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Applied Biotechnology, Bioengineering, Science, Stanford News, Technology

Dr. Prakash goes to Washington

Dr. Prakash goes to Washington

Prakash at White House

It’s not every day that a researcher gets to hang out at the White House – so Wednesday was rather unusual for Stanford bioengineer Manu Prakash, PhD. Prakash, inventor of the 50-cent microscope, called the Foldscope, and a $5 chemistry kit, participated in the White House’s first-ever Maker Faire that day. He called it an “inspiring event” and tweeted the above photo from his time there.

And for those interested in learning more, a paper on the Foldscope was published online this week in PLOS One.

Previously: Stanford microscope inventor invited to first White House Maker Faire, The pied piper of cool science tools, Music box inspires a chemistry set for kids and scientists in developing countries, Free DIY microscope kits to citizen scientists with inspiring project ideas and Stanford bioengineer develops a 50-cent paper microscope
Photo by Manu Prakash

Behavioral Science, Bioengineering, Neuroscience, Research, Stanford News, Technology

Party animal: Scientists nail “social circuit” in rodent brain (and probably ours, too)

Party animal: Scientists nail "social circuit" in rodent brain (and probably ours, too)

party animalStimulating a single nerve-cell circuit among millions in the brain instantly increases a mouse’s appetite for getting to know a strange mouse, while inhibiting it shuts down the same mouse’s drive to socialize with the stranger.

Stanford brain scientist and technology whiz Karl Deisseroth, MD, PhD, is already renowned for his role in developing optogenetics, a technology that allows researchers to turn on and turn off nerve-cell activity deep within the brain of a living, freely roving animal so they can see the effects of that switching in real time. He also pioneered CLARITY, a method of rendering the brain – at least if it’s the size of of a mouse’s – both transparent and porous so its anatomy can be charted, even down to the molecular level, in ways previously deemed unimaginable.

Now, in another feat of methodological derring-do detailed in a new study in Cell, Deisseroth and his teammates incorporated a suite of advanced lab technologies, including optogenetics as well as a couple of new tricks, to pinpoint a particular assembly of nerve cells projecting from one part to another part of the mouse brain. We humans’ brains obviously differ in some ways from those of mice. But our brains have the same connections Deisseroth’s group implicated in mice’s tendency to seek or avoid social contact. So it’s a good bet this applies to us, too.

Yes, we’d all like to be able to flip a switch and turn on our own “party animal” social circuitry from time to time. But the potential long-term applications of advances like this one are far from frivolous. The new findings may throw light on psychiatric disorders marked by impaired social interaction such as autism, social anxiety, schizophrenia and depression.From my release on this study:

“Every behavior presumably arises from a pattern of activity in the brain, and every behavioral malfunction arises from malfunctioning circuitry,” said Deisseroth, who is also co-director of Stanford’s Cracking the Neural Code Program. “The ability, for the first time, to pinpoint a particular nerve-cell projection involved in the social behavior of a living, moving animal will greatly enhance our ability to understand how social behavior operates, and how it can go wrong.”

Previously: Lightning strikes twice: Optogenetics pioneer Karl Deisseroth’s newest technique renders tissues transparent, yet structurally intact, Researchers induce social deficits associated with autism, schizophrenia in mice, Anti-anxiety circuit found in unlikelybrain region and Using light to get muscles moving
Photo by Gamerscore blog

Chronic Disease, Public Health, Research, Technology

More evidence that text message programs can help in managing diabetes

mobile_phone_6.16.14Previous research has shown that automated daily text messages can increase medication adherence among diabetic patients and reduce their repeated visits to the emergency room. Now new research offers more evidence that text-message-based programs are an effective tool in helping in those with type 2 diabetes improve their glycemic control.

For the study, researchers from the Scripps Whittier Diabetes Institute partnered with a San Diego-based community clinic providing care to a large percentage of Latino patients with type 2 diabetes. A group of 126 patients were randomly assigned to receive either standard care alone or standard care combined with frequent text messages. According to a release:

Standard care consisted of regular visits with a primary care physician and a brief computerized presentation conducted in English or Spanish that included; diabetes nutrition standards; desired targets for blood sugar, cholesterol and blood pressure; and medications recommended to achieve control.

For the text messaging group, the same standard care was provided but in addition messages were sent to their mobile devices at random times throughout the week. The messages focused on healthy nutrition tips, the benefits of physical activity and medication adherence, and requests to check blood sugar and send back results. Two to three messages were sent each day at the beginning of study enrollment, and the frequency tapered off over a six-month period.

“At the six-month mark, we found that the Dulce Digital [study] participants had a significantly larger decrease in hemoglobin A1c test levels than the control group,” said [Athena Philis-Tsimikas, MD, corporate vice president for the Scripps Whittier Diabetes Institute.]

Noting the promise of mobile phones to aide low-income populations in managing chronic diseases, Philis-Tsimikas said in the release, “We found that by using text messages we were able to circumvent many of the barriers these patients face, such as lack of transportation or childcare, while still being able to expand the reach of diabetes care and education.”

The findings were presented on Friday at the 74th Scientific Sessions of the American Diabetes Association in San Francisco.

Previously: Text message program helps smokers “stay focused on quitting”, Text message reminders shown effective in boosting flu shot rates among pregnant women and Texts may help people with diabetes manage care
Via HealthCanal
Photo by Wolfman-K

Patient Care, Technology

Listening to the stethoscope’s vitals

p013296.jpg“What will happen to bookshelves?”, bibliophiles lamented with the ascent of the e-book, mourning the loss of the feel of paper pages between their fingers and the smell of rich mahogany encasing their many leather-bound books. Now, physicians may be wondering the same thing about stethoscopes. As ultrasound machines become smaller, cheaper and more portable, a recent BMJ article notes, some doctors propose that point-of-care scans may replace the stethoscope as “the symbol of the profession.”

In a BMJ blog post responding to the original article, Rhy Davies, a medical student at Imperial College London, writes an “Ode to a stethoscope” summarizing the history of the instrument, its medical pros and cons and the meanings it embodies. He writes:

And can you boldly stride into the hospital canteen with an ultrasound device the way you can with a stethoscope? Slung around the neck, it declares to the world that, yes, everything will be fine now that the medical student is here. (Actually, that’s infuriating. Can we all agree to stop doing that?)

Lastly, what of one of the greatest uses of the stethoscope? In a hectic emergency room or a busy GP surgery, when the earbuds go in and the diaphragm is laid meaningfully on the chest, the stethoscope ferries the doctor or student to that quiet mental space…..what will become of that little space where the doctor or student can synthesise, diagnose, and reflect? Will the next generation of ultrasounds have an app for that?

Previously: Med school friendships from classroom to clinicsThe OMG Factor: Curbing your enthusiasm during clinical rotations and Students design special stethoscope for use in space, noisy places
Photo by PhotosNormandie

Big data, Genetics, Stanford News, Technology, Videos

Ann Wojcicki discusses personalized medicine: “In the next 10 years everyone will have their genome”

Ann Wojcicki discusses personalized medicine: "In the next 10 years everyone will have their genome"

The 2014 Big Data in Biomedicine conference was held here last month, and keynote speakers, panelists, moderators and attendees are now available on the Stanford Medicine YouTube channel. To continue the discussion of how big data can be harnessed to benefit human health, we’ll be featuring a selection of the videos this month on Scope.

Ann Wojcicki, CEO and co-founder of personal-genetics company 23andMe, delivered a keynote speech at Big Data in Biomedicine in 2013 about empowering patients and the importance of owning one’s genetic data. Returning this year to the conference as an attendee, Wojcicki spoke in a Behind the Scenes at Big Data interview about, among other things, her early interest in genes, her belief that genetics are an important part of preventative care, and her desire for a framework where patient communities can easily participate, and potentially direct, medical research. She also discussed the status of 23andMe in the U.S. Food and Drug Administration authorization process and sounded a hopeful note about patients’ future access to their genetic information. “I believe that in the next 10 years everyone will have their genome,” she said.

Previously: When it comes to your genetic data, 23andMe’s Anne Wojcicki says: Just own it

Health Policy, Media, Public Health, Research, Technology

Lack of adoption of social media among health-policy researchers = missed opportunity

Lack of adoption of social media among health-policy researchers = missed opportunity

Despite the opportunity for connecting directly with the public and policy makers, health-policy researchers have yet to rapidly adopt social media-tools in communicating news about their work, according to a study recently published in Health Affairs.

The survey of more than 200 health and health-policy researchers (primarily MDs and PhDs) found that 14 percent of participants reported using Twitter and an estimated 21 percent used blogs or Facebook in the past year to discuss their findings. However, 65 percent of individuals utilized press releases, media interviews or other traditional media channels. Lead author David Grande, MD, MPA, said in a release that the low adoption of social media among these experts “could be a significant missed opportunity to expose a larger audience to important health news and findings.”

Grande and colleagues identified four factors preventing researchers from participating in social media: the belief that the culture of social media is frequently at odds with that of research, perceived professional risk, low confidence in ability to use social media, and uncertainties about how effective the tools are at disseminating research. Educating researchers about how to use social media and best practices could alleviate these concerns and increase adoption, said the authors. They concluded:

Public investments in research on health and health care are substantial. It is essential to maximize the returns on those investments by making research a key component of the process of developing, implementing, and refining health policies. Historically, the communication gap between researchers and policy makers has been large. Social media are a new and relatively untested tool, but they have the potential to create new communication channels between researchers and policy makers that can help narrow that gap. Determining how health researchers can best use and adapt this new technology to communicate evidence to policy makers should be a priority for universities, research funders, and scientists.

Previously: More reasons for doctors and researchers to take the social-media plunge, A reminder to young physicians that when it comes to social media, “it’s no longer about you”, How using Twitter can benefit researchers and How can physicians manage their online persona? KevinMD offers guidance
Via PsychCentral

Events, Stanford News, Technology

Stanford Medicine partners with TEDMED on “first-ever gathering on the West Coast”

Stanford Medicine partners with TEDMED on "first-ever gathering on the West Coast"

TED_MED_2010

Stanford Medicine has been named a medical research institution partner for TEDMED, an annual global event dedicated to exploring the promise of technology and potential of human achievement in health and medicine. Jay Walker, TEDMED curator and chairman, commented on the partnership in a release, saying, “Stanford and TEDMED share a passionate belief in the value of building multi-disciplinary communities as we strive for a better tomorrow in health and medicine.

School of Medicine Dean Lloyd Minor, MD, also shared his enthusiasm over joining forces with TEDMED on its “first-ever gathering on the West Coast.” He commented, “There could not be a more exciting time for Stanford Medicine and TEDMED as the world comes together to focus on the unprecedented opportunities in biomedicine today.

The three-day conference, which will be held Sept. 10-12, consists of a live, digitally-linked event held simultaneously in San Francisco and Washington, D.C. The University of California, San Francisco will also serve as a medical research institution partner.

Previously: Exploring popular health myths and how they influence health-care decisions, Stanford geneticist discusses genomics and medicine in TEDMED talk, What if obesity has nothing to do with overeating? and Re-imagining first response with an all-volunteer rescue service
Photo by Jamais Cascio

Autism, Big data, Stanford News, Technology, Videos

Using Google Glass to help individuals with autism better understand social cues

Using Google Glass to help individuals with autism better understand social cues

The 2014 Big Data in Biomedicine conference was held here last month, and keynote speakers, panelists, moderators and attendees are now available on the Stanford Medicine YouTube channel. To continue the discussion of how big data can be harnessed to benefit human health, we’ll be featuring a selection of the videos this month on Scope.

At the Big Data in Biomedicine 2014 conference, Dennis Wall, PhD, associate professor of pediatrics in systems medicine at Stanford, discussed how he and colleagues are leveraging home videos and a seven-point parent questionnaire to diagnose autism. In a pair of Behind the Scenes at Big Data videos, Wall discusses the research and its potential to speed up the standard diagnosis process, as well as another project aimed at using Google Glass to help autistic individuals better read others’ emotions. Watch the above clip to learn how the wearable technology could be used for a new type of behavioral therapy.

Previously: Rising to the challenge of harnessing big data to benefit patients and Home videos could help diagnose autism, says new Stanford study

Big data, Stanford News, Technology

What computation tells us about how our bodies work

What computation tells us about how our bodies work

Last week, as the 2014 Big Data in Biomedicine conference came to a close, a related story about the importance of computing across disciplines posted on the Stanford University homepage. The article describes research making use of the new Stanford Research Computing Center, or SRCC (which we blogged about here). We’re now running excerpts from that piece about the role computation, as well as big data, plays in medical advances.

cup of coffeeAs you sip your morning cup of coffee, the caffeine makes its way to your cells, slots into a receptor site on the cells’ surface, and triggers a series of reactions that jolt you awake. A similar process takes place when Zantac provides relief for stomach ulcers, or when chemical signals produced in the brain travel cell-to-cell through your nervous system to your heart, telling it to beat.

In each of these instances, a drug or natural chemical is activating a cell’s G-protein coupled receptor (GPCR), the cellular target of roughly half of all known drugs, says Vijay Pande, PhD, a professor of chemistry and, by courtesy, of structural biology and computer science at Stanford. This exchange is a complex one, though. In order for caffeine or any other molecule to influence a cell, it must fit snuggly into the receptor site, which consists of 4,000 atoms and transforms between an active and inactive configuration. Current imaging technologies are unable to view that transformation, so Pande has been simulating it using his Folding@Home distributed computer network.

So far, Pande’s group has demonstrated a few hundred microseconds of the receptor’s transformation. Although that’s an extraordinarily long chunk of time compared to similar techniques, Pande is looking forward to accessing the SRCC to investigate the basic biophysics of GCPR and other proteins. Greater computing power, he says, will allow his team to simulate larger molecules in greater detail, simulate folding sequences for longer periods of time, and visualize multiple molecules as they interact. It might even lead to atom-level simulations of processes at the scale of an entire cell. All of this knowledge could be applied to computationally design novel drugs and therapies.

“Having more computer power can dramatically change every aspect of what we can do in my lab,” says Pande, who is also a Stanford Bio-X affiliate. “Much like having more powerful rockets could radically change NASA, access to greater computing power will let us go way beyond where we can go routinely today.

Previously: Computing our evolution, Learning how to learn to readPersonal molecular profiling detects diseases earlier, New computing center at Stanford supports big data and Nobel winner Michael Levitt’s work animates biological processes
Photo by Toshiyuki IMIA

Big data, Genetics, Stanford News, Technology

Computing our evolution

Computing our evolution

Last week, as the 2014 Big Data in Biomedicine conference came to a close, a related story about the importance of computing across disciplines posted on the Stanford University homepage. The article describes research making use of the new Stanford Research Computing Center, or SRCC (which we blogged about here). We’re now running excerpts from that piece about the role computation, as well as big data, plays in medical advances.

The human genome is essentially a gigantic data set. Deep within each person’s 6 billion data points are minute variations that tell the story of human evolution, and provide clues to how scientists can combat modern-day diseases.

To better understand the causes and consequences of these genetic variations, Jonathan Pritchard, PhD, a professor of genetics and of biology, writes computer programs that can investigate those linkages. “Genetic variation effects how cells work, both in healthy variation and in response to disease, which ultimately regulates organism-level phenotypes,” Pritchard says. “How natural selection acts on phenotypes, that’s what causes evolutionary changes.”

Consider, for example, variation in the gene that codes for lactase, an enzyme that allows mammals to digest milk. Most animals don’t express lactase after they’ve been weaned from their mother’s milk. In populations that have historically revolved around dairy farming, however, Pritchard’s algorithms have shown that there has been strong long-term selection for expressing the genes that allow people to process milk. There has been similarly strong selection on skin pigmentation in non-Africans that allow better synthesis of vitamin D in regions where people are exposed to less sunlight.

The methods used in these types of investigations have the potential to yield powerful medical insights. Studying variations in gene regulation within a population could reveal how and where particular proteins bind to DNA, or which genes are expressed in different cell types – information that could be applied to design novel therapies. These inquiries can generate hundreds of thousands of data sets, which can only be parsed with clever algorithms and machine learning.

Pritchard, who is also a Stanford Bio-X affiliate, is bracing for an even bigger explosion of data; as genome sequencing technologies become less expensive, he expects the number of individual genomes to jump by as much as a hundredfold in the next few years. “There are not a lot of problems that we’re fundamentally unable to handle with computers, but dealing with all of the data and getting results back quickly is a rate limiting step,” Pritchard says. “Having access to SRCC will make our inquiries go easier and more quickly, and we can move on faster to making the next discovery.”

Previously: Learning how to learn to readPersonal molecular profiling detects diseases earlier and New computing center at Stanford supports big data

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