Physicists curate list of COVID-19 projects to join

As we continue to deal with the global COVID-19 pandemic, biomedical researchers are racing to understand the virus that causes the disease, to evaluate its spread, and to develop tests, treatments and vaccines.

Physicists are volunteering to assist in these efforts, using their skills in data analytics, machine learning, simulation, software, computing, hardware development and project management. And an organization called Science Responds is helping to match them with projects that need their support.

As Savannah Thais, a postdoctoral researcher in high-energy physics and a co-founder of Science Responds, reported at the April meeting of the American Physical Society, physicists are assisting with a variety of types of projects, divided into the following categories:

Epidemiology

Epidemiology is the branch of medical science that studies public health problems and events in order to understand what causes them, how they are distributed among populations and possible ways to control them. Epidemiologists investigate diverse problems including pollution, foodborne illnesses, natural disasters and infectious diseases such as COVID-19.

Science Responds is connecting physicists with epidemiological projects that are working to model how the virus that causes COVID-19 might spread. Physicists hope to help address a major problem that the experts making these models face: incorporating data from a multitude of dissimilar sources.

Thais says physicists have the background and experience needed to provide epidemiologists this kind of support.

“We don’t think physicists should be building their own epidemiological models from scratch, because they don’t have the domain expertise of an epidemiologist or biologist about infectious diseases,” she says. But “physicists can be most effective by providing their computing and statistics skills to interdisciplinary research.”

One epidemiology project Science Responds encourages volunteers to join is HealthMap, which displays data about COVID-19 cases across the globe over time via an openly accessible website and mobile app. HealthMap integrates and filters data from diverse, publicly available sources—including online news aggregators and reports from governments and agencies such as the World Health Organization—and then creates intuitive visualizations of the state of the outbreak by location.

Other modeling projects use analyses of the genomic features of previously studied viruses to help estimate unreported COVID-19 cases; integrate health and hospital resource data to inform localized risk predictions; and incorporate information from previous animal and human outbreaks to improve model accuracy.

Diagnosis

An important part of dealing with an epidemic is determining who has the disease, but shortages of testing supplies have made diagnosis a challenge. Science Responds promotes projects that are trying to address this gap in different ways.

Some projects use artificial intelligence to process visual or audio data. The project CAD4COVID, for example, builds off an existing technology that has been highly successful in diagnosing tuberculosis through the analysis of chest X-rays. The project COVID Voice Detector, on the other hand, is collecting audio recordings to develop an AI that can recognize signs of COVID-19 infection in a patient’s voice.

Other projects are building tools to predict who is likely to experience the most severe effects of COVID-19. These machine-learning-based efforts identify indicators such as markers that appear in blood tests or specific features from lung biopsies to predict the likelihood of long-term hospitalization or death.

Treatments and cures

The race to develop COVID-19 vaccines and treatments begins with understanding the physical structure of the virus. On this front, Science Responds collaborators are providing key support for an effort called Folding@Home, which uses computer simulations to map out the proteins the SARS-CoV-2 virus uses to reproduce and suppress a patient’s immune system. Physicists are helping to develop the protein-folding simulations, but they are also playing a pivotal role in looking for help from anyone with a computer that Folding@Home can use remotely to run folding simulations.

In addition, physicists are helping process the massive amount of data related to the SARS-CoV-2 genome. They’re hoping to identify molecules that are important to the growth and spread of the virus and to understand its mutations.

Science Responds collaborators are also aiding efforts to use machine learning to identify drugs that could be repurposed to treat COVID-19. For example, they are using natural-language-processing algorithms to comb through a massive database of scholarly articles, called CORD-19, for relevant ideas. Other projects are using deep-learning-based models with existing data to predict how commercially available drugs will interact with the virus.

Supporting hospitals and healthcare systems

Science Responds participants are volunteering on projects to support frontline workers who are providing medical care to COVID-19 patients. These efforts include developing models to help predict hospital overload and to allow for the sharing of resources such as mechanical ventilators and personal protective equipment.

One example is the CHIME project, which gathers information on hospital resources and predicts when the needs of patients will exceed an institution’s capacity. CHIME has already been deployed in several hospitals, including the University of Pennsylvania Health System.

Another project in this area is COVID Care Map, which is using open-source data to map existing supplies of hospital beds, ventilators and other resources needed to care for COVID-19 patients such as available staff.

Other projects highlighted by Science Responds are aimed at improving telehealth. Enhanced at-home care could reduce the spread of COVID-19 by eliminating unnecessary hospital visits and improving access to care for rural areas.

Researchers are helping to develop AI-based chatbots that can be used to assess possible infections, educate patients and call on human providers when necessary. Other projects are working to combine in-home sensors and cameras with AI-assisted technologies to remotely monitor the health of vulnerable populations.

Socio-economic response

Finally, Science Responds volunteers are also working to address what they call “second-order effects,” not directly related to healthcare.

Some projects deal with infodemiology, research into what we can learn from user-contributed, health-related content on the internet. Researchers are analyzing millions of real-time tweets related to COVID-19 to answer questions like: How are people reacting to the outbreak? How is Twitter being used to pass on vital information? How is Twitter being abused to spread false information, panic and hate?

Physicists with data-analysis and data-engineering expertise can volunteer for projects aimed at bringing attention to at-risk populations. Thais leads a project that is developing a COVID-19 Vulnerability Index, an AI-based predictive model used to identify communities at high risk of socio-economic and health impacts associated with the spread of COVID-19.

The index looks at a wide range of measures, such as whether community members have access to home Wi-Fi, whether they are affected by non-COVID health issues such as diabetes, and whether healthcare resources are available to them.

Are you a physicist looking to volunteer? Thais recommends checking out the Science Responds website, which lists projects organized by their required skills, highlights available data sources, computing resources and funding opportunities, and provides instructions for getting connected.

Illustration by Sandbox Studio, Chicago with Ana Kova

This is a reposting of my news feature, courtesy of Symmetry magazine.

 

Why do viruses like the coronavirus sometimes steal our sense of smell?

When you catch a severe cold, your nose stuffs up, you can’t smell anything and food tastes funny. Fortunately, most people regain their sense of smell once the cold runs its course. But for others, the complete (anosmia) or partial (hyposmia) loss of the sense of smell is permanent.

I spoke with Zara Patel, MD, a Stanford associate professor of otolaryngology, head and neck surgery, and director of endoscopic skull base surgery, to learn more about her research on olfactory disorders. In particular, we discussed her recent study on the possible association between post-viral olfactory loss and other cranial neuropathies, which are disorders that impair your nerves and ultimately your ability to feel or move. She also described how her work pertains to the COVID-19 pandemic.  

How does a virus impair someone’s sense of smell?

A variety of viruses can attack the cranial nerves related to smell or the mucosal tissue that surrounds those nerves. Cranial nerves control things in our head and neck — such as the nerves that allow us to speak by using our vocal cords, control our facial motion, hear and smell.

For example, COVID-19 is just one type of disease caused by a coronavirus. There are many other types of coronaviruses that cause colds and upper respiratory illnesses, as well as rhinoviruses and influenza viruses. Any of these viruses are known to cause inflammation, either directly around the nerve in the nasal lining or within the nerve itself. When the nerve is either surrounded by inflammatory molecules or has a lot of inflammation within the nerve cell body, it cannot function correctly — and that is what causes the loss or dysfunction of smell. And it can happen to anyone: young and old, healthy and sick.

How did your study investigate olfactory loss?

In my practice, I see patients who have smell dysfunction. But I’m also a sinus and skull base surgeon, so I have a whole host of other patients with sinus problems and skull-based tumors who don’t have an olfactory loss. So we did a case-control study to compare the incidence of cranial neuropathies — conditions in which nerves in the brain or brain stem are damaged — in two patient groups. Ninety-one patients had post-viral olfactory loss and 100 were controls; and they were matched as closely as possible for age and gender.

We also looked at family history of neurologic diseases — such as Alzheimer’s disease, Parkinson’s disease and stroke.

What did you find?

Patients with post-viral olfactory loss had six-times higher odds of having other cranial neuropathies than the control group — with an incidence rate of other cranial nerve deficits of 11% and 2%, respectively. Family history of neurologic diseases was associated with more than two-fold greater odds of having a cranial nerve deficit. Although we had a small sample size, the striking difference between the groups implies that it is worthwhile to research this with a larger population.

Our findings suggest that patients experiencing these pathologies may have inherent vulnerabilities to neural damage or decreased ability of nerve recovery — something beyond known risk factors like age, body mass index, co-morbidities and the duration of the loss before intervention. For example, there may be a genetic predisposition, but that is just an untested theory at this point.

How does this work pertain to COVID-19?

Smell loss can be one of the earliest signs of a COVID-19 infection. It can sometimes be the only sign. Or it can present after other symptoms. Although it may not affect every patient with COVID-19, loss of smell and taste is definitely associated with the disease. In some countries, including France, they’ve used this as a triage mechanism. People need to know that these symptoms can be related to the COVID-19 disease process so they aren’t going about their lives like normal and spreading the virus.

The pandemic also might impact how we treat patients with olfactory dysfunction in general. When someone has a viral-induced inflammation of the nerve, we sometimes treat it with steroids to decrease the inflammation. But treating COVID-19 patients with steroids might be a bad idea because of its effect on the inflammatory processes going on in their heart and lungs.

What advice do you have for people who have an impaired sense of smell?  

First, if you lose your sense of smell and it isn’t coming back after all the other symptoms have gone away, seek care as soon as possible. If you wait too long, there is much less that we can do to help you. Interventions, including olfactory training and medications, are more effective when you are treated early.

Second, if you lose your sense of smell or taste during this pandemic and you don’t have any other symptoms, contact your doctor. The doctor can decide whether you need to be tested for COVID-19 or whether you need to self-isolate to avoid being a vector of the virus in your family or community.

Image by carles

This is a reposting of my Scope story, courtesy of Stanford School of Medicine.

Defend or delay? Grad students must decide whether to present their thesis virtually

Graduate students who are trying to finish their degrees amid the COVID-19 pandemic are finding, after years of research and months of preparation, that the big day of defending their thesis has to be delayed or done remotely.

Faced with a new order to shelter at her off-campus home, Anjali Bisaria, a graduate student in chemical and systems biology at Stanford, decided to forge ahead. She works in the lab of Tobias Meyer, PhD,  where they study how human cells move and divide to build, maintain and repair tissues and organs.

On the scheduled date and time, Bisaria logged into a Zoom session and defended her research to a virtual audience of advisors, classmates, friends and family members. She then virtually met with just her faculty examinees. After being declared a doctor, she celebrated with her lab via yet another Zoom session.

“I know it was the right thing to do to keep the community safe,” she said in a Stanford news story. “But it was a little bit sad because this is likely my last quarter on campus. So to not be able to interact with my classmates and not be able to enjoy that honeymoon phase of grad school felt unceremonious.”

Soon, microbiology and immunology graduate student Kali Pruss will face the same decision. Her in-person PhD oral is currently scheduled for May 22 at Munzer Auditorium on Stanford campus.

“I haven’t yet decided whether I’ll proceed with my defense via Zoom or delay my defense to later in the summer, in hopes that I would be able to have an in-person defense,” Pruss told me. “I was planning on staying through the summer, taking a writing quarter anyway. Thankfully, this gives me some flexibility in terms of timing.”

As a member of the lab run by Justin Sonnenburg, PhD, Pruss studies how Clostridium difficile — a bacteria that commonly causes diarrhea and colitis — adapts to the inflammation that it generates, she said.

Pruss is currently writing a paper on her research, but the pandemic is impacting that too. She told me that she’s doing more data analysis and relying less on experiments than she normally would — and she’s a bit worried about how this approach will be received.

“I’m concerned with how this is going to affect the review process, and whether I’ll be able to successfully address reviewer comments asking for additional experiments for my papers,” she said.

She added, “Ultimately, though, I feel incredibly privileged and grateful to be able to continue working remotely towards my dissertation. The question of how my research is being impacted, and whether to postpone my defense, has been a minor concern in the scope of what is currently happening at Stanford and around the world.”

Given the extension of the Bay Area’s shelter-at-home order to last through at least May 3, Pruss’s hopes of defending in-person on May 22 may not be realized. So, her extended family — from Wisconsin, Indiana and Illinois — canceled their travel arrangements. They hope to come in late summer if she delays her defense and sheltering orders have been lifted.  

Regardless of how she defends her thesis, she plans to celebrate her upcoming educational milestone.

“This is the one time we, as PhD students, get to celebrate our time in grad school as an accomplishment,” she said.

After graduation, Pruss plans to join Jeffrey Gordon’s lab at Washington University School of Medicine in St. Louis as a postdoc. Ultimately, she plans to run her own academic lab.

Photo by Anjali Bisaria

This is a reposting of my Scope story, courtesy of Stanford School of Medicine.