March 2018 – Scientists Talk Funny

Learning from health-related social media posts: A Q&A

About 6,000 tweets are sent every second and they aren’t all about celebrities. Posts about health or illness can be tremendously valuable to health care professionals, allowing them to track trends, spot epidemics and assess the quality of services provided by health facilities, to name just a few uses.

But how can the researchers make sense of this flood of data? To find out, I spoke with Sidhartha Sinha, MD, an assistant professor of medicine at Stanford, who analyzes social media posts to better understand patient and societal perceptions.

What sparked your interest in online data?

“While there are certainly downsides with working with unstructured data from sources such as social media and online patient forums, there are also tremendous advantages, including the scope of patients we can ‘reach.’

For example, in our work analyzing data from an online patient forum for patients with inflammatory bowel disease, we are able to access tens of thousands of posts from patients with IBD. These patients are describing a variety of issues around their experience with the disease — such as their therapy side effects (some of which have not been seen before and may offer early insights), psychosocial issues with chronic disease, and opinions regarding treatments and interventions. By analyzing this data, we are in effect ‘listening’ to these patients’ experiences and hopefully gaining insights to better treat the disease.”

I understand you’ve also used online data to better understand public sentiment — could you describe that?

“One of the most important things health care providers do is try to prevent disease. And one of the best means to do this is through disease screening. However, millions of people do not get age-appropriate screening for diseases such as breast cancer or colon cancer. My group’s initial work targeted understanding the perceptions around cancer screening tools. Understanding how people feel about these screening interventions — particularly on the scale we’re able to examine using social media — allows us to not only identify barriers, but also further ascertain methods that work.”

How did you do that?

“Tens of thousands of tweets mentioning screening tests are created weekly. And while there are clear limitations to the quality of data and its generalizability, the sheer volume of data that we can access is much larger than most other means such as conventional surveys, which carry their own significant limitations. So we developed and validated a machine learning algorithm to classify sentiment (positive, negative, or neutral) around mentions of three common cancer screening tools: colonoscopy, mammography and PAP smears.

We found more negative sentiment expressed for colonoscopy and more positive sentiment for mammography. For example, the words ‘fear’ and ‘pain’ were commonly associated with negative sentiment. We also found that posts that were negative in sentiment spread more rapidly through social media than positive posts.”

How are these findings being used?

“Knowing the types of postings that reach more users, and some of the common issues expressed in them, could certainly influence how professional societies develop outreach interventions to improve engagement with preventive health efforts.

Based on our initial findings, we are developing additional algorithms to hopefully butter understand patient and societal perceptions of disease. We are also now engaged with professional societies such as the Crohn’s and Colitis Foundation to provide organizations with improved methods to understand patient needs and promote health.”

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

Big bacteria may be easier to kill, new research suggests

The size of a cell is intrinsicThe size of a cell is intrinsically linked with its genetic makeup, growth rate and other fundamental properties. What would happen if scientists could control the size of pathogens?

That possibility isn’t completely outlandish: Stanford researchers have discovered a genetic “tuning knob” that can enlarge or shrink bacteria across a wide range — and this knob can be used to fatten up the bacteria to increase their susceptibility to certain antibiotics, as recently reported in Current Biology.

The research team is led by KC Huang, an associate professor of bioengineering and of microbiology and immunology at Stanford. Huang explained in a recent Stanford Engineering news article:

“Most strategies to killing bacteria are linear: you find a very specific target and block it with a drug. These findings point in the direction of totally orthogonal therapies, in which you predispose cells to death by tweaking a global property like size.”

The researchers found that a single protein in E. coli, called MreB, acts as a master regulator of cell size by coordinating the construction of cell walls. So they manufactured many copies of the E. coli’s DNA, changing in each copy just one of the 347 letters in MreB’s genetic code. Using fluorescence-activated cell sorting, they then separated the individual cells with different sizes to create a library of cell-size mutants.

The team used this library to study how size impacts a cell’s physiology, including how bacterium grow and survive. For instance, they treated the various E. coli mutants with several antibiotics and found that larger E. coli were more sensitive to the drugs. A larger cell has more surface area and that increases the drug uptake, they said in the paper.

Huang said he hopes their techniques can be applied to other bacteria and used to help human health in the future. He added:

“While we don’t yet know how to twist this bacterial size dial in patients, it’s good to have such an exciting new therapeutic approach as antibiotic resistance becomes increasingly prevalent.”

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

Developing “guided missiles” to attack cancer: A podcast featuring a Stanford bioengineer

Chemotherapy attacks cancer by killing cells that are rapidly dividing. But this leads to serious side effects, like intestinal upset and hair fallout, because these normal cells grow quickly.

So researchers like Jennifer Cochran, PhD, a professor and the chair of bioengineering at Stanford, are developing more targeted cancer therapies, dubbed “guided missiles.” She recently described her work to professor and radio show Russ Altman, MD, PhD, on an episode of the Sirius radio show The Future of Everything.

“We, and others, have developed novel proteins that can selectively target cancer cells and then we can attach cargo to them — this is where the missile analogy comes in,” Cochran told Altman. “The cargo that we attach, things like chemotherapy, can then be selectively targeted to the tumor.” The idea is to precisely deliver to the tumor a more poisonous dose than you could deliver systemically, she said.

One way to do this is to bioengineer antibodies, which are molecules that recognize and help neutralize foreign substances like bacteria. However, Cochran’s lab took a slightly different approach. She explained to Altman:

“As amazing as antibodies are, they can have some limitations in that they are very large in terms of molecular size so they have trouble wiggling into a tumor. So we’ve created smaller versions of tumor-targeting proteins that can hopefully penetrate into tumors better. And we’ve then chemically attached chemotherapy molecules to deliver a punch to the cancer cells.”

In order to develop these proteins, her team is expediting protein evolution in a test tube — making favorable properties that would normally evolve over millions of years happen in just a few weeks. To do this, the team uses genetic manipulation to create millions of slightly different protein variants, tests them with high-throughput screening in just a few hours, identifies the ones most desirable for a certain task, and then determines these variants’ DNA sequences.

For example, they used this evolutionary process on a peptide, a small fragment of protein, from the seeds of a plant known as a squirting cucumber to turn the molecule into a favorable drug scaffold. “We ran the protein through this evolution process to create a tumor-targeting protein that we then hooked the chemotherapy agents on to,” said Cochran.

Cochran’s group is also investigating immunotherapy applications for her proteins. She is teaming up with Dane Wittrup, PhD, a professor in chemical engineering and biological engineering at Massachusetts Institute of Technology, who has developed new ways to use the immune system. By combining Cochran’s tumor-targeting technology with Wittrup’s insights into immunotherapy, they are able to give a “one-two punch” and activate multiple factors of the immune system to more effectively attack cancer, she said.

Her research team is also interested in applying their work to other diseases. She explained to Altman:

“We’ve been applying them for cancer, but you can use the same approach to deliver therapies to other types of disease tissue. We have really only just scratched the surface of what we can do. A big driver of this has been the interdisciplinary culture of collaborative research at Stanford. We’ve been working together with physicians, clinicians, scientists, engineers and physicists to tackle really challenging problems.”

Cochran’s bioengineered proteins are not yet available to patients. However, some tumor-targeting molecules are already approved by the U.S. Food and Drug Administration and many more are in the pipeline. “There are a number of molecules that are FDA approved and you might have heard commercials for them,” she told Altman. “But they only work for a subset of patients. So the question is: how do we make them work better for a larger subset of patients?”

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

BrainPost: Neuroscience summarized and delivered to your inbox

Like most busy professionals, neuroscientists have trouble keeping up with everything that’s going on in their field. They just don’t have enough time to read all the papers being published.

Neuroscientists Kasey Hemington and Leigh Christopher, PhD, a Stanford postdoctoral researcher, want to help. They created a new weekly e-newsletter, called BrainPost, that sends easy-to-read summaries of the latest neuroscience publications into their readers’ inbox. To learn more, I spoke with Christopher recently.

What inspired you to create BrainPost?

“Throughout my PhD and during my postdoc, I noticed two trends. First, when I talked to other neuroscientists, they were often unaware of research going on in closely related fields. I know that science is specialized, but it dawned on me that if scientists themselves are unable to keep up with other research, there was no way that members of the general public could even begin to stay on top of the latest advances. The second trend is one of too much data. I think with big data comes big confusion. We have too much to consume and therefore we often choose not to consume at all, because it’s overwhelming.

We wanted to simplify the process of consuming neuroscience, which is constantly changing. We also wanted to make the information easily accessible when open access to the original scientific publications is not an option. Hopefully, BrainPost can help make neuroscience convenient, fun and digestible.”

Who is your primary target audience?

“BrainPost summaries provide a little more information than traditional science journalism aimed at the general public. We primarily want to improve awareness about new neuroscience research within the science community. This means anyone who is engaging with neuroscience: a researcher, graduate student, undergraduate student, biotech employee, policy maker, clinician, psychologist, science journalist or science enthusiast. We want to encourage cross-discipline communication and collaboration.”

What is your selection and writing process?

“We choose recently published online articles from reputable journals that we feel are high quality and move neuroscience forward. We would love to cover more, but for now, we are limited by time as only myself and Kasey are working on the newsletter. In the future, we want to bring on more writers.

We send out all of our summaries to authors before publishing the e-newsletter. We’re able to incorporate their edits and comments to ensure our summaries are accurate and don’t sensationalize the findings or misguide the reader.

We hope to eventually cover most of the latest neuroscience publications on our website, acting as a continuously updated resource for neuroscience. Our ultimate goal is to expand and have customized newsletters on topics of interest, as well as a repository of summaries on our website.”

Why do you encourage readers to connect directly with the study authors?

“Kasey had this great idea to engage scientists by asking them to comment and to respond on social media. Social media can have a positive impact on the way we communicate about science. We want readers to start discussions with study authors to help create a more cohesive community amongst people engaging with neuroscience. When scientists are more social and vocal about their work, it helps to get the word out and for them to be better understood.

All of the scientists who we’ve reached out to on Twitter so far have been very enthusiastic and responsive. I think they’re excited to have their work recognized, since the academic world does not always offer enough of this recognition. BrainPost will hopefully help with that.”

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

On writing about female physicians and the Grand Canyon: A Q&A

As a voracious reader, I particularly enjoy mystery novels featuring a female detective or medical examiner. And as physicians know so well, medical mysteries can be just as gripping, and surprising, as crimes. So I was eager to read the novel, Only Rock is Real, about a female doctor with a family practice at the Grand Canyon. I spoke recently with the book’s author, Sandra Miller, MD, who is a writer and retired family physician.

What motivated you to write novels?

I have always written poetry and essays, but crafting a novel pushes my writing to another level. The process of weaving a plot — while creating compelling and authentic characters, developing their growth and showing their stumbles — is riveting to me. The greatest compliment is when readers tell me they feel like they know my characters personally and care about them.

I’m also on a mission to promote family medicine and women physicians through fiction. I really want to encourage physicians to write, and especially to write fiction. There is little medical fiction being written currently, with the exception of the crime scene/thriller genre. I would love to see more fiction about everyday physicians and their trials and joys. And I welcome with any medical writers who want to brainstorm, share or seek feedback about their work.

How did you develop the main character, Dr. Abby Wilmore?

Like most fictional characters, Abby is partly a conglomerate of people I have known and partly made up. Every physician wants to be highly competent and strives for excellence, but there are many potholes along that path. Perfectionism and anxiety are common in doctors; finding your peace with an ever changing and critical career like medicine is no small task. I wanted to show how her confidence builds and then derails — the ups and downs of successes and errors, real or perceived, in both her professional and personal life. I wanted to show how very human physicians are.

How did you select which patient cases to include?

I tried to use a mix of cases representing a typical day: some common and some less common, some routine prevention and occasionally a very difficult case. I also wanted to include a mix of physical and mental health issues. I guess the teacher in me is always lurking, because I also selected cases where readers can learn about topics like diabetes, the morning after pill and contraception, heat injury and flu vaccines.

I keep them as realistic as I can. Sometimes you know the diagnosis immediately and other times it takes detective work. Sometimes you’re wrong because people aren’t textbooks and they don’t always follow the rules. I’ve put much effort into making all the science — medicine, geology and astronomy — as accurate as I can.

Why did you set your books in national parks?

For the last thirty years of my career in academic medicine, I helped train family medicine residents who often did a rotation at the Grand Canyon clinic. And I have friends who worked there for years. I know their stories, the human dynamics in such unusual places. Only a few national parks actually support a physician.

In addition, I have always felt a deep connection to the natural world. We’re all constructed of the same molecules; all follow the same rules of development and decay. The wonders around us are simply stunning and worth celebrating.

How do you describe your books?

I’m calling my books ‘evidence-based medical adventures.’ There is romance and a bit of a thriller plot, but the books are also filled with tons of real medicine, science and the quandaries physicians face every day. And the poetry of the night sky and the rock under our feet, not to mention the value of humor.

Are there similarities between writing and being a family physician?

I think it helps for both to know you can never know everything. And that much of life comes at us in tones of gray. Being a family physician certainly gives you a broad view of the world and the vagaries of the human mind. You need to know as much as you possibly can and you need to know what you don’t know. You keep trying your best. I think this experience helped me as a writer.

Photo by DomCarver

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

Use your range hood for a healthier home, advises indoor air quality expert Brett Singer

Most Americans don’t realize cooking can be a major source of indoor air pollutants, unless they’ve recently burned something on the stove. But studies have shown that cooking-related contaminants can cause health problems such as respiratory illness and asthma attacks.

To learn more, I spoke with Brett Singer, PhD, a scientist at Berkeley Lab who investigates indoor air quality. Recently, he measured the levels of pollutants emitted from gas cooking burners and ovens in several Bay Area homes. I asked him about this study and for advice on how to reduce cooking pollutants.

Are harmful pollutants emitted when cooking?

“A gas burner almost always produces significant quantities of nitrogen dioxide, which is a respiratory irritant. Depending on the burner configuration, it can also produce carbon monoxide, which is regulated by the Environmental Protection Agency. In general, newer cooktop burners don’t produce much carbon monoxide because of design improvements. Finally, the gas produces ultrafine particles, smaller than 100 nanometers, which are dangerous because they can move around your body in ways that larger particles can’t.

Electric burners don’t produce carbon monoxide and produce only small amounts of nitrogen dioxide. But an electrical coil burner can produce ultrafine particles, particularly when you first turn it on.

Cooking food on either type of burner also produces fine particles and some organic chemicals, including acrolein and polynuclear aromatic hydrocarbons that are known to be hazardous. Frying, broiling and other cooking at high temperatures generally produces more pollutants.

However, these pollutants can be easily addressed with good kitchen ventilation, which is especially important if you live in a small home.”

What did your in-home study find?

“We went into moderately sized homes — eight 1,400 to 2,500-square-foot homes and one small apartment — with common, well-functioning equipment that had been in use for a few years. We measured the concentrations of pollutants in the kitchen and elsewhere as we boiled and steamed water on the cooktop and/or oven, with and without ventilation. We found issues in half of these homes and that’s not good. In four of the homes, we showed that the gas-cooking burners emitted enough nitrogen dioxide to exceed the health standards for outdoor air.”

What are your tips to minimize these cooking pollutants?

“The first tip is to ventilate when you cook, and to ventilate more the more you cook. Range hoods are the most effective way to do this, if your range hood actually moves air out of the kitchen. If you have a range hood that just recirculates air back into the kitchen, you need to use another exhaust fan — for example, from a nearby bathroom — or open windows.

You also need to use your hood or exhaust fan regularly. Based on several surveys, many people only occasionally use them. People report not using them because they’re noisy, because people forget to turn them on or because they aren’t needed unless removing smoke, odors and moisture — like when frying something stinky. Those are good reasons to use ventilation, but people can’t sense pollutants, so they may not be ventilating sometimes when it’s really needed.

If you’re buying a new range hood, buy a quiet one that you like. If it isn’t quite as efficient but you’re happy with it and you’ll use it, then great. To improve on that, a range hood needs to have higher flow rates and cover the front burners.

Beyond that, almost any range hood works better if you cook on the back burners. If you put it on a low speed and cook on a single back burner, then you’ll typically capture 50 to 70 percent of the pollutants.”

What is the ultimate goal of your research?

“The goal of our work on kitchen ventilation is to help people cook all they want — with gas or electric — without exposing themselves to harmful air pollutants. This is an important part of our broader work on high performance homes that use very little energy and provide a healthier environment for their occupants. We try to provide the science to inform builders, retrofit contractors and the general public.”

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

Tackling the “childcare-conference conundrum”

Attending conferences is a critical part of professional development, particularly for early-stage academic researchers. At these meetings, scientists further their careers by presenting their research discoveries and networking with potential collaborators, employers and funding agencies.

However, many early-stage researchers are moms who are primary caretakers of their children, which makes it difficult to attend conferences that lack childcare accommodations. Recently, a group of women scientists came together to address this “childcare-conference conundrum.”

The group, called a Working Group of Mothers in Science, was spearheaded by Rebecca Calisi, PhD, an assistant professor at the University of California, Davis. Last fall, she reached out to other women scientists after attending a large neuroscience conference — including Stanford’s Erin Gibson, PhD, a research scientist in neurology, and Lauren O’Connell, PhD, an assistant professor of biology — and this led to the formation of the group of almost 50 women last December.

The working group wants to help conferences establish safe and effective childcare options for all working parents with young children. They argue that solving the childcare-conference conundrum will help primary caretakers, foster scientific advancements and innovation by allowing a population of scientists to remain engaged, and benefit the conferences themselves and businesses associated with them.

“While childcare disproportionately affects women and their career mobility especially in the sciences, we want to bring attention to this problem as it can impact all parents from breast-feeding mothers to fathers who are the primary caretakers,” explained Gibson. “Relatively simple changes could dramatically affect the lives of primary caregivers at these conferences. And the more well-trained scientists we can keep in science by not leaving them out due to childcare restrictions, the more the entire scientific community benefits.”

In an editorial published this week in the Proceedings of the National Academy of Sciences, the group outlined four concrete recommendations for organizations:

Provide financial support for individually arranged childcare for smaller conferences and onsite childcare for larger ones.
Select family-friendly dates, venues and daily schedules.
Provide adequate facilities and equipment, including lactation areas with storage lockers for breast pumps and refrigeration for expressed milk; baby-changing facilities in all bathrooms and dedicated playroom space.
Establish a conference-specific parent social network.

The authors wrote that the adoption of these practices will send a strong and positive message, as well as support an inclusive family-friendly environment.

“I have never had a positive experience attending a conference after having children, whether I was nursing either of my two daughters or just wanting them to attend,” Gibson told me. “We hope this op-ed can help guide future conferences to provide resources for working parents. I hope within the next year to attend conferences where all scientists feel included, especially those with children.”

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

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