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Big data, BigDataMed15, Precision health, Public Health, Research, Videos

How the FDA is promoting data sharing and transparency to support innovations in public health

How the FDA is promoting data sharing and transparency to support innovations in public health

Keynote talks and presentations from the 2015 Big Data in Biomedicine conference at Stanford are now available on the Stanford YouTube channel. To continue the discussion of how big data can be harnessed to improve the practice of medicine and enhance human health, we’re featuring a selection of the videos on Scope.

At the 2014 Big Data in Biomedicine conference, Taha Kass-Hout, MD, chief health informatics officer for the U.S. Food and Drug Administration, announced that the federal agency was launching OpenFDA, a scalable search and big-data analytics platform. In May, he returned to the Big Data in Biomedicine stage to offer an update on the initiative and discuss how the FDA is continuing to foster access and transparency of big data in government.

During his talk, Kass-Hout shared some eye-popping statistics about the information available through OpenFDA. The platform houses close to 70,000 product labels for pharmaceuticals; nearly four million reports on adverse events or malfunctions of medical devices; 41,000 records on recalls of foods, pharmaceuticals or devices and over four and a half million reports of adverse events or side-effects of drugs.

He outlined future plans to build a similar public, cloud-based platform to compliment the Obama Administration’s Precision Medicine Initiative. Watch the full talk to learn more about these exciting efforts to unlock the rapidly growing reservoir of biomedical data and spur innovation in public health.

Previously: A look at the MyHeart Counts app and the potential of mobile technologies to improve human health, Discussing patient participation in medical research: “We had to take this into our own hands,” A look at aging and longevity in this “unprecedented” time in history, Mining Twitter to identify cases of foodborne illness and Discussing access and transparency of big data in government

Public Health, Public Safety, Research, Sports

Study shows football helmet safety tests may not capture common cause of concussions

Study shows football helmet safety tests may not capture common cause of concussions

boy-164286_1280The football helmet is perhaps the most iconic piece of safety equipment there is, but we’re just now beginning to understand how helmets can — and should — protect the brain.

Blows that rotate the head are known to cause brain trauma, yet a new Stanford study (subscription required) has found that this kind of movement isn’t included in the tests currently used to evaluate a football helmet’s safety.

In the study, bioengineer David Camarillo, PhD, and his team investigated the types of head movements that cause concussions using computer models of the brain and data collected from Stanford football players wearing mouthguards instrumented with accelerometers (device that measures changes in velocity).

Using the computer model, they found that the brain’s movement increases when the head oscillates (moves back and forth) at 15-20 hertz and it completes a single oscillation in about 50 milliseconds. The field data from the accelerometers showed that the players typically experience head oscillations around 20 hertz.

When the research team compared these results to the scenarios used to test the safety of football helmets, they found a mismatch. The standard tests used to evaluate football helmet safety (acceleration tests and a test that drops a helmet-wearing dummy head from various heights) fail to include the rotational movements known to cause concussions; they also generate faster head oscillations (100 hertz); and measure head acceleration for only 15-36 milliseconds.

“The problem with having a model that doesn’t re-create what players actually experience in the field, is that you could optimize a helmet to perform well in the drop test that unintentionally performs poorly in the field,” said Fidel Hernandez, a doctoral candidate in mechanical engineering and one of the study’s lead authors, in a Stanford News story.

This is a big deal because roughly 70 percent of football players in the United States who rely on helmets to keep their head’s precious cargo safe are under the age of 14, and they receive, on average, a whopping 240 hits to the head each season.

Camarillo and his team hope their findings can be used to make more realistic and useful helmet tests.

Previously: Stanford bioengineers and clinicians team up to shed light on how concussions affect the brainForces at work in concussions more complicated than previously thought, new Stanford study revealsNow that’s using your head: Bike-helmet monitor alerts emergency contacts after a crash and Study shows concussion recovery may take longer for female, younger athletes
Image courtesy of Pixbay

Behavioral Science, In the News, Infectious Disease, Research, Stanford News

Irrational fear of contagion fuels xenophobia, Stanford study shows

Irrational fear of contagion fuels xenophobia, Stanford study shows

face-mask-98640_1280I have a very distinct memory of my grandfather dying from leukemia in an Iowa hospital. I peered in through a glass window, too scared to don the white mask and gown to visit him myself, even though the protections were for him, not me. Granted, I was eight. But fear of disease, and fear of those who have disease, makes perfect sense to me, even now.

But, that realization is tempered by knowledge of the harmful effects of irrational fear, the topic of a recent study by a team of Stanford researchers. As described in a recent Graduate School of Business story:

Throughout history, minority or “out” groups have been blamed for the spread of infectious disease. In medieval Europe, for instance, Jews and gypsies were among those accused of spreading the deadly bubonic plague. In 1793, during the yellow fever epidemic in Philadelphia, local officials singled out actors, vaudevillians, and artists for transmitting the disease. But what is it about the fear of contagion that makes otherwise rational people buy into rumors about those they consider to be outsiders?

Organizational behavior researchers Hayagreeva Rao, PhD, and recent graduate Sunasir Dutta, PhD, developed an online pilot study where one group was told a new strain of flu had emerged, then asked about their views on immigration. The control group was simply asked about immigration.

Not surprisingly, the group told about the flu was less likely to support immigrant legalization. Dutta said he is convinced the results would be even more striking in the real world:

Practically speaking, the implications are clear: “Don’t do immigration reform during flu season,” says Rao.

The study also demonstrates the power of rumors to spur fear, even ethnic violence, Dutta said. And it illustrates the need for proactive, responsive communications, particularly in the beginning stage of epidemics when irrational fears can germinate.

Previously: Fear factor: Using virtual reality to overcome phobias, Fear of recurrence an issue for some cancer survivors and Looks of fear and disgust help us to see threats, study shows
Image by Openicons

Events, Medical Education, Medical Schools, Stanford News

Aspiring young doctors learn the ropes during Stanford summer program

Aspiring young doctors learn the ropes during Stanford summer program

CSI participants - 560

Deep in the basement laboratory of Stanford’s Falk Cardiovascular Research Center, 31 high-school and college students stood in awed silence as surgeon Paul Chang, MD, demonstrated on the room’s large screen how to dissect a pig’s heart. After a moment of watching him point out the valves, atria, ventricles and arteries of the organ, students excitedly grabbed the surgical tools in front of them and began their work.

“This is so cool,” exclaimed Daria Arzy, a student at Harvard-Westlake High School in Los Angeles. “I’m more of a hands-on person, so I really enjoy this kind of thing.”

Heart dissection is just one sliver of the Stanford Medicine Clinical Summer Internship, a new program by the Division of General Medical Disciplines that was designed to provide a diverse group of students with an up-close and personal look at the field of medicine.

Department of Medicine Chair Bob Harrington, MD, greeted the participants on their first day and encouraged them to enjoy their time on the Stanford campus. “This is an amazing place,” he shared. “I’m still excited to come to work each day.”

Throughout the course of the two-week program, students learned the foundations of patient care, including how to take a patient’s medical history and vital signs, how to perform a physical exam, and how to administer ultrasounds and injections; practiced surgical techniques; and heard from cardiologists, neurologists, and other experts. “We encountered so many different perspectives,” said Kathy Zhang, a premed student at Vanderbilt University. “It was wonderful to meet medical professionals from different backgrounds and career pursuits.”

The students also had the opportunity to travel to the roof of Stanford Hospital to tour the school’s 50-foot Life Flight helicopter and to visit Stanford’s Center for Immersive and Simulation-based Learning, where they learned how to manage and treat infectious diseases.

During a guest lecture, Chloe Chien, MD, a Stanford medical student graduate and the COO of Homemade, a social healthy cooking program, shared her journey from medical student to startup co-founder. “When I was training to become a surgeon, I suddenly realized that I wanted to help prevent and heal lifestyle diseases like obesity and diabetes,” she said. “So I spoke to patients with chronic diseases to better understand what they were going through.” Chien later engaged the students in a lively discussion about the barriers to healthy lifestyle change, and offered three principles for healthy living: “Cook your own food, listen to your body, and eat whole, natural ingredients.”

On the final day, program organizers handed out certificates and offered their closing remarks to the group: “6 hours in the Stanford anatomy lab, 20 injected oranges, and 31 dissected sheep brains and pig hearts. By any numerical measure, this week has been impressive,” said Program Manager Misty Mazzara. “But this week was never about numbers.  It was about bringing bright young students together to introduce them to the practice of medicine.” Eva Weinlander, MD, who co-organized the internship with Sarita Khemani, MD, agreed, adding: “We have been lucky to spend time with all of you. You’ve all been so enthusiastic, professional, and supportive of each other during this journey.”

As the ceremony came to a close, participants lingered in the auditorium — hugging, taking photos, and exchanging contact information. One student echoed the sentiments of many when she yelled: “Don’t worry everyone, I’m coming back next year!”

Lindsey Baker is the communications manager for Stanford’s Department of Medicine. More photos from the internship program can be found on this Flickr page.

Previously: What’s it like to be an internal medicine resident at Stanford?At Stanford Cardiovascular Institute’s annual retreat, a glimpse into the future of cardiovascular medicine and A look at one high-school student’s summer internship experience at Stanford
Photo by Lindsey Baker

Cancer, Chronic Disease, Dermatology, Stanford News, Surgery, Transplants

Rebuilding Cassie’s smile: A lung transplant patient’s struggle with skin cancer

lung patientWhen I first met Cassie Stockton, she was seated in an exam chair in Stanford’s dermatology clinic, getting cosmetic skin treatments. Lovely and young, just 21 years old, it seemed a bit silly. How could she possibly need injectable lip fillers or laser skin treatments?

I knew Stockton had a lung transplant at 15 and that the immunosuppressant drugs she was required to take to keep her body from rejecting the donated lungs had made her susceptible to skin cancer. But it wasn’t until I researched her story in depth that I truly understood how she ended up needing regular cosmetic treatments here.

As I explain in my recently published Stanford Medicine article, her story began at birth:

Born premature, [Cassie] was intubated the first two weeks of life, then sent home with her mother and an oxygen tank. She remained on oxygen 24 hours a day for the first two years of her life. Eventually, she was diagnosed with bronchopulmonary dysplasia, a chronic lung disorder …

Sixteen years later, the donated gift of new lungs saved her life – but it left scars, both emotional and physical:

The day Stockton woke up out of the anesthesia six years ago after a 13-hour surgery at the Transplant Center at Lucile Packard Children’s Hospital Stanford, she breathed in oxygen with newly transplanted lungs, and breathed out sobs. Tears streamed down her face. “At first, I thought she was in pain,” says her mother, Jennifer Scott, who stood by her side. But that wasn’t it. Stockton was overwhelmingly sad because she now knew her new lungs were the gift of a child. It was Dec. 6, 2009, just before Christmas. The death of someone else’s child had given her a whole new life.

And now:

Every four months, she and her fiancé make the four-hour drive from their home in Bakersfield, California, past the oil rigs and cattle farms to Stanford’s Redwood City-based dermatology clinic for her skin cancer screening. It’s been two years of treatments: freezings, laserings, a total of eight outpatient skin surgeries — the most significant resulting in the removal of the left half of her lower lip. The dermatologic surgeon removes the skin cancers, and then gets to work to repair the damage. “It’s heart-breaking to have to remove the lip of a 21-year-old woman,” says Tyler Hollmig, MD, clinical assistant professor of dermatology and director of the Stanford Laser and Aesthetic Dermatology Clinic, who leads Stockton’s treatment and keeps her looking like the young woman she is, restoring her skin, rebuilding her lip, making sure she keeps her smile.

Stockton doesn’t complain about any of the struggles she’s had post transplant. She knows she got a second chance at life. And, she tells me, it’s her job to take care of the lungs given to her by that child who died.

Previously: This summer’s Stanford Medicine magazine shows some skin
Photo by Max Aguilera-Hellweg

Clinical Trials, Ethics, Research, Stanford News

Should patients pay their way into clinical trials?

Should patients pay their way into clinical trials?

Photo of U.S. currency and a pharmaceutical capsuleIn a time of shrinking federal research budgets, here’s one idea for a solution: charge patients to participate in clinical trials.

Patients’ payment could fund studies that would not otherwise be conducted, said a group of medical ethicists led by Ezekiel J. Emanuel, MD, PhD, the former White House health-policy adviser who now chairs the Department of Medical Ethics and Health Policy at the University of Pennsylvania. Emanuel was asked by a group of academic investigators to review the legality and ethics of charging for enrollment in an early-phase clinical trial; he and his co-authors examine the pros and cons.

No laws or regulations prohibit pay-to-play, said the authors, and it has some upsides. By putting their money where their mouth is, patients could be demonstrating deep engagement with the research protocol, and affirming their informed consent. Their payment could be seen as a direct, Kickstarter-style version of a charitable contribution to medical research, or as an analogue to permissible payment for experimental treatments outside the confines of a clinical trial. Last but not least, there is a liberty argument, that “people should have the freedom to do whatever they want with their own money as long as they are not harming others or diminishing their rights and opportunities,” said the authors, whose perspective essay (subscription required) appears today in Science Translational Medicine.

But before going full libertarian, the authors put on the brakes. Let’s be honest, they said, this is less about a collaborative partnership than a potentially desperate need to save one’s own life; less about a charitable impulse than purchasing a service. It will skew research toward the health needs of the wealthy and could interfere with research integrity: A paying participant may be less willing to accept randomization to a control group or more reluctant to disclose symptoms and side effects. For their part, investigators might feel pressure to bend inclusion or removal criteria, or not to terminate a study. Ultimately, the authors conclude that pay-to-play is generally unethical, and warrants legislative and regulatory attention.

Co-author Govind Persad, JD, a Stanford graduate student in philosophy, told me he’s particularly concerned about participants feeling pressure to pay: “There is this real psychological pressure, if you or your kid are sick or in this desperate position, to do something that not only you wouldn’t have done, but that you see as having this direct, imminent benefit to yourself out of proportion to the benefit it’s likely to have.”

Persad hopes the essay will ignite an “educated debate” among researchers, policy makers, potential donors to medical research and people who stand to benefit from interventions to be studied in clinical trials. “An issue for people to think about going forward is: If we need more research into Condition X but pay-to-play is not the way, what would be some other good ways to try to expand the universe of trials?”

Related: A look at crowdfunding clinical trials, Can crowdfunding boost public support and financing for scientific research, Stanford forum on the future of health care in America posted online and When it comes to health-care spending, U.S. is “on a different planet”
Photo by David Goehring

Autoimmune Disease, Genetics, Immunology, Science, Stanford News, Technology

Women and men’s immune system genes operate differently, Stanford study shows

Women and men's immune system genes operate differently, Stanford study shows

A new technology for studying the human body’s vast system for toggling genes on and off reveals that genes connected with the immune system switch on and off more frequently than other genes, and those same genes operate differently in women and men. What’s more, the differences in gene activity are mostly not genetic.

A couple of years ago, geneticists Howard Chang, MD, PhD; Will Greenleaf, PhD, and others at Stanford invented a way to map the epigenome – essentially the real time on/off status of each of the 22,000 genes in our cells, along with the switches that control whether each gene is on or off.

Imagine a fancy office vending machine that can dispense 22,000 different drinks and other food items. Some selections are forever pumping out product; other choices are semi permanently unavailable. Still others dispense espresso, a double espresso or hot tea depending on which buttons you push. The activity of the 22,000 genes that make up our genomes are regulated in much the same way.

That’s a lot to keep track of. But Chang and Greenleaf’s technology, called ATAC-seq, makes it almost easy to map all that gene activity in living people as they go about their lives. Their latest study, published in Cell Systems, showed that the genes that switch on and off differently from person to person are more likely to be associated with autoimmune diseases, and also that men and women use different switches for many immune system genes. That sex-based difference in activity might explain the much higher incidence of autoimmune diseases in women — diseases like multiple sclerosis, lupus and rheumatoid arthritis.

The team took ordinary blood samples from 12 healthy volunteers and extracted immune cells called T cells. T cells are easy to isolate from a standard blood test and an important component of the immune system. With T cells in hand, the team looked at how certain genes are switched on and off, and how that pattern varied from individual to individual. Chang’s team also looked at how much change occurred from one blood draw to the next in each volunteer.

Chang told me, “We were interested in exploring the landscape of gene regulation directly from live people and look at differences. We asked, ‘How different or similar are people?’ This is different from asking if they have the same genes.”

Even in identical twins, he said, one twin could have an autoimmune disease and the other could be perfectly well. And, indeed, the team reported that over a third of the variation in gene activity was not connected to a genetic difference, suggesting a strong role for the environment. “I would say the majority of the difference is likely from a nongenetic source,” he said.

Previously: Caught in the act! Fast, cheap, high-resolution, easy way to tell which genes a cell is using
Photo by Baraka Office Support Services

Infectious Disease, Medical Education, Public Health, Research, Stanford News

A how-to guide on “galvanizing medical students” to administer flu vaccines

A how-to guide on "galvanizing medical students" to administer flu vaccines

image001Stanford’s Flu Crew, an initiative that gets medical students out into the campus and greater community administering flu vaccines, recently published a paper validating the importance of such initiatives for medical education and public health, and enumerating its best practices so other programs can follow in its footsteps.

Rachel Rizal and Rishi Mediratta were Flu Crew’s co-directors when we first wrote about their work in 2012. Rizal is now a fifth-year student and Mediratta a pediatrics resident at Stanford. They are lead authors on the article, “Galvanizing medical students in the administration of influenza vaccines: the Stanford Flu Crew,” which appears in the journal Advances in Medical Education and Practice.

I learned a lot about Flu Crew in an email exchange with Rizal, Mediratta, and a host of people they said were instrumental in this accomplishment. Catherine Zaw, a Stanford undergraduate who is a co-author on the recent paper, told me,”The Flu Crew concept has already spread to a couple of schools around the Bay Area, including UCSF, and I hope that with the publication of the paper, more medical schools will consider adopting it.”

The article is essentially a blueprint for replicating Flu Crew in other institutions. It describes Flu Crew’s innovative online-based curriculum, created by former Stanford medical student Kelsey Hills-Evans, MD (which she discussed in a post earlier this week). It lays out the planning needed to coordinate vaccination events, which in their case involves the medical school, undergraduate volunteers, the Vaden Student Health Center, Stanford’s Occupational Health Clinic, and community institutions like churches, libraries, and homeless shelters. And finally, it explains the impact on medical students’ attitudes to population health, as one of its main goals as a service-learning program is to provide students with experience in public health and patient interactions early on in their career.

Imee DuBose, MPH, who worked as operations manager at Occupational Health and was inspired by the “impressive professionalism” of Flu Crew’s student leadership to shift her career to student advising, told me: “As a public health professional, I see Flu Crew promoting community health through collaboration, and as a student affairs professional, I see student development and growth – this project combines the best of both worlds.”

Rizal and Mediratta’s successors for the two-year director position, Lauren Pischel and Michael Zhang, were also co-authors. Pischel explained that she thinks public health and preventative medicine are incredibly important in medical education.

“Campaigns like this link the individual you see sitting before you in clinic with the health of the population at large,” she said “I would like to see this paper be used to talk about how we can effectively integrate public health teaching and experience into medical school. There is quite a bit of room to grow in this direction.”

Previously: Stanford Medicine grads urged to break out of comfort zoneAn ounce of action is worth a ton of theory: Med student encourages community engagementFrenemies: Chronic cytomegalovirus infection boosts flu vaccination efficacyFlu Near You campaign aims to improve monitoring of flu outbreaks, vaccinations and Student “Flu Crew” brings no-cost flu vaccinations to the community
Related: The Flu Crew: Med students provide vaccinations to the community
Photo, of medical student Lichy Han administering a flu vaccine to Dean Lloyd Minor, MD, in 2012, courtesy of Imee Diego DuBose

Humor, Media, Medicine and Society, Neuroscience, Research, Stanford News

Did extraterrestrials chew up my news release, or does artificial intelligence still have a ways to go?

Did extraterrestrials chew up my news release, or does artificial intelligence still have a ways to go?

UFO

Almost two years ago, in a Scope blog entry titled “Can Joe Six-Pack compete with Sid Cyborg?” I posed the question: “Just how long will it be before we can no longer tell our computers from ourselves?”

I think it’s safe to say we’re not there yet. Either that, or extraterrestrials have been reading my news releases and finding them puzzling.

Last week we put out a news release I’d written about a dramatic discovery by Stanford radiologists Mike Zeineh, MD, PhD, Brian Rutt, PhD, and their colleagues. In brief, they’d analyzed postmortem slabs of brain tissue from people diagnosed with Alzheimer’s, compared them with equivalent brain-tissue slabs taken from people who’d died without any Alzheimer’s-like symptoms, and noticed some striking and intriguing differences. In a key brain region essential to memory formation, Zeineh and Rutt had spotted – only in Alzheimer’s brains, not normal ones – iron deposits engulfed by mobile inflammatory cells. This observation’s potentially big implications were plenty newsworthy.

It so happened that, on the day we issued the release, a high-powered five-day-long meeting on Alzheimer’s sponsored by the eponymous Alzheimer’s Association was in session in Washington, D.C. As a result, many of the brain-oriented science writers to whom my news release was targeted were preoccupied.

I was a little anxious about that. So, the other day, I turned to my favorite search engine to see if the release had managed to get some traction in the popular press. As I’d feared, the Washington conference had sucked up a lot of the oxygen in the earthly neuroscience arena.

But apparently, the release had done better in Outer Space. I saw that it had been picked up by, for example, Red Orbit (a website that I’ve always assumed, based on its name, emanates from Mars).

My eyes were next drawn to a link to an unfamiliar outfit called AZ News, which bills itself in a tagline as an “International Online News Site.” I clicked on the link, and saw a news report with the same title as my release. I started reading the text below.

The first words were: “In autopsy mind hankie from people not diagnosed with Alzheimer’s…” I don’t know what an “autopsy mind hankie” is, but I suspect it’s a mind-blower.

I checked our release. That’s not what I’d written at all. What I’d said was, “In postmortem brain tissue from people not diagnosed with Alzheimer’s…”

It seemed pretty clear that the release had been translated into some language – I had no idea which – and then, for some reason, reverse-translated back into English. I read on.

Continue Reading »

Scope Announcements, Stanford News

Stanford Medicine is on Instagram

Stanford Medicine is on Instagram

Do you use Instagram? We do! Stanford Medicine recently launched a feed designed to capture the best of its places and people (the images above are among the ones posted this month), and we hope you’ll follow along.

Previously: Introducing the Scope magazine on Flipboard and 100,000 followers for @StanfordMed

Stanford Medicine Resources: