Research

A close friend recently told me about the post-traumatic stress disorder research of Stanford’s Emma Seppala, PhD, whom she knows from the yoga community in Madison, Wisc. (Seppela did her postdoctoral work there.) It was amazing stuff, I was told (and what a small world, I thought.)

And so, I was eager to hear yesterday about one of Seppala’s studies, which found that yoga-based breathing exercises dramatically decreased PTSD in veterans – and that the effect lasted a full one year after the study period.

As Brooke Donald reports:

Twenty-one male veterans of the Iraq and Afghanistan wars participated. Half took part in the intervention, a seven-day workshop that emphasized a set of breathing techniques from the Sudarshan Kriya Yoga practice. The rhythmic breathing patterns exercised during this practice are meant to relax participants physically and mentally, and reduce symptoms of anxiety, depression and stress.

“Some people think of it as yoga, but it’s really more breathing – an active breathing intervention,” Seppala explained.

Before and after the workshop, which lasted three hours a day, the veterans completed questionnaires about how they were feeling. They also underwent cognitive and physiological tests to measure how they responded to loud noises and other startling stimuli.

The questionnaires were given and the tests were taken again a month after the workshop, then a year after.

Seppala called the results “extraordinary.”

Traditional PTSD is not effective for a large chunk of veterans, Seppala said, and this study provides numbers to back up anecdotal evidence that yogic breathing techniques can be helpful. She hopes that “having the data will help move this kind of treatment forward in a more substantial way” and will garner the attention of policymakers.

Seppala, the associate director of the Center for Compassion and Altruism Research and Education here, is now preparing the study for publication. Her work and that of University of Wisconsin’s Richard Davidson, PhD, was recently featured in the documentary “Free the Mind.”

Previously: Using mindfulness therapies to treat veterans’ PTSD, As soldiers return home, demand for psychologists with military experience grows, Stanford and other medical schools to increase training and research for PTSD, combat injuries and Can training soldiers to meditate combat PTSD?
Photo of veteran Adam Burn practicing yogic breathing techniques by Linda Cicero

A short survey that asks patients to assess their walking ability could be helpful in predicting a person’s risk of cardiovascular disease, as well as mortality risks from any cause. That’s according to a Stanford study recently published online in the journal Circulation.

The Walking Impairment Questionnaire, also known as the WIQ, is currently used to predict risks of peripheral artery disease, a narrowing of the arteries that causes limited circulation to the limbs. The authors of this new study wanted to see if the WIQ, which can be filled out by patients while waiting for their doctor appointments, might be helpful in predicting other health risks.

“A 70-year-old patient’s ability to walk six minutes is a great predictor of cardiovascular risks,” said Kevin Nead, a Stanford medical student and the first author of the study. “But most people are seen in 15-minute doctor visits. They’re not going to be doing a walking test.” Perhaps, he reasoned, a subjective test like this 17-question survey could be used instead.

Nead and his colleagues, who examined questionnaire results from more than 1,700 patients, found that the use of the WIQ alone successfully predicted cardiovascular outcomes. In addition, when the survey was used in conjunction with other common clinical tests such as blood pressure measurements and blood tests, it significantly improved the ability to predict mortality not just from cardiovascular disease but from any cause.

“In an era of increasing expense for medical costs, this work suggests that the WIQ, an extremely simple and economical tool, may significantly improve our ability to prognosticate risk,” Nead told me.

Photo by timparkinson

This afternoon, leading figures from academia, industry, government and philanthropic foundations will gather at the Big Data in Biomedicine conference at Stanford to explore the vast opportunities for mining the growing volume of public health data and develop new ways to prevent, diagnose and treat disease.

The event runs today through Friday and features 32 speakers representing large information-technology corporations, startups, venture-capital firms and the research community. As a reminder, those unable to attend in person can tune in to the live webcast and submit questions for panelists by visiting the conference website.

Additionally, we’ll be live tweeting the conference keynote speeches by Anne Wojcicki, CEO and co-founder of personal-genetics company 23andMe (which starts around 1 PM Pacific time today) and David Ewing Duncan, author of Experimental Man, as well as other proceedings from the conference. You can follow the tweets on the @SUMedicine feed or by using the hashtag #bigdatamed.

Previously: Big Data in Biomedicine conference opens this week, Stanford computer scientist shows stem cell researchers the power of big data, Atul Butte discusses why big data is a big deal in biomedicine and Stanford and Oxford team up for conference on “big data’s” role in biomedicine

Science Insider took another look yesterday at the effects of the budget sequestration on research. After describing the potential harms of the NIH’s recently announced 5 percent budget cut - “part of a larger pattern of declining funding over the past decade” – reporter Jocelyn Kaiser points out another troubling aspect of sequestration:

NIH leaders say that the sequester’s most severe effect is the chilling message it sends to young scientists. In testimony last week, [NIH Director Francis Collins, MD, PhD,] quoted a former student who is finishing a Ph.D. at the Massachusetts Institute of Technology. She’s seen her role models struggle with funding. “I can’t erase the fear that this is my future,” Collins quoted her writing.

“We’re putting an entire generation of U.S. scientists at risk,” Collins warned. “If they go away, they won’t come back.”

Previously: Sequestration hits the NIH – fewer new grants, smaller budgets, NIH director polls Twitter for real-world responses to budget cutbacks and As budget sequester nears, a call for Congress to protect funding for scientific and medical research

Each year the National Science Foundation runs a video contest for young IGERT-funded scientists to communicate to the public about their research, and viewers are encouraged to vote for their favorite videos by liking them on Facebook.

One of the entries in this year’s contest comes from a group of Stanford graduate students who show how the brain plans movement and discuss their work on neural prostheses - biomedical devices for restoring movement to individuals with paralysis or lost limbs. The students, who are all part of the Stanford Center for Mind, Brain and Computation, conduct their work in the labs of electrical engineer Krishna Shenoy, PhD, whose research we’ve written about in the past, and Surya Ganguli, PhD, an assistant professor of applied physics.

The take-away message of the video, student Sergey Stavisky told me yesterday, is that “neural prosthetics are an exciting class of medical technology with the potential to improve the lives of individuals with paralysis,” but that to develop better ones, “we still need to learn a lot about the basic science of how the brain controls movement.”

The video, called “Neural Prosthetics: Understanding Reach Planning,” is worth checking out, as are many of the other entries, whose topics range from “virtual blood vessels” to the use of stem cells to revitalize skeletal muscle. Voting is open until 7 PM Pacific time Thursday.

Previously: Researchers find neurons fire rhythmically to create movement and Stanford researchers uncover the neural process behind reaction time
Via Erica Seigneur from NeuroTalk
Video still courtesy of Sergey Stavisky

The Big Data in Biomedicine conference kicks off at Stanford this week. The event, which will be held at the School of Medicine’s Li Ka Shing Center for Learning and Knowledge, is bringing together leading figures from academia, industry, government and philanthropic foundations to discuss the burgeoning opportunities for mining the vast amounts of biomedical data housed in public databases. Here’s a look at the schedule.

For those unable to attend the conference in person, the event will be webcasted via the Big Data in Biomedicine website. Throughout the three-day event, we’ll also be live tweeting the keynote talks from Anne Wojcicki, CEO and co-founder of personal-genetics company 23andMe, and David Ewing Duncan, author of Experimental Man, as well as other proceedings from the conference. You can follow the tweets on the @SUMedicine feed or by using the hashtag #bigdatamed.

Previously: Obama’s new open-data policy aims to boost access to federal data for entrepreneurs, researchers, Stanford computer scientist shows stem cell researchers the power of big data, Atul Butte discusses why big data is a big deal in biomedicine and Stanford and Oxford team up for conference on “big data’s” role in biomedicine
Photo by Wellcome Images

Stanford engineers have developed a nanoparticle that could lead to a new way to purify water. In a press release, writer Andrew Myers provides details on the work – which involves the use of magnetism to clear the synthetic “nanoscavenger” from the water – and describes researchers’ hope to “create a ‘one-pot solution’ that tackles water afflicted by a diverse mixture of contaminants.” Given that 1.6 million people die each year from diarrheal diseases stemming from lack of access to safe drinking water and basic sanitation, such purification technology could have big public-health implications.

Previously: Waste not, want not, say global sanitation innovators

In this short animation, John Hengeveld, marketing director for high performance computing at Intel, shares his story of undergoing an appendectomy and learning that, as a result of a burst appendix, a rare and cancer-causing material was now circulating in his body. Currently, there are few good treatment options for his condition, but Hengeveld hopes that by harnessing computers to perform scientific research this could change. Watch the video to learn how computers can help researchers accelerate the scientific process by simulating biomedical experiments to develop new methods of fighting disease.

Previously: Obama’s new open-data policy aims to boost access to federal data for entrepreneurs, researchers and Stanford computer scientist shows stem cell researchers the power of big data

Last night I listened squeamishly to my 13-year-old daughter and her friends compete in a (loud!) Fear-Factor-type eating contest in the other room (a sample dish: gummi worms covered in coleslaw – shudder). Fortunately for her (and all of us, really), the old adage “you are what you eat” is a vast oversimplification of nutrition science; many factors actually influence our overall health and body composition.

A similar simplification existed at one time in genetics, when it was believed that the DNA sequence of our genes determined our biological destiny. But over time scientists have learned that many variables affect how, when and even to what degree these genes are expressed, or transformed, into proteins. For instance, I may have the same DNA sequence for gene A as my friend, but I may make more, or fewer, molecules of protein A than she does, and therefore have a significantly different biological outcome. Unfortunately, it’s been difficult to accurately quantify and compare protein levels among individuals and groups.

Now research led by Stanford geneticists Hua Tang, PhD, and Michael Snyder, PhD, published yesterday in Nature (subscription required), has shown that these variations in gene expression levels are inherited over generations. In other words, your levels of expression of individual genes is likely to be similar to that of your parents. What’s more, genes involved in common processes tend to vary in similar ways – indicating a high degree of coordination of expression. As Tang explained in an e-mail to me:

We’ve found that the abundance of many proteins varies considerably among individuals, and we have identified numerous DNA variants that may influence the protein expression of a neighboring gene. We also showed that proteins that co-vary tend to have related biological functions or physical interactions.

The researchers used a sophisticated variation of a technique called quantitative mass spectrometry to determine the relative level of nearly 6,000 proteins in cells from 95 people from around the world. Until recently, most researchers relied on an indirect, and inexact, method that estimated protein levels within a cell based on the prevalence of RNA messages encoding that protein. Co-first author and research associate Sophie Candille, PhD, (who co-authored the research with postdoctoral scholar Linfeng Wu, PhD) explained:

RNA is in fact an intermediary molecule in the expression of the protein-coding genome. Proteins are the end product and active agents of the cell but their quantification has been challenging and therefore has lagged behind that of RNA.

By analyzing which proteins co-vary, the researchers were able to identify new functional groups that hint at previously unknown protein networks and interactions. Postdoctoral scholar and co-first author Linfeng Wu, PhD, concluded:

This research is important because many proteins are involved in the human immune response and diseases such as cancer. Therefore, the DNA variants that influence gene expression at the protein level are likely to be associated with disease phenotypes.

As Wu explained, the researchers are particularly interested in understanding how variation in protein expression levels affects disease risk or physical attributes. In my case, I can’t help wondering whether I have a genetic predisposition to nausea when I hear talk of eating bananas with Baconnaise or Spam with chocolate sauce (gag). But maybe, my reaction isn’t all that unusual?

Previously: Stanford geneticist talks tracking biological data points and personalized medicine

The importance of the physician-scientist is the focus of a new Perspective piece in the New England Journal of Medicine. Writing that an increasing number of MDs have moved away from the laboratory and into clinical practice, and calling the shortfall of new physician-researchers a “national, if not global, concern,” Michael M. Gottesman, MD, outlines how the National Institutes of Health is working to reverse the trend. And he notes that the awarding of the 2012 Nobel Prize in Chemistry (which went to Robert Lefkowitz, MD, and Stanford’s Brian Kobilka, MD, both trained in cardiology) “should remind us of the critical role that clinician-scientists have played in formulating the seminal concepts that govern modern biomedical science.”

Previously: Funding basic science leads to clinical discoveries, eventually, Why basic research is the venture capital of the biomedical world, At press conference, Nobel Laureate Brian Kobilka discusses his research and “irrational optimism” and Stanford’s Brian Kobilka wins 2012 Nobel Prize in Chemistry