch and is used to create a visual recording of the blood flow. This same mechanism can also be used to create moving images of the heart’s walls. 

A potential game changer in the clinic

For many people, blood flow is not something that is measured during a regular visit to the physician. It is usually assessed after a patient shows some signs of cardiovascular problems, or if a patient is at high risk.

The standard blood flow exam itself can be time consuming and labor intensive. A trained technician presses a handheld ultrasound probe against a patient’s skin and moves it from one area to another until it’s directly above a major blood vessel. This may sound straightforward, but results can vary between tests and technicians.

Since the patch is simple to use, it could solve these problems, said Sai Zhou, a materials science and engineering Ph.D. student at UC San Diego and co-author of the study. “Just stick it on the skin, then read the signals. It’s not operator dependent, and it poses no extra work or burden to the technicians, clinicians or patients,” he said. “In the future, patients could wear something like this to do point of care or continuous at-home monitoring.”

In tests, the patch performed as well as a commercial ultrasound probe used in the clinic. It accurately recorded blood flow in major blood vessels such as the carotid artery, which is an artery in the neck that supplies blood to the brain. Having the ability to monitor changes in this flow could, for example, help identify if a person is at risk for stroke well before the onset of symptoms.

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Ultrasound patch wired to its full experimental setup.

The researchers point out that the patch still has a long way to go before it is ready for the clinic. Currently, it needs to be connected to a power source and benchtop machine in order to work. Xu’s team is working on integrating all the electronics on the patch to make it wireless.

Paper: “Continuous monitoring of deep-tissue haemodynamics with stretchable ultrasonic phased arrays.” Co-authors include Baiyan Qi*, Zhuorui Zhang*, Mitsutoshi Makihata, Boyu Liu, Yi-hsi Huang, Hongjie Hu, Yue Gu, Yimu Chen, Yusheng Lei, Shu Chien and Erik Kistler, UC San Diego; Taeyoon Lee, Yonsei University and Korea Institute of Science and Technology; and Kyung-In Jang, Daegu Gyeonbuk Institute of Science and Technology, Republic of Korea.

*These authors contributed equally

This work was supported by the National Institutes of Health (grant 1R21EB027303-01A1) and the Center for Wearable Sensors at the UC San Diego Jacobs School of Engineering.

UC San Diego among six U.S. institutions in new Wu Tsai Human Performance Alliance

The Joe and Clara Tsai Foundation makes a $220M commitment to create the Wu Tsai Human Performance Alliance, to advance human well-being through the study of peak performance

July 21, 2021--The University of California San Diego is one of six universities invited to participate in the Wu Tsai Human Performance Alliance, which publicly launched on July 21, 2021. 

The Wu Tsai Human Performance Alliance is a scientific collaboration that aims to transform human health on a global scale through the discovery and translation of the biological principles underlying human performance. 

The Alliance was created through a $220M philanthropic investment from the Joe and Clara Tsai Foundation after philanthropists Clara Wu Tsai and Joe Tsai identified an opportunity for broad societal impact by using new insights into the scientific principles underlying athletic performance to improve human fitness and thriving. 

“Scientific funding has traditionally been focused on the study of diseases,” said Clara Wu Tsai, founder of the Wu Tsai Human Performance Alliance. “We are taking the opposite approach and studying the human body at its healthiest and most vital, to enable the thriving of all people – from an Olympic Gold Medal-level athlete to a grandfather lacking the mobility to enjoy a full life.”

The Alliance is a public-private partnership comprised of scientists, clinicians, engineers, coaches, athletes and innovators from UC San Diego; as well as Stanford University; Boston Children’s Hospital, a Harvard Medical School Affiliate; University of Kansas; University of Oregon; and the Salk Institute for Biological Studies. 

The big-picture motivation of the Alliance extends to empowering all humans to perform at peak physical, intellectual and emotional capacity. 

"UC San Diego is one of six world-renowned institutions selected to help launch the Wu Tsai Human Performance Alliance," said UC San Diego Chancellor Pradeep K. Khosla. "We are uniquely equipped to help build upon fundamental, applied and clinical expertise to empower all people to perform at peak physical, intellectual and emotional capacity. UC San Diego brings to the Alliance dynamic, multi-scale modelling expertise as well as the capacity to generate bedrock experimental and clinical data that will drive new ‘living models’ of human performance and recovery. We look forward to continuing our tradition of collaborative research with friends and new partners."

 

The UC San Diego arm of the Alliance is led by Andrew McCulloch, a professor in the departments of Bioengineering and Medicine at UC San Diego and director of UC San Diego’s campus-wide Institute of Engineering in Medicine.

UC San Diego activities within the Alliance are organized around two grand challenges: a scientific project, the Multiscale Athlete, led by McCulloch; and an applied project, the Triton Center for Performance and Injury Science, led by Sam Ward, a professor in the departments of Orthopaedic Surgery and Radiology at UC San Diego Health. 

Multiscale Athlete 

For the Multiscale Athlete "moonshot" project, UC San Diego researchers are creating new generations of computational models of the musculoskeletal system. The new models will go well beyond representing a static picture of the muscles, bones, tendons and ligaments in the human body. The goal, instead, is to bring these mathematical models "to life" by incorporating biological processes so that a person’s whole-body athletic model can change and adapt over time to reflect things like injuries or changes in training regimens. 

The researchers are using the term "multiscale" because biological research is performed at multiple "scales." From small to large, these biological scales include the genetic, molecular, cellular, tissue, and organ systems scales. Through the Multiscale Athlete project and the Alliance’s Digital Athlete project at Stanford University, the UC San Diego researchers aim to weave new information and insights from all these different biological scales into whole-body mathematical models of athletic performance.

 

One of the big goals of these living models is to provide useful insights and predictions that are based on what is actually happening, at multiple scales, in a person’s muscles, bones, ligaments and tendons at any given time based on things like a particular exercise regime, a specific diet, an injury, or the details of an individual’s sleep patterns. 

"Our multiscale modeling teams are critical glue that will connect the other research teams across the Alliance. We are a synergistic layer that will make the Alliance much greater than the sum of the individual parts," said McCulloch. "UC San Diego is a recognized world-leader in multiscale modeling of living systems. It’s tremendously exciting to have this opportunity to apply our expertise to the important challenge of understanding the science of human performance and improving human thriving."

Triton Center for Performance and Injury Science

What makes the difference between being a good athlete and a great athlete? Can we predict when a dancer is at risk of injury? What can accelerate an athlete’s recovery? 

These are the kinds of questions that drive the UC San Diego researchers, and the larger efforts of the Alliance more generally. 

"The goal is to understand how the underlying biology behaves in many different human performance contexts," said Ward, who leads the Triton Center for Performance and Injury Science at UC San Diego, which is one of the Innovation Hubs of the Alliance.

"Our concept is to figure out how to fold dynamic models of molecular biology, cell biology and physiology into larger scale models of human movement to aid decision making related to performance, training, and recovery. You can ask questions and do experiments in models that you can’t do in humans. But to make the models useful, you need to get great experimental data and rigorous validation to make sure that the models represent what’s actually happening in the human body during and after training, performance, and recovery."

 

With a new "biobank" of tissue samples, ethically collected from athletes as well as laboratory animals, UC San Diego-led teams will generate new biological measurements that will feed into the engineering models in order to accurately represent what’s happening in the human body during and after exercise training and injury. 

"What sorts of training or rest will be most effective for a baseball pitcher near the end of a long season? How do we precisely pair a therapy to a specific individual with a specific injury? To make these kinds of mappings, you need to understand what’s happening biologically in the underlying tissues," said Ward.

It is the interaction between mechanics and biology that the UC San Diego team believes will create breakthroughs in our understanding of peak athletic performance, and peak human performance, more generally. 

"If you don’t understand what’s going on with the underlying biological ‘state’ of tissues, in the cells themselves, you can’t make a prediction about what is going to cause an injury, improve training, or accelerate healing," said Ward. 

Putting the pieces together

Through the Multiscale Athlete moonshot project and the Performance and Injury Science innovation hub, the UC San Diego teams are pulling in the same direction. 

UC San Diego researchers will use tissue samples from the biobank to run laboratory experiments looking for biological information at multiple scales that offers insights on athletic performance, or injury recovery.  

One of the likely scenarios is the following: first, researchers identify genetic, molecular or cellular information in laboratory experiments on tissue samples that point to new ideas about athletic performance or recovery after exercise or after injury. Laboratory experiments will inform and validate the team’s computer simulations, which will inspire additional experiments. 

The researchers will then be able to apply insights that emerge from this feedback loop between laboratory experiments and computational models to predict what will occur in humans, in terms of anatomy and physiology. Biomarkers in sweat, saliva or blood of human athletes; or information that can be picked up via non-invasive imaging tools, will help the research teams translate their insights to humans.   

To dive deeper into the actual experiences of elite athletes, the UC San Diego researchers are also collaborating with UC San Diego Athletics and other groups in the San Diego community. 

“In athletics, as in life, we know that injuries occur when demand exceeds capacity. The Wu Tsai Human Performance Alliance provides an excellent opportunity to understand better the success factors driving physical readiness associated with optimal performance in sport and life," said Matt Kritz, PhD, Senior Associate Athletic Director for Athletic Performance and Health at UC San Diego.

Scientific advances and successes that emerge from the Alliance will be freely accessible to everyone—to scientists, to athletes and coaches, to clinicians and health care personnel, to technology designers, and to the general public. The aim is to enable people with all kinds of bodies to thrive at every stage of life.

 

UC San Diego projects and collaborators include:

Multiscale Models of Musculoskeletal Tissue States

Andrew McCulloch, UC San Diego Departments of Bioengineering and Medicine

Systems Biology of Musculoskeletal Tissue States

Padmini Rangamani, UC San Diego Department of Mechanical and Aerospace Engineering
Pradipta Ghosh, UC San Diego School of Medicine 

Mechanobiology of Cell and Matrix interactions

Adam Engler, UC San Diego Department of Bioengineering
Stephanie Fraley, UC San Diego Department of Bioengineering 

Biomechanics of Musculoskeletal Tissues

Daniela Valdez-Jasso, UC San Diego Department of Bioengineering
Andrew McCulloch, UC San Diego Department of Bioengineering

Performance Evolution

Kimberly Cooper, UC San Diego Division of Biological Sciences 

Triton Center for Performance and Injury Science

Sam Ward, UC San Diego Health Sciences
Robert Sah, UC San Diego Department of Bioengineering
UC San Diego Athletics
Rady Children’s Hospital  

UC San Diego among six U.S. institutions in new Wu Tsai Human Performance Alliance

The Joe and Clara Tsai Foundation makes a $220M commitment to create the Wu Tsai Human Performance Alliance, to advance human well-being through the study of peak performance

July 21, 2021--The University of California San Diego is one of six universities invited to participate in the Wu Tsai Human Performance Alliance, which publicly launched on July 21, 2021. 

The Wu Tsai Human Performance Alliance is a scientific collaboration that aims to transform human health on a global scale through the discovery and translation of the biological principles underlying human performance. 

The Alliance was created through a $220M philanthropic investment from the Joe and Clara Tsai Foundation after philanthropists Clara Wu Tsai and Joe Tsai identified an opportunity for broad societal impact by using new insights into the scientific principles underlying athletic performance to improve human fitness and thriving. 

“Scientific funding has traditionally been focused on the study of diseases,” said Clara Wu Tsai, founder of the Wu Tsai Human Performance Alliance. “We are taking the opposite approach and studying the human body at its healthiest and most vital, to enable the thriving of all people – from an Olympic Gold Medal-level athlete to a grandfather lacking the mobility to enjoy a full life.”

The Alliance is a public-private partnership comprised of scientists, clinicians, engineers, coaches, athletes and innovators from UC San Diego; as well as Stanford University; Boston Children’s Hospital, a Harvard Medical School Affiliate; University of Kansas; University of Oregon; and the Salk Institute for Biological Studies. 

The big-picture motivation of the Alliance extends to empowering all humans to perform at peak physical, intellectual and emotional capacity. 

"UC San Diego is one of six world-renowned institutions selected to help launch the Wu Tsai Human Performance Alliance," said UC San Diego Chancellor Pradeep K. Khosla. "We are uniquely equipped to help build upon fundamental, applied and clinical expertise to empower all people to perform at peak physical, intellectual and emotional capacity. UC San Diego brings to the Alliance dynamic, multi-scale modelling expertise as well as the capacity to generate bedrock experimental and clinical data that will drive new ‘living models’ of human performance and recovery. We look forward to continuing our tradition of collaborative research with friends and new partners."

 

The UC San Diego arm of the Alliance is led by Andrew McCulloch, a professor in the departments of Bioengineering and Medicine at UC San Diego and director of UC San Diego’s campus-wide Institute of Engineering in Medicine.

UC San Diego activities within the Alliance are organized around two grand challenges: a scientific project, the Multiscale Athlete, led by McCulloch; and an applied project, the Triton Center for Performance and Injury Science, led by Sam Ward, a professor in the departments of Orthopaedic Surgery and Radiology at UC San Diego Health. 

Multiscale Athlete 

For the Multiscale Athlete "moonshot" project, UC San Diego researchers are creating new generations of computational models of the musculoskeletal system. The new models will go well beyond representing a static picture of the muscles, bones, tendons and ligaments in the human body. The goal, instead, is to bring these mathematical models "to life" by incorporating biological processes so that a person’s whole-body athletic model can change and adapt over time to reflect things like injuries or changes in training regimens. 

The researchers are using the term "multiscale" because biological research is performed at multiple "scales." From small to large, these biological scales include the genetic, molecular, cellular, tissue, and organ systems scales. Through the Multiscale Athlete project and the Alliance’s Digital Athlete project at Stanford University, the UC San Diego researchers aim to weave new information and insights from all these different biological scales into whole-body mathematical models of athletic performance.

 

One of the big goals of these living models is to provide useful insights and predictions that are based on what is actually happening, at multiple scales, in a person’s muscles, bones, ligaments and tendons at any given time based on things like a particular exercise regime, a specific diet, an injury, or the details of an individual’s sleep patterns. 

"Our multiscale modeling teams are critical glue that will connect the other research teams across the Alliance. We are a synergistic layer that will make the Alliance much greater than the sum of the individual parts," said McCulloch. "UC San Diego is a recognized world-leader in multiscale modeling of living systems. It’s tremendously exciting to have this opportunity to apply our expertise to the important challenge of understanding the science of human performance and improving human thriving."

Triton Center for Performance and Injury Science

What makes the difference between being a good athlete and a great athlete? Can we predict when a dancer is at risk of injury? What can accelerate an athlete’s recovery? 

These are the kinds of questions that drive the UC San Diego researchers, and the larger efforts of the Alliance more generally. 

"The goal is to understand how the underlying biology behaves in many different human performance contexts," said Ward, who leads the Triton Center for Performance and Injury Science at UC San Diego, which is one of the Innovation Hubs of the Alliance.

"Our concept is to figure out how to fold dynamic models of molecular biology, cell biology and physiology into larger scale models of human movement to aid decision making related to performance, training, and recovery. You can ask questions and do experiments in models that you can’t do in humans. But to make the models useful, you need to get great experimental data and rigorous validation to make sure that the models represent what’s actually happening in the human body during and after training, performance, and recovery."

 

With a new "biobank" of tissue samples, ethically collected from athletes as well as laboratory animals, UC San Diego-led teams will generate new biological measurements that will feed into the engineering models in order to accurately represent what’s happening in the human body during and after exercise training and injury. 

"What sorts of training or rest will be most effective for a baseball pitcher near the end of a long season? How do we precisely pair a therapy to a specific individual with a specific injury? To make these kinds of mappings, you need to understand what’s happening biologically in the underlying tissues," said Ward.

It is the interaction between mechanics and biology that the UC San Diego team believes will create breakthroughs in our understanding of peak athletic performance, and peak human performance, more generally. 

"If you don’t understand what’s going on with the underlying biological ‘state’ of tissues, in the cells themselves, you can’t make a prediction about what is going to cause an injury, improve training, or accelerate healing," said Ward. 

Putting the pieces together

Through the Multiscale Athlete moonshot project and the Performance and Injury Science innovation hub, the UC San Diego teams are pulling in the same direction. 

UC San Diego researchers will use tissue samples from the biobank to run laboratory experiments looking for biological information at multiple scales that offers insights on athletic performance, or injury recovery.  

One of the likely scenarios is the following: first, researchers identify genetic, molecular or cellular information in laboratory experiments on tissue samples that point to new ideas about athletic performance or recovery after exercise or after injury. Laboratory experiments will inform and validate the team’s computer simulations, which will inspire additional experiments. 

The researchers will then be able to apply insights that emerge from this feedback loop between laboratory experiments and computational models to predict what will occur in humans, in terms of anatomy and physiology. Biomarkers in sweat, saliva or blood of human athletes; or information that can be picked up via non-invasive imaging tools, will help the research teams translate their insights to humans.   

To dive deeper into the actual experiences of elite athletes, the UC San Diego researchers are also collaborating with UC San Diego Athletics and other groups in the San Diego community. 

“In athletics, as in life, we know that injuries occur when demand exceeds capacity. The Wu Tsai Human Performance Alliance provides an excellent opportunity to understand better the success factors driving physical readiness associated with optimal performance in sport and life," said Matt Kritz, PhD, Senior Associate Athletic Director for Athletic Performance and Health at UC San Diego.

Scientific advances and successes that emerge from the Alliance will be freely accessible to everyone—to scientists, to athletes and coaches, to clinicians and health care personnel, to technology designers, and to the general public. The aim is to enable people with all kinds of bodies to thrive at every stage of life.

 

UC San Diego projects and collaborators include:

Multiscale Models of Musculoskeletal Tissue States

Andrew McCulloch, UC San Diego Departments of Bioengineering and Medicine

Systems Biology of Musculoskeletal Tissue States

Padmini Rangamani, UC San Diego Department of Mechanical and Aerospace Engineering
Pradipta Ghosh, UC San Diego School of Medicine 

Mechanobiology of Cell and Matrix interactions

Adam Engler, UC San Diego Department of Bioengineering
Stephanie Fraley, UC San Diego Department of Bioengineering 

Biomechanics of Musculoskeletal Tissues

Daniela Valdez-Jasso, UC San Diego Department of Bioengineering
Andrew McCulloch, UC San Diego Department of Bioengineering

Performance Evolution

Kimberly Cooper, UC San Diego Division of Biological Sciences 

Triton Center for Performance and Injury Science

Sam Ward, UC San Diego Health Sciences
Robert Sah, UC San Diego Department of Bioengineering
UC San Diego Athletics
Rady Children’s Hospital  

Calling all couch potatoes: this finger wrap can let you power electronics while you sleep

ALT TEXT
This thin, flexible strip can be worn on a fingertip and generate small amounts of electricity when a person’s finger sweats or presses on it.

July 13, 2021 -- A new wearable device turns the touch of a finger into a source of power for small electronics and sensors. Engineers at the University of California San Diego developed a thin, flexible strip that can be worn on a fingertip and generate small amounts of electricity when a person’s finger sweats or presses on it.

What’s special about this sweat-fueled device is that it generates power even while the wearer is asleep or sitting still. This is potentially a big deal for the field of wearables because researchers have now figured out how to harness the energy that can be extracted from human sweat even when a person is not moving.

This type of device is the first of its kind, said co-first author Lu Yin, a nanoengineering Ph.D. student at the UC San Diego Jacobs School of Engineering. “Unlike other sweat-powered wearables, this one requires no exercise, no physical input from the wearer in order to be useful. This work is a step forward to making wearables more practical, convenient and accessible for the everyday person.”

The new wearable energy harvester is described in a paper published July 13 in Joule.

The device also generates extra power from light finger presses—so activities such as typing, texting, playing the piano or tapping in Morse code can also become sources of energy.

“We envision that this can be used in any daily activity involving touch, things that a person would normally do anyway while at work, at home, while watching TV or eating,” said Joseph Wang, a professor of nanoengineering at the UC San Diego Jacobs School of Engineering and the study’s senior author. “The goal is that this wearable will naturally work for you and you don’t even have to think about it.”

The device derives most of its power from sweat produced by the fingertips, which are 24-hour factories of perspiration. It’s a little-known fact that the fingertips are one of the sweatiest spots on the body; each one is packed with over a thousand sweat glands and can produce between 100 to 1000 times more sweat than most other areas on the body.

“The reason we feel sweatier on other parts of the body is because those spots are not well ventilated,” said Yin. “By contrast, the fingertips are always exposed to air, so the sweat evaporates as it comes out. So rather than letting it evaporate, we use our device to collect this sweat, and it can generate a significant amount of energy.”

But not just any sweat-fueled device can work on the fingertip. Collecting sweat from such a small area and making it useful required some innovative materials engineering, explained Yin. The researchers had to build different parts of the device to be super absorbent and efficient at converting the chemicals in human sweat into electrical energy.

Yin worked on this project with UC San Diego nanoengineering Ph.D. students Jong-Min Moon and Juliane Sempionatto, who are the study’s other co-first authors, as part of a team led by Wang, who is also the director of the Center for Wearable Sensors at UC San Diego. Wang and his team pioneered sweat-fueled wearables 8 years ago. Since then, they have been building on the technology to create new and better ways to power wearables using sustainable sources, such as the wearers themselves and their surroundings.

This latest energy harvesting technology is especially unique in that it could serve as a power source anytime, anywhere. It does not have the same limitations as, say, solar cells, which only work under sunlight, or thermoelectric generators, which only work when there’s a large temperature difference between the device and the surroundings.

How it works

The device is a thin, flexible strip that can be wrapped around the fingertip like a Band-Aid. A padding of carbon foam electrodes absorbs sweat and converts it into electrical energy. The electrodes are equipped with enzymes that trigger chemical reactions between lactate and oxygen molecules in sweat to generate electricity. Underneath the electrodes is a chip made of what’s called a piezoelectric material, which generates additional electrical energy when pressed.

As the wearer sweats or presses on the strip, the electrical energy gets stored in a small capacitor and is discharged to other devices when needed.

The researchers had a subject wear the device on one fingertip while doing sedentary activities. From 10 hours of sleep, the device collected almost 400 millijoules of energy—this is enough to power an electronic wristwatch for 24 hours. From one hour of casual typing and clicking on a mouse, the device collected almost 30 millijoules.

And this is just from one fingertip. Strapping devices on the rest of the fingertips would generate 10 times more energy, the researchers said.

“By using the sweat on the fingertip—which flows out naturally regardless of where you are or what you’re doing—this technology provides a net gain in energy with no effort from the user. This is what we call a maximum energy return on investment,” said Wang.

“Compare this to a device that harvests energy as you exercise,” explained Yin. “When you are running, you are investing hundreds of joules of energy only for the device to generate millijoules of energy. In that case, your energy return on investment is very low. But with this device, your return is very high. When you are sleeping, you are putting in no work. Even with a single finger press, you are only investing about half a millijoule.”

In other experiments, the researchers connected their energy harvester to an electronic system consisting of a chemical sensor connected to a small low-power display, which shows a numerical reading of the sensor’s data. Either pressing the energy harvester 10 times every 10 seconds or simply wearing it on the fingertip for two minutes was enough to power both the sensor and the display. In one experiment, the researchers hooked up their device to a vitamin C sensor that they developed in the lab. They had a subject take a vitamin C pill and then use the finger-powered system to read their vitamin C level. In another experiment, the researchers showed that their system could also be used with a lab-built sodium sensor to read the sodium ion level of a saltwater solution.

“Our goal is to make this a practical device,” said Yin. “We want to show that this is not just another cool thing that can generate a small amount of energy and then that’s it—we can actually use the energy to power useful electronics such as sensors and displays.”

To that end, the team is making further improvements to the device so that it is more efficient and durable. Future studies will include combining it with other types of energy harvesters to create a new generation of self-powered wearable systems.

Paper: “A Passive Perspiration Biofuel Cell: High Energy Return on Investment.” Co-authors include Muyang Lin, Mengzhu Cao, Alexander Trifonov, Fangyu Zhang, Zhiyuan Lou, Jae-Min Jeong, Sang-Jin Lee and Sheng Xu, UC San Diego.

This work was supported by the Center for Wearable Sensors at the UC San Diego Jacobs School of Engineering. 

Artificial Intelligence Could Be New Blueprint for Precision Drug Discovery

Mathematical approach could transform drug development by searching for disease targets, then predicting if a drug will be successful

July 12, 2021--Writing in the July 12, 2021 online issue of Nature Communications, researchers at University of California San Diego describe a new approach that uses machine learning to hunt for disease targets and then predicts whether a drug is likely to receive FDA approval. 

The study findings could measurably change how researchers sift through big data to find meaningful information with significant benefit to patients, the pharmaceutical industry and the nation’s health care systems. 

Pradipta Ghosh, MD, is senior author of the study and professor in the departments of Medicine and Cellular and Molecular Medicine at UC San Diego School of Medicine.

“Academic labs and pharmaceutical and biotech companies have access to unlimited amounts of ‘big data’ and better tools than ever to analyze such data. However, despite these incredible advances in technology, the success rates in drug discovery are lower today than in the 1970s,” said Dr. Pradipta Ghosh, senior author of the study and professor in the departments of Medicine and Cellular and Molecular Medicine at UC San Diego School of Medicine. 

“This is mostly because drugs that work perfectly in preclinical inbred models, such as laboratory mice, that are genetically or otherwise identical to each other, don’t translate to patients in the clinic, where each individual and their disease is unique. It is this variability in the clinic that is believed to be the Achilles heel for any drug discovery program.” 

In the new study, Ghosh and colleagues replaced the first and last steps in preclinical drug discovery with two novel approaches developed within the UC San Diego Institute for Network Medicine (iNetMed), which unites several research disciplines to develop new solutions to advance life sciences and technology and enhance human health. 

The researchers used the disease model for inflammatory bowel disease (IBD), which is a complex, multifaceted, relapsing autoimmune disorder characterized by inflammation of the gut lining. Because it impacts all ages and reduces the quality of life in patients, IBD is a priority disease area for drug discovery and is a challenging condition to treat because no two patients behave similarly.

“Our study shows how the likelihood of success in phase III clinical trials, for any target, can be determined with mathematical precision,” said Debashis Sahoo, PhD, co-senior author of the study who leads PreCSN and is associate professor in the departments of Pediatrics and Computer Science at UC San Diego School of Medicine and UC San Diego. 

 “Our approach could provide the predictive horsepower that will help us understand how diseases progress, assess a drug’s potential benefits and strategize how to use a combination of therapies when current treatment is failing,” Sahoo said.

The first step, called target identification, used an artificial intelligence (AI) methodology developed by The Center for Precision Computational System Network (PreCSN), the computational arm of iNetMed. The AI approach helps model a disease using a map of successive changes in gene expression at the onset and during the progression of the disease. What sets this mapping apart from other existing models is the use of mathematical precision to recognize and extract all possible fundamental rules of gene expression patterns, many of which are overlooked by current methodologies. 

Soumita Das, PhD, is co-senior author of the study, director of the HUMANOID center and an associate professor in the Department of Pathology at UC San Diego School of Medicine.

The underlying algorithms ensure that the identified gene expression patterns are ‘invariant’ regardless of different disease cohorts. In other words, PreCSN builds a map that extracts information that applies to all IBD patients. 

“In head-to-head comparisons, we demonstrated the superiority of this approach over existing methodologies to accurately predict ‘winners’ and ‘losers’ in clinical trials,” said Ghosh. 

The last step, called target validation in preclinical models, was conducted in a first-of-its-kind Phase ‘0’ clinical trial using a living biobank of organoids created from IBD patients at The HUMANOID Center of Research Excellence (CoRE), the translational arm of iNetMed. 

The Phase ‘0’ approach involves testing the efficacy of the drugs identified using the AI model on human disease organoid models—cultured human cells in a 3D environment that mimic diseases outside of the body. In this case, an IBD-afflicted gut-in-a-dish. 

“The ‘phase 0’ trial concept was developed because most drugs fail somewhere between phases I and III. Before proceeding to patients in the clinic, ‘phase 0’ tests efficacy in the human disease models, where ineffective compounds can be rejected early in the process, saving millions of dollars,” said Soumita Das, PhD, co-senior author of the study, director of the HUMANOID center and an associate professor in the Department of Pathology at UC San Diego School of Medicine.

Biopsy tissues for the study were taken during colonoscopy procedures involving IBD patients. Those biopsies were used as the source of stem cells to grow organoids. 

“There were two major surprises. First, we saw that despite being away from the immune cells in the gut wall and the trillions of microbes that are in the gut lining, these organoids from IBD patients showed the tell-tale features of a leaky gut with broken cell borders,” said Das.

“Second, the drug identified by the AI model not only repaired the broken barriers, but also protected them against the onslaught of pathogenic bacteria that we added to the gut model. These findings imply that the drug could work in both acute flares as well as for maintenance therapy for preventing such flares.”

The researchers found the computational approach had a surprisingly high level of accuracy across diverse cohorts of IBD patients, and together with the Phase ‘0’ approach, they developed a first-in-class therapy to restore and protect the leaky gut barrier in IBD. 

Debashis Sahoo, PhD, is co-senior author of the study who leads PreCSN and is associate professor in the departments of Pediatrics and Computer Science at UC San Diego School of Medicine and UC San Diego

The authors said next steps include testing if the drug that passed the human phase ‘0’ trial in a dish can pass phase III trials in clinic; and whether the same methodologies can be used with other diseases, ranging from diverse types of cancers and Alzheimer’s disease to non-alcoholic fatty liver disease. 

“Our blueprint has the potential to shatter status quo and deliver better drugs for chronic diseases that have yet to have good therapeutic solutions,” said Ghosh.

Co-authors include: Lee Swanson, Ibrahim Sayed, Gajanan Katkar, Stella-Rita Ibeawuchi, Yash Mittal, Rama Pranadinata, Courtney Tindle, Mackenzie Fuller, Dominik Stec and John Chang, all with UC San Diego. 

This study was supported in part, the National Institutes of Health (grants AI141630, DK107585, R56 AG069689, UG3TR003355, UG3TR002968, R01-AI55696, T32 DK 007202, 1TL1TR001443, 3R01DK107585-02S1), the DiaComp Pilot and Feasibility Award (R00-CA151673, R01-GM138385), Padres Pedal the Cause/C3 Collaborative Translational Cancer Research Award (#PTC2017), the Leona M. and Harry B. Helmsley Charitable Trust and The American Association of Immunologists Intersect Fellowship Program for Computational Scientists and Immunologists. 

Disclosure: Soumita Das, Debashis Sahoo and Pradipta Ghosh have a patent on the methodology.

Ishwar K. Puri named USC vice president for research

Women in Engineering --Anna Pridmore, P.E., Ph.D.

Machine learning enhances non-verbal communication in online classrooms

If concertmaster (top left) looks at her camera, it will appear to the musicians that she is looking at all of them. But gaze tracking system shows she is looking at Walter (second row center), and labels the concertmaster’s video feed with the cue “Walter” so the entire class knows intended gaze recipient. The cue updates continuously when she looks at another musician – establishing non-verbal communication with the ensemble.

June 21, 2021--Researchers in the Center for Research on Entertainment and Learning (CREL) at the University of California San Diego have developed a system to analyze and track eye movements to enhance teaching in tomorrow’s virtual classrooms – and perhaps future virtual concert halls.

UC San Diego music and computer science professor Shlomo Dubnov, an expert in computer music who directs the Qualcomm Institute-based CREL, began developing the new tool to deal with a downside of teaching music over Zoom during the COVID-19 pandemic.

“In a music classroom, non-verbal communication such as facial affect and body gestures is critical to keep students on task, coordinate musical flow and communicate improvisational ideas,” said Dubnov. “Unfortunately, this non-verbal aspect of teaching and learning is dramatically hampered in the virtual classroom where you don’t inhabit the same physical space.”

To overcome the problem, Dubnov and Ph.D. student Ross Greer recently published a conference paper on a system that uses eye tracking and machine learning to allow an educator to make ‘eye contact’ with individual students or performers in disparate locations – and lets each student know when he or she is the focus of the teacher’s attention.

The researchers built a prototype system and undertook a pilot study in a virtual music class at UC San Diego via Zoom.

“Our system uses a camera to capture the presenter’s eye movements to track where they are looking on screen,” explained Greer, an electrical and computer engineering Ph.D. student in UC San Diego’s Jacobs School of Engineering. “We divided the screen into 91 squares, and after determing the location of the teacher’s face and eyes, we came up with a ‘gaze-estimation’ algorithmm that provides the best estimate of which box – and therefore which student – the teacher is looking at.”

As the system recognizes a change in where the teacher is looking, the algorithm determines the identity of the student and tags his or her name on screen so everyone knows whom the presenter is focusing on.

In the pilot study, Dubnov and Greer found the system to be highly accurate in estimating the presenter’s gaze – managing to get within three-quarters of an inch (2cm) of the correct point on a 27.5 x 13 inches (70x39cm) screen. “In principle,” Greer told New Scientist magazine, “the system should work well on small screens, given enough quality data.”

One downside, according to Dubnov: the further the presenter is from the camera, the eyes become smaller and harder to track, resulting in less accurate gaze estimation. Yet with better training data, higher-quality camera resolution, and further advances in tracking facial and body gestures, he thinks the system could even allow the conductor to wield a baton remotely and conduct a distributed symphony orchestra -- even if every musician is located somewhere else.

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Ross Greer and Shlomo Dubnov, Eye-Tracking Software Could Make Video Calls Fee More LifelikeProceedings of CSME (2021), ISBN: 978-989-758-502-9  DOI: 10.5220/0010539806980708

Bio-inspired hydrogel protects the heart from post-op adhesions

Researchers developed a device to spray the hydrogel during surgeries. Download high resolution version of this image on Flickr.  Image credit:  UC San Diego Jacobs School of Engineering / David Baillot

June 18, 2021-- A hydrogel that forms a barrier to keep heart tissue from adhering to surrounding tissue after surgery was developed and successfully tested in rodents by a team of University of California San Diego researchers. The team of engineers, scientists and physicians also conducted a pilot study on porcine hearts, with promising results.

They describe their work in the June 18, 2021 issue of Nature Communications.

In rats, the hydrogel prevented the formation of adhesions altogether. In a small pilot study, porcine hearts treated with the hydrogel experienced less severe adhesions that were easier to remove. In addition, the hydrogel did not appear to cause chronic inflammation. 

Adhesions--organ tissue sticking to surrounding tissue--are a relatively common problem when surgeons need to operate again at the same site, which happens in 20 percent of cases every year in cardiac surgery. Re-operations are particularly common when the patients are children suffering from cardiac malformations--as the child’s heart grows, additional interventions are needed. 

Adhesions form within the first 30 days post-op and can complicate operations and increase the risk of mortality during interventions. In some cases, they can also interfere with proper heart function or completely prevent a repeat surgery. One of the paper’s senior authors, UC San Diego bioengineering professor Karen Christman, experienced this when one of her uncles couldn’t have  a heart valve repaired because of severe adhesions. 

“Our work is an engineering solution driven by a medical problem,” said Christman, who co-founded a company, Karios Technologies, to bring the hydrogel into the clinic. “And now it’s poised to significantly improve cardiac surgery, both for adults and children.”

The work brought together not only bioengineers and physicians, but also chemists and materials scientists.  

In academic medical centers such as UC San Diego, most surgeons conduct repeat operations and encounter adhesions fairly regularly. In this study, in rats, 70 percent of animals in the control group developed severe adhesions. 

Currently there are no FDA approved products marketed for preventing adhesions after heart surgery.  “This product will have a significant impact on the lives of many patients who potentially require repeat operations, either on the heart or anywhere else in the body,” said Dr. Michael M. Madani, chair of the Division of Cardiovascular and Thoracic Surgery at UC San Diego Health and one of the paper’s co-authors.

How it’s made

By contrast, the hydrogel developed by bioengineers in Christman’s lab is designed specifically to meet both the patients’ and surgeons’ needs. It’s sprayable, so easy to apply. Once sprayed onto tissue, it binds to the heart muscle and turns into a soft, elastic coating that creates a protective barrier, while still allowing for movement. The gel can be easily removed from tissue and dissolves after more than four to six weeks. 

The biggest challenge was making sure that the hydrogel attaches strongly  enough to the heart but doesn’t swell, as swelling can put dangerous pressure on the heart. Christman and team used what’s known as crosslinking chemistry, which consists of linking two molecules together with a covalent bond, to accomplish this. Masaki Fujita, the paper’s first author and a visiting scientist in the Department of Bioengineering at UC San Diego, had the idea of using a compound known as catechol, similar to what mussels use to adhere to rocks, to ensure the hydrogel stayed in place on the heart. 

Catechol contains an amino acid, L-dopa, that is a muscle binding protein. In this case, it was added to the gel base, a water soluble polymer, known as PEG. The result is a hydrogel that sticks onto the organ it is applied to, but then creates a protective barrier that lasts at least up to four weeks before dissolving. By that point, adhesions are less likely to form. To the researchers’ knowledge, it’s the first time this type of formulation has been used for preventing adhesions after surgery.

Spraying device

Left: a rodent heart treated with the hydrogel post-op shows little to no adhesions two weeks post-op. Right: a heart from the control rodent group shows severe adhesions.

Researchers also designed a device to safely and accurately spray the hydrogel inside the area where open heart surgery is being performed. The device houses the hydrogel’s two main components in two different chambers. Each component is made of PEG with different reactive groups that crosslink together to form the hydrogel. One of the solutions also includes the catechol-modified PEG to ensure it stays on the heart. The two mix as they exit the device, forming a gel. The process is akin to using two cans of spray paint, for example blue and yellow, to create a third color, green. 

Next steps and bigger picture

The next step is to do a large-scale trial in pigs to refine dosage and examine how the hydrogel binds to sutures and drains. The ultimate goal is to conduct a human pediatric study in 18 months to two years and bring the product to the FDA for approval in five years.

Karios Technologies is licensing the technology from UC San Diego.  “We want feedback from surgeons,” Gregory, CEO of Karios Technologies said. “We designed this material specifically for use on the heart and ease of use by the surgeon.”

The technology could easily translate to other organs also requiring multiple operations and susceptible to adhesions, researchers said. 

The work was funded by the National Heart, Lung and Blood Institute through the UC Center for Accelerated Innovation, and the National Center for Advancing Translational Sciences through the UC San Diego Center for Clinical and Translational Research Institute. 

Christman co-founded and holds equity interest in Karios Technologies, a startup that aims to commercialize the hydrogel technology. Dr. Madani is a consultant for the company. Christman, Fujita and Madani are inventors on patents and patent applications related to the work. 

 

Imperfections in jewels used as sensors for new quantum materials

'It Feels Like I'm Talking into a Void': How Do We Improve the Virtual Classroom?

 

A pseudonymous snapshot of a discussion-based lecture at UC San Diego. Most students are not sharing videos and all are muted except the one person who is speaking.

June 17, 2021--The COVID pandemic precipitated a major shift to virtual learning—an unplanned test of whether these technologies can scale effectively. But did they?

Researchers in the UC San Diego Department of Computer Science and Engineering wanted to look beyond the anecdotal evidence to better understand where remote education fell short and how we might improve it. In a study presented at the Association for Computing Machinery’s Conference on Human Factors in Computing Systems (CHI), the team examined faculty and student attitudes towards virtual classrooms and proposed several technological refinements that could improve their experience, such as flexible distribution of student video feeds and enhanced chat functions.

“We wanted to understand instructor and student perspectives and see how we can marry them,” said Nadir Weibel, a computer science associate professor and senior author on the paper. “How can we improve students’ experience and give better tools to instructors?”

The project was initiated and led by computer science Ph.D. student and first author Matin Yarmand. With coauthors Scott Klemmer, a professor of cognitive science and computer science, and Carnegie Mellon University Ph.D. student Jaemarie Solyst, the team interviewed seven UC San Diego faculty members to better understand their experience. Their primary fault with online learning is that many students never turn their cameras on.

“When I’m presenting the lecture content, it feels like I’m talking into a void,” said one professor. “How do I tell whether students are engaged?” asked another. “You have no sense if people are getting it or not getting it.”

The researchers then distributed student surveys. The 102 responses they showed—not surprisingly—that students resist turning on their cameras and often remain muted. Some don’t want their peers to see them; others are eating or performing unrelated tasks; some are unaware video feedback helps instructors; and a hardcore few see no need to turn their cameras on at all.

While students feel awkward asking questions on video, they overwhelmingly like chat functions, which make them more likely to participate. “I’m more comfortable asking questions in chat, since I feel less like I’m interrupting the lecture,” said one respondent. The survey also showed chat rooms drive more community among students. As a result, the authors propose that text communication could promote student engagement and community, even in in-person classrooms.

Students also have trouble connecting with instructors. Online classes lack opportunities for short conversations and questions that can happen during “hallway time” before and after live lectures.

Gathering together, virtually

The Gather lounge contains the instructor’s office in the middle and many other spaces for student collaboration. The red ellipses indicate small group interactions that are taking place before the lecture starts.

In response to these concerns, the researchers have suggested potential solutions. Technology that reads social cues, such as facial expressions or head nods, could provide invaluable feedback for instructors. Video feeds could also be refined to make instructors the center of attention, as they are in real-life classrooms, rather than one of many co-equal video boxes.

Increased chat use could improve both online and in-person classes, as some students have always been reluctant to call attention to themselves.

Weibel and colleagues have also been exploring how virtual reality environments could improve online learning. Using a tool called Gather, they have been testing an instructor lounge, in which students and faculty could meet before or even during class.

“The way Gather works is you move your avatar around in the space, and if it gets close enough to somebody, you can have a one-to-one conversation with just that person,” said Weibel. “Nobody else is part of it. People can just come and talk to me directly or chat with their friends and peers.”

The team is also working on a natural language processing bot that could make the experience more interactive. For example, if two people are struggling on the same assignment, it could connect them to improve collaboration or point to additional resources on Canvas.

The authors believe online classes, such as MOOCs, which were popular before COVID, will continue into the future. Weibel hopes this research and other efforts will refine the technology and improve the online learning experience.

“Some classes will be back in person,” he said. “Some will be only online and some will be hybrid, but I think online learning is probably here to stay.”

AI predicts how patients with viral infections, including COVID-19, will fare

This image shows specialized lung cells (resembling a beaded necklace) that may mount a cytokine storm in response to some viral infections.

June 17, 2021--Debashis Sahoo, a professor in the UC San Diego Department of Computer Science and Engineering and of pediatrics at UC San Diego School of Medicine, along with other researchers at the School of Medicine have used an artificial intelligence algorithm to sift through terabytes of gene expression data — which genes are “on” or “off” during infection — to look for shared patterns in patients with past pandemic viral infections, including SARS, MERS and swine flu.

Two telltale signatures emerged from the study, published June 11, 2021 in eBiomedicine. One, a set of 166 genes, reveals how the human immune system responds to viral infections. A second set of 20 signature genes predicts the severity of a patient’s disease. For example, the need to hospitalize or use a mechanical ventilator. The algorithm’s utility was validated using lung tissues collected at autopsies from deceased patients with COVID-19 and animal models of the infection.

Sahoo co-led the study with Dr. Pradipta Ghosh, professor of cellular and molecular medicine at UC San Diego School of Medicine and Moores Cancer Center, and Soumita Das, associate professor of pathology at UC San Diego School of Medicine.

“These viral pandemic-associated signatures tell us how a person’s immune system responds to a viral infection and how severe it might get, and that gives us a map for this and future pandemics,” said Ghosh.

During a viral infection, the immune system releases small proteins called cytokines into the blood. These proteins guide immune cells to the site of infection to help get rid of the infection. Sometimes, though, the body releases too many cytokines, creating a runaway immune system that attacks its own healthy tissue. This mishap, known as a cytokine storm, is believed to be one of the reasons some virally infected patients, including some with the common flu, succumb to the infection while others do not.

But the nature, extent and source of fatal cytokine storms, who is at greatest risk and how it might best be treated have long been unclear.

“When the COVID-19 pandemic began, I wanted to use my computer science background to find something that all viral pandemics have in common — some universal truth we could use as a guide as we try to make sense of a novel virus,” Sahoo said. “This coronavirus may be new to us, but there are only so many ways our bodies can respond to an infection.”

The data used to test and train the algorithm came from publicly available sources of patient gene expression data — all the RNA transcribed from patients’ genes and detected in tissue or blood samples. Each time a new set of data from patients with COVID-19 became available, the team tested it in their model. They saw the same signature gene expression patterns every time.

From a simple blood draw, gene expression patterns associated with pandemic viral infections could provide clinicians with a map to help define patients’ immune responses, measure disease severity, predict outcomes and test therapies.

“In other words, this was what we call a prospective study, in which participants were enrolled into the study as they developed the disease and we used the gene signatures we found to navigate the uncharted territory of a completely new disease,” Sahoo said.

By examining the source and function of those genes in the first signature gene set, the study also revealed the source of cytokine storms: the cells lining lung airways and white blood cells known as macrophages and T cells. In addition, the results illuminated the consequences of the storm: damage to those same lung airway cells and natural killer cells, a specialized immune cell that kills virus-infected cells.

“We could see and show the world that the alveolar cells in our lungs that are normally designed to allow gas exchange and oxygenation of our blood, are one of the major sources of the cytokine storm, and hence, serve as the eye of the cytokine storm,” Das said. “Next, our HUMANOID Center team is modeling human lungs in the context of COVID-19 infection in order to examine both acute and post-COVID-19 effects.”

The researchers think the information might also help guide treatment approaches for patients experiencing a cytokine storm by providing cellular targets and benchmarks to measure improvement.

To test their theory, the team pre-treated rodents with either a precursor version of Molnupiravir, a drug currently being tested in clinical trials for the treatment of COVID-19 patients, or SARS-CoV-2-neutralizing antibodies. After exposure to SARS-CoV-2, the lung cells of control-treated rodents showed the pandemic-associated 166- and 20-gene expression signatures. The treated rodents did not, suggesting that the treatments were effective in blunting cytokine storm.

“It is not a matter of if, but when the next pandemic will emerge,” said Ghosh, who is also director of the Institute for Network Medicine and executive director of the HUMANOID Center of Research Excellence at UC San Diego School of Medicine. “We are building tools that are relevant not just for today’s pandemic, but for the next one around the corner.”

Co-authors of the study include: Gajanan D. Katkar, Soni Khandelwal, Mahdi Behroozikhah, Amanraj Claire, Vanessa Castillo, Courtney Tindle, MacKenzie Fuller, Sahar Taheri, Stephen A. Rawlings, Victor Pretorius, David M. Smith, Jason Duran, UC San Diego; Thomas F. Rogers, Scripps Research and UC San Diego; Nathan Beutler, Dennis R. Burton, Scripps Research; Sydney I. Ramirez, La Jolla Institute for Immunology; Laura E. Crotty Alexander, VA San Diego Healthcare System and UC San Diego; Shane Crotty, Jennifer M. Dan, La Jolla Institute for Immunology and UC San Diego.

Funding for this research came, in part, from the National Institutes for Health (grants R00-CA151673, R01-GM138385, R01-AI141630, CA100768, CA160911, R01DK107585, R01-AI155696, R00RG2628, R00RG2642 and U19-AI142742), UC San Diego Sanford Stem Cell Clinical Center, La Jolla Institute for Immunology Institutional Funds, and VA San Diego Healthcare System.

Researchers translate a bird's brain activity into song

Study demonstrates the possibilities of a future speech prosthesis for humans

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Zebra finch. Photo by iStock_thawats

June 16, 2021 -- It is possible to re-create a bird’s song by reading only its brain activity, shows a first proof-of-concept study from the University of California San Diego. The researchers were able to reproduce the songbird’s complex vocalizations down to the pitch, volume and timbre of the original.

Published June 16 in Current Biology, the study lays the foundation for building vocal prostheses for individuals who have lost the ability to speak.

“The current state of the art in communication prosthetics is implantable devices that allow you to generate textual output, writing up to 20 words per minute,” said senior author Timothy Gentner, a professor of psychology and neurobiology at UC San Diego. “Now imagine a vocal prosthesis that enables you to communicate naturally with speech, saying out loud what you’re thinking nearly as you’re thinking it. That is our ultimate goal, and it is the next frontier in functional recovery.”

The approach that Gentner and colleagues are using involves songbirds such as the zebra finch. The connection to vocal prostheses for humans might not be obvious, but in fact, a songbird’s vocalizations are similar to human speech in various ways. They are complex, and they are learned behaviors.

“In many people’s minds, going from a songbird model to a system that will eventually go into humans is a pretty big evolutionary jump,” said Vikash Gilja, a professor of electrical and computer engineering at UC San Diego who is a co-author on the study. “But it’s a model that gives us a complex behavior that we don’t have access to in typical primate models that are commonly used for neural prosthesis research.”

The research is a cross-collaborative effort between engineers and neuroscientists at UC San Diego, with the Gilja and Gentner labs working together to develop neural recording technologies and neural decoding strategies that leverage both teams’ expertise in neurobiological and behavioral experiments.

The team implanted silicon electrodes in male adult zebra finches and monitored the birds’ neural activity while they sang. Specifically, they recorded the electrical activity of multiple populations of neurons in the sensorimotor part of the brain that ultimately controls the muscles responsible for singing.

The researchers fed the neural recordings into machine learning algorithms. The idea was that these algorithms would be able to make computer-generated copies of actual zebra finch songs just based on the birds’ neural activity. But translating patterns of neural activity into patterns of sounds is no easy task.

“There are just too many neural patterns and too many sound patterns to ever find a single solution for how to directly map one signal onto the other,” said Gentner.

To accomplish this feat, the team used simple representations of the birds’ vocalization patterns. These are essentially mathematical equations modeling the physical changes—that is, changes in pressure and tension—that happen in the finches’ vocal organ, called a syrinx, when they sing. The researchers then trained their algorithms to map neural activity directly to these representations.


Bird song sample: number of a bird in the study, followed by its own natural recorded song and then the reproduced, biomechanical version of the same song.

This approach, the researchers said, is more efficient than having to map neural activity to the actual songs themselves.

“If you need to model every little nuance, every little detail of the underlying sound, then the mapping problem becomes a lot more challenging,” said Gilja. “By having this simple representation of the songbirds’ complex vocal behavior, our system can learn mappings that are more robust and more generalizable to a wider range of conditions and behaviors.”

The team’s next step is to demonstrate that their system can reconstruct birdsong from neural activity in real time.

Part of the challenge is that songbirds’ vocal production, like humans’, involves not just output of the sound but a constant monitoring of the environment and constant monitoring of the feedback. If you put headphones on humans, for example, and delay when they hear their own voice, disrupting just the temporal feedback, they’ll start to stutter. Birds do the same thing. They’re listening to their own song.  They make adjustments based on what they just heard themselves singing and what they hope to sing next, Gentner explained. A successful vocal prosthesis will ultimately need to work on a timescale that is similarly fast and also intricate enough to accommodate the entire feedback loop, including making adjustments for errors.

“With our collaboration,” said Gentner, “we are leveraging 40 years of research in birds to build a speech prosthesis for humans—a device that would not simply convert a person’s brain signals into a rudimentary set of whole words but give them the ability to make any sound, and so any word, they can imagine, freeing them to communicate whatever they wish.”

Paper: “Neurally driven synthesis of learned, complex vocalizations.” Co-authors include Ezequiel M. Arneodo, Shukai Chen and Daril E. Brown, all at UC San Diego.

This work was supported by the National Institutes of Health (grant R01DC018446), the Kavli Institute for the Brain and Mind (IRG no. 2016-004), the Office of Naval Research (MURI N00014-13-1-0205) and a Pew Latin American Fellowship in the Biomedical Sciences.

Declaration of interests: Vikash Gilja is a compensated consultant of Paradromics, Inc., a brain-computer interface company.

Genetically engineered nanoparticle delivers dexamethasone directly to inflamed lungs

June 16, 2021--Nanoengineers at the University of California San Diego have developed immune cell-mimicking nanoparticles that target inflammation in the lungs and deliver drugs directly where they’re needed. As a proof of concept, the researchers filled the nanoparticles with the drug dexamethasone and administered them to mice with inflamed lung tissue. Inflammation was completely treated in mice given the nanoparticles, at a drug concentration where standard delivery methods did not have any efficacy. 

The researchers reported their findings in Science Advances on June 16.

Schematic of a genetically engineered cell membrane-coated nanoparticle designed to deliver dexamethasone to inflamed lungs. Credit: Zhang Lab

What’s special about these nanoparticles is that they are coated in a cell membrane that’s been genetically engineered to look for and bind to inflamed lung cells. They are the latest in the line of so-called cell membrane-coated nanoparticles that have been developed by the lab of UC San Diego nanoengineering professor Liangfang Zhang. His lab has previously used cell membrane-coated nanoparticles to absorb toxins produced by MRSA; treat sepsis; and train the immune system to fight cancer. But while these previous cell membranes were naturally derived from the body’s cells, the cell membranes used to coat this dexamethasone-filled nanoparticle were not.

Liangfang Zhang, a professor of nanoengineering at UC San Diego, has been developing cell membrane-coated nanoparticles for over a decade.

“In this paper, we used a genetic engineering approach to edit the surface proteins on the cells before we collected the membranes. This significantly advanced our technology by allowing us to precisely overexpress certain functional proteins on the membranes or knockout some undesirable proteins,” said Zhang, who is a senior author of the paper. 

Joon Ho Park, a graduate student in Zhang’s lab and first author of the paper, said the researchers noticed that when endothelial cells become inflamed, they overexpress a protein called VCAM1, whose purpose is to attract immune cells to the site of inflammation. In response, the immune cells express a protein called VLA4, which seeks out and binds to VCAM1. 

“We engineered cell membranes to express the full version of VLA4 all the time,” said Park. “These membranes constantly overexpress VLA4 in order to seek out VCAM1 and the site of inflammation. These engineered cell membranes allow the nanoparticle to find the inflamed sites, and then release the drug that’s inside the nanoparticle to treat the specific area of inflammation.”

While the nanoparticle won’t directly enhance the efficacy of the drug—dexamethasone in this case—concentrating it at the site of interest may mean a lower dosage is required. This study showed that the dexamethasone accumulated at the site of interest at higher levels, and faster, than standard drug delivery approaches. 

“We’re delivering the exact same drug used in the clinic, but the difference is we’re concentrating the drugs to the point of interest,” said Park. “By having these nanoparticles target the inflammation site, it means a larger portion of the medicine will wind up where it’s needed, and not be cleared out by the body before it can accumulate and be effective.”

The researchers note that this genetically engineered cell membrane approach is a platform technology that in theory can be used to target not only inflammation in other areas of the body— VCAM1 is a universal signal of inflammation—but much broader use cases as well.

“This is a versatile platform, not just for lung inflammation but any type of inflammation that upregulates VCAM1,” said Park. “This technology can be generalized; this engineered cell membrane-coated nanoparticle doesn’t have to overexpress VLA4, it could be swapped out to another protein that can target other areas of the body or accomplish other goals.”

Nanoengineering graduate student Joon Ho Park is first author of the study.
 

To engineer the cell membranes to overexpress the VLA4 protein, Park and the team start with packaging VLA4 genes into a viral vector. They then insert this reprogrammed viral vector into lab-grown host cells derived from mice. The cells incorporate the genes that the viral vector is carrying into their own genome and as a result, produce membranes that constantly overexpress VLA4. 

The researchers’ next step is to study the process using human cell membranes, instead of mice cell membranes, that are engineered to express the human version of VLA4. There are still many steps needed before the technology could be tested in human clinical trials, but the researchers say that these early results from the platform technology are encouraging. 

“By leveraging the established gene editing techniques, this study advances the cell membrane-coated nanoparticles to a new level and opens up new opportunities for targeted drug delivery and other medical applications”, concluded by Zhang.  

Paper: “Genetically engineered cell membrane–coated nanoparticles for targeted delivery of dexamethasone to inflamed lungs.” Co-authors include Yao Jiang, Jiarong Zhou, Hua Gong, Animesh Mohapatra, Jiyoung Heo, Weiwei Gao, and Ronnie H. Fang.

This work was supported by the National Institutes of Health (R01CA200574) and the Defense Threat Reduction Agency Joint Science and Technology Office for Chemical and Biological Defense (HDTRA1-18-1-0014).

Titans of industry, academia team up to advance engineering in medicine

Generosity of Shu and K.C. Chien and Peter Farrell to be recognized through named research collaboratory in Franklin Antonio Hall

June 10, 2021--When renowned UC San Diego bioengineer Shu Chien completed medical school in 1953, he wanted to find ways to make technological advancements in healthcare that would improve human lives. To do so, he had to find an engineer to collaborate with, since physicians and engineers were largely siloed professions at the time.

Peter Farrell, founder of sleep-disordered breathing medical device company ResMed, experienced something similar when completing his bioengineering Ph.D. research into treatments with the artificial kidney, working under the guidance of two advisors: one a nephrologist, and the other an engineer.

“Many years ago, if you talked to leaders in medical school about engineering, they’d say ‘Oh we’re not very interested in that,” said Chien. “But today, almost every major medical school leadership would like to have an engineering presence, and conversely leadership in engineering would like to have biomedical engineering complementation.”

Chien went on to earn a Ph.D. in physiology, and helped to create the engineering-meets-medicine world he was looking for as a young physician. The great success of his efforts are reflected in advances made by former students and colleagues around the world and right here at UC San Diego where the Bioengineering Department is ranked No. 3 in the nation according to U.S. News & World Report and No.1 according to the National Research Council of the U.S. National Academies.

Chien's research includes work critical to our understanding of how blood flows in the cardiovascular system. He is one of only a handful of individuals to be awarded the U.S. National Medal of Science and to be voted into all three National Academies (Science, Medicine and Engineering).

As founder of ResMed, Peter Farrell’s development of a machine that helps people with sleep apnea breathe better while asleep has transformed lives and led to greater understanding of the link between sleep-disordered breathing and chronic illnesses such as diabetes and hypertension. The concept of nasal CPAP (continuous positive airway pressure) was pioneered by Dr. Colin Sullivan at the University of Sydney Medical School to treat obstructive sleep apnea. Farrell came to the interface of engineering and medicine as an engineer. He is an elected member of the National Academy of Engineering, and served as founding director of biomedical engineering at the University of New South Wales, Sydney before becoming vice president of research and development at Baxter Healthcare, Japan.

Farrell was research and development vice president at Baxter for five years before founding ResMed, where he remains Chairman of the Board. ResMed sells 360,000 medical devices a month and 1.2 million masks of various types in more than 140 countries to treat sleep apnea, COPD and other respiratory conditions. ResMed is listed on the New York Stock Exchange (RMD) and employs 7,500 people.

Chien and Farrell agree that while the silos that once kept engineering and medicine as distinctly separate from one another have been breaking down, there is still room for improvement.

“Without engineering, medicine is just not going to advance at the level that it should,” said Farrell. “The participation of both fields is not only here to stay, it’s vital for healthcare in general. Engineers and physicians, pharmaceutical scientists and biologists all need to be working together, as a team. In the good programs, like UC San Diego, the silos have virtually disappeared.”

The UC San Diego Institute for Engineering in Medicine, which Chien founded, with Farrell sitting on the advisory board, is a prime example of how engineering and medicine have converged on campus. The Institute facilitates the integration of engineering principles and novel technologies with biomedical and translational research.

KC and Shu Chien

As the silos between engineering and medicine continue to dissolve, there is a growing need on campus for facilities where engineers, physicians and medical researchers can work in the same physical research ecosystems. Shu Chien and his wife, KC, recently joined forces with Peter Farrell to support this vision.

The Chiens and Farrell each recently donated $1.5 million to support programmatic expansion of engineering and medicine on campus. A large collaborative research facility for engineering and medicine in the Jacobs School’s newest building, Franklin Antonio Hall, will be named in recognition of their generosity.

The named Chien-Farrell Institute for Engineering in Medicine Collaboratory will serve as a hub for research at the interface of engineering and medicine. This collaborative research facility is one of 13 such "collaboratories" within the Jacobs School's newest building, Franklin Antonio Hall.

The Chien-Farrell Collaboratory will bring faculty, students, researchers and industry partners from different fields together in the same space, to facilitate the types of truly interdisciplinary, collaborative research required to solve society’s greatest challenges in medicine and healthcare.

“Today, one young person can get trained and have knowledge in all of these fields,” said Chien. “Nevertheless, one person cannot do as much as people collaborating together—we’re limited beings, so we still need a group to work together. That’s the beauty of interdisciplinary research: different people with different expertise mutually beneficial to each other. When we work together like this, the total of our efforts is much greater than the sum of each individual’s work.”

The Chien-Farrell Collaboratory in particular and Franklin Antonio Hall more generally will focus not only on collaborations among researchers from disparate fields, but among academic teams and industry partners as well.

“Entrepreneurship is not about risk taking, it’s about opportunity seeking,” said Farrell “Industry and academia all need to be part of the same ecosystem with the same goals. They support each other in a loop where the best ideas are fed into the marketplace to generate revenue, where a portion of the profit flows back to academia in research support coupled with potential equity. This new Collaboratory and Franklin Antonio Hall accelerate that loop, delivering good ideas which solve problems into the marketplace. Everybody benefits: it can help the campus, the students, society as a whole.”

“I'm really very honored to share the naming of the building with Peter,” said Chien. “He and his company Resmed have made tremendous contributions to the science and engineering of respiratory and sleep problems. I myself am a beneficiary of their product with sleep apnea, so I personally am grateful for that.”

“Shu is a pleasure to work with and a good guy to be involved with,” said Farrell. “He gets it. I have a lot of respect for him.”

Franklin Antonio Hall

In addition to the Chien-Farrell Collaboratory, 12 more of these large research facilities make up the heart of Franklin Antonio Hall. Each collaboratory will house a collection of professor-led research groups from different but related disciplines. Together, these complementary research teams will pursue grand-challenge research in areas like renewable energy technologies, smart cities and smart transportation, wearable and robotics innovations, and digital privacy and security. The building is designed to maximize the circulation and collaboration of UC San Diego faculty, students, professional research staff, and industry partners.

Franklin Antonio Hall will also serve as an important new facility for undergraduate and graduate-student learning, both inside and outside the classroom. The building will provide critical workspace for Jacobs School undergraduate student organizations that are participating in national design competitions. Teams of students will design, build and test their projects in this new collaborative environment. Teams will cycle through the space annually to best serve the growing number of nationally ranked student teams.

Franklin Antonio Hall is named after UC San Diego alumnus Franklin Antonio in recognition of his incredible $30 million gift to the UC San Diego Jacobs School of Engineering. The approximately 186,000 square foot university building is projected to be completed in early 2022.

Philanthropic gifts, like the gift from Shu and K.C. Chien and Peter Farrell, contribute to the Campaign for UC San Diego—a university-wide comprehensive fundraising effort concluding in 2022. Alongside UC San Diego’s philanthropic partners, the university is continuing its nontraditional path toward revolutionary ideas, unexpected answers, lifesaving discoveries and planet-changing impact. Visit the Campaign for UC San Diego website to learn more.

World's largest outdoor earthquake simulator undergoes major upgrade

June 9, 2021-- A major upgrade to the world’s largest outdoor earthquake simulator reached a milestone mid-April when the facility’s floor--all 300,000 lbs of it--was put back into place. When completed this fall, the simulator will have the ability to reproduce multi-dimensional earthquake motions with unprecedented accuracy to make structures and their residents safer during strong shakes.

The simulator, or shake table,  will be able to test the world’s heaviest and tallest structures to gauge how well they would withstand various types of earthquakes. The shake table will be equipped with the ability to reproduce all the six possible movements of the ground, known as six degrees of freedom. The first test following the upgrade will feature a full-scale, 10-story, cross-laminated timber building. 

The shake table's platen, or floor, is put back into place by two cranes at the Englekirk Structural Engineering Center. 

“This facility will save a large number of human lives by making the places we live and work in safer during earthquakes,” said Joel Conte, the shake table’s principal investigator and a professor of structural engineering at the University of California San Diego. Conte and colleagues lay out the details of the upgrade in a paper published in January 2021 in Frontiers in Built Environment

In the paper, researchers also detail the impact that the shake table has had on building and design codes since it opened in 2004. 

In  San Francisco, approximately 6,000 “soft-story” wood-frame buildings are being retrofitted to make them safer in strong earthquakes. Full-scale testing of retrofit systems for these soft-story wood-frame buildings was performed on the UC San Diego shake table in 2013. Professor John van de Lindt from Colorado State University, who led this project, played a key role in writing the guidelines for the retrofit of these buildings.

In 2008, a test led by Professors Robert Fleischman of the University of Arizona and Jose Restrepo of UC San Diego led to new recommendations on how precast concrete floors, known as diaphragms, should be built into parking garage structures to improve their seismic behavior.

In 2011 and 2012, during a series of landmark tests, a team tested elevators and stairs inside a full-size, six-story building. The findings led to new, better guidelines for the way these components should be connected to buildings’ structural frames so they don’t detach during a quake.

How it works
 

Principal investigator Joel Conte (right), who is also a professor of structural engineering at UC San Diego, and Koorosh Lotfizadeh, the table's operations manager, inspect the platen. 

The principle behind the table is relatively simple: various structures are built on top of the facility’s floor, or platen, which is connected to a series of horizontal and vertical actuators, or pistons, that move back and forth, simulating earthquake motions. The movements follow precise earthquake records that researchers have gathered from around the world.

The facility is transitioning from one degree of freedom--the ability to move structures backwards and forwards--to six degrees of freedom, adding the ability to move up and down, left to right, as well as pitch, roll and yaw motions. To understand these last three, think of an airplane in flight: pitch is when the nose of the airplane goes up and its tail goes down; roll is when one wing dips and the other lifts; and yaw is when the plane’s whole body slides from left to right. 

Two additional horizontal actuators were added to two existing ones in a new configuration in order to move the table horizontally forwards and backwards; left to right; and to make a yaw motion. The six existing actuators that move the table up and down were hooked up to a new, stronger hydraulic power source. 

Why do six degrees of freedom matter? 

Tests on a soft-story structure helped design guidelines to retrofit these buildings. 

Reproducing earthquake motions in six degrees of freedom is key because during a temblor, the ground might move in more than one direction. For example, during the 1994 Northridge earthquake in the Los Angeles area, bridge columns punched through bridge decks, hinting at a strong vertical ground motion component. Similarly, during the 1971 San Fernando earthquake, the buildings twisted and swayed, hinting that the ground was probably rotating.

Principal investigator Conte says he believes results of prior tests would have revealed additional ways to make buildings safer if they had been done in six degrees of freedom rather than one.

More power, better sensors

The upgrade will also add a new, state-of-the-art sensing and data collection system with a total of 768 channels to carry information coming from a wide range of sensors, including high-definition cameras, strain gauges, accelerometers and more. The software controlling the shake table also will be upgraded. 

In addition, the mechanism that powers the shake table also been expanded and connected to a hydraulic power system whose capacity has quadrupled. 
 

Students thrive in program focused on diversifying undergraduate engineering at UC San Diego

First cohort of ACES Scholars graduate after completing NSF-funded program supporting students from backgrounds traditionally underrepresented in engineering

Xavier Perez, Yoon Jung Choi and Armando Godoy-Velasquez are members of the first cohort of ACES Scholars.

June 9, 2021--Among the more than 1,400 undergraduate engineering and computer science students earning bachelor’s degrees from the University of California San Diego Jacobs School of Engineering this year, are Xavier Perez, Yoon Jung Choi, and Armando Godoy-Velasquez, who are all members of the first cohort of ACES Scholars. Students in the National Science Foundation-funded Academic Community for Engineering Success (ACES) Scholars program are highly motivated students from economically and educationally underserved backgrounds; nearly all are Pell grant eligible, many are the first in their family to attend college, and many are women or from underrepresented groups in engineering. 

Perez, Choi and Godoy-Velasquez say their participation in the ACES Scholars program was crucial in not only helping them make it to graduation, but to leave their undergraduate years with research experience, internships, and involvement in student organizations under their belts, and offers to attend graduate school and industry careers in hand.

ACES Scholars Program

UC San Diego is one of six universities in the NSF-funded Redshirt in Engineering Consortium, which aims to support low income students through an engineering degree by intervening in the crucial first two years on campus. The program was formed in 2016, and UC San Diego’s Redshirt-funded ACES Scholars program started in the fall of 2017. The Consortium takes its name from the practice of redshirting in college athletics, with the idea of providing extra support to help promising engineering students complete a bachelor’s degree.

“This NSF funding has boosted our ability to provide comprehensive support and improve undergraduate student success here at the Jacobs School," said Pamela Cosman, the UC San Diego PI for the NSF award and a professor in the Department of Electrical and Computer Engineering. Cosman served as Associate Dean for Students of the Jacobs School of Engineering from September 2013 to December 2016. "This NSF investment has allowed us to reach more students, and to engage with them on multiple levels, through programs administered through our IDEA Engineering Student Center."

Summer Engineering Institute at the Jacobs School

ACES Scholars receive a scholarship to participate in the IDEA Engineering Student Center's five-week Summer Engineering Institute before the fall quarter of their first year even begins. The goal of this summer program for incoming Jacobs School undergraduates is to strengthen students' technical preparation and study skills while also offering community building activities to help the students develop a supportive peer network and a familiarity with campus life. As part of the program, students take an academic enrichment course such as ENG 15 "Engineer your Success" as well as a foundational technical engineering course. 

"The Summer Engineering Institute is about building community, making friends, and focusing on the skills and strategies that set our students up for academic and personal success at the Jacobs School of Engineering," said Mechanical and Aerospace Engineering professor Olivia Graeve, who is wrapping up her service as Faculty Director of the IDEA Engineering Student Center this summer. "It's quite gratifying to see so many incoming Jacobs School students coming together through the Summer Engineering Institute. I wish this program had existed when I was an engineering undergraduate here at UC San Diego."

Faculty and Peer Mentorship

Another key component of the ACES program is mentorship. ACES Scholars are paired with a faculty mentor and peer mentor to help answer questions, direct the students to useful contacts, and provide another layer to the support network. ACES Scholars also attend weekly discussions with ACES Program advisor Jessica Baldis and their whole cohort during fall quarter, and monthly or quarterly meetings for the rest of the program.

ACES Scholars have access to professional and technical development workshops, including resume preparation help, which is particularly important because the internship cycle in engineering starts early in the year and many students have never gone through the steps needed to land an engineering internship. ACES Scholars also have access to many additional resources provided by the IDEA Center, including coding workshops, guest speakers, and scholarships. 

Below are snapshots of how the three students have thrived at the Jacobs School thanks in part to the ACES Program. 

"In different ways, each of these students made the most of, and benefited greatly from, early access to community building; research; and peer, staff and faculty mentorship," said UC San Diego nanoengineering professor Darren Lipiomi, the incoming Faculty Director of the IDEA Engineering Student Center. "The ACES Scholars program is a powerful example of how a little extra support and guidance to students at the start of their undergraduate careers can transform careers and lives."

Xavier Perez

Electrical engineering student Xavier Perez has been involved in so much on and off campus it’s hard to keep track of it all. He’s been active in groups ranging from the Society of Hispanic Professional Engineers to intramural soccer; was selected as one of five UC San Diego students for the UC LEADS research program; and conducted award-winning research in Professor Vikash Gilja’s Translational Neuroengineering Lab. He credits his willingness to make these connections and seek out these opportunities to the ACES Scholars program, which helped him get his footing before school even started. 

“The Summer Engineering Institute was amazing,” Perez said. “It opened all these doors as they introduced me to the world of engineering at UC San Diego. With the two classes we got the chance to take--I took ECE5 as well as ENG10--I met the professor I have done research with up until today.”

After meeting Gilja through ECE5, Perez jumped at the opportunity to do research in his lab through the STARS and UC LEADS programs. After fielding offers from Columbia University and UC Irvine, Perez chose to pursue his PhD at UC San Diego, in none other than Gilja’s lab. He’ll be earning his doctorate in electrical engineering with a focus on medical devices and systems. 

His current research has contributed to a neurally-driven speech prosthesis, based on studying the neural activities of song birds. Perez designed a custom recording studio to record the birds’ songs that is 10 times less expensive than the existing professional installation system being used.

Aside from the SEI and meetings with his faculty mentor, Perez said the friends he made through ACES were crucial to his success.

“That’s the other part -- the ACES Scholar community helped me come to UC San Diego with a  group of friends already, which was very helpful. I still talk to all my ACES friends; I even lived with two of them off campus. Another part of the ACES program I really enjoyed was the cohort meetings we had. That was impactful in the sense that it brought us all together once a month or once a quarter such that we could see everyone all together.”
 

Yoon Jung Choi

For chemical engineering student Yoon Jung Choi, the ACES Scholars program was all about making connections. For example, her peer mentor when she first arrived at UC San Diego was an active member of Engineers for a Sustainable World. This introduction to the group and a couple of its members convinced the sustainability-focused Choi to get involved as well. She was an active member of ESW all four years, and served in leadership roles. 

Similarly, her ACES faculty mentors gave her the encouragement and know-how to reach out to her professors. She has been conducting research for the last two years in Professor Ping Liu’s lab, focused on developing new battery technologies.

“I worked on multiple research projects and I also got my name on two publications from that. From this research group I got exposure to the fundamentals of lithium ion batteries, and different experimental techniques to make them and characterize them.”

Choi also appreciated the ACES Scholars regular cohort meetings and discussions. 

“That was very helpful because it provides space for people to mingle and form a community. They also allow people to help each other, clarify concepts in classes, and just hang out with your peers. I think the Jacobs School of Engineering does a great job of forming community; ACES is a great example of that.”

Choi will intern at the NASA Glenn Research Center this summer, before heading to UC Berkeley to earn her master’s degree.

Armando Godoy-Velasquez

Armando Godoy-Velasquez was introduced to structural engineering in a rather unusual way.

“I heard about structural engineering when I was watching a Netflix show called Prison Break,’ he said. “The main character is a structural engineer so I looked it up and started researching about structural engineering, and it really interested me. I liked building things and designing things, and a couple of my family members work in construction so it’s always intrigued me.”

After learning that UC San Diego is the only school in the nation with an undergraduate structural engineering degree, his mind was made up.

It’s all come full circle for Godoy-Velasquez, who accepted a full time position as a field engineer with Turner Construction, after having interned for the company for the past year.  His current project involves, you guessed it, renovating and upgrading the electrical, mechanical, and plumbing systems in a local prison. He’s also worked on commercial office renovations, and may get the opportunity to work on the new San Diego Airport terminal.

Godoy-Velasquez is more than qualified for the job. Thanks to his ACES faculty mentor, he started conducting research in the Powell Laboratory during his first year on campus.

“I worked on a project for the California Earthquake Agency, researching how homes built before the 1980s were prone to more damage during earthquakes,” Godoy-Velasquez said. “So we built walls inside the Powell Lab, then tested them against earthquakes and studied their performance. Then we rebuilt them reinforced with plywood sheeting and compared the differences in performance with reinforcement and without reinforcement.”

During his time at UC San Diego, Godoy-Velasquez played on the men’s club soccer team, was a member of the Tau Kappa Epsilon fraternity, was a member of SHPE, and also joined the Associated Schools of Construction Design-Build project team. Their project was sponsored by Clarke Construction company, which was building the new Sixth College at UC San Diego, so a lot of their homework was based off those real, current, plans. 

In addition to his ACES faculty mentor providing an early research opportunity, Godoy-Velasquez said the Summer Engineering Institute was also critical to his success. 

“SEI was a really crucial program for me. I’m still friends with everyone I met in SEI; that’s pretty much been my main study group in college. When I started off my first quarter after SEI, I felt like I wasn’t a freshman. That was thanks to SEI, all the workshops we had, I felt like I’d been there for a year already.”

He had such a positive experience that he returned the following year as a peer facilitator to help incoming students get the same jump start that he did. 

“The peer mentors during my SEI year were really cool, and I still keep in touch with them. They helped me out even after SEI. Being able to give that back to incoming students was really great.”

Super productive 3D bioprinter could help speed up drug development

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The high-throughput 3D bioprinting setup performing prints on a standard 96-well plate. Images adapted from Biofabrication

June 8, 2021 -- A 3D printer that rapidly produces large batches of custom biological tissues could help make drug development faster and less costly. Nanoengineers at the University of California San Diego developed the high-throughput bioprinting technology, which 3D prints with record speed—it can produce a 96-well array of living human tissue samples within 30 minutes. Having the ability to rapidly produce such samples could accelerate high-throughput preclinical drug screening and disease modeling, the researchers said.

The process for a pharmaceutical company to develop a new drug can take up to 15 years and cost up to $2.6 billion. It generally begins with screening tens of thousands of drug candidates in test tubes. Successful candidates then get tested in animals, and any that pass this stage move on to clinical trials. With any luck, one of these candidates will make it into the market as an FDA approved drug.

The high-throughput 3D bioprinting technology developed at UC San Diego could accelerate the first steps of this process. It would enable drug developers to rapidly build up large quantities of human tissues on which they could test and weed out drug candidates much earlier.

“With human tissues, you can get better data—real human data—on how a drug will work,” said Shaochen Chen, a professor of nanoengineering at the UC San Diego Jacobs School of Engineering. “Our technology can create these tissues with high-throughput capability, high reproducibility and high precision. This could really help the pharmaceutical industry quickly identify and focus on the most promising drugs.”

The work was published in the journal Biofabrication.

The researchers note that while their technology might not eliminate animal testing, it could minimize failures encountered during that stage.

“What we are developing here are complex 3D cell culture systems that will more closely mimic actual human tissues, and that can hopefully improve the success rate of drug development,” said Shangting You, a postdoctoral researcher in Chen’s lab and co-first author of the study.

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Examples of the geometries that the high-throughput 3D bioprinter can rapidly produce.

 

The technology rivals other 3D bioprinting methods not only in terms of resolution—it prints lifelike structures with intricate, microscopic features, such as human liver cancer tissues containing blood vessel networks—but also speed. Printing one of these tissue samples takes about 10 seconds with Chen’s technology; printing the same sample would take hours with traditional methods. Also, it has the added benefit of automatically printing samples directly in industrial well plates. This means that samples no longer have to be manually transferred one at a time from the printing platform to the well plates for screening.

“When you’re scaling this up to a 96-well plate, you’re talking about a world of difference in time savings—at least 96 hours using a traditional method plus sample transfer time, versus around 30 minutes total with our technology,” said Chen.

Reproducibility is another key feature of this work. The tissues that Chen’s technology produces are highly organized structures, so they can be easily replicated for industrial scale screening. It’s a different approach than growing organoids for drug screening, explained Chen. “With organoids, you’re mixing different types of cells and letting them to self-organize to form a 3D structure that is not well controlled and can vary from one experiment to another. Thus, they are not reproducible for the same property, structure and function. But with our 3D bioprinting approach, we can specify exactly where to print different cell types, the amounts and the micro-architecture.”

How it works

To print their tissue samples, the researchers first design 3D models of biological structures on a computer. These designs can even come from medical scans, so they can be personalized for a patient’s tissues. The computer then slices the model into 2D snapshots and transfers them to millions of microscopic-sized mirrors. Each mirror is digitally controlled to project patterns of violet light—405 nanometers in wavelength, which is safe for cells—in the form of these snapshots. The light patterns are shined onto a solution containing live cell cultures and light-sensitive polymers that solidify upon exposure to light. The structure is rapidly printed one layer at a time in a continuous fashion, creating a 3D solid polymer scaffold encapsulating live cells that will grow and become biological tissue.

The digitally controlled micromirror array is key to the printer’s high speed. Because it projects entire 2D patterns onto the substrate as it prints layer by layer, it produces 3D structures much faster than other printing methods, which scans each layer line by line using either a nozzle or laser.

“An analogy would be comparing the difference between drawing a shape using a pencil versus a stamp,” said Henry Hwang, a nanoengineering Ph.D. student in Chen’s lab who is also co-first author of the study. “With a pencil, you’d have to draw every single line until you complete the shape. But with a stamp, you mark that entire shape all at once. That’s what the digital micromirror device does in our technology. It’s orders of magnitude difference in speed.”

This recent work builds on the 3D bioprinting technology that Chen’s team invented in 2013. It started out as a platform for creating living biological tissues for regenerative medicine. Past projects include 3D printing liver tissues, blood vessel networks, heart tissues and spinal cord implants, to name a few. In recent years, Chen’s lab has expanded the use of their technology to print coral-inspired structures that marine scientists can use for studying algae growth and for aiding coral reef restoration projects.

Now, the researchers have automated the technology in order to do high-throughput tissue printing. Allegro 3D, Inc., a UC San Diego spin-off company co-founded by Chen and a nanoengineering Ph.D. alumnus from his lab, Wei Zhu, has licensed the technology and recently launched a commercial product.

Paper: “High throughput direct 3D bioprinting in multiwell plates.” Co-authors include Xuanyi Ma, Leilani Kwe, Grace Victorine, Natalie Lawrence, Xueyi Wan, Haixu Shen and Wei Zhu.

This work was supported in part by the National Institutes of Health (R01EB021857, R21AR074763, R21HD100132, R33HD090662) and the National Science Foundation (1903933, 1937653).

Class of 2021 students honored at Ring Ceremony

The recipients of the 2021 Jacobs School of Engineering Awards of Excellence

June 8, 2021-- In addition to UC San Diego’s commencement ceremonies, the Jacobs School of Engineering will honor the class of 2021 at its annual Ring Ceremony on Saturday, June 12. During the Ceremony, graduating engineering and computer science students will receive their class ring, and recite together the Jacobs School of Engineering oath, vowing to practice engineering with integrity and high ethical standards. 

Six students who have made significant contributions to their department and the Jacobs School community, will also be honored with Awards of Excellence. 

Watch the Ring Ceremony live here: https://jacobsschool.ucsd.edu/idea/programs/ring-ceremony  And learn more about these impressive graduates below. 


Bioengineering: Aoife O’Farrell

 Aoife O’Farrell was drawn to bioengineering because of the excitement of the field; there is still so much to discover about how our bodies work, and how we can treat disease. She wanted to find ways to transfer medical discoveries from the lab to patients that need them, and had the opportunity to do so as an undergraduate researcher at the UC San Diego Moores Cancer Center.

“I am most excited by the opportunities in the field of immunoengineering - designing novel therapeutics to modulate the immune system to treat cancer and autoimmune disease. I currently work at the Moores Cancer Center, studying how immune checkpoint blockade inhibitors can best be used to treat certain types of cancer, and hope to continue similar work in the future to aid patients currently unresponsive to standard of care.”

After graduating, she’s pursuing a PhD in bioengineering at the University of Pennsylvania, with funding from the NSF Graduate Research Fellowship Program. She plans to continue her immunoengineering and immo-oncology research, and hopes to eventually become a professor at a public university. 

Aside from coursework and hands-on research with Dr. Robert Saddawi-Konefka in the Gutkind Lab at Moores, O’Farrell was involved in several organizations that helped shape her time on campus: she worked as a Campus Ambassador (tour guide) for three years; and served as an officer in both Engineers without Borders and the Biomedical Engineering Society (BMES).

As the project lead for Engineers Without Borders’  Project FogCatchers, O'Farrell led a team of 15 students to develop technology to aid those without access to clear water, and authored two successful research grants to fund this work. As BMES’ Vice President External, she helped run Bioengineering Day in 2020, including a quick pivot to a virtual event, and planned the Bioengineering Career Fair in 2021. 

Her advice to students is to be willing to try things that make you uncomfortable.

“It sounds cliche, but I think the best advice I can give is to say “yes” to things,” O’Farrell said. “There were a lot of times where I felt uncomfortable about jumping into something (like leading an engineering-based project team, or writing a research grant to ask for funding) but being willing to try anyways opened so many doors that I never would have experienced otherwise. There’s a lot of support on campus at UC San Diego to help with  whatever it is you want to learn.”

 

Computer Science and Engineering: Priyal Suneja

Priyal Suneja’s favorite class was always math, until a basic programming class in high school got her curious about how the words she was typing could make the computer perform certain functions. 

“In order to learn exactly how that pipeline worked, I decided to pursue CS as a major,” Suneja said.

After graduating with the Department’s Award of Excellence, Suneja is heading to the University of Washington, Seattle, for a PhD in Systems and Networking. 

While at UC San Diego, she served as a computer science tutor, conducted research in operating systems, and was involved in the Women in Computing student organization, serving as president this year.

“I started out as a member of WIC and then proceeded to serve as a board member. I had the privilege to serve as WIC’s president over this last year.”

Her advice for students is to get to know your peers and professors.

“My journey at UC San Diego would have been starkly different had I not met the friends and mentors that I met. They made me realize the importance of enjoying what I do, and helped me believe that I could do anything that I set my mind to. I owe all the fun parts of my four years at UC San Diego to the people that I met here.”

 

Electrical and Computer Engineering: Geeling Chau

To computer engineering student Geeling Chau, electrical and computer engineering is magic. 

“Electrical engineering is the magic that has enabled the life changing technological advancements we've seen in the past few decades. Through doing robotics in high school and taking a hands-on interactive device design course, I was fortunate to see first hand the utility of studying this field and gain the confidence that I could take a step into understanding this magic.”

At UC San Diego, she’s applied this magic to brain computer interface work, through research in Professor Vikash Gilja’s Translational Neuroengineering Lab. She specifically worked on a project trying to detect emotional signals from a user playing video games. Chau also conducted research in the Voytek Lab on a data science project on parameterizing power spectral features on working memory neural signals, and with the de Sa Lab on building real-time BCIs for detecting focus levels.

In addition to research, Chau has been involved in the IEEE Honor Society, Eta Kappa Nu (HKN), serving as an officer for three years. While president of HKN, she co-founded the NeuroTech club, which has grown to span more than seven departments at UC San Diego. As a computer engineering student, she also worked as a tutor in the Computer Science and Engineering Department. 

After graduating with the ECE Award for Excellence, Chau is heading to CalTech to pursue a PhD in Computation and Neural Systems. She hopes to contribute to the field of neural engineering, and the next generation of brain computer interface technologies.

Her advice to students?

“There's a lot you can do as an engineering student at UC San Diego - be strategic in what opportunities you choose, and remember why you chose it -- this really helped me get through times that felt tough. You will be pushed to your limits, but remember that being in that uncomfortable state is how you will grow the fastest.”

 

Mechanical and Aerospace Engineering: Luca Scotzniovsky

Luca Scotzniovsky was amazed by planes as a child, and was intrigued by how an object so large and heavy could even get off the ground. This translated into a serious interest in physics in high school, and eventually to aerospace engineering. After being involved in aerospace engineering organizations and conducting research in two different labs at the Jacobs School, he found his calling.

“Upon working in the Large-Scale Design Optimization Lab, I found the path I wanted to follow once I finished my undergraduate career,” Scotzniovsky said.

He will return to UC San Diego next year to pursue a Ph.D. in mechanical and aerospace engineering, working in Professor John Hwang’s Large-Scale Design Optimization Lab, conducting fluid mechanics-based optimization and modeling for urban air mobility vehicles.

During his undergraduate years, Scotzniovsky played on the Men’s Club Soccer Team, including two years as president and captain. He was also a member of Design-Build-Fly, and conducted research in Hwang’s lab, as well in Professor David Saintillan’s lab, where he focused on data analysis of a DNA Loop Extrusion model. 

Scotzniovsky makes no bones about it--engineering is challenging. But focusing on the basics and having a support network will make the journey possible, and enjoyable.

“You can ask anyone in the Jacobs School of Engineering and they will agree that engineering is plain hard, and everyone has had a tough time with it at some point. My experiences have shown me that you really get out what you put into it and that the basic concepts are crucial to really understand the more complex subtopics within engineering. Another thing, which I wish I knew earlier, is that the experience of joining major-related organizations is not only interesting but just as important when it comes to learning and gaining relevant expertise. The one thing that shouldn't stop you from applying for a club, lab, or internship is your course-related experience, especially since the opportunity will provide the proper tools to succeed.”

 

Nanoengineering: Zoe Li

Chemical engineering student Zoe Li came to campus with a career plan in place: she wanted to be a teacher. Working as a teaching assistant in the nanoengineering and math departments, as well as working as a physics tutor in the PATHS program, helped her decide she would specialize in science and STEM education.

 After graduating with the Department of Nanoengineering’s Award of Excellence, Li, who double majored in psychology with a minor in education, will return to UC San Diego for the one-year master’s of education plus teaching credential program, before shaping the next generation of scientists and engineers as a secondary science teacher. 

“I’ve had a lot of jobs in education; I’ve taught pretty much everything from theater when I was younger, and writing, and now I’m teaching more of the STEM subjects like math, science and computer science,” she said. “So it’s been a shift for me. I thought I was going to be an English teacher when I was in high school, but now I’m like ‘Science is cool too’!”

In addition to these teaching roles, on campus Li also worked as a Resident Assistant for three years in Marshall and Revelle colleges, and is an EcoNaut for Housing, Dining and Hospitality, educating students on their latest sustainability goals and calls to action. This year, that included educating students about HDH’s new reusable to-go containers. 

Her advice for students is to find a group of friends you can commiserate with--which can include professors! 

“What got me through these years was having a good group of friends in all my classes. Every time I felt like I could just drop out of chemical engineering and just be a psychology major, my friends would say ‘No, we need to take these classes together!’ In chemical engineering we take almost all our classes with the same cohort so you get to know thm super well. That’s what got me through it, getting to know friends. My other advice is be friends with your professors. They get you through it too.”
 

Structural Engineering: Janelle Coleen Dela Cueva

In high school, Janelle Coleen Dela Cueva was involved in extracurriculars including auto mechanics and woodshop, where she got to work on cars and build birdhouses. 

“ I had so much fun working on these projects that I felt pursuing a degree in structural engineering would allow me to continue designing and creating throughout my entire life. When it comes to coursework, I found that solving problems with a practical application of theory solidified my love for engineering.”

After graduating with the Award of Excellence, Dela Cueva will return to UC San Diego to pursue a PhD in structural engineering, researching advanced aerospace composites.

As an undergraduate, Dela Cueva was involved with the Society of Civil and Structural Engineers (SCSE), serving as Social Chair and VP Internal, and also conducted research as a UC Leadership Excellence through Advanced Degrees (UC LEADS) undergraduate fellowship, having the opportunity to be first author on a paper characterizing fracture in carbon fiber composites. 

Through her roles with SCSE, Dela Cueva had a particular focus on outreach to younger students, and creating a supportive environment for all students at UC San Diego. 

“I found that plan and action go hand in hand to push forward solutions for issues affecting students of color.  In my many roles, I led a team of 5 students to create and promote professional development opportunities for students in my department. Transforming ideas into many initiatives, I created opportunities for young engineers through general body meetings, scientific writing workshops, and industry panels. Through SCSE, I started out teaching local middle schoolers about seismic engineering with our Seismic Outreach initiative and moved onto building houses in Tijuana. I experienced firsthand the integral role engineering plays in impacting the community and I wanted to continue being a part of that throughout my career.”

Her advice to students is to take advantage of every opportunity available, but not at the expense of your own well-being. 

“Over the four years that I have spent studying at UC San Diego, I learned that taking the time to rest will really let your work shine. I also believe that it’s important to not be disheartened by failures, but rather take the chance to learn from them. There will inevitably be times that you don’t succeed at first, but with great effort and support from the people around you things will always work out in the end.”

Doing this allowed her to not only survive her undergraduate years, but enjoy the process too.

“I had a lot of fun. The Jacobs School of Engineering has one the most diverse set of opportunities to grow in engineering. The hands-on experience and education that I received on advanced aerospace composite manufacturing was a rare opportunity that is seldom found at other schools. I feel genuinely lucky and grateful to be able to complete my undergraduate at this institution."

Stabilizing gassy electrolytes could make ultra-low temperature batteries safer

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Artistic rendering of a battery separator that condenses gas electrolytes into liquid at a much lower pressure. The new separator improves battery performance in the extreme cold by keeping more electrolyte, as well as lithium ions, flowing in the battery. Credit: Chen group

 

June 7, 2021 -- A new technology could dramatically improve the safety of lithium-ion batteries that operate with gas electrolytes at ultra-low temperatures. Nanoengineers at the University of California San Diego developed a separator—the part of the battery that serves as a barrier between the anode and cathode—that keeps the gas-based electrolytes in these batteries from vaporizing. This new separator could, in turn, help prevent the buildup of pressure inside the battery that leads to swelling and explosions.

“By trapping gas molecules, this separator can function as a stabilizer for volatile electrolytes,” said Zheng Chen, a professor of nanoengineering at the UC San Diego Jacobs School of Engineering who led the study.

The new separator also boosted battery performance at ultra-low temperatures. Battery cells built with the new separator operated with a high capacity of 500 milliamp-hours per gram at -40 C, whereas those built with a commercial separator exhibited almost no capacity. The battery cells still exhibited high capacity even after sitting unused for two months—a promising sign that the new separator could also prolong shelf life, the researchers said.

The team published their findings June 7 in Nature Communications.

The advance brings researchers a step closer to building lithium-ion batteries that can power vehicles in the extreme cold, such as spacecraft, satellites and deep-sea vessels.

This work builds on a previous study published in Science by the lab of UC San Diego nanoengineering professor Ying Shirley Meng, which was the first to report the development of lithium-ion batteries that perform well at temperatures as low as -60 C. What makes these batteries especially cold hardy is that they use a special type of electrolyte called a liquefied gas electrolyte, which is a gas that is liquefied by applying pressure. It is far more resistant to freezing than a conventional liquid electrolyte.

But there’s a downside. Liquefied gas electrolytes have a high tendency to go from liquid to gas. “This is the biggest safety issue with these electrolytes,” said Chen. In order to use them, a lot of pressure must be applied to condense the gas molecules and keep the electrolyte in liquid form.

To combat this issue, Chen’s lab teamed up with Meng and UC San Diego nanoengineering professor Tod Pascal to develop a way to liquefy these gassy electrolytes easily without having to apply so much pressure. The advance was made possible by combining the expertise of computational experts like Pascal with experimentalists like Chen and Meng, who are all part of the UC San Diego Materials Research Science and Engineering Center (MRSEC).

Their approach makes use of a physical phenomenon in which gas molecules spontaneously condense when trapped inside tiny, nanometer-sized spaces. This phenomenon, known as capillary condensation, enables a gas to become liquid at a much lower pressure.

The team leveraged this phenomenon to build a battery separator that would stabilize the electrolyte in their ultra-low temperature battery—a liquefied gas electrolyte made of fluoromethane gas. The researchers built the separator out of a porous, crystalline material called a metal-organic framework (MOF). What’s special about the MOF is that it is filled with tiny pores that are able to trap fluoromethane gas molecules and condense them at relatively low pressures. For example, fluoromethane typically condenses under a pressure of 118 psi at -30 C; but with the MOF, it condenses at just 11 psi at the same temperature.

“This MOF significantly reduces the pressure needed to make the electrolyte work,” said Chen. “As a result, our battery cells deliver a significant amount of capacity at low temperature and show no degradation.”

The researchers tested the MOF-based separator in lithium-ion battery cells—built with a carbon fluoride cathode and lithium metal anode—filled with fluoromethane gas electrolyte under an internal pressure of 70 psi, which is well below the pressure needed to liquefy fluoromethane. The cells retained 57% of their room temperature capacity at -40 C. By contrast, cells with a commercial separator exhibited almost no capacity with fluoromethane gas electrolyte at the same temperature and pressure.

The tiny pores of the MOF-based separator are key because they keep more electrolyte flowing in the battery, even under reduced pressure. The commercial separator, on the other hand, has large pores and cannot retain the gas electrolyte molecules under reduced pressure.

But tiny pores are not the only reason the separator works so well in these conditions. The researchers engineered the separator so that the pores form continuous paths from one end to the other. This ensures that lithium ions can still flow freely through the separator. In tests, battery cells with the new separator had 10 times higher ionic conductivity at -40 C than cells with the commercial separator.

Chen’s team is now testing the MOF-based separator on other electrolytes. “We are seeing similar effects. We can use this MOF as a stabilizer to adsorb various kinds of electrolyte molecules and improve the safety even in traditional lithium batteries, which also have volatile electrolytes.”

Paper: “Sub-Nanometer Confinement Enables Facile Condensation of Gas Electrolyte for Low-Temperature Batteries.” Co-authors include Guorui Cai*, Yijie Yin*, Dawei Xia*, Amanda A. Chen, John Holoubek, Jonathan Scharf, Yangyuchen Yang, Ki Kwan Koh, Mingqian Li, Daniel M. Davies and Matthew Mayer, UC San Diego; and Tae Hee Han, Hanyang University, Seoul, Korea.

*These authors contributed equally to this work

This work was supported by NASA’s Space Technology Research Grants Program (ECF 80NSSC18K1512), the National Science Foundation through the UC San Diego Materials Research Science and Engineering Center (MRSEC, grant DMR-2011924) and startup funds from the Jacobs School of Engineering at UC San Diego. This work was performed in part at the San Diego Nanotechnology Infrastructure (SDNI) at UC San Diego, a member of the National Nanotechnology Coordinated Infrastructure, which is supported by the National Science Foundation (grant ECCS-1542148). This research used resources of the National

Energy Research Scientific Computing Center, a DOE Office of Science User Facility supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. This work also used the Extreme Science and Engineering Discovery Environment (XSEDE), and the Comet and Expanse supercomputers at the San Diego Supercomputing Center, which is supported by National Science Foundation (grant ACI-1548562).

NASA's Perseverance inspires UC San Diego's Yonder Dynamics

Several members of the Yonder Dynamics team, with their rover Apathy

By Melissa Hernandez

June 3, 2021--NASA’s latest feat, the landing of its rover Perseverance on Mars this past February, inspired the nation and world, as people were able to watch in near real-time as the autonomous robot touched down on Mars. Perseverance has an important job: gathering soil samples and other intel on the red planet to answer the age-old question: Is there life on Mars? This accomplishment was particularly exciting for the Yonder Dynamics student robotics team at the Jacobs School of Engineering at UC San Diego, which builds a Mars rover of their own each year in a bid to compete in the international University Rover Challenge (URC) hosted by The Mars Society.

 Rovers that are accepted to the competition are tasked with tackling challenges similar to what Perseverance faces, including autonomously collecting soil samples, traversing difficult terrain to deliver a payload, repairing broken equipment on a mock lander, and autonomously navigating to a set site. Though the in-person URC competition was cancelled in 2020 and 2021 due to COVID-19, the Yonder Dynamics team and their rover, Apathy, were one of 36 teams from around the world that qualified for a pared down remote competition in June 2021, with teams competing at their own campuses. Watch footage of their rover here.

Fourth-year biophysics student and Yonder Dynamics Project Manager and Science Team Lead Luke Piszkin, said watching the Perseverance’s landing was inspirational. 

“The NASA rovers have been a huge inspiration for us at Yonder, especially the students on the science sub-team. The goal of the science team is to develop ways for our rover to look for signs of life in the environment to find out if there is life on other planets,” Piszkin said. “We’ve mimicked the Perseverance’s way of detecting life on our rover by using a high-powered spectroscopy laser to use light scattering to detect organic molecules in the soil, which would give us clues of past life."

Yonder’s 2020 rover, Apathy, was one of 36 from around the world that qualified for the University Rover Challenge competition before it was cancelled due to COVID-19 restrictions. This wasn’t the only setback the team would face in 2020. Yonder Dynamics also had to make changes to the way they functioned as a robotics team, as the pandemic forced them into a fully remote workflow, which is especially challenging for a team building a physical robot. Despite not having access to their rover or being able to work in-person, the team was able to not only complete a submission to the virtual 2021 competition, but they were even able to make improvements to Apathy, including a complete revamp of the electronics of the rover, an improvement to the code underpinning its autonomous tasks, and mechanical improvements to Apathy’s robotic arm.

Electrical team lead and second-year electrical engineering student Karl Johnson, notes the changes the electrical team has been able to make. 

“We changed a lot of the wiring on our rover from a breadboard, which is not optimal and very complicated. This year we decided to learn more about printed circuit board design, and we’ve designed and printed our own PCBs to put on the rover,” Johnson said. “Even without access to the rover we can design the boards to then replace the existing breadboards once we have physical access to the rover. It provides an opportunity for all the electronics team members to contribute to the rover.”

 The country-wide shutdown not only affected the Yonder team in terms of the way they work on the rover, but it affected their approach to planning their future as an organization on campus. Their entire recruitment process was completed online.

Fourth-year computer science student and Software co-lead Cyrus Cowley explained that the software team was able to create a simulated version of Apathy, which allowed them to work on the autonomous tasks, without accessing the actual robot.

“Because of COVID-19, we have been focusing a lot on simulation. We’ve gone through and taken our entire software stack and simulated it. It can run on any member of the software team’s computer,” Cowley said. “We can launch the simulation with just two commands. We rethought our approach to our autonomous traversal task entirely, and things have gone pretty well.”

On the mechanical side of things, Johnson highlighted that not having physical access to their hardware was a blow to the mechanical team. To deal with this, they created CAD replicas of the mechanics of the robot, using these simulated versions of their hardware to test out changes and new additions. Through this form of remote designing, the mechanics team has been able to visualize the future physical changes that will be done to the rover. 

 “We have been able to improve a lot of aspects that have been flaws in our design through our CAD models,” Johnson said. “When we get back to physically working on it, these  will help us improve the mechanics of our rover.”

“We promoted recruitment events normally as we would before and much like we would’ve done in person we had a general body meeting for potential new members,” Johnson said. “This year we had a pretty good turnout for interviews, fortunately, but with things being virtual it is difficult to keep retention with new members.”

The new robotic arm that the Yonder team designed for Apathy.

Despite the circumstances, the Yonder Team was able to submit the System Acceptance Review documents required to earn a spot in the University Rover Challenge; these consist of a five-minute video and a seven-page report detailing the ins and outs of their rover. Their hard work paid off when they found out that Apathy was one of only 36 from around the world to score highly enough to qualify for the pared down version of the competition being held remotely in 2021. Unfortunately, since each competing team needs to setup their own course on their own campus this year due to COVID considerations, the Yonder Dynamics team made the tough decision to not compete.

“Unfortunately, we will not be participating in the virtual competition this year because we do not have the time or resources to set up the courses for ourselves,” said Piszkin. “But seeing Apathy score so well was a really great feeling, knowing that all the time and effort we put in during the last year made a difference. Although we have to miss this year's virtual competition, we are looking forward to competing for the presumably in-person URC 2022.”

The team first qualified for the competition in 2017, and has since qualified in 2018 and 2020. Their latest rover, Apathy, is a nod to the team’s culture.

“We just thought it was funny,” said Piszkin. “It sort of represents the style of Yonder: we don't take ourselves too seriously.”

Light-shrinking material lets ordinary microscope see in super resolution

Square, semi-transparent material held against light.
This light-shrinking material turns a conventional light microscope into a super-resolution microscope. Credit: Junxiang Zhao

June 1, 2021 -- Electrical engineers at the University of California San Diego developed a technology that improves the resolution of an ordinary light microscope so that it can be used to directly observe finer structures and details in living cells.

The technology turns a conventional light microscope into what’s called a super-resolution microscope. It involves a specially engineered material that shortens the wavelength of light as it illuminates the sample—this shrunken light is what essentially enables the microscope to image in higher resolution.

“This material converts low resolution light to high resolution light,” said Zhaowei Liu, a professor of electrical and computer engineering at UC San Diego.

Closeup of a microscope stage.
The material mounted on the stage of an inverted microscope. Credit: Junxiang Zhao

“It’s very simple and easy to use. Just place a sample on the material, then put the whole thing under a normal microscope—no fancy modification needed.”

The work, which was published in Nature Communications, overcomes a big limitation of conventional light microscopes: low resolution. Light microscopes are useful for imaging live cells, but they cannot be used to see anything smaller. Conventional light microscopes have a resolution limit of 200 nanometers, meaning that any objects closer than this distance will not be observed as separate objects. And while there are more powerful tools out there such as electron microscopes, which have the resolution to see subcellular structures, they cannot be used to image living cells because the samples need to be placed inside a vacuum chamber.

“The major challenge is finding one technology that has very high resolution and is also safe for live cells,” said Liu.

The technology that Liu’s team developed combines both features. With it, a conventional light microscope can be used to image live subcellular structures with a resolution of up to 40 nanometers.

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Artistic rendering of the new super resolution microscopy technology. Animal cells (red) are mounted on a slide coated with the multilayer hyperbolic metamaterial. Nanoscale structured light (blue) is generated by the metamaterial and then illuminates the animal cells. Image credit: Yeon Ui Lee

 

The technology consists of a microscope slide that’s coated with a type of light-shrinking material called a hyperbolic metamaterial. It is made up of nanometers-thin alternating layers of silver and silica glass. As light passes through, its wavelengths shorten and scatter to generate a series of random high-resolution speckled patterns. When a sample is mounted on the slide, it gets illuminated in different ways by this series of speckled light patterns. This creates a series of low resolution images, which are all captured and then pieced together by a reconstruction algorithm to produce a high resolution image.

Microscope images displayed in orange against a black background.
Comparison of images taken by a light microscope without the hyperbolic metamaterial (left column) and with the hyperbolic metamaterial (right column): two close fluorescent beads (top row), quantum dots (middle row), and actin filaments in Cos-7 cells (bottom row). Adapted from Nature Communications

The researchers tested their technology with a commercial inverted microscope. They were able to image fine features, such as actin filaments, in fluorescently labeled Cos-7 cells—features that are not clearly discernible using just the microscope itself. The technology also enabled the researchers to clearly distinguish tiny fluorescent beads and quantum dots that were spaced 40 to 80 nanometers apart.

The super resolution technology has great potential for high speed operation, the researchers said.  Their goal is to incorporate high speed, super resolution and low phototoxicity in one system for live cell imaging.

Liu’s team is now expanding the technology to do high resolution imaging in three-dimensional space. This current paper shows that the technology can produce high resolution images in a two-dimensional plane. Liu’s team previously published a paper showing that this technology is also capable of imaging with ultra-high axial resolution (about 2 nanometers). They are now working on combining the two together.

Paper title: “Metamaterial assisted illumination nanoscopy via random super-resolution speckles.” Co-authors include: Yeon Ui Lee*, Junxiang Zhao*, Qian Ma*, Larousse Khosravi Khorashad, Clara Posner, Guangru Li, G. Bimananda M. Wisna, Zachary Burns and Jin Zhang, UC San Diego.

*These authors contributed equally to this work

This work was supported by the Gordon and Betty Moore Foundation and the National Institutes of Health (R35 CA197622). This work was performed in part at the San Diego Nanotechnology Infrastructure (SDNI) at UC San Diego, a member of the National Nanotechnology Coordinated Infrastructure, which is supported by the National Science Foundation (grant ECCS-1542148).

A 'self-stirring' pill enhances drug bioavailability

Self-propelling microparticles enhance the dissolution of drugs in the stomach, achieving better bioavailability without the side effects of high dosing.

May 28, 2021 -- The majority of drugs we take are administered orally, and while this route is easy for patients, safe, and effective, there are many hurdles to overcome before a drug molecule can be delivered to a desired organ or location in the body. This is not always a bad thing and your body does a fairly good job at keeping foreign molecules and parasites out. However, ensuring drugs are absorbed at levels high enough to elicit a desired therapeutic outcome can be challenging.

One of the main parameters to assess drug performance is bioavailability, which is defined as the fraction of dosed drug that reaches systemic circulation. Achieving high bioavailability depends strongly on drug solubility, stability in the stomach, and its absorption in the GI tract, among other factors. One way around this is high dosing, but this can be dangerous and result in undesired side effects. Needless to say, efficient absorption through this route is often difficult to achieve.

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Top row: Images of aspirin-loaded static (white) and microstirring pills (black). Bottom row: The tube used to perform the pill administration by oral gavage. Images courtesy of Advanced Science

From modifying the structure of drug molecules to developing sophisticated formulation systems, researchers are exploring new and innovative ways to safely enhance drug bioavailability. In a recent study published in Advanced Science, researchers at the University of California San Diego report the development of a microstirring pill platform with built-in mixing capability to enhance drug uptake and bioavailability.

“For over a decade we have been working on using micromotor-based active transport to improve the delivery of drugs,” said Joseph Wang, a professor of nanoengineering at UC San Diego and co-corresponding author of the study. “Our recent efforts have been aimed at bridging the field of microrobots with the pharmaceutical industry. Our goal has been to greatly increase the bioavailability of oral drugs by incorporating a built-in stirring capability into traditional drug tablets.”

To accomplish this, Wang, an expert in the field of microrobotics, reached out to UC San Diego nanoengineering professor Liangfang Zhang, who is himself an expert in drug design and delivery and the study's other corresponding author. They hypothesize that including chemically-powered microstirrers into a pharmaceutical pill could enhance the drug dissolution and dispersion in the stomach, leading to faster absorption and increased bioavailability.

The researchers note that their “smart pill” platform is safe. “Similar to conventional oral pills, the self-stirring pills cause no damage to the stomach,” said Wang.

Zhang and Wang’s pill contains embedded “microengines” called Janus microparticles made from magnesium microparticles that are partially coated with a thin layer of titanium dioxide. The fabrication process leaves a small opening in the particle’s structure through which microbubbles generated via an internal chemical reaction can exit and shoot the microparticle around.

“Embedding microscopic stirrers into a pill matrix offers significantly faster pill disintegration and dissolution,” explained Wang. “Since the encapsulated drugs and microstirrers are decoupled, the drug loading is not affected or compromised by the microstirrer.”

In vivo studies using animal models demonstrated that the enhanced pills greatly improved the absorption and bioavailability of aspirin, both immediately post administration and at longer time scales. “Considering [these] encouraging results, we anticipate a high likelihood of clinical translation of the microstirring pill technology,” said Wang.

“In principal, the microstirrer pill can be broadly applicable for numerous types of oral drugs. The concept thus has a very high translation potential: adding only one excipient material (the synthetic microstirrers) into the pill formulation without changing anything else.”

Source: Advanced Science News

Thin, large-area device converts infrared light into images

May 27, 2021 -- Seeing through smog and fog. Mapping out a person’s blood vessels while monitoring heart rate at the same time—without touching the person’s skin. Seeing through silicon wafers to inspect the quality and composition of electronic boards. These are just some of the capabilities of a new infrared imager developed by a team of researchers led by electrical engineers at the University of California San Diego.

The imager detects a part of the infrared spectrum called shortwave infrared light (wavelengths from 1000 to 1400 nanometers), which is right outside of the visible spectrum (400 to 700 nanometers). Shortwave infrared imaging is not to be confused with thermal imaging, which detects much longer infrared wavelengths given off by the body.

The imager works by shining shortwave infrared light on an object or area of interest, and then converting the low energy infrared light that’s reflected back to the device into shorter, higher-energy wavelengths that the human eye can see.

“It makes invisible light visible,” said Tina Ng, a professor of electrical and computer engineering at the UC San Diego Jacobs School of Engineering.

While infrared imaging technology has been around for decades, most systems are expensive, bulky and complex, often requiring a separate camera and display. They are also typically made using inorganic semiconductors, which are costly, rigid and consist of toxic elements such as arsenic and lead.

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The new infrared imager is thin and compact with a large-area display. Credit: Ning Li

The infrared imager that Ng’s team developed overcomes these issues. It combines the sensors and the display into one thin device, making it compact and simple. It is built using organic semiconductors, so it is low cost, flexible and safe to use in biomedical applications. It also provides better image resolution than some of its inorganic counterparts.

The new imager, published recently in Advanced Functional Materials, offers additional advantages. It sees more of the shortwave infrared spectrum, from 1000 to 1400 nanometers—existing similar systems often only see below 1200 nanometers. It also has one of the largest display sizes of infrared imagers to date: 2 square centimeters in area. And because the imager is fabricated using thin film processes, it is easy and inexpensive to scale up to make even larger displays.

Energizing infrared photons to visible photons

The imager is made up of multiple semiconducting layers, each hundreds of nanometers thin, stacked on top of one another. Three of these layers, each made of a different organic polymer, are the imager’s key players: a photodetector layer, an organic light-emitting diode (OLED) display layer, and an electron-blocking layer in between.

The photodetector layer absorbs shortwave infrared light (low energy photons) and then generates an electric current. This current flows to the OLED display layer, where it gets converted into a visible image (high energy photons). An intermediate layer, called the electron-blocking layer, keeps the OLED display layer from losing any current. This is what enables the device to produce a clearer image.

This process of converting low energy photons to higher energy photos is known as upconversion. What’s special here is that the upconversion process is electronic. “The advantage of this is it allows direct infrared-to-visible conversion in one thin and compact system,” said first author Ning Li, a postdoctoral researcher in Ng’s lab. “In a typical IR imaging system where upconversion is not electronic, you need a detector array to collect data, a computer to process that data, and a separate screen to display that data. This is why most existing systems are bulky and expensive.”

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The imager sees the word "EXIT" concealed by smog (left). An image of the setup without smog (right). Courtesy of Ning Li/Advanced Functional Materials 

Another special feature is that the imager is efficient at providing both optical and electronic readouts. “This makes it multifunctional,” said Li. For example, when the researchers shined infrared light on the back of a subject’s hand, the imager provided a clear picture of the subject’s blood vessels while recording the subject’s heart rate.

The researchers also used their infrared imager to see through smog and a silicon wafer. In one demonstration, they placed a photomask patterned with “EXIT” in a small chamber filled with smog. In another, they placed a photomask patterned with “UCSD” behind a silicon wafer. Infrared light penetrates through both smog and silicon, making it possible for the imager to see the letters in these demonstrations. This would be useful for applications such as helping autonomous cars see in bad weather and inspecting silicon chips for defects.

The researchers are now working on improving the imager’s efficiency.

Paper title: “Organic Upconversion Imager with Dual Electronic and Optical Readouts for Shortwave Infrared Light Detection.” Co-authors include Naresh Eedugurala and Jason D. Azoulay, University of Southern Mississippi; and Dong-Seok Leem, Samsung Electronics Co., Ltd.

This work was supported by the National Science Foundation (ECCS-1839361) and Samsung Advanced Institute of Technology. The work was performed in part at the San Diego Nanotechnology Infrastructure (SDNI) at UC San Diego, a member of the National Nanotechnology Coordinated Infrastructure, which is supported by the National Science Foundation (grant ECCS-1542148). 

Sustainable method to 3D print steel wins big at Triton Innovation Challenge

May 26, 2021--Engineers, physicians, biologists and business students at UC San Diego showcased their environmentally focused technologies at the ninth annual Triton Innovation Challenge business competition. A startup developing a 3D printing technique that can manufacture steel cheaper than existing methods, with no carbon emissions and minimal wasted scrap metal, earned the $7,000 Grand Prize.

The Triton Innovation Challenge is a business competition focused on fostering creativity and bringing to the spotlight commercially promising, environmentally focused technologies generated by students, staff and faculty from across UC San Diego. The competition is hosted by the Jacobs School of Engineering, Rady School of Management and Scripps Institution of Oceanography, and showcases startups or technologies that come from, are inspired by, or directly impact nature. The competition is funded by the William and Kathryn Scripps Family Foundation.

Jacobs School of Engineering materials science Ph.D. students Andy Zhao and Olivia Dippo are the founders of Green Steel Printing, which won Grand Prize at the Triton Innovation Challenge.

On May 21, five teams presented their ventures virtually to a panel of five judges and an audience, with $12,500 worth of prizes on the line: a Grand Prize of $7,000; Runner Up earning $4,000; and an Audience Choice award of $1,500. All the competing teams participated in a pitch-prep workshop and received other training and networking opportunities as part of the Challenge program. 

Green Steel Printing, a venture founded by Jacobs School of Engineering materials science Ph.D. students Olivia Dippo and Andy Zhao, earned the Grand Prize for their solution to reducing carbon emissions and metal waste in the steel manufacturing industry. Current steel manufacturing processes take iron oxide ore, and burn coal or natural gas to reduce the ore into iron, which is then converted to steel. This accounts for 7 percent of global carbon dioxide emissions. 

“For every ton of steel produced, 1.8 tons of carbon dioxide is emitted,” said Zhao. “There’s an inherent carbon price you have to pay to produce steel; there are fossil fuels embedded in the steel supply chain.” 

The traditional process of manufacturing steel parts is subtractive, meaning companies purchase large blocks of steel, and then remove material until they reach the desired shape and size of the part they’re building, resulting in a lot of scrap metal waste.

Green Steel aims to solve both of these problems by combining metal 3D printing, with green hydrogen technology, to generate steel with no carbon emissions, and significantly less scrap metal waste. Their patent pending 3D printing process is also projected to be cheaper than existing methods.

“Inspired by metal 3D printing and inspired by using green hydrogen as a replacement for fossil fuels, we have come up with our Green Steel printer,” said Dippo. “The two inputs are iron oxide ore—which is how the material comes out of the earth—and green hydrogen. These two things are mixed together in a reaction zone that forms iron powder. We can add additional alloying elements such as carbon in order to make steel, and at the very bottom of the machine we have our print head, where we can print the desired shapes.”

In the future, they plan to partner with aerospace or automotive companies to produce steel parts.

Dippo and Zhao are securing additional funding and lab space to further develop their steel 3D printing machine, and hope to have a prototype complete in about a year. 

The judges selected Lichen Lab as the Triton Innovation Challenge Runner Up. Lichen Lab, founded by biology alumnus Will Landry, developed and sells an alarm to help lab users keep their fume hoods closed, not only improving lab safety, but reducing energy consumption and saving money as well. When these fume hoods are left open when not in use, they waste upwards of $1,000 in energy per hood annually.

The Audience Choice award went to SynBioEnergy, founded by bioengineering PhD student Tyler Myers. SynBioEnergy uses a bioreactor to treat wastewater and desalinate water, using the components filtered out of the water as a biofuel to power the device. They plan to market the small-scale device to wineries and agricultural industries needing to meet state wastewater treatment regulations. 

Other Triton Innovation Challenge finalists include Algeon Materials, founded by Rady School of Management students, which leverages ocean derived materials like kelp to create plastic alternatives, initially in the retail space for items like hangers; and Kryos Cooling, led by a UC San Diego physician and faculty in the School of Public Health, which is developing a cooling vest for the increasing number of people living in hot climates, or who work outside in the summer. 

In addition to the Triton Innovation Challenge, Scripps Oceanography and Rady School of Management are now launching another innovation program, startBlue, on campus this fall. The startBlue accelerator program is currently accepting applications from San Diego-based innovators, engineers, and scientists who are working to solve ocean-related challenges. The deadline to apply for the fall cohort is July 2, 2021. Visit the startBlue website to learn more.

Improved maps for self-driving vehicles win Research Expo 2021

May 25, 2021-- From monitoring the structural integrity of airplane wings, to improving lithographic 3D printing processes, to creating better maps for self-driving cars, this year’s Research Expo symposium showcased the depth and breadth of work done by graduate engineering and computer science students at the University of California San Diego Jacobs School of Engineering.

Computer science Ph.D. students David Paz-Ruiz and Hengyuan Zhang took the top prize, the Lea Rudee Outstanding Poster Award, in addition to the Best Poster Award for the Department of Computer Science and Engineering. Their work focuses on improving the maps that self-driving vehicles use to navigate the world. They worked under the direction of Henrik Christensen, director of UC San Diego’s Contextual Robotics Institute and a professor in the computer science department.

David Paz-Ruiz Hengyuan Zhang

Paz-Ruiz and Zhang are tackling a problem that makes it hard for self-driving cars to scale up: most rely on high-definition (HD) maps, with resolution as small as one centimeter, which are manually labeled.

The computer scientists instead created what is known as semantic maps--2D data based on camera images overlapping with point cloud maps. The maps contain information about drivable areas, crosswalks, sidewalks, and lane markings. 

“Unlike HD maps, our maps do not include centimeter level annotations for the trajectories that the vehicle can follow,” Paz-Ruiz said. “Instead, we seek to generate these in real time.” 

“Our semantic maps are generated without human labeling effort and can be continuously updated if the environment was to change in the future,” Zhang added. 

Researchers can build a semantic map of campus in just a few hours. By contrast, an HD map would take weeks. In addition, the researchers’ maps can be used across different robots and different vehicles. 

“At UCSD we are studying how smart vehicles can be used in urban areas such the university campus or a parking lot at the airport to assist people with daily tasks” adds Prof. Christensen 

This year, the 39th annual Research Expo event was held virtually, with students submitting video presentations ahead of time, and answering questions about their work during the live event from judges, alumni and industry representatives. In all, 250 people attended the event. 

In addition to Paz-Ruiz and Zhang, one research project from each of the Jacobs School’s six departments was recognized. They are listed below, with links to their video presentations: 

Bioengineering

Sandhya Sihra

"A Heart-to-Heart Worth Having"

Computer Science and Engineering

David Paz and Hengyuan Zhang

"Towards Autonomous Vehicle Navigation without HD Maps"

Electrical and Computer Engineering

Ross Greer

“Trajectory Prediction in Autonomous Driving with a Lane Heading Auxiliary Loss”

Mechanical and Aerospace Engineering

Jessica Medrado

"Fundamentals of water-evaporation processes for renewable energy application"

NanoEngineering

David Wirth and Justin Hochberg

"A Highly Expandable Foam for Lithographic 3D Printing"

Structural Engineering

Adrielly Hokama Razzini

"Structural Health Monitoring of an Airplane’s Wings Using Gaussian Process Regressors"


 

Zexiang Xu wins Chancellor's Dissertation Medal

Undergraduate researchers earn Goldwater Scholarship

May 13, 2021-- Three UC San Diego undergraduate students with impressive academic and research credentials were selected to receive the Goldwater Scholarship, designed to foster and encourage outstanding students to pursue research careers in the fields of the natural sciences, engineering and mathematics. The Goldwater Scholarship, which provides students up to $7,500 toward tuition, books and fees, is the preeminent undergraduate award of its type in these fields.

The scholarship is named in honor of Senator Barry Goldwater, and this year was administered in partnership with the Department of Defense National Defense Education Programs.

Bioengineering students Aditi Gnanasekar and Claire Zhang, and physics student Mara Casebeer, received the scholarship in recognition of their research contributions and plans to pursue careers in research.

Aditi Gnanasekar

Aditi Gnanasekar was interested in biology, computer science and technology from an early age, but was not sure how to combine all three fields until she discovered the Bioengineering: Biotechnology major at UC San Diego.

“There is definitely a lot of computation within the biotech track, but it also has a focus on chemical engineering concepts and biomolecular techniques as well, so it’s the perfect blend of those disciplines,” said Gnanasekar.

She has applied her bioengineering know-how as an undergraduate researcher in the lab of Professor Weg Ongkeko at the UC San Diego School of Medicine, analyzing RNA sequences to extract information on immune cell expression, ultimately working toward characterizing cancers on the molecular level.

“Recently, I’ve been working on research into the intratumor microbiome, and specific microbes that are characterized in specific tumors,” Gnanasekar said. “We think it’s pretty interesting that there are microbes that are only present in certain tumors, and think they could play a critical role in determining the clinical outcome of cancer.”

After earning her bachelor’s degree, Gnanasekar plans to pursue an M.D./Ph.D., enabling her to continue this type of research while also working hands-on with patients.

In addition to earning the Goldwater Scholarship, Gnanasekar is also one of just 11 Jacobs School of Engineering students in the class of 2022 to receive the prestigious Jacobs School Scholar award, supported by school namesakes Dr. Irwin and Joan Jacobs. Jacobs Scholars are selected for demonstrated academic achievement, leadership, commitment to community, and innovative potential, and become a close community of scholars during their undergraduate years.

Outside of the classroom, Gnanasekar played intramural sports, sung in a capella groups, and volunteered with UC San Diego StRIVE, assisting adults with disabilities. But research was her main passion.

“My lab is really important—they’re like a second family to me.”

She advises students interested in research to stick with it, even when the going gets tough.

“One of the biggest lessons I’ve learned from doing scientific research and being part of a lab is being really patient,” she said. “Research is hard and you need to be persistent—you can't expect to get published right away or for your experiments to work out your way. A lot of times experiments will fail; that's totally expected and fine. And even if they do fail, that doesn't mean the research was useless or you didn't get anything out of it. That information is still very important.”

Claire Zhang 

As a young student, Claire Zhang was intrigued by both patient-facing clinical medicine and the technical innovations required to better manage disease. An early hands-on introduction to biomedical research solidified her desire to do both, and helped her see a path to do so.

Now a bioengineering student at UC San Diego, Zhang plans to earn an M.D./Ph.D. after graduation, with a goal of improving computational precision medicine by unifying molecular, cellular and physiological data as a physician scientist. She got a taste for what this can look like as an undergraduate researcher in the lab of Dr. Kevin King, from the Departments of Medicine and Bioengineering. Zhang used tools like single-cell RNA sequencing to study diseases in which the immune system becomes activated even though there is no infection, including heart attacks.

“Dr. King has been an incredible role model and crucial source of support and mentorship over the past two years, and inspired my interest in pursuing a physician-scientist career myself,” said Zhang.

She hopes to put the medical and computational skills she’s learning to use to synthesize all the various data points we can learn about an individual‒ from genetics to heart rate to sleep habits‒into actionable information.

“We’ve gotten quite good at drawing conclusions from each of these types of data on their own, but synthesizing information from all of these diverse sources to make holistic personalized predictions about one’s risk for disease, or what drugs will be most effective for someone, could truly revolutionize clinical medicine.”

Like Gnanasekar, Zhang is also a Jacobs School Scholar, one of the 11 Jacobs School of Engineering students in the class of 2022 to receive the prestigious full-ride scholarship award that is supported by school namesakes Dr. Irwin and Joan Jacobs.

In addition to the Jacobs Scholars community and her research, Zhang is involved in the International Health Collective, a student-run nonprofit that operates a monthly free clinic in Tijuana, Mexico, and is a member of the Theta Tau professional engineering fraternity.

Her advice for current and future students?

“Take advantage of opportunities to grow, even (and sometimes especially) if they make you uncomfortable. Apply to that internship that you don’t think you’ll get into, email that professor whose research sounded interesting, try out a few student orgs!”

Mara Casebeer

Mara Casebeer, a biological physics student with a minor in chemistry, has been captivated by the power of physics since high school.

“My junior year of high school I had an amazing physics teacher who showed me everything that physics could do,” she said. “We had one lab where we had to calculate the angle we needed to release a ball in order to get it to land in a basket. On the first try, based off our calculations, we got it right in the basket, nothing but net. And that blew my mind, that simple physics equations can predict what’s happening in the natural world so easily.”

As an undergraduate researcher at the Scripps Institution of Oceanography, Casebeer now harnesses the power of physics to study how radio frequency cell-to-cell communications and high-frequency electromagnetic waves interact with biological systems. She models how DNA behaves and changes in these high-frequency environments.

After graduating in 2022, Casebeer plans to earn a doctorate in biological physics, and continue conducting research in experimental and computational biophysics. At UC San Diego, Casebeer is also a supplemental physics instructor through the Teaching and Learning Commons, an experience which has affirmed her goal of becoming a professor one day, combining her love of research and teaching.

Outside of research, coursework and teaching, Casebeer is also co-president of the Warren Honor Society, plays intramural soccer and clarinet in the chamber ensemble and is part of the Undergraduate Women in Physics organization.

Her advice to current and future students?

“Don’t be afraid to put yourself out there in terms of research‒it can never hurt to talk to a professor after class about their research, or email them. It can be really intimidating but if it’s something you’re passionate about it’ll be worth it.”

Bioengineering student earns Strauss Scholarship

May 13, 2021--UC San Diego bioengineering undergraduate Zina Patel was selected to receive the $15,000 Strauss Scholarship, awarded to outstanding students developing social change or public service projects. Patel is one of only 14 students to receive the scholarship, which aims to prepare future leaders by encouraging them to undertake a high-impact venture and providing the funds to get started.

Patel’s project, called This Able, is a free online platform that connects college students with disabilities interested in joining the workforce, to mentors with disabilities already in the workforce. The goal is to not only provide mentorship, but to also provide these students with tailored expertise to bolster their job applications by assisting with resumes, interview preparation and more.

“The goal of this effort is to guide the next generation of those with disabilities and empower them by providing mentorship and networking opportunities,” said Patel. “I hope that This Able will serve as an avenue to increase employment rates for the special needs community and help cultivate a diverse and inclusive workforce, setting a precedent for the post-COVID world. My long-term and ultimate goal is to hand This Able off to web developers with disabilities who can run the platform, making it uniquely for those with disabilities by those with disabilities.”

Patel was inspired to create This Able as a volunteer at TRACE Alternative School in San Diego, where she witnessed talented job applicants being passed over for jobs they seemed to be qualified for. According to the Bureau of Labor and Statistics, only 18 percent of people with disabilities were employed in 2020. 

“As a volunteer at TRACE, I have heard countless stories from students about unsuccessful job applications,” Patel said. “ More often than not, it’s because of their disability and stigmas/stereotypes surrounding that. They are often seen as a liability rather than an asset, who will bring a fresh perspective to the table. And I wanted to do something about this because I personally knew those students who were the faces behind the rejection letters. I knew their potential that many companies didn’t recognize. That’s my motivation for This Able — to help the students I’ve worked with and others like them secure a job and secure their independence.”

Patel said her engineering courses have prepared her well for not only the technical skills required to build out a platform like This Able, but also in the critical thinking and problem solving skills necessary for undertaking a project of this scale. 

“Another key component that I really love about engineering and entrepreneurship is customer development — going out in the community to talk to the people who will be using the technologies I create and getting their perspectives to drive the development of my projects,” she said.

Patel is doing that now for This Able, working with the UC San Diego Office for Students with Disabilities to conduct user testing. She hopes to launch the platform in the fall. 

On campus, Patel has been active in the Student-run Intercommunicative and Vocational Education (StRIVE) group, which aims to assist adults with disabilities in the critical age range of 18-22 with their transition to independent living; that’s how she taught and interacted with young adults with disabilities at TRACE, and is also part of the reason she’s studying engineering. Patel entered UC San Diego as a molecular and cellular biology student, but an experience during her freshman year convinced her that bioengineering was a better fit. 

“While volunteering at an autism center in India during my freshman year, I noticed that many of the students had no access to or could not afford assistive technology,” she said. “In fact, the school itself did not have an elevator for those in wheelchairs. Back in the US, I was a volunteer for an alternative school where all students had at least one form of assistive technology. Seeing the gap between students with disabilities and assistive technology in the country my ancestors come from, I decided to pursue a career in bioengineering to better understand the creation of medical devices so that I could one day give back to those students in need.”

Personalized sweat sensor reliably monitors blood glucose without finger pricks

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A handheld device combined with a touch sweat sensor (strip at right) measures glucose in sweat, while a personalized algorithm converts that data into a blood glucose level. Image courtesy of ACS Sensors

May 10, 2021 -- Many people with diabetes endure multiple, painful finger pricks each day to measure their blood glucose. Now, engineers at the University of California San Diego have developed a device that can measure glucose in sweat with the touch of a fingertip, and then a personalized algorithm provides an accurate estimate of blood glucose levels.

The work was published recently in ACS Sensors.

According to the American Diabetes Association, more than 34 million children and adults in the U.S. have diabetes. Although self-monitoring of blood glucose is a critical part of diabetes management, the pain and inconvenience caused by finger-stick blood sampling can keep people from testing as often as they should. And while scientists have developed ways to measure glucose in sweat, levels of the sugar are much lower than in blood, and they can vary with a person’s sweat rate and skin properties. As a result, the glucose level in sweat usually doesn’t accurately reflect the value in blood.

To obtain a more reliable estimate of blood sugar from sweat, a team led by UC San Diego nanoengineering professor Joseph Wang and Juliane Sempionatto, a nanoengineering Ph.D. student in Wang’s lab, devised a system that could collect sweat from a fingertip, measure glucose and then correct for individual variability.

The researchers made a touch-based sweat glucose sensor with a polyvinyl alcohol hydrogel on top of an electrochemical sensor, which was screen-printed onto a flexible plastic strip. When volunteers placed their fingertip on the sensor surface for one minute, the hydrogel absorbed tiny amounts of sweat. Inside the sensor, glucose in the sweat underwent an enzymatic reaction that resulted in a small electrical current that was detected by a handheld device.

The researchers also measured the volunteers’ blood sugar through a standard finger prick test, and they developed a personalized algorithm that could translate each person’s sweat glucose to their blood glucose levels. In tests, the algorithm was more than 95% accurate in predicting blood glucose levels before and after meals. To calibrate the device, a person with diabetes would need a finger prick only once or twice per month. But before the sweat diagnostic can be used to manage diabetes, a large-scale study must be conducted, the researchers say.

The work was supported by the UC San Diego Center for Wearable Sensors and the National Research Foundation of Korea.

Paper title: “Touch-Based Fingertip Blood-Free Reliable Glucose Monitoring: Personalized Data Processing for Predicting Blood Glucose Concentrations.”

This system helps robots better navigate emergency rooms

May 10, 2021-- Computer scientists at the University of California San Diego have developed a more accurate navigation system that will allow robots to better negotiate busy clinical environments in general and emergency departments more specifically.  The researchers have also developed a dataset of open source videos to help train robotic navigation systems in the future. 

The team, led by Professor Laurel Riek and Ph.D. student Angelique Taylor, detail their findings in a paper for the International Conference on Robotics and Automation taking place May 30 to June 5 in Xi’an, China.  

The project stemmed from conversations with clinicians over several years. The consensus was that robots would best help physicians, nurses and staff in the emergency department by delivering supplies and materials. But this means robots have to know how to avoid situations where clinicians are busy tending to a patient in critical or serious condition. 

“To perform these tasks, robots must understand the context of complex hospital environments and the people working around them,” said Riek, who holds appointments both in computer science and emergency medicine at UC San Diego. 

Taylor and colleagues built the navigation system, the Safety Critical Deep Q-Network (SafeDQN), around an algorithm that takes into account how many people are clustered together in a space and how quickly and abruptly these people are moving. This is based on observations of clinicians’ behavior in the emergency department. When a patient’s condition worsens, a team immediately gathers around them to render aid. Clinicians’ movements are quick, alert and precise. The navigation system directs the robots to move around these clustered groups of people, staying out of the way.

“Our system was designed to deal with the worst case scenarios that can happen in the ED,” said Taylor, who is part of Riek’s Healthcare Robotics lab at the UC San Diego Department of Computer Science and Engineering. 

The team trained the algorithm on videos from YouTube, mostly coming from documentaries and reality shows, such as “Trauma: Life in the ER” and “Boston EMS.”  The set of more than 700 videos is available for other research teams to train other algorithms and robots.

Researchers tested their algorithm in a simulation environment, and compared its performance to other state-of-the-art robotic navigation systems. The SafeDQN system generated the most efficient and safest paths in all cases. 

Next steps include testing the system on a physical robot in a realistic environment. Riek and colleagues plan to partner with UC San Diego Health researchers who operate the campus’ healthcare training and simulation center. 

The algorithms could also be used outside of the emergency department, for example during search and rescue missions. 

Ph.D. student Sachiko Matsumoto and undergraduate student Wesley Xiao also contributed to the paper. 

Social Navigation for Mobile Robots in the Emergency Department

Angelique M. Taylor, Sachiko Mastumoto, Wesley Xiao and Laurel Riek, University of California San Diego
http://cseweb.ucsd.edu/~lriek/papers/taylor-icra-2021.pdf


 

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May 8, 2021

Programs help Jacobs School undergraduates make the most of research experiences

GEAR and ERSP set engineering and computer science students up for success as researchers

May 6, 2021 -- As a first year bioengineering major at UC San Diego, Kanksha Patel had heard that there were opportunities to do research in professors’ labs as an undergraduate, but she didn't know how to get started or what lab to join.

Emily Tang liked physics but, as a first year, wasn't clear what her nanoengineering major was all about or if it was really for her. 

These two University of California San Diego engineering undergraduates broadened their understanding of what it means to study engineering -- and transformed their college experiences -- by getting involved in engineering research through a Jacobs School of Engineering program called GEAR

GEAR stands for Guided Engineering Apprenticeship in Research, and it's run by the IDEA Engineering Student Center here at the UC San Diego Jacobs School of Engineering. The program is modeled off a similar program for computer science undergraduates at the Jacobs School of Engineering called the Early Research Scholars Program (ERSP)

ERSP was launched by Christine Alvarado, who is a professor in the Department of Computer Science and Engineering and also Associate Dean for Students for the Jacobs School of Engineering. 

Both GEAR and ERSP bring second-year undergraduates into university research labs where they work on team projects that contribute to the actual research mission of the lab. In both programs, in addition to mentorship from people within the research lab, students get outside guidance, mentorship and community building opportunities. Students with no previous research experience and students from traditionally underrepresented groups in engineering and computer science are particularly encouraged to apply. Applications are due in the spring, and the programs run from fall through the spring of the following academic year. 

One of the unique aspects of these programs is that the students are systematically required to discover and truly understand the big picture "Why" of the research lab they have joined. 

"Challenging undergraduate students to understand the big picture 'Why' of the research laboratory they are working in gives them the ability to understand why their contribution matters, why the intermediate step they are responsible for is important," said Ekaterina (Katya) Evdokimenko, Ph.D.

Evdokimenko teaches the two-credit ENG 20 "Introduction to Engineering Research" course which all GEAR students take during the first-quarter of their three-quarter GEAR experience. The students cover a lot of ground in ENG 20, all of it tied to making the most of their first research experience in a lab and building on the experience in order to open more opportunities and eventually a fulfilling career. 

The final ENG 20 project is a customized research proposal which the students use as a roadmap for their research project which continues for the next two quarters. 

"Each week you log something different," said Patel, the bioengineering major who was embedded in Karsten Zengler's microbiology lab which is part of the Center for Microbiome Innovation at UC San Diego. The students learn how to communicate effectively within a research lab environment, including teasing out the big-picture goals of the lab and learning how to communicate with the professor who leads the lab as well as graduate students, research scientists and other lab group members to keep them updated.

Emily Tang felt intimidated by the prospect of joining nanoengineering professor Zheng Chen's battery lab, but she found a supportive environment and developed a research project to test the efficiency of lithium ion batteries with varying electrolyte concentrations. 

"GEAR gave me more direction in what nanoengineering even is," said Tang. "I'm a nanoengineering major with an environmental studies minor. Renewable energy is something that bridges these interests."

Building on the momentum from her research experience, Tang enrolled in a graduate-level nano-scale energy course taught by world-renowned battery pioneer and nanoengineering professor Shiley Meng

GEAR and ERSP are specifically designed for undergraduates who have never worked in a professor's research lab and aim to give all students, no matter their past experiences, the tools and support necessary for success. 

"The biggest thing about the GEAR program for me is that it's introductory. I didn't know what research was like," said Tang. 

Patel learned about herself through the experience. "I wasn't sure if I would like research and the lab environment." After going through GEAR, she said, "I decided I really like research. I want to pursue research after graduation."

Both Patel and Tang were in the first cohort of GEAR students during the 2019-2020 school year. They both thrived and went on to serve as tutors for the Fall 2020 GEAR class, ENG 20, taught by Evdokimenko. 

"I think the GEAR experience helps students understand if they WANT to be an engineer or if they WANT to be in an engineering research lab," said Evdokimenko. "Students need to understand what it means to be an engineer."

"I think the GEAR experience helps students to understand what it means to be an engineer, what exactly engineers do, and what the word 'research' implies," said Evdokimenko. 

The ERSP and GEAR programs give Jacobs School of Engineering students opportunities to answer these questions. 

"This idea of engaging sophomores in research is a little bit out there," said Alvarado in a video showcasing ERSP. "People take time to warm up to the idea that sophomores can do something meaningful in a research project." 

In addition to inspiring the Jacobs-School-wide program, ERSP has also inspired similar programs at a handful of universities including UC Santa Barbara. 

ERSP was originally supported with funding from the National Science Foundation and is currently funded through the Department of Computer Science and Engineering here at UC San Diego. GEAR is supported through the Jacobs School of Engineering, and the pilot year was partially funded through support from the Office for Equity, Diversity, and Inclusion (EDI) at UC San Diego.

UC San Diego runs a wide range of programs that help undergraduate students get involved in research. There is a Student Research portal on TritonLink and also a campus-wide Undergraduate Research website.

We need to build more EV fast-charging stations, researchers say

The campus is home to one of the largest, most diverse range of electric vehicle charging stations at any university in the world.

May 5, 2021-- A team of engineers recommends expanding fast-charging stations for electric vehicles as campuses and businesses start planning for a post-pandemic world. 

The recommendation is based on a study of charging patterns for electric vehicles on the University of California San Diego campus from early January to late May of 2020, after the university moved most of its operations online. Researchers say the findings can be applied to a broader range of settings. 

“Workplace charging is a critical enabler of carbon-free transportation as the electrons consumed primarily come from solar power plants, as opposed to at-home charging, which occurs at night and relies more on fossil fuel power plants,” said Jan Kleissl, the paper’s senior author and a professor of environmental engineering at UC San Diego.

It’s the first time that a research team gathered information on workplace charging patterns for electric vehicles during the COVID-19 pandemic. As expected, charging declined dramatically once most campus operations became remote. Also as expected, charging at the campus’ medical center was less impacted as medical facilities continued most in-person operations and healthcare workers and patients kept using those charging stations. 

This reflects nationwide trends. Vehicle travel in the United States declined by about 40 percent from mid-March to mid-April 2020, according to the National Bureau of Economic Research.

But DC fast chargers that provide a full charge in about half an hour were less affected than what is known as Level 2 chargers, which provide a full charge over eight hours. Energy dispatched at Level 2 chargers on the main UC San Diego campus decreased by 84 percent. DC fast charging initially dropped by 67 percent. These stations quickly returned to near-normal usage in a short period of time, unlike Level 2 charging stations. 

“This finding reinforces ongoing efforts to deploy at least an additional 20 DCFCs primarily on the perimeter of campus in order to serve both UC San Diego commuters as well as the general public in need of recharging,” said Byron Washom, the UC San Diego director of strategic energy initiatives and one of the paper’s coauthors.

The team details their findings in the March 23 issue of the Journal of Renewable and Sustainable Energy. 

Only four out of 100 stations in the study were fast-charging. More broadly, in the United States, only a tiny fraction of charging stations are fast-charging, and most of those only serve Tesla vehicles. For example, California has about 31,800 EV charging stations. Of those, almost 3000 are Tesla supercharging stations, only available to Tesla vehicles. An additional 470 are DCFC stations managed by California-based Chargepoint. 

The study looked at 100 charging stations in 28 parking structures. Specifically, researchers found that from March 11 to May 20, 2020: 

  • Charging on the main campus dropped by 84 percent from pre-pandemic levels
  • Charging dropped by 50 percent at the parking structures at the UC San Diego medical center locations
  • Charging at DC fast charging stations initally dropped by 67 percent before going back up to near pre-pandemic levels 

Charging will likely not resume back to normal even  after the pandemic ends, researchers say. 

“Commuting patterns based on five days a week in the office are unlikely to  resume, however, as employers may allow more telecommuting even after the end of the pandemic,” Kleissl said. . 

That may be good news as the anticipated dramatic increase in EV adoption over the coming years would otherwise strain the existing charging infrastructure, he  added.

Impact of the Coronavirus Pandemic on Electric Vehicle Workplace Charging

Graham McClone, Jan Kleissl, Byron Washom, Sushil Silwal, University of California San Diego


 

The Wave Beneath Their Wings

The intricate dance between waves, wind, and gliding pelicans is worked out for the first time

April 21, 2021-- It’s a common sight: pelicans gliding along the waves, right by the shore. These birds make this kind of surfing look effortless, but actually the physics involved that give them a big boost are not simple. 

Researchers at the University of California San Diego have recently developed a theoretical model that describes how the ocean, the wind and the birds in flight interact in a recent paper in Movement Ecology.

This cartoon illustrates the equation that describes the physics of wave slope-soaring. 

UC San Diego mechanical engineering PhD student Ian Stokes and adviser Professor Drew Lucas of UC San Diego’s Department of Mechanical and Aerospace Engineering and Scripps Institution of Oceanography found that pelicans can completely offset the energy they expend in flight by exploiting wind updrafts generated by waves through what is known as wave-slope soaring. In short, by practicing this behavior, seabirds take advantage of winds generated by breaking waves to stay aloft.

The model could be used to develop better algorithms to control drones that need to fly over water for long periods of time, the researchers said. Potential uses do not stop there.

“There’s a community of biologists and ornithologists that studies the metabolic cost of flight in birds that can use this and see how their research connects to our estimates from theory. Likewise, our model generates a basic prediction for the winds generated by passing swell, which is important to physicists who study how the ocean and atmosphere interact in order to improve weather forecasting,” Stokes said. 

“This is an interesting project because it shows how the waves are actually moving the air around, making wind. If you're a savvy bird, you can optimize how you move to track waves and to take advantage of these updrafts. Since seabirds travel long distances to find food, the benefits may be significant,” Lucas said. 

Stokes and Lucas are, of course, not the first scientists to study the physics of the atmosphere that pelicans and other birds are hardwired to intuit so they can conserve energy for other activities. For centuries, humans have been inspired by the sight of birds harnessing the power and patterns of the winds for soaring flight.

That’s how it started with Stokes, who is now in the second year of his PhD at UC San Diego. As a UC Santa Barbara undergraduate, Stokes, a surfer and windsurfer in his off hours, needed a project for his senior physics class and thought of the birds that would accompany him on the waves. When he looked closer, he appreciated the connection between their flight dynamics and the study of environmental fluid dynamics, a speciality of scientists at UC San Diego. The project ultimately turned into a master’s thesis with Lucas, drawing inspiration from oceanographers at Scripps who seek to understand the interactions between the ocean and atmosphere.

Wave-slope soaring is just one of the many behaviors in seabirds that take advantage of the energy in their environment. By tapping into these predictable patterns, the birds are able to forage, travel, and find mates more effectively. 

“As we appreciate their mastery of the fluid, ever-changing ocean environment, we gain insight into the fundamental physics that shape our world,” said Lucas.

Pelicans glide above the waves, a behavior known as wave-slope soaring.
Photo: Simone Staff

 

Computer Scientists Discover Vulnerability Affecting Computers Globally

From left, clockwise: Dean Tullsen, professor, and Ph.D. student Mohammadkazen Taram at UC San Diego, teamed up with UC San Diego alumnus and UVA professor Ashish Venkat. 

April 30, 2021--Computer scientists at the University of California San Diego with researchrs at the University of Virginia School of Engineering to uncover a line of attack that breaks current defenses against Spectre, a devastating hardware flaw in computers eqwuipped with Intel and AMD processors. This means that billions of computers and other devices across the globe are just as vulnerable today as they were when Spectre was first announced.

The team reported its discovery to international chip makers in April and will present the new challenge at a worldwide computing architecture conference, the International Symposium on Computer Architecture, or ISCA, in June.

Led by Ashish Venkat, a UVA professor and UC San Diego alumni, with Dean Tullsen, a professor in the Department of Computer Science and Engineering at UC San Diego, the researchers found a new way for hackers to exploit something called a “micro-op cache,” which speeds up computing by storing simple commands and allowing the processor to fetch them quickly and early in the speculative execution process. Micro-op caches have been built into Intel computers manufactured since 2011.

The UC San Diego/UVA team reverse-engineered certain undocumented features in Intel and AMD processors. They have detailed the findings in their paper: “I See Dead µops: Leaking Secrets via Intel/AMD Micro-Op Caches.”

These two UC San Diego and UVA teams have collaborated before, including on a paper UC San Diego Ph.D. student Mohammadkazem Taram presented at the ACM International Conference on Architectural Support for Programming Languages and Operating Systems in April 2019. The paper, “Context-Sensitive Fencing: Securing Speculative Execution via Microcode Customization,” which introduced one of just a handful more targeted microcode-based defenses developed to stop Spectre in its tracks, was recently selected as a Top Pick in Hardware and Embedded Security among papers published in the six-year period between 2014 and 2019.

Read the full story from UVA about their research and its impact here.

CAREER awards for three researchers at UC San Diego Contextual Robotics Institute

May 15, 2021--Three researchers at the Contextual Robotics Institute at UC San Diego have received CAREER awards from the National Science Foundation in 2021. Their work ranges from robot mapping, to invertebrate locomotion, to autonomous robotic surgery. 

The projects’ descriptions are below.

Nikolai Atanasov

Atanasov’s project, “Active Bayesian Inference for Collaborative Robot Mapping" is an integrated research and education career development effort. It aims to design motion planning algorithms that enable robots to actively reduce uncertainty about their environment. Theoretically, this is an active Bayesian inference problem, aiming to achieve optimal control of a sensing and probabilistic estimation process. Practically, this is the goal of reproducing the curiosity that humans and animals exhibit when exploring an unknown environment on a robot system. The project considers collaboration among multiple robots to collaboratively explore and build a map of their environment. Applications include environmental monitoring, disaster response, and security and surveillance.
https://www.nsf.gov/awardsearch/showAward?AWD_ID=2045945

Nicholas Gravish

Gravish's NSF CAREER award is entitled "The exceptional biomechanics of legged locomotion in the microcosmos". When viewed in relative terms, the fastest legged animals on the planet are the smallest of invertebrates.  These remarkable feats of movement are enabled by strong limbs, robust foot attachment mechanics, and resilient exoskeleton structures and these feats are unmatched in current insect-scale robotics. In this proposal we will study the legged movement performance in small invertebrates to reveal a set of radically different locomotor constraints and opportunities, enabled by favorable geometric and dynamic scaling laws. By elucidating principles of legged movement in small animals we seek to extrapolate these concepts to the insect-scale robots built in the Gravish lab. Overall the goal of this proposal is to better understand the rules of mobility and locomotion for scientific and engineering gain. 
https://www.nsf.gov/awardsearch/showAward?AWD_ID=2048235&HistoricalAwards=false

 Michael Yip

Yip's NSF CAREER award, entitled "Contextually Informed Autonomous Robotic Surgery", will investigate how doctors use an understanding of the geometry and mechanics of human anatomy to guide their actions in surgery, and imbue surgical robots with this knowledge. By defining anatomical context for surgical robots, robots will be able to evaluate and optimize safe plans and trajectories in autonomous procedures, particularly those that involve stabilizing patients during first response. Yip's NIH Trailblazer award, entitled "Robotically controlled intraluminal instruments for flexible endoscopic intervention", investigates the design of handheld robotic catheters that may be used with flexible bronchoscopes for biopsying lung cancer. The work hypothesizes that handheld robotics may potentially offer a low-cost and more accessible solution today's expensive robot-assisted surgical diagnoses and interventional procedures and a potentially more complete diagnosis than with passive, manually controlled instruments.
https://www.nsf.gov/awardsearch/showAward?AWD_ID=2045803&HistoricalAwards=false


 

Building a voice assistant for older adults

April 28, 2021-- Computer scientists at the University of California San Diego received an Amazon Research Award to develop a voice assistant to better communicate with older adults. Their initial goal is to create a system capable of understanding and answering the medical questions of adults over age 65.

The way the elderly sometimes struggle to use voice assistants like Alexa or Siri may often be joked about, but the problem is real: data show that adults over 65—a demographic expected to double between 2010 and 2050—tend to give up on using these tools after several unsuccessful attempts at getting their questions answered. 

The problem is that existing natural language processing (NLP) systems—the artificial intelligence models used to train computers to understand spoken and written human language—are trained to understand short, formal questions. This is fine for people who grew up with computer technology and know how to phrase their questions to be understood by the device. But older adults are used to speaking to people, not machines, and often struggle to pare down longer or conversational  questions to a sentence the artificial intelligence underpinning the voice assistants can understand.   

“Our job is to bridge that gap,” said Khalil Mrini, the UC San Diego computer science PhD student who will be supported by the Amazon Research Award to work on the project. “We’re working on technology that will flip the burden: instead of having older adults change or reformulate their question, we want the AI to be able to learn and understand the older adult.”

Computer science PhD student Khalil Mrini is working to make human language technology accessible to more populations.

To accomplish this, Mrini, a graduate student in UC San Diego computer science Professor Ndapa Nakashole’s lab, is working to create an end-to-end question answering system that can: 1) shorten the user’s question down to its key components, 2) match the shortened medical question to a frequently asked question from a database of 17,000 medical questions sourced from the National Institutes of Health; and 3) select the relevant portions of the corresponding longer answer to share with the user. 

Mrini has already completed the first step—training the AI to summarize a long question into a shorter one—which he did by training the NLP model jointly on summarizing questions and a classification task called question entailment, in which the model learns to tell if by answering a short question, the initial longer question has been addressed. 

“We found that if you’re training on both summarization—which is basically feeding longer user questions and the model learns to generate the short question—and at the same time training on question entailment, that classification task, then you’re able to generate better results,” said Mrini.

This question summarization AI model can be implemented as a standalone feature into existing voice assistants like Alexa, or integrated as a first step into any question answering system, where it can shorten user questions.

The team is still working on getting the tool to match the question with one in a pool of FAQs—in this case provided by the NIH—and then have the AI select the relevant pieces of a longer answer to read back to the user. 

Computer science Professor Ndapa Nakashole’s research focuses on developing algorithms that enable computers to understand and generate human language.

"The potential impact of this work is substantial because it aims to broaden the population of people who can benefit from conversational agents, by targeting an important segment of the population, older adults,” said Nakashole.

Making AI more inclusive

Why did this segment of the population need an add-on feature after the fact? Why were their user needs not considered in initial voice assistant testing? It’s a problem Mrini says is pervasive in AI systems and training, and one that he and researchers in the VOLI team are trying to rectify.

“Among users of existing question answering systems, older adults are underrepresented,” he said. “It stems from a lack of representation among internet users, which escalates into not having a lot of data about this particular demographic and so on. You have a problem that escalates into a lack of data, and if there’s no data, you can’t train an algorithm to meet their specific needs.”

Mrini is intimately familiar with this problem. As a native of Morocco, he noticed that virtually no AI models worked for his native language, Darija, a form of Arabic spoken in Morocco. 

“I realized there were—and still are—close to no NLP models or AI models that work well for my native language. So my first ever project was making data so that AI can be trained for my native language,” Mrini said.

He’s interned at Adobe Research and the Alexa group at Amazon, working to make AI models that can predict the syntax of a sentence in an interpretable way, and summarize the important takeaways of longer articles, respectively. 

“The global goal of my research is to make human language technology more interpretable and more accessible to wider audiences,” Mrini said. “Now I’m mainly working on English-language technology, but to make it more accessible for marginalized or underrepresented audiences, so older adults in this case.”

This project is part of the larger VOLI effort, (Voice Assistant for Quality of Life and Healthcare Improvement in Aging Populations) led by natural language processing researchers including Nakashole, along with geriatric physicians, and human computer interaction researchers at UC San Diego. One of the key goals of this NIH-funded project is to develop a personalized and context-aware voice-based digital assistant to improve the quality of life and the healthcare of older adults. Ultimately, the researchers hope the device will enable older adults to remain independent and optimize interactions with healthcare and service providers.

The principal investigators on the NIH grant are:
Qualcomm Institute Research Scientist Emilia Farcas; computer science Professors Ndapa Nakashole and Nadir Weibel; geriatric physician Dr. Alison Moore; and internal medicine physician and biomedical informatician Dr. Michael Hogarth.

UC San Diego joins Bytecode alliance to build safer software foundations for the Internet

The nonprofit is focused on building an ecosystem to advance the unique advantages of WebAssembly

April 28, 2021 -- The University of California San Diego has joined The Bytecode Alliance, a nonprofit organization dedicated to creating new software foundations and building on standards such as WebAssembly and WebAssembly System Interface (WASI). UC San Diego is part of a cross-industry collaboration alongside other new members Arm, DFINITY Foundation, Embark Studios, Google and Shopify to support the alliance, which was incorporated by Fastly, Intel, Mozilla and Microsoft.  

These organizations share a vision of a WebAssembly ecosystem that fixes cracks in today’s software foundations that are holding the industry and its software supply chains back from a secure, performant, cross-platform and cross-device future. 

Computer science professor Deian Stefan says, "they will contribute tools and techniques for a more secure software ecosystem"

“WebAssembly is quickly becoming the de facto intermediate representation for building secure systems. WebAssembly takes a principled approach to security and gives us just the right building blocks to build the next generation secure and high-assurance systems,” said Deian Stefan, an assistant professor in the Department of Computer Science and Engineering at the UC San Diego Jacobs School of Engineering. “It’s a core part of the sandboxing and high-assurance security toolkits we are developing at UC San Diego.”  

UC San Diego researchers and collaborators have developed the RLBox framework that uses WebAssembly to sandbox libraries, the CT-Wasm language extension for writing secure crypto code in WebAssembly, the Swivel compiler that mitigates Spectre attacks and the VeriWasm tool that verifies the safety of native compiled WebAssembly.

 “As members of the Bytecode Alliance we hope to help shape the direction of WebAssembly and contribute tools and techniques that will amplify the alliance’s vision towards a more secure software ecosystem,” Stefan said.

The Bytecode Alliance, founded in 2019, has helped bring attention to the inherent weaknesses in predominant models for building software, which rely heavily on composing up to thousands of third-party modules without security boundaries between them. These weaknesses in the software supply chain have historically been instrumental in breaching government systems, critical infrastructure services, and a large number of companies, as well as in stealing personal information of hundreds of millions, perhaps even billions of people. 

Neural implant monitors multiple brain areas at once, provides new neuroscience insights

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SEM images of the neural implant’s microelectrode array. Images courtesy of Nature Neuroscience

April 27, 2021 -- How do different parts of the brain communicate with each other during learning and memory formation? A new study by researchers at the University of California San Diego takes a first step at answering this fundamental neuroscience question.

The study was made possible by developing a neural implant that monitors the activity of different parts of the brain at the same time, from the surface to deep structures—a first in the field. Using this new technology, the researchers show that diverse patterns of two-way communication occur between two brain regions known to play a role in learning and memory formation—the hippocampus and the cerebral cortex. The researchers also show that these different patterns of communication are tied to events called sharp-wave ripples, which occur in the hippocampus during sleep and rest.

The researchers published their findings Apr. 19 in Nature Neuroscience.

“This technology has been developed particularly for studying interactions and communications between different brain regions simultaneously,” said co-corresponding author Duygu Kuzum, a professor of electrical and computer engineering at the UC San Diego Jacobs School of Engineering. “Our neural implant is versatile; it can be applied to any area of the brain and can enable study of other cortical and subcortical brain regions, not just the hippocampus and cerebral cortex.”

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The neural implant connected to a customized printed circuit board.

“Little is known about how various brain regions work together to generate cognition and behavior,” said Takaki Komiyama, a professor of neurobiology and neurosciences at UC San Diego School of Medicine and Division of Biological Sciences, who is the study’s other co-corresponding author. “In contrast to the traditional approach of studying one brain area at a time, the new technology introduced in this study will begin to allow us to learn how the brain as a whole works to control behaviors and how the process might be compromised in neurological disorders.”

The neural implant is made up of a thin, transparent, flexible polymer strip fabricated with an array of micrometer-sized gold electrodes, onto which platinum nanoparticles have been deposited. Each electrode is connected by a micrometers-thin wire to a custom-printed circuit board. Kuzum’s lab developed the implant. They worked with Komiyama’s lab to perform brain imaging studies in transgenic mice.

Engineering a multi-use neural probe

What makes this neural implant unique is that it can be used to monitor activity in multiple brain regions at the same time. It can record electrical signals from single neurons deep inside the brain, like in the hippocampus, while imaging large areas like the cerebral cortex.

“Our probe enables us to combine these modalities in the same experiment seamlessly. This cannot be done with current technologies,” said Xin Liu, an electrical and computer engineering Ph.D. student in Kuzum’s lab. Liu is a co-first author of the study along with Chi Ren, a recent UC San Diego biological sciences Ph.D. graduate who is now a postdoctoral researcher in Komiyama’s lab, and Yichen Lu, an electrical and computer engineering Ph.D. student in Kuzum’s lab.

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The flexible neural probe allows the working distance of the microscope to be close to the surface (top), while a conventional probe with rigid parts makes the working distance (red arrows) much farther (bottom).

Several design features make multi-region monitoring possible. One is that this probe is flexible. When it is inserted deep into the brain to monitor a region like the hippocampus, the part that sticks out of the brain can be bent down and make room for a microscope to be lowered close to the surface to do imaging of the cerebral cortex at the same time. Conventional neural probes are rigid, so they get in the microscope’s way; as a result, they cannot be used to monitor deep brain structures while imaging the brain’s surface. And even though the UC San Diego team’s neural probe is soft and flexible, it is engineered to withstand buckling under pressure during insertion.

Another important feature is that this probe is transparent, so it gives the microscope a clear field of view. It also does not generate any shadows or additional noise during imaging.

Exploring fundamental neuroscience questions

The motivation for this study was getting to the root of how different cognitive processes, such as learning and memory formation, occur in the brain. Such processes involve communication between the hippocampus and cerebral cortex. But how exactly does this communication happen? And which brain region initiates this communication: the hippocampus or the cerebral cortex? These types of questions have been left unanswered because it is very difficult to study these two brain regions simultaneously, said Kuzum.

“We were interested in investigating the nature of cortical-hippocampal interactions, so we built a technology to explore this neuroscience problem,” she said.

The researchers used their probe to monitor the activity of the hippocampus and the cerebral cortex in transgenic mice. Specifically, they monitored activity before, during and after oscillations that occur in the hippocampus called sharp-wave ripples.

Their experiments revealed that communication between the hippocampus and cerebral cortex is two-sided: sometimes the cortex initiates communication, other times it’s the hippocampus. This is an important first clue for understanding inter-region communication in the brain, the researchers said.

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L-R: Co-first authors Xin Liu, Chi Ren and Yichen Lu.

“The hippocampal-cortical interaction is important in memory consolidation and retrieval,” said Ren. “The two-sided communication we reported here is different from the conventional notion that the cortex passively receives the information from the hippocampus. Instead, the cortex is actively involved in encoding information into the brain and may play an instructive role during memory consolidation and retrieval.”

“We can now begin new studies to unlock how processes like learning and memory happen,” said Kuzum. “For example, when the brain acquires new information, how does the hippocampus transfer the memory to the cortex for storage, or does the cortex send a cue to transfer the memory? Our findings show that communication can be initiated by either, but to go beyond that we’d need to do behavioral studies.”

ALT TEXT
Examples of different cortical activity patterns during sharp-wave ripples.

This study also reveals that there are diverse and distinct modes of communication between the hippocampus and the cerebral cortex. The researchers found that the hippocampus communicates with at least eight different parts of the cerebral cortex every time sharp-wave ripples occur. Further, each of these eight cortical activity patterns is tied to a different population of neurons in the hippocampus.

“These findings suggest that the interactions between brain regions, not only between cortex and hippocampus, can be fundamentally diverse and flexible. Therefore, multiple brain regions can efficiently work together to generate cognition and behavior that rapidly adapt to changing environments,” said Ren.

Paper title: “Multimodal neural recordings with Neuro-FITM uncover diverse patterns of cortical-hippocampal interactions.” Co-authors of the study include Yixiu Liu, Jeong-Hoon Kim and Stefan Leutgeb, all at UC San Diego.

This research was supported by the Office of Naval Research (N000142012405 and N00014162531), the National Science Foundation (ECCS-2024776, ECCS-1752241 and ECCS-1734940), and the National Institutes of Health (R21 EY029466, R21 EB026180, DP2 EB030992, R01 NS091010A, R01 EY025349, R01 DC014690, R21 NS109722 and P30 EY022589).

From self-driving cars, to drones, to healthcare robotics: UC San Diego at ICRA 2021 preview

April 26, 2021-- A record number of papers from robotics faculty at the University of California San Diego were accepted to the 2021 International Conference on Robotics and Automation taking place in Xi’an.China, May 30 to June 5. 

From helping robots navigate the ER, to making it easier for autonomous drones to fly around obstacles, to teaching robots how to suture wounds, the papers demonstrate the breath and depths of robotics research taking place at the UC San Diego Contextual Robotics Institute. 

“It is encouraging to see the strong growth in submissions in all areas of robotics research,” said Henrik Christensen, director of the robotics institute, which includes more than 50 faculty and more than 100 graduate students. “In spite of COVID-19 and all the challenges it presents, our research work continues in full force.”

Below is a list of papers accepted to the conference, in alphabetical order by department, with summaries and links. 

Department of Computer Science and Engineering

Looking Farther in Parametric Scene Parsing with Ground and Aerial Imagery

 

Raghava Modhugu, Harish Rithish Sethuram, Manmohan Chandraker, C.V. Jawahar

In this paper, researchers demonstrate the effectiveness of using aerial imagery as an additional modality to overcome challenges in road scene understanding. We propose a novel architecture, Unified, that combines features from both aerial and ground imagery to infer scene attributes. 

http://cdn.iiit.ac.in/cdn/cvit.iiit.ac.in/images/ConferencePapers/2021/Scene_attributes___ICRA_2021.pdf

Auto-calibration Method Using Stop Signs for Urban Autonomous Driving Applications

 

Yunhai Han, Yuhan Liu, David Paz, Henrik Christensen
Researchers developed an approach to calibrate sensors for self-driving cars using recognition of traffic signs, such as stop signs. The approach is based on detection, geometry estimation, calibration, and recursive updating. Results from natural environments are presented that clearly show convergence and improved performance.

https://arxiv.org/abs/2010.07441

Social Navigation for Mobile Robots in the Emergency Department

 

Angelique Taylor, Sachiko Mastumoto, Wesley Xiao, and Laurel D. Riek
In this paper, we introduce the Safety-Critical Deep Q-Network (SafeDQN) system, a new acuity-aware navigation system for mobile robots.

http://cseweb.ucsd.edu/~lriek/papers/taylor-icra-2021.pdf

Temporal Anticipation and Adaptation Methods for Fluent Human-Robot Teaming

 

Tariq Iqbal and Laurel D. Riek
In this paper, we introduce TANDEM: Temporal Anticipa- tion and Adaptation for Machines, a series of neurobiologically- inspired algorithms that enable robots to fluently coordinate with people. TANDEM leverages a human-like understanding of external and internal temporal changes to facilitate coordination.

http://cseweb.ucsd.edu/~lriek/papers/iqbal-riek-icra-2021.pdf

 

Department of Electrical and Computer Engineering

Mesh Reconstruction from Aerial Images for Outdoor Terrain Mapping Using Joint 2D-3D Learning

 

Q. Feng, N. Atanasov
This paper develops a joint 2D-3D learning approach to reconstruct local meshes at each camera keyframe, which can be assembled into a global environment model. Each local mesh is initialized from sparse depth measurements.
https://arxiv.org/abs/2101.01844

Coding for Distributed Multi-Agent Reinforcement Learning

 

B. Wang, J. Xie, N. Atanasov
We propose a coded distributed learning framework, which speeds up the training of MARL algorithms in the presence of stragglers, while maintaining the same accuracy as the centralized approach. As an illustration, a coded distributed version of the multi-agent deep deterministic policy gradient(MADDPG) algorithm is developed and evaluated
https://arxiv.org/abs/2101.02308

Non-Monotone Energy-Aware Information Gathering for Heterogeneous Robot Teams

X. Cai, B. Schlotfeldt, K. Khosoussi, N. Atanasov, G. J. Pappas, J. How
This work proposes a distributed planning approach based on local search, and shows how to reduce its computation and communication requirements without sacrificing algorithm performance.
https://arxiv.org/abs/2101.11093

Active Bayesian Multi-class Mapping from Range and Semantic Segmentation Observations

 

A. Asgharivaskasi, N. Atanasov
This work develops a Bayesian multi-class mapping algorithm utilizing range-category measurements. We derive a closed-form efficiently computable lower bound for the Shannon mutual information between the multi-class map and the measurements.
https://arxiv.org/abs/2101.01831

Learning Barrier Functions with Memory for Robust Safe Navigation

 

K. Long, C. Qian, J. Cortes, N. Atanasov
This paper investigates safe navigation in unknown environments, using onboard range sensing to construct control barrier functions online. To represent different objects in the environment, we use the distance measurements to train neural network approximations of the signed distance functions incrementally with replay memory. This allows us to formulate a novel robust control barrier safety constraint which takes into account the error in the estimated distance fields and its gradient.
https://arxiv.org/abs/2011.01899

Generalization in reinforcement learning by soft data augmentation

 

Nicklas Hansen, Xiaolong Wang
Instead of learning policies directly from augmented data, we propose SOft Data Augmentation (SODA), a method that decouples augmentation from policy learning. Specifically, SODA imposes a soft constraint on the encoder that aims to maximize the mutual information between latent representations of augmented and non-augmented data, while the RL optimization process uses strictly non-augmented data.
https://nicklashansen.github.io/SODA/

Bimanual Regrasping for Suture Needles using Reinforcement Learning for Rapid Motion Planning

 

Z.Y. Chiu, F. Richter, E.K. Funk, R.K. Orosco, M.C. Yip
In this work, we present rapid trajectory generation for bimanual needle regrasping via reinforcement learning (RL). Demonstrations from a sampling-based motion planning algorithm is incorporated to speed up the learning. In addition, we propose the ego-centric state and action spaces for this bimanual planning problem, where the reference frames are on the end-effectors instead of some fixed frame.
https://arxiv.org/pdf/2011.04813.pdf

Real-to-Sim Registration of Deformable Soft-Tissue with Position-Based Dynamics for Surgical Robot Autonomy

 

F. Liu, Z. Li, Y. Han, J. Lu, F. Richter, M.C. Yip
In this work, we propose an online, continuous, real-to-sim registration method to bridge from 3D visual perception to position-based dynamics(PBD) modeling of tissues. The PBD method is employed to simulate soft tissue dynamics as well as rigid tool interactions for model-based control.
https://arxiv.org/abs/2011.00800

Model-Predictive Control of Blood Suction for Surgical Hemostasis using Differentiable Fluid Simulations

 

J. Huang*, F. Liu*, F. Richter, M.C. Yip
We investigate the integration of differentiable fluid dynamics to optimizing a suction tool's trajectory to clear the surgical field from blood as fast as possible. The fully differentiable fluid dynamics is integrated with a novel suction model for effective model predictive control of the tool.
https://arxiv.org/abs/2102.01436

SuPer Deep: A Surgical Perception Framework for Robotic Tissue Manipulation using Deep Learning for Feature Extraction

 

J. Lu, A. Jayakumari, F. Richter, Y. Li, M.C. Yip
In this work, we overcome the challenge by exploiting deep learning methods for surgical perception. We integrated deep neural networks, capable of efficient feature extraction, into the tissue reconstruction and instrument pose estimation processes.
https://arxiv.org/pdf/2003.03472.pdf

Data-driven Actuator Selection for Artificial Muscle-Powered Robots

 

T. Henderson, Y. Zhi, A. Liu, M.C. Yip
To accelerate the development of artificial muscle applications, researchers developed a data driven approach for robot muscle actuator selection using Support Vector Machines (SVM). This first-of-its-kind method gives users insight into which actuators fit their specific needs and actuation performance criteria, making it possible for researchers and engineers with little to no prior knowledge of artificial muscles to focus on application design. It also provides a platform to benchmark existing, new, or yet-to-be-discovered artificial muscle technologies.
https://arxiv.org/abs/2104.07168

Optimal Multi-Manipulator Arm Placement for Maximal Dexterity during Robotics Surgery

 

J. Di, M. Xu, N. Das, M.C. Yip
Engineers created a method to generate the optimal manipulator base positions for the multi-port da Vinci surgical system that minimizes self-collision and environment-collision, and maximizes the surgeon's reachability inside the patient. The metrics and optimization strategy are generalizable to other surgical robotic platforms so that patient-side manipulator positioning may be optimized and solved.
J. Di, M. Xu, N. Das, M.C. Yip
https://arxiv.org/abs/2104.06348

MPC-MPNet: Model-Predictive Motion Planning Networks for Fast, Near-Optimal Planning under Kinodynamic Constraints

 

L. Li, Y.L. Miao, A.H. Qureshi, M.C. Yip
We present a scalable, imitation learning-based, Model-Predictive Motion Planning Networks framework that quickly finds near-optimal path solutions with worst-case theoretical guarantees under kinodynamic constraints for practical underactuated systems. Our framework introduces two algorithms built on a neural generator, discriminator, and a parallelizable Model Predictive Controller (MPC).
https://arxiv.org/pdf/2101.06798.pdf

Autonomous Robotic Suction to Clear the Surgical Field for Hemostasis using Image-based Blood Flow Detection

 

F. Richter, S. Shen, F. Liu, J. Huang, E.K. Funk, R.K. Orosco, M.C. Yip
In this work, we present the first, automated solution for hemostasis through development of a novel probabilistic blood flow detection algorithm and a trajectory generation technique that guides autonomous suction tools towards pooling blood. The blood flow detection algorithm is tested in both simulated scenes and in a real-life trauma scenario involving a hemorrhage that occurred during thyroidectomy.
https://arxiv.org/abs/2010.08441

Department of Mechanical and Aerospace Engineering

Scalable Learning of Safety Guarantees for Autonomous Systems using Hamilton-Jacobi Reachability

 

Sylvia Herbert, Jason J. Choi, Suvansh Qazi, Marsalis Gibson, Koushil Sreenath, Claire J. Tomlin
In this paper we synthesize several techniques to speed up computation: decomposition, warm-starting, and adaptive grids. Using this new framework we can update safe sets by one or more orders of magnitude faster than prior work, making this technique practical for many realistic systems.
https://arxiv.org/abs/2101.05916

Planning under non-rational perception of uncertain spatial costs

 

Aamodh Suresh and Sonia Martinez
This work investigates the design of risk- perception-aware motion-planning strategies that incorporate non-rational perception of risks associated with uncertain spatial costs. Our proposed method employs the Cumulative Prospect Theory (CPT) to generate a perceived risk map over a given environment.
https://arxiv.org/pdf/1904.02851.pdf


 

Three from UC San Diego Elected to American Academy of Arts and Sciences

From left: Ananda Goldrath, Eileen Myles and Stefan Savage

April 23, 2021, San Diego, CA -- Three members of the University of California San Diego community, including two professors and one professor emeritus, have been elected to the American Academy of Arts and Sciences—one of the oldest and most esteemed honorary societies in the nation.

Ananda Goldrath, Eileen Myles and Stefan Savage are among the Academy’s 2021 class of 252 members. They join fellow 2021 classmates who are artists, scholars, scientists and leaders in the public, non-profit and private sectors, including: civil rights lawyer and scholar Kimberlé Crenshaw; computer scientist Fei-Fei Li; composer, songwriter, and performer Robbie Robertson; and media entrepreneur and philanthropist Oprah Winfrey. 

The American Academy of Arts and Sciences has honored exceptionally accomplished individuals and engaged them in advancing the public good for more than 240 years. Professor Walter Munk was the first UC San Diego faculty member elected to the Academy. Since then, more than 80 faculty from disciplines that span the entire campus have received this prestigious honor. 

"This year, our faculty are being recognized for three vastly different fields of study: immunology, literature, and cybersecurity,” said UC San Diego Chancellor Pradeep K. Khosla. “Having the oldest and most distinguished American national academy honor the career accomplishments of these prestigious faculty both honors their individual successes and spotlights the breadth of expertise and influence of our Triton faculty. UC San Diego’s well-established prowess in science, technology and art offers a truly well-rounded experience for our students, our researchers and our collaborative faculty.”

In the statement announcing this year's new Academy members, David Oxtoby, President of the American Academy said, “The past year has been replete with evidence of how things can get worse; this is an opportunity to illuminate the importance of art, ideas, knowledge, and leadership that can make a better world.”

Following is more information about each of UC San Diego’s newest Academy members:

Ananda Goldrath
Goldrath is a Tata Chancellor’s Professor in the Division of Biological Sciences and former chair of the Molecular Biology Section. Her work as an immunologist has contributed to the understanding of transcriptional networks that govern the formation and maintenance of long-lived protective immunity. Goldrath’s research explores the mechanistic basis underlying memory T cell differentiation as a strategy to program the immune system to meet pathogens or malignancies in the tissues where they first pose a threat. This information has made it possible to beneficially manipulate the immune system to eliminate infection and malignancies. Goldrath is a Pew Scholar and Leukemia and Lymphoma Society Fellow and a member of the Immunological Genome Project, the Leadership Council of the Program in Immunology and Scientific Advisory Committee of the San Diego Center for Precision Immunotherapy at UC San Diego.

Eileen Myles
Myles, professor emeritus of fiction writing in the Department of Literature, began their career in New York City in 1974 as a poet, novelist, public talker and art journalist. While at UC San Diego from 2002 to 2007, they taught courses in poetry writing, short fiction, writing between genres and the libretto, among others. Also during this time, they wrote the libretto for the opera “Hell,” composed by Michael Webster with productions in 2004 and 2006. Myles is the recipient of a Guggenheim Fellowship, a Creative Capital/Andy Warhol Foundation Arts Writers grant, four Lambda Literary Awards, the Shelley Award from the Poetry Society of America, and a 2014 artist grant from the Foundation for Contemporary Arts. In 2016 they received a Creative Capital grant and the Clark Prize for Excellence in Art Writing and, in 2019, a poetry award from the American Academy of Arts and Letters. The Publishing Triangle honored Myles with the Bill Whitehead Award for Lifetime Achievement in 2020, recognizing writers in the LGBT community. Their 22 books include “For Now” (2020), “evolution” (2018), “Afterglow” (2017), “I Must Be Living Twice/new & selected poems” (2015) and “Chelsea Girls” (1994).

Stefan Savage
Savage is a cybersecurity researcher who holds an expansive view of the field. He and colleagues bring together computer science and the social sciences in their work by taking into account economics, policy and regulations, not just technology. His team has been instrumental in pointing out security vulnerabilities in cars, which have been addressed by the automotive industry’s regulatory bodies and manufacturers. They have tracked the financial transactions responsible for funding email spam campaigns and botnets around the world. The data has been used by government agencies and credit card companies to block these transactions. Savage and colleagues also have designed ways to measure and pinpoint the source of attacks that cripple the internet and large websites, known as distributed denial of service attacks. Savage has received numerous awards for his work, including a McArthur fellowship in 2017, the ACM Prize in Computing in 2015, and three test of time awards from leading academic computer security organizations. He holds the Irwin and Joan Jacobs Chair at the Jacobs School of Engineering and is a professor in the UC San Diego Department of Computer Science and Engineering.

In addition to these three faculty members, alumna Angela Davis is also part of this year’s class of fellows. A well known activist who is now on faculty at the University of California Santa Cruz, Davis earned a master’s degree from the Department of Philosophy at UC San Diego in 1969. She worked closely with philosopher Herbert Marcuse. Her likeness is now part of the Price Center’s Black Legacy Mural, and she is also portrayed on the walls of the Che Cafe. 

The American Academy of Arts & Sciences was founded in 1780 by John Adams, John Hancock and others who believed the new republic should honor exceptionally accomplished individuals and engage them in advancing the public good. The 2021 members join the company of those elected before them, including Benjamin Franklin and Alexander Hamilton in the eighteenth century; Ralph Waldo Emerson and Maria Mitchell in the nineteenth; Robert Frost, Martha Graham, Margaret Mead, Milton Friedman and Martin Luther King, Jr. in the twentieth; and more recently Joan C. Baez, Judy Woodruff, John Lithgow, and Bryan Stevenson. International Honorary Members include Charles Darwin, Albert Einstein, Winston Churchill, Laurence Olivier, Mary Leakey, John Maynard Keynes, Akira Kurosawa and Nelson Mandela.

Combining nanomaterials in 3D to build next-generation imaging devices

Man wearing a labcoat.
Oscar Vazquez-Mena. Photos by Erik Jepsen/University Communications

April 12, 2021 -- For years, two-dimensional nanomaterials just one or a few atoms thick have been all the rage in the world of materials science. Take graphene, for example. This one-layer sheet of carbon atoms yields a material that is hundreds of times stronger than steel, highly conductive and super-flexible.

Oscar Vazquez-Mena, a professor of nanoengineering at the UC San Diego Jacobs School of Engineering, is taking these types of materials to the next dimension. His research focuses on integrating different nanoscale materials together in 3D to create an entirely new generation of devices for environmental monitoring, energy harvesting and biomedical applications.

“It opens up so many more possibilities for what we could do with our nanoengineering tools,” said Vazquez-Mena, who recently received a five-year, $500,000 CAREER Award through the National Science Foundation for one such project.

The project involves combining graphene with semiconducting nanoparticles called quantum dots to create devices that can “see” a broad range of different wavelengths of light, such as infrared and ultraviolet, that are invisible to the human eye. These devices, called multi-spectrum photodetectors, could enable cameras to take pictures of infections, poisonous gases and harmful radiation; check for food quality or contamination; and monitor air and water quality. They could also aid vision at night and when it’s foggy.

Closeup of an electronic chip.
Chips integrating graphene and quantum dots.

Vazquez-Mena’s approach would make these devices ultra-thin. “Because we are working with nanomaterials, we can in principle engineer very thin photodetectors on the order of one micrometer, which could easily be integrated into smartphones and other mobile devices for convenient deployment outside of the lab,” he said.

An aspect of this project that is near and dear to Vazquez-Mena is mentoring and training the next generation of nanoengineers. He will be developing hands-on nanoengineering fabrication workshops for pre-college students, particularly underrepresented students at schools that may have limited resources and laboratory equipment.

This builds on Vazquez-Mena’s ongoing work promoting STEM education and research among migrant communities and children of deported parents, as well as UC San Diego transfer students. In recognition of his outreach work, Vazquez-Mena has been named an Emerging Scholar in 2020 by Diverse: Issues in Higher Education magazine. He was also recently named an Outstanding Engineering Educator by San Diego County Engineering Council.

“In my career, I had plenty of support and opportunities, so for me it is very important to provide these two things to students who come from underserved communities and have a strong desire to make discoveries and contribute to our society through science and technology,” said Vazquez-Mena.

At the start of 2020, Vazquez-Mena started a pilot program to help new Latinx/Chicanx transfer students at UC San Diego get involved in research activities. The program, called Research Paths for LatinX Students, is supported by the university’s Latinx/Chicanx Academic Excellence Initiative. Students attend Saturday sessions where they learn about the importance of research, different research opportunities on campus and strategies to join a lab. During the pandemic, the program shifted to offering virtual workshops on Coding, Arduino controllers and Machine Learning for students to continue learning at home.

Imaging the brain with ultrasound

In another project, Vazquez-Mena is stacking nanostructures to build 3D arrays that can allow ultrasound to go through the skull and do non-invasive imaging and stimulation of the human brain. Such technology would be useful for treating brain disease and trauma without having to open the skull or insert wires and implants in the brain. It could also allow physicians to rapidly diagnose brain trauma in patients without having to perform costly MRI scans.

Getting ultrasound through the skull and into the brain is no easy task. The human skull is relatively thick and dense, so it either reflects or absorbs ultrasound waves before they can make it to the brain.

To get past this barrier, Vazquez-Mena is engineering a special kind of material—called a metamaterial—composed of nanostructures that can cancel the reflections created by the skull and essentially redirect ultrasound waves to go through it. The metamaterial is made of nanometers-thin membranes of silicon nitride and microscale acoustic cavities. Both components are arranged together in a 3D array that can enable the material to manipulate sound waves in ways that cannot be done with conventional materials.

“This is another example of building 3D constructions based on nanomaterials that achieve new and exciting properties,” said Vazquez-Mena.

This project is funded by a prestigious Director’s Fellowship awarded to Vazquez-Mena by the Defense Advanced Research Projects Agency (DARPA). The multidisciplinary work involves collaboration with UC San Diego mechanical and aerospace engineering professors James Friend and Nicholas Boechler, who are experts in ultrasound acoustics, and with UC San Diego rheumatology professor Monica Guma.

In 2018, Vazquez-Mena received a DARPA Young Faculty award (YFA) to pursue this project. The DARPA YFA recognizes rising stars in junior research positions who are pursuing basic science research and provides $500,000 of funding for a two-year period. As one of the program’s top-performing awardees, Vazquez-Mena was selected for the highly competitive DARPA Director’s Fellowship, which provides up to $500,000 of additional funding and support.

UC San Diego researchers developing COVID-19 vaccine technology -- no refrigeration or second dose needed

Understudied Mutations Have Big Impact on Gene Expression

Variable number tandem repeats modulate genes associated with Alzheimer's disease, obesity, cancer and other conditions

Vineet Bafna, a professor in the UC San Diego Department of Computer Science and Engineering and senior author on the paper

April 9, 2021-- An international team of researchers led by computer scientists at the University of California San Diego have identified 163 variable number tandem repeats (VNTRs) that actively regulate gene expression. In a paper published in Nature Communications this week, the researchers provide new insights into this understudied mechanism, how it may drive disease and other traits and could ultimately impact patient care.

VNTRs are common genomic variations that appear as repeated DNA sequences longer than six base pairs.

“VNTRs have been difficult to identify through sequencing information, particularly short reads,” said Vineet Bafna, a professor in the UC San Diego Department of Computer Science and Engineering and senior author on the paper. “We developed a fast computational method to identify these variations, which gave us a new lens to observe their potential impact on gene expression and disease.”

While VNTRs are one of the most common genetic variations, detecting them has been both challenging and expensive. As a result, genome-wide association studies have mostly ignored VNTRs, excluding a potentially rich repository of disease-causing mutations.

Using the new method they developed, researchers found more than 10,000 VNTRs in a group of 652 people. Of those, 163 changed the way genes were expressed in 46 different tissue types. Nearly half had a particularly strong impact on Alzheimer’s disease, familial cancers, diabetes and other conditions.

“We looked closely at these 163 VNTRs to understand their impact,” said UC San Diego computer science Ph.D. student Mehrdad Bakhtiari. “One was affecting expression levels of a gene called AS3MT, which has been implicated in schizophrenia. The tandem repeat controls gene expression and the expression affects the disease.”

A new neural-network based method

The new computational method,  called adVNTR-NN, rapidly finds VNTRs  in short read genomic sequencing data. Short read technology breaks up DNA samples into relatively small pieces and uses sophisticated algorithms to piece together complete sequences. Popularized by Illumina, short reads are the most common, and least expensive, form of next-generation sequencing.

“Our computational method runs quite fast and it works in the most cost-effective sequencing technologies,” said Bakhtiari, the first author on the paper. “So, it should be easy to scale and easy to use for people outside of research settings, for example, hospitals.”

Next steps

The authors have high confidence in these results, as 91% of the initial findings were validated in two other cohorts. However, there is still more work to do. The researchers want to better quantify the impact VNTRs have on specific genes, as well as determining whether there is indeed a causal link between certain VNTRs and the diseases they have been linked to.

“We’re learning more about the importance of complex and repetitive regions of the genome and the roles they play in human traits,” said Melissa Gymrek, assistant professor in the Computer Science and Engineering department and the School of Medicine and coauthor on the paper. “VNTRs  have been almost impossible to look at in most available sequencing datasets on a large scale.”

The team also wants to study specific conditions, such as autism spectrum disorder, to better understand patients’ VNTR profiles and how those influence their conditions.

“These findings open a whole new window to study the role VNTRs play in gene expression,” said Bafna. “Given that these sequences are physically larger than single nucleotide polymorphisms and are also quite prevalent, these efforts could eventually have a major impact on patient care.”

In addition to Bafna, Bakhtiari, and Gymrek, paper coauthors include Jonghun Park of the Computer Science and Engineering Department, Yuan-Chun Ding and Susan L. Neuhausen of the Beckman Research Institute of City of Hope, Sharona Shleizer-Burko of UC San Diego Department of Medicine, and Bjarni V. Halldórsson and Kári Stefánssonde of CODE Genetics, Reykjavik, Iceland.

 

 

testing

April 9, 2021

Diversifying the ranks of engineering faculty

UC San Diego Jacobs School of Engineering joins program to diversify engineering faculty

The University of California San Diego Jacobs School of Engineering has partnered with University of Michigan to strengthen a program that addresses the lack of diversity in the engineering academia. 

The program, NextProf Pathfinder, is a two-day program developed at Michigan Engineering and aimed at first and second-year PhD students, as well as students in masters programs, in an effort to keep them pursuing careers in academia.

It’s the newest program in a larger effort that began in 2012 as NextProf. To date, more than 144 women and people from underrepresented groups who attended its workshops have achieved tenure-track faculty positions. And UC San Diego Jacobs School of Engineering is the third institution to partner with Michigan Engineering on a NextProf program.

At workshops, participants hear from top faculty and deans from around the U.S. to gain a better understanding of academic life and how to achieve a position in it. They learn best practices in applying and networking for positions, how to set up a lab and what kind of work/life balance they can expect, for example. NextProf Pathfinder, designed for earlier-stage students, teaches participants what types of experiences they should seek out to best position themselves. The NextProf workshops for later-stage students and postdocs focus more on how to leverage those experiences and communicate about them.

The two schools will partner on the NextProf Pathfinder program going forward, with the institutions swapping hosting duties each year. This year, the program will be in Ann Arbor, from October 17-19. The conference will be in San Diego in 2022.

“One of the reasons I’m particularly excited about this partnership is that, given UCSD’s location and the demographics of that region of the country, it will make our workshops more accessible to Latinx graduate students,” said Lola Eniola-Adefoso, a U-M professor of chemical engineering and a University Diversity and Social Transformation Professor. “Latinx faculty members are dramatically underrepresented in academia and this is an important step toward changing that.”

For UC San Diego Jacobs School of Engineering, NextProf Pathfinder represents an important move forward in its broader efforts to create learning and research environments where all engineering and computer science students, staff and faculty thrive.
 

Karen L. Christman, Associate Dean for Faculty, Professor of Bioengineering, UC San Diego Jacobs School of Engineering 

“NextProf Pathfinder is one concrete step in a larger effort to create a broader academic culture where all students—and in particular students who are traditionally underrepresented in engineering—are empowered with the knowledge the networks, the role models and the momentum needed to establish fulfilling and meaningful careers,” said Karen Christman, associate dean for faculty and professor of bioengineering at UC San Diego Jacobs School of Engineering. “Critical to this project is ensuring that students who are traditionally underrepresented in engineering have all that they need to make the jump from graduate student to engineering professor and head of an independent lab. That’s what NextProf Pathfinder is designed to do.”

Engineering is a field which, despite efforts going back decades, remains stubbornly white and male. The number of female faculty members is trending upward in recent years, but only slowly. And the percentage of people from underrepresented groups in faculty positions has been flat for roughly two decades.

Such a monolithic engineering culture has repercussions for society-at-large, as we’ve seen illustrated recently by facial recognition technologies that aren’t accurate for Black faces, for example. Increasing the diversity of academic engineering researchers and educators is seen as an essential step in advancing technologies that don’t exacerbate inequities.

But the current lack of diversity in professor roles can make non-white and non-male candidates feel unwelcome or devalued, Eniola-Adefoso says. Each one that opts for something outside academia, in favor of a career where they feel more at home, can perpetuate the cycle.

NextProf Pathfinder is the newest part of the larger NextProf effort co-founded in 2012 by Alec D. Gallimore, the Robert J. Vlasic Dean of Engineering, the Richard F. and Eleanor A. Towner Professor, an Arthur F. Thurnau Professor, and a professor of aerospace engineering.

NextProf began as a program for third- to fifth-year PhD students and recent doctoral graduates from anywhere in the nation. Since that time it has expanded to three workshops:

  • NextProf Engineering, founded in 2015, is held every spring at U-M and is open to all engineering students and postdocs at U-M.
  • NextProf Pathfinder, founded in 2018, is open to first- and second-year PhD students and master’s students considering a PhD. Before a COVID-19 hiatus in 2020, it had welcomed 73 participants from 32 institutions in its first two years.
  • NextProf Nexus, an expansion of the original NextProf workshop, began in 2018 when the University of California, Berkeley joined as a partner and sponsoring institution. Georgia Tech joined the following year. Now, the three partner universities take turns hosting it.


Katherine Adler is a fifth-year PhD candidate in civil and environmental engineering at Cornell University. She was once a participant in both the NextProf Nexus and Pathfinder programs.

“The Nexus program provided more concrete tools to which I refer as I refine my faculty application materials,” Adler said. “After attending these workshops, I can better visualize my path to becoming a successful research faculty member and better understand the high expectations for faculty candidates.”

Testing

April 3, 2021

Test

UC San Diego Engineering Ranks #9 in U.S. News and World Report Best Engineering Schools Rankings

March 30, 2021 - For the second year in a row, the University of California San Diego Jacobs School of Engineering has ranked #9 in the nation in the influential U.S. News & World Report Rankings of Best Engineering Schools. 

This #9 ranking is up from #11 two years ago, #12 three years ago, #13 four years ago, and #17 five years ago.  

“The Jacobs School of Engineering has earned its ninth place among the nation’s most innovative, distinctive and prestigious engineering schools,” said UC San Diego Chancellor Pradeep K. Khosla. “UC San Diego’s engineers and computer scientists regularly collaborate with students, faculty and staff across our $1.4 billion dollar research enterprise. This unique cooperative, cross-discipline connectivity sparks discoveries and drives innovations that garner national and global recognition."

The Jacobs School of Engineering at UC San Diego leverages engineering and computer science for the public good through education, research and transfer of innovation to society. The #9 ranking brings welcome attention to the Jacobs School's work to create and strengthen interrelated education, research and innovation ecosystems.

“Ranking ninth in the nation is a tribute to the hard work, grit and excellence of our students, staff, faculty, industry partners, collaborators and friends," said Albert P. Pisano, Dean of the UC San Diego Jacobs School of Engineering. "I look at rankings as recognition rather than definition. It's wonderful to be recognized for some of the ways we are strengthening and growing as a school and as a community."

Research relevance

The UC San Diego Jacobs School of Engineering has launched 14 Agile Research Centers and Institutes since 2014. This effort has driven deeper collaborations within the Jacobs School and across the UC San Diego campus. It has also driven deeper interactions between Jacobs School research teams and collaborators in industry and government labs. The goal is to tackle fundamental, relevant challenges that no individual research lab or company is likely to solve alone. This process of taking on difficult, interdisciplinary challenges involving academia, industry and government provides engaging training and learning environments for Jacobs School of Engineering students. These students go on to graduate as an empowered innovation workforce. 

The most recent institute is a cross-campus collaboration, co-launched with the UC San Diego Division of Physical Sciences, called the UC San Diego Institute for Materials Discovery and Design. Researchers deeply involved in this Institute recently won a prestigious National Science Foundation (NSF) Materials Research Science and Engineering Center (MRSEC)

A few recent research results that have emerged from cross-disciplinary research projects tied to agile research centers and institutes include: a skin patch bringing us closer to wearable, all-in-one health monitor; a robot that doesn't need electronics; and a nano-scale particle for better COVID-19 tests.

San Diego regional innovation ecosystems

The fact that the UC San Diego Jacobs School of Engineering has established itself as a top-nine engineering school adds to San Diego's momentum as a world-class, well-rounded hub for technology and innovation. 

In addition to its #9 ranking, the Jacobs School of Engineering at UC San Diego is the largest engineering school on the U.S. West Coast, according to the latest enrollment data from ASEE. In Fall 2020, the Jacobs School enrolled 9,174 students. The Jacobs School has awarded nearly 15,000 degrees over the last 6 years. 

"The UC San Diego Jacobs School of Engineering is educating the innovation workforce the nation needs," said Pisano. "And more than ever, as a region, we are employing this innovation workforce here in San Diego."

Creating more and better environments for training this innovation workforce is one of the motivations behind Franklin Antonio Hall, which is UC San Diego's new engineering building. It is on schedule to open in Spring 2022.

Students from all across campus will take classes in Franklin Antonio Hall, which will serve as a national model for how to build innovation ecosystems with physical roots and virtual collaboration infrastructure with national and international impact. This is how engineering for the public good will get done in the future.

Bioengineering climbs to #3

In the same US News & World Report Rankings, the Department of Bioengineering at the UC San Diego Jacobs School of Engineering ranked #3 in the nation. This is up from #4 last year in the same ranking. Bioengineering at UC San Diego has ranked among the top four programs in the nation every year for more than a decade.

"The UC San Diego Department of Bioengineering has been inventing and re-inventing the field of bioengineering for more than 50 years, and it continues to take the field in new and exciting directions. I'm thrilled that we have moved up to #3 in the nation," said UC San Diego professor and chair of bioengineering Kun Zhang. "Some of the most influential work that helped launch the field of bioengineering happened here at UC San Diego. Today, our campus remains an incredibly open and vibrant environment. This enables us to recruit some of the most talented young investigators, and continue exploring the next frontiers and embracing non-traditional research directions in the realm of bioengineering."

Bioengineers from UC San Diego recently made headlines around the world for newly published work advancing an effort to develop a gene therapy for chronic pain that could offer a safer, non-addictive alternative to opioids

One of the newest bioengineering faculty at UC San Diego is Lingyan Shi, who is developing new methods and systems for recording what is happening within live cells

Jacobs School rankings

Highly ranked doctoral programs in engineering at the Jacobs School: bioengineering (3); computer engineering (14); electrical engineering (16); aerospace engineering (17); mechanical engineering (17); civil engineering (20).

The full listing of Jacobs School rankings:
2022 US News & World Report Rankings of Best Engineering Schools are here

 

New ways of looking inside living cells

From developing new imaging platforms, to asking new biological questions, and developing new disease diagnostics, UC San Diego bioengineering professor Lingyan Shi is pushing the boundaries of what's possible when we look inside living cells.

UC San Diego bioengineering professor Lingyan Shi

By Becky Ham

March 29, 2021-- Energy from an exquisitely targeted photon can vibrate the chemical bond of molecules like a pluck on a guitar string. Instead of music, these vibrational frequencies allow University of California San Diego bioengineering professor Lingyan Shi to see specific molecules within a living cell.

The cutting-edge imaging technologies used by Shi, who leads the Laboratory of Optical Bioimaging and Spectroscopy at UC San Diego, are a mouthful: stimulated Raman scattering (SRS) microscopy, multiphoton fluorescence microscopy (MPF), and resonance Raman microscopy (RRS). However, they all use light of specific wavelengths to probe chemical vibrational bonds in biological tissues.   

Different molecules such as fats, proteins, and DNA have distinct vibrational modes, and produce a subtle, yet distinct photo-spectral output. This allows researchers to identify these molecules with high chemical and spatial resolution. The powerful techniques don’t disturb living tissues, so they can be used across a variety of applications. For instance, SRS microscopy can generate a digital histological image of a biopsy in mere minutes, without the use of any chemical dyes and minimal sample preparation. Digital histology, which can mimic the staining seen in traditional histology  techniques (see figure 2), may make its way into the operating room as an intraoperative technique that saves time and improves surgical performance. Another application of Raman-based technologies includes the probing of metabolic dynamics and compositions. Various tissues and even diseases like cancer are marked by distinct metabolic changes. Understanding these dynamics will aid in early detection and better understanding of such diseases and nutrition. 

As one of the world’s leading experts in ultrafast optical imaging, the new Assistant Professor of Bioengineering at the UC San Diego Jacobs School of Engineering has no shortage of ideas about the potential of Raman-based technologies. “When we are developing a new technology, a new tool,” she says, “it will definitely inspire us to ask new biological questions.” 

Seeing without Disturbing

One of those questions is: how can we observe very small molecules in the body, without disturbing their natural functions? For her doctoral research, Shi had been tagging very small drug molecules with fluorescent probes to watch how they passed through the blood-brain barrier. But on the molecular scale, “if we consider size of the drug as a ping-pong ball, but the attached fluorescent particle was like another ping-pong ball or even bigger,” she explained. The bulky fluorescent label on the drugs was likely perturbing the drug’s behavior (such as its permeability and diffusion coefficient) in the body.

A 2014 seminar by her postdoctoral mentor Wei Min at Columbia University illustrated how stimulated Raman scattering microscopy could solve this problem. “At the time, I was very biological problem-oriented, and this was just a great tool for my research,” Shi says. “But when I got to know more and more about the technology, I realized that biological questions and imaging technology are mutually inspirational. It’s not unidirectional.”

Today, no single imaging technique reigns supreme in Shi’s lab. She and her students work with a variety of platforms, depending on the biological question at hand. Some techniques are better at seeing deep into living tissue, Shi explains, while others can probe a broader range of chemical bonds. She has also pioneered new ways of using heavy water to tag molecules with an isotope of hydrogen called deuterium (Fig. 3), to follow the metabolic activities under different physiological or pathological conditions. 

As mentioned, a powerful application centers on detecting metabolic changes that occur during tumor formation, when energy-hungry cancer cells metabolize differently than healthy cells. Shi recently led a study that combined several techniques to detect early metabolic changes that distinguish triple-negative breast cancer from less aggressive cancer types.

Triple-negative breast cancer predominantly affects Black and Latina women, and is difficult to detect early in the disease. “But the optical imaging technology we’re developing can tell you a lot about metabolic changes at a very early stage,” says Shi. “Early-stage diagnosis is critical to increase the survival rate among these women and reduce their cost of treatment.

“Homebuilt” Lab

Many of the imaging systems Shi and her students use are not commercially available yet, and they combine instrumentation and probes to fit their needs. “It’s like a homebuilt microscopy platform in my lab,” Shi says.

The researchers are always tinkering with the platforms to improve the image resolution and sensitivity to the optical signal. Shi holds 6 patents as a co-inventor related to optical imaging and is interested in commercializing or licensing some of these technologies.

“The application of these technologies is still in the infant stage,” she explains. “I think we need to do more educational presentations to show what kinds of information we can achieve, and to demonstrate how useful it is.”

Shi is excited to welcome research collaborators at UC San Diego, from biological scientists to genetics experts, and she is eager to mentor passionate students from underrepresented minorities in her lab, at every level from undergraduate to postdoc. 

“We’re very motivated here at UCSD, and the atmosphere is great. I enjoy seeing students become aware of something they didn’t know about before,” she says. “It’s a very happy moment.”

Shi joined the UC San Diego faculty in October 2019, and she says COVID-19 has made setting up a lab more difficult in some ways. At first it was challenging to source supplies, but lately she’s been more worried that the pandemic will keep her from throwing lab dinner parties and birthday celebrations that usually “bring us all together and make it feel like a family.”

“But I try to think positively about it,” Shi says. “This has also given me more time to think about the future research directions we want to explore.”

Research Expo 2021

Robot, heal thyself

Nanoengineers develop self-repairing microbots

March 17, 2021--Living tissue can heal itself from many injuries, but giving similar abilities to artificial systems, such as robots, has been extremely challenging. Now, researchers at the University of California San Diego reporting in Nano Letters have developed small, swimming robots that can magnetically heal themselves on-the-fly after breaking into two or three pieces. The strategy could someday be used to make hardier devices for environmental or industrial clean up, the researchers say. Watch a video of the self-healing swimmers here.

Scientists have developed small robots that can “swim” through fluids and carry out useful functions, such as cleaning up the environment, delivering drugs and performing surgery. Although most experiments have been done in the lab, eventually these tiny machines would be released into harsh environments, where they could become damaged.

Swimming robots are often made of brittle polymers or soft hydrogels, which can easily crack or tear. Senior author and UC San Diego nanoengineering professor Joseph Wang and colleagues wanted to design swimmers that could heal themselves while in motion, without help from humans or other external triggers.

The researchers made swimmers that were 2 cm long (a little less than an inch) in the shape of a fish that contained a conductive bottom layer; a rigid, hydrophobic middle layer; and an upper strip of aligned, strongly magnetic microparticles. The team added platinum to the tail, which reacted with hydrogen peroxide fuel to form oxygen bubbles that propelled the robot.

When the researchers placed a swimmer in a petri dish filled with a weak hydrogen peroxide solution, it moved around the edge of the dish. Then, they cut the swimmer with a blade, and the tail kept traveling around until it approached the rest of the body, reforming the fish shape through a strong magnetic interaction.

The robots could also heal themselves when cut into three pieces, or when the magnetic strip was placed in different configurations. The versatile, fast and simple self-healing strategy could be an important step toward on-the-fly repair for small-scale swimmers and robots, the researchers say.

Coronavirus circulated undetected months before first COVID-19 cases in Wuhan, China

Study dates emergence as early as October 2019; simulations suggest in zoonotic viruses in most cases die out naturally before causing a pandemic.

The SARS-CoV-2 virus under a microscope. Photo credit: National Institute of Allergy and Infectious Diseases

March 24, 2021--Using molecular dating tools and epidemiological simulations, bioinformaticians and computer scientists at the University of California San Diego, with colleagues at the University of Arizona and Illumina, Inc., estimate that the SARS-CoV-2 virus was likely circulating undetected for at most two months before the first human cases of COVID-19 were described in Wuhan, China, in late-December 2019.

Writing in the March 18, 2021 online issue of Science, they also note that their simulations suggest that the mutating virus dies out naturally more than three-quarters of the time without causing an epidemic.

“Our study was designed to answer the question of how long could SARS-CoV-2 have circulated in China before it was discovered,” said senior author Joel O. Wertheim, associate professor in the Division of Infectious Diseases and Global Public Health at the UC San Diego School of Medicine.

“To answer this question, we combined three important pieces of information: a detailed understanding of how SARS-CoV-2 spread in Wuhan before the lockdown, the genetic diversity of the virus in China, and reports of the earliest cases of COVID-19 in China. By combining these disparate lines of evidence, we were able to put an upper limit of mid-October 2019 for when SARS-CoV-2 started circulating in Hubei province.”

The epidemiological models were designed and run by Ph.D. student Jonathan Pekar, in the UC San Diego bioinformatics program, who is also part of Wertheim’s research group. 

Niema Moshiri, an assistant teaching professor in computer science at the Jacobs School, coded the simulations used in this Science paper. 

Niema Moshiri, an assistant teaching professor in the UC San Diego Department of Computer Science and Engineering, created all the code behind the epidemiological simulations, which can be found here and here on GitHub. The simulations are based on a robust framework for the simultaneous simulation of a transmission network and viral evolution, as well as simulation of sampling imperfections of the transmission network and of the sequencing process. 

Cases of COVID-19 were first reported in late December 2019 in Wuhan, located in the Hubei province of central China. The virus quickly spread beyond Hubei. Chinese authorities cordoned off the region and implemented mitigation measures nationwide. By April 2020, local transmission of the virus was under control but, by then, COVID-19 was pandemic with more than 100 countries reporting cases.

SARS-CoV-2 is a zoonotic coronavirus, believed to have jumped from an unknown animal host to humans. Numerous efforts have been made to identify when the virus first began spreading among humans, based on investigations of early-diagnosed cases of COVID-19. The first cluster of cases — and the earliest sequenced SARS-CoV-2 genomes — were associated with the Huanan Seafood Wholesale Market, but study authors say the market cluster is unlikely to have marked the beginning of the pandemic because the earliest documented COVID-19 cases had no connection to the market.

Regional newspaper reports suggest COVID-19 diagnoses in Hubei date back to at least Nov. 17, 2019, suggesting the virus was already actively circulating when Chinese authorities enacted public health measures.

In the new study, researchers coupled epidemiological simulations with molecular clock evolutionary analyses to try to home in on when the first, or index, case of SARS-CoV-2 occurred. “Molecular clock” is a term for a technique that uses the mutation rate of genes to deduce when two or more life forms diverged — in this case, when the common ancestor of all variants of SARS-CoV-2 existed, estimated in this study to as early as mid-November 2019.

Molecular dating of the most recent common ancestor is often taken to be synonymous with the index case of an emerging disease. However, said co-author Michael Worobey, professor of ecology and evolutionary biology at University of Arizona: “The index case can conceivably predate the common ancestor — the actual first case of this outbreak may have occurred days, weeks or even many months before the estimated common ancestor. Determining the length of that ‘phylogenetic fuse’ was at the heart of our investigation.”

Based on this work, the researchers estimate that the median number of persons infected with SARS-CoV-2 in China was less than one until Nov. 4, 2019. Thirteen days later, it was four individuals, and just nine on December 1, 2019. The first hospitalizations in Wuhan with a condition later identified as COVID-19 occurred in mid December.

Study authors used a variety of analytical tools to model how the SARS-CoV-2 virus may have behaved during the initial outbreak and early days of the pandemic when it was largely an unknown entity and the scope of the public health threat not yet fully realized.

These tools included epidemic simulations based on the virus’s known biology, such as its transmissibility and other factors. In just 29.7 percent of these simulations was the virus able to create self-sustaining epidemics. In the other 70.3 percent, the virus infected relatively few persons before dying out. The average failed epidemic ended just eight days after the index case.

“Typically, scientists use the viral genetic diversity to get the timing of when a virus started to spread,” said Wertheim. “Our study added a crucial layer on top of this approach by modeling how long the virus could have circulated before giving rise to the observed genetic diversity.”

“Our approach yielded some surprising results. We saw that over two-thirds of the epidemics we attempted to simulate went extinct. That means that if we could go back in time and repeat 2019 one hundred times, two out of three times, COVID-19 would have fizzled out on its own without igniting a pandemic. This finding supports the notion that humans are constantly being bombarded with zoonotic pathogens.”

Wertheim noted that even as SARS-CoV-2 was circulating in China in the fall of 2019, the researchers’ model suggests it was doing so at low levels until at least December of that year.

“Given that, it’s hard to reconcile these low levels of virus in China with claims of infections in Europe and the U.S. at the same time,” Wertheim said. “I am quite skeptical of claims of COVID-19 outside China at that time.”

The original strain of SARS-CoV-2 became epidemic, the authors write, because it was widely dispersed, which favors persistence, and because it thrived in urban areas where transmission was easier. In simulated epidemics involving less dense rural communities, epidemics went extinct 94.5 to 99.6 percent of the time.

The virus has since mutated multiple times, with a number of variants becoming more transmissible.

“Pandemic surveillance wasn’t prepared for a virus like SARS-CoV-2,” Wertheim said. “We were looking for the next SARS or MERS, something that killed people at a high rate, but in hindsight, we see how a highly transmissible virus with a modest mortality rate can also lay the world low.”

Konrad Scheffler, Illumina, Inc. was also a co-author.

Funding for this research came, in part, from the National Institutes of Health (grants AI135992, AI136056, T15LM011271), the Google Cloud COVID-19 Research Credits Program, the David and Lucile Packard Foundation, the University of Arizona and the National Science Foundation (grant 2028040).


 

Welcome to the Jacobs School, Class of 2025

Why Commercialization of Carbon Capture and Sequestration has Failed and How it Can Work

Credibility of incentives - a function of policy and politics - is a key, researchers say

Despite extensive support, 80 percent of projects that seek to commercialize carbon capture and sequestration technology have ended in failure. Credit: Coatesy/iStock

March 22, 2021 - There are 12 essential attributes that explain why commercial carbon capture and sequestration projects succeed or fail in the U.S., University of California San Diego researchers say in a recent study published in Environmental Research Letters

The paper was coauthored by Jacobs School alumnus Ryan Hanna, now an assistant research scientist at UC San Diego. 

Carbon capture and sequestration (CCS) has become increasingly important in addressing climate change. The Intergovernmental Panel on Climate Change (IPCC) relies greatly on the technology to reach zero carbon at low cost. Additionallyit is among the few low-carbon technologies in President Joseph R. Biden’s proposed $400 billion clean energy plan that earns bipartisan support. 

In the last two decades, private industry and government have invested tens of billions of dollars to capture CO2 from dozens of industrial and power plant sources. Despite the extensive support, these projects have largely failed. In fact, 80 percent of projects that seek to commercialize carbon capture and sequestration technology have ended in failure. 

“Instead of relying on case studies, we decided that we needed to develop new methods to systematically explain the variation in project outcome of why do so many projects fail,” said  lead author Ahmed Y. Abdulla, research fellow with UC San Diego’s Deep Decarbonization Initiative and assistant professor of mechanical and aerospace engineering at Carleton University. “Knowing which features of CCS projects have been most responsible for past successes and failures allows developers to not only avoid past mistakes, but also identify clusters of existing, near-term CCS projects that are more likely to succeed.”

He added, “By considering the largest sample of U.S. CCS projects ever studied, and with extensive support from people who managed these projects in the past, we essentially created a checklist of attributes that matter and gauged the extent to which each does.”

Credibility of incentives and revenues is key

The researchers found that the credibility of revenues and incentives—functions of policy and politics—are among the most important attributes, along with capital cost and technological readiness, which have been studied extensively in the past.

“Policy design is essential to help commercialize the industry because CCS projects require a huge amount of capital up front,” the authors, comprised of an international team of researchers, note. 

The authors point to existing credible policies that act as incentives, such as the 2018 expansion of the 45Q tax credit. It provides companies with a guaranteed revenue stream if they sequester CO2 in deep geologic repositories.

The only major incentive companies have had thus far to recoup their investments in carbon capture is by selling the CO2 to oil and gas companies, who then inject it into oil fields to enhance the rate of extraction—a process referred to as enhanced oil recovery.

The 45Q tax credit also incentivizes enhanced oil recovery, but at a lower price per CO2 unit, compared to dedicated geologic CO2 storage.   

Beyond selling to oil and gas companies, CO2 is not exactly a valuable commodity, so few viable business cases exist to sustain a CCS industry on the scale that is necessary or envisioned to stabilize the climate.

“If designed explicitly to address credibility, public policy could have a huge impact on the success of projects,” said David Victor, co-lead of the Deep Decarbonization Initiative and professor of industrial innovation at UC San Diego’s School of Global Policy and Strategy.

Results with expert advice from project managers with real-world experience

While technological readiness has been studied extensively and is essential to reducing the cost and risk of CCS, the researchers looked beyond the engineering and engineering economics to determine why CCS continues to be such a risky investment. Over the course of two years, the researchers analyzed publicly available records of 39 U.S. projects and sought expertise from CCS project managers with extensive, real-world experience. 

They identified 12 possible determinants of project outcomes, which are technological readiness, credibility of incentives, financial credibility, cost, regulatory challenges, burden of CO2 removal, industrial stakeholder opposition, public opposition, population proximity, employment impact, plant location, and the host state’s appetite for fossil infrastructure development.

To evaluate the relative influence of the 12 factors in explaining project outcomes, the researchers built two statistical models and complemented their empirical analysis with a model derived through expert assessment.

The experts only underscored the importance of credibility of revenues and incentives; the vast majority of successful projects arranged in advance to sell their captured CO2 for enhanced oil recovery. They secured unconditional incentives upfront, boosting perceptions that they were resting on secure financial footing.

The authors conclude models in the study—especially when augmented with the structured elicitation of expert judgment—can likely improve representations of CCS deployment across energy systems. 

“Assessments like ours empower both developers and policymakers,” the authors write. “With data to identify near-term CCS projects that are more likely to succeed, these projects will become the seeds from which a new CCS industry sprouts.”

Co-authors include Jacobs School alumnus Ryan Hanna, assistant research scientist at UC San Diego; Kristen R Schell, assistant professor at Carleton University; and Oytun Babacan, research fellow at Imperial College London. 

Artificial neuron device could shrink energy use and size of neural network hardware

Goto Flickr
SEM image of the artificial neuron device. Images courtesy of Nature Nanotechnology

March 18, 2021 -- Training neural networks to perform tasks, such as recognizing images or navigating self-driving cars, could one day require less computing power and hardware thanks to a new artificial neuron device developed by researchers at the University of California San Diego. The device can run neural network computations using 100 to 1000 times less energy and area than existing CMOS-based hardware.

Researchers report their work in a paper published Mar. 18 in Nature Nanotechnology.

Neural networks are a series of connected layers of artificial neurons, where the output of one layer provides the input to the next. Generating that input is done by applying a mathematical calculation called a non-linear activation function. This is a critical part of running a neural network. But applying this function requires a lot of computing power and circuitry because it involves transferring data back and forth between two separate units—the memory and an external processor.

Now, UC San Diego researchers have developed a nanometer-sized device that can efficiently carry out the activation function.

“Neural network computations in hardware get increasingly inefficient as the neural network models get larger and more complex,” said corresponding author Duygu Kuzum, a professor of electrical and computer engineering at the UC San Diego Jacobs School of Engineering. “We developed a single nanoscale artificial neuron device that implements these computations in hardware in a very area- and energy-efficient way.”

The new study was performed as a collaboration between UC San Diego researchers from the Department of Electrical and Computer Engineering (led by Kuzum, who is part of the university's Center for Machine-Integrated Computing and Security) and a DOE Energy Frontier Research Center (EFRC led by physics professor Ivan Schuller), which focuses on developing hardware implementations of energy-efficient artificial neural networks.

The device implements one of the most commonly used activation functions in neural network training called a rectified linear unit. What’s particular about this function is that it needs hardware that can undergo a gradual change in resistance in order to work. And that’s exactly what the UC San Diego researchers engineered their device to do—it can gradually switch from an insulating to a conducting state, and it does so with the help of a little bit of heat.

This switch is what’s called a Mott transition. It takes place in a nanometers-thin layer of vanadium dioxide. Above this layer is a nanowire heater made of titanium and gold. When current flows through the nanowire, the vanadium dioxide layer slowly heats up, causing a slow, controlled switch from insulating to conducting.

Chips on a circuit board
Left: Closeups of the synaptic device array (top) and the activation, or neuron, device array (bottom). Right: A custom printed circuit board built with the two arrays.

“This device architecture is very interesting and innovative,” said first author Sangheon Oh, an electrical and computer engineering Ph.D. student in Kuzum's lab. Typically, materials in a Mott transition experience an abrupt switch from insulating to conducting because the current flows directly through the material, he explained. “In this case, we flow current through a nanowire on top of the material to heat it and induce a very gradual resistance change.”

To implement the device, the researchers first fabricated an array of these so-called activation (or neuron) devices, along with a synaptic device array. Then they integrated the two arrays on a custom printed circuit board and connected them together to create a hardware version of a neural network.

The researchers used the network to process an image—in this case, a picture of Geisel Library at UC San Diego. The network performed a type of image processing called edge detection, which identifies the outlines or edges of objects in an image. This experiment demonstrated that the integrated hardware system can perform convolution operations that are essential for many types of deep neural networks.

A building shaped like an upside-down pyramid
Image of Geisel Library used for edge detection (left). Output of the convolution operations for the lateral filter (center) and vertical filter (right).

The researchers say the technology could be further scaled up to do more complex tasks such as facial and object recognition in self-driving cars. With interest and collaboration from industry, this could happen, noted Kuzum.

“Right now, this is a proof of concept,” Kuzum said. “It’s a tiny system in which we only stacked one synapse layer with one activation layer. By stacking more of these together, you could make a more complex system for different applications.”

Paper: “Energy Efficient Mott Activation Neuron for Full Hardware Implementation of Neural Networks.”

This work was supported by the Office of Naval Research, Samsung Electronics, the National Science Foundation, the National Institutes of Health, a Qualcomm Fellowship and the U.S. Department of Energy, Office of Science through an Energy Frontier Research Center.

How to speed up muscle repair

Drawing of muscle fiber
Illustration of skeletal muscle fiber. Credit: Kavitha Mukund

March 17, 2021 -- A study led by researchers at the University of California San Diego Jacobs School of Engineering provides new insights for developing therapies for muscle disease, injury and atrophy. By studying how different pluripotent stem cell lines build muscle, researchers have for the first time discovered how epigenetic mechanisms can be triggered to accelerate muscle cell growth at different stages of stem cell differentiation.

The findings were published Mar. 17 in Science Advances.

“Stem cell-based approaches that have the potential to aid muscle regeneration and growth would improve the quality of life for many people, from children who are born with congenital muscle disease to people who are losing muscle mass and strength due to aging,” said Shankar Subramaniam, distinguished professor of bioengineering, computer science and engineering, and cellular and molecular medicine at UC San Diego and lead corresponding author on the study. “Here, we have discovered that specific factors and mechanisms can be triggered by external means to favor rapid growth.”

The researchers used three different human induced pluripotent stem cell lines and studied how they differentiate into muscle cells. Out of the three, one cell line grew into muscle the fastest. The researchers looked at what factors made this line different from the rest, and then induced these factors in the other lines to see if they could accelerate muscle growth.

They found that triggering several epigenetic mechanisms at different time points sped up muscle growth in the “slower” pluripotent stem cell lines. These include inhibiting a gene called ZIC3 at the outset of differentiation, followed by adding proteins called beta-catenin transcriptional cofactors later on in the growth process.

“A key takeaway here is that all pluripotent stem cells do not have the same capacity to regenerate,” Subramaniam said. “Identifying factors that will prime these cells for specific regeneration will go a long way in regenerative medicine.”

Next, the team will explore therapeutic intervention, such as drugs, that can stimulate and accelerate muscle growth at different stages of differentiation in human induced pluripotent stem cells. They will also see whether implanting specific pluripotent stem cells in dystrophic muscle can stimulate new muscle growth in animals. Ultimately, they would like to see if such a stem cell-based approach could regenerate muscle in aging humans.

Paper: “Temporal mechanisms of myogenic specification in human induced pluripotent stem cells.” Co-authors of the study include Priya Nayak, UC San Diego; Alexandre Colas, Sanford Burnham Prebys Medical Discovery Institute; Mark Mercola, Stanford University; and Shyni Varghese, Duke University.

Defending human-robot teams against adversaries goal of computer science grant

Computer science professor Kamalika Chaudhuri is part of a MURI grant going to multiple institutions. Her work is on Cohesive and Robust Human-Bot Cybersecurity Teams.  

March 16, 2021-- UC San Diego computer science professor Kamalika Chaudhuri is part of a multi-university team that has won a prestigious US Department of Defense Multidisciplinary University Research Initiative (MURI) Award to develop rigorous methods for robust human-machine collaboration against adversaries. 

Chaudhuri will receive $750,000 to fund her research on the project titled Cohesive and Robust Human-Bot Cybersecurity Teams, which aims to develop rigorous parameters for Human-Bot Cybersecurity teams with the goal of developing a cohesive team that is not vulnerable to active human and machine learning (ML) adversaries. 

“We now know how to develop machine learning methods that are robust to adversaries, yet in many applications, humans work in coordination with machine learning software, and adversaries can still disrupt the process,” said Chaudhuri, whose research interests lie in the foundations of trustworthy machine learning. “This project will investigate in detail how that can happen, and how we can design algorithms and tools to be robust to these adversaries."

Cybersecurity is the most challenging task that the Department of Defense (DoD) faces today. A typical human analyst in a cybersecurity task has to deal with a plethora of information, such as intrusion logs, network flows, executables, and provenance information for files. Real cybersecurity scenarios are even more challenging: an active adversarial environment, with large amounts of information and techniques that neither humans nor machines can handle alone. 

In addition to human analysts, machine learning (ML) bots have become part of these cybersecurity teams. ML bots reduce the burden on human analysts by filtering information, thus freeing up cognitive resources for tasks related to the high-level mission.

The team will first focus on ways to build trust within the HBCT by investigating techniques to produce explanations for the human analysts of how the ML bots work. These explanations will be presented in an appropriate vocabulary for the analysts and will be specific to the task of the HBCT, providing valuable insight for the human analysts so they will trust the ML model and reduce manual effort.

The group will also research how analysts integrate information to arrive at decisions, as well as their mental models of how bots operate. This will allow them to take a step towards automating the decision-making process. Moreover, the mental model can help design robust ML models that are more specific to the task of the HBCT.

Adaptability will be key as well. Human-bot team dynamics change as new adversaries with different capabilities arise, and adversaries adapt in response to new team strategies. Adversaries interactive learning must be taken into account to develop methods for the entire team to adaptto adversaries in an interactive manner.

Chaudhuri and her research group will develop methods that can improve generalization capabilities of current machine learning methods to rare inputs, bolster the quality of explanations provided by them and design principled solutions for adversarial robustness. 

“This will build on some of our prior and current work in the area of interactive learning, as well as principled methods for defending against adversaries,” she said. 

Since its inception in 1985, the tri-Service MURI program has convened teams of investigators with the hope that collective insights drawn from research across multiple disciplines could facilitate the advancement of newly emerging technologies and address the Department’s unique problem sets. Complementing the Department’s single-investigator basic research grants, the highly competitive MURI program has made immense contributions to both national defense and society at large. Innovative technological advances from the MURI program help drive and accelerate current and future military capabilities and find multiple applications in the commercial sector.

Seven universities comprise the research team, which is led by Somesh Jha at the University of Wisconsin-Madison: Carnegie Mellon University, University of California San Diego, Pennsylvania State University, University of Melbourne, Macquarie University, and University of Newcastle. Benjamin Rubinstein of the University of Melbourne will lead the Australian team, or AUSMURI, funded by the Australian Government. The team brings together diverse expertise spanning computer security, machine learning, psychology, decision sciences, and human-computer interaction

 


 

Researchers at UC San Diego Unveil New Interactive Web Tool for Visualizing Large-Scale Phylogenetic Trees

March 17, 2021

The proliferation of sequencing technologies and an ever-increasing focus on ‘omic studies over the past several years have spawned massive quantities of data and many tools to process and analyze the results. As these tools have evolved, so has the need for even greater scale and the ability to visualize complex data sets in more efficient ways.

Born of these needs for advancement, a team of researchers with the Center for Microbiome Innovation (CMI) at the University of California San Diego (UC San Diego), led by Kalen Cantrell and Marcus W. Fedarko, unveiled EMPress, a new interactive visualization tool, in an article published in mSystems on March 16, 2021. The paper, entitled “EMPress Enables Tree-Guided, Interactive, and Exploratory Analyses of Multi-omic Data Sets,” showcases the tool’s functionality, versatility, and scalability, and explores some of the potential applications in visualization and data analysis.

"Although there are many excellent existing tools for visualizing trees, we wanted to create a tool that could be used within a web browser and could scale to really large trees," Fedarko remarked when discussing the development process. "Another motivation was that there were many custom features that no existing tool, to our knowledge, supported - for example, the ability to interactively link samples in an ordination with a phylogenetic tree, showing the sequences contained within each sample, or going the opposite way, the samples containing a given sequence."

Aside from interactively integrating ordinations with trees, EMPress also introduces the ability to animate a tree’s changes over time. While other tools have included a temporal dimension to trees, the ability to animate the tree alongside an ordination is a novel feature that the team believes will enhance the exploratory analysis of ‘omic data sets.

What began as an undergraduate project at UC San Diego’s Early Research Scholars Program has since grown into a collaboration that spans both academia and industry. The team at CMI has worked closely with IBM Research’s Artificial Intelligence for Healthy Living Center throughout the process, as well as researchers at the Simons Foundation, Cornell University, and Justus Liebig University.

Developing a tool that was not only web-based but capable of storing, processing, and visualizing such large phylogenetic trees presented numerous challenges. As the scale of microbiome and other ‘omic studies has continued to grow, so too has the technical complexity required to accommodate and analyze the large, complex data sets those studies produce.

FIG 1 Earth Microbiome Project paired phylogenetic tree (including 756,377 nodes) and unweighted UniFrac ordination (including 26,035 samples). (a) Graphical depiction of EMPress’ unified interface with fragment insertion tree (left) and unweighted UniFrac sample ordination (right). Tips are colored by their phylum-level taxonomic assignment; the barplot layer is a stacked barplot describing the proportions of samples containing each tip summarized by level 1 of the EMP ontology. Inset shows summarized sample information for a selected feature. The ordination highlights the two samples containing the tip selected in the tree enlarged to show their location. (b) Subset of EMP samples with pH information: the inner barplot ring shows the phylum-level taxonomic assignment, and the outer barplot ring represents the mean pH of all the samples where each tip was observed. (c) pH distributions summarized by phylum-level assignment with median pH indicated by dotted lines. Interactive figures can be accessed at https://github.com/knightlab-analyses/empress-analyses.

"We resolved some of these issues by creating our own custom WebGL, shaders which are capable of visualizing millions of points, and implementing high-performance data structures such as the balanced parentheses tree that helped drastically reduce the memory footprint of EMPress," according to Cantrell. As the code has been refined and optimized through several phases of development, it has enabled the analysis of larger and larger data sets, including a tree with over 750,000 nodes. 

While the article in mSystems represents the tool’s formal unveiling, it has already seen use in several studies and applications. Researchers at the CMI utilized EMPress in their recently published analysis of the composition and microbial load of the human oral microbiome. Additionally, epidemiologists with UC San Diego’s Return to Learn program have been using the tool to help manage the university’s response to the COVID-19 pandemic. These applications have provided critical feedback and facilitated improvements to continue streamlining the analyses for which EMPress is designed.

As development continues, there are several planned features, including the ability to explore time-series data, potential anomaly detection, implementing support for annotating various types of data, and further improving performance to allow for larger data sets. The tool’s source code is available on GitHub, and the team is eager to see how their peers expand upon their work.

“Just as EMPress builds on the many existing tree visualization tools in the literature (iTOL, PHYLOViZ, Anvi'o, SigTree, FigTree, ggtree, TopiaryExplorer, MicroReact, Archaeopteryx, etc.), we're sure that other tools will pop up soon enough that build on the concepts used in EMPress -- we look forward to seeing how the landscape of these tools changes in the future,” Fedarko added.

 

FIG 2 EMPress is a versatile exploratory analysis tool adaptable to various ‘omics data types. (a) RoDEO differential abundance of microbial functions from metatranscriptomic sequencing of COVID-19 patients (n = 8) versus community-acquired pneumonia patients (n = 25) and versus healthy control subjects (n = 20). The tree represents the four-level hierarchy of the KEGG enzyme codes. The barplot depicts significantly differentially abundant features (P , 0.05) in COVID-19 patients. Clicking on a tip produces a pop-up insert tabulating the name of the feature, its hierarchical ranks, and any feature annotations. (b) Global FoodOmics Project LC-MS data. Stacked barplots indicate the proportions of samples (n = 70) (stratified by food) containing the tips in an LC-MS Qemistree of food-associated compounds, with tip nodes colored by their chemical superclass. (c) De novo tree constructed from 16S rRNA sequencing data from 32 oral microbiome samples. Samples were taken before (n = 16) and after (n = 16) subjects (n = 10) brushed their teeth; each barplot layer represents a different differential abundance method’s measure of change between before- and after-brushing samples. The innermost layer shows estimated log-fold changes produced by Songbird, the middle layer shows effect sizes produced by ALDEx2, and the outermost layer shows the W-statistic values produced by ANCOM (see Materials and Methods). The tree is colored by tip nodes’ phylum-level taxonomic classifications. Interactive figures can be accessed at https://github.com/knightlab-analyses/empress-analyses.

 

Additional co-authors include Gibraan Rahman, Daniel McDonald, Yimeng Yang, Thant Zaw, Antonio Gonzalez, Mehrbod Estaki, Qiyun Zhu, Erfan Sayyari, George Armstrong, Anupriya Tripathi, Julia M. Gauglitz, Clarisse Marotz, Nathaniel L. Matteson, Cameron Martino, Se Jin Song, Austin D. Swafford, Pieter C. Dorrestein, Kristian G. Andersen, Yoshiki Vázquez-Baeza, and Rob Knight, all at UC San Diego; Stefan Janssen at Justus Liebig University; Niina Haiminen and Laxmi Parida at the IBM Thomas J. Watson Research Center; Kristen L. Beck and Ho-Cheol Kim at the IBM Almaden Research Center; James T. Morton at the Simons Foundation; Jon G. Sanders at Cornell University; and Anna Paola Carrieri at IBM Research Europe.

This piece was written by CMI’s contributing editor Cassidy Symons

Writing a New Chapter on Innovation

UC San Diego establishes local chapter of National Academy of Inventors

 

March 17, 2021 - The University of California San Diego is the first University of California campus to establish a chapter of the National Academy of Inventors (NAI), a move that will help the campus build and sustain a more robust innovation ecosystem. This designation provides tools and resources to help UC San Diego raise the profile of its inventions and technologies, encourage innovations on campus and educate student entrepreneurs.

“Invention is in our DNA,” said Chancellor Pradeep K. Khosla, an NAI fellow who was recognized for his work in enhancing cybersecurity. “Since 2014, UC San Diego has seen a 153% increase in licensed startups, a 120% increase in industry funding, and a 78% increase in licenses. Just last year, our research program generated more than 500 new invention disclosures, including over 200 new patents. Establishing a local NAI chapter will help further develop our students, create stronger connections to the region’s flourishing community of inventors, and showcase UC San Diego’s growing research prowess.”

An NAI chapter designation gives the UC San Diego community access to networks and tools that can facilitate inventorship and entrepreneurism in students, faculty and staff. Chapter members will be able to participate in annual meetings, network with inventors around the world and meet participants from organizations like the U.S. Patent and Trademark Office. They’ll also be able to submit articles to NAI’s journal Technology and Innovation.

The chapter will have a faculty advisory board to discuss metrics for success and programming opportunities, as well as strategic priorities for the coming year. The inaugural board includes faculty from across campus, including Health Sciences, the Rady School of Management and the Jacobs School of Engineering to ensure representation across UC San Diego’s innovation ecosystem.

Innovation programming helps faculty and students potentially turn research into products, such as this wearable patch that can heat or cool the skin. (cr: David Baillot/UC San Diego Jacobs School of Engineering)

“Students, staff and faculty from all parts of campus will be most welcome in the new chapter," said Albert P. Pisano, dean of the UC San Diego Jacobs School of Engineering. "Speaking as an engineer, educator and inventor, I know firsthand that we get the best solutions when we look at challenges from all directions. We need everyone at the innovation and invention table.” 

Pisano was inducted into the National Academy of Inventors in 2019  based on the impact of medical devices that treat arterial diseases, currently being commercialized via a startup company.

While NAI fellows are inducted into the academy through a formal nomination process, chapter members will apply locally through UC San Diego’s Office of Innovation and Commercialization. Students will have the unique opportunity to become honorary members and have access to mentorship and professional development resources.

TODAY’S INNOVATION FOR TOMORROW’S WORLD

Student entrepreneurs are supported by programs like The Basement and will be able to join the NAI chapter as honorary members. (cr: Erik Jepsen/UC San Diego)

The university’s commitment to innovation and entrepreneurship runs deep and goes beyond the campus borders. While programs like Institute for the Global EntrepreneurThe Basement and StartR at the Rady School of Management support students and faculty in their startup endeavors, capital projects like the Design and Innovation Building and Downtown Park & Market “The U” promise to strengthen the connection between the campus and industry partners, government entities and community members.

“UC San Diego prioritizes innovation, technology transfer and entrepreneurship for the sustained economic prosperity of the region,” said Associate Vice Chancellor for Innovation and Commercialization Paul Roben. “Our recent designation as an NAI Chapter will allow us to connect with world-renowned inventors, while nurturing and mentoring innovators, business owners and the workforce of tomorrow.” 

Upcoming events supporting and celebrating campus innovation include the grand opening of the Design and Innovation Building, a Student Inventor and Startup Showcase focused on “Enriching Human Life and Society,” and the NAI Investor Awards.

“Launching an official NAI Chapter is an amazing step at creating a united innovation ecosystem on campus and within your community to celebrate and share the importance of academic innovation and invention,” said NAI Director Jayde Stewart. “The NAI is honored and proud to have you as members and look forward to celebrating the successes of your students and faculty innovators through your local Chapter.”

The National Academy of Inventors was founded in 2010 to recognize and encourage inventors, enhance the visibility of academic technology, and educate and mentor innovation-minded students. NAI boasts over 1,000 fellows and 250 institutions worldwide. In total, the fellows have formed more than 9,000 companies and generated over $190 billion from nearly 11,000 licensed inventions. UC San Diego is home to 13 NAI fellows, including current and emeritus faculty.

Writing a New Chapter on Innovation

UC San Diego establishes local chapter of National Academy of Inventors

March 17, 2021--The University of California San Diego is the first University of California campus to establish a chapter of the National Academy of Inventors (NAI), a move that will help the campus build and sustain a more robust innovation ecosystem. This designation provides tools and resources to help UC San Diego raise the profile of its inventions and technologies, encourage innovations on campus and educate student entrepreneurs.

“Invention is in our DNA,” said Chancellor Pradeep K. Khosla, an NAI fellow who was recognized for his work in enhancing cybersecurity. “Since 2014, UC San Diego has seen a 153% increase in licensed startups, a 120% increase in industry funding, and a 78% increase in licenses. Just last year, our research program generated more than 500 new invention disclosures, including over 200 new patents. Establishing a local NAI chapter will help further develop our students, create stronger connections to the region’s flourishing community of inventors, and showcase UC San Diego’s growing research prowess.”

An NAI chapter designation gives the UC San Diego community access to networks and tools that can facilitate inventorship and entrepreneurism in students, faculty and staff. Chapter members will be able to participate in annual meetings, network with inventors around the world and meet participants from organizations like the U.S. Patent and Trademark Office. They’ll also be able to submit articles to NAI’s journal Technology and Innovation.

The chapter will have a faculty advisory board to discuss metrics for success and programming opportunities, as well as strategic priorities for the coming year. The inaugural board includes faculty from across campus, including Health Sciences, the Rady School of Management and the Jacobs School of Engineering to ensure representation across UC San Diego’s innovation ecosystem.

Innovation programming helps faculty and students potentially turn research into products, such as this wearable patch that can heat or cool the skin. (cr: David Baillot/UC San Diego Jacobs School of Engineering)

“Students, staff and faculty from all parts of campus will be most welcome in the new chapter," said Albert P. Pisano, dean of the UC San Diego Jacobs School of Engineering. "Speaking as an engineer, educator and inventor, I know firsthand that we get the best solutions when we look at challenges from all directions. We need everyone at the innovation and invention table.” 

Pisano was inducted into the National Academy of Inventors in 2019  based on the impact of medical devices that treat arterial diseases, currently being commercialized via a startup company.

While NAI fellows are inducted into the academy through a formal nomination process, chapter members will apply locally through UC San Diego’s Office of Innovation and Commercialization. Students will have the unique opportunity to become honorary members and have access to mentorship and professional development resources.

TODAY’S INNOVATION FOR TOMORROW’S WORLD

 

The university’s commitment to innovation and entrepreneurship runs deep and goes beyond the campus borders. While programs like Institute for the Global EntrepreneurThe Basement and StartR at the Rady School of Management support students and faculty in their startup endeavors, capital projects like the Design and Innovation Building and Downtown Park & Market “The U” promise to strengthen the connection between the campus and industry partners, government entities and community members.

“UC San Diego prioritizes innovation, technology transfer and entrepreneurship for the sustained economic prosperity of the region,” said Associate Vice Chancellor for Innovation and Commercialization Paul Roben. “Our recent designation as an NAI Chapter will allow us to connect with world-renowned inventors, while nurturing and mentoring innovators, business owners and the workforce of tomorrow.” 

Upcoming events supporting and celebrating campus innovation include the grand opening of the Design and Innovation Building, and a Student Inventor and Startup Showcase focused on “Enriching Human Life and Society.”

Student entrepreneurs are supported by programs like The Basement and will be able to join the NAI chapter as honorary members. (cr: Erik Jepsen/UC San Diego)

“Launching an official NAI Chapter is an amazing step at creating a united innovation ecosystem on campus and within your community to celebrate and share the importance of academic innovation and invention,” said NAI Director Jayde Stewart. “The NAI is honored and proud to have you as members and look forward to celebrating the successes of your students and faculty innovators through your local Chapter.”

The National Academy of Inventors was founded in 2010 to recognize and encourage inventors, enhance the visibility of academic technology, and educate and mentor innovation-minded students. NAI boasts over 1,000 fellows and 250 institutions worldwide. In total, the fellows have formed more than 9,000 companies and generated over $190 billion from nearly 11,000 licensed inventions. UC San Diego is home to 13 NAI fellows, including current and emeritus faculty.

Swift Sewage-Sifting System Boosts Efforts to Forecast and Mitigate the Spread of COVID-19

March 11, 2021- 

As the COVID-19 pandemic proliferated in early 2020, tracking the spread of a frequently asymptomatic virus presented a novel challenge for public health officials. Diagnostic testing was often unavailable and not fast enough to act as a useful forecasting tool.

While symptoms can take several days to appear, the virus immediately begins replicating in the gastrointestinal tract, and traces of it end up in the infected individuals’ stool. Researchers at the University of California San Diego (UC San Diego) quickly determined that testing sewage for viral markers would allow for earlier detection of infections and potential outbreaks.

The wastewater sampling initiative began as a pilot program on the UC San Diego campus in the summer of 2020 with only six collection sites but quickly grew as they determined that environmental testing was a key to preventing the spread of COVID-19. However, the manual work involved in concentrating samples was a roadblock to scaling the surveillance program beyond the university.

“Viral concentration is typically the biggest bottleneck in wastewater analyses since it's laborious and very time-consuming. Here, we optimized that step via automation with liquid-handling robots,” said Smruthi Karthikeyan, a postdoctoral researcher at UC San Diego School of Medicine. The automated system not only increases the number of samples that can be processed concurrently - 24 in 40 minutes - it also removes the potential for human error and accelerates the timeline from the collection of samples to viral detection, enabling a more rapid response to positive results.

This project marked the first collaboration between the Center for Microbiome Innovation (CMI) and the Center for Machine-Integrated Computing & Security (CMICS), both research centers are part of UC San Diego Jacobs School of Engineering. The system is described in a new paper entitled “High-Throughput Wastewater SARS-CoV-2 Detection Enables Forecasting of Community Infection Dynamics in San Diego County”, published March 2, 2021, in mSystems.

As a result of the increased scale at which wastewater samples were tested, the team could track viral detection patterns from a far higher-level perspective than before. “In this paper, we observed strong correlations and forecasting potential between viral content in daily wastewater samples from the Point Loma wastewater treatment plant and positive COVID-19 cases reported for San Diego county when modeled with temporal information,” according to Nancy Ronquillo, a graduate student researcher with the CMICS.

While the system is already enabling health officials to forecast the spread of COVID-19 with greater speed and accuracy, efforts continue to expand what data can be extracted from wastewater. Karthikeyan noted that performing viral genome sequencing of the samples could help track the prevalence of different variants of SARS-CoV-2 and model the impact they’re having on viral spread throughout the community. On a more granular level, the team is studying the dynamics of viral shedding and transmission at UC San Diego, which will ultimately aid the university in safely reopening the campus under the Return to Learn program.

"The Center for Microbiome Innovation and Center for Machine-Integrated Computing & Security collaboration accelerated the trace viral pathogen detection modeling in large-scale wastewater sampling throughout San Diego," remarked Andrew Bartko, executive director of the CMI. "We're grateful to contribute to this interdisciplinary team and generate impactful developments in the fight against COVID-19. We look forward to leveraging our complementary technologies and expertise in the future."

Additional co-authors include Pedro Belda-Ferre, Destiny Alvarado, Tara Javidi, Christopher A. Longhurst, and Rob Knight, all at UC San Diego.


 

Tracking infection dynamics in San Diego County. (A) Map showing the San Diego sewer mains (depicted in purple) that feed into the influent stream at the primary wastewater treatment plant (WWTP) at Point Loma. Overlaid are the cumulative cases recorded from the different zip codes in the county during the course of the study. The caseload was counted by cases per zip code from areas draining into the WWTP. The sizes of the circles are proportional to the diagnostic cases reported from each zone, and the color gradient shows the number of cases per 100,000 residents. (B) Daily new cases reported by the county of San Diego. (C) SARS-CoV-2 viral gene copies detected per liter of raw sewage determined from N1 Cq values corrected for PMMoV (pepper mild mottle virus) concentration. All viral concentration estimates were derived from the processing of two sample replicates and two PCR replicates for each sample (error bars show the standard deviations [SD]).

 

This piece was written by CMI’s contributing editor Cassidy Symons

 

Structural engineers get hands-on experience with composite materials

Students test the performance of the blades they designed and built using composite materials.

March 11, 2021-- Structural engineering students at the Jacobs School got hands-on experience designing, manufacturing and analyzing structures made from composite materials through the Design of Composite Structures course, held in-person thanks to UC San Diego’s Return to Learn policies.

“This is actually a pretty unique class that I don't think you find in engineering departments across the country in terms of the subject matter, and also that it’s taught at the undergrad level,” said Hyonny Kim, a professor of structural engineering at UC San Diego. “Composite materials are high performance materials used to make aerospace structures and space structures. They’re extremely light, strong, and stiff. The class is about how we design them, manufacture them, and quantitatively analyze them.”

The course, held in the fall quarter, started off in a reduced-capacity setting indoors, with half of the students completing a lab project one week, and the other half the following week. When county COVID-19 requirements shifted to outdoor only-education, Kim and his team of dedicated graduate teaching assistants moved the course outside. 

“I felt and observed that the students really enjoyed this,” said Kim. “I think they got a lot out of it, coming to campus, having some direct interaction with instructors. There was a lot of good learning as well as just the psychological benefits of feeling engaged with school, being able to have some social interaction with their teammates. I think it was all around really good for all the students.”

Kim and the TAs prepared individual lab kits for each student taking the course remotely.

In order to make this lab course work for the 26 students in-person as well as the 17 students taking the course remotely, Kim and the TAs created individual kits for each of the three lab projects, that students picked up or had shipped to them.

For the labs, students first made a flat plate with carbon fiber/epoxy composite to get accustomed to the process of using composite materials. They then made a carbon fiber structural channel beam with a different type of composite that is what’s called pre-impregnated (prepreg), where the epoxy is already combined with the fibers; this prepreg material is what most high-end aerospace structures are made with. For the third lab, students made beams out of fiberglass with a foam core. 

They put this understanding of composites to use for the final project: a competition to see which team could build the most efficient wind turbine blades using a glass fiber/epoxy composite. The student teams had to figure out what angle and configuration to set the blades; build them as light and aerodynamic as possible; and have them generate the most power from a controlled fixed-speed wind source. 

Students working on lab assignments outside.

Each team of five students included two who were completely remote, and were responsible for designing the 3D-printed part that was used to position their team’s blades in the wind turbine. 

“We really tried to give everyone, including the remote students, as close to a hands-on role as possible,” Kim said, noting that after months of quarantining and being isolated from friends, instructors and the campus, students seemed to really appreciate the opportunity to meet safely in person. 

Students made carbon fiber structural channel beams with prepreg material.

“The class seemed to work really well,” said Kim “I really emphasized the right culture to the students: a no blame, no shame culture where if they, lets say, got sick or were exposed or had concerns because of X, Y or Z, they didn’t need to justify telling me they couldn’t or shouldn’t come to class that week. I broadcast that message really clearly, and I thought the students were fantastic. They were excellent and very responsible about that.”

Many of these students are now in the structural engineering capstone design course this quarter, co-taught by Kim, who is also teaching a Repair of Aerospace Structures class that also conducts labs outside. 

Computer science student brings Black beauty products to UC San Diego

Jaida Day, a math-computer science student, started Black Beauty Near You to make beauty products more accessible for UC San Diego students. Photos courtesy of Jaida Day.

March 11, 2021--When Jaida Day arrived at UC San Diego to begin her undergraduate studies, she found a welcoming campus environment, peers and faculty to push her academically, beautiful beaches and opportunities to get involved in student organizations. But she also found there was something missing.

“I grew up in Los Angeles where I could go down the street and find the products I need for my hair and my skin, things of that sort, because there are other people who look like me in that area,” said Day. “But coming to La Jolla, I realized the beauty supply stores, the CVS, even the markets on campus, they don't have what I need for my hair and skin.”

Her options? Drive 30 minutes to the closest beauty supply that carried the items she needed; order her hygiene necessities online and have them shipped; or stock up at home during breaks and bring the products back to campus with her. With no car and only a few trips home each year, she recognized she wasn’t the only student facing this dilemma, and decided to take action.

“I was talking to my mom about it and she said ‘Well, you should come up with something to fix that.’ So that’s pretty much how Black Beauty Near You came about.”

The mathematics-computer science student put her web development skills to use, and launched her Black Beauty Near You business with a goal of making Black hair and skin care products more accessible to UC San Diego students. Through her website, people can order brushes, combs, bobby pins, braid charms, scalp oil, edge control, durags, makeup and other items they need.

For a time, Black Beauty Near You had a physical setup in the Black Resource Center’s The Shop, but with COVID-19 restrictions, sales are now all online. Day delivers the items to students on campus, and frequently changes up her inventory to reflect student requests.

To Day, this is just the first step, a stopgap measure until more permanent solutions are put in place. The UC San Diego Black Student Union—of which Day is co-publicity manager—is working with university administration to try and get more of these products that Black students need in markets on campus.

“My mind goes far. I know this isn't the only school where there's not Black beauty products on campus, and it would be nice if there could be better access to these items at more universities. It doesn’t have to be through Black Beauty Near You, but perhaps in the future I’ll find a way to help universities get these products on their campus, because I think it’s just a disconnect of knowing what is needed.”

In addition to working towards her math-computer science major—a combination of the mathematical theory and methods used in computer science, along with computer programming, structure, and algorithms—Day is also the web development chair of the Women in Computing undergraduate student organization, and was an intern for the Black Resource Center (BRC). She has a knack for finding ways to use her technical skills to empower her communities.

Day selling her products at the Black Resource Center's The Shop. With COVID-19 restrictions, sales are now all online.

As a BRC intern, Day organized an event called Engineering Orgs Near You, bringing engineering student organizations to the Black Resource Center to recruit new members and share what they do. For her internship final project, she created a website called Magnifying San Diego, where people new to campus can find information on local places to hang out, get their hair or nails done, eat, or find a therapist, with a focus on the Black community.

“Jaida is a brilliant, motivated, and self-less scholar and person. She was an exemplar as an intern at the BRC, but she has also continued to be a dedicated and active member of the Black community at UC San Diego,” said Porsia Curry, director of the Black Resource Center. “Her yearlong project not only blew us away, but continues to be a tremendous resource for Black students. Our center and community are better because of her contributions.”

As WiC’s web development chair, she led the development of the group’s new website, developed entirely from scratch.

“I had never done that before, I had always used templates to develop a website, but never from scratch,” said Day. “So, I was nervous. But WiC is the best community ever; they’re so welcoming, so supportive, so helpful. Myself and some of our other board members got together virtually every week over the summer to work on the website, and we got it done.”

Her advice to students is to branch out and try new things.

“If I had never gone to that first WiC meeting, I would have never had this supportive community in my actual major. Because it’s one thing to hang around with people I identify with as my race, but it’s another to be with people who get the struggle of being a computer science student. So definitely try to find your community or communities on campus. Go to those different org meetings, you never know what you’ll find.”

Always thinking big picture, Day also had advice for increasing underrepresented groups in the computer science field as a whole, and here at UC San Diego.

For starters, more computer science camps and coding programs like Kode with Klossy, where Day got her first introduction to computer science, are needed, particularly in underserved areas.

“The summer after my junior year I did a two-week coding boot camp program through Kode with Klossy, and I thought OK that’s what I want to do; I know I’m good at math and think I like computer science, so why not do both,” said Day. “More of those programs and classes in schools or even like the coding camp I did would be a good start, just so students can have the option to see if they like it. Because if I hadn’t done that coding camp, I would not be a computer science student. I couldn't even tell you what I’d be doing.”

Looking closer to campus, Day said she knows the UC San Diego admissions team is researching ways to reach more diverse groups of students and encourage them to attend UC San Diego, but emphasized the importance of this work.

“I probably only know one Black woman computer science student in each grade level,” she said. “We have to do better at bringing in more Black CS students. It’s isolating in class, and while I’ve gotten over it, it can be really isolating as a first year student when you come in and don’t see anyone that looks like you. We definitely have to do better with that.”

In October 2020, the Jacobs School of Engineering launched a Student and Faculty Racial Equity Task Force to assess and improve its efforts to create equitable learning and working environments, as one piece of UC San Diego’s larger efforts to address this issue. Learn more through the Office of Equity, Diversity and Inclusion. The Department of Computer Science and Engineering and the Division of Physical Sciences (which administers the Math-Computer Science major) are also actively engaged in addressing diversity issues.

With gene therapy, scientists develop opioid-free solution for chronic pain

March 10, 2021 -- A gene therapy for chronic pain could offer a safer, non-addictive alternative to opioids. Researchers at the University of California San Diego developed the new therapy, which works by temporarily repressing a gene involved in sensing pain. It increased pain tolerance in mice, lowered their sensitivity to pain and provided months of pain relief without causing numbness.

The researchers report their findings in a paper published Mar. 10 in Science Translational Medicine.

The gene therapy could be used to treat a broad range of chronic pain conditions, from lower back pain to rare neuropathic pain disorders—conditions for which opioid painkillers are the current standard of care.

woman in business attire
Ana Moreno, UC San Diego bioengineering alumna and CEO and co-founder of Navega Therapeutics

“What we have right now does not work,” said first author Ana Moreno, a bioengineering alumna from the UC San Diego Jacobs School of Engineering. Opioids can make people more sensitive to pain over time, leading them to rely on increasingly higher doses. “There’s a desperate need for a treatment that’s effective, long-lasting and non-addictive.”

The idea for such a treatment emerged when Moreno was a Ph.D. student in UC San Diego bioengineering professor Prashant Mali’s lab. Mali had been investigating the possibility of applying CRISPR-based gene therapy approaches to rare as well as common human diseases. Moreno’s project focused on exploring potential therapeutic avenues. One day, she came across a paper about a genetic mutation that causes humans to feel no pain. This mutation inactivates a protein in pain-transmitting neurons in the spinal cord, called NaV1.7. In individuals lacking functional NaV1.7, sensations like touching something hot or sharp do not register as pain. On the other hand, a gene mutation that leads to overexpression of NaV1.7 causes individuals to feel more pain.

When Moreno read this, it clicked. “By targeting this gene, we could alter the pain phenotype,” she said. “What’s also cool is that this gene is only involved in pain. There aren’t any severe side effects observed with this mutation.”

Non-permanent gene therapy

Moreno had been working on gene repression using the CRISPR gene editing tool as part of her dissertation. Specifically, she was working with a version of CRISPR that uses what’s called “dead” Cas9, which lacks the ability to cut DNA. Instead, it sticks to a gene target and blocks its expression.

Moreno saw an opportunity to use this approach to repress the gene that codes for NaV1.7. She points out an appeal of this approach: “It’s not cutting out any genes, so there are no permanent changes to the genome. You wouldn’t want to permanently lose the ability to feel pain,” she said. “One of the biggest concerns with CRISPR gene editing is off-target effects. Once you cut DNA, that’s it. You can’t go back. With dead Cas9, we’re not doing something irreversible.”

Mali, who is a co-senior author of the study, says that this use of dead Cas9 opens the door to using gene therapy to target common diseases and chronic ailments.

“In some common diseases, the issue is that a gene is being misexpressed. You don’t want to completely shut it down,” he said. “But if you could turn down the dose of that gene, you could bring it to a level where it is not pathogenic. That is what we are doing here. We don’t completely take away the pain phenotype, we dampen it.”

Moreno and Mali co-founded the spinoff company Navega Therapeutics to work on translating this gene therapy approach, which they developed at UC San Diego, into the clinic. They teamed up with Tony Yaksh, an expert in pain systems and a professor of anesthesiology and pharmacology at UC San Diego School of Medicine. Yaksh is a scientific advisor to Navega and co-senior author of the study.

Early lab studies

The researchers engineered a CRISPR/dead Cas9 system to target and repress the gene that codes for NaV1.7. They administered spinal injections of their system to mice with inflammatory and chemotherapy-induced pain. These mice displayed higher pain thresholds than mice that did not receive the gene therapy; they were slower to withdraw a paw from painful stimuli (heat, cold or pressure) and spent less time licking or shaking it after being hurt.

The treatment was tested at various timepoints. It was still effective after 44 weeks in the mice with inflammatory pain and 15 weeks in those with chemotherapy-induced pain. The length of duration is still being tested, researchers said, and is expected to be long-lasting. Moreover, the treated mice did not lose sensitivity or display any changes in normal motor function.

To validate their results, the researchers performed the same tests using another gene editing tool called zinc finger proteins. It’s an older technique than CRISPR, but it does the same job. Here, the researchers designed zinc fingers that similarly bind to the gene target and block expression of NaV1.7. Spinal injections of the zinc fingers in mice produced the same results as the CRISPR-dead Cas9 system.

“We were excited that both approaches worked,” Mali said. “The beauty about zinc finger proteins is that they are built on the scaffold of a human protein. The CRISPR system is a foreign protein that comes from bacteria, so it could cause an immune response. That’s why we explored zinc fingers as well, so we have an option that might be more translatable to the clinic.”

The researchers say this solution could work for a large number of chronic pain conditions arising from increased expression of NaV1.7, including diabetic polyneuropathy, erythromelalgia, sciatica and osteoarthritis. It could also provide relief for patients undergoing chemotherapy.

And due to its non-permanent effects, this therapeutic platform could address a poorly met need for a large population of patients with long-lasting (weeks to months) but reversible pain conditions, Yaksh said.

“Think of the young athlete or wounded war fighter in which the pain may resolve with wound healing,” he said. “We would not want to permanently remove the ability to sense pain in these people, especially if they have a long life expectancy. This CRISPR/dead Cas9 approach offers this population an alternative therapeutic intervention—that’s a major step in the field of pain management.”  

Researchers at UC San Diego and Navega will next work on optimizing both approaches (CRISPR and zinc fingers) for targeting the human gene that codes for NaV1.7. Trials in non-human primates to test for efficacy and toxicity will follow. Researchers expect to file for an IND and to commence human clinical trials in a couple years.

Paper title: “Long-lasting Analgesia via Targeted in situ Repression of NaV1.7.” Co-authors include Fernando Alemán, Glaucilene F. Catroli, Matthew Hunt, Michael Hu, Amir Dailamy, Andrew Pla, Sarah A. Woller, Nathan Palmer, Udit Parekh, Daniella McDonald, Amanda J. Robers, Vanessa Goodwill, Ian Dryden, Robert F. Hevner, Lauriane Delay and Gilson Gonçalves dos Santos.

This work was supported by UC San Diego Institutional Funds and the National Institutes of Health (grants R01HG009285, RO1CA222826, RO1GM123313, R43CA239940, R43NS112088, R01NS102432, R01NS099338).

Disclosure: Ana Moreno, Fernando Alemán, Prashant Mali and Tony Yaksh have a financial interest in Navega Therapeutics. The terms of these arrangements have been reviewed and approved by the University of California San Diego in accordance with its conflict of interest policies.

'Wearable microgrid' uses the human body to sustainably power small gadgets

March 9, 2021 -- Nanoengineers at the University of California San Diego have developed a “wearable microgrid” that harvests and stores energy from the human body to power small electronics. It consists of three main parts: sweat-powered biofuel cells, motion-powered devices called triboelectric generators, and energy-storing supercapacitors. All parts are flexible, washable and can be screen printed onto clothing.

The technology, reported in a paper published Mar. 9 in Nature Communications, draws inspiration from community microgrids.

“We’re applying the concept of the microgrid to create wearable systems that are powered sustainably, reliably and independently,” said co-first author Lu Yin, a nanoengineering Ph.D. student at the UC San Diego Jacobs School of Engineering. “Just like a city microgrid integrates a variety of local, renewable power sources like wind and solar, a wearable microgrid integrates devices that locally harvest energy from different parts of the body, like sweat and movement, while containing energy storage.” 

Stretchable electronics on a white long sleeved shirt
The wearable microgrid uses energy from human sweat and movement to power an LCD wristwatch and electrochromic device. Photos by Lu Yin

The wearable microgrid is built from a combination of flexible electronic parts that were developed by the Nanobioelectronics team of UC San Diego nanoengineering professor Joseph Wang, who is the director of the Center for Wearable Sensors at UC San Diego and corresponding author on the current study. Each part is screen printed onto a shirt and placed in a way that optimizes the amount of energy collected.

Biofuel cells that harvest energy from sweat are located inside the shirt at the chest. Devices that convert energy from movement into electricity, called triboelectric generators, are positioned outside the shirt on the forearms and sides of the torso near the waist. They harvest energy from the swinging movement of the arms against the torso while walking or running. Supercapacitors outside the shirt on the chest temporarily store energy from both devices and then discharge it to power small electronics.

Harvesting energy from both movement and sweat enables the wearable microgrid to power devices quickly and continuously. The triboelectric generators provide power right away as soon as the user starts moving, before breaking a sweat. Once the user starts sweating, the biofuel cells start providing power and continue to do so after the user stops moving.

“When you add these two together, they make up for each other’s shortcomings,” Yin said. “They are complementary and synergistic to enable fast startup and continuous power.” The entire system boots two times faster than having just the biofuel cells alone, and lasts three times longer than the triboelectric generators alone.

The wearable microgrid was tested on a subject during 30-minute sessions that consisted of 10 minutes of either exercising on a cycling machine or running, followed by 20 minutes of resting. The system was able to power either an LCD wristwatch or a small electrochromic display—a device that changes color in response to an applied voltage—throughout each 30-minute session.

Greater than the sum of its parts

Stretchable electronics on a white shirt
Biofuel cells harvest energy from sweat.

The biofuel cells are equipped with enzymes that trigger a swapping of electrons between lactate and oxygen molecules in human sweat to generate electricity. Wang’s team first reported these sweat-harvesting wearables in a paper published in 2013. Working with colleagues at the UC San Diego Center for Wearable Sensors, they later updated the technology to be stretchable and powerful enough to run small electronics.

The triboelectric generators are made of a negatively charged material, placed on the forearms, and a positively charged material, placed on the sides of the torso. As the arms swing against the torso while walking or running, the oppositely charged materials rub against each and generate electricity.

Stretchable electronics on a white shirt
Triboelectric generator harvests energy from movement.

Each wearable provides a different type of power. The biofuel cells provide continuous low voltage, while the triboelectric generators provide pulses of high voltage. In order for the system to power devices, these different voltages need to be combined and regulated into one stable voltage. That’s where the supercapacitors come in; they act as a reservoir that temporarily stores the energy from both power sources and can discharge it as needed.

Yin compared the setup to a water supply system.

“Imagine the biofuel cells are like a slow flowing faucet and the triboelectric generators are like a hose that shoots out jets of water,” he said. “The supercapacitors are the tank that they both feed into, and you can draw from that tank however you need to.”

Stretchable electronics on a white shirt
Supercapacitors store energy and discharge it to other electronic devices that the user is wearing.

All of the parts are connected with flexible silver interconnections that are also printed on the shirt and insulated by waterproof coating. The performance of each part is not affected by  repeated bending, folding and crumpling, or washing in water—as long as no detergent is used.

The main innovation of this work is not the wearable devices themselves, Yin said, but the systematic and efficient integration of all the devices.

“We’re not just adding A and B together and calling it a system. We chose parts that all have compatible form factors (everything here is printable, flexible and stretchable); matching performance; and complementary functionality, meaning they are all useful for the same scenario (in this case, rigorous movement),” he said.

Other applications

This particular system is useful for athletics and other cases where the user is exercising. But this is just one example of how the wearable microgrid can be used. “We are not limiting ourselves to this design. We can adapt the system by selecting different types of energy harvesters for different scenarios,” Yin said.

The researchers are working on other designs that can harvest energy while the user is sitting inside an office, for example, or moving slowly outside.

Paper: “A Self-Sustainable Wearable Multi-Modular E-Textile Bioenergy Microgrid System.” Co-authors include Kyeong Nam Kim*, Jian Lv*, Farshad Tehrani, Muyang Lin, Zuzeng Lin, Jong-Min Moon, Jessica Ma, Jialu Yu and Sheng Xu.

*These authors contributed equally to this work.

This work was supported by the UC San Diego Center for Wearable Sensors and the National Research Foundation of Korea.

Adhesion, contractility enable metastatic cells to go against the grain

Schematic of cells migrating over a step gradient. For durotactic cells, higher tractions and longer bond lifetimes on the stiff side drive adhesion maturation and net migration toward the stiffer substrate. For adurotactic cells, tractions balance across the boundary due to longer bond lifetimes on the soft side of the step gradient.

March 9, 2021--Bioengineers at the University of California San Diego and San Diego State University have discovered a key feature that allows cancer cells to break from typical cell behavior and migrate away from the stiffer tissue in a tumor, shedding light on the process of metastasis and offering possible new targets for cancer therapies. 

It has been well documented that cells typically migrate away from softer tissue to stiffer regions within the extracellular matrix—a process called durotaxis. Metastatic cancer cells are the rare exception to this rule, moving away from the stiffer tumor tissue to softer tissue, and spreading the cancer as they migrate. What enables these cells to display this atypical behavior, called adurotaxis, and migrate away from the stiffer tumor hasn’t been well understood.

Building off previous research led by bioengineers in UC San Diego Professor Adam Engler’s lab, which found that weakly adherent, or less sticky, cells migrated and invaded other tissues more than strongly adherent cells, the team has now shown that the contractility of these weakly adherent cells is what enables them to move to less stiff tissue. By chemically reducing the contractility of weakly adherent cells, they become durotactic, migrating toward stiffer tissue; increasing the contractility of strongly adherent cells makes them migrate down the stiffness gradient. The researchers reported their findings on March 9 in Cell Reports. 

“The main takeaway here is that the less adherent, more contractile cells are the ones that don’t exhibit typical durotactic behavior,” said Benjamin Yeoman, a bioengineering PhD student in the joint program at UC San Diego and SDSU, and first author of the study. “But beyond that, we see this in several different types of cancer, which opens up the possibility that maybe there’s this commonality between different types of carcinomas that could potentially be a target for a more universal treatment.”

To find out what enables this atypical behavior, Yeoman first used computational models developed in bioengineer Parag Katira’s lab in the SDSU Department of Mechanical Engineering, to try and pinpoint what was different about the cells that were able to move against the stiffness gradient. The models showed that changing a cell’s contractile force could modulate the cell’s adhesion strength in an environment of a certain stiffness, which would change their ability to be durotactic. To confirm the computational results, Yeoman used a microfluidic flow chamber device designed for previous research on cell adherence in Engler’s lab, to experiment with the contractility of real cancer cells from breast cancer, prostate cancer and lung cancer cell lines. 

“It worked perfectly,” said Katira, co-corresponding author of the paper. “It was really an ideal collaboration, where you have experimental results that show something is different; then you have a computational model that predicts it and explains why something is happening; and then you go back and do experiments to actually test if that’s going on. All of these blocks fell into place to bring this interesting result.”

The microfluidic cell-sorting device developed in Engler’s lab allowed the researchers to isolate cells based on adhesion strength. Credit: Benjamin Yeoman

The parallel plate flow chamber device used to test the computational theory was designed by engineers in Engler’s lab studying the effect of adherence on cell metastasis and cancer recurrence, and first described in Cancer Research in February 2020. Using this patent pending device, the researchers now isolated cells based on adhesion strength, and seeded them onto photopatterned hydrogels with alternating soft and stiff profiles. The researchers used time-lapse video microscopy to watch how the cells moved, and found that strongly adherent cells would durotax, moving to stiffer sections, while weakly adherent cells would migrate to softer tissue. 

After investigating several potential mechanisms within the cell enabling this behavior, the team focused on contractility as a key marker of its ability to adurotax. By modulating the number of active myosin motors within the cell— a marker of contractile ability—they were able to get previously durotactic cells to migrate away from stiffer tissue, and previously adurotactic, weakly adherent cells to migrate up the stiffness gradient.

The researchers hope that this work, and the further development of the microfluidic cell sorting device, will enable better assessments of disease prognosis in the future. Their ultimate aim is to be able to use the parallel plate flow chamber as a way to measure the metastatic potential of a patient’s cells, and use that as a predictor for cancer recurrence to drive more effective treatments and outcomes. 

“Understanding the mechanisms that govern invasion of many different tumor types enables us to better use this device to sort and count cells with weak adhesion and their percentage in a tumor, which may correlate with poor patient outcomes,” said Adam Engler, professor of bioengineering at UC San Diego and co-corresponding author of the paper. 

The researchers cautioned that this discovery doesn’t preclude other mechanisms from playing a role in the metastasis of cells. It does, however, highlight the important role that adherence and contractility do play, which needs to be studied further.

“The point is not to say that nothing else can drive cells away from a tumor,” said Katira. “There could be other drivers for metastasis, but this is clearly an important mechanism, and the fact that cells can do this across lung, breast and pancreatic cancer cells tells us this is generalizable.”

Going forward, the engineers plan to study other parameters that may contribute to adurotaxis; investigate the effect of different types of tumor environments on a cell’s ability to adurotax; and move from the individual cell scale to the population scale, to see how adhesion and contractility function and can be modulated when there is a mixed population of cells with unique mechanical properties.

This project was funded by grants from the National Science Foundation, National Institutes of Health and the Army Research Office. 

Three-layered masks most effective against large respiratory droplets

The droplet impacting on the mask surface is recorded at 20,000 frames per second. These time sequence images of droplet impingement on a single-, double-, and triple-layer masks show the total number count of atomized droplets is significantly higher for the single-layer mask in comparison with the double-layer mask, while only a single droplet penetrates through the triple-layer mask. Credit: Basu et al, Science Advances, March 5 2021

March 5, 2021-- If you are going to buy a face mask to protect yourself and others from COVID-19, make sure it’s a three-layered mask. You might have already heard this recommendation, but researchers have now found an additional reason why three-layered masks are safer than single or double-layered alternatives. 

While this advice was originally based on studies that showed three layers prevented small particles from passing through the mask pores, researchers have now shown that three-layered surgical masks are also most effective at stopping large droplets from a cough or sneeze from getting atomized into smaller droplets. These large cough droplets can penetrate through the single- and double-layer masks and atomize to much smaller droplets, which is particularly crucial since these smaller droplets (often called aerosols) are able to linger in the air for longer periods of time. Researchers studied surgical masks with one, two and three layers to demonstrate this behavior. 

The researchers reported their results in Science Advances on March 5

The team notes that single and double-layer masks do provide protection in blocking some of the liquid volume of the original droplet and are significantly better than wearing no mask at all. They hope their findings on ideal mask pore size, material thickness, and layering could be used by manufacturers to produce the most effective masks designs.

Using a droplet generator and a high-speed time-lapse camera, the team of engineers from the University of California San Diego, Indian Institute of Science and University of Toronto found that, counterintuitively, large respiratory droplets containing virus emulating particles (VEPs) actually get atomized when they hit a single-layer mask, and many of these VEPs pass through that layer. Think of it like a water droplet breaking into smaller droplets as it’s being squeezed through a sieve. For a 620 micron droplet—the size of a large droplet from a cough or sneeze—a single-layer surgical mask only restricts about 30 percent of the droplet volume; a double-layer mask performs better, restricting about 91 percent of the droplet volume; while a three layer mask has negligible, nearly zero droplet ejection. This video illustrates the research as well.

“While it is expected that large solid particles in the 500–600-micron range should be stopped by a single-layer mask with average pore size of 30 micron, we are showing that this is not the case for liquid droplets,” said Abhishek Saha, professor of mechanical and aerospace engineering at UC San Diego and a co-author of the paper. “If these larger respiratory droplets have enough velocity, which happens for coughs or sneezes, when they land on a single-layer of this material it gets dispersed and squeezed through the smaller pores in the mask.” 

Schematic diagram of viral load getting trapped inside the mask layer. Droplets and virus are not drawn to scale. Basu et al, Science Advances, March 5 2021

This is a problem. Droplet physics models have shown that while these large droplets are expected to fall to the ground very quickly due to gravity, these now smaller, 50-80 micron-sized droplets coming through the first and second layer of a mask will linger in the air, where they can spread to people at larger distances. 

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

“We do droplet impact experiments a lot in our labs,” said Saha. “For this study, a special generator was used to produce a relatively fast-moving droplet. The droplet was then allowed to land on a piece of mask material—that could be a single layer, double, or triple layer, depending on which we’re testing. Simultaneously, we use a high-speed camera to see what happens to the droplet.”

Using the droplet generator, they’re able to alter the size and speed of the droplet to see how that affects the flow of the particle. 

Going forward, the team plans to investigate the role of different mask materials, as well as the effect of damp or wet masks, on particle attrition. 

Coronavirus-like particles could ensure reliability of simpler, faster COVID-19 tests

Series of test tubes containing yellow and pink liquid
RT-LAMP test samples showing positive (yellow) and negative (pink) results. Image credit: Soo Khim Chan

March 2, 2021 -- Rapid COVID-19 tests are on the rise to deliver results faster to more people, and scientists need an easy, foolproof way to know that these tests work correctly and the results can be trusted. Nanoparticles that pass detection as the novel coronavirus could be just the ticket.

Such coronavirus-like nanoparticles, developed by nanoengineers at the University of California San Diego, would serve as something called a positive control for COVID-19 tests. Positive controls are samples that always test positive. They are run and analyzed right alongside patient samples to verify that COVID-19 tests are working consistently and as intended.

The positive controls developed at UC San Diego offer several advantages over the ones currently used in COVID-19 testing: they do not need to be kept cold; they are easy to manufacture; they can be included in the entire testing process from start to finish, just like a patient sample; and because they are not actual virus samples from COVID-19 patients, they do not pose a risk of infection to the people running the tests.

Researchers led by Nicole Steinmetz, a professor of nanoengineering at UC San Diego, published their work in the journal Biomacromolecules.

This work builds on an earlier version of the positive controls that Steinmetz’s lab developed for the RT-PCR test, which is the gold standard for COVID-19 testing. The positive controls in the new study can be used not only for the RT-PCR test, but also for a cheaper, simpler and faster test called the RT-LAMP test, which can be done on the spot and provide results in about an hour.

Having a hardy tool to ensure these tests are running accurately—especially for low-tech diagnostic assays like the RT-LAMP—is critical, Steinmetz said. It could help enable rapid, mass testing of COVID-19 in low-resource, underserved areas and other places that do not have access to sophisticated testing equipment, specialized reagents and trained professionals.

Upgraded positive controls

Goto Flickr
Coronavirus-like nanoparticles, made from plant viruses and bacteriophage, could serve as positive controls for the RT-LAMP test. Image credit: Soo Khim Chan

The new positive controls are essentially tiny virus shells—made of either plant virus or bacteriophage—that house segments of coronavirus RNA inside. The RNA segments include binding sites for both of the primers used in the PCR and LAMP tests.

“This design creates an all-in-one control that can be used for either one of these assays, making it very versatile,” said first author Soo Khim Chan, who is a postdoctoral researcher in Steinmetz’s lab.

The team developed two types of positive controls. One was made from plant virus nanoparticles. To make them, the researchers infected cowpea plants in the lab with cowpea chlorotic mottle virus and then extracted the viruses from the plants. Afterwards, the researchers removed the virus’ RNA and replaced it with a custom-made RNA template containing specific yet non-infectious sequences from the SARS-CoV-2 virus. The resulting nanoparticles consist of coronavirus RNA sequences packaged inside plant virus shells.

The other positive control was made from bacteriophage nanoparticles. It involved a similar recipe. The researchers infected E. coli bacteria with custom-made plasmids—rings of DNA—that contain specific fragments of sequences (which are also non-infectious) from the SARS-CoV-2 virus, as well as genes coding for surface proteins of a bacteriophage called Qbeta. This process caused the bacteria to produce nanoparticles that consist of coronavirus RNA sequences packaged inside bacteriophage shells.

The plant virus and bacteriophage shells are key to making these positive controls so sturdy. They protect the coronavirus RNA segments from breaking down at warmer temperatures—tests showed that they can be stored for a week at temperatures up to 40 C (104 F). The shells also protect the RNA during the first step of the PCR and LAMP tests, which involves breaking down cells in the sample—via enzymes or heat—to release their genetic material for testing.

These protections are not present in the positive controls currently used in COVID-19 testing (naked synthetic RNAs, plasmids or RNA samples from infected patients). That’s why existing controls either require refrigeration (which makes them inconvenient to handle, costly to ship and store) or have to be added at a later stage of the test (which means that means scientists will not know if something went wrong in the first steps).

As a next step, the researchers are looking to partner up with industry to implement this technology. The positive controls can be adapted to any established RT-PCR or RT-LAMP assay, and using them would help negate false readouts, Steinmetz’s team said.  Plus, these positive controls can be easily produced in large quantities by molecular farming in plants or microbial culture fermentation, which is good news for translating them to large-scale manufacturing.

“With mutants and variants emerging, continued testing will be imperative to keep the population safe,” Steinmetz said. “The new technology could find utility in particular for at-home tests, which may have a higher rate of false readouts due to the less controlled experimental conditions.”

Paper title: “Virus-Like Particles as Positive Controls for COVID-19 RT-LAMP Diagnostic Assays.”

This work was funded in part by the National Science Foundation (RAPID CBET-2032196 and RAPID CMMI-2027668) and the University of California (UCOP-R00RG2471 and a Galvanizing Engineering in Medicine Award).

KRISTEN VACCARO AND THE SCIENCE OF SOCIAL MEDIA

 

February 11, 2021 -- New assistant professor Kristen Vaccaro came to UC San Diego’s Computer Science and Engineering Department from the University of Illinois Urbana-Champaign, where she recently earned her Ph.D. After spending several years in chilly Illinois, she’s pleased to be wintering in San Diego.

“It was very cold,” said Vaccaro, “and very  flat. It’s been a pleasure to go hiking again.”

Weather notwithstanding, Vaccaro chose CSE because she was impressed by the faculty and students here.

“It was a virtual visit, which was weird,” she said. “I hadn't been to San Diego before, so I was really coming in blind, but I had so much fun on the visit, talking with everyone. That was 90% of my decision.”

Understanding Social Media

Vaccaro earned her B.A. in physics at Reed College, worked as a software engineer at the MITRE Corporation for several years and circled back to grad school at the University of Illinois. Her research focuses on giving users more say in how social media works.

“My work looks at how we can design machine learning systems to improve user agency and control,” said Vaccaro. “There are increasingly large numbers of decisions that get made about people through automated decision-making systems. How can we take a more human-centered approach when building these systems? How do we give people a sense of agency?”

These can be tricky questions. Sometimes people get too many choices and are simply overwhelmed. Facebook already has more than 100 control settings, but most people don’t know how to effectively use them. In fact, Vaccaro’s research has identified a kind of control setting placebo effect, which she likens to the Close Door button on an elevator. Nobody has any idea what it does – if anything.

“We did one study where we gave people control setting access for their newsfeeds,” she said. “Sometimes the control settings worked properly, but in some cases we also coded them to      malfunction. People were just as satisfied with the malfunctioning settings as the functioning ones.”

Vaccaro and others have also identified a variety of social media folk theories – which can lead to odd tricks people adopt to customize their feeds. Some people like a post and subsequently hide it. They want to show their friend some love; however, they don’t want the algorithm to show them similar posts.

Does liking and hiding work? Nobody really knows. Outside of Facebook, there’s no way to run a controlled experiment where people can change their news feed on one screen and leave the other alone. However, understanding these folk theories can offer new design insights.

“The control settings are there,” said Vaccaro. “People care about them, but they don't know where they are, and they can't tell whether they're working. Maybe we can take the more natural ways people have of thinking about a platform and leverage those to curate control settings, be their virtual valet.”

Vaccaro also wonders if current design is too seamless, hiding what’s really going on under the hood. She thinks a more “seamful” approach, in which people can see problems in real time and react appropriately, might be more helpful. She compares it to hearing an unnerving rattle in your car.

In addition, Vaccaro wants to help people understand their privacy choices and improve their experience when they disagree with a platform. “How can you design content moderation systems so that people have a say in how their community is governed?” she asks.

Teaching and Learning

Vaccaro likes to incorporate student-driven elements into her courses. It engages her classes and sometimes offers unique topics. During one fall quarter class, she let students to pick 10% of the topics.

“Some of the student choices were things I would've picked already, like AR/VR,” she said. “Others were things I absolutely would not have chosen myself. The students wanted to talk about depression and stress and how that connects to  social media. I would never, in a million years, have picked that topic. But the students were interested, and it led to a great discussion.”

Outside the classroom, she has been exploring San Diego, particularly the excellent hiking. “I go out weekdays, early in the morning, so there’s less traffic – Torrey Pines, Peñasquitos, Cowles Mountain. I have two books on San Diego area hikes, and I hope to do them all.”

Meet computer scientist Kristen Vaccaro and the science of social media

CSE Assistant Professor Kristen Vaccaro is one of four new faculty members to join the distinguisehd community of CSE faculty over the next two academic years. 

March 2, 2021 -- New assistant professor Kristen Vaccaro came to UC San Diego’s Department of Computer Science and Engineering from the University of Illinois Urbana-Champaign, where she recently earned her Ph.D. After spending several years in chilly Illinois, she’s pleased to be wintering in San Diego.

“It was very cold,” said Vaccaro, “and very flat. It’s been a pleasure to go hiking again.”

Weather notwithstanding, Vaccaro chose UC San Diego because she was impressed by the faculty and students here.

“It was a virtual visit, which was weird,” she said. “I hadn't been to San Diego before, so I was really coming in blind, but I had so much fun on the visit, talking with everyone. That was 90% of my decision.”

Understanding Social Media

Vaccaro earned her bachelor's in physics at Reed College, worked as a software engineer at the MITRE Corporation for several years and circled back to grad school at the University of Illinois. Her research focuses on giving users more say in how social media works.

“My work looks at how we can design machine learning systems to improve user agency and control,” said Vaccaro. “There are increasingly large numbers of decisions that get made about people through automated decision-making systems. How can we take a more human-centered approach when building these systems? How do we give people a sense of agency?”

These can be tricky questions. Sometimes people get too many choices and are simply overwhelmed. Facebook already has more than 100 control settings, but most people don’t know how to effectively use them. In fact, Vaccaro’s research has identified a kind of control setting placebo effect, which she likens to the Close Door button on an elevator. Nobody has any idea what it does – if anything.

“We did one study where we gave people control setting access for their newsfeeds,” she said. “Sometimes the control settings worked properly, but in some cases we also coded them to malfunction. People were just as satisfied with the malfunctioning settings as the functioning ones.”

Vaccaro and others have also identified a variety of social media folk theories – which can lead to odd tricks people adopt to customize their feeds. Some people like a post and subsequently hide it. They want to show their friend some love; however, they don’t want the algorithm to show them similar posts.

Does liking and hiding work? Nobody really knows. Outside of Facebook, there’s no way to run a controlled experiment where people can change their news feed on one screen and leave the other alone. However, understanding these folk theories can offer new design insights.

“The control settings are there,” said Vaccaro. “People care about them, but they don't know where they are, and they can't tell whether they're working. Maybe we can take the more natural ways people have of thinking about a platform and leverage those to curate control settings, be their virtual valet.”

Vaccaro also wonders if current design is too seamless, hiding what’s really going on under the hood. She thinks a more “seamful” approach, in which people can see problems in real time and react appropriately, might be more helpful. She compares it to hearing an unnerving rattle in your car.

In addition, Vaccaro wants to help people understand their privacy choices and improve their experience when they disagree with a platform. “How can you design content moderation systems so that people have a say in how their community is governed?” she asks.

Teaching and Learning

Vaccaro likes to incorporate student-driven elements into her courses. It engages her classes and sometimes offers unique topics. During one fall quarter class, she let students pick 10% of the topics.

“Some of the student choices were things I would've picked already, like AR/VR,” she said. “Others were things I absolutely would not have chosen myself. The students wanted to talk about depression and stress and how that connects to  social media. I would never, in a million years, have picked that topic. But the students were interested, and it led to a great discussion.”

Outside the classroom, she has been exploring San Diego, particularly the excellent hiking. “I go out weekdays, early in the morning, so there’s less traffic – Torrey Pines, Peñasquitos, Cowles Mountain. I have two books on San Diego area hikes, and I hope to do them all.”

Weakness is strength for this low-temperature battery

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Simulated structures of the binding between a lithium ion and electrolyte molecules. Image courtesy of John Holoubek/Nature Energy

February 25, 2021 -- Nanoengineers at the University of California San Diego have discovered new fundamental insights for developing lithium metal batteries that perform well at ultra-low temperatures; mainly, that the weaker the electrolyte holds on to lithium ions, the better. By using such a weakly binding electrolyte, the researchers developed a lithium metal battery that can be repeatedly recharged at temperatures as low as -60 degrees Celsius—a first in the field.

Researchers report their work in a paper published Feb. 25 in Nature Energy.

In tests, the proof-of-concept battery retained 84% and 76% of its capacity over 50 cycles at -40 and -60 degrees Celsius, respectively. Such performance is unprecedented, researchers said.

Other lithium batteries that have been developed for use in sub-freezing temperatures are capable of discharging in the cold but need warmth when charging. That means an extra heater must be brought on board to use these batteries in applications such as outer space and deep-sea exploration. The new battery, on the other hand, can be both charged and discharged at ultra-low temperature.

This work—a collaboration between the labs of UC San Diego nanoengineering professors Ping Liu, Zheng Chen and Tod Pascal—presents a new approach to improving the performance of lithium metal batteries at ultra-low temperature. Many efforts so far have focused on choosing electrolytes that don’t freeze up so easily and can keep lithium ions moving quickly between the electrodes. In this study, UC San Diego researchers discovered that it’s not necessarily how fast the electrolyte can move the ions, but how easily it lets go of them and deposits them on the anode.

“We found that the binding between the lithium ions and the electrolyte, and the structures that the ions take in the electrolyte, mean either life or death for these batteries at low temperature,” said first author John Holoubek, a nanoengineering Ph.D. student at the UC San Diego Jacobs School of Engineering.

The researchers made these discoveries by comparing battery performance with two types of electrolytes: one that binds weakly to lithium ions, and one that binds strongly. Lithium metal battery cells with the weakly binding electrolyte performed better overall at -60 degrees Celsius; it was still running strong after 50 cycles. In contrast, cells with the strongly binding electrolyte stopped working after just two cycles.

After cycling the cells, the researchers took them apart to compare the lithium metal deposits on the anodes. The differences were also stark. Deposits were smooth and uniform in the cells with the weakly binding electrolyte, but chunky and needle-like in the cells with the strongly binding electrolyte. 

Details matter

The differences in battery performance all come down to nanoscale interactions, the researchers said. “How lithium ions interact with the electrolyte at the atomic level not only enables sustainable cycling at very, very low temperature, but also prevents dendrite formation,” Chen said.

To understand why, the team took a detailed look at these interactions using computational simulations and spectroscopic analysis. In one of the electrolytes, called diethyl ether (or DEE), the researchers observed molecular structures consisting of lithium ions weakly bound to the surrounding electrolyte molecules. In the other electrolyte, called DOL/DME, the researchers observed structures that feature strong binding between the ions and electrolyte molecules.

These structures and binding strengths are important, the researchers said, because they ultimately dictate how lithium deposits on the anode surface at low temperature. In weakly bound structures like those observed in the DEE electrolyte, Holoubek explained, lithium ions can easily leave the electrolyte’s hold, so it doesn’t take much energy to get them to deposit anywhere on the anode surface. This is why deposits are smooth and uniform in DEE. But in strongly bound structures, like those in DOL/DME, more energy is needed to pull lithium ions away from the electrolyte. As a result, lithium will prefer to deposit where the anode surface has an extremely strong electric field—anywhere there’s a sharp tip. And lithium will continue to pile up on that tip until the cell short circuits. This is why deposits are chunky and dendritic in DOL/DME.

“Figuring out the different types of molecular and atomic structures that lithium forms, how lithium coordinates with certain atoms—these details matter,” said Pascal, who directed the computational studies. “By understanding fundamentally how these systems come together, we can come up with all kinds of new design principles for the next generation of energy storage systems. This work demonstrates the power of nanoengineering, where figuring out what happens at the small scale enables the design of devices at the large scale.”

Compatible cathode

These fundamental insights enabled the team to design a cathode that’s compatible with the electrolytes and anode for low-temperature performance. It is a sulfur-based cathode made with materials that are low-cost, abundant and environmentally benign—no expensive transition metals are used.

“The significance of this work is really two-fold,” said Liu, whose lab designed the cathode and has been optimizing the cycling performance of such a cathode in DEE for normal conditions. “Scientifically, it presents insights that are contrary to conventional wisdom. Technologically, it is the first rechargeable lithium metal battery that can deliver meaningful energy density while being fully operated at -60 C. Both aspects present a complete solution for ultra-low temperature batteries.”

Paper title: “Tailoring Electrolyte Solvation for Li Metal Batteries Cycled at Ultra-Low Temperature.”

This work was supported by a NASA Space Technology Graduate Research Opportunity, and in part by a NASA early career faculty award and by the U.S. Department of Energy.

Protecting our oceans with AI Technology: Q&A with Saakib Akbany of Remora

Human-centered mobility and transportation options for disadvantaged communities is the goal of new partnership

UC San Diego researchers are working hand in hand with community organizations and the San Diego Association of Governments

Feb. 24, 2021--The University of California San Diego is teaming up with several community-based organizations and the San Diego Association of Governments to improve access to transportation for the county’s low-income and underserved neighborhoods. The team is adopting a human-centered design approach to their work to try and repair the harm done by car-oriented transportation policies of the past. 

The project was selected this month to be part of the inaugural Civic Innovation Challenge, a partnership of the National Science Foundation, the Department of Energy and the Department of Homeland Security. The competition’s goal is to empower communities to tackle issues such as transit, housing affordability and operating safe schools during the COVID-19 pandemic. 

The UC San Diego team is one of 52 groups across 30 states to receive a $50,000 award during the first stage of the competition. The teams have four months to refine their projects, after which NSF will select a smaller number of groups to receive awards of up to $1 million for ready-to-implement pilot projects with the potential to produce scalable, sustainable and transferable solutions to address community-identified challenges. 

The UC San Diego team is headed by Todd Hylton and Colleen Emmenegger of the  Contextual Robotics Institute and the Design Lab. Contextual Robotics Institute Director Henrik Christensen is also a co-principal investigator on the grant.  Thanks to the $50,000 NSF award, researchers will assess the challenges and feasibility of an integrated mobility service with representative communities. With the help of partner community organizations, they will conduct day-in-a-life interviews and real-world observations. They will also deploy questionnaires and wearable sensors in several disadvantaged communities.

Working with SANDAG, the team will employ data-driven methodologies including the analysis demographic data, transportation services data, survey data and transportation modeling in these same communities.

The project’s primary research objective is to assess the integration of these techniques and their utility in understanding the needs of disadvantaged communities and in formulating solutions that are both responsive and feasible. 

In the project’s second stage, the team will implement an integrated mobility pilot in one of these communities that is responsive to the real needs of the community; addresses the long-term strategic plan for transportation and sustainability in the region; and can be expanded to other communities in the region. 

“We anticipate that the pilot will demonstrate improved access to employment, recreation, shopping, education and public transit via the integration of mobility services including, for example, pooled ride-hailing, neighborhood electric vehicles, microtransit, e-scooters, e-bikes, and carshare,” Hylton said. 

The project intends not only to address needs in particular San Diego communities, but also to inform SANDAG’s planners about the types of services, incentives, and operating models that are needed to ensure alignment with a community’s needs as they implement a bold vision of the 2021 Regional Plan known as the “5 Big Moves.”


 

Computer scientist studies the importance of extra-chromosomal DNA

With ground-breaking approaches and a new company, Vineet Bafna and colleagues are taking a different path to control cancer

CSE Professor Vineet Bafna is working to determine how ecDNA drives cancer, which could eventually lead to new anti-cancer therapies. 

Feb. 23, 2021--Cancer is a genetic disease that can lay waste to DNA. In many cases, error correction mechanisms mutate, removing the quality control circuits that maintain genes, setting the stage for more mutations.

But sometimes the changes are even more profound. Chunks of DNA are duplicated and break away from their home chromosomes, forming small, circular islands of extrachromosomal DNA (ecDNA). Under a microscope, chromosomes look like they’ve been hit by a sledgehammer.

UC San Diego Computer Science and Engineering (CSE) Professor Vineet Bafna is fascinated by ecDNA and is working with biologists to measure its impact. These structural changes, and the associated gene duplications, can amplify genes that drive rampant cell division, as well as genes that make tumors treatment resistant, giving them an outsized impact on cells.

“There’s been a lot of research that suggests high copies of oncogenes – genes that are proliferative in nature – lead to poor outcomes,” says Bafna. “But what is not clear is how these copy number variations arise. How is it a gene can make 20, 50, 100 copies?”

Bafna and colleagues are working to answer these questions and help determine how ecDNA drives cancer. They hope these insights will eventually lead to new anti-cancer therapies.

Taking an Algorithmic Approach

Since the human genome was sequenced, many researchers have focused almost exclusively on single letter changes in oncogenes and how these affect cellular function. While this has been a fruitful path, structural changes to chromosomes have been somewhat neglected. Working closely with UC San Diego pathology professor Paul Mischel and others, Bafna has been developing computational approaches to identify ecDNA and other chromosomal changes.

“The question I’m interested in is: How can we determine what is causing a complex structural rearrangement based on a genomic signature?” said Bafna.

The Bafna lab developed machine learning techniques to detect ecDNA in cellular images. These techniques can spot ecDNA when cultured cancer cells enter metaphase, the second stage of cell division, when chromosomes become quite compact.

From there, it’s just a matter of counting. Conducted jointly with the Mischel lab, these studies have analyzed thousands of images and found ecDNA in virtually every cancer subtype – hiding in plain sight.

Unfortunately, these imaging techniques are difficult to deploy with patient tumors, from which only DNA, isolated from chromosomes, can be extracted. To get around this, Bafna and colleagues examine short (150 to 300 base pair) ecDNA fragments in tumor samples and compare them to reference genomes. If the two ends of these ecDNA fragments match a reference chromosome, this strongly indicates the region detached from that chromosome.

Working with Mischel and Professor Roel Verhaak at the Jackson Laboratory in Maine, Bafna applied these genomic methods to more than 3,000 tumor samples and found ecDNA in over 20% of the tumors, with higher frequencies in glioblastomas, lung and kidney cancers.

Grand Challenges    

These structural defects have become increasingly important for the scientific community. Interrogating ecDNA is one in a series of Cancer Grand Challenges, which offer $25 million awards to researchers who can answer important questions about cancer pathology.

“What are the biological mechanisms involved in ecDNA generation?” asked Bafna. “What's the role of ecDNA in the evolution of cancer? Can we model and predict ecDNA evolution? Can we target any vulnerabilities therapeutically? These are questions we’ve been trying to answer anyway, so this is a big deal for us.”

The researchers also believe it’s time to translate their discovery research into treatments. Two years ago, Bafna and Mischel co-founded Boundless Bio, a San Diego life sciences company working to find ecDNA-focused therapeutics.

“We are taking what we’ve learned about ecDNA vulnerabilities and identifying molecules that could potentially target those vulnerabilities,” says Bafna. “We believe this will give us another tool to fight cancer.”

New material is next step toward stable high-voltage long-life solid-state sodium-ion batteries

The Zr-Cl unit and the orange/brown "cloud" that surrounds the green Zr shows rotation.

Feb. 23, 2021-- A team of researchers designed and manufactured a new sodium-ion conductor for solid-state sodium-ion batteries that is stable when incorporated into higher-voltage oxide cathodes. This new solid electrolyte could dramatically improve the efficiency and lifespan of this class of batteries. A proof of concept battery built with the new material lasted over 1000 cycles while retaining 89.3% of its capacity--a performance unmatched by other solid-state sodium batteries to date. 

Researchers detail their findings in the Feb. 23, 2021 issue of Nature Communications. 

Solid state batteries hold the promise of safer, cheaper, and longer lasting batteries. Sodium-ion chemistries are particularly promising because sodium is low-cost and abundant, as opposed to the lithium required for lithium-ion batteries, which is mined at a high environmental cost. The goal is to build batteries that can be used in large-scale grid energy storage applications, especially to store power generated by renewable energy sources to mitigate peak demand. 

“Industry wants batteries at cell-level to cost $30 to $50 per kWh,” about one-third to one-fifth of what it costs today, said Shirley Meng, a professor of nanoengineering at the University of California San Diego, and one of the paper’s corresponding authors. “We will not stop until we get there.”

The work is a collaboration between researchers at UC San Diego and UC Santa Barbara, Stony Brook University, the TCG Center for Research and Education in Science and Technology in Kolkata, India, and Shell International Exploration, Inc.

For the battery described in the Nature Communications study, researchers led by UC San Diego nanoengineering professor Shyue Ping Ong ran a series of computational simulations powered by a machine learning model to screen which chemistry would have the right combination of properties for a solid state battery with an oxide cathode. Once a material was selected as a good candidate, Meng’s research group experimentally fabricated, tested, and characterized it to determine its electrochemical properties. 

By rapidly iterating between computations and experiments, the UC SanDiego team settled on a class of halide sodium conductors made up of sodium, yttrium, zirconium and chloride. The material, which they named NYZC, was both electrochemically stable and chemically compatible with the oxide cathodes used in higher voltage sodium-ion batteries. The team then reached out to researchers at UC Santa Barbara to study and understand the structural properties and behavior of this new material.

NYZC is based on Na3YCl6, a well-known material that is unfortunately a very poor sodium conductor. Ong suggested substituting zirconium for yttrium because it would create vacancies and increase the volume of the cell battery unit, two approaches that increase the conduction of sodium ions. Researchers also noted that, in conjunction with the increased volume, a combination of zirconium and chloride ions in this new material undergoes a rotating motion, resulting in more conduction pathways for the sodium ions. In addition to the increase in conductivity, the halide material is much more stable than materials currently used in solid-state sodium batteries. 

“These findings highlight the immense potential of halide ion conductors for solid-state sodium-ion battery applications,” said Ong. “Further, it also highlights the transformative impact that large-scale materials data computations coupled with machine learning can have on the materials discovery process.”

Next steps include exploring other substitutions for these halide materials and increasing the battery’s overall power density, along with working to scale up the manufacturing process. 

The technology has been licensed by UNIGRID, a startup co-founded by UC San Diego NanoEngineering professor Zheng Chen; Erik Wu, a Ph.D. alumnus from Meng’s research group; and Darren H. S. Tan, one of Meng’s Ph.D. students. Meng is the company’s technical advisor.

Funding to support this work was provided by the Energy & Biosciences Institute through the EBI-Shell program and NSF.

The video below shows a simulation of the ZrCl6 unit rotating.

Tracking melting points above 4000 degrees Celsius

With a new grant, a UC San Diego engineer is developing a better platform to study new materials that melt above 4000 degrees Celsius

February 23, 2021: A materials engineer at the University of California San Diego is leading the development of a new research platform for studying high-performance materials, in particular new materials that melt above 4000 degrees Celsius (C). UC San Diego nanoengineering professor Kenneth Vecchio is leading the project, which is funded by a new $800,000 grant from the US Office of Naval Research (ONR), through the Defense University Research Instrumentation Program (DURIP).

The research platform will be built to specifically address the challenges of studying new materials that melt at temperatures higher than 4000C, which is approximately 80 percent of the temperature of the surface of the sun.

This platform will become a national resource for engineers and other researchers who are pushing the limits of materials science. There are many industrial, energy, space and defense applications that would benefit from new solid materials that perform reliably at record-breaking, ultra-high temperatures. Applications include the containment walls for fusion reactors, leading edges of air vehicles that travel five or more times the speed of sound, and new industrial material machining methods. (The tips of cutting tools, for example, can experience temperatures above 3000C at high machining speeds. New cutting tool materials with much higher melting temperatures would enable faster manufacturing.)

Creating and then characterizing materials that don't melt until exposed to ultra-high temperatures presents multiple challenges. In addition to creating candidate materials, researchers need to be able to characterize these materials to demonstrate performance. One of the key metrics is the temperature at which materials melt.

When working at temperatures around 4000C, nothing is simple. For example, how do you test the melting point of new materials that melt at temperatures higher than any containers you might try to hold them in? How do you heat a sample to temperatures in the 4000C range while precisely controlling the temperature? Or how do you determine exactly when a sample at such extreme conditions actually melts?

These are some of the issues that Vecchio and his team plan to solve via an experimental platform he designed and will build thanks to $800K in new funding from the ONR DURIP grant.

New Materials that melt at temperatures higher than 4000C

How do you increase the melting point of materials that already melt at ultra-high temperatures? For the past five years, Vecchio has led a UC San Diego project funded by the ONR Multidisciplinary University Research Initiatives (MURI) Program to focus on this.

The team is taking a new approach to this difficult task. To make sense of their strategy, you first need to know that there are two physical phenomena that largely determine the temperature at which a solid material melts into a liquid.

The first phenomenon is enthalpy. Enthalpy describes the energy associated with keeping a material in its solid form. The higher the enthalpy, the stronger the bond between the two atoms will be, and the higher you have to heat the material to melt it by breaking those bonds.

The second phenomenon is entropy. Entropy is associated with disorder and describes the energy driving the atoms to separate.  

"Melting in a solid occurs when the entropy becomes high enough to exceed the enthalpy," said Vecchio.

Ultra-high-temperature materials development is usually focused on enthalpy. But researchers seem to have reached the limits of the enthalpy approach, at least for materials that do not react with oxygen. The roadblock is due to the fact that the enthalpy of bonding between atoms is largely fixed. That means that once you find materials with the highest enthalpy of bonding, there is little room for increasing the melting temperature of that material via enthalpy.  

In their quest for materials that melt at ever higher temperatures, Vecchio and his team at the UC San Diego Jacobs School of Engineering have turned to the other phenomenon controlling melting temperature: entropy.

Most people have a vague sense that entropy has something to do with chaos or disorder. That notion will come in handy for understanding this new approach to developing materials with record-breaking melting temperatures.
 

Kenneth Vecchio UC San Diego
UC San Diego nanoengineering professor Kenneth Vecchio

"A liquid has a very high level of entropy. Atoms are moving all around in a liquid, that's entropy. If we can make a solid look like a liquid, in terms of its free energy, then there will be less driving force to change from the solid to the liquid state," said Vecchio.

Making a solid "look" like a liquid means increasing the inherent entropy of the material when it's a solid. That's what Vecchio has set out to do. Their strategy is to increase the disorder in new high-temperature solid materials by mixing large numbers of different atoms together.

"We create disorder through atomic mixing," said Vecchio.  

By taking this approach, the researchers are making their solid materials structurally appear more similar to the atomic state of that material's liquid form. This reduces the driving force for the solid to "want" to melt, which can lead to an increase in the temperature at which it melts.

For example, silicon carbide (SiC) is a well-known material with an ultra-high melting point of 2730C. But it would be useful to have related materials that melt at even high temperatures.

Following the entropy-focused approach in previous research, Vecchio and his collaborators replaced the Si atoms with equal amounts of five different metals, which led to new materials with even higher melting temperatures. These new materials, called, high-entropy carbides, or more broadly high-entropy ceramics, are discussed in a research article published in the journal Acta Materialia in 2019.

Vecchio and his team are pursuing another use of entropy as well. More entropy can be added to a solid-material system by adding other molecular and atomic-bonding variations that alone would not increase the melting temperature. But when you add enough of them into the system, the diversity of molecular elements and bonding scenarios further increases entropy, which can increase the temperature at which the solid melts into a liquid.

Researchers must be able to experimentally validate melting temperature and other properties for these kinds of approaches to materials development to lead to new useful materials. That's where the new platform comes in.

High Temperature-X-ray Diffraction platform

The new High Temperature-X-ray Diffraction platform being funded by the ONR DURIP grant to UC San Diego is designed to enable the heating of a sample region to 4500C, while measuring its temperature very accurately, and detecting the onset of melting.
 

Concept for integration of laser heating and high temperature pyrometry into an x-ray diffraction platform to achieve measurement of melting above 4000C.

The system components include: a platform that enables high-speed measurements called a high brightness X-ray diffraction platform; a high power laser to locally heat a small region of a material sample; and a high-tech thermometer (a pyrometer) that records temperatures up to 4500C by measuring the wavelength of light emitted from the heat source.

"The integration of these three tools is a fascinating engineering challenge," said Vecchio.

In order to overcome the 'container problem' in which a container melts before the experimental sample it is supposed to be holding, Vecchio plans to use sample materials as their own containers.

"We will only heat a small circular region in the middle of the sample using the laser," he said.

The remaining perimeter of the sample that is not exposed to the laser will serve as the container that holds the sample as it melts from solid to liquid.

"I look forward to being able to share this unique platform with researchers across the country," said Vecchio. "People have been trying to devise systems to measure melting temperatures of these types of materials, but their biggest scientific problem is they have no method to verify what structure the sample has at the perceived onset of melting. My design will solve this problem," explained Vecchio. "By building our melting system inside an x-ray diffraction platform, we will be able to exactly know the structure and type of material present right at the point of melting, and we will be able to completely verify melting as it has a completely different X-ray diffraction result compared to a solid sample."

He estimates that the facility will be up and running by the end of 2022.

The funded ONR DURIP proposal is entitled “Thermodynamic Measurements of Entropy-Stabilized Ultra-high Temperature Materials.” University of California San Diego NanoEngineering Professor Kenneth Vecchio is the Principal Investigator (PI) on the grant. (ONR award number: N00014-20-1-2872).

Engineer inducted into prestigious biomedical institution

Padmini Rangamani, a professor in the Department of Mechanical and Aerospace Engineering at UC San Diego, is part of the 2021 class of AIMBE Fellows. 

Feb. 22, 2021--Padmini Rangamani, a professor at the Jacobs School of Engineering, has been inducted into the College of Fellows of the American Institute for Medical and Biological Engineering (AIMBE). She was recognized for outstanding contributions to multiscale computational modeling of cellular mechanobiology including spatial signal transduction and membrane trafficking processes.

The College of Fellows comprises the top 2 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. AIMBE Fellows are recognized for their contributions in teaching, research and innovation.

A formal induction ceremony will be held during AIMBE’s 2021 Annual Event on March 26. Rangamani will be inducted along with 174 colleagues who make up the AIMBE Fellow Class of 2021, including two other UC San Diego researchers, Samuel Ward and Jiang Du from the UC San Diego School of Medicine. They join a total of 37 UC San Diego AIMBE Fellows. 

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. 

Her work uses a combination of novel mechanical theories and computational  approaches to simulate  many aspects of cellular membranes, in collaboration with experimentalists. Her areas of focus include transport phenomena in biological membranes, influence of cell shape on biochemical activation of signaling networks and morphological and topological changes to lipid membranes mediated by proteins and cytoskeletal forces.

In addition to her research, Rangamani has been active in advocating for women in science and under-represented groups in science. She recently was part of a group of women deans, chairs and distinguished faculty that authored a call to action to fund Black scientists, published in the journal Cell. Karen Christman, a Jacobs School’s associate dean and a bioengineering professor, was also part of the group. 

Rangamani also was a coauthor of a paper in PLOS Computational Biology titled “Ten simple rules for women principal investigators during a pandemic.” It’s perhaps important to note that despite its title, the article is careful to say that the cardinal rule is that there are no rules. So all 10 points outlined are in fact suggestions. Also despite its title, Rangamani says most of the 10 points outlined in the publication can apply to all caregivers juggling work and caregiving during the pandemic. 

AIMBE’s mission is to recognize excellence in, and advocate for, the fields of medical and biological engineering in order 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 in order to enhance and extend the lives of people all over the world. They have also successfully advocated 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


 

This robot doesn't need any electronics

Walking quadruped is controlled and powered by pressurized air

Photos: http://bit.ly/airwalkerpictures

Feb. 17, 2021--Engineers at the University of California San Diego have created a four-legged soft robot that doesn’t need any electronics to work. The robot only needs a constant source of pressurized air for all its functions, including its controls and locomotion systems. 

The team, led by Michael T. Tolley, a professor of mechanical engineering at the Jacobs School of Engineering at UC San Diego, details its findings in the Feb. 17, 2021 issue of the journal Science Robotics.

“This work represents a fundamental yet significant step towards fully-autonomous, electronics-free walking robots,” said Dylan Drotman, a Ph.D. student in Tolley’s research group and the paper’s first author. 

Applications include low-cost robotics for entertainment, such as toys, and robots that can operate in environments where electronics cannot function, such as MRI machines or mine shafts. Soft robots are of particular interest because they easily adapt to their environment and operate safely near humans. 

Most soft robots are powered by pressurized air and are controlled by electronic circuits. But this approach requires complex components like circuit boards, valves and pumps--often outside the robot’s body. These components, which constitute the robot’s brains and nervous system, are typically bulky and expensive. By contrast, the UC San Diego robot is controlled by a light-weight, low-cost system of pneumatic circuits, made up of tubes and soft valves, onboard the robot itself. The robot can walk on command or in response to signals it senses from the environment. 

“With our approach, you could make a very complex robotic brain,” said Tolley, the study’s senior author. “Our focus here was to make the simplest air-powered nervous system needed to control walking.” 

The robot is controlled by complex pneumatic circuits made up tubes and soft valves and powered by pressurized air. 
More pictures: http://bit.ly/airwalkerpictures

The robot’s computational power roughly mimics mammalian reflexes that are driven by a neural response from the spine rather than the brain. The team was inspired by neural circuits found in animals, called central pattern generators, made of very simple elements that can generate rhythmic patterns to control motions like walking and running.

To mimic the generator’s functions, engineers built a system of valves that act as oscillators, controlling the order in which pressurized air enters air-powered muscles in the robot’s four limbs. Researchers built an innovative component that coordinates the robot’s gait by delaying the injection of air into the robot’s legs. The robot’s gait was inspired by sideneck turtles. 

The robot is also equipped with simple mechanical sensors--little soft bubbles filled with fluid placed at the end of booms protruding from the robot’s body. When the bubbles are depressed, the fluid flips a valve in the robot that causes it to reverse direction. 

The Science Robotics paper builds on  previous work by other research groups that developed oscillators and sensors based on pneumatic valves, and adds the components necessary to achieve high-level functions like walking. 

How it works

The robot is equipped with three valves acting as inverters that cause a high pressure state to spread around the air-powered circuit, with a delay at each inverter.

Each of the robot’s four legs has three degrees of freedom powered by three muscles. The legs are angled downward at 45 degrees and composed of three parallel, connected pneumatic cylindrical chambers with bellows. When a chamber is pressurized, the limb bends in the opposite direction. As a result, the three chambers of each limb provide multi-axis bending required for walking. Researchers paired chambers from each leg diagonally across from one another, simplifying the control problem. 

A soft valve switches the direction of rotation of the limbs between counterclockwise and clockwise. That valve acts as what’s known as a latching double pole, double throw switch--a switch with two inputs and four outputs, so each input has two corresponding outputs it’s connected to. That mechanism is a little like taking two nerves and swapping their connections in the brain. 

Next steps

In the future, researchers want to improve the robot’s gait so it can walk on natural terrains and uneven surfaces. This would allow the robot to navigate over a variety of obstacles. This would require a more sophisticated network of sensors and as a result a more complex pneumatic system. 

The team will also look at how the technology could be used to create robots, which are in part controlled by pneumatic circuits for some functions, such as walking, while traditional electronic circuits handle higher functions. 

This work is supported by the Office of Naval Research, grant numbers N00014-17-1-2062 and N00014-18-1-2277.

Electronics-free pneumatic circuits for controlling soft legged robots

Dylan Drotman, Saurabh Jadhav, David Sharp, Christian Chan and Michael T. Tolley, Department of Mechanical and Aerospace Engineering and Contextual Robotics Institute, UC San Diego


 

Delving into Drool's Droves of Data: Quantifying the Microbial Load in Human Saliva

As anyone who has woken up to a blast of morning breath can attest, the human mouth plays host to a vibrant and diverse blend of microbes. Along with its obvious olfactory output, the oral microbiome impacts the digestive tract, immune system, and nearly every other facet of human health.

The mix of bacteria and fungi that comprise the oral microbiome has been studied extensively, yet the actual quantity has been largely untested. How many microbes are at work in the mouth throughout the day? And what are the potential health ramifications of both understanding and managing the microbial load?

Researchers from the Center for Microbiome Innovation at UC San Diego, led by Clarisse Marotz and corresponding author Karsten Zengler, designed a study to measure not just the composition of the oral microbiome, but the microbial load as well, and how it’s affected by daily activities such as eating and brushing one’s teeth. The results, entitled “Quantifying live microbial load in human saliva samples over time reveals stable composition and dynamic load,” were published in mSystems on February 16, 2021.

"While the proportion of bacteria can be the same, the overall numbers can vary from a few to trillions, showcasing the extreme dynamics of our microbial ecosystems,” according to Marotz. “We wanted to quantify how much microbial load can fluctuate in a healthy, host-associated microbiome over time."

The study was performed by collecting salivary samples from participants at specific intervals throughout the day and cross-referenced against perturbations such as meals and dental hygiene. The samples were measured for flow rate, tested for both microbial load and composition, and treated with propidium monoazide, which enabled tests to assess the mix and mass of active microbes.

By removing relic DNA from dead or inactive cells, the study provided a much clearer picture of how the quantity of living microbes ebbs and flows. “These results highlight the importance of removing dead cell signal in microbiome experiments, especially in longitudinal studies where variations over time can be masked by DNA from dead microbes of previous timepoints,” Marotz remarked when discussing the impact of the findings.

Daily dynamics of the human saliva microbiome. The percentage of live microbial cells collected in unstimulated saliva (for 5 minutes) normalized to the first timepoint; samples were collected throughout the course of a day starting from right after waking to before going to bed.

Based on these results, the team is embarking on further studies to determine how these methods can be adapted to other sample sites and microbiomes within the human body. If current testing methods based on the relative abundance of dead bacteria can be refined to focus on live microbes, researchers hope that this will allow for a deeper understanding of how variations in microbial activity are indicators of both health conditions and the progression of diseases.

Additional co-authors include Perris Navarro, Joanna Coker, Pedro Belda-Ferre, and Rob Knight, all at UC San Diego, as well as James T. Morton at the Simons Foundation.

 

 

 

This piece was written by CMI’s contributing editor Cassidy Symons

New skin patch brings us closer to wearable, all-in-one health monitor

February 15, 2021 -- Engineers at the University of California San Diego have developed a soft, stretchy skin patch that can be worn on the neck to continuously track blood pressure and heart rate while measuring the wearer’s levels of glucose as well as lactate, alcohol or caffeine. It is the first wearable device that monitors cardiovascular signals and multiple biochemical levels in the human body at the same time.

“This type of wearable would be very helpful for people with underlying medical conditions to monitor their own health on a regular basis,” said Lu Yin, a nanoengineering Ph.D. student at UC San Diego and co-first author of the study published Feb. 15 in Nature Biomedical Engineering. “It would also serve as a great tool for remote patient monitoring, especially during the COVID-19 pandemic when people are minimizing in-person visits to the clinic.”

Such a device could benefit individuals managing high blood pressure and diabetes—individuals who are also at high risk of becoming seriously ill with COVID-19. It could also be used to detect the onset of sepsis, which is characterized by a sudden drop in blood pressure accompanied by a rapid rise in lactate level.

Wearable patch on a person's arm
This soft, stretchy patch can monitor the wearer’s blood pressure and biochemical levels at the same time.

One soft skin patch that can do it all would also offer a convenient alternative for patients in intensive care units, including infants in the NICU, who need continuous monitoring of blood pressure and other vital signs. These procedures currently involve inserting catheters deep inside patients’ arteries and tethering patients to multiple hospital monitors.

“The novelty here is that we take completely different sensors and merge them together on a single small platform as small as a stamp,” said Joseph Wang, a professor of nanoengineering at UC San Diego and co-corresponding author of the study. “We can collect so much information with this one wearable and do so in a non-invasive way, without causing discomfort or interruptions to daily activity.”

The new patch is a product of two pioneering efforts in the UC San Diego Center for Wearable Sensors, for which Wang serves as director. Wang’s lab has been developing wearables capable of monitoring multiple signals simultaneously—chemical, physical and electrophysiological—in the body. And in the lab of UC San Diego nanoengineering professor Sheng Xu, researchers have been developing soft, stretchy electronic skin patches that can monitor blood pressure deep inside the body. By joining forces, the researchers created the first flexible, stretchable wearable device that combines chemical sensing (glucose, lactate, alcohol and caffeine) with blood pressure monitoring.

“Each sensor provides a separate picture of a physical or chemical change. Integrating them all in one wearable patch allows us to stitch those different pictures together to get a more comprehensive overview of what’s going on in our bodies,” said Xu, who is also a co-corresponding author of the study.

Patch of all trades

The patch is a thin sheet of stretchy polymers that can conform to the skin. It is equipped with a blood pressure sensor and two chemical sensors—one that measures levels of lactate (a biomarker of physical exertion), caffeine and alcohol in sweat, and another that measures glucose levels in interstitial fluid.

The patch is capable of measuring three parameters at once, one from each sensor: blood pressure, glucose, and either lactate, alcohol or caffeine. “Theoretically, we can detect all of them at the same time, but that would require a different sensor design,” said Yin, who is also a Ph.D. student in Wang’s lab.

The blood pressure sensor sits near the center of the patch. It consists of a set of small ultrasound transducers that are welded to the patch by a conductive ink. A voltage applied to the transducers causes them to send ultrasound waves into the body. When the ultrasound waves bounce off an artery, the sensor detects the echoes and translates the signals into a blood pressure reading.

The chemical sensors are two electrodes that are screen printed on the patch from conductive ink. The electrode that senses lactate, caffeine and alcohol is printed on the right side of the patch; it works by releasing a drug called pilocarpine into the skin to induce sweat and detecting the chemical substances in the sweat. The other electrode, which senses glucose, is printed on the left side; it works by passing a mild electrical current through the skin to release interstitial fluid and measuring the glucose in that fluid.

The researchers were interested in measuring these particular biomarkers because they impact blood pressure. “We chose parameters that would give us a more accurate, more reliable blood pressure measurement,” said co-first author Juliane Sempionatto, a nanoengineering Ph.D. student in Wang’s lab.

“Let’s say you are monitoring your blood pressure, and you see spikes during the day and think that something is wrong. But a biomarker reading could tell you if those spikes were due to an intake of alcohol or caffeine. This combination of sensors can give you that type of information,” she said.

Wearable patch on a person's neck
Wearing the patch on the neck provides optimal readout.

In tests, subjects wore the patch on the neck while performing various combinations of the following tasks: exercising on a stationary bicycle; eating a high-sugar meal; drinking an alcoholic beverage; and drinking a caffeinated beverage. Measurements from the patch closely matched those collected by commercial monitoring devices such as a blood pressure cuff, blood lactate meter, glucometer and breathalyzer. Measurements of the wearers’ caffeine levels were verified with measurements of sweat samples in the lab spiked with caffeine.

Engineering challenges

One of the biggest challenges in making the patch was eliminating interference between the sensors’ signals. To do this, the researchers had to figure out the optimal spacing between the blood pressure sensor and the chemical sensors. They found that one centimeter of spacing did the trick while keeping the device as small as possible.

The researchers also had to figure out how to physically shield the chemical sensors from the blood pressure sensor. The latter normally comes equipped with a liquid ultrasound gel in order to produce clear readings. But the chemical sensors are also equipped with their own hydrogels, and the problem is that if any liquid gel from the blood pressure sensor flows out and makes contact with the other gels, it will cause interference between the sensors. So instead, the researchers used a solid ultrasound gel, which they found works as well as the liquid version but without the leakage.

“Finding the right materials, optimizing the overall layout, integrating the different electronics together in a seamless fashion—these challenges took a lot of time to overcome,” said co-first author Muyang Lin, a nanoengineering Ph.D. student in Xu’s lab. “We are fortunate to have this great collaboration between our lab and Professor Wang’s lab. It has been so fun working together with them on this project.”

Next steps

Wearable patch with cables attached at the bottom
The current prototype of the patch needs to be connected with cables to a benchtop machine and power source.

The team is already at work on a new version of the patch, one with even more sensors. “There are opportunities to monitor other biomarkers associated with various diseases. We are looking to add more clinical value to this device,” Sempionatto said.

Ongoing work also includes shrinking the electronics for the blood pressure sensor. Right now, the sensor needs to be connected to a power source and a benchtop machine to display its readings. The ultimate goal is to put these all on the patch and make everything wireless.

“We want to make a complete system that is fully wearable,” Lin said.

Paper: “An epidermal patch for the simultaneous monitoring of haemodynamic and metabolic biomarkers.”

This research was supported by the UC San Diego Center of Wearable Sensors and the National Institutes of Health (grant no. 1R21EB027303-01A1). 

Engineers earn NASA grant to enable flying taxis

An artist’s conception of an urban air mobility environment. Credit: NASA / Lillian Gipson

February 12, 2021-- Imagine fleets of small aircraft able to vertically take off and land from helipads in urban areas, transporting people to and from work; or shuttles with preset routes flying people to the airport or other major hubs.

This futuristic system of flying taxis and shuttles is one step closer to reality thanks to a team of engineers led by the University of California San Diego. They received a $5.8 million University Leadership Initiative grant from NASA to create computational design tools that will help US companies develop more efficient air taxi designs, faster.

“This project is part of a growing field called urban air mobility, an exciting vision enabling point-to-point, on-demand air travel within densely populated areas,” said John Hwang, professor of mechanical and aerospace engineering at the Jacobs School of Engineering at UC San Diego and principal investigator for the project. “We will combine multidisciplinary computational models of urban air mobility vehicles and advanced design optimization algorithms to develop methods and tools for rapidly designing safe, quiet, and affordable vehicle concepts.”

This three-year project will result in a set of open-source simulation and optimization tools that companies can use to design the optimal electric vertical take off and landing (eVTOL) aircraft for their needs. Given several input parameters such as number of passengers, desired cruise speed, and range requirement, these tools will allow engineers to determine the optimal number and shape of rotors, wing shape, structural design, propulsion system sizing, and other design aspects that yield the most cost-efficient vehicle while ensuring it is safe and operates quietly. In addition, the researchers will use these tools to perform vehicle configuration trade studies on safety, noise, and cost, to help companies make their design decisions.

“Given a computational model, state-of-the-art design optimization algorithms can efficiently search for the optimal values of up to tens of thousands of design parameters that minimize or maximize some specified objective, such as vehicle operating cost," said Hwang. "We will develop models for all aspects of the aircraft – such as aerodynamics, structures, acoustics, battery, and motor performance – and leverage these optimization algorithms to navigate the most complex and unintuitive aspects of the eVTOL aircraft design problem.”

Early roll out of this new class of vehicles is expected within five years, with a market study commissioned by NASA estimating these services will be profitable by the 2030s. In fact, United Airlines and startup Archer Aviation just inked a deal to purchase 200 of these eVTOL aircraft, expected to debut in 2024.

Ultimately, this new kind of transportation – a hybrid between a helicopter, airplane and drone – is intended to save time, while limiting travel-related carbon emissions in urban areas by operating purely on electricity.

“The goal of urban air mobility is to ease traffic congestion and reduce travel times. For example, a 90-minute ground commute to a downtown workplace could be reduced to a 15-minute air taxi flight,” said Hwang.

University Leadership Initiative

The team, led by Hwang, is one of five academic groups that received the University Leadership Initiative (ULI) award from NASA. ULI was created to initiate a new type of interaction between NASA’s Aeronautics Research Mission Directorate and US universities, with academic researchers taking the lead on their own research projects that further NASA’s mission.

In addition to Hwang, the team includes UC San Diego engineers David Kamensky, Alicia Kim, and Shirley Meng. The team also includes Seongkyu Lee from UC Davis; Chris Mi from San Diego State University; Andrew Ning from Brigham Young University; Jeffrey Chambers and Adam Grasch from Aurora Flight Sciences; and Tyler Winter of M4 Engineering. In all, the researchers bring expertise in computational modeling and optimization, topology optimization, batteries, acoustics, electric motors, aerodynamics, composite materials, and concept design.

Key aspects of the ULI include a focus on transitioning the research results to industry or government partners to bring them to market; providing research opportunities for students; and promoting greater diversity in the aeronautics field through increased participation of underrepresented groups in engineering.

This project will have an industry advisory board consisting of both established aircraft companies and eVTOL startups. The team will also institute an aeronautics internship program for students, to enhance and coordinate recruiting and mentoring of undergraduate student researchers across all four universities involved. The internship will be run in partnership with the Academic Enrichment Program at UC San Diego, which has experience managing internship programs for first-generation, low-income and underrepresented students in engineering.

In Memoriam: Juan C. Lasheras, Distinguished Mechanical and Aerospace Engineering Professor

February 9, 2021: Juan C. Lasheras, University of California San Diego distinguished professor of Mechanical and Aerospace Engineering and Bioengineering, passed away on February 1, 2021 after a brief battle with cancer. He was 69 years old.  
 

Juan Lasheras
Juan C. Lasheras

Lasheras was a brilliant scholar, a visionary leader, a supportive mentor, a dedicated educator and a larger-than-life presence in the Department of Mechanical and Aerospace Engineering (MAE) and in the Jacobs School of Engineering. More than that, he was a beloved friend and dear colleague.  

Lasheras was instrumental in founding the Aerospace Engineering program at UC San Diego and in forming the Department of Mechanical and Aerospace Engineering (MAE). In 1999, when the Department of Applied Mechanics and Engineering Sciences (AMES) split into the Department of Mechanical and Aerospace Engineering (MAE) and the Department of Structural Engineering, Juan served as the first Chairman of the new MAE department.  

He was also the founding director of the Center for Medical Devices at UC San Diego, and served as the Interim Dean of Engineering in 2012. Since 2007, he held the Stanford S. and Beverly P. Penner Endowed Chair in Engineering or Applied Sciences.  

Beyond UC San Diego, Lasheras received multiple distinctions and awards. He was a member of the National Academy of Engineering, the National Academy of Inventors, and the Spanish Royal Academy of Engineering. He held honorary doctoral degrees from the Universidad Politécnica de Madrid and from Universidad Carlos III.  

Lasheras was born in Valencia, Spain and spent most of his formative years near Murcia where his father, a mathematician by training, was stationed as a Colonel at the Air Force Academy. At age 18, Lasheras began his studies at the Universidad Politécnica de Madrid in Aeronautical Engineering. However, his academic plans were disrupted at the end of his first year by his father's passing. To provide for his family, he moved back to Murcia and, in the following years, worked as a teacher and director of a preparatory school for air force cadet candidates. During that period, Juan was unable to attend college lectures in Madrid, located 300 miles away, and prepared for course exams using class notes shared by his classmates. Despite these challenges, Juan managed to graduate at the top of his class.  

Upon graduation in 1977, Lasheras secured a Guggenheim fellowship to continue his studies at Princeton University, under the guidance of Professor Irv Glassman, a renowned combustion scientist. It was at Princeton that Lasheras began to develop his skills as a creative experimentalist. He designed a combustion facility from scratch that, for the first time, allowed investigation of the mechanisms for explosive (disruptive) burning of multicomponent and emulsified fuel droplets. His pioneering work caught the attention of the research department at the Shell corporation, which hired him as a Research Scientist in 1981 to direct the combustion group at the Royal Dutch Shell Laboratory in Amsterdam.  

In 1983, Lasheras returned to the US as an Assistant Professor in the Department of Mechanical Engineering at the University of Southern California. In the following years, Lasheras used his experimental skills to investigate a number of fluid dynamics problems related to aerospace propulsion applications. For example, his experiments helped clarify the structure and stability of turbulent mixing layers and jets, as well as the regimes of liquid atomization relevant to the design of rocket engines. It was during his time in Los Angeles that Lasheras met Alexis, whom he married in 1985.  

Already a renowned experimentalist, Lasheras joined UC San Diego as Professor in the AMES Department in 1991. While he maintained an active research program addressing flow problems for engineering applications, he also developed an interest in biomedical applications following the deaths of two of his sisters at an early age. With initial guidance from Professor Shu Chien, Distinguished Professor of Bioengineering and Medicine at UC San Diego, Lasheras was able to build a brilliant career working at the interfaces between mechanics, biology, and medicine in a short time.  

Lasheras' work has led to significant advances in biomechanics. He addressed a wide variety of problems and applications at the macroscopic level, including endovascular techniques to induce and control mild hypothermia, unsteady blood flows and the risk of rupture of aortic and intracranial arterial aneurysms. More recently, his work encompassed cerebrospinal flow in the central nervous system and its role in intrathecal drug delivery procedures. His contributions are equally important at the cellular level, including development of a novel, three-dimensional cell-traction-force microscopy method and clarification of some of the biochemical pathways for the generation of the traction forces exerted by cells during migration. Although his work was driven by a fundamental interest in the underlying physical mechanisms, he always remained a true engineer with an interest in the ultimate applications. He held nearly fifty patents, including one for an endovascular blood-cooling catheter that served as a heat exchanger, the first device approved by the FDA to rapidly cool the body temperature after cardiac arrest to protect the brain from the resulting damage.                                                

The research style of Lasheras combined an outstanding ability to identify relevant problems in need of further understanding and quantification along with a profound knowledge of the key physical and biological elements involved. Mastering the central physical phenomena and describing them in a clear and concise manner, he was able to design insightful experiments that revealed the underlying phenomena with minimum associated complexity. Although an experimentalist by training, he was interested in complex problems that require an interdisciplinary approach. His success was a result of his remarkable ability to form and motivate research teams that included individuals from different disciplines who were able to contribute a wide range of research tools. Juan's exceptional interpersonal and communication skills were key in enabling and promoting the collaborative work of people with completely different backgrounds, successfully facilitating the harmonious interaction of biologists and medical doctors with electrical, mechanical, and aerospace engineers.  

Lasheras was also an exceptional communicator. He was known for his ability to explain very complex ideas in simple terms. In any given laboratory meeting he could explain the different roles of viscous and pressure forces in blood flow to a doctor, and then turn around and explain the physiology of a red cell to an engineer. These communication skills made him an extremely effective and well-liked teacher. Students gave him the highest recommendations, and he was awarded the Teacher of the Year Award by the MAE department on multiple occasions and by the Engineering Division’s Tau Beta Pi Engineering Honor Society. He was always sought by campus colleagues to serve on Academic Senate faculty committees.  

Lasheras was extremely generous with his time. He somehow seemed to have endless hours available for either serious discussion or friendly conversation, and he handled both with ease. He never turned down a request when his help or advice was needed. For many years, he served as Chairman of the Board of Advisors at Universidad Carlos III in Spain, where he helped organize their Bioengineering program, along with his friend Shu Chien. It has become the leading program in the country.

Lasheras was also very active in service to the scientific community, notably as an Associate Editor of the Journal of Fluid Mechanics and as a participant in activities of the American Physical Society (APS) and the National Institutes of Health (NIH). Besides spending time as Secretary/Treasurer of the Division of Fluid Mechanics of APS and later as Chair of that division, Lasheras was a member of the APS Executive Council. He chaired the Organizing Committee for two annual meetings, having previously received the F. Frenkiel Award for Fluid Dynamics from APS and having been elected an APS Fellow. He was also strongly involved in NIH studies and served as a Permanent Member of the Study Section on Modeling and Analysis of Biological Systems for seven years. Lasheras contributed deep consideration and time to these activities, always trying to make sure that what was done would be best for the scientific community.  

Beyond all of his professional accomplishments and accolades, Lasheras was a caring and generous person. He had a profound impact on many students, staff, and faculty at UC San Diego. This legacy is evident in countless anecdotes they shared including certain impactful career advice, his role in bringing them to UC San Diego, and the help that he graciously offered to them or to their relatives regarding personal challenges.  

Outside of work, he was an excellent golfer and a skilled chef. In his cooking, he applied the same creativity he used in the laboratory, always ready to try new recipes. He and Alexis loved to entertain friends, students, and colleagues and hosted many memorable gatherings in their La Jolla home.  

Lasheras leaves an extraordinary academic legacy, not only in his scientific contributions but also in the innumerable graduate and undergraduate students, postdocs and colleagues that have benefitted from his teaching and mentorship.  

He is survived by Alexis, his wife of over 35 years, his siblings, Maruja, Arsenio, and Teresa, and his nephews and nieces, Javier, Carmen, Jose Maria, Arsenio, Luz, Jaime, and Robbie.

Elizabeth H. Simmons
Executive Vice Chancellor

Albert P. Pisano
Dean, Jacobs School of Engineering

George Tynan
Professor and Chair, Department of Mechanical and Aerospace Engineering

Deepfake detectors can be defeated, computer scientists show for the first time

February 8, 2021-- Systems designed to detect deepfakes --videos that manipulate real-life footage via artificial intelligence--can be deceived, computer scientists showed for the first time at the WACV 2021 conference which took place online Jan. 5 to 9, 2021.

Researchers showed detectors can be defeated by inserting inputs called adversarial examples into every video frame. The adversarial examples are slightly manipulated inputs which cause artificial intelligence systems such as machine learning models to make a mistake. In addition, the team showed that the attack still works after videos are compressed.

“Our work shows that attacks on deepfake detectors could be a real-world threat,” said Shehzeen Hussain, a UC San Diego computer engineering Ph.D. student and first co-author on the WACV paper. “More alarmingly, we demonstrate that it’s possible to craft robust adversarial deepfakes in even when an adversary may not be aware of the inner workings of the machine learning model used by the detector.”

In deepfakes, a subject’s face is modified in order to create convincingly realistic footage of events that never actually happened. As a result, typical deepfake detectors focus on the face in videos: first tracking it and then passing on the cropped face data to a neural network that determines whether it is real or fake. For example, eye blinking is not reproduced well in deepfakes, so detectors focus on eye movements as one way to make that determination. State-of-the-art Deepfake detectors rely on machine learning models for identifying fake videos.

The extensive spread of fake videos through social media platforms has raised significant concerns worldwide, particularly hampering the credibility of digital media, the researchers point out. “If the attackers have some knowledge of the detection system, they can design inputs to target the blind spots of the detector and bypass it,” said Paarth Neekhara, the paper’s other first coauthor and a UC San Diego computer science student.

Researchers created an adversarial example for every face in a video frame. But while standard operations such as compressing and resizing video usually remove adversarial examples from an image, these examples are built to withstand these processes. The attack algorithm does this by estimating over a set of input transformations how the model ranks images as real or fake. From there, it uses this estimation to transform images in such a way that the adversarial image remains effective even after compression and decompression.

The modified version of the face is then inserted in all the video frames. The process is then repeated for all frames in the video to create a deepfake video. The attack can also be applied on detectors that operate on entire video frames as opposed to just face crops.

The team declined to release their code so it wouldn’t be used by hostile parties.

High success rate

Researchers tested their attacks in two scenarios: one where the attackers have complete access to the detector model, including the face extraction pipeline and the architecture and parameters of the classification model; and one where attackers can only query the machine learning model to figure out the probabilities of a frame being classified as real or fake. In the first scenario, the attack's success rate is above 99 percent for uncompressed videos. For compressed videos, it was 84.96 percent. In the second scenario, the success rate was 86.43 percent for uncompressed and 78.33 percent for compressed videos. This is the first work which demonstrates successful attacks on state-of-the-art Deepfake detectors.

“To use these deepfake detectors in practice, we argue that it is essential to evaluate them against an adaptive adversary who is aware of these defenses and is intentionally trying to foil these defenses,” the researchers write. “We show that the current state of the art methods for deepfake detection can be easily bypassed if the adversary has complete or even partial knowledge of the detector.”

To improve detectors, researchers recommend an approach similar to what is known as adversarial training: during training, an adaptive adversary continues to generate new deepfakes that can bypass the current state of the art detector; and the detector continues improving in order to detect the new deepfakes.

Adversarial Deepfakes: Evaluating Vulnerability of Deepfake Detectors to Adversarial Examples

*Shehzeen Hussain, Malhar Jere, Farinaz Koushanfar, Department of Electrical and Computer Engineering, UC San Diego

Paarth Neekhara,  Julian McAuley, Department of Computer Science and Engineering, UC San Diego


 

Music and computer science professor studies the sounds of COVID

Researchers analyze coughs, vocal utterances to detect COVID-19 infection

UC San Diego music and computer science professor Shlomo Dubnov

February 5, 2021-- Millions of people already use Fitbit and other devices to monitor and track a variety of personal health metrics. Now, a researcher at the University of California San Diego has published data indicating that analyzing voice signals can detect COVID-19 infection when compared with sample audio clips from healthy speakers.

In a research paper on “Robust Detection of COVID-19 in Cough Sounds,” published in the February 2021 issue of Springer Nature’s SN Computer Science journal, UC San Diego music and computer science professor Shlomo Dubnov and colleagues spell out initial results of their work analyzing samples of coughs and utterances from patients diagnosed with the SARS-Cov2 virus against a control group of healthy subjects.

“This work displays high potential for evaluating and automatically detecting COVID-19 from web-based audio samples of an individual’s coughs and vocalizations,” said Dubnov, who co-authored the paper with Lebanese American University professor Pauline Mouawad and recent Jacobs School of Engineering alumnus Tammuz Dubnov. “We showed the robustness of our method in detecting COVID-19 in cough sounds with an overall mean accuracy of 97 percent.” With samples of the sustained vowel sound ’ah’, the accuracy was 99 percent.

“Now we’re kind of hopeful that some of this will be useful for actual applications,” add the paper’s senior author.

The project originated in a master’s thesis by Dubnov’s son Tammuz, who completed his M.S. degree in engineering sciences in UC San Diego’s Mechanical and Aerospace Engineering department in 2020. His topic: “Signal Analysis and Classification of Audio Samples from Individuals Diagnosed with COVID-19”.  Tammuz completed his degree while running a startup, Zuzor, which he founded in 2015.

“My thesis was using artificial intelligence and audio, then COVID happened,” recalls the UC San Diego alumnus. “So that was kind of the genesis of it. I was already doing a lot of work in deep learning, and I was already doing a lot of machine learning before that.  So I wondered: how we could we use this maybe to diagnose something?”

After completing his thesis, Tammuz wanted to continue the research and approached his father at UC San Diego, who was also focused on machine learning and audio – but for different applications. “I've been working on voice or musical instrument sounds, but also on singing and spoken voice,” said Dubnov, a longtime participant in the Qualcomm Institute at UC San Diego. “We're talking pretty much about sound texture, of the little details of sound, the repetition of small sound elements. We had these techniques as part of our research toolkit, so it was sort of a leap of faith to see if we could actually discriminate between COVID and non COVID.”

The machine-learning models developed for the study were “trained” on data (self-submitted audio samples) collected by the Corona Voice Detect project, a partnership between Carnegie Mellon University and the Israel-based company Voca.ai. The recordings contained audio of each individual coughing three times and then uttering the sustained vowel “ah”.

The researchers applied a combined method from nonlinear dynamics to detect COVID-19 in vocal signals – offering a reliability that could also allow detection at an earlier stage. “The robust results of our model have the potential to substantially aid in the early detection of the disease on the onset of seemingly harmless coughs,” said professor Dubnov.

The researchers insist that their model is not intended for independently diagnosing COVID-19. “I wouldn't rely on an AI to diagnose or not diagnose,” insisted Tammuz. “We're hoping more to position it like an early warning system for doctors.”

Shlomo Dubnov agrees. “It would hopefully help physicians decide whether standard tests may be necessary for a diagnosis,” he said. “It also offers a non-invasive way to do surveillance testing at the population level, including analyzing vocal sounds from microphone arrays in public spaces.”

Example of graphical sound 'fingerprints' indicating a COVID-19-related dry cough.

“COVID is a terrible respiratory disease that we're all facing now, but I'm optimistic that the vaccine will work and COVID will hopefully be a thing of the past,” said Tammuz. “But as part of this project, I ended up talking to a lot of doctors and maybe the bright side of all this is that this technology can be used for other diseases.”

Indeed, there are audio signatures associated with a broad array of medical conditions, ranging from asthma and chronic obstructive pulmonary disease to bronchitis, tuberculosis and congestive heart failure. “We have a whole list of diseases that it could be beneficial for,” he explained. “So that's kind of the commercial opportunity here.”

Professor Dubnov is now teaming with his son’s software company Zuzor on a joint proposal for a Small Business Innovation Research (SBIR) seed grant from the National Science Foundation. Their goal: to aggregate much larger datasets related to different diseases – data they will need in order to train models to do much deeper feature extraction that, for instance, would allow them to differentiate cough sounds across many different diseases.

Said Zuzor’s Tammuz Dubnov: “There are diseases that have a huge impact on many, many lives, so if we can help even a little bit with that, that could have really big implications.”

Lightening the data center energy load

UC San Diego engineers earn ARPA grant to enable efficiency through photonics

A proof-of-concept setup for an optically switched network. Photo by David Baillot

February 3, 2021-- Electrical engineers and computer scientists at UC San Diego are on the front lines of global efforts to reduce the energy used by data centers. The potential impact is great: the US government estimates that data centers currently consume more than 2.5% of U.S. electricity. This figure is projected to double in about eight years due to the expected growth in data traffic. 

The UC San Diego Jacobs School of Engineering team has been awarded a total of $7.5 million from the US Advanced Research Projects Agency-Energy (ARPA-E) and the California Energy Commission to advance nation-wide efforts to double data center energy efficiency in the next decade through deployment of new photonic— light based—network topologies. 

In particular, the UC San Diego team is focused on developing solutions to enable the thousands of computer servers within a data center to communicate with each other over advanced light and laser-based networks that replace existing electrical switches with optical switches developed within the ARPA-E program. 

“The photonic devices we’re developing aren’t actually used within the servers per se: instead, the devices connect the servers within the datacenter network using a more efficient optical  network,” said George Papen, a professor of electrical and computer engineering at UC San Diego and co-principal investigator on the project. 

“By removing bottlenecks in the network, the computer servers, which account for the majority of power in the data center, operate more efficiently. Our project, supported by ARPA-E, aims to double the server power efficiency by transforming the network into a high-speed interconnect free of these bottlenecks,” said George Porter, a professor of computer science at UC San Diego and co-principal investigator.

What’s an optical switch?

So how do these data center networks pass bits of information and computation commands around today? They use a technology called electrical packet switching, in which a message is broken down into smaller groups, or packets of data. These packets of data are converted to electrical signals and sent through a cable to a network switch, where they’re routed to the desired location and pieced back together into the original message. Network switches are physical, electrical devices with ports for wired connections, that direct the flow of data from many machines.

Unlike electronic switches, optical switches aren’t bound by the limitations of electronics to transmit data. Instead, optical switches make direct “light path” connections from input ports to output ports. Since no conversion between optical and electrical data is required at every switch, optical switches don’t have the latency or electronic logjam issues that existing network switches have, and require less power to route data. 

Using an optical network instead of an electrical network can produce a more efficient network with a larger data rate to each server. This can increase the energy efficiency of the servers, which consume most of the energy in a data center. One goal of the project is to demonstrate that the cost of such an optical network can drop below the cost of adding the additional semiconductor chips required to get the same data rate on existing electrical networks. 

“It would be lower cost in part because you’re using less energy, but also in part because if you wanted to build a very high speed network using existing commercial technology, the cost of adding additional chips to build bigger switches increases dramatically,” said Porter. “It’s not a linear relationship of double-the-speed for double-the-money; you can think of it almost like double the speed for quadruple the cost. On the other hand, optics, at these very high speeds, follows a more linear cost relationship.”

Developing a proof-of-concept

In phase one of the Lightwave Energy Efficient Datacenters (LEED)  project in the  ARPA-E Enlitened program, which ran from 2017-2019, Papen, Porter and UC San Diego colleagues Joe Ford, a professor in the Department of Electrical and Computer Engineering, and Alex Snoeren, a professor in the Department of Computer Science and Engineering, developed the photonic technology and network architecture required to enable this scale of optical switching. The collaboration between electrical engineers—who designed a new type of optical switch—and computer scientists—who developed the protocol to allow it to work at a data center scale—was key. 

Their success hinged on a new type of optical switch conceptualized by UC San Diego alumnus Max Mellette, co-founder and CEO of spinout company inFocus Networks. Instead of the full crossbar architecture that was previously used, which allows any node in the data center to talk to any other node, his idea was to create a switch that had more limited connectivity, thereby enabling faster speeds.

The key insight was to develop a network protocol that would enable this faster but less-connected architecture to communicate in a way that would still deliver the performance required. By working closely with computer scientists led by Porter and Snoeren, the team made it happen. 

By the end of Phase 1, this new optical switch was functional, able to run applications and receive data in a testbed setting. Now in Phase 2, the team is working with collaborators at Sandia National Laboratories on scaling up the architecture to function with larger amounts of data and more nodes. The goal for Phase 2 is a realistic testbed demonstration that an optical network architecture provides significant value to end-users. 

A storied history of photonics

There was a good reason this UC San Diego team was selected for the Enlitened program: it was here that, more than a decade ago, then-postdoc Porter was part of a research team also including Papen, that assembled and demonstrated the first data center testbed using an optically switched network. The paper describing this work has been cited more than 1,000 times.

Since then, Porter, Papen, Ford, Snoeren and colleagues in both the electrical engineering and computer science departments and the Center for Networked Systems have worked closely to further develop and refine the technology, and work towards making it a commercially viable reality. 

“We were the first to show we could build testbeds with optically switched networks for data centers,” Porter said. “Papen and I have been meeting multiple times a week for 10 years, supervising students together, and working on this optical data center concept for a decade; it’s a real example of what can happen when computer scientists and electrical engineers work closely together.” 

While their optical data center is still in the proof-of-concept phase, researchers agree there will come a time when the cost of adding more and more semiconductor chips to drive faster speeds simply won’t be cost competitive, putting aside the energy concerns. At that point, optical systems will become much more appealing. It’s hard to know when exactly that will be, but researchers predict it could be as soon as five years from now, and likely within 10. 

“Nonetheless, there's so much work to do to be able to validate that indeed if we can’t continually scale chips, what applications should we first apply optical switching? That will take a significant effort to sort  out,” Papen said. The researchers are working with national labs and private companies to test optical switches on various live applications to help answer this question.

Difficult, future-looking work such as this optical data center project is a perfect example of the role academic research institutions play in the innovation ecosystem.

“This is a really hard problem to solve, and hard problems take a long time,” Papen said. “Being able to devote the time to this, and collaborate with faculty and students from across the entire engineering school, is what makes this type of transformative development possible.”

Islands without structure inside metal alloys could lead to tougher materials for transportation, energy and defense

January 29, 2021: An international team of researchers produced islands of amorphous, non-crystalline material inside a class of new metal alloys known as high-entropy alloys. 

This discovery opens the door to applications in everything from landing gears, to pipelines, to automobiles. The new materials could make these lighter, safer, and more energy efficient.  

The team, which includes researchers from the University of California San Diego and Berkeley, as well as Carnegie Mellon University and University of Oxford, details their findings in the Jan. 29 issue of Science Advances. 

“These present a bright potential for increased strength and toughness since metallic glasses (amorphous metals) have a strength that is vastly superior to that of crystalline metals and alloys,” said Marc Meyers, a professor in the Department of Mechanical and Aerospace Engineering at UC San Diego, and the paper’ s corresponding author. 

Using transmission electron microscopy, which can identify the arrangement of atoms, the researchers concluded that this amorphization is triggered by extreme deformation at high velocities. It is a new deformation mechanism that can increase the strength and toughness of these high entropy alloys even further.

Proposed hierarchical deformation mechanism paradigm for the equi- atomic CrCoNi-based HEAs subjected to increasing degrees of deformation.

The research is based on seminal work by Brian Cantor at the University of Oxford, and Jien-Wei Yeh at National Tsing Hua University in Taiwan. In 2004, both researchers led teams that reported the discovery of high-entropy alloys. This triggered a global search for new materials in the same class, driven by numerous potential applications in the transportation, energy, and defense industries.

 “Significant new developments and discoveries in metal alloys are quite rare,” Meyers said. 

Amorphization in extreme deformation of the CrMnFeCoNi high-entropy alloy

Shiteng Zhao and Robert O. Ritchie, University of California Berkeley; Zezhou Li, Wen Yang and Marc A. Meyers, University of California San Diego; Chaoyi Zhu, Carnegie Mellon University; Zhouran Zhang, David E. J. Armstrong and Patrick S. Grant, University of Oxford.  


 

Women in STEM: Picture a Scientist

Bioengineering Diversity Council's Town Hall addresses issues of gender parity

January 29, 2021: Women from all different stages of their scientific careers, from undergraduate students through the UC San Diego Vice Chancellor for Research, met virtually to share their experiences as women in STEM for the UC San Diego Bioengineering Diversity Council’s Winter Quarter Town Hall. Stephanie Fraley, professor of bioengineering and chair of the Bioengineering Diversity Council, mediated a discussion among six panelists addressing topics from the film “Picture a Scientist,” including gendered harassment and discrimination. 

In addition to Fraley, the panelists included Sandra Brown, UC San Diego Vice Chancellor for Research; Dr. Sangeeta Bhatia, professor of engineering at MIT and director of the Marble Center for Cancer Nanomedicine at MIT; Daniela Valdez-Jasso, a professor of bioengineering at UC San Diego; Maya Rowell, a bioengineering PhD student and a Jacobs School Racial Equity Fellow; and Rafaela Simoes-Torigoe, a bioengineering undergraduate student. 

During the discussion, the panelists shared their experiences navigating the “minority time tax,” developing a work-life balance, setting boundaries for the diversity-promoting efforts they’re asked to participate in, and addressing the outright bullying and stereotyping they’ve witnessed. The group also shared some actionable steps to create a truly inclusive research community. 

Read a thorough recap of the discussion here. 

The UC San Diego Bioengineering Diversity Council promotes the interests and advancement of women and minorities in the bioengineering department at the Jacobs School of Engineering. 

A call to end funding discrimination against Black scientists in the United States

Network of female biomedical engineering researchers issues call to action in Cell

Karen Christman, one of the paper's co-authors, is an associate dean at the Jacobs School and a professor in the UC San Diego Department of Bioengineering.

January 26, 2021: Representatives from a network of women deans, chairs and distinguished faculty in biomedical engineering are calling upon the National Institutes of Health and other funding agencies to address disparities in allocating support to Black researchers.  The group made the call to action in the Jan. 26, 2021 issue of the journal Cell

Two engineering faculty at the University of California San Diego are coauthors: Karen Christman, associate dean at the Jacobs School of Engineering and bioengineering professor, and Padmini Rangamani, professor of mechanical and aerospace engineering. 

In examining the racial inequities and injustices that prevent Black faculty from equitably contributing to science and achieving their full potential, insufficient federal funding for research by Black scientists rose to the top as a key issue. 

According to studies of the allocation of National Institutes of Health research funding,  Black applicant award rates for research funding has stood at about 55 percent of that of white principal investigators of similar academic achievement.  Despite internal reviews of the reasons behind this disparity, and promises to do better, the funding gap continues. 

Efforts have been made to improve the pipeline to encourage Black students to prepare for and enter careers as researchers and college and university faculty. But once on the job, lack of research funding can derail these careers.  Many universities look to faculty members’ ability to support their research as part of their decisions on tenure and promotions. As a result, NIH funding disparity can end the careers of Black scientists.  In addition, without adequate research funding, these scientists can become discouraged and leave their professions.  

 

This means that fewer Black scientists remain to serve as role models and mentors for the next generation.  It also means that many important research questions vital to society are not being asked, because the perspectives, creativity, and knowledge of a diverse population of scientists are not being tapped. The public also does not see the faces or hear the voices of Black scientific experts speaking on vital issues.  

The authors of the paper make several recommendations on how research funding disparities can be eliminated.  Among the steps funding agencies might take are:

Explicitly state that racism persists in the U.S. research enterprise and that it must be expelled

Develop federal funding institute policies to immediately achieve racial funding equity

Incorporate diversity into research proposal scoring criteria; prioritize research teams that exemplify diversity; and diversify proposal review panels

Train funding agency leadership and staff as well as grant reviewers and recipients, to recognize and stop racism

“Scientific colleagues, let us each use our voices and actions to now overcome our profession’s racism and serve as antiracist agents of change,” the researchers wrote in Cell. 

They recommended ways  individual scientists and universities, colleges and institutes can move forward.  These recommendations include recognizing how they might be unintentionally contributing to systemic racism in their academic roles.  Academia, they write, must also move forward from statements of solidarity to transformative organizational changes.

In closing, the authors also look to the private sector, such as philanthropists and industrial leaders whose companies depend on scientific innovation, and to foundations and professional societies, to help offset racial disparities in research funding. The biotech company Genentech is held up as an example of leadership in reducing racial disparities in science, with its creation of a research funding awards program for Black scientists. 

Together, private and public sectors can enhance the creativity and innovation of their science and bring forward the greater good of society by funding innovative ideas and robust talents of Black scientists.

The corresponding authors on the paper, “Fund Black Scientists,” are senior author Omolola Eniola-Adefeso, the University Diversity and Social Transformation Professor of Chemical Engineering at the University of Michigan, and lead author Kelly R. Stevens, Assistant Professor of Bioengineering and Laboratory Medicine and Pathology at the University of Washington School of Medicine and UW College of Engineering.  Stevens also is an investigator at the UW Medicine Institute for Stem Cell and Regenerative Medicine. 

Other engineering faculty researchers co-authoring the paper are: Kristyn S. Masters University of Wisconsin-Madison; Princess Imoukhuede and Lori A. Setton, Washington University St. Louis; Karmella A. Haynes, Emory University; Elizabeth Cosgriff-Hernandes and Shelly Sakiyama-Elbert, University of Texas at Austin; Muyinatu A. Lediju Bell, Johns Hopkins University; Padmini Rangamani and Karen Christman, University of California San Diego; Stacey Finley, University of Southern California;  Rebecca Willits and Abigail N. Koppes, Northeastern University; Naomi Chesler, University of California-Irvine; Josephine Allen, University of Florida, Gainesville; Joyce N. Wong, Boston University; Hana El-Samad and Tejal Desai, University of California San Francisco also contributed to the Cell paper. 

 

 


 

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Sourcing Viral Surveillance Supplies at the Pharmacy: Understanding Consumer-Grade Materials' Viability as SARS-CoV-2 Testing Media

As the COVID-19 pandemic grew and quickly took hold of the world, one of the biggest challenges in the response efforts was determining the most effective approach to monitoring the virus’s spread. That task has become all the more critical as regional and national governments have been tasked with balancing the protection of public health against the reality that society is ill-equipped to handle a prolonged shutdown.

Even as rapid research led to more efficient testing methods, early efforts to detect SARS-CoV-2 - the virus that causes COVID-19 - were hampered by a lack of available materials approved by public health agencies such as the CDC and WHO. Questions quickly arose as to whether more widely available sampling supplies were viable alternatives.

To address these questions, a team of researchers at the Center for Microbiome Innovation at UC San Diego set out to determine whether consumer-grade materials were a safe replacement, as well as testing whether alternative storage solutions were viable options for preserving and transporting samples. Their findings, titled “Feasibility of using alternative swabs and storage solutions for paired SARS-CoV-2 detection and microbiome analysis in the hospital environment,” were published in Microbiome Journal on January 22, 2021.

"One of the main problems at the beginning of the pandemic in the US was supply chain shortages. Since medical- and research-grade swabs are used for sample collection during testing, we wanted to determine if consumer-grade swabs were a possible option for COVID-19 screening and testing," according to Jeremiah J Minich of the Scripps Institute of Oceanography at UC San Diego, one of the paper's lead authors.

The study approached this problem by performing a series of viral detection experiments using five different consumer-grade swabs composed of varying materials, as well as one CDC-approved swab as a control. All of the swabs were then placed in 95% ethanol and evaluated in terms of RNase activity.

Prior to this study, it was generally believed that consumer-grade swabs would contain too many contaminants to serve as sampling materials effectively. "However, our work showed that, at least in the case of SARS-CoV-2 detection, wooden-shafted and cotton-tipped swabs are suitable, provided the material is extracted from the swab head itself rather than relying on the material to be present in the surrounding fluid which is typically assessed for viral presence" noted corresponding author Austin D. Swafford, Director of Research-Innovations at the Center for Microbiome Innovation.

These findings are a boon to government and health agencies in their work to safely reopen educational and economic sectors of society. The ability to monitor the built environment for the virus using readily available materials allows for orders of magnitude more testing than previously thought.

"As we continue our efforts to monitor the environment for SARS-CoV-2 in public settings such as our hospitals, campus, and K-12 schools, we seek to provide a path to scalable, affordable monitoring. Consumer-grade surface swabs will enable a wider range of applications where the deployment of clinical-grade materials is not economically feasible," said co-author Rob Knight, professor and director of the Center for Microbiome Innovation at UC San Diego. Those efforts are expected to pay dividends quickly via UC San Diego’s Safer at School Early Alert (SASEA) program. SASEA will soon be utilizing inexpensive and readily available surface detection methods - informed largely by this study’s results - to help provide a safe path for San Diego-area students to return to their classrooms.

Comparison of CDC-approved SYN swabs, consumer-grade CGp, and bulk TMI swab congruence compared to clinical-grade hospital tests using synthetic-tipped plastic-shafted NP swabs for twenty participants in the clinical setting. a SARS-CoV-2-positive patients (n = 16) sampled with three swab types across three environments: nares, floor, and bedrail. “+” samples (dark grey = SYN, red = CGp, blue = TMI) refer to samples which tested positive for SARS-CoV-2 out of the total samples tested for that particular swab type (light-grey bar). Percentage of positive tests per swab type are below the x axis for each environmental sample. b SARS-CoV-2-negative patients (n = 4) with three swab types across three environments: nares, floor, and bedrail.

While the paper’s findings have wide-ranging implications, the benefits of deploying consumer-grade supplies to detect the virus are particularly significant in developing nations, where supply chain shortages presented even greater logistical challenges. Dr. Miguel Angel Garcia Bereguiain, of Universidad de Las Americas in Quito, Ecuador, noted the implications for his nation’s response to the pandemic. "Ecuador has experienced supply shortages at different levels of SARS-CoV-2 diagnosis, from swabs to PCR kits. During the swab shortage, public health authorities could have asked local producers to provide cotton swabs to avoid diagnosis disruption," he commented. "With this new information available, hopefully in the coming future, this problem will be avoided."

Following this research, there are further ongoing studies centered upon expanding and refining the ability to detect SARS-CoV-2 in the built environment as a means of reducing the pandemic’s spread, as well as better informing the response to future viral threats. “Hopefully, the lessons we've learned here can help set the stage for a more rapid, affordable, and widespread, perhaps citizen-scientist accessible, response to monitoring and combating current and future outbreaks,” Swafford added when discussing the study’s conclusions.

Additional co-authors include Farhana Ali, Clarisse Marotz, Pedro Belda-Ferre, Leslie Chiang, Justin P. Shaffer, Carolina S. Carpenter, Daniel McDonald, Jack Gilbert, Sarah M. Allard, Eric E Allen, and Daniel A. Sweeney, all at UC San Diego.

 This piece was written by CMI’s contributing editor Cassidy Symons

IMDD Seminar: The Innovation Ecosystem at UC San Diego

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Ten suggestions for female faculty and staff during the pandemic

Padmini Rangamani, a professor in the Department of Mechanical and Aerospace Engineering, is a coauthor of an article in PLOS Computational Biology giving tips for working women to navigate the pandemic. 

File photo from 2014

January 21, 2021: When university campuses sent students, staff and faculty members home in March, Padmini Rangamani, a professor at the University of California San Diego, suddenly found herself running her research lab remotely, teaching her classes online, and supervising her two children, ages 10 and 13, who are also learning online. 

To deal with the stress the situation created, Rangamani turned to a support network of fellow female faculty members around the United States. They chatted and texted and eventually decided to write a scholarly article with recommendations for all other female principal investigators in academia. 

The article, “Ten simple rules for women principal investigators during a pandemic,” was published recently in PLOS Computational Biology.  It’s perhaps important to note that despite its title, the article is careful to say that the cardinal rule is that there are no rules. So all 10 points outlined are in fact suggestions. Also despite its title, Rangamani says most of the 10 points outlined in the publication can apply to all caregivers juggling work and caregiving during the pandemic. 

“Without in-person school or daycare, and without after-school programs, there is really no way for caregivers to function at full capacity at work,” Rangamani said. 

In addition,  such concerns have not been discussed openly in the workplace, the authors felt. Their real fear is then that talent nurtured through the years will be lost in one fell swoop--and  their main goal is to try and change this. Rangamani and fellow co-authors want to normalize conversations about juggling work and family obligations. “If you want to say ‘I can’t meet at this time, because I need to be on a Zoom with my kids, that doesn’t mean you’re not serious about your job or not doing your job well,” she said. “We want to reduce this perception bias.”

This is particularly important to maintain equity and diversity within an organization, Rangamani added. “We need to be extremely vigilant to ensure that those who are particularly vulnerable do not exit the system,” she said. Single parents, those who are taking care of elderly parents and relatives, and parents whose children have special services are especially at risk, she added. “The intense pressure of being ‘on’ all the time is simply not realizable right now.” 

While the paper outlines some changes that can be made at a campus-wide or even university system level, Rangamani is focused on a smaller scale: an office or a department for example. It is much easier to get these smaller groups together and have genuine conversations about what the individual needs are and what can be done to get our colleagues through this intensely difficult period without sacrificing quality or fairness.. “There are measures you can take at the grassroots level,” she said. 

In order to normalize these conversations about work-life balance Rangamani hopes that leadership will empower those who hesitate to ask for help to do so. 

Here are the 10 suggestions that the paper outlines to cope during the pandemic: 

  1. Find a peer group of women to provide professional support.
    “The authors are all members of an online group for women PIs in biomedical engineering, which has historically served as a sounding board for professional concerns. We have found that maintaining these connections has been essential over the course of our careers and are even more important during this quarantine period.”
  2. Say no to requests to do anything outside of your main responsibilities
    “If you can’t do them now, you can offer a time when you might be able to do them; the requesting party will need to recognize that your future schedule could go through upheaval as surges of the disease hit different areas and restrictions change. “
  3. Drop something
    “True, your house might not be as clean as you would like, and you may be eating more frozen pizza than you normally would tolerate. Remember that you are not the only person accepting this as your “new normal.” We can’t forget that the goal during a pandemic is survival—if you are keeping yourself physically and mentally healthy, you are more than succeeding.”
  4. When you have energy to do more than the minimum, use it to support women and underrepresented groups
    “We recognize that advocacy of this nature is a privilege, and not everyone is able to do so safely. If you are in the position to support women and underrepresented groups and have the energy, pick a cause and lean into it. Also, recognize that this action can take many forms, some of which may be a better fit for your individual situation.”
  5. Remember, you know yourself best
    “You know the things that have historically helped you relieve stress. Make a list of 10 of them. Some of them may not be an option during quarantine (oh, how some of us miss writing in coffee shops). But for those that are an option, try to do 1 of them every now and then.”
  6. It’s OK to push back
    “Perpetuating the myth that we can all work to the same degree (or better!) than we did a few months ago is very damaging to many women PIs. When you hear statements such as “everyone is writing more grants now” and “since we have more time, let’s have a virtual conference about this topic,” it’s more than OK to push back that this is not your reality, regardless of the reason.”
  7. Remember, you have some flexibility to make your own schedule
    “If there are pockets of time where you find yourself able to focus better than others, do your best to protect them. Block these times on your calendar—both in the near future and in the upcoming months by declining invitations for extraneous responsibilities.”
  8. Whatever help you can get, take it
    “Perhaps your kids are old enough that they can even help with some of your work—1 of the authors tried (unsuccessfully) to engage her son in doing analysis on ImageJ (NIH, Bethesda, Maryland). Another purchased a 3D printer and recruited her daughter to help print parts for an OpenSPIM setup.”
  9. Do your best to remember that others are struggling too—be empathetic and work to build a community
    “We suggest that each situation is approached with empathy, while maintaining your standards and accountability. For example, empathy may mean that when you assign a task to a group member or staff, you ask them whether the timeline is feasible. If it’s not, that may be a sign that in the future you should aim to give them more advance notice. If a pattern of not completing work continues, it is then time to ask for an explanation. Recognize that just as no one is fully aware of your situation, you are not completely aware of your colleague’s situation.” 
  10. Don’t lose your sense of humor
    “We know, there is nothing funny about this situation. Many of us have needed or will need space to grieve deeply. However, our experience is that where you can share a laugh, you should.”

 Rangamani herself does her best to implement some of these suggestions. She prioritizes the well-being of her own research group over other zoom meetings; protects her research time; and does not schedule meetings at lunch time, if she can help it.

“While there is a light at the end of the tunnel in the form of vaccines,” Rangamani also notes, “this global health crisis may be a once-in-a-lifetime opportunity for the academy to take a close look at how we can empower our vulnerable colleagues and make policy changes to change our culture for the better.”

The authors put rule, or rather suggestion, 10 in practice, by including a list of humorous rules and tips in a supplemental file.

“Service expectations are now completely fulfilled by raising scientifically literate humans of our own and science communication by way of family conversations, Facebook and Twitter debates,” they write. 




 

UC San Diego Alumnus at Helm of Company Behind First At-Home COVID Test

Erik Engelson, a UC San Diego bioengineering and microbiology alumnus, is president and CEO of Lucira Health.

January 21, 2021: In November 2020, Lucira Health received emergency use authorization for the first rapid at-home COVID-19 test from the U.S. Food and Drug Administration. Erik Engelson, a UC San Diego bioengineering and microbiology alumnus, is president and CEO of Lucira Health, which was founded by UC Berkeley bioengineering alumni.

The Lucira COVID-19 All-In-One Test Kit is a molecular test that uses a simple nasal swab to return results in 30 minutes, anywhere, any time. The test is currently available by prescription in select medical centers. Engelson describes the test as a key tool, along with vaccines, in the arsenal required to slow the spread of COVID-19.

The test uses a real-time loop mediated amplification reaction, and works by swirling the self-collected sample swab in a vial that is then placed in the test unit. In 30 minutes or less, the results can be read directly from the test unit’s light-up display. The Lucira test is simple to operate and is completely self-contained for one-time use. Its accuracy is similar to that of PCR tests that are run in high-complexity central labs.

Engelson earned a bachelor’s degree in microbiology and a master’s in bioengineering from UC San Diego. He has led several medical device startups through to acquisition by companies including Medtronic and Stryker, was a partner at medical device incubator The Foundry, and is a venture partner at ShangBay Capital, to name a few career highlights.

He spoke about the process of getting the COVID-19 test kit through FDA emergency use authorization, his time at UC San Diego, and advice for students, in this Q&A.

Q: Lucira had been working on at-home test kits before COVID-19; what was the initial use case for this product?

A: The company was started in 2013, and I joined about two years ago. The original use case was for influenza. Just as central lab testing was extended to point-of-care (POC), Lucira’s technology is now extending POC to anytime/anywhere testing. From a public health standpoint, it is helpful to keep infectious individuals out of circulation. But how is one to know they are infectious if they can’t test themselves at home? With influenza for example, antiviral medications are generally effective only if taken within 48 hours of symptom onset. Many people don’t go to the doctor at all for flu, and when they do, it’s typically three to five days post-symptom onset, and by then it’s too late for an antiviral. As a result, it would be helpful both to individuals as well as the public health to be able to diagnose flu and other infectious diseases at home.

Q: When you and the Lucira team saw the COVID-19 pandemic developing, was there a decision to pivot and rapidly develop a test for this virus instead?

A: There was a pivot. Fortunately, the Lucira test platform is easily adapted to new assays (tests). Within months, our assay team demonstrated that they had developed an effective COVID-19 assay. This was then integrated into our test platform. Meanwhile, the pandemic was continuing, and the decision to prioritize the COVID-19 test was an easy one.

Q: What were some of the main challenges from an engineering and management perspective to getting the COVID-19 at-home test to and through FDA EUA?

A: I give the technical team huge kudos for the work they did in realizing the vision of transforming a central lab molecular diagnostic that runs on large machines, to a tiny, fully disposable handheld device. Significant thoughtfulness by the engineers and biologists who developed this product went into the design. My role was to build an experienced team of other important functions, including commercialization, clinical/regulatory, finance manufacturing/supply chain and quality, around the technical team. I also brought in additional capital. The transition from technology development to a commercial stage company can be challenging, but the risk can be reduced with an experienced team.

Because our test is intended to eventually be a consumer product, it was critical to not only have strong clinical and bench performance, but also to demonstrate that people of all backgrounds could successfully run the Lucira test from its simple, one-page instruction. This is known as usability testing, and significant effort went into creating easy-to-understand instructions along with a simple-to-use test.

Q: Looking back, were there any formative courses, research experiences, or student organizations from your time at UC San Diego that helped prepare you for this experience of rushing a product to FDA EUA in the middle of a pandemic?

A: Originally a New Yorker, my time both at UC San Diego as well as in La Jolla in general in earlier, quieter days was wonderful. UC San Diego was transformative for me in so many ways: socially, academically. I was lucky to find a perfect academic challenge. My biggest takeaways from the UC San Diego experience were a joy of learning and seeing the beginnings of what I was capable of accomplishing. These attributes remain with me today.

I studied microbiology as an undergrad followed by bioengineering in graduate school. The lab research was interesting, but I craved business. It was really the intersection of business and technology that interested me. It’s important to understand that every technical decision within a company also has a business element. How can engineers and scientists make these decisions if they don’t receive accounting and finance at a minimum? I am delighted that the Rady School of Management is there now, and the Institute for the Global Entrepreneur, the Basement, all these new programs to give students exposure to business and entrepreneurship. I would have loved to have taken business classes in my UC San Diego days—how great if current science and engineering students have this opportunity.

Q: Advice for students who want to work in the biotech industry or aspire to a role such as yours?

A: If there’s a chance of doing an internship for the summer in a company, that can be helpful and illuminating. And I would suggest that students take it upon themselves to find companies that could be of interest and just to reach out. Don’t hesitate, just reach out, even to the CEO. He or she will redirect the inquiry most likely.

When I was at UC San Diego, Hybritech was the only startup on the Mesa. I wrote to the CEO and I still have the response letter in which he stated that “we only have five employees right now, so we're not really set up for this”. That’s ok, and I greatly appreciated his reply. Just reach out, take it upon yourself. Exercise your entrepreneurial gene, and don’t expect the system to create opportunities for you. I know the university has programs to try and make connections and that’s great too, but just go for it, be a self-starter and create your own opportunities.

As you construct your resume and cover letters, emphasize not only technical skills but also the critical softer skills such as your experiences collaborating with others, natural leadership and followership skills, independent as well as group problem-solving. Examples always help. Failure is an important teacher, and insights from such experiences can be useful to convey.

Q: Lucira was co-founded by a couple of UC Berkeley engineering alumni. Why did you decide to get involved with Lucira, and what does this say about the UC system?

A: I always pick companies based on the people as well as the market, and the people at Lucira were just stellar. They had toiled for years on the challenging problem of developing the technology. One of the company’s investors recruited me to Lucira. My predecessor had done a really great job of positioning the technology and company.

The UC system rocks. It’s clear that investment in higher education feeds the economy. That’s exactly what we’re witnessing here, and we see it over and over. I am a proponent of higher education and California is lucky to have such an impressive university system.

Engelson is President and CEO of Lucira Health. He is a Trustee Emeritus of the UC San Diego Foundation; Initial Chairman of the Board of Trustees of UC San Diego’s Bioengineering Department; a member of the UC San Diego Division of Biological Sciences Dean’s Leadership Council; and an elected fellow of the American Institute for Medical and Biological Engineering (AIMBE).

This piece originally ran in ThisWeek. 

Making masks smarter and safer against COVID-19

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January 21, 2021: A new tool for monitoring COVID-19 may one day be right under your nose. Researchers at the University of California 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. (Read an updated FAQ with project leader and UC San Diego nanoengineering professor Jesse Jokerst on the Jacobs School blog.)

The project, which received $1.3 million from the National Institutes of Health, 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. It is part of the NIH’s Rapid Acceleration of Diagnostics Radical (RADx-rad) program for COVID-19.

“In many ways, masks are the perfect ‘wearable’ sensor for our current world,” said Jesse Jokerst, professor of nanoengineering at the UC San Diego Jacobs School of Engineering and lead principal investigator of the project. “We’re taking what many people are already wearing and repurposing them so we can quickly and easily identify new infections and protect vulnerable communities.”

The team will create test strips, or stickers, that can be put on any mask (N95, surgical or cloth). They will be designed to detect the presence of protein-cleaving molecules, called proteases, that are produced from infection with the SARS-CoV-2 virus.

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Prototype test strip before use (top) and after use, showing a negative result (bottom).

The idea is that as the user breathes through the mask, particles—including SARS-CoV-2 proteases if the user is infected—will accumulate in the test strip. At the end of the day or during a mask change, the user will conduct the test. The test strip is equipped with a blister pack that the user will squeeze, releasing nanoparticles that change color in the presence of the SARS-CoV-2 proteases. A control line on the test strip will show what a positive result should look like. It would be similar to checking the results of a home pregnancy test.

Jokerst notes that the strips are not meant to replace current COVID-19 testing protocols.

“Think of this as a surveillance approach, similar to having a smoke detector in your house,” he said. “This would just sit in the background every day and if it gets triggered, then you know there’s a problem and that’s when you would look into it with more sophisticated testing,”

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Set of test strips.

The test strips can be easily mass produced via roll-to-roll processing. This would keep costs down to a few cents per strip. “We want this to be affordable enough for daily testing,” Jokerst said. This would allow facilities at high risk such as group homes, prisons, dialysis clinics and homeless shelters to monitor for new infections earlier and more frequently to reduce spread, he said.

Jokerst is teaming up with researchers at UC San Diego School of Medicine to test the strips first on COVID-19-positive saliva samples, then on patients and healthcare workers at Veterans Affairs San Diego Healthcare System.

Co-investigators on the team are William Penny, professor of clinical medicine, and cardiologist at VA San Diego Healthcare System, Louise Laurent, professor of obstetrics, gynecology and reproductive sciences, and Rob Knight, professor of pediatrics, bioengineering and computer science and engineering, and director of the Center for Microbiome Innovation at UC San Diego.

Potential tool against future outbreaks

This technology can translate to future coronavirus outbreaks, Jokerst said. “The proteases we’re detecting here are the same ones present in infections with the original SARS virus from 2003 as well as the MERS virus, so it would not be too far of a stretch to imagine that we could still benefit from this work later on should future pandemics emerge.”

And even with vaccination efforts underway, this surveillance approach could be deployed in parts of the world where vaccines are not yet available or still limited in distribution.

Materials science approach to mask safety

In addition to this work, Jokerst and his team, in collaboration with UC San Diego nanoengineering professor Ying Shirley Meng, have conducted in-depth research on masks to answer a burning question that surfaced early on in the pandemic: Can N95 respirators be safely reused after being disinfected?

The answer, they found, is yes.

Since the start of the COVID-19 pandemic, health care workers have been facing shortages of personal protective equipment. Researchers and medical centers across the U.S. have found ways to decontaminate and reuse N95 respirators to help keep health care workers safe while serving on the front lines. Jokerst, Meng and colleagues wanted to explore exactly how safe and effective the respirators are for reuse.

A paper detailing this work was published in ACS Applied Materials & Interfaces. UC San Diego materials science Ph.D. student Wonjun Yim is the first author on the study.

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SEM images of the filter layer in an N95 respirator before heat treatment (left) and after (right).

The UC San Diego researchers studied the materials science properties of N95 and KN95 respirators before and after decontamination—the process involved heating the respirators in an oven at 70 C (158 F) for 30 minutes at a time, three times total. They used a filtration apparatus to count how many particles in the air are captured by the respirators. They also examined the fibers of the respirators under an electron microscope.

The team discovered that after the heat treatment, the respirators were able to filter out 90 percent of airborne particles—a small drop from their original 95 rating. They also saw no changes in the structure, density or width of the fibers.

“These masks are more reusable than people think. This is good knowledge to have, to know that these still offer significant protection after being heated multiple times,” Jokerst said.

“People right now don’t understand what happens when you breathe on a piece of cloth all day,” he said. “These studies will lay the foundation to get us thinking about how we can use our masks in safer and smarter ways.”

Wearables: Where Are We?

The latest from Jacobs School of Engineering professors and alumni pioneering the industry.

IMDD Seminar: Introduction and Materials for Quantum Communication

Dr. Bhagawan Sahu on January 28

Five UC San Diego teams receive $100,000 to support groundbreaking research

Dominique Meyer and Henry Zhang are fusing diverse sensor systems to advance autonomous vehicles. Photo taken prior to COVID-19 pandemic.

January 19, 2021: The Qualcomm Innovation Fellowship (QIF) recognizes creative Ph.D. students, providing them with funding, mentoring and other resources to pursue innovative research. This year, five UC San Diego Jacobs School of Engineering teams were awarded fellowships – four from Computer Science and Engineering and one from Electrical and Computer Engineering.

“This is the most QIF awards UC San Diego has ever received in a single year,” said Sorin Lerner, chair of the computer science department. “We are honored by Qualcomm’s commitment to our students and excited to watch them solve important and impactful research problems.”

Each team will receive $100,000 from Qualcomm to pursue cutting-edge research on autonomous vehicles, natural language processing and other areas.

“It is great to see the UC San Diego engineering graduate students thrive as participants in the Qualcomm Innovation Fellowship program,” said John Smee, Qualcomm’s vice president of Engineering. “Congratulations to all of the student finalists and winners this year.”

Team: Dominique Meyer (Ph.D. 2021) and Henry Zhang (Ph.D. 2024)
Advisors: Professor Henrik Christensen, Director of the Contextual Robotics Institute; Professor Falko Kuester, Structural Engineering; Professor Todd Hylton, Mechanical and Aerospace Engineering and Executive Director of the Contextual Robotics Institute
Project: Spatiotemporal Fusion of Radar, Vision and LIDAR Data for Autonomous Driving

Autonomous vehicles use different sensor types to adapt to road conditions, traffic, weather and other hazards. The value of each sensor type shifts as circumstances change around the vehicles.

Multiple sensing technologies improve performance, but also pull heavily on the vehicle’s minimal processing power.

Building on work conducted at the Autonomous Vehicle Laboratory and DroneLab, Meyer and Zhang are developing a system that adjusts how sensor data is fused based on driving conditions  to create a dynamic sensor fusion algorithm.

“The work on sensor fusion for autonomous driving vehicles the QIF fellows in my group are conducting is a rich data science problem of modeling sensors, fusion of information and generating actionable knowledge to operate in a dynamic and uncertain world,” said Christensen. “Qualcomm’s support for our students is invaluable for their studies, building direct links to real-world problems and helping them establish a broader world view.”

Team: Shuyang Li (Ph.D. 2022) and Bodhisattwa Prasad Majumder (Ph.D. 2022)
Advisor: CSE Associate Professor Julian McAuley
Project: Toward Personalized and Multimodal Conversational Recommender Systems

Working in the Julian McAuley lab, Li and Majumder have been investigating natural language processing to develop a conversational recommender system. The team was one of ten finalists in the Amazon Alexa Prize 2019-2020 for their efforts to build dialog systems that conduct engaging conversations with users.

Li’s research focuses on machine learning for text generation (recipes, news and dialog) and learning from unstructured fact collections. Majumder has designed more personalized and empathetic machine learning systems. He has published on language and dialog generation, common sense reasoning and information extraction.

“We believe this approach can be particularly impactful in a variety of user-facing applications, such as recommendation engines in product marketplaces, ad-targeting systems and customer support,” said McAuley. “For these applications, we must provide explanations that are interpretable by laypeople, and those explanations should be personalized to each individual user. Conversational frameworks increase accessibility, facilitate new forms of interaction and make recommender systems more empathetic.”

Team: Minghua Liu (Ph.D 2024) and Xiaoshuai Zhang (Ph.D. 2024)
Advisor: Computer Science Assistant Professor Hao Su
Project: Learning-Based 3D Mesh Reconstruction

3D reconstruction captures an object’s shape and appearance from sensor data, providing insights that cannot be easily gleaned from 2D observations.

3D data can be presented in several formats, such polygon meshes, which capture geometric shapes more efficiently, making them ideal for autonomous driving. While creating high-quality 3D meshes from point clouds is a prerequisite for many applications, current approaches can be problematic.

To overcome these limitations, the team is developing ways to better handle ambiguous structures, noise and incomplete data to create a system that supports robotics, autonomous driving, augmented reality and other applications.

Team: Sai Bi (Ph.D. 2021) and Zhengquin Li (Ph.D. 2021)
Advisors: Comptuer Science Assistant Professor Manmohan Chandraker and Professor Ravi Ramamoorthi
Project: Physically Motivated Deep Inverse Rendering from Sparse Inputs

Image formation is a complex process, in which lighting, materials and geometry interact to determine final appearance. Inverse rendering reconstructs a scene from a small set of images or sometimes a single image.

Current methods require expensive, carefully calibrated setups, or assume simplified physical models, reducing performance. Even deep learning methods have problems addressing limited data.

“The human eye is sensitive to all these details,” said Chandraker. “That’s why removing these artifacts is so important. For a true augmented reality experience, everything has to be just right.”

Bi and Li are developing inverse rendering networks that require only light-weight setups to handle complex visual effects, such as spatially varying lighting and global illumination. This work could potentially turn mobile phones into powerful augmented reality and 3D modeling devices.

Team: Casey Hardy (Ph.D. 2021) and Abdullah Abdulslam (Ph.D. 2021)
Advisors: Electrical Engineering Assistant Professor Hanh-Phuc Le and Associate Professor Patrick Mercier
Project: Vertical Hybrid Power Delivery for High-Performance Processors and Digital Systems

As data processing requirements increase for mobile devices and autonomous vehicles, the industry needs higher performing processors. However, as performance increases, so do power demands.

Mobile devices must maximize battery life and minimize heat generation, limiting their performance. Autonomous vehicles rely on input/output (I/O) processor pins to handle large amounts of sensor data. However, a large number of pins are needed for power delivery. As a result, power demands can generate data processing bottlenecks. Hardy and Abdulslam are using a novel power converter architecture to operate at optimal efficiency while reducing power losses.

The team’s preliminary analysis shows this architecture can increase power delivery efficiency by up to 12 percent, as well as reducing heat generation and increasing I/O pin availability for laptops, smart phones and autonomous vehicles.

“We really appreciate Qualcomm (QTI) and the QIF program to support us on this project and the opportunity to work closely with QTI engineers to benefit from their immense mass-production experiences for the success of our project,” said Le. “With this support, we are excited to tackle one of the most urgent and challenging problems in modern high-performance computing systems, power delivery and management.”

Computer scientist named inaugural holder of the Halicioglu Endowed Chair in Memory Systems

CSE Professor Steven Swanson is the inaugural holder of the HalicioÄŸlu Endowed Chair in Memory Systems

UC San Diego Computer Science and Engineering (CSE) Professor Steven Swanson is building computer systems that explore how new memory technologies will impact the future of computing.

In recognition of his impressive body of research to create software to support persistent memory, Swanson was recently named the inaugural holder of the HalıcıoÄŸlu Chair in Memory Systems at UC San Diego. The $1 million chair is part of a larger $18.5 million gift made in 2013 to the department by CSE alumnus Taner HalıcıoÄŸlu ’96.

The chair provides a dedicated source of funds, in perpetuity, for the chair holder’s scholarly activities as well as support for graduate students.

“In the face of the COVID-19 pandemic, Professor Swanson’s work is more important than ever before,” said UC San Diego Chancellor Pradeep K. Khosla. “His research, teaching and mentorship not only push the boundaries of human understanding, they inspire our academic community to continue innovating, experimenting and discovering. These efforts are critical to our mission as a public research university.”

The chair is named after HalıcıoÄŸlu, who was Facebook’s first full-time employee when it had only 15 computer servers and 250,000 users. Now he spurs startups in San Diego as an angel investor and is also a lecturer in the computer science department. He’s been recognized as a 2020 Computer Science Distinguished Alumnus, a 2019 Chancellor’s Medalist and a UC San Diego 2019 Outstanding Alumnus.

“Taner’s incredible generosity and support of innovation and the work of Steven Swanson will impact our department, our university and our world for years to come,” said  Sorin Lerner. chair of the Department of Computer Science and Engineering.

“Endowed chairs give faculty members the freedom to pursue revolutionary ideas, inspire the next generation of innovators, and transform our society in fundamental ways,” Swanson said. “I am privileged to be able further this kind of work at UC San Diego and CSE.”

Impacting the Future of Computing

Swanson is the director of the UC San Diego Non-Volatile Systems Laboratory, where his group builds computer systems to explore how new memory technologies will impact the future of computing, with a focus on non-volatile memories that allow programmers to build long-lived data structures that can survive system crashes and power failures.

“This requires the data structures to be extremely robust, but that is hard because systems can fail in so many different ways,” he said.

Their recent research has made it easier for programmers to build these robust data structures. “Rather than relying on the programmer to get it right, we have built a compiler that automatically checks for the properties these data structures need.  This means less testing, fewer bugs and better reliability,” he said. 

Swanson has also been working with colleagues to develop a new course and lab (CSE142 and CSE142L) that teach students how to fully utilize the powerful features that modern processors provide. 

“Based on our experience of what really matters to software developers, we take the students on a ‘grand tour’ of modern CPUs and then have them apply what they’ve learned to optimize machine learning workloads,” he said.

HalıcıoÄŸlu’s gift has also created the HalicioÄŸlu Chair in Computer Architecture at UC San Diego, which is held by Professor Hadi Esmaeilzadehand the Ronald L. Graham Chair of Computer Science held by Professor Ravi Ramamoorthi, both in the computer science deparment. 

New Method Makes Better Predictions of Material Properties Using Low Quality Data

Multi-fidelity approach also enables property prediction for disordered materials

A schematic of the multi-fidelity graph networks approach to more accurately predict material properties.

Advancements in energy technologies, healthcare, semiconductors and food production all have one thing in common: they rely on developing new materials—new combinations of atoms—that have specific properties enabling them to perform a needed function. In the not-too-distant past, the only way to know what properties a material had was by performing experimental measurements or using very expensive computations.

More recently, scientists have been using machine learning algorithms to rapidly predict the properties that certain arrangements of atoms would have. The challenge with this approach is it requires a lot of highly accurate data to train the model, which often does not exist.

By combining large amounts of low-fidelity data with the smaller quantities of high-fidelity data, nanoengineers from the Materials Virtual Lab at UC San Diego have developed a new machine learning method to predict the properties of materials with more accuracy than existing models. Crucially, their approach is also the first to predict the properties of disordered materials—those with atomic sites that can be occupied by more than one element, or can be vacant. They detailed their multi-fidelity graph networks approach on January 14 in Nature Computational Science.

“When you are designing a new material, one of the key things you want to know is if the material is likely to be stable, and what kind of properties it has,” said Shyue Ping Ong, a professor of nanoengineering at the UC San Diego Jacobs School of Engineering and the paper’s corresponding author. “The fundamental problem is that valuable accurate data, such as experimental measurements, is difficult to come by, even though we have large databases of less accurate computed properties. Here, we try to get the best of both worlds – combine the large low-fidelity data and the smaller high-fidelity data to improve the models’ accuracy in high value predictions.”

While other multi-fidelity approaches exist, these methods do not scale well or are limited to only two fidelities of data. They are not as accurate or dynamic as this new multi-fidelity graph network approach, which can work with an unlimited number of data fidelities and can be scaled up very quickly.

In this paper, the nanoengineers looked specifically at materials’ band gaps—a property used to determine electrical conductivity, the color of the material, solar cell efficiency, and more —as a proof-of-concept. Their multi-fidelity graph networks led to a 22–45% decrease in the mean absolute errors of experimental band-gap predictions, compared to a traditional single-fidelity approach. The researchers also showed that their approach can predict high-fidelity molecular energies accurately as well.

“There is no fundamental limitation as to what properties this can be applied to,” said Ong. “The question is which kind of properties we have data on.”

In the near term, Ong’s team plans to use this new method to develop better materials for energy storage, photovoltaic cells and semiconductor devices.

While predicting the properties of ordered materials, the team made another serendipitous discovery—in the graph deep learning model they use, atomic attributes are represented as a learned length-16 embedding vector. By interpolating these learned embedding vectors, the researchers found they were able to also create a predictive model for disordered materials, which have atomic sites that can be occupied by more than one element or can be vacant at times, making them harder to study using traditional methods.

“While the bulk of computational and machine learning works have focused on ordered materials, disordered compounds actually form the majority of known materials,” said Chi Chen, an assistant project scientist in Ong’s lab, and first author of the paper. “Using this approach, multi-fidelity graph network models can reproduce trends in the band gaps in disordered materials to good accuracy.”

This opens the door to much faster and more accurate design of new materials to meet key societal needs.

“What we show in this work is you can actually adapt a machine learning algorithm to predict the properties of disordered materials. In other words, now we are able to do materials discovery and prediction across the entire space of both ordered and disordered materials rather than just ordered materials,” said Ong. “As far as we know, that is a first.”

The work was supported by the Materials Project, an open-science initiative to make the properties of all known materials publicly available to accelerate materials innovation, funded by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Materials Sciences and Engineering Division (DE-AC02-05-CH11231: Materials Project program KC23MP). All data and models from this work have also been made publicly available via the Materials Virtual Lab’s megnet repository on Github

Study Finds Neglected Mutations May Play Important Role in Autism Spectrum Disorder

UC San Diego and UCLA researchers find tandem repeats, which are also associated with Huntington’s disease, may contribute to ASD

Melissa Gymrek, a professor at UC San Diego, is the paper's corresponding author. 

January 13, 2021: Mutations that occur in certain DNA regions, called tandem repeats, may play a significant role in autism spectrum disorders, according to research led by Melissa Gymrek, assistant professor in the UC San Diego Department of Computer Science and Engineering and School of Medicine. The study, which was published in Nature on Jan. 13, was co-authored by UCLA professor of human genetics Kirk Lohmueller and highlights the contributions these understudied mutations can make to disease.

“Few researchers really study these repetitive regions because they’re generally non-coding--they do not make proteins; their function is unclear; and they can be difficult to analyze,” said Gymrek. “However, my lab has found these tandem repeats can influence gene expression, as well as the likelihood of developing certain conditions such as ASD.”   

In the paper, the lab studied around 1,600 “quad” families, which include mother, father, a neurotypical child and a child with ASD. Specifically, they were looking for de novo mutations, which appear in the children but not the parents. This analysis, led by UC San Diego graduate student and first author Ileena Mitra, identified an average of 50 de novo mutations at tandem repeats in each child, regardless of whether they were affected by autism. 

On average, there were more mutations in ASD children, and while the increase was statistically significant, it was also relatively modest. However, using a novel algorithmic tool developed by UC San Diego bioengineering undergraduate and second author Bonnie Huang, the researchers showed tandem repeat mutations predicted to be most evolutionarily deleterious were found at higher rates in ASD children.

“In our initial analysis, the ratio between the number of mutations in ASD children and neurotypical children was around 1.03, so barely above one,” said Gymrek. “However, after we applied Bonnie’s tool, we found relative risk increased about two-and-a-half fold. The kids with autism had more severe mutations compared to the controls.”

Finding so many previously undiscovered tandem repeat mutations is significant, as it matches the number of point mutations (single alterations in the A, C, G, T bases that make up DNA) typically found in each child.

The study also produced a wealth of information about the many factors that can influence these de novo mutations. For example, children with older fathers had more tandem repeat mutations, quite possibly because sperm continues to divide – and accumulate mutations – during a man’s lifetime. However, the changes in repeat length coming from mothers were often larger, though the reasons for this are unclear.

“The mutations from dad tended to be plus or minus one copy,” said Gymrek. “However, mutations from mom were usually plus or minus two or more copies, so we’d see more dramatic events when they came from the mother.” 

This approach highlighted a number of genes that had already been linked to ASD, as well as new candidates, which the lab is now exploring.

“We want to learn more about what these novel ASD genes are doing,” said Gymrek. “It’s exciting because repeats have so much more variation compared to point mutations. We can learn quite a bit from a single location on the genome.”

Patterns of de novo tandem repeat mutations and their role in autism

The team includes UC San Diego researchers Ileena Mitra, Bioinformatics and Systems Biology Program; Bonnie Huang, Department of Bioengineering; Nima Mousavi, Department of Electrical and Computer Engineering; Nichole Ma, Department of Medicine; Michael Lamkin, Department of Electrical and Computer Engineering; Richard

Yanicky, Department of Medicine; Sharona Shleizer-Burko, Department of Medicine; and Melissa Gymrek; and Kirk E. Lohmueller from the departments of Ecology and Evolutionary Biology and Human Genetics at UCLA. 

UC San Diego professor Bernhard O. Palsson named Y.C. Fung Endowed Chair in Bioengineering

University of California San Diego professor Bernhard O. Palsson  has been named the Y.C. Fung Endowed Chair in Bioengineering at the Jacobs School of Engineering. Palsson is also a professor of pediatrics, and Director of the Center for Biosustainability.   

January 13, 2021: University of California San Diego professor Bernhard O. Palsson  has been named the Y.C. Fung Endowed Chair in Bioengineering at the Jacobs School of Engineering. Palsson is also a 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.

"Bernhard Palsson is a true intellectual pioneer and international thought leader who knows how to translate fundamental research into biotechnological impact. The positive outcomes of his research, and the work done by the many people he has educated and mentored, are breathtaking," said Albert P. Pisano, dean of the UC San Diego Jacobs School of Engineering. "Bernhard truly exemplifies the can-do, will-do, must-do spirit of Y.C. Fung and the endowed chair professorship created in his honor.” 

"I am honored to be awarded this chair as Y.C. Fung has been one of my role models, was one of the founders of our field, and was such an honorable and dignified individual. I shared many memorable moments with him in my early years at UCSD. I have fond memories of him and admire his legacy," said Palsson. (More about Y.C. Fung: Bioengineering Pioneer Y.C. Bert Fung Turns 100; Obituary for Y.C. Bert Fung

"Following Shu Chien who was the first and only holder of the Y.C. Fung Endowed Chair in Bioengineering adds to the prestige of the history of the chair. I can only hope to be able to continue this history of excellence. These are big shoes to fill," said Palsson. (More about Shu Chien: Pioneering bioengineer Shu Chien retires after 31 years at UC San Diego)

Palsson was named for the 7th year in a row as one of the world’s most influential researchers in their fields, according to a December 2020 research citation report from the Web of Science Group. His most cited paper, entitled, “What is flux balance analysis?” was published in Nature Biotechnology in 2010. He was inducted into the National Academy of Engineering in 2006.

Palson previously held the Pierre Galletti Chair in Bioengineering Innovation in the Department of Bioengineering at the UC San Diego Jacobs School of Engineering where he is a senior faculty member in the Department of Bioengineering, which ranks 4th in the nation for biomedical/bioengineering (US News and World Report Ranking of Best Engineering Schools, published March 2020). Bioengineering has ranked among the top four programs in the nation every year for more than a decade.

"Dr. Palsson is an outstanding world leader in systems biology and genome-scale modeling in bacteria and human cells," said UC San Diego bioengineering professor emeritus Shu Chien. "He is an inspiring educator who has written definitive textbooks on Systems Biology and Tissue Engineering, in the true tradition of Professor Fung. He is an ideal holder of the Y.C. Fung endowed chair."

Remembering UC San Diego engineering professor Siavouche Nemat-Nasser

University of California San Diego engineering professor emeritus Siavouche "Sia" Nemat-Nasser passed away on January 4, 2021 due to complications of acute myeloid leukemia (AML). He was 84 years old.  

January 13, 2021: University of California San Diego engineering professor emeritus Siavouche "Sia" Nemat-Nasser passed away on January 4, 2021 due to complications of acute myeloid leukemia (AML). He was 84 years old. 

Professor Nemat-Nasser was a Distinguished Professor of Mechanics and Materials in the Department of Mechanical and Aerospace Engineering at the UC San Diego Jacobs School of Engineering. He officially retired from UC San Diego in 2019 but remained active as a researcher through his Center of Excellence for Advanced Materials (CEAM). 

He was born in Tehran, Iran, and immigrated to the US in 1958 to complete his undergraduate degree at Sacramento State College (now University). He earned his MS and PhD degrees from UC Berkeley in 1961 and 1964, respectively.

He joined the UC San Diego faculty twice, first from 1966 to 1970. He went on to a brilliant 15-year career at Northwestern University. He then returned to the UC San Diego faculty in 1985 where he served as the Director of CEAM until his retirement.

Upon his return to UC San Diego, he set out to create a materials science program, which included helping to recruit a series of young and talented scholars. He went on to serve as the Founding Director of the Materials Science and Engineering Program, which remains an integrated campus-wide graduate degree program that has achieved global recognition. Nemat-Nasser also initiated a program on the mechanical behavior of materials. Both programs became magnets for researchers globally, and recognition by the community followed, along with support from the National Science Foundation which funded the Institute for Mechanics and Materials at UC San Diego where Nemat-Nasser played an important role. 

In many contexts and with many different material types, he studied how materials fail and why. His work enabled the design of more resistant, useful, and safer materials for a wide range of applications, including building materials for civil infrastructure; materials for space stations that can withstand meteorite impacts; and materials for biotechnology and defense.

Renowned both as a strong theoretician and innovative experimentalist, he studied a broad range of advanced materials including ceramics, ceramic composites, high strength alloys and superalloys, rocks and geomaterials, and advanced metallic and polymeric composites with electromagnetic, self-healing, and self-sensing functionality; ionic polymer-metal composites as soft actuators/sensors, and shape-memory alloys. 

In addition, Nemat-Nasser and his research teams developed or co-developed many of the novel research instruments used in their laboratories.

Over a prolific academic career, he published more than 500 scientific articles which have over 33,000 citations according to Google Scholar. 

Nemat-Nasser served as Founding editor in chief of the journal Mechanics of Materials, a position he held for 37 years until his retirement. He also authored, co-authored or edited over 20 books and proceedings including the book series Mechanics Today and the book series Mechanics of Elastic and Inelastic Solids. Notable scholarly works include his book Micromechanics: Overall Properties of Heterogeneous Materials (with co-author M. Hori), and Plasticity, A Treatise on Finite Deformation of Heterogeneous Inelastic Materials.

In 2001, he was elected a member of the National Academy of Engineering for pioneering micromechanical modeling and novel experimental evaluations of the responses and failure of modes of heterogeneous solids and structures. Among his numerous honors, he received the highest awards in mechanics, the Timoshenko Medal in 2008, and the ASME Gold Medal in 2013 (see video).

Teaching and mentoring were crucial to Nemat-Nasser. He advised more than 70 PhD students and 30 post-doctoral researchers during his career, and throughout, taught undergraduate courses in mechanics and mathematics. In 2015 he was awarded the UC San Diego Academic Senate Distinguished Teaching Award for his teaching of undergraduate students which integrated inventive and alternative teaching methods that were simple yet highly effective. 

In a 2008 UCSD TV video segment, he expressed his passion for teaching and training future generations of researchers. He relished the process of working with graduate students who then would be intellectual partners from whom he could learn. Many of his former students and postdocs have become leaders in the field of mechanics.  

Academic awards that bear Sia Nemat-Nasser's name have been created with both the American Society of Mechanical Engineers (ASME) focused on underrepresented minorities and women in engineering, and the Society for Experimental Mechanics (SEM). 

In 2016, Nemat-Nasser and his wife Éva generously established the Roghieh Chehre-Azad Distinguished Professorship within the UC San Diego Division of Arts and Humanities to foster new projects and future works exploring the music, art, literature and history of Persian culture at UC San Diego.

At the time, Nemat-Nasser noted that the gift served to honor his mother "Chehre-Azad,” a well-known actor in Iran who pursued her passion of acting at great personal risk when women performing on stage in Iran was taboo.

He was fond of the Persian poets Ferdowsi, and Omar Khayyam, who also was a great mathematician and astronomer. Nemat-Nasser himself translated poetry from Farsi to English. He also wrote his own poetry in Farsi, illustrated it, and translated it into English. 

A person of great energy, discipline, and dedication, he swam for one hour every day until 2018. In past years, he was known to enter La Jolla Cove at night and swim alone in the ocean, to the dismay of his wife Éva. 

Nemat-Nasser is survived by his wife Éva, six children: Michaela, Elizabeth, Katherine, David, Syrus, Shiba, and grandchildren: Lilith, DJ, Jack, and Arastoo. 

The family has asked that in lieu of flowers, gifts can be made to the Roghieh Chehre-Azad Distinguished Professorship at UC San Diego (K3993).

$1.2 Million Grant Funds a New Generation of Healthcare Telemanipulation Robots

UC MRPI award will develop advanced telehealth robots to protect healthcare workers and help isolated people connect with their communities.

January 12, 2021: Researchers at UC San Diego, UCLA, UC Irvine and San Diego State University have been awarded a $1.2 million UC Multicampus Research Programs and Initiatives (MRPI) grant to develop an advanced class of mobile telemanipulation robots. These easy-to-operate, low-cost  robots called UC Iris will be used to grasp objects, open doors and perform other tasks to advance telehealth, allowing healthcare workers to safely conduct remote exams and providing quarantined Californians a safe way to interact outside their homes.

“COVID-19 is exacerbating societal inequities and will continue to affect our existence for years to come,” said project lead Laurel Riek,  a professor in UC San Diego’s Computer Science and Engineering department and director of the university’s Healthcare Robotics Lab. “Two groups are at extremely high risk for infection, adverse physical and mental health outcomes and extended isolation: Frontline healthcare workers and people who cannot leave their homes due to high infection risk. This project will develop new telehealth robotic technologies to support both groups.”

A healthcare worker can remotely operate UC-Iris to safely treat isolated patients (left). People at high risk of infection unable to leave home can use UC-Iris to engage with their communities, such as an art class with friends at a cultural center (left).

Entitled Robot-facilitated Health Equity in Post-Pandemic California and Beyond, the team      will develop state-of-the-art mobile robots with advanced tactile sensing, manipulation, and haptics technologies (which transmit information through touch). This will allow operators to feel truly immersed in a remote location and give them a sense of presence and touch. Veronica Santos, professor of Mechanical and Aerospace Engineering and director of the Biomechatronics Lab at UCLA, and Veronica Ahumada-Newhart, human-robot interaction scientist at UC Irvine and director of the Technology and Social Connectedness Lab are co-principal investigators on the team.      

For healthcare workers, these new  robots will help conduct remote exams. Throughout the COVID-19 pandemic,  clinicians have largely relied on static telehealth technologies, such as Zoom and telemedicine carts, to reduce infection risks. However, they must physically deliver these technologies; train patients to use them; and troubleshoot technical issues – all at the patient’s bedside – mitigating their benefits. In addition, existing technologies lack touch and independent mobility, key features many clinicians need. 

Outside of hospitals, millions are at high risk for infection, including people with cancer, those with suppressed immune systems and older adults. These individuals have been further isolated by the pandemic, putting them at increased risk for depression, suicide, dementia and other conditions. 

To address this, the team will advance inexpensive, user-friendly robotic systems that give quarantined people new opportunities to “leave” home and interact with society.

“We will be designing new haptic interfaces, tactile sensing modalities and shared control methods for telemanipulation,” said Riek. “For healthcare workers, these robots will enable new ways to safely treat patients. For people who are isolated, they will provide new opportunities to engage with their loved ones and their communities.”  

Laurel Riek, the project lead and a professor in UC San Diego’s Computer Science and Engineering department and director of the university’s Healthcare Robotics Lab

The researchers will also study optimal ways to deploy the technology. The team will work closely with healthcare workers across the UC system, including emergency medicine specialists and hospitalists, to integrate UC Iris into critical care settings. They will also explore how these robots can improve quality of life for isolated groups and increase their independence. 

“We are specifically focused on Latino communities, as they are the most tragically affected by COVID-19 in California, representing 71% of fatalities among those 18 to 64,” said Riek. “We will explore ways the robots can help them engage and feel included in their communities without risking in-person gatherings.”

The Team

The multidisciplinary research team includes internationally-recognized experts in robotics, haptics, health informatics and psychology.

  • Dr. Laurel Riek (UC San Diego) will lead the overall project, coordinating research activities across the UC campuses, and leading development of the new mobile telemanipulation robotic system, including creating new shared control methods.
  • Dr. Veronica Santos (UCLA) brings expertise in artificial tactile sensing/perception, grasp and manipulation with human, prosthetic and robotic hands to lead development of new haptics technologies that support teleoperator embodiment.
  • Dr. Veronica Ahumada-Newhart (UCI) is an expert in health informatics and developmental psychology and will lead efforts to develop telerobots that support robot-mediated inclusion.
  • Dr. Tania Morimoto (UC San Diego) contributes expertise in human-in-the-loop interfaces, including low-cost haptics, to accommodate a wide range of age and experience levels. Morimoto will lead efforts to create new haptic display technology.
  • Dr. Jacquelynne Eccles (UCI), one of the leading developmental scientists of her generation, will support virtual inclusion efforts on the project.
  • Dr. Kristen Wells (SDSU), brings extensive expertise in clinical psychology and behavioral science, particularly in health equity and health disparities.

Ocean acidification is transforming California mussel shells

New analyses reveal how over 60 years a critical marine species has responded to ocean acidification

By Mario Aguilera

UC San Diego researchers have found that the shells of California mussels, a critical species found along the Pacific Coast, are weakening as a result of ocean acidification.

The large mollusk known as the California mussel makes its home in the rocky shoreline along the Pacific Coast from Mexico to Alaska. Considered a “foundational” animal, Mytilus californianus provides homes for hundreds of other species and offers a rich food source for species ranging from spiny lobsters to humans.

As the waters off our coasts change due to human influences, scientists at the University of California San Diego are finding that the composition of California mussel shells is weakening as it becomes more tolerant of acidic conditions.

Scientists have known that rising levels of human-produced carbon dioxide that are increasingly absorbed into the world’s oceans will have an impact on sea life. But as ocean waters increasingly acidify, tracking impacts on specific species has been difficult to gauge over time. Most of what we know about species’ responses to acidifying waters comes from short-term experiments that suggest these increases in ocean acidity—causing a lowering of seawater pH and less availability of carbonate ions to make shells—can lead to less fortified shells and more vulnerable animals.

But not every species from these studies responds the same way, with some even appearing to do better under these conditions. This makes long-term studies looking at how increases in temperature and ocean acidification impact species extremely valuable for understanding and ultimately making predictions about future vulnerability of these species.

UC San Diego Biological Sciences graduate students Elizabeth Bullard and Alex Neu traveled the Pacific Coast from La Jolla to Washington state collecting mussels that would form a comparison to mussels collected in the 1950s.

Comparing new data with samples collected in the 1950s, UC San Diego Division of Biological Sciences graduate student Elizabeth Bullard and Professor Kaustuv Roy found that ocean acidification is transforming the composition of California mussel shells from mostly the mineral aragonite to the mineral calcite. The results are published in the Proceedings of the National Academy of Sciences.

Aragonite is much stronger than calcite and makes for a better shell to protect against predators and wave energy, two things that are expected to increase with warming waters. Calcite, on the other hand, is much weaker but does not dissolve as easily as aragonite—making a better shell material if the waters are acidifying. Experts had expected aragonite, the stronger of the two substances, to emerge as the dominant mussel shell mineral due to its preference to form in warmer waters. Instead, the new study has shown that the weaker but more stable calcite mineral is now the dominant shell substance, a response linked to increases in ocean water acidity.

“We found that these mussels are indeed secreting more calcite today than they were 60 years ago,” said Bullard. “Lower pH eats away the shells these animals are able to create, so it’s considered a major problem for marine organisms. There are 303 species that are associated with the California mussel, so if we lose the mussel we lose other species, some of which are really important to things like our fisheries and recreation.”

In the late 1950s, Caltech scientist James Dodd traveled the Pacific Coast from La Jolla to Washington state, collecting mussels along the way. His specimen sampling led to a valuable baseline of information about mussels and their shell composition, including the ratio of aragonite to calcite. One of the results of his work was a stark geographical contrast between cold northern waters, where mussels mostly featured calcitic shells, with the warmer southern waters where aragonite was the dominant shell mineral.

Professor Olivia Graeve with members of her lab

To find out how the shell mineral profile has changed across six decades, Bullard similarly traveled the coastline with her lab mate, graduate student Alex Neu, in 2017 and 2018 to collect new specimens in a survey that geographically replicated Dodd’s sampling. With more than 100 shell samples collected, Bullard then spent days meticulously grinding each shell down to a fine dust to dissect their composition—up to 16 hours of grinding for one shell in some cases.

“If you put too much heat or pressure on aragonite it will convert to calcite,” said Bullard. “Calcite is extremely stable but aragonite isn’t. In order to really make sure the ratio is accurate you have to be super careful and hand grind the specimens down to a super fine powder.”

Finally, project collaborator Professor Olivia Graeve and her materials science group in the UC San Diego Jacobs School of Engineering conducted X-ray diffraction analysis on each sample to determine their mineral profiles.

“By combining our expertise in crystallography of materials with our collaborator’s expertise in ecology, we were able to make a real impact on our understanding of humans’ long-term effects on other species,” said Graeve. “This type of interdisciplinary research is what’s required to continue advancing science and engineering for the benefit of our world.”

The results told a new story. Instead of a geographical boundary between north and south California mussel shells, the new survey revealed that acidic waters are reducing shell aragonite throughout the coast, leading to calcite as the dominant shell mineral.

“James Dodd’s data fit in a world where the balance of temperature and ocean pH was very different from that today,” said Roy, a professor in the Section of Ecology, Behavior and Evolution (EBE). “For me it was surprising how big the effect was in 60 years. That’s not a huge amount of time as these things go, but the effect was striking.”

The researchers were surprised to find that ocean pH and changing amounts of carbonate availability, not temperature, played such a strong role in influencing shell mineralogy. It’s a finding that would not be possible without Dodd’s critical baseline work.

“This study highlights the importance of utilizing long-term data sets and large spatial comparisons to understand and test predictions about species responses to a changing world,” the authors write in the paper.

Bullard and Roy are now probing deeper into shell viability questions. They are conducting lab experiments to test how this change from aragonite to calcite might impact the strength and overall function of the mussel shell.

Co-authors of the paper include: Elizabeth Bullard, Ivan Torres, Tianqi Ren, Olivia Graeve and Kaustuv Roy.

A grant from NASA and the Jeanne Marie Messier Memorial Endowment Fund (EBE) supported this research.

2020 Jacobs School student highlights

Alumna spotlight: Bridget Benson, electrical engineering professor at Cal Poly

Moving forward, looking back

The Jacobs School of Engineering is preparing to emerge from the pandemic stronger and more relevant than ever

How will the UC San Diego Jacobs School of Engineering emerge on the other side of the COVID-19 pandemic? The ground has shifted in many ways, and it's up to us to respond, evolve and adapt.

As we look back at 2020 and move forward in 2021, there are two high-level moves we are also making. These moves are designed to ensure the Jacobs School emerges more ready than ever to confront the challenges, injustices, and societal and innovation needs laid bare by the pandemic.

First, the Jacobs School has initiated and strengthened a series of culture-building programs. The goal is to ensure that we empower all of our students, faculty and staff to do the creative and innovative technical work they are so capable of (more details below).

Second, we are facilitating critical national and international conversations on research. In particular, how academia, industry and government can partner and collaborate in new ways. The goal is to build on the existing research enterprise in order to increase the pull through of innovation to society. Getting this right will inevitably lead to an ever more diverse and empowered innovation workforce.

"Framed by this work on culture building and more effective research partnerships, I'm pleased and humbled to share some of the momentum we've built this year and over the last handful of years," said Albert P. Pisano, Dean of the UC San Diego Jacobs School of Engineering. "I offer my deepest gratitude to everyone in our Jacobs School community."

A few of our Jacobs School 2020 wins are captured in this video.



Jacobs School Momentum: looking back and looking forward

World-class faculty
We have hired more than 130 new faculty into the Jacobs School over the last 7 years. More than 36% of these new professors are women and/or from other groups traditionally underrepresented in engineering and computer science.

Growing research enterprise
At $212M, our research expenditures are up 34% over the last 5 years.

Rising reputation
We jumped to #9 in the nation this year, in the closely watched US News and World Report Best Engineering Schools rankings. This is up from #17 just four years ago.

Innovation workforce
We have awarded nearly 15,000 Jacobs School degrees over the last 6 years. More than 9,170 talented students enrolled in Fall 2020.

Research relevance
We have launched 14 new agile research centers and institutes since 2014 to drive deeper and more relevant collaborations that tackle the fundamental challenges no research lab or company can solve alone.

Franklin Antonio Hall
We are on schedule for our Spring 2022 opening of Franklin Antonio Hall. Our new building will serve as a model for how to build innovation ecosystems with physical roots and virtual infrastructure with national and international impact. This is how engineering for the public good will get done in the future.

Culture building
As I mentioned above, we are working hard to build a school culture where every student, staff member and professor is empowered to bring their whole self to the classroom, lab, office, and screen. Just this year, we launched the Student and Faculty Racial Equity Task Force; the Racial Equity Fellows Program; the Jacobs School Research Ethics Initiative; and the Jacobs School Anthropology, Performance, and Technology Program. The Jacobs School is a key part of the new Changemaker Institute at UC San Diego. We are also celebrating 10 years of the IDEA Engineering Student Center; and we are proud to be collaborating with our UC San Diego Office for Equity, Diversity, and Inclusion.

 

 

Jacobs School alumni kickstart Dean's Scholars of Excellence program

December 15, 2020-- Education is the great equalizer.

Jacobs School of Engineering alumni Mary Bui-Pham and Dan Pham have seen this play out in their own lives, having both arrived in the U.S. as Vietnamese immigrants who didn’t speak English or have any money to their names-- Mary with her family at age 13 and Dan in his 20s. Yet they were able to work their way up to leadership roles at top tech firms like Yahoo, HP, and Indeed, all thanks to an education.

“I think of myself coming to the U.S., 13 years old, not knowing any English; my father going from being the administrator of a fairly famous research institute to getting a job as a stock clerk in the hospital because his degrees were not recognized, and my mother having to take a seamstress job in a shirt factory even though she didn’t know how to sew,” said Bui-Pham. “Fast forward to now, and I have a Ph.D., I’m a senior leader for a company that helps millions of people get jobs, and I just gave my school an endowed scholarship. All within my lifetime. And all because I got an education and I worked hard. Why can’t that story be replicated again and again?”

The Bui Pham family in front of Geisel Library at UC San Diego.

It will be replicated more frequently thanks to the Bui-Pham family, who have donated the funds to endow a scholarship supporting 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 engineering students.  Their gift launched the larger Jacobs School of Engineering Dean’s Scholars of Excellence program, a school-wide scholarship program meant to advance equal access to a Jacobs School education.  

Thanks to a $10,000 seed gift from an anonymous Jacobs School faculty emeritus, gifts of any amount can now be directed to the Dean’s Scholars of Excellence program, supporting these student scholarships. 

"We have a responsibility to ensure that a Jacobs School education is accessible to as many students as possible. Diversity is critical to innovation, and moving forward as a nation, we must find more and more effective ways to tap our entire talent pool," said Albert P. Pisano, Dean of the UC San Diego Jacobs School of Engineering. "Mary and Dan understand on a personal level the effect that education can have on one person, and the transformative impact it can have on a society. I’m grateful and honored to work with them to launch the Dean’s Scholars of Excellence program, providing outstanding students with the financial support to pursue their academic goals.”

Bui-Pham earned her Ph.D. in Chemical Engineering at the UC San Diego Jacobs School of Engineering, where she met Dan, a master’s student also working in Professor Kal Seshadri’s lab one summer. It was fireworks-- or more like an explosion-- from the beginning; a pressure gauge on a gas tank Dan was using for an experiment malfunctioned, causing a minor explosion, but catching Mary’s attention in the process. They’ve been together since. 

After earning her Ph.D., Bui-Pham conducted research as a postdoctoral scholar, doing computational modeling of flames. Her computational background set her up for a job with NetGravity, which eventually merged with Google. She then went to Yahoo, where she was the chief-of-staff for the division of Publisher Products, before moving into her current role as Vice President of Strategy and Operations at Indeed, where she helps shape and implement the employment platform’s long-term roadmap. After earning his master’s degree in mechanical engineering at the Jacobs School, Dan worked at disk drive design and storage firm Quantum Corporation, before working his way up from procurement and software engineer to Program Manager at Hewlett Packard.

“I’ve always been very grateful to UC San Diego,” Bui-Pham said. “I made amazing friends, I met my husband, I had the best time in grad school, and I want to pay it forward.”

The inaugural Bui Pham Family Engineering Endowed Scholarship recipient will be named in Fall 2021. The family hopes that their gift and the larger Dean’s Scholars of Excellence program will help propel students with the drive to succeed on a trajectory similar to the one they’ve lived. 

“I think 10 years from now we’ll have a whole generation of amazingly educated, productive citizens, who would be also thinking about ‘how do I pay it forward,’” Bui-Pham said. “We all need to have that gratitude and understand that you don't get anywhere by yourself. We all stand on others’ shoulders. Sometimes just a tiny boost is all we need.”

The goal of the Dean’s Scholars of Excellence program is to continue advancing equal access and success for the most promising engineering minds from all communities. With the help of visionary supporters, we can shape the next generation of diverse problem-solvers who will rise to the challenge of creating tomorrow’s sustainable technologies. To support students through the Dean’s Scholars of Excellence program, select the Jacobs School Dean's Scholars of Excellence fund here. For more information, contact: David Strachan, Director of Development, (858) 761-1379, dstrachan@eng.ucsd.edu

The Bui Pham’s gift contributes to the Campaign for UC San Diego—a university-wide comprehensive fundraising effort concluding in 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.

UC San Diego Celebrates 25 Years of Wireless Research Leadership

December 15, 2020-- The University of California San Diego Center for Wireless Communications (CWC) is celebrating 25 years of partnering with industry to push the bounds of wireless technologies while training the wireless workforce of the future. 

At the UC San Diego Center for Wireless Communication's 5G and Beyond Forum in November 2020, researchers from academia, industry and government presented on both 5G innovations and visions for 6G. The symposium also looked back at some of the Center’s impactful research and activities over the last three decades.

Looking forward, UC San Diego is engaging in national and international conversations focused on creating wireless research ecosystems and infrastructure through public-private partnerships that facilitate both innovation and workforce development. The general idea is to create scalable research ecosystems and infrastructure that can be accessed virtually and encourage development of future wireless technologies, use-case exploration for 6G and beyond, and the training of tomorrow's wireless workforce.

"I'm thrilled to be actively engaged with the Center for Wireless Communications, and all of our faculty, industry partners, and the wider wireless research community. We are working together to ensure that we have the wireless research infrastructure necessary to drive innovation and empower future generations of wireless engineers," said Albert P. Pisano, Dean of the UC San Diego Jacobs School of Engineering.

Wireless firms are already partnering with researchers at UC San Diego and elsewhere to create research infrastructure such as digital replicas of wireless networks. Building on this kind of shared, virtual research infrastructure will be crucial for collecting the data necessary to bring 6G-enabled technologies to fruition, explained Sujit Dey, who is an electrical and computer engineering professor at UC San Diego and Director of the Center for Wireless Communications.

“The Center for Wireless Communications has invested a lot of time into creating application-specific network testbeds -- we’re doing it for our smart transportation program for connected autonomous vehicles, as well as our connected health program for mixed-reality remote healthcare" said Dey. "We’re lucky to have industry partners that make this realistic, but it’s not possible for everyone to be doing this. I hope industry, academia and government can come together in creating digital replicas, digital twins, to not only have testbeds nationally, but to have these digital twins that replicate real situations and gather tremendous amounts of data we otherwise could not. For example with driving, we cannot drive unsafely. But with a digital twin you could get that data.”

Making transportation smarter

In addition to looking deep into the 6G future and beyond, researchers are also innovating and improving 5G connectivity. At the CWC Forum, UC San Diego engineers shared several research areas they’re focused on, including smart transportation and the hardware required to enable up to a trillion connected devices.

A session on connected and autonomous vehicles featured a number of projects at the UC San Diego Jacobs School of Engineering that are focused on improving how well self-driving cars can “see” and communicate with each other.

One example is a technology developed by the lab of UC San Diego electrical and computer engineering professor Dinesh Bharadia that could enable self-driving cars to navigate safely in bad weather. It consists of multiple radar sensors working together like multiple eyes to create a fuller view of the road, even when it’s not clear outside. The setup can accurately predict the dimensions of a car moving in fog. Bharadia is working with Toyota and Honda for further research and development. He says this new technology could provide a cheap alternative to lidar.

Improving self-driving cars’ vision will also require reconciling images taken by sensors at different viewpoints. A camera from a vehicle and a camera from a lamp post, for example, can both see the same object, but they might not know it is the same because they are viewing it from different angles, said Truong Nguyen, a professor of electrical and computer engineering at UC San Diego. To address this issue, Nguyen and his lab developed algorithms that can find features that are common between these pictures and match them to objects. The algorithms work in both 2D images and 3D point clouds. The researchers are currently optimizing the algorithms for real-time computation.

As more cars and streets become outfitted with cameras and sensors, an emerging opportunity and challenge will be fusing live data from all of these different sources, obtaining intelligent perception of the environment, and sharing the insights with all the vehicles and even other road users like pedestrians and bicyclists.

Sujit Dey, the Center for Wireless Communications director, is working with CWC colleagues and industry partners to develop intelligent roadside units to perform these tasks. The idea is that vehicles—both autonomous and human-driven—would send data from on-board cameras, radar and lidar sensors to the roadside units, which would fuse and process the data, and then provide enhanced perception to vehicles and other road users to improve advanced driver assistance systems, and to autonomous vehicles for more efficient path planning and navigation. Because all of this hefty computer processing will consume a lot of power, Dey and colleagues are building units that are powered by renewable energy so they can reduce their carbon footprint.

Connected vehicle technologies will also require high-throughput data rates. Millimeter wave directional beams can accommodate these increases in data use, but the problem is they are susceptible to blockage from buildings and human bodies. They are also hard to manage when tracking moving objects.

UC San Diego electrical and computer engineering professor Xinyu Zhang is exploring ways to make millimeter wave technology practical for connected vehicle applications. His lab built a testbed at the UC San Diego campus to explore the feasibility and challenges of millimeter wave-connected vehicles. The researchers discovered that millimeter waves can boost link speed by orders of magnitude in best case scenarios, but this requires deploying a significantly large number of base stations on site. The good news, Zhang noted, is that since road segments have simple geometries, base stations can easily “spot-light” on vehicles using their directional beams to maintain connectivity. The researchers are exploring machine learning algorithms that can make the base stations intelligent enough to harness such advantages.

Circuits for a more connected world

The future will experience an explosive growth in the number of connected devices being used worldwide. By 2035, we can expect that number to be a trillion, said UC San Diego electrical and computer engineering professor Patrick Mercier.

But to get to that number, engineers need to figure out how to improve the power management of these devices, he noted. The battery life of a typical IoT device ranges from a few hours to a few days. The largest fraction of that battery power is being spent by the radio subsystems.

By only waking up a wireless device when necessary, the wake-up receiver (chip stack to the left of the penny) can cut down on power use and extend battery life. The system includes a miniaturized antenna (gold-colored plate below the receiver). Photos by David Baillot/UC San Diego Jacobs School of Engineering

Mercier’s lab is working on solving this power problem by building ultra-low power wake-up radios. As their name implies, these radios wake up a device only when it needs to communicate and perform its function. This allows the device to stay dormant the rest of the time and reduce power use. The latest wake-up radio from the Mercier lab boasts a power consumption of 4.4 microwatts and is compatible with both WiFi and Bluetooth. Mercier says the technology could improve the battery life of small IoT devices from months to years.

A number of UC San Diego electrical engineering professors are at the cutting edge of building hardware elements for next generation 5G systems. These include power amplifiers with highly efficient supply modulators (Peter Asbeck and Hanh-Phuc Le); phased arrays that transmit and receive over a wide band (Gabriel Rebeiz); and digital phase-locked loops with state-of-the-art performance (Ian Galton).

Envisioning 6G

While 5G connectivity is still being rolled out and improved for users around the globe, wireless industry and academic leaders are already exploring what the next generation of connectivity—6G—will look like, and starting the research required to enable it.

A panel of experts from Samsung Research, Qualcomm, Nokia, Ericsson and UC San Diego agreed that the specific technical capabilities of 6G are still being hashed out, but some rough estimates do exist.

While 5G connectivity in 2021 is expected to have speeds of 100 gigabits per second and latency of 500 microseconds, 6G connectivity is expected to increase the speed of transmission to 1 terabyte per second, with latency as low as 100 microseconds.

Use cases for these high data rates and low latency include truly immersive extended reality experiences, as well as mobile holograms and "digital twins" which refers to recreating physical entities in a virtual world to study, alter and interact with them.

The panelists also agreed that they expect 6G connectivity should be entering the wireless market within the next 10 years, perhaps as early as 2028. What research is required from academic researchers to enable these speed and latency improvements?

On the semiconductor side, improving radio-frequency integrated circuits (RFICs) to function at terahertz bandwidth will be key. In addition to moving into terahertz bandwidth, research into dynamic spectrum sharing options is needed.

“The wireless industry is incredibly grateful for the existence of the Center for Wireless Communications,” said Martha Dennis, a technologist, venture capitalist and a member of the CWC’s founding executive council at the recent CWC 25th anniversary forum. Over the center’s 25 year lifespan, more than 40 companies have become members.

As wireless technologies are incorporated into more and more industries, services and products, the number and diversity of companies partnering with CWC is sure to rise.   

Bioengineering alumnus named to Forbes 30 Under 30

Major Upgrade Under Way at the World's Largest Outdoor Shake Table

Dec. 14, 2020 -- Earlier this year in San Diego, two giant cranes lifted the 330,000 lb. steel  floor, or platen, off the world’s largest outdoor shake table, revealing a complex network of pipes, wires and catwalks. 

This was the first step in a major $16.3 million upgrade to the seismic simulator funded by the National Science Foundation. Over the next 10 months, the facility will undergo major construction. When completed in October 2021, the shake table will be able to reproduce multi-dimensional earthquake motions with unprecedented accuracy. 

“We take a lot of pride in having such accuracy,”  said Joel Conte, principal investigator of the UC San Diego shake table and a professor in the Department of Structural Engineering. 

“It’s very, very difficult to achieve on such a large shake table.” 

“We will be able to replicate, in full 3D, the combined effect of all the motions of an earthquake applied to a structure, as well as the interaction between soil and building, and soil liquefaction,” he added. 

The principle behind the table is relatively simple: various structures are built on top of the facility’s floor, or platen, which is connected to a series of horizontal and vertical actuators, or pistons that move back and forth, simulating earthquake motions. The movements follow precise earthquake records researchers have gathered from around the world.

Each structure on the table is wired with hundreds of sensors recording how it fared during earthquake simulations--the data acquisition system will be completely overhauled during the upgrade as well. Data analysis from the tests has led to many changes in the nation’s building codes in the shake table’s 15-year history.

Until this year, the facility could only simulate backward and forward ground motions, or what is known as one degree of freedom. Thanks to the NSF funds, it is getting more actuators, and more power, so that it can also simulate up and down, left and right, as well as pitch, roll and yaw motions, which is known as six degrees of freedom (6-DOF).

Reproducing earthquake motions in 6-DOF is key because during a temblor, the ground may move in any direction. For example, during the 1994 Northridge earthquake in the Los Angeles area, bridge columns punched through bridge decks, hinting at a strong vertical ground motion component. Similarly, during the 1971 San Fernando earthquake, the buildings twisted and swayed, hinting that the ground was probably rotating. 

“We will be able to achieve the ultimate level of validation for new retrofit methods, new materials, new components and new construction methods,” Conte said. 

After the upgrade, the facility also will be able to test the tallest and heaviest test specimens in the world, from multi-story buildings, to bridge columns, bridge bents, and wind turbines, with a full range of ground motions that can occur during an earthquake.

Shake table impact

Professor Joel Conte is the principal investigator at UC San Diego's shake table. 

In the 15 years of operations of the shake table, known as the LHPOS,T in its one degree of freedom configuration, a total of 34 major research projects have been tested on the shake table. The research has led to important changes in design codes for commercial and residential structures and new insights into the seismic performance of geotechnical systems, such as foundations, tunnels and retaining walls. It also has helped validate the use of innovative technologies to make buildings more likely to withstand earthquakes.

For example, in San Francisco, approximately 6,000 soft-story wood-frame buildings are being retrofitted to make them safer in strong earthquakes. Full-scale testing of retrofit systems for these “soft-story” wood frame buildings on the UC San Diego shake table, led by Professor John van de Lindt from Colorado State University, was critical to make this possible.

Research by Professor Jose Restrepo at UC San Diego, co-principal investigator for the NSF upgrade grant, and Professor Robert Fleischman at the University of Arizona, led to new design standards for so-called floor diaphragms, which transfer seismic forces from building floors to columns, walls and eventually foundations.

10-story building test

The first structure to undergo tests on the shake table after the upgrade will be a full-scale 10-story building made from cross-laminated timber. The goal of these tests, led by Shiling Pei, a professor at the Colorado School of Mines, will be to gather critical fundamental data to design wood buildings as tall as 20 stories that do not suffer significant damage during large earthquakes. That is, not only can occupants leave the building unharmed, but they can also return and resume living in the building shortly after an earthquake.

The operation and maintenance of the UC San Diego shake table is currently funded through a five-year grant from NSF’s Natural Hazards Engineering Research Infrastructure (NHERI) Program.

 

A smart ring shows it's possible to detect fever before you feel it

Advance could pave the way for early warning system on COVID-19 and flu using wearables

Subjects used the Oura ring to track their temperature. 

Dec. 14, 2020 -- Temperature data collected by wearable devices worn on the finger can be reliably used to detect the onset of fevers, a leading symptom of both COVID-19 and the flu, according to a team of researchers from the University of California San Diego, UC San Francisco and MIT Lincoln Lab.

Researchers published their results in a paper titled  “Feasibility of continuous fever monitoring using wearable devices” in the Dec. 14 issue of the journal Scientific Reports. They emphasize that the study is a proof-of-concept effort with data from only 50 participants reporting COVID-19. 

The Scientific Reports paper is the first published result from TemPredict, a study of more than 65,000 people wearing a ring manufactured by Finnish startup Oura, that records temperature, heart rate, respiratory rate and levels of activity. The goal of the study is to develop an algorithm that can predict the onset of symptoms such as fever, cough and fatigue, which are characteristic of COVID-19. Researchers say they hope to reach that goal by the end of the year. They also hope the algorithms will allow public health officials to act faster to contain the virus’ spread.  

“This isn’t just a science problem, it’s a social problem,” said Benjamin Smarr, the paper’s corresponding author and a  professor in the Department of Bioengineering and the Halicioglu Data Sciences Institute at UC San Diego. “With wearable devices that can measure temperature, we can begin to envision a public COVID early alert system.”

But users from diverse backgrounds  would need to feel safe sharing their data for such efforts to really work, Smarr added.  The data is stripped of all personal information, including location, and each subject is known by a random identifying number.

Smarr is TemPredict’s data analytics lead. Ashley Mason, a professor in the Department of Psychiatry and the Osher Center for Integrative Medicine at UC San Francisco, is the principal investigator of the study. 

“If wearables allow us to detect COVID-19 early, people can begin physical isolation practices and obtain testing so as to reduce the spread of the virus,” Mason said. In this way, an ounce of prevention may be worth even more than a pound of cure.” 

Wearables such as the Oura ring can collect temperature data continuously throughout the day and night, allowing researchers to measure people’s true temperature baselines and identify fever peaks more accurately. “Temperature varies not only from person to person but also for the same person at different times of the day,” Smarr said. 

The study, he explains, highlights the importance of collecting data continuously over long periods of time. Incidentally, the lack of continuous data is also why temperature spot checks are not effective for detecting COVID-19. These spot checks are the equivalent of catching a syllable per minute in a conversation, rather than whole sentences, Smarr said. 

Benjamin Smarr, a professor in the Department of Bioengineering and the Halicioglu Data Science Institute, is the paper's corresponding author. 

In the Scientific Reports paper, Smarr and colleagues noticed that fever onset often happened before subjects were reporting symptoms, and even to those who never reported other symptoms. “It supports the hypothesis that some fever-like events may go unreported or unnoticed without being truly asymptomatic,” the researchers write. “Wearables therefore may contribute to identifying rates of asymptomatic [illness] as opposed to unreported illness, [which is] of special importance in the COVID-19 pandemic.”

The 50 subjects in the study all owned Oura rings and had had COVID-19 before joining TemPredict. They provided symptom summaries for their illnesses and gave researchers access to the data their Oura rings had collected during the period when they were sick. The signal for fever onset was not subtle, Smarr said. “The chart tracking people who had a fever looked like it was on fire.” 

The data collected as part of the subsequent TemPredict study included 65,000 subjects, and these data will be stored at the San Diego Supercomputer Center at UC San Diego, where a team led by Ilkay Altintas is building a portal to enable other researchers to access these data for other analyses. 

“The data collected has great potential to be linked with other datasets making individual and societal scale models be combined to further understand the disease,” said Ilkay Altintas, the chief data science officer at the San Diego Supercomputer Center, who is . The easier we can make to share the data and optimize the use of it through digital technologies, the quicker other researchers will make use of it in their studies.”

Researchers also are keeping up efforts to recruit a diverse pool of subjects that reflects the U.S. population. 

“We need to make sure that our algorithms work for everyone,” Smarr said. 

In future, researchers plan to expand their early detection methods to other infectious diseases, such as the flu. 

Smarr has worked as a consultant with Oura within the last 12 month and received compensation, although not during this research project. 

Feasibility of continuous fever monitoring using wearable devices

Benjamin Smarr, UC San Diego Department of Bioengineering and Halicioglu Data Science Institute

Kirstin Aschbacher, UC San Francisco and Oura

Sarah M. Fisher, Anoushka Chowdhary, Kerena Puldon, Adam Rao, Frederick Hecht and Ashley E. Mason UCSF

Stephan Dilchert, City University of New York and preValio LLC, Minneapolis

Passing of Shao-chi Lin, Professor Emeritus of Engineering at UC San Diego

Shao-chi Lin, Professor Emeritus of Engineering at the University of California San Diego, died on October 8, 2020 at the age of 95. He is remembered by former students and colleagues as a talented and caring teacher, mentor and researcher; and an active member of the campus community.

Lin was an internationally renowned engineer who specialized in gas dynamics, which has applications in many areas including the re-entry of spacecraft into earth's atmosphere after space travel.

UC San Diego Professor Emeritus Forman Williams remembers Lin as an experimentalist who had excellent theoretical understanding, which is a powerful combination. Lin's dual strengths in theory and experimentation fed his passion for making real-world impacts through research, teaching, and mentorship.

UC San Diego professor Sol Penner recruited Lin to UC San Diego in 1964, where he joined the newly formed Aerospace and Mechanical Engineering Sciences (AMES) Department as a professor of engineering physics.

A world-class mentor

Lin taught and mentored many UC San Diego students over the years. Two students who earned PhDs under his guidance, and who were driven, like Lin, by a desire to make real-world impacts, are Robert Akins BA ’74, M.S. ’77, Ph.D. ’83, and Richard Sandstrom, BA ’72, M.S. ’76, Ph.D. ’79.

Grounded in expertise on excimer lasers that were part of Lin's research program at UC San Diego, Akins and Sandstrom founded Cymer. This San Diego based company grew to lead the world in the design and manufacture of laser light sources used for making computer chips for computers, phones and many other electronic devices.

"He was a strong intersection of a practical hardware guy and a very good theoretician," said Sandstrom, who explained that Lin instilled the importance of backing up experimental research with a good theoretical foundation. Lin pushed his students to keep asking themselves "What's behind it?"

There are different kinds of personalities you find among professors, explained Akins. "Some are extremely academic, some are outward focused. Dr. Lin was able to blend very strong academics with being very involved in real life," said Akins. "In one of his graduate classes on gas dynamics, the only question on the final was to calculate the peak temperature on the heat shield of a re-entering Apollo space capsule. It was as short as that. You had to come up with a ballpark answer."

Akins fondly recalled Lin's ability to quickly walk through a calculation rationale, making numerous assumptions and calculating units, and then asking students to check his calculations. "You would find he was pretty close, maybe 10% off. He could do that again and again and again."