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Education, Patient Care, Technology, Videos

Physician-writer Abraham Verghese on ritual, technology and medical training

Physician-writer Abraham Verghese on ritual, technology and medical training

stethoscope-448614_1280Listening to Abraham Verghese, MD, is always a treat, so I quickly clicked on a recently published Q&A featuring Verghese in conversation with Steven Stack, MD, president of the American Medical Association.

Of particular interest were comments on changes in the training of medical students. Here’s Verghese:

There have been some striking changes. For one thing, the model that you probably trained under and certainly I trained under — an intense focus on the patient and the bedside and rounds going from bed to bed — I think it’s been sort of kidnapped in a sense by the workstation.

One of the great disappointments students have when they come on the wards is… in the first two years they’re learning physical diagnosis, and they’re so excited to learn how to read the body as a text. And they arrive on the wards, and their moment of awakening, almost disillusionment, is to find that the currency on the wards does not revolve around the patient. It revolves much more around the computer. For many of them, it’s a moment of crisis. I think it actually leads many of them away from primary care, which is not a good trend.

Verghese also weighs in on the importance of touch and how a physical exam is a ritual akin to baptism or graduation. Two videos round out the post, where Verghese and Stack (the youngest AMA president since 1854!) discuss the excessive use of tests and Verghese’s motivation to begin writing books.

Previously: Abraham Verghese: “It’s a great time for physician leaders to embrace design thinking”, Abraham Verghese: “There is no panacea for an investment of time at the bedside with students and Physician-author Abraham Verghese encourages journalists to tell the powerful stories of medicine
Photo by HolgersFotografie


Education, Health Costs, In the News, Patient Care, Research, Stanford News, Technology

Medical errors caused by doctors not examining their patients

Medical errors caused by doctors not examining their patients

800px-Child_examined_by_doctorStories of shocking medical errors that occur because doctors miss something during a physical exam — or forget to examine a patient at all — are common. Every physician knows them, says Stanford physician Abraham Verghese.

A missed breast mass in a patient that presents with chest pain. A missed gunshot wound in a patient wheeled into the emergency room. A missed pregnancy in a patient with a large belly.

But little has been done to quantify this type of medical error. In a first step toward creating data-based measurements of medical errors due to inadequacies in the physical exam, a study published recently in the American Journal of Medicine reports on a collection of 208 such occurrences, and their consequences.

I think of it as my worst nightmare, that a patient will slip through my grasp with a diagnosable or treatable condition.

Researchers collected the incidents from responses to surveys sent to 5,000 physicians asking for first-hand stories of such medical errors. The cause of the oversights in the 208 responses was most often a failure to perform the physical examination at all — in 63 percent of the cases, the study states. Other times, errors were caused by misinterpretating or overlooking physical signs.

“I think of it as my worst nightmare, that a patient will slip through my grasp with a diagnosable or treatable condition,” says Verghese, who is known as a champion of bedside medicine. “I call it the ‘low hanging fruit,'” he says, referring to the simple yet essential process of conducting the physical exam — and its low cost.

The consequences of these mostly preventable mistakes varied from missed or delayed diagnoses in 65 percent of the patients, to incorrect diagnosis in 27 percent or unnecessary treatment in 18 percent, the study says.

“We are talking about missing things that are very common, a mass, or a sore or a heart murmur or something in the lungs, that leads you down the wrong path,” says John Ioannidis, MD, senior author of the study. “This is something that happens everyday, and it’s something that could be corrected to a good extent.”

A well-known report conducted by the Institute of Medicine titled, “To Err is Human,” found that medical errors cause nearly 100,000 deaths per year, according to the study. The extent to which physical examination errors contribute to this figure remains uncertain and, as a result, little has been done to prevent them, it says.

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Bioengineering, Evolution, Research, Science, Stanford News, Technology

Fast-forwarding evolution to select suitable proteins

Fast-forwarding evolution to select suitable proteins

4286076672_2763323a1e_zNature churns out new versions of proteins in response to environment changes or random mutations. Sometimes the new versions work better than old. Other times, not.

But now, Stanford researchers have developed a super speedy technique to test millions of versions of a certain protein to see which one works best.

A Stanford news release explains:

The researchers call their tool µSCALE, or Single Cell Analysis and Laser Extraction.

The “µ” stands for the microcapillary glass slide that holds the protein samples. The slide is roughly the size and thickness of a penny, yet in that space a million capillary tubes are arrayed like straws, open on the top and bottom.

The microcapillary glass slide, roughly the size and thickness of a penny, holds the protein samples.

The power of µSCALE is how it enables researchers to build upon current biochemical techniques to run a million protein experiments simultaneously, then extract and further analyze the most promising results.

The research was led by Jennifer Cochran, PhD, associate professor of bioengineering and Thomas Baer, PhD, executive director of the Stanford Photonics Research Center.

The system is easy to use with numerous applications, Baer said.

“Evolution, the survival of the fittest, takes place over a span of thousands of years, but we can now direct proteins to evolve in hours or days,” Cochran said in the release.

Previously: Proteins from pond scum revolutionize neuroscience, Study shows toothed whales have persisted millions of years without two common antiviral proteins and Computing our evolution
Photo by Alexander Boden

Genetics, Microbiology, Technology

The art of exploring the fecal-ome

The art of exploring the fecal-ome

Monet Cathé Monet La_Cathédrale_de_Rouen.yellowThe community of bacteria living inside our own guts is about as local an ecosystem as we’re likely to find. So you’d think navel-gazing biologists would already know all about it. But several barriers have made this ecosystem nearly as inaccessible as the forests of the Amazon River were for 18th century naturalists.

One problem has been that bacteria have traditionally been studied by growing them in glass or plastic dishes containing a “culture medium,” typically a sort of gelatin concoction containing mystery ingredients like calf serum. Lots of bacteria grow well on this stuff, but even more don’t. And most of what we know about bacteria comes from studies of the short of list bacteria that will grow in the lab.

Advances in genomics have revealed the presence of new species of bacteria everywhere biologists have looked. But, apparently, even that diversity is just the tip of the iceberg.

Computer scientists and geneticists at Stanford recently collaborated on a technique and uncovered an amazing amount of diversity in the gut contents of a human male, who volunteered a fecal sample. In the sample, the Stanford team found not just lots of species, but also lots of sub-strains — as many as five different strains of a single species. You can read more about the technique in the press release I wrote about the study, which appeared today in Nature Biotechnology.

The work’s similarity to an incredibly tough jigsaw puzzle captured my imagination.

Geneticist Michael Snyder, PhD, who is a senior author on the paper, explained to me that it’s now pretty easy to assemble the genome of a single person or bacterium from the short strands of DNA in a sample.

But when you have a mix of lots of different species, he said, it’s like assembling 100 jigsaw puzzles from a single pile of pieces from all those different jigsaw puzzles. Not only do you have to fit the pieces together, but you have to know which puzzle or species each piece came from.

If the jigsaw puzzles are as different as, say, a Van Gogh Sunflowers painting and Ansel Adams’ “Moonrise, Hernandez, New Mexico”, you wouldn’t have much trouble separating the pieces. But what if you’ve got several strains of the same bacterial species? That’s the equivalent of a mix of puzzles all depicting different versions of Monet’s paintings of Cathedral Rouen.

Previously: Microbiome explorations stoke researcher’s passionAt TEDMED 2015: How microbiome studies could improve the future of humanityInvestigating the human microbiome: “We’re only just beginning and there is so much more to explore
Monet image courtesy of KnightSerbia

Biomed Bites, Stanford News, Technology

When proteins go bad: Quality control inside the cells

When proteins go bad: Quality control inside the cells

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

The enthusiasm of Tom Wandless, PhD, in this video is contagious. Wandless, a professor of chemical and systems biology, injects vigor into the science of protein folding.

Just as in a factory assembly line, sometimes cells produce blooper proteins. And that’s no good: These abnormal proteins can lead to diseases such as Parkinson’s or Huntington’s diseases, Wandless said.

Wandless and his team are currently working to understand how cells distinguish correct from incorrect proteins. “How the cell uses quality control machinery to recognize and ultimately degrade these proteins is a very important question, not only for basic sciences, but ultimately for disease as well,” Wandless says in the video above.

Making inroads on diseases like Parkinson’s alone would be quite an accomplishment, he says. “But what has excited me even more is the potential for understanding the role of protein degredation in disease we don’t even understand yet.”

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

Previously: Decoding proteins using your very own super computer, Nobel winner Michael Levitt’s animates biological processes and Packed and ready to go: The link between DNA folding and disease

Applied Biotechnology, Events, Genetics, Research, Stanford News, Technology

Stanford Genome Technology Center retreat highlights interdepartmental synergy

Stanford Genome Technology Center retreat highlights interdepartmental synergy

IMG_0108The recent Stanford Genome Technology Center retreat drove home for me why it’s a great idea to put biochemists, geneticists, engineers, and physicians in a lab together.

Set up in 1989 to establish automated methods for the Human Genome Project, SGTC works to increase the speed, accuracy, and cost-effectiveness of genomic, biomedical, and diagnostic technologies. The center integrates personnel from Stanford’s departments of genetics, biochemistry, medicine, and electrical engineering. At the two-day retreat, researchers presented their latest work in areas like synthetic biology, genome sequencing applications, single-cell approaches, and devices for cellular and molecular detection.

Since I joined SGTC this summer, I’ve gotten a firsthand view of the benefits of combining engineers and biologists. As our engineer Rahim Esfandyarpour, PhD, told me, “We have a lot of solutions – you biologists just need to tell us what the problems are.” The solutions presented at the retreat ranged from ‘sequencing by seeing’ – literally reading DNA molecules under an electron microscope – to a nanopipetting technology that noninvasively takes tiny samples from individual cells, to electrical ‘needles’ that can detect interactions between individual cells or even molecules, to wearable devices that quantify molecules in sweat.

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Events, Research, Science, Technology

At TEDMED 2015: Thinking about “breaking through” the valley of death in science

At TEDMED 2015: Thinking about "breaking through" the valley of death in science

This year’s TEDMED was held Nov. 18-20 in Palm Springs, Calif. Stanford Medicine is a medical research institution partner of TEDMED, and a group of MD and PhD students who represented Stanford at the conference will be sharing their experiences here. 

“I am #BreakingThrough the ‘valley of death.’”

That’s what I wore on my nametag last week at TEDMED. The theme of this year’s conference was “Breaking Through,” and every delegate was asked to write a brief statement that illustrates an area of health care that they’re most passionate about.

The “valley of death” refers to the vast gap in the landscape of biomedical therapeutic development between academia and industry. Traditionally, an academic institution and industry have played two separate but equally important roles in the lengthy and expensive process of bringing new medical innovations to the patient. Academic researchers investigate new mechanisms, pathways and methods, making discoveries that yield promise. Industry then takes these experimental innovations and conducts product development, safety profiling, clinical trials, and manufacturing and distribution, ensuring that extensively tested, safe and efficacious products are widely made available.

However, this transition between academia and industry is not always a smooth one. The pharmaceutical industry is notorious for its extreme risk aversion with new products – and with an average cost of $1B, a 10-year path to FDA approval, and a failure rate north of 95 percent, who can blame them? Meanwhile, most academic labs are neither equipped to nor interested in spending the resources to conduct important yet labor-intensive preclinical work (which, quite frankly, won’t help a scientist graduate, secure tenure, or win a Nobel Prize). And so, because of this, potentially beneficial therapeutics are liable to languish in the valley of death between discovery and human trials.

On Thursday, Stanford professor Daria Mochly-Rosen, PhD, took the TEDMED stage to describe her own experience crossing that valley on the TED stage. In the early 2000s her lab had discovered a novel class of compounds for reducing cardiac injury after heart attack. After receiving universal rejections from pharma companies that they hoped would license the compounds, Mochly-Rosen and one of her graduate students reluctantly took matters into their own hands, left the university, and started KAI Therapeutics to bring their compounds into clinical trials. Long story short, they were eventually wildly successful and acquired by Amgen after demonstrating efficacy in Phase II clinical trials. The experience drove Mochly-Rosen to start the Stanford’s SPARK program, which offers a variety of resources – including classes, industry mentors and grants – to help scientists here survive their own journeys through the valley of death.

As a scientist developing new potential tools for diagnosis and therapy, and as someone who works frequently with early-stage life science companies, I spend a disturbing amount of time thinking about the valley of death. But to me, the valley is much deeper and wider than what it means for pharmaceutical development. It spans similar challenges in medical devices, diagnostics, and even digital health solutions.

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Big data, Medical Apps, Patient Care, Precision health, Research, Stanford News, Technology

Precision health in practice: Using HealthKit to monitor patients’ blood-sugar levels

Precision health in practice: Using HealthKit to monitor patients' blood-sugar levels

Rajiv Kumar and patient - 560

Imagine having to keep track of your diabetic son’s constantly changing blood sugar levels by typing each individual reading into an email. Then, once in the doctor’s office, having to spend a chunk of your precious time with your clinician waiting for her to download that data.

That was the plight of Lori Atkins, whose son has Type 1 diabetes, until this March, when the Atkins joined a pilot project involving Apple’s HealthKit. Pediatric endocrinologist Rajiv Kumar, MD, is using HealthKit – a new technology that can securely share health data with third-party applications – to more easily monitor the blood-sugar levels of 10 patients.

A recent Inside Stanford Medicine article describes the project:

Patients like Blake wear a continuous glucose monitor that sends 288 blood-sugar readings a day to an Apple mobile device through Bluetooth. The data is securely transmitted via HealthKit into the patient’s electronic medical record at Stanford Children’s Health through the MyChart app.

The system also improves clinical outcomes, Kumar said: “Our endocrinologists are now able to easily assess large volumes of blood-sugar data between clinic visits — and quickly identify trends that could benefit from insulin dosing regimen changes.”

Kumar is planning to expand the use of the app to more of his patients.

Previously: A look at the MyHeart Counts app and the potential of mobile technologies to improve human health, Harnessing mobile health technologies to transform human health and A picture is worth a thousand words: Researchers use photos to see how Type 1 diabetes affects kids
Photo by Norbert von der Groeben

Bioengineering, Cancer, Imaging, Public Safety, Research, Stanford News, Technology

A new way to scan for plastic explosives could someday detect cancerous tumors

A new way to scan for plastic explosives could someday detect cancerous tumors

14591799636_128fbe50ee_zSci-fi shows and superhero films are full of gadgets and beings that have the power to remotely scan their environment for hidden things. For us mere mortals this superability may sound unachievable, but now Stanford engineers are working to develop a safe and portable way to detect concealed objects by scanning with microwaves and ultrasound.

As this Stanford Report story explains, the idea began with a challenge posed by the Defense Advanced Research Projects Agency: Design a way to detect buried plastic explosives from a safe distance without touching the surface of the ground.

A team of electrical engineers led by assistant professor Amin Arbabian, PhD, and research professor Pierre Khuri-Yakub, PhD, took up the challenge, paying homage to the scanning device made popular by sci-fi show Star Trek in the process. They created a tricorder-like device that senses the ultrasonic waves created by objects as they expand and contract when warmed by electromagnetic energy (e.g., light and microwaves).

Here’s the really interesting part: Because everything expands and contracts when heated — but not at identical rates — this scanning tool could have medical applications as well. For example, blood vessels that sprout from cancerous tumors absorb heat differently than surrounding tissue. So, blood vessels radiating from tumors could appear as “ultrasound hotspots” when scanned with the tricorder device.

The team is working to make this device ready to detect the presence of tumors and other health anomalies sometime within the next decade or so.

Previously: Beam me up! Detecting disease with non-invasive technology and Tiny size, big impact: Ultrasound powers miniature medical implant
Photo by Joe Haupt

Big data, Patient Care, Stanford News, Technology

OrderRex taps decisions of thousands of “doctors like me”

OrderRex taps decisions of thousands of "doctors like me"

chen_vaAs a new clinician, Stanford’s Jonathan Chen, MD, PhD, struggled to treat patients with unfamiliar conditions. He yearned to ask one or, even better, dozens of more experienced physicians for advice.

For most people, that would be a passing wish. But not for Chen, who has a PhD in computer science and experience working as a software developer. (Oh yeah, he also started college when he was 13).

A recent article from the Center for Health Policy and Center for Primary Care and Outcomes Research (CHP/PCOR) describes Chen’s next steps:

“I thought about how the Amazon product-recommender algorithm works and thought, `Can we do this for medical decision-making?’” said the 34-year-old Chen, a VA Medical Informatics Fellow at Stanford Health Policy.

So instead of, other people who bought this book also liked this book, how about: Other doctors who ordered this CT scan also ordered this medication.

“What if there was that kind of algorithm available to me at the point of care?” he asked. “It doesn’t tell me the right or wrong answer, but I bet this would be really informative and help me make better decisions for my patients.”

Chen’s idea differs from the Green Button concept, which draws on thousands of medical records to search for patients with similar conditions. Instead, Chen is trying to capture doctor’s decision-making process by developing a digital platform to mine electronic medical records; he calls his project OrderRex.

It “looks for ‘doctors like me,’ and anticipates what the doctor wants before they ask for it,” Chen explains in the article.

Chen received a five-year National Institutes of Health grant and is working to develop OrderRex with the guidance of his mentor, bioinformatician Russ Altman, MD, PhD.

Previously: Push-button personalized treatment guidance for patients not covered by clinical-trial results, Big Data in Biomedicine panelists: Genomics’ future is bright, thanks to data-science tools and Euan Ashley discusses harnessing big data to drive innovation for a healthier world 
Photo by Joseph Matthews/VA Palo Alto

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