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Cancer, Imaging, In the News, Research, Technology

Stanford instructor called out for his innovative – and beautiful – imaging work

Stanford instructor called out for his innovative - and beautiful - imaging work

breast cancer cells

I’ll skip the name word play – it’s just too obvious – but I won’t skip Michael Angelo’s work. Angelo, MD, a pathology instructor at Stanford, developed a new imaging technique that labels antibodies with metallic elements, then uses an ion beam to scan the tissue, revealing up to 100 proteins at once in a single cancer cell.

This technique, called multiplexed ion beam imaging, or MIBI, captured the attention of the National Institutes of Health, which featured Angelo in its NIH Director’s Blog this week. The images are lovely to look at, but also quite useful to learn more about tissue types.

Here’s Angelo describing the image above:

Angelo used MIBI to analyze a human breast tumor sample for nine proteins simultaneously—each protein stained with an antibody tagged with a metal reporter. Six of the nine proteins are illustrated here. The subpopulation of cells that are positive for three proteins often used to guide breast cancer treatment (estrogen receptor a, progesterone receptor, Ki-67) have yellow nuclei, while aqua marks the nuclei of another group of cells that’s positive for only two of the proteins (estrogen receptor a, progesterone receptor). In the membrane and cytoplasmic regions of the cell, red indicates actin, blue indicates vimentin, which is a protein associated with highly aggressive tumors, and the green is E-cadherin, which is expressed at lower levels in rapidly growing tumors than in less aggressive ones.

Taken together, such “multi-dimensional” information on the types and amounts of proteins in a patient’s tumor sample may give oncologists a clearer idea of how quickly that tumor is growing and which types of treatments may work best for that particular patient.  It also shows dramatically how much heterogeneity is present in a group of breast cancer cells that would have appeared identical by less sophisticated methods.

Angelo was given a NIH Director’s Early Independence Award last fall, and he’s ramping up his investigations of breast cancer.

Events, Science, Science Policy, Stanford News, Technology

The challenge – and opportunity – of regulating new ideas in science and technology

The challenge – and opportunity – of regulating new ideas in science and technology

running image

Innovation in science and technology holds promise to improve our lives. But disruptive business models, do-it-yourself medical devices, and open platforms also introduce corporate and personal risks. How can the public stay safe from unknown consequences as a company’s product or service matures? In a recent panel co-sponsored by Stanford’s Rock Center for Corporate Governance and Center for Law and the Biosciences, experts in law, business, and ethics discussed what happens when science and technology outrun the law.

Talk of drones, app-based car services, and music-sharing technologies teased out key issues currently disrupting legal paradigms. But biomedical science took center stage. “Health is more regulated than any other [area]” said panelist Hank Greely, JD, the Deane F. and Kate Edelman Johnson Professor of Law and director of the Center for Law and the Biosciences. He characterized the FDA’s processes as useful in slowing innovation in the health space but noted that rigorous pre-market regulation “won’t work in most parts of the economy.”

What happens when regulation is beyond reach? Greely noted that even if the FDA could limit an entrepreneurial company, it couldn’t conquer the DIY market. He referenced a procedure known as transcranial direct current stimulation, which, by applying electrodes to the head, can feel like “Adderall through a wire” or alter a person’s mood according to placement. A transmitting device is so simple to make, Greely said, “the hardest part will be finding an open Radio Shack.”

Moderator Dan Siciliano, JD, faculty director of the Rock Center and professor of the practice of law, asked the panelists which under-regulated technologies they found frightening. Vapor cigarettes, answered Eleanor Lacey, JD, for luring youth through fruit flavors and targeting them through advertising channels prohibited for regular cigarettes. (As previously reported on Scope, the FDA announced last spring that it would regulate the sale, but not marketing, of e-cigarettes.)

Lacey, vice president, general counsel and secretary of SurveyMonkey, discussed regulation issues involving health information that is transmitted on the company’s platform, where users own their data. She pointed to instances of users creating surveys on which respondents shared HIPAA-protected information, admitted suicidal thoughts, or confessed to crimes. The company cooperates with law enforcement in a very narrow set of sensitive situations but also upholds neutrality of the user-owned space and the user right to control the content: “You don’t want us to be able to shut it down,” Lacey said.

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Genetics, In the News, Medicine and Society, Research, Science, Technology

A leader in the Human Genome Project shares tale of personalized medicine, from 1980 until today

A leader in the Human Genome Project shares tale of personalized medicine, from 1980 until today

2559447601_005b33ae7d_zEric Lander, PhD, warned the several hundred people who came to hear him speak on the Stanford campus earlier this week that he wasn’t giving a traditional data-packed scientific presentation.

Instead, the founding director of the Broad Institute and veteran of the Human Genome Project — who Google’s Eric Schmidt introduced — promised to tell a story, a yarn about, as he put, the biomedicine of the East Coast meeting the technological innovation of the West Coast. (He couched the statement and admitted that yes, the West Coast does have a bit of biomedicine.)

So here goes:

Once upon a time, 35 years ago, in a land ruled by punk rock and big hair, scientists worked hard to pinpoint the genetic cause of cystic fibrosis, a disease caused by a single mutation. It was slow, hard work, but they persevered and found the gene.

Wouldn’t it be wonderful to know all the human genes, some scientists speculated, buoyed by their preliminary success. Cancer could be vanquished. Genetic disorders a thing of the past. But getting to that point might take as long as 2,000 years.

Enter the Human Genome Project (HGP) in 1990. A collaborative effort of 16 research centers in six countries, the team “industrialized biology,” cranking out a code for the 3 billion base pairs that make up the human genome.

Of equal importance, the HGP was advocating the importance of public access to genetic material. It faced a challenge from a rival private company, Celera, who proposed creating a subscription database with the genetic information.

The HGP also had to contend with hype, Lander said: With a banner-headline, the New York Times had proclaimed in 2000 “Genetic code of human life is cracked by scientists.”

But really, the scientists had little more than a gigantic text — ATCGGCTATATAATCG — that Lander likened to the Rosetta Stone. By comparing it with the genomes of mice, dogs, rats, cats, dolphins and many other critters, scientists worldwide were able to decipher it piece by piece.

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Biomed Bites, Research, Technology, Videos

Decoding proteins using your very own super computer

Decoding proteins using your very own super computer


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

A quick review: DNA codes for RNA, which directs the formation of proteins, the body’s teensy building blocks and messengers. But like individual widgets, proteins still aren’t ready for prime time as soon as they pop off the assembly line.

First they must be folded, partnered with other proteins and crafted into a three-dimensional shapes. Then, they can go about the work of life.

Stanford biochemist Vijay Pande, PhD, has been studying proteins for quite some time, and early on he realized that experimentally, proteins aren’t that easy to examine. They’re small and they rely on precise environmental cues. Once stripped from the cell, proteins behave and assemble differently, perhaps even not at all.

“So we take a very different approach,” Pande says in the video above:

We’ve been pioneering new simulation methods to not just be able to look at the problem experimentally, but to use large-scale computer simulations to understand why proteins would fold correctly, or why they would not fold correctly such as in the case with disease.

By using a very unusual approach where we get people around the world to donate computer time to us, we assembled the most powerful supercomputer in the world to tackle problems like protein folding and protein misfolding.

More than 183,000 computers now contribute to Pande’s project, Folding@home. Perhaps yours will be 183,001.

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

Previously: Using a smartphone and the Folding@home app to advance disease research, What computation tells us about how our bodies work and Nobel winner Michael Levitt’s work animates biological processes

Applied Biotechnology, Stanford News, Technology

Stanford team produces free Braille notetaker app

Stanford team produces free Braille notetaker app

brailleIn 2011, we showed you a video demonstration of an app that enables visually impaired people to type on a touchscreen tablet. Over the past few years, Sohan Dharmaraja, PhD, and Adrian Lew, PhD, completely redesigned the prototype they first developed with New Mexico State University student Adam Duran at Stanford’s Army High-Performance Computing Research Center. Now, their app, called iBrailler Notes, is ready for prime time.

This finished product, as Dharmajara and Lew explain in a recent story in Stanford Report, looks nothing like the original prototype that caught the media’s eye over three years ago. “Creating a prototype is relatively easy when your audience is a handful of fellow classmates. We did it almost as a whim to see if we could do it,” Dharmaraja said. “But creating a real app, that potentially millions might rely upon every day, is a whole other ballgame.”

Redesigning the app was no small feat because the final design had to be intuitive for users that may have little to no experience with touchscreen technology. As Dharmaraja explains, several of their test subjects had never used a tablet before:

Our testers did not know what a tablet computer or a touchscreen was, much less how to use them. We had to teach them how to use a touchscreen before they could tell us how to improve our products.

Dharmajara and Lew patterned their iBrailler Notes app after the traditional eight-keyed Perkins Brailler. What makes iBrailler Notes unique is the app enables the user to type regardless of where they position their fingers on the touchscreen—the user simply places eight to ten fingers on the touchscreen and the app automatically encircles each fingertip with a key. More from the article:

“We constantly pushed ourselves to innovate because being born with a disability shouldn’t mean you get left out of today’s technology revolution,” Dharmaraja said. “When you see the smile of someone doing something that you and I take for granted, it’s motivating.”

Lew added, “We think the time was well-spent to get it right.”

Previously: Developing a touchscreen Braille writerTennis, anyone? New York Times examines tennis for the blindMap of the Carina Nebula for the visually impairedRubik’s Cube for the visually impairedThe blind can see, and The mind maps the visual world with minimal means.
Photo courtesy of Sohan Dharmaraja

Patient Care, SMS Unplugged, Technology

Why technology won’t destroy the doctor-patient relationship

Why technology won't destroy the doctor-patient relationship

SMS (“Stanford Medical School”) Unplugged is a forum for students to chronicle their experiences in medical school. The student-penned entries appear on Scope once a week; the entire blog series can be found in the SMS Unplugged category.

doctor in iPadMany aspects of medicine have changed over the course of human history. Schools of thought shifted from humorism to evidence-based medicine, while the standard of care evolved from bleeding to our modern cornucopia of interventions.

Yet across centuries, the doctor-patient relationship has remained relatively constant – a physician would physically interact with the patient and then come to conclusions on how to treat him or her. However, new technologies and innovative delivery models have begun to erode this cornerstone of medical practice, raising questions about whether they are ultimately helpful or harmful.

I was first introduced to non-traditional models of medical care the summer after my freshmen year of college. I worked with a doctor who has an extensive background in telemedicine, which broadly implies the use of technology to expand access to medical care. In practice, that might mean seeing patients via videoconference, having patients take pictures of lesions, remote monitoring, or a number of other applications. Moving forward, it may even allow patients to conduct their own physical on a smartphone.

Inspired by my experience, I started to explore other ways we can reach patients without bringing them into the doctor’s office. One strategy is to use social media to engage patients. Another is to make use of retail health clinics – clinics in shopping centers or pharmacies that are equipped to handle one-off, minor medical complaints. (If you’re interested, I have written in more detail about each of these models here, here, and here).

Almost invariably, the first criticism brought against these strategies is that they’ll interfere with the doctor-patient relationship. It’s true that they can influence the dynamic between a patient and physician and should be evaluated carefully. But in my experience, critiques tend to overlook three major aspects of technology that actually improve the doctor-patient relationship.

First, new tools in health-care delivery don’t replace the physician with a technological brave new world. To the contrary, they create a doctor-patient relationship for patients who otherwise wouldn’t have a doctor at all. Many of these tools are targeted towards patients who live in underserved communities and give them an effective way to communicate with a doctor.

Take rural populations as an example. Suppose a patient has a condition that requires a specialist consult. Do you think the patient would rather: (1) take a day off from his or her job and drive three hours to a tertiary care center; or (2) remotely connect with a specialist who can clear up the problem? Most patients would likely prefer the second scenario, and may defer care if they don’t have that option.

Second, the doctor-patient relationship is especially relevant to patients who have complicated medical issues. If patients are able to handle minor complaints outside of the doctor’s office, physicians will have more time to spend with the patients who need the most help.

Finally, these approaches empower patients to take responsibility for their own health. Once again, let’s consider this in in the context of an example. One common stereotype in medicine is that of the non-compliant patient – maybe someone who has high blood pressure, high cholesterol, etc., but doesn’t take his or her medication, make diet modifications, or exercise. At present, a doctor might require this patient to come in for a check-up every few months. And yet nothing changes.

But if the doctor gives that same patient the tools to monitor their health on a day-to-day basis, the patient may take on a greater sense of ownership for their well-being and start making some changes. As medical students, we regularly hear that we’re in an era of patient-centered care. Technological tools that give patients more health information don’t hurt the doctor-patient relationship; they serve as another means to connect us.

Medicine is a constantly evolving field. New strategies have the potential to change the way we practice. But it’s worth remembering that a different doctor-patient relationship can be a better doctor-patient relationship.

Akhilesh Pathipati is a second-year medical student at Stanford. He is interested in issues in health-care delivery.

Photo by NEC Corporation of America

Genetics, Science, Stanford News, Technology

Major genomics exhibit, staffed with Stanford volunteers, now open in San Jose

Major genomics exhibit, staffed with Stanford volunteers, now open in San Jose

Abbey Thompson, a Stanford PhD candidate, gives tour of Genome exhibit at the The Tech Museum of Innovation in San Jose on Wednesday, February 4, 2015. ( Norbert von der Groeben/Stanford School of Medicine )

Last week I checked out the museum exhibit “Genome: Unlocking Life’s Code,” which just arrived at the Tech Museum of Innovation in San Jose.

Created to honor the 10-year anniversary of the completion of the Human Genome Project by the National Institutes of Health and the Smithsonian Institution, the exhibit’s goal is to demystify the science of genetics. It includes demonstrations of the equipment used in sequencing the human genome, videos about the practical and ethical implications of having your own genome sequences, and interactive exhibits that let you explore which genetically-determined characteristics — like hair color or even being lactose intolerant — you might have. There is a section devoted to determining ancestry from your DNA; it turns out that we humans all hail from east Africa.

The part of exhibit I can’t get out of my mind was made up of transparent cylinders filled with sand. It was a comparison of the genomes of different species. We humans are, of course, a complex species and so is our genome, with 20,000 genes. But amoebas and barley (yes, the grain) have bigger genomes than we do!

Volunteer docents, many from the Stanford genetics community, are ready to answer questions from visitors of all ages. Michael Cherry, PhD, professor of genetics, has trained as a docent for the exhibit. Members of his lab team have volunteered, too.

“It is good for us to learn how to communicate our science to the general public — to explain things that seem basic to us,” Cherry said in an Inside Stanford Medicine article I wrote on the exhibit. “Visitors tell us what is important to them; they stimulate us.”

The Tech Museum and Stanford’s Genetics Department have a long-term relationship. For more than a decade, the department has sponsored Stanford at the Tech, a program that aims to explain the science of genetics to the general public.

“It is so critical that we reach the public,” Michael Snyder, PhD, professor and chair of genetics told me. “We are undergoing a genetics revolution, where everyone can get their DNA sequence determined, and it will transform the way medicine is practiced.”

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Patient Care, Stanford News, Technology

Medical student-turned-entrepreneur harnesses Google Glass to improve doctor-patient relationship

Medical student-turned-entrepreneur harnesses Google Glass to improve doctor-patient relationship

Pelu - 560

When third-year Stanford medical student Pelu Tran began clinical rotations and started caring for patients in the summer of 2012, he experienced firsthand how paperwork, documentation and billing coding can leave “little time for the patient-physician relationship.” He shared his frustrations with Biodesign classmate and Stanford MBA graduate Ian Shakil and, after the pair tested out an early version of Google Glass, the solution became clear: develop a platform based on the wearable technology that automates the record-keeping process for doctors.

Tran, who was recently named to Forbes’ “30-Under-30: Healthcare,” and Shakil founded Augmedix and have raised a total of $23 million in venture capital funding. A story published today in Inside Stanford Medicine explains how the company has dramatically cut the number of hours doctors spend on record keeping:

Contracting with Google Glass, Augmedix provides the much-publicized internet-connected headgear, which looks and feels like a pair of eye glasses, to doctors on a monthly subscription basis. Physicians wear the headgear during appointments with patients and use verbal cues to instantly access a patient’s electronic medical records and transcribe the doctor-patient conversation. A thumbnail-sized screen appears in the corner of the right eye of the device, which also has a camera and a microphone. The visit gets live streamed directly to Augmedix, which then uses a combination of software and human support to type notes into the patient’s electronic medical records. When the doctor’s visit is complete, so is the record-keeping.

According to Tran, physicians who use the service have been able to reduce the number of hours spent record keeping from an average of 17 a week down to just two — or even fewer. “It literally changes the lives of the doctors we work with,” he said. “They’re getting back 15-hours a week to spend with family, with friends, with patients, to provide care. That is the whole point.”

The service is currently available for use in 35 clinics across 11 states and growing. Although Google recently announced that it will stop selling Glass to consumers, the company will continue to contract with companies such as Augmedix that have a specialized use for the technology.

Previously: Using Google Glass to help individuals with autism better understand social cues, Using Google Glass to improve quality of life for Parkinson’s patients and Abraham Verghese uses Google Glass to demonstrate how to begin a patient exam
Photo courtesy of Augmedix

Global Health, Media, Patient Care, Pediatrics, Research, Technology, Videos

OPENPediatrics offers opportunity to help physicians, and sick children, worldwide

OPENPediatrics offers opportunity to help physicians, and sick children, worldwide

6948764580_97d353e8d4_zAs chief of critical care at Boston Children’s Hospital, Jeffrey Burns, MD, MPH, was asked to consult on the case of a young girl who fell ill while vacationing with her family in Guatemala. He had treated a similar case in the U.S. before, but he encountered unexpected technological hurdles.

That spurred Burns — working with many partners, including IBM — to create OPENPediatrics.org, a platform that allows physicians to share skills and resources to treat sick children. Burns described his hopes for the site in a 2014 article in Medtech Boston:

Our goal was to create something called a community of practice where instead of being broad and thin like a MOOC (Massive Open Online Classes), we would be narrow and much more deep, and the content would actually be peer reviewed by doctors and nurses who care for critically ill children, because those are essentially our primary users,” Burns says.

The site, which launched last year, offers forums for health-care workers worldwide to share experiences and a multimedia library with videos and animations — including some interactive features — on everything from nasopharyngeal suctioning to Faciltating Parent Presence During Invasive Procedures.

Burns and his team have been thinking how to leverage the platform to support research.

(A confession: I learned about OPENPediatrics through an article in Wesleyan magazine. Stanford’s Cardinal brethren on the East Coast, Wes, like Stanford fosters interdisciplinary projects and, I’m proud to say, is the alma mater of two of us in the medical school’s relatively small Office of Communication.)

Previously: Stanford undergrad works to redistribute unused medications and reduce health-care costs, Stanford Medicine X: From an “annual meeting to a global movement”  and Euan Ashley discusses harnessing big data to drive innovation for a healthier world
Photo by Intel Free Press

Health Costs, Medicine and Society, Medicine X, Technology

The power of social media: How one man uses it to help amputees get prosthetics

The power of social media: How one man uses it to help amputees get prosthetics

Stanford’s Medicine X is a catalyst for new ideas about the future of medicine and health care. This new series, called The Engaged Patient, provides a forum for some of the patients who have participated in or are affiliated with the program. The latest installment comes from Medicine X ePatient Joe Riffe.

Allie - smallWe’re all familiar with social media. We spend our days updating our Facebook statuses, tweeting our latest attempt at being funny, or using Instagram to show off our last meal. Social media is an excellent way to connect with friends and family; some people have even gained celebrity status all through the social-media movement. Social media has sparked revolutions as well. The Occupy Wall Street Movement, for example, was largely driven by the power of a hashtag.

This power is also accessible to patients to start a David versus Goliath type war. I use the power of social media to help amputees get prosthetics, and in this piece I’ll tell you two of these stories. The first is about Allie; the second is a recent story about my own battle to get a prosthetic.

I met Allie in the hospital after a mutual friend asked me to meet her and her family to show them that being an amputee doesn’t mean you can’t live the life you want to live. I immediately connected with Allie. I wanted to be her mentor; she the Luke to my Obi Wan. Allie didn’t have insurance at that time, and I couldn’t stand the thought of this young girl, just starting her life, not having access to the best prosthetics available. I explained to her that with the right prosthetic, anything is possible.

A local prosthetic company had gotten to Allie before the prosthetist I use was able to meet with her and her family. They convinced the family that due to Allie’s lack of insurance she would have to settle for the best prosthetic she could afford – and not the best available like she deserved. Allie suffered on this prosthetic for months. The ill-fitting socket and knee didn’t suit the lifestyle of an active 20-year old.

After nearly a year of suffering, Allie found herself with insurance and made her way to the prosthetist I use. He quickly saw the need for her to have access to the best technology available and had his team start creating a prosthetic for her.

There are many hoops to jump through when trying to get a prosthetic leg. The biggest obstacle is that advanced technology comes with a hefty price tag. Luckily, the office she goes to now knows how to get through these hoops fairly quickly.

Allie made it though this process fairly quickly and received a letter from her insurance company promising to pay for the advanced prosthetic. Then, they began the stall tactic. They waited months, delaying the payment required to order the prosthetic that Allie so desperately needed.

That was when I came in. With one tweet – just one tweet – I was able to expedite the payment for her prosthetic limb. Why does this company prevent amputees from returning to their lives by approving high-quality prosthetics then not paying for them, I wrote to my hundreds of followers. A few days later I was greeted on Facebook by the photo above: Allie with her new leg.

Unadulterated joy!

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