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Big data, BigDataMed15, Events, Medicine and Society, Microbiology, Research, Technology

At Big Data in Biomedicine, Nobel laureate Michael Levitt and others talk computing and crowdsourcing

At Big Data in Biomedicine, Nobel laureate Michael Levitt and others talk computing and crowdsourcing

Levitt2Nobel laureate Michael Levitt, PhD, has been using big data since before data was big. A professor of structural biology at Stanford, Levitt’s simulations of protein structure and movement have tapped the most computing power he could access in his decades-long career.

Despite massive advances in technology, key challenges remain when using data to answer fundamental biological questions, Levitt told attendees of the second day of the Big Data in Biomedicine conference. It’s hard to translate gigabytes of data capturing a specific biological problem into a form that appeals to non-scientists. And even today’s supercomputers lack the ability to process information on the behavior of all atoms on Earth, Levitt pointed out.

Levitt’s address followed a panel discussion on computation and crowdsourcing, featuring computer-science specialists who are developing new ways to use computers to tackle biomedical challenges.

Kunle Olukotun, PhD, a Stanford professor of electrical engineering and computer science, had advice for biomedical scientists: Don’t waste your time on in-depth programming. Instead, harness the power of a domain specific language tailored to allow you to pursue your research goals efficiently.

Panelists Rhiju Das, PhD, assistant professor of biochemistry at Stanford, and Matthew Might, PhD, an associate professor of computer science at the University of Utah, have turned to the power of the crowd to solve problems. Das uses crowdsourcing to answer a universal problem (folding of RNA) and Might has used the crowd for a personal problem (his son’s rare genetic illness).

For Das, an online game called Eterna – and its players – have helped his team develop an algorithm that much more accurately predicts whether a sequence of RNA will fold correctly or not, a key step in developing treatments for diseases that use RNA such as HIV.

And for Might, crowdsourcing helped him discover other children who, like his son Bertrand, have an impaired NGLY1 gene. (His story is told in this New Yorker article.)

Panelist Eric Dishman, general manager of the Health and Life Sciences Group at Intel Corporation, offered conference attendees a reminder: Behind the technology lies a human. Heart rates, blood pressure and other biomarkers aren’t the only trends worth monitoring using technology, he said.

Behavioral traits also offer key insights into health, he explained. For example, his team has used location trackers to see which rooms elderly people spend time in. When there are too many breaks in the bathroom, or the person spends most of the day in the bedroom, health-care workers can see something is off, he said.

Action from the rest of the conference, which concludes today, is available via live-streaming and this app. You can also follow conversation on Twitter by using the hashtag #bigdatamed.

Previously: On the move: Big Data in Biomedicine goes mobile with discussion on mHealthGamers: The new face of scientific research?, Half-century climb in computer’s competence colloquially captured by Nobelist Michael Levitt and Decoding proteins using your very own super computer
Photo of Michael Levitt by Saul Bromberger

Big data, BigDataMed15, Events, Medicine and Society, Research, Technology

On the move: Big Data in Biomedicine goes mobile with discussion on mHealth

On the move: Big Data in Biomedicine goes mobile with discussion on mHealth

17910585102_33293fefe7_zIda Sim, MD, PhD, would like to prescribe data as easily as she orders a blood test or a prescription for antibiotics. Sim, a professor of medicine at the University of California-San Francisco, told attendees of a Big Data in Biomedicine panel on mHealth yesterday afternoon that she doesn’t want access to data collected willy-nilly, with little regard for the patient’s health condition or needs.

Instead, she wants to tailor data collection to the individual patient. For example, there’s no need to collect activity data for a competitive marathoner, but it would be useful for a sedentary computer programmer.

And she doesn’t care how patients collect their data; they can “bring their own device,” Sim, who also co-directs of biomedical informatics at the UCSF Clinical and Translational Sciences Institute, said.

The design of those devices is integral to the quality of the data developed, pointed out panelist Ram Fish, vice president of digital health at Samsung. He said his team starts with “small data,” making sure devices such as their Simband watch accurately records biomarkers such as blood pressure or heart rate in a single individual, before expanding it to the population level.

He said he’s most keen on developing tools that make a real difference in health, such as the detection of abnormal heart rhythms, a project still in the works.

And speaking of new tools, Stanford’s Euan Ashley, MD, PhD, associate professor of medicine and of genetics, shared some early results from the cardiovascular app MyHeart Counts, which Stanford introduced in March to great acclaim.

Ashley reported that the study has yielded information about the link between sleep patterns and happiness (those who go to bed late and get up late are less happy than others) and about geographic patterns of produce consumption (South Dakota users out-eat Californians when it comes to fruits and veggies). The project’s team is just starting to delve into some of its other findings, which include correlations between the 6-minute timed walk and overall health.

“We’re in a really new era and one we don’t really understand,” Ashley said.

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Media, Medicine and Society, Technology

Upset stomachs and hurting feet: A look at how people use Twitter for health information

Upset stomachs and hurting feet: A look at how people use Twitter for health information

MedCity News ran an incredibly informative article earlier this week on how people use social media – and more specifically, Twitter – to consume and discuss health information. Reporting on a recent talk from Twitter engineer Craig Hashi at Cleveland Clinic’s ePatient Experience: Empathy + Innovation Summit, Neil Versel shared:

Some 40 percent of consumers believe that information they found on social media affects how they deal with their health, [Hashi] said. A quarter of Internet users with chronic illnesses look for people with similar health issues. And 42 percent search online for reviews of health products, treatments and providers.

Twitter processes 23,000 weekly tweets with the words “feet hurt,” and the frequency naturally increases as the day and the work week go on, though many people tweet that when they get home on Saturday night as well. “Dr. Scholl’s can actually come in and reach these people,” Hashi suggested.

“Allergy” tweets mostly occur between March and June, Hashi said. “Sunscreen” also peaks in the late spring and summer. “Uncomfortable tummies” is highest on Thanksgiving, with lesser spikes at Christmas and on Super Bowl Sunday. Hashi said that Tums advertised on Twitter around Thanksgiving.

And for those who question the value of Twitter, or don’t quite understand its place in health care, these figures might give you pause: “The volume of information available on Twitter is staggering, Hashi said. There are half a billion tweets send every day. There will be more words on Twitter in the next two years than in all books ever printed. An analysis Hashi put together found that there were 44 million cancer-related tweets in the 12 months ending in March 2015, and traffic spiked in October, which happens to be Breast Cancer Awareness Month.”

Previously: Finding asthma outbreaks using Twitter: How social media can improve disease detectionAdvice for young doctors: Embrace TwitterTwitter 101 for patientsBertalan Meskó discusses how mobile technologies can improve the delivery of health care and What to think about when using social media for health information

Events, LGBT, Medical Schools, Medicine and Society, Patient Care

Advice for clinicians on addressing gender- and sex-related issues

Advice for clinicians on addressing gender- and sex-related issues

2633907150_6303146d75_zFor great patient care, a doctor needs to understand the patient’s life and the patient needs to feel comfortable sharing. This can be especially challenging when it comes to the LGBT community, which was part of the impetus for a talk on the Stanford Medicine campus last week. The event focused on challenges faced by sexual and gender minorities (SGM) in medicine, not just as patients, but as physicians and medical students as well.

Matthew Mansh, a fourth-year Stanford medical student; Gabriel Garcia, PhD, professor of medicine and associate dean of medical school admissions at Stanford; and Mitchell Lunn, a research fellow at UCSF and a graduate of Stanford’s medical school, are all part of Stanford’s LGBT Medical Education Research Group. After hearing the three speak, I walked away with a greater understanding of how important and challenging it is for doctors to have intimate conversations with their patients.

Of the three, Lunn’s talk was the most oriented towards helping practitioners be more sensitive about  He began by laying out some terminology (terms are moving away from assuming two genders – bisexual is falling out of favor, for example), but emphasized that even the most sophisticated labeling won’t tell you which organs patients have or which sex acts they’re doing. Providers have to ask and be comfortable with the terms they should use to ask, Lunn said.

Coming from an anthropology background, I know how hard it can be to not make assumptions. But Lunn emphasized that it’s crucial for clinicians to try: Patients overwhelmingly answer when asked about things in their lives, and they subsequently receive better care, such as screenings for HIV and hepatitis. Among the barriers to providers asking about sex and gender practice/expression are fears of being intrusive, cultural differences, ignorance regarding the clinical relevance of such questions, patient’s lack of genital complaints, and uncertainty of how to ask. Most of these can be combated with provider education; as for how to ask, Lunn says it doesn’t matter as long as the doctor’s questioning makes no assumptions and is the same for everyone.

Intake forms could ask preferred pronouns, for example. Stigmatizing language like “atypical practices” and questions like “Are you married?” should be avoided. Questions about sex and gender practices can be grouped with those about drug use, wearing a seat belt, and going to the dentist – the goal is to normalize these conversations; people don’t want to be targeted or singled out. In every intake visit, Lunn says to his patient: “I talk to my patients about gender identity – do you know what I mean by that?” Crack the door like this and most who are gender nonconforming will go through it, he assures.

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Humor, Medical Education, Medicine and Society

University of Glasgow medical student makes learning anatomy a feast for the senses

Areo Oli_Mike McCormick_560

If you’ve ever heard the phrase “you are what you eat” and playfully wondered which part of you is composed of coffee and sweets, take a peek at the gallery of artwork called CandyAnatomy. These candy creations are the work of Mike McCormick, a medical student at the University of Glasgow. Recently, I reached out to McCormick to learn more about his inventive works of art and how they came to be. Here’s what he had to say.

How did CandyAnatomy begin?

CandyAnatomy was born out of the realization that I could be as nerdy as I wanted and the only repercussion was that it might make me a better doctor. [While getting] my previous degree, Physiology (Hons) at the University of Edinburgh, I’m pretty sure I would be laughed out of town for being so embarrassing, but medicine rewards absorbing as much information as you can. I would draw muscles, nerves and blood supply with a sharpie on my arm; convert anything I could to mimic a biological system; and candy was just so full of possibilities that would also make tasty snacks!

Do your creations help you learn the material you study in medical school, or does the art serve another purpose?

Yes, the creations do make it easier for me to learn the subject. I take time to consider what sweets most resemble the cells or structures in question; this helps me remember. Good examples might be the Aero Bubbles, whose high surface area resembles alveoli, or using a jelly snake to remind me about serpentine receptors.

Why did you choose to use candy in your artwork? Do you have a sweet tooth?

Ha, ha – honestly I’m a child of two dentists, so candy is probably forbidden! But… I’m showing candy can be used for something other than eating, so perhaps that’s setting a better example from a dental perspective! I actually just use the candy because the colors make for a very vibrant image, people want to eat them, and because I don’t actually eat them they will last longer before they go out of date. I’ve used a little SavouryAnatomy, but it doesn’t last very long!

What inspired the artwork (featured above) “Aero-Oli”?

I had been searching for an idea to detail the site of gaseous exchange. We had been doing a few weeks of respiratory anatomy and pathology, and I didn’t just want to produce two lungs out of candy, as it’s not very eye-catching. When shopping, I spotted the Aero Bubbles and I just had to [use them]. I like this image because it explores the structure [at different magnifications, much] like switching the power of a microscope. It shows the smooth muscle around the bronchioles that play an important role in asthma, and it also details the capillary network (surrounding the alveoli) that oxygenates the blood and removes waste products.

Thinking about your future, what area of medicine are you planning to pursue?

In the future I’m considering becoming a surgeon because I like working with my hands, dissecting and learning anatomy. However, pediatrics might be another alternative as clearly CandyAnatomy would be a good way to explain medical situations to children.

Previously: Image of the Week: A playful take on the human respiratory systemImage of the Week: VeggieanatomyImage of the Week: Quilled anatomyKitchen anatomy: Brain carved from a watermelon and Virtual dissection table helps teach human anatomy
Via Laughing Squid
Artwork courtesy of Mike McCormick

Events, Health and Fitness, Medicine and Society, Stanford News

Stanford Medicine’s community open house happening on May 16

Stanford Medicine's community open house happening on May 16

health matters logo 15

Mark your calendar for Health Matters, Stanford Medicine’s community open house, being held this year on Saturday, May 16. There will be wellness dogs and a helicopter, chair massages, tasty food and plenty of informative presentations on topics ranging from breast cancer and dementia to exercise and diet.

And, it’s all free (except for the tasty food).

A few of the presentations include:

  • “Dispelling the myths: Realistic strategies for maintaining cognitive health and preventing dementia” with Frank Longo, MD, PhD
  • “Tips for safe workouts: How to stay healthy and injury-free” with Jason Dragoo, MD
  • “Anti-inflammatory foods” with Kylie Chen, RD
  • “Approaching the second half of life with health and vitality: The latest research on longevity and aging” with Anne Brunet, PhD
  • “Teen mental health and your family — Practical information and insights”, a panel presentation

Throughout the day, the Life Flight helicopter is expected to be available, as will be the canine stars of the Pet-Assisted Wellness (PAWs) program. The pavilion will also feature a look at the MyHeart Counts heart-health app, cooking demonstrations, emergency preparation information and Stanford experts available to answer your health questions.

The event will be held at the Li Ka Shing Center for Learning and Knowledge. If certain talks particularly strike your fancy, register here to reserve a space. Some events, such as the medical school session for high school students, will or have already filled up.

Previously: Stanford Medicine to open its doors to community during Health Matters event, An ounce of action is worth a ton of theory: Med student encourages community engagement and Stanford Medicine community gathers for Health Matters event

Biomed Bites, Genetics, Medicine and Society, Microbiology, Research, Science, Videos

From yeast to coral reefs: Research that extends beyond the lab

From yeast to coral reefs: Research that extends beyond the lab

Welcome to Biomed Bites, a weekly feature that introduces readers to some of Stanford’s most innovative researchers. 

John Pringle, PhD, focused most of his career on yeast. Easy to culture in the lab, yeast offer scientists a malleable model to learn about all types of cells, including human cells.

As a professor of genetics, he still does a bit of that. But now, his heart is focused on saving the world’s coral reefs – no small task given that these living ecosystems are vulnerable to temperature changes, carbon dioxide concentrations and overfishing.

Pringle’s research concentrates on a small sea anemone known as Aiptasia pallida, as he explains in the video above:

We picked an experimental system that has huge advantages over the corals themselves and we try to learn basic things about their molecular and cellular biology that will help us with the more complex and less experimentally tractable system of the reefs.

Just as with his yeast work, the lessons learned from the anemones are directly applicable to human well-being. “Corals are important to hundreds of millions of people around the world for livelihood and for the beauty they bring and the food they provide,” he says. “We have the hopes that by doing basic research, we’ll contribute to an understanding of how coral reefs might be preserved.”

Learn more about Stanford Medicine’s Biomedical Innovation Initiative and about other faculty leaders who are driving biomedical innovation here.

Previously: Bubble, bubble, toil and trouble — yeast dynasties give up their secrets, Yeast advance understanding of Parkinson’s disease, says Stanford study and My funny Valentine — or, how a tiny fish will change the world of aging research

Global Health, Medicine and Society

What I learned about emergency preparedness from spending 36 post-earthquake hours in Nepal

What I learned about emergency preparedness from spending 36 post-earthquake hours in Nepal

Nepal_guest_postI recently spent two weeks in Nepal starting a clinical trial for HandHero, an innovative hand splint that our team developed in Design for Extreme Affordability at Stanford, in partnership with ReSurge International. It was a very successful trip, with patients recruited and partnerships formed, and I was nearly on my way home when the earthquake struck. I recently detailed my experience in a guest blog post, and now I would like to share some of the lessons I learned about emergency preparedness. The following tips are by no means comprehensive, but they’re the key steps I would take next time I travel abroad – and they may be useful to those conducting field research or other work in developing countries.

  • Before departure: Give your close family and friends back home a list of your local contacts. Include phone numbers and a description of who these people are and the planned nature of your interactions (ie. “I will be spending most days working with this person.”). In the event of a natural disaster, it may be faster for your loved ones to contact you than vice versa.
  • Upon arrival: Get a local phone or SIM card. In Nepal, a traveler’s pack SIM card with ample local and international call, text, and data cost US $10. While voice reception could be weak, ability to send and receive texts was invaluable.
  • Cash: Always have more than enough local currency in your wallet or stored separately. Most ATMs and banks will close in the immediate aftermath of a disaster.
  • Sustenance: Pack a few energy bars for emergencies only. Bring a personal water filtration device. Keep in mind that while food and drinking water may seem sufficient immediately after a serious disaster, supplies will be hard to find and increasingly costly in the days to come.
  • Airport: Reliable information may not always be available, and airline call centers can be hard to reach. Physically going to the airport may be your best bet, and ask a trusted native speaker for help seeking out the right personnel.
  • U.S. Embassy: Keep the phone number and address of your country’s embassy handy. They can provide both logistical and practical support and will tell you whether or not there is a planned evacuation of citizens via armed forces.

AirportIf faced with a decision between leaving the country and staying on the ground to try and help with recovery efforts, consider carefully. Do you have specific skills relevant to the situation at hand? Do you speak the language? Could you be of more help staying in the country or back home raising awareness and support? While it may be extremely compelling to stay, it might not always be the best option depending on your situation.

Finally, take good care of yourself upon your eventual return. My first few days back in the Bay Area seemed very surreal, as the reality of what occurred only hit home after the adrenaline died down. Unforgettable life experiences often happen when we least expect, and the best we can do is to stay equipped with communication capabilities and basic supplies.

Jana Lim is a PhD candidate in neurosciences at Stanford. Her thesis research focuses on molecular mechanisms of associative learning in C. elegans. Lim’s involvement in Design for Extreme Affordability stems from her long-standing interest in sustainable development and her desire to create more applied solutions to existing social issues.

Previously: “Still many unknowns”: Stanford physician reflects on post-earthquake Nepal, Day 6: Heading for home after treating Nepal earthquake victims, Day 4: Reaching beyond Kathmandu in treating Nepal earthquake victims, Day 2: “We have heard tales of miraculous survival” following Nepal earthquake and Day 1: Arriving in Nepal to aid earthquake victims
Photos by Jana Lim

Global Health, Health Disparities, Health Policy, In the News, Medicine and Society

Why millions lack access to surgery: A conversation with Stanford surgeon Thomas Weiser

Why millions lack access to surgery: A conversation with Stanford surgeon Thomas Weiser


In the United States, many routine surgeries are just that: routine. They may or may not correct the condition, but the likelihood of death or of life-changing complications are minimal.

But if you live in a poorer nation, surgery — even a cesarean birth — is quite risky and hard to procure. For as many as 5 billion people, these basic procedures are out of reach, according to a recent report by the Lancet Commission, the focus of a recent Scope post and many other news articles.

There are numerous reasons for this surgical gap, as Stanford surgeon Thomas Weiser, MD, who contributed to the report, explains in an Inside Stanford Medicine Q&A.

First, surgery “requires a strong and continuous supply chain, highly technical skills and ongoing training, and intensive management to organize such services,” Weiser said. In addition, most aid programs focus on a specific disease, while surgery is a therapy, leaving it outside the bounds of most international development programs, he said.

So what does the future hold? Weiser is optimistic:

I hope that these findings and the new data presented in the commission report will increase attention and awareness of the vital role surgical care plays in a health system. Ideally, we will see increased leadership from organizations like the WHO and the World Bank in the form of attempts to standardize data collection, identify high-performing health systems, publicize successful programs and promote their adoption and replication in other health settings, and support improved investments in surgical capacity and quality improvement as a way to strengthen the health system more generally.

Previously: Billions lack surgical care; report calls for change, Stanford Medicine magazine opens up the world of surgery and Global health expert: Economic growth provides opportunity to close the “global health gap”
Photo by skeeze

Events, In the News, Medical Education, Medicine and Society

Former Brown University President Ruth Simmons challenges complacency on diversity

Former Brown University President Ruth Simmons challenges complacency on diversity

Ruth SimmonsWhen Ruth Simmons went away to college from a poor section of Houston, she didn’t have enough money to buy clothes. Now, after serving as the president of Brown University and of Smith College, Simmons, PhD, has not only the money, but also the flexibility to select which speaking invitations she accepts.

And at first, Simmons admitted Friday at the third talk in the Dean’s Lecture Series, she was tempted to decline the request to speak on diversity. After a lifetime of refusing to be defined as the “black” woman or the “poor” girl, she didn’t want to be known as a diversity expert.

But: “My initial cynicism gave way to the concern I have for the state of diversity in higher education and society at large,” she said. Just look at the recent events in Baltimore, she said; clearly something is amiss.

Nationwide, there is strong support for the abstract concept of diversity, Simmons said. “But when disassembling diversity into its component parts, support fractures depending on what was at issue.” When pressed about issues such as fair pay, employment opportunities and integration, communities disintegrate into divergent factions.

And in the past, people stuck together in like-minded communities, wary of what she called the “jangle and discord of clashing opinions.” With advances in technology, and the increasing diversity of the U.S., isolation and insulation are no longer possible, she said.

Modeling ways to live together, while airing and respecting difference views, is a responsibility that students and faculty at elite universities need to take on, Simmons said. And universities must be prepared to institutionalize debates and create processes for disagreement. Inherent in the protection of diversity is the protection of free speech, she said.

Top universities should also not shy away from high expectations related to diversity. And their efforts to enhance and support diversity in all forms — race, income, sexual orientation, gender — should go beyond “laissez-faire statements on inclusion.” She lauded Dean Lloyd Minor, MD, for his efforts.

Minor agreed that “diversity is close to my heart.” He said he is motivated by the “fundamental belief that diversity makes us better as individuals and as society, but also because diversity is critical for the work we’re trying to achieve here at Stanford Medicine. In order to lead the biomedical revolution, we must have a diverse community.”

Previously: Panel on diversity calls for transformative change in society, courageous leadership from individuals, Intel’s Rosalind Hudnell kicks off Dean’s Lecture Series on diversity and Diversity is initial focus of new Stanford lecture series
Photo by Norbert von der Groeben

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