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Big data, Events, FDA, NIH, Stanford News, Technology

Discussing access and transparency of big data in government

Discussing access and transparency of big data in government


The Big Data in Biomedicine conference of 2014 continued today with discussion around how troves of information are being stored, organized, accessed and applied in a way that’s useful to stakeholders across health care.

Yesterday afternoon, Stanford bioengineer Russ Altman, PhD, introduced keynote speaker Philip Bourne, PhD, who earlier this year began his post as the first permanent associate director for data science at the National Institutes of Health. Altman was part of the search committee that selected Bourne as part of an initiative of NIH Director Francis Collins, MD, PhD, to make use of biomedical research datasets and lead the way in coordinating effective use of Big Data.

Bourne discussed some of the factors motivating thinking on big data at the NIH, including open access to information, which was also a focus of U.S. Chief Technology Officer Todd Park‘s conference presentation. Bourne noted that currently 70 percent of research that’s funded cannot be reproduced – a statistic “of great concern to the NIH” that’s driving ongoing reproducibility studies there. But what worried him most, he said, is sustainability: How can growing databases be accommodated within the NIH’s flat budget? (“We can’t go on like this,” he said.) How can labs retain talent when competing with industry’s larger salaries offered to top scientists? (“It’s a loss to the field if you spend money making a biomedical scientist and they leave the field.”) Bourne also seeks to address “broken” areas of scholarship – a paper with “16,000 citations” that no one reads – and the reward system.

Among his solutions are applying business models to promote sustainability of research, introducing policies to ensure funding is allocated where it is most needed, sharing infrastructure where possible and treating biomedical scientists more like tenured academics. Bourne also described an NIH data commons to provide Dropbox-type storage and a collaborative compute environment for scientists.

Co-operating and data-sharing were key this morning as the conference audience heard from Taha Kass-Hout, MD, the U.S. Food and Drug Administration‘s first chief health informatics officer. He described the importance of big data to the regulatory agency’s mission “to protect and promote the public health” and in promoting information-sharing with transparency and protection of privacy. The new, scalable search and big-data analytics platform openFDA comprises more than 100 public access data sets within the FDA and  allows users to access data and run queries through APIs. ”It’s not just about the data,” Kass-Hout told the audience. Ask rather, “How can you build a community around that data?

Previously: U.S. Chief Technology Officer kicks off Big Data in BiomedicineBig Data in Biomedicine conference kicks off tomorrowBig Data in Biomedicine technical showcase to feature companies’ innovations related to big data and Euan Ashley discusses harnessing big data to drive innovation for a healthier world
Photo of Bourne by Saul Bromberger

Big data, Events, Stanford News, Technology

U.S. Chief Technology Officer kicks off Big Data in Biomedicine

U.S. Chief Technology Officer kicks off Big Data in Biomedicine

Dean - smallThis morning, the 2014 Big Data in Biomedicine conference kicked off at the Li Ka Shing Center for Learning and Knowledge. The School of Medicine’s dean, Lloyd Minor, MD, welcomed the nearly 500 in-person attendees and many more joining via the free live stream of sessions over the course of three days. Minor emphasized collaboration – with conference sponsor Li Ka Shing and between co-hosts Stanford Medicine and the University of Oxford, and within the scientific community – to harness “the vast potential of technology, data and biomedicine to transform human health for the 21st century.”

Oxford’s Martin Landray, PhD, FCRP, and Stanford University President John Hennessy, PhD, spoke before yielding the floor to keynote speaker Todd Park, chief technology officer of the United States. An enthusiastic Park shared, “No topic excites me more than the incredible power data has to fuel innovation.” He referenced the 2010 paper “Where Are the Health Care Entrepreneurs? The Failure of Organizational Innovation in Health Care” to preface comments noting how, over the last few years and with the help of government programs, innovators have begun to increase efficiency, lower costs and improve outcomes in health care.

Todd ParkProvisions of the Affordable Care Act, for example, have helped to innovate care and payment models, Park said, noting a shift of payment away from volume and towards value of care. He said that “democratizing data,” evidenced by the Open Data Initiative of 2009 and a May 2013 executive order by President Obama to make open and affordable access to government information the norm, and financial incentives to use electronic health records have contributed to an acceleration of change in the field.

Through the Blue Button Movement, patients have gained access to their own health information online. “This has everything to do with big data,” Park said. And while privacy remains the chief concern of some, he noted many are eager to donate their data for research to improve health outcomes for themselves and others.

Park insisted that “there has never been a better time to be a health-care innovator” than the present, offering these departing words: “May the force be with you.”

Previously: Big Data in Biomedicine conference kicks off tomorrowChief technology officer of the United States to speak at Big Data in Biomedicine conferenceBig Data in Biomedicine technical showcase to feature companies’ innovations related to big data and U.S. Chief Technology Officer discusses health-care reform’s effects on innovation
Photo of Lloyd Minor (top) by Saul Bromberger; photo of Todd Park from @cdbustamante

Big data, Events, Stanford News

Big Data in Biomedicine conference kicks off tomorrow

Big Data in Biomedicine conference kicks off tomorrow

big_data_051514Thought leaders and innovators from academia, information technology companies, venture capital firms and public health institutions will gather tomorrow on the Stanford campus for the annual Big Data in Biomedicine conference.

The three-day event, which is cosponsored by Stanford and Oxford University, will explore ways to capitalize on the rapidly growing amount of biomedical data to improve the practice of medicine and human health. Keynote speakers include Todd Park, chief technology officer of the United States; Philip Bourne, PhD, associate director for data science at the National Institutes of Health; David Glazer, director of engineering at Google; Taha Kass-Hout, MD, the U.S. Food and Drug Administration’s first chief health informatics officer; and Vinod Khosla, MBA, founder of Khosla Ventures and a co-founder of Sun Microsystems.

Those unable to attend in person can tune in to the live webcast via the conference website. Additionally, we’ll be live tweeting the keynote talks, as well as other proceedings from the conference; you can follow the coverage on the @SUMedicine feed or by using the hashtag #bigdatamed.

Previously: Professor Margot Gerritsen discusses how “algebra is not just useful, it’s also inherently beautiful”, Chief technology officer of the United States to speak at Big Data in Biomedicine conference, Big Data in Biomedicine technical showcase to feature companies’ innovations related to big data and Euan Ashley discusses harnessing big data to drive innovation for a healthier world
Photo by Saul Bromberger

Applied Biotechnology, Events, Infectious Disease, Research, Stanford News, Videos

Stanford microbiologist’s secret sauce for disease detection

Stanford microbiologist's secret sauce for disease detection

Last week, John Boothroyd, PhD, kicked off Stanford’s first Disease Detective lecture series with a fascinating tale about how his lab invented a simple biochemical “secret sauce” that revolutionized the detection of viral and bacterial infections like HIV, Hepatitis C and gonorrhea.

“It mostly started as a sketch on a piece of paper, then later became Gen-Probe’s core technology, which won them the 2004 National Medal of Technology,” explained Boothroyd, a Stanford professor of microbiology and immunology.

What Boothroyd invented, in collaboration with postdoctoral researchers James Burg and Philippe Pouletty, is called Transcription-Mediated Amplification.

Before this discovery, detecting a snippet of disease-specific DNA in a sample of cells was like finding a needle in a haystack. To increase a test’s accuracy, a lab technician would try to coax the target DNA into replicating itself through hours of tedious time-and- temperature-sensitive steps.

Boothroyd and his team’s new process consisted of a simple recipe of primers and enzymes that, after optimization by Gen-Probe, tricked a target snippet of DNA into automatically creating 10 billion copies of itself in less than an hour. This ultimately enabled the development of cheaper and faster disease tests.

In 2012 Boothroyd was ushered into the Stanford Inventor’s Hall of Fame because of this patent, which is among the top-ten revenue-generating inventions Stanford. He has six other patented inventions, including one that makes antigen production for the testing of toxoplasmosis infections far more efficient. Another detects toxoplasmosis in the amniotic fluid of pregnant women. He describes this research in the video above.

Looking back on his career choices, one thing that Boothroyd is grateful for is being able to combine his two loves at Stanford — basic research and teaching — while leaving the business of running a company to his patent licensees.

To the lecture hall filled with student researchers worried about the “postdocalypse,” the shortage of tenure-track research positions in academia, he gave this advice:

“I think the [postdocalypse] negativity is overstated. You have to have faith in yourself. You have to do what you want to do. If you’re enjoying your work and it’s a stepping stone to where you’re going, relax and see what happens.”

The next Disease Detective lecture will be held during fall quarter 2014. Watch for details on the Stanford Predictives and Diagnostics Accelerator webpage.

Previously: Patrick House discusses Toxoplasma gondii, parasitic mind control and zombies, Cat guts, car crashes, and warp-speed Toxoplasma infections, and NIH study supports screening pregnant women for toxoplasmosis

Events, Medicine and Society, Stanford News

Stanford Medicine community gathers for Health Matters event

Stanford Medicine community gathers for Health Matters event

Health Matters attendeeWhere else can you spend a Saturday morning learning from an NFL Hall of Famer what to look for when you suspect a concussion in your child, getting unique perspectives from a Pulitzer Prize-winning author about the biography of cancer or listening to tips on maintaining your cognitive health from an expert in the field?

On Saturday, Stanford Medicine hosted a free community day at the Li Ka Shing Center for Learning and Knowledge. Members of the communities surrounding the Stanford campus came to interact with School of Medicine faculty leaders, hear about the latest discoveries in medicine and explore an interactive pavilion that highlighted advances in medical technology, disease prevention and treatment. This year’s Health Matters, which also featured a Med School Morning program for teens, attracted more than 500 guests to the Stanford campus for a day of learning, fun and exploration.

The event featured keynote speaker Siddhartha Mukherjee, MD, PhD, Pulitzer Prize winning author of the New York Times bestseller The Emperor of All Maladies. Mukherjee, who attended Stanford as an undergrad, shared his view of cancer being one of humanity’s greatest challenges and discussed the long-recorded history of the disease. Mukherjee, speaking from a stage in the Berg auditorium – named after his mentor, the Nobel Prize-winning chemist Paul Berg, PhD – eloquently described cancer as “a disease in which normalcy and illness are intertwined.” But also remarked that, “There is hope as we enter the age of targeted therapy.”

Young and SteinbergOther Stanford Medicine faculty gave presentations on topics ranging from sleep health and dementia prevention to big data for biomedicine and mental health and well-being. One highly attended session included neurosurgeon Gary Steinberg, MD, PhD, and former San Francisco 49er Steve Young. The two, who discussed sports-related concussions and brain injuries, also introduced the new Stanford Concussion and Traumatic Brain Injury Center. Set to open in the coming year, the center will provide a national center for the treatment of athletes, veterans and the community with state-of-the art diagnostic technology and availability 24 hours a day, seven days a week. Young said of the new center, “The fact that local parents will now have a resource,24/7 to bring their child and get some real help – that’s a really good thing.”

girl with FoldscopeIn addition to attending sessions, many explored the Health Pavilion exhibits featuring interactive displays from throughout Stanford Medicine. Guests were excited to see up-close the work of Manu Prakash, MD, PhD, to get hands-on with his revolutionary “Foldscope” and learn more about it’s potential applications. The Stanford Clinical Anatomy division’s virtual and 3D imaging technologies were a hit among kids and adults alike.  But the favorite of the day seemed to be Stanford Life Flight and their crew who, in celebration of the program’s 30-year anniversary, gave tours of the helicopter to many lucky guests.

To learn more about the program and speakers and view recordings of some of the sessions, visit the event website. For information on future community events and to hear more about wellness topics and medical innovations at Stanford Medicine, follow @StanfordHealth on Twitter.

Eileen DiFranco is director of communications and media in the Office of Medical Center Development at Stanford.

Previously: Stanford Life Flight celebrates 30 years, Stanford Medicine to open its doors to community during Health Matters event, Stanford bioengineer develops a 50-cent paper microscope and Cancer’s Pulitzer Prize winner: Siddhartha Mukherjee, MD
Photos by Alex Johnson

Events, Global Health, Stanford News, Women's Health

2014 Stanford Women’s Health Forum to focus on global health

2014 Stanford Women's Health Forum to focus on global health

I’ll be spending next Wednesday afternoon at the Fifth Annual Stanford Women’s Health Forum, where the best thing about the event is also its most frustrating: There are a lot of good speakers. How does one choose between hearing about the power of training adolescent girls to say no to unwanted sexual advances, and learning from Shuchi Anand, MD, MS, a Stanford nephrologist and epidemiologist who tracks gender-related risk factors for chronic disease in developing regions?

Such difficult choices have been typical of the abundant schedule for each year’s forum, organized by the Stanford WDSM Center, previously known by its longer title, the Stanford Center for Health Research on Women and Sex Differences in Medicine. WSDM selects a theme for the forum and doubles the opportunities for audiences by offering two talks each hour. Last year’s forum focused on breast cancer and featured keynote speaker Susan Love, MD, a breast cancer specialist and leukemia survivor. This year’s theme is global health, and the impressive list of speakers begins with Ruth Levine, PhD, director of the global development and population program at the William and Flora Hewlett Foundation.

In addition to the talks, whose moderators include Jesse Draper, creator and host of “The Valley Girl Show,” the event features  informational presentations on the Stanford Health Library, Stanford Hospital’s Aging Adult Services and Navigation Services programs, lung CT screening, new breast cancer screening technologies, peripheral artery disease diagnostics, and the medical application of the latest in immersive 3-D technologies.

The free event is held at the Arrillaga Alumni Center on the Stanford campus, and those who are interested can register here. For those who can’t make the event, WSDM will post videos of its forum on its YouTube channel.

Previously: Empowerment training prevents rape of Kenyan girls, Videos from Stanford 2013 Women’s Health Forum available online and At Stanford event, cancer advocate Susan Love talks about “a future with no breast cancer”

Events, Stanford News

A spotlight on TEDxStanford’s “awe-inspiring” and “deeply moving” talks

A spotlight on TEDxStanford's "awe-inspiring" and "deeply moving" talks

Jill Helms - smallThe third annual TEDxStanford event, themed “Above and Beyond,” took place on campus Saturday. Thirty-one talks and performances covered a wide range of subjects, including biotech, earth sciences, art, education and medicine.

A Stanford Report article notes today, “While all the talks and performances were thought-provoking and awe-inspiring, some were also deeply moving,” and goes on to describe a presentation by cystic fibrosis patient Isabel Stenzel Byrnes, who received a double-lung transplant 10 years ago at Stanford Hospital. At last year’s event, the piece notes, she shared the stage with her twin sister, Anabel, who died eight months ago.

More from the article:

Emotions also ran high when Jill Helms, [PhD,] a professor of plastic and reconstructive surgery at Stanford School of Medicine, talked about the concept of beauty and our perception of the face.

“Face-recognition is hard-wired in us,” Helms said, noting that we prize symmetry, balance and proportion. That creates a challenge, though, for people whose faces don’t fit our view of beauty.

When children whose faces don’t fit the ideal realize that they’re different, they turn inward, Helms said, her voice shaking. She challenged the audience to look past appearances. “Let’s reconsider beautiful,” she said.

Previously: Tickets for TedxStanford 2014 go on sale MondayKrishna Shenoy discusses the future of neural prosthetics at TEDxStanfordFilm about twin sisters’ double lung transplants and battle against cystic fibrosis available online and Living – and thriving – with cystic fibrosis
Photo of Jill Helms by Aaron Kehoe

Events, Stanford News

Health Matters happening at Stanford tomorrow

Health Matters happening at Stanford tomorrow

As a reminder, Stanford Medicine’s Health Matters event is happening Saturday at the Li Ka Shing Center for Learning and Knowledge. Hundreds of community members are coming to campus to attend sessions on a variety of medicine and science-related topics and to learn about the latest advancements in medicine and health. (Added bonus for football fans: Former San Francisco 49er Steve Young will be one of the speakers; he and neurosurgeon Gary Steinberg, MD, PhD, will discuss sports-related concussions.)

Conference organizers will be live tweeting the activities; you can follow the coverage starting at 10 AM Pacific time tomorrow on the @StanfordHealth feed or by using the hashtag #HealthMatters.

Previously: Can’t be at Stanford for Health Matters? Follow along on social media and Stanford Medicine to open its doors to community during Health Matters event

Events, Global Health, Stanford News

A day of celebration and education for Stanford School of Medicine alumni

A day of celebration and education for Stanford School of Medicine alumni

welcome back alum - smallLast Saturday, more than 300 School of Medicine alumni and their guests returned to campus for Alumni Day. The annual event, which saw record-high attendance this year, brings together medical alumni of all ages, encouraging them to stay engaged with the university and their former classmates. Held at the Li Ka Shing Center for Learning and Knowledge, the day featured educational sessions led by prominent Stanford leaders in global health and wrapped up with a celebratory social evening on campus.

Wolfe - smallThe morning kicked off with a keynote presentation from Nathan Wolfe, DSc, a Stanford visiting professor and author of The Viral Storm. Wolfe began with a short lesson on the history of human discovery of microorganisms and emphasized that we still have much left to explore when it comes to the smallest living things in our universe. He argued that a critical part of fighting the next major epidemic is to simply identify- and contain- the virus that would otherwise cause it. “In the process of interrogating the microbial species that are in our world,” Wolfe concluded, “we’re going to find things that have the potential to harm us, and stop them before they can.”

The agenda included a variety of educational sessions in medicine and the biosciences, including a joint presentation by consulting associate professors of medicine Rajiv Doshi, MD, and Chris Shen, MD, who discussed how their respective biodesign programs in India and Singapore are revolutionizing the use of medical devices in those countries. Among the many devices they discussed, Shen described a special stent that was created with Singapore’s aging population in mind. For those who require aortic valve replacement, this device is able to conform to different types of aortic shapes, is removable, and helps protect against stroke – a significant side effect of current therapies.

Doshi explained that in India, neonatal hearing screenings are not required and many people are still giving birth outside of hospitals. Stanford-India Biodesign has developed 22 products to date, including a low-cost, reusable neonatal hearing screening device that leverages technology available in the U.S. and allows testing to be done very cheaply. More important than the devices themselves, however, are the fellows who are educated in these programs. “Our true product is the people that we train,” Doshi said. “Over the course of a lifetime, they’re going to create a massive impact.”

alum - smallAnother notable speaker was S.V. Mahadevan, MD, director of Stanford Emergency Medical International, who participated in a panel discussion about introducing medical resources to underdeveloped countries. Mahadevan was instrumental in setting up India’s first international paramedic training institute, Nepal’s first emergency medical services system, and Cambodia’s first emergency medicine strengthening program. His presentation highlighted the growth of India’s emergency medical services system over the last decade. “In much of the world, emergency care doesn’t exist,” he told the audience. “In 2005, India’s EMS system cared for zero people. Today, it cares for 750 million people.”

Later in the evening, alumni and their guests raised a glass and reminisced with classmates at a reception hosted by the dean followed by a formal class dinner. Classes ending in ’4 and ’9 celebrated a milestone together this year including the Class of 1964, a very special group in the history of the School of Medicine who gathered to commemorate their 50th reunion. “Ours was the first five-year class to graduate on the Stanford campus,” said 1964 class representative Don Goffinet, MD. “The best class ever!”

Brittany Malitsky is associate director of the Stanford University Medical Center Alumni Association. Alumni Day is sponsored by the alumni association and is open to all graduates of degree programs at the School of Medicine, as well as former residents, interns, postdocs, and fellows.

Previously: Hunt or be hunted: Tracking the next big pandemics
Photos by Mark Estes

Events, Medicine and Literature, Medicine and Society, Stanford News

Inside Abraham Verghese’s bag, a collection of stories

Inside Abraham Verghese's bag, a collection of stories

What’s inside Abraham Verghese’s medical bag? Visit the Smithsonian Institution’s National Museum of Natural History to see. Verghese, MD, vice chair for the theory and practice of medicine and a physician at Stanford, is one of the notable Indian Americans featured in the exhibition “Beyond Bollywood: Indian Americans Shape the Nation,” which runs through August 2015 in D.C. and then will tour the U.S.

An article in The Caravan dives into the diversity and complexity of experiences lived by Indian Americans in the United States and opens this way:

IN JOHNSON CITY, Tennessee, in 1982, an Ethiopia-born, India-trained medical resident named Abraham Verghese coveted Dr Steven Berk’s doctor bag. He saved enough money to purchase one for himself, then rubbed it with neatsfoot oil to approximate the well-worn, talismanic quality of his mentor’s bag. Verghese then filled it with his kit—eye drops, calipers, prescription pads—and his hopes of assimilating into the American medical establishment.

Verghese’s bag, one of the exhibition’s hundreds of objects on display, is coupled with the physician-author’s memories from earlier in his career: “I had to ask someone how to tie my tie with a thinner knot so I could fit in,” the article notes. “And the only way I could eat the bland hospital food was to put Tabasco sauce on everything.”

The piece continues:

Verghese’s words capture the familiar dual imperative of immigrant life: on the one hand, fitting in, with a tie knot of appropriate girth; on the other, maintaining one’s tastes, through the strategic application of chilli-approximating Tabasco. His story reminds us that even blue- and white-collar immigrants have to negotiate resistance to the perceived “Third World invasion” of the United States, whether through neutralising accents or by softening the stiffness of difference with neatsfoot oil.

Previously: Abraham Verghese shares what’s in his lab coatStanford’s Abraham Verghese honored as both author and healer,  Stanford’s Abraham Verghese = “today’s most creative person” and Abraham Verghese’s Cutting for Stone: Two years as a New York Times best seller

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