COVID-19: the Jacobs School community engages
San Diego, Calif., updated on May 15, 2020 -- The UC San Diego Jacobs School of Engineering community is stepping up to address many challenges that the COVID-19 pandemic has put before us. This web story highlights is a cross section of projects that Jacobs School faculty, students, staff and alumni have launched in response to COVID-19. Some of these efforts are sure to grow into larger, sustained efforts. Others will morph or conclude as needs and available resources change. Through it all, our commitment to bold innovation for the public good remains.
Know of a COVID-19 project at the Jacobs School of Engineering?
Reach out to communications director Daniel Kane at: email@example.com
June 19, 2020
Understanding COVID-19 through genome analysis
Pavel Pevzner, a professor in the Department of Computer Science and Engineering, has receivd a $300,000 grant from the National Science Foundation through the Early-concept Grants for Exploratory Research (EAGER) mechanism, to study COVID-19. The project is called: Assembling the Immunoglobulin Loci Across Mammalian Species and Across the Human Population.
June 8, 2020
A better way to split ventilators
The COVID crisis has resulted in equipment shortages, including ventilators. Increasing ventilation capacity by sharing them between two or more patients is one option, but it has many risks. Dr. Lonnie Petersen, from the Jacobs School, and Dr. Sidney Merritt, from the School of Medicine, developed a process that would allow use of a ventilator to service two patients at the same time, addressing and solving key safety issues. The research has been accepted for publication by the journal Critical Care. More information:
June 4, 2020 udpate
Engineers at the University of California San Diego are developing low-cost, low-power wearable sensors that can measure temperature and respiration--key vital signs used to monitor COVID-19. The devices would transmit data wirelessly to a smartphone, and could be used to monitor patients for viral infections that affect temperature and respiration in real time. The research team plans to develop a device and a manufacturing process in just 12 months.
May 15, 2020 update
Real-time quantitative detection of protease activity
Patients with severe COVID-19 infections have higher levels of plasmin protease activity in their blood. This enzyme is thought to enhance the virulence and infectivity of SARS-CoV-2 virus by cleaving the viral spike protein. The UC San Diego team developed a sensor that can rapidly quantify protease activity in biological fluids. The new work appears in Nature Scientific Reports and is led by UC San Diego electrical engineering professor Drew Hall and UC San Diego Skaggs School of Pharmacy professor Anthony O’Donoghue. In their new assay, magnetic nanoparticles are immobilized to the surface of a giant magnetoresistive spin-valve sensor using peptides. Cleavage of these peptides by a target protease in a biofluid releases the magnetic nanoparticles resulting in a time-dependent change in the local magnetic field. The team has validated this assay to quantify proteases in urine and is currently modifying this assay to quantify plasmin in blood.
May 5, 2020 updates
UCSD Privacy-preserving COVID-19 Contact Tracing Apps
Two teams in the Electrical and Computer Engineering (ECE) Department at UC San Diego are developing new cell phone applications for more accurate, private COVID-19 contact tracing. Led by electrical engineering faculty Dinesh Bharadia and Farinaz Koushanfar, the applications use wireless sensing and close integration with health systems, respectively, to monitor an infected person’s social interactions, while preserving the user’s privacy.
UCSD & TU Darmstadt Privacy-preserving COVID-19 Bluetooth Contact Tracing App
Lead by Professor Farinaz Koushanfar
Prof. Koushanfar in collaboration with Technical University Darmstadt has developed a novel privacy-preserving Bluetooth-based smart phone app for COVID-19 contact tracing. Contact tracing can be used to record and discover the social exposure of people with close contact to patients tested positive with COVID-19. The resulting app is aimed for integration within the UCSD myHealth website, which is based on the widely used Epic medical platform to perform contact tracing for patients and healthcare professionals. We are also working closely with Qualcomm on learning their Bluetooth measurement data and models for integration within our app. Koushanfar is tightly collaborating with the TU Darmstadt since they have successfully launched the beta testing of their tracing app. The tracing app complies to both privacy regulations of Germany and California. To download the beta application go to https://tracecorona.net/download-tracecorona/
Meanwhie, BluBLE, an app under development in the Wireless Communications Sensing and Networking Laboratory, which is in the electrical engineering department, provides each user with a customized risk profile to determine their chances of contracting COVID-19. Now available on android and iOS, BluBLE uses infrastructure provided by Google and Apple to launch a novel algorithm that accounts for environmental context, including the exact distance between two people, their activity level (e.g. walking or jogging), whether the interaction took place in an indoor or outdoor environment, and the position of a person’s phone. All of this information is gathered while keeping each user anonymous.
Using voice to detect COVID-19
Researchers at UC San Diego are part of a collaborative, multinational effort to use changes in voice to detect COVID-19. They are gathering voice and coughing audio samples from people who both have and have not tested positive for COVID-19. Then, researchers including those at UC San Diego, are using algorithms and neural networks to pick out differences in the patterns between the two groups, with a goal of being able to detect if someone has the virus simply by them speaking or coughing into their phone or computer microphone. Computer scientists, electrical engineers and mechanical engineers at the Jacobs School are contributing to the analysis of open source data collected by several different companies and institutions, including Voca.ai, Vocalis, Carnegie Mellon University and MIT.
Shlomo Dubnov, a professor in the Departments of Music and Computer Science and Engineering, is leading UC San Diego’s involvement in the project, and is using tools he and his lab developed to analyze musical sounds. UC San Diego researchers, including mechanical engineering graduate student Tammuz Dubnov and his startup company Zuzor, are also developing and repurposing tools to be able to deploy these detection algorithms over apps and web browsers.
UV-Drone: Mobile Disinfection Platform for Community Facilities with Minimum Human Exposure
Disinfecting areas that have been exposed to COVID-19 using conventional methods of washing and cleaning surfaces with disinfecting liquid and materials, exposes the most disadvantaged workers on the frontlines and increases the risk of exposure and disease contraction for the cleaning crew. Professor Tara Javidi is leveraging her DetecDrone research platform developed at UC San Diego to significantly improve on the process of UV-based disinfection. In addition to providing a cost effective and agile non-contact UV-C sterilization, the researchers envision the first Do It Yourself (DIY) prototype of a drone platform for delivering non-contact mobile UV sterilization unit (UVerizeDrone) for community facilities such as schools, institutions of higher education, offices, daycare centers, businesses and community centers. Javidi is Co-Director of the Center for Machine-Integrated Computing and Security (MICS) at the UC San Diego Jacobs School of Engineering. Learn more on the MICS COVID-19 page.
UC San Diego Team Delivers Protective Equipment to Hospitals in Baja California
The COVID-19 pandemic is impacting the availability of personal protective equipment (PPE) supplies in Baja California, and researchers with UC San Diego are engineering solutions to help. Nadir Weibel, an associate professor in the Department of Computer Science and Engineering and head of the Human-Centered and Ubiquitous Computing Lab, is collaborating with university colleagues, government and industry to develop PPE solutions and to transport ing supplies, like masks and face shields, to hospitals in Baja.
So far, the team in collaboration with the CAICE lab and the Scripps Institution of Oceanography has produced, tested and delivered 3,000 face shields, with around 1,100 masks on the way. The protocols to make this equipment have been published on Earth 2.0, a curated clearinghouse started by UC San Diego faculty and students for COVID-19 information and solutions.
Researchers Awarded NSF Grant to Apply Epidemic Model to COVID-19
Behrouz Touri and Massimo Franceschetti, both on faculty in the Department of Electrical and Computer Engineering Department at UC San Diego, have secured funding from the National Science Foundation to address COVID-19 using the Susceptible Infectious Recovered (SIR) mathematical model. The two researchers are in the early stages of adapting the SIR model to the current pandemic, in the hopes of identifying policies that effectively reduce the number of COVID-19 infections and mortalities, while limiting the cost to the economy. In time, the researchers hope to provide officials and policymakers at the city and regional level with insight into the efficacy of social distancing, stay-at-home orders and other guidelines.
Privacy-preserving COVID-19 Discovery
Several research labs worldwide, both on the industrial and university side, are focused on sequencing the COVID-19 virus and studying its interactions in-vivo and in-vitro. In several cases, sharing the data and models is not possible due to privacy and IP issues, impeding collaboration for achieving a faster discovery. Professor Farinaz Koushanfar’s lab provides one-of-a-kind provable privacy-preserving methodologies, based on verified cryptographic protocols, which enable collaboration among the various entities in an encrypted domain. With this method, the privacy of the IP/content owners is not compromised, while new collaborations and discoveries are uniquely enabled. In particular, multiple research labs will be able to jointly work on the encrypted version of the aggregated data without disclosing their sensitive information to any other research lab. These state-of-the-art technologies provide a secure platform such that the confidentiality of the data during computation is guaranteed. The platform also assured the correctness of the computation; the result is equivalent to running the underlying algorithm on the cleartext (unencrypted) data. The platform will remove several critical obstacles in the global-scale study of COVID-19, and in turn, will accelerate the process of finding new recovery mechanisms. Koushanfar is Co-Director of the Center for Machine-Integrated Computing and Security (MICS) at the UC San Diego Jacobs School of Engineering. Learn more on the MICS COVID-19 page.
Robust AI for Automated and Accelerated Literature and Trend COVID-19 Systemization of Knowledge
Professor Farinaz Koushanfar is leading development of novel robust and safe accelerated methodologies, based on natural language processing (NLP) to systemize knowledge discovery in the COVID-19 domain. While several disparate entities are working in research on the topic, and a multitude of sources are publishing news on a daily basis, their platform is interactive, allowing researchers and public health professionals to follow the many updates. NLP-based methods are useful for automated knowledge discovery but suffer from the existence of unreliable sources, data poisoning and fake news. This effort focuses on making the automated knowledge search systematic, safe and robust, while we simultaneously address scalability through new hardware/software/algorithm co-design. Koushanfar is Co-Director of the Center for Machine-Integrated Computing and Security (MICS) at the UC San Diego Jacobs School of Engineering. Learn more on the MICS COVID-19 page.
A Controlled Response to COVID-19
Electrical engineering rofessors Massimo Franceschetti and Behrouz Touri are proposing a generalization of Susceptible Infectious Recovered (SIR) model for inhomogeneous population. Using tools from optimal control and nonlinear control and based on the proposed mean-field model, they are working to find the optimal-cost containment policy to meet the local health-care provider's care capacity.
May 4, 2020 update
Protecting medical staff during procedures and providing non-invasive respiratory support
Researchers have desgined and build a large enclosure that extracts exhaled aerosols and droplets from COVID-19 patients, providing health care workers with a safety barrier. The vaccum exhaused isolation locker, or VEIL, is currently being used on five patients. "We hope that the properties of the VEIL will increase the number of options for non-invasive respiratory support for COVID19 patients without increasing the risk of viral contagion," researchers write. They've made 20 of the devices so far and plan to manufacture 90 more as soon as possible. The team includes Dr. Timothy Morris, a pulmonologist at UC San Diego, James Friend, a professor the Department of Mechanical and Aerospace Engineering at UC San Diego, his PhD student Gopesh Tivawala and other physicians and researchers at the Jacobs School of Engineering, the UC San Diego School of Medicine and the Qualcomm Institute. More information: http://friend.ucsd.edu/veil/
Friend, Tivawala and colleagues also partnered with Dr. Alexander Girgis, a UC San Diego anesthesiologist, to build a device that protects medical staff from aerosols and droplets from COVID-19 patients during intubation and extubation. The team built about 20 of the devices. You can watch a demonstration of how the device is used here: http://friend.ucsd.edu/madbox/
April 20, 2020 update
Plant-based COVID-19 Vaccine
Nanoengineers at UC San Diego received NSF funding for their work to develop a COVID-19 vaccine that is based on a plant virus. The team’s goal is to use plants to create a stable, easy to manufacture vaccine that can be shipped around the globe. It will be packaged in slow-release microneedle patches that patients can wear on the arm to painlessly self-administer the vaccine in a single dose. The work is being led by nanoengineering professors Nicole Steinmetz and Jon Pokorski. Read the full story.
Earth2.0 / COVID Collective Response System
The UC San Diego community is part of the new, interdisciplinary Earth2.0 initiative, which focuses on leveraging emerging digital technologies to harness, coordinate and empower citizen-centric activities that can quickly surface problems and crowd source innovations, resource management or development. The Earth2.0 / COVID Collective Response System supports front-line clinicians and researchers who need help answering questions, performing tasks or locating resources in real-time by engaging a local network of experts ranging from clinical researchers, to scientists and engineers (faculty, staff and students) to help provide solutions. UC San Diego researchers include computer science professor Nadir Weibel, who is also with the Design Lab; computer science professor and Contextual Robotics Institute Director Henrik Christensen; and Qualcomm Institute Director and electrical engineering professor Ramesh Rao. You can read the story here.
April 17,2020 update
UC San Diego Researchers Optimize Microbiome Tool for Computer GPUs
Researchers at UC San Diego have been applying their high-performance computing expertise by porting the popular UniFrac microbiome tool to graphic processing units (GPUs) in a bid to increase the acceleration and accuracy of scientific discovery, including urgently needed COVID-19 research. Learn more.
April 13, 2020 update
IBM and UC San Diego to pivot AI for Healthy Living collaboration to take on COVID-19 pandemic
UC San Diego and IBM are building on the existing AI for Healthy Living (AIHL) collaboration in order to help tackle the COVID-19 pandemic. AI for Healthy Living is a multi-year partnership leveraging a unique, pre-existing cohort of adults in a senior living facility to study healthy aging and the human microbiome as part of IBM's AI Horizons Network of university partners. “In this challenging time, we are pleased to be leveraging our existing work and momentum with IBM through the AI for Healthy Living collaboration in order to address COVID-19,” said Rob Knight, UC San Diego professor of pediatrics, computer science, and bioengineering and Co-Director of the IBM-UCSD Artificial Intelligence Center for Healthy Living. Knight is also Director of the UC San Diego Center for Microbiome Innovation.
April 2, 2020 updates
Engineers and doctors team up to retrofit and 3D-print ventilators
A team of engineers and physicians at UC San Diego is working to turn emergency hand-held ventilators into devices that can work autonomously for long periods of time, without human input. Ventilators are medical devices that push air in and out of a patient’s lungs when they are unable to breathe on their own. One of the primary symptoms of COVID-19 is difficulty breathing; approximately 1 percent of people who contract the virus require ventilation to support their recovery — sometimes for weeks. Read the full story. Watch the video. Read the story in STAT.
Researchers work on early warning system for COVID-19
To better understand early signs of coronavirus and the virus' spread, physicians around the country and data scientists at UC San Diego are working together to use a wearable device to monitor more than 12,000 people, including thousands of healthcare workers. The effort has started at hospitals in the San Francisco Bay Area and at the University of West Virginia. The team includes bioengineer Ben Smarr, and computer scientists Rob Knight and Ilkay Altintas. Read the full story. An early press report ran in the San Francisco Chronicle. Read the KPBS story. Read the US News story.
Crowdsourcing SARS-CoV-2 info
A crowdsourced research effort based at the University of California San Diego School of Medicine, has expanded its capabilities to now allow citizen-scientists around the world to help collect crucial information about SARS-CoV-2, the novel coronavirus causing a COVID-19 pandemic. “We are now positioned to collect data that will help drive epidemiological studies of where the virus is and isn’t, and help researchers determine who is at greatest risk, who is already immune, how the virus is transmitted and how it spreads through a population,” said UC San Diego professor Rob Knight, co-founder of The Microsetta Initiative. Knight is Director of the Center for Microbiome Innovation at the UC San Diego Jacobs School of Engineering and holds appointments in the departments of Bioengineering and Computer Science and Engineering. Read the story in This Week @ UC San Diego.
A smart scale to detect COVID-19
A smart scale installed below patients’ beds can detect sleep duration, cough, heartbeats and respiration. A team of engineers and physicians who developed the device are hoping it will be able to detect respiratory and cardiac changes that occur before patients develop COVID-19 related pneumonia. Hundreds of devices have been manufactured and they are currently in patients’ homes throughout San Diego County. The effort is led by bioengineering professor Dr. Kevin King, who is also a practicing cardiologist with UC San Diego Health, and bioengineering professor Todd Coleman.
COVID-19 sequencing analysis in real time
Bioinformatics researcher (and computer science teaching professor) Niema Moshiri created an automated tool that analyzes in real time genomic coronavirus open-source datasets from the Global Initiative on Sharing All Influenza Data (GISAID). The tool outputs results in a way that is more user-friendly for public health and biology researchers. Some of the information that can be extracted from analysis includes the virus' most likely evolutionary history; information about the common ancestors of viral samples; and information about how recent each version of the virus is in given clusters of patients. This could help health officials determine effective policies to contain the virus and to potentially design therapeutics. Moshiri received a $200,000 RAPID grant from the National Science Foundation for the work, with computer science professor Tajana Rosing. The tool can be found here on Github. Read Moshiri's related article in The Conversation, which also appeared in many US newspapers, including the San Francisco Chronicle.
UV light- and heat-based decontamination system
Nanoengineering professor Jesse Jokerst is part of a team at UC San Diego developing a process to decontaminate N95 masks with UV light and heat so they can be safely reused. The work, which is still in the experimental stages, aims to address the shortage of protective masks for health care workers.
Imaging medical masks at the nanoscale
Nanotechnology researchers led by Prof. Shirley Meng are evaluating the effectiveness of improvised medical masks using scanning electron microscope (SEM) technology available at UC San Diego’s Nano3, which is a nanofabrication cleanroom facility that is part of the Qualcomm Institute. This technique can image structures whose dimensions are much smaller than the novel Coronavirus, providing researchers a means to accurately gage the effectiveness of various personal protection equipment materials.
Qualcomm Institute Prototyping Lab
Researchers and engineers at UC San Diego's Qualcomm Institute Prototyping Lab are evaluating the use of 3D printing technologies and rapid prototyping techniques to create safe and effective medical equipment and gear, such as ventilator components and face shields. Teams are also exploring the possibility of using 3D printers to produce large quantities of the nasal swabs needed for COVID-19 testing. Read the full story.
Non-invasive Spleen Ultrasound Treatment for COVID-19 Patients
Based on established results that show stimulation of the vagus nerve (the longest cranial nerve in the body) can produce anti-inflammatory effects that can help prevent sepsis-related mortality, UC San Diego researchers affiliated with the Qualcomm Institute are developing and testing Focused Ultrasound Spleen Stimulation, or FUSS, as a potential treatment for the hospitalized COVID-19 patient. FUSS engages the vagus cholinergic anti-inflammatory reflex to potentially aid the body’s response to the virus. The project is a collaboration between Qualcomm Institute and UC San Diego Health researcher Dr. Imanuel Lerman and bioengineering professor Todd Coleman and electrical engineering professor Truong Nguyen from the Jacobs School.
The Pacific Research Platform, a National Science Foundation-supported project, overseen by Larry Smarr, the Harry E. Gruber Professor in Computer Science and Engineering, has lent its distributed computing and storage powers to help in the fight against COVID-19. Within the last two weeks, more than half of the distributed system’s 600 GPUs have been made available to the global Folding@home effort to study the dynamics of how viral proteins interact with human receptors. Smarr says this shows how quickly the system’s resources are able to be repurposed to support an urgent and critical need such as combating the novel coronavirus.
Sharing mass spectrometry data
UC San Diego researchers created an open-data community resource for sharing of mass spectrometry data and (re)analysis results for all experiments pertinent to the global SARS-CoV-2 pandemic. The resource, called CoronaMassKB, is designed for the rapid exchange of data and results among the global community of scientists working towards understanding the biology of SARS-CoV-2/COVID19 with the goal of accelerating the emergence of effective responses to this global pandemic. The project is led by computer science professor Nuno Bandeira.
Crowd-Sourcing Pandemic Management
Michael Barrow, a PhD candidate in the research group of computer science professor Ryan Kastner, is leading efforts to mitigate shortages in ventilators and critical care specialists. He and his team are developing a universal control system to help produce high-quality, safe DIY ventilators. (This effort is related to the ventilator projects listed above being led by mechanical and aerospace engineering professors James Friend and Lonnie Petersen.) They are also developing a telemedicine platform that allows specialists to focus on the patients who need them most while less-trained clinicians can monitor more stable patients and query as necessary.
Using robots to combat COVID-19
Can robots be effective tools in combating the COVID-19 pandemic? A group of leaders in the field of robotics, including Henrik Christensen, director of UC San Diego’s Contextual Robotics Institute, say yes, and outline a number of examples in an editorial in Science Robotics. They say robots can be used for clinical care such as telemedicine and decontamination; logistics such as delivery and handling of contaminated waste; and reconnaissance such as monitoring compliance with voluntary quarantines. Read the full story. Read coverage in Wired. Read news coverage in The Washington Post.
SEDS students join ventilator challenge
Students from the Students for the Exploration and Development of Space (SEDS) organization are turning their attention to a challenge to design a low-cost, simple, easy-to-use and easy-to-build ventilator that can serve COVID patients, in an emergency timeframe. What SEDS brings to the table is experience with High Oxygen Environment safety, and 3D-printing and fluid system experience. A UC San Diego emergency medicine resident is providing medical input. More information on the Code Life Ventilator Challenge. More information on SEDS at UC San Diego.
Jacobs School Alumni Projects
Fluxergy, a medical diagnostic company based in Irvine, California, that designs and builds rapid point-of-care diagnostic testing devices, collaborated with UC San Diego Health faculty to test a system to diagnose COVID-19 in under an hour. On March 30 they submitted an Emergency Use Authorization (EUA) to the U.S. Food and Drug Administration (FDA) in the hopes that their device can be deployed in medical settings within the next few weeks, making it possible for healthcare systems to test for the virus in under an hour, at the point-of-care. Most of the team behind Fluxergy met as engineering students at the Jacobs School of Engineering, where they were members of the Formula Society of Automotive Engineers (SAE) team, now known as Triton Racing, as undergraduates. Learn more about Fluxergy: https://fluxergy.com/ Read the April 9 story in This Week @ UC San Diego.
Nanome, a company founded by Jacobs School of Engineering alumni and that spent its earliest days in the Qualcomm Institute Innovation Space (QIIS), is providing researchers with a virtual reality platform to visualize and study the novel coronavirus. Nanome develops open-access virtual reality software that creates a shared virtual space for researchers to collaborate with one another and interact with 3D models of molecules. Currently, Nanome’s team is working with collaborators from around the world to use their virtual reality software to examine the protein structures that allow the novel coronavirus to attach to healthy cells. Learn more: https://nanome.ai/
flashPub—a QIIS-incubated company on a mission to make scientific publishing smarter, smaller and faster—is organizing a global campaign of researchers to model outbreak scenarios at the city scale. The group will be rapidly publishing the modeling results and organizing data into an interactive map. Their goal is to predict when a city is going to hit a tipping point of hospitalizations in order to inform preparation and resource allocation decisions. Learn more: https://www.flashpub.io/
Know of a COVID-19 project at the Jacobs School of Engineering?
Reach out to communications director Daniel Kane at: firstname.lastname@example.org
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