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Big data, Bioengineering, NIH, Research, Science Policy, Stanford News

$23 million in NIH grants to Stanford for two new big-data-crunching biomedical centers

$23 million in NIH grants to Stanford for two new big-data-crunching biomedical centers

More than $23 million in grants from the National Institutes of Health – courtesy of the NIH’s Big Data to Knowledge (BD2K) initiative – have launched two Stanford-housed centers of excellence bent on enhancing scientists’ capacity to compare, contrast and combine study results in order to draw more accurate conclusions, develop superior medical therapies and understand human behaviors.

Huge volumes of biomedical data – some of it from carefully controlled laboratory studies, increasing amounts of it in the form of electronic health records, and a building torrent of data from wearable sensors – languish in isolated locations and, even when researchers can get their hands on them, are about as comparable as oranges and orangutans. These gigantic banks of data, all too often, go unused or at least underused.

But maybe not for long. “The proliferation of devices monitoring human activity, including mobile phones and an ever-growing array of wearable sensors, is generating unprecedented quantities of data describing human movement, behaviors and health,” says movement-disorders expert Scott Delp, PhD, director of the new National Center for Mobility Data Integration to Insight, also known as the Mobilize Center. “With the insights gained from subjecting these massive amounts of data to  state-of-the-art analytical techniques, we hope to enhance mobility across a broad segment of the population,” Delp told me.

Directing the second grant recipient, the Center for Expanded Data and Retrieval (or CEDAR), is Stanford’s Mark Musen, MD, PhD, a world-class biomedical-computation authority. As I wrote in an online story:

[CEDAR] will address the need to standardize descriptions of diverse biomedical laboratory studies and create metadata templates for detailing the content and context of those studies. Metadata consists of descriptions of how, when and by whom a particular set of data was collected; what the study was about; how the data are formatted; and what previous or subsequent studies along similar lines have been undertaken.

The ultimate goal is to concoct a way to translate the banter of oranges and orangutans, artichokes and aardvarks now residing in a global zoo (or is it a garden?) of diverse databases into one big happy family speaking the same universal language, for the benefit of all.

Previously: NIH associate director for data science on the importance of “data to the biomedicine enterprise”, Miniature wireless device aids pain studies and Stanford bioengineers aim to better understand, treat movement disorders

Bioengineering, Biomed Bites, Neuroscience, Research, Videos

Deciphering “three pounds of goo” with Stanford neurobiologist Bill Newsome

Deciphering "three pounds of goo" with Stanford neurobiologist Bill Newsome

Thursday means it’s time for Biomed Bites, a weekly feature that highlights some of Stanford’s most compelling research and introduces readers to innovative scientists from a variety of disciplines. If you aren’t hooked on this series yet, you will be after hearing from this neuroscientist.

Stanford neurobiologist Bill Newsome, PhD, doesn’t invent new drugs, develop creative treatments or diagnose mysterious afflictions. He mostly uses moving dots to study vision. So it makes sense that even Newsome’s own mother asks the point of his research.

Newsome, who directs the Stanford Neuroscience Institute, fields the question with grace in the video above:

I  am interested in the brain as a biological organ that gives rise to intelligence. We study vision because we believe it’s going to give us certain cues how the brain actually works and understanding the mechanisms by which the brain produces behavior will help us understand all kinds of diseases of the brain… how thought and decision-making and memory and attention go wrong in diseases like schizophrenia, in diseases like depression.

It’s not about the dots. It’s about deciphering the brain, which Newsome calls “three pounds of goo” by gesturing toward his own goo-container. (It’s a well-known goo-container: Newsome also co-chairs the federal BRAIN Initiative). How does what you see influence what you do? What you think? What you don’t see?

Newsome has spent more than 40 years poking around in the brain and he knows it works much better than any of our most advanced attempts to replicate it. Think of all the applications for a machine that can not only see, but can also make decisions based on what it spots. But now, Newsome says, the best artificial intelligence vision systems are only as perceptive as a fly or an ant.

The notion is that if we can understand how real biological vision works, we can build artificial intelligence systems that can do vision much, much better than our current ones can… and we can improve our lives in many ways.

Basic bio it is, and basically very important.

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

Previously: Even old brains can stay healthy, says Stanford neurologist, Marked improvement in transplant success on the way, says Stanford immunologist and Discover the rhythms of life with a Stanford biologist

Addiction, Bioengineering, Mental Health, Neuroscience, Stanford News, Stroke

Neuroscientists dream big, come up with ideas for prosthetics, mental health, stroke and more

Neuroscientists dream big, come up with ideas for prosthetics, mental health, stroke and more

lightbulbs

So there you are, surrounded by some of the smartest neuroscientists (and associated engineers, biologists, physicists, economists and lawyers) in the world, and you ask them to dream their biggest dreams. What could they achieve if money and time were no object?

That’s the question William Newsome, PhD, asked last year when he became director of the new Stanford Neurosciences Institute. The result is what he calls the Big Ideas in Neuroscience. Today the institute announced seven Big Ideas that will become a focus for the institute, each of which includes faculty from across Stanford schools and departments.

In my story about the Big Ideas,I quote Newsome:

The Big Ideas program scales up Stanford’s excellence in interdisciplinary collaboration and has resulted in genuinely new collaborations among faculty who in many cases didn’t even know each other prior to this process. I was extremely pleased with the energy and creativity that bubbled up from faculty during the Big Ideas proposal process. Now we want to empower these new teams to do breakthrough research at important interdisciplinary boundaries that are critical to neuroscience.

The Big Ideas are all pretty cool, but I find a few to be particularly fascinating.

One that I focus on in my story is a broad collaboration intended to extend what people like psychiatrist Robert Malenka, MD, PhD, and psychologist Brian Knutson, PhD, are learning about how the brain makes choices to improve policies for addiction and economics. Keith Humphreys, PhD, a psychiatry professor who has worked in addiction policy and is a frequent contributor to this blog, is working with this group to help them translate their basic research into policy.

Another group led by bioengineer Kwabena Boahen, PhD, and ophthalmologist E.J. Chichilnisky, PhD, are working to develop smarter prosthetics that interface with the brain. I spoke with Chichilnisky today, and he said his work develop a prosthetic retina is just the beginning. He envisions a world where we as people interface much more readily with machines.

Other groups are teaming up to take on stroke, degenerative diseases, and mental health disorders.

One thing that’s fun about working at Stanford is being able to talk with really smart people. It’s even more fun to see what happens when those smart people dream big. Now, they face the hard work of turning those dreams into reality.

Previously: This is your brain on a computer chip, Dinners spark neuroscience conversation, collaboration and Brain’s gain: Stanford neuroscientist discusses two major new initiatives
Photo by Sergey Nivens/Shutterstock

Applied Biotechnology, Bioengineering, Events, Medical Education, Stanford News, Technology

Stanford physicians and engineers showcase innovative health-care solutions

Stanford physicians and engineers showcase innovative health-care solutions

scholar-poster

A “breathalyzer” that noninvasively determines if patients have unsafe levels of ammonia in their blood. The discovery of a previously approved drug that also fights the Dengue virus. A smartphone-based eye-imaging system that can be used to diagnose vision problems remotely.

These are a few of the 40-plus inventions and clinical solutions presented at the first annual Spectrum Innovation Research Symposium, held last Friday at the Stanford School of Medicine. The event demonstrated the power of bringing together teams of physicians, bioinformaticists and engineers to apply new technologies and ideas to challenging medical problems. Also showcased were budding physician-scientists supported by the Spectrum KL2 and TL1 clinical research training awards. (In the photo above, Colleen Craig, MD, an endocrinology fellow, describes a novel treatment that she’s developing for gastric-bypass patients who suffer from severely low blood sugar.)

The buzz is that it’s going to be a good year for health-care breakthroughs

Spectrum, the recipient of Stanford’s NIH Clinical and Translational Science Award, annually gives up to $50,000 to investigator teams for year-long projects in the areas of drug discovery, medical technologies, predictives/diagnostics, population health sciences and community engagement. This program also provides these teams with training and mentoring to help them move their ideas rapidly from bench to bedside and into the community.

“These modest pilot awards have been immensely successful in stimulating innovative ideas across the spectrum of translational research,” said Spectrum’s director, Harry Greenberg, MD. “They have lead to new inventions that promote individual’s health, new ways of improving the health of the populations and new efforts to assist our surrounding community on health issues.”

As this year’s grantees were rolling up their poster presentations, next year’s scholars were rolling up their sleeves to finish their 2014-15 Spectrum grant proposals, which are due in a few days.

It’s been a pivotal year in medical technology, with the launch of an unprecedented number of game-changing inventions, such as the Mini-ION, a $900 USB-powered DNA sequencer, and Apple HealthKit, a health-and-fitness dashboard and developer kit. In the coming year, these will provide Stanford scholars with amazing technology platforms from which to launch medical solutions that are better, faster and cheaper.

“We are in the middle of amazing biomedical innovation here in Silicon Valley,” said Atul Butte, MD, PhD, and faculty director of the diagnostics/predictives program. “Spectrum enables us to fund the earliest of early technologies, more risky than even the usual angel investments, but with higher potential impacts. In the end, this gets technologies to patients and families that much sooner.”

Because of this, anticipation among the grant-approval committee members at the symposium was high — the buzz is that it’s going to be a good year for health-care breakthroughs.

Previously: Spectrum awards innovation grants to 23 projects, Stanford awarded more than $45 million to spur translational research in medicine, As part of annual tradition, budding physician-scientists display their work, and New class of physician-scientists showcase research
Photo by Kris Newby

Bioengineering, Imaging, Research, Stanford News, Videos

How CLARITY offers an unprecedented 3-D view of the brain’s neural structure

How CLARITY offers an unprecedented 3-D view of the brain's neural structure

Last year, Stanford bioengineer Karl Deisseroth, MD, PhD, and colleagues in his lab announced their development of CLARITY, a process that renders tissue transparent, sparking excitement among the scientific community. As explained in the above video, released yesterday by the National Science Foundation, researchers had been unable to directly study the human brain’s circuitry because much of the organ is covered in an opaque tissue. But using CLARITY researchers can “chemically dissolve the opaque tissue in a post-mortem brain, and in place of that tissue, they insert a transparent hydrogel that keeps the brain intact and provides a window into the brain’s neural structure and circuitry.” For this reason, the technique is “hailed as an important advance in whole-brain imaging.”

Previously: Process that creates transparent brain named one of year’s top scientific discoveries, An in-depth look at the career of Stanford’s Karl Deisseroth, “a major name in science”, Peering deeply – and quite literally – into the intact brain: A video fly-through and Lightning strikes twice: Optogenetics pioneer Karl Deisseroth’s newest technique renders tissues transparent, yet structurally intact

Applied Biotechnology, Bioengineering, Cancer, Research, Stanford News

New “decoy” protein blocks cancer from spreading

New "decoy" protein blocks cancer from spreading

14299-metastasis_news

Cancer becomes most deadly when it’s on the move – jumping from the breast to the brain or the pancreas to the liver and then onward.

But now, a team of Stanford researchers led by radiation biologist Amato Giaccia, PhD, and bioengineer Jennifer Cochran, PhD, have created a protein that may be able to thwart the metastasis.

They published their results this week in Nature Chemical Biology.

“This is a very promising therapy that appears to be effective and nontoxic in preclinical experiments,” Giaccia said in a Stanford release. ”It could open up a new approach to cancer treatment.”

The researchers created a protein that mimics Axl, a protein found on the surface of cancer cells. This decoy protein intercepts incoming messages – intended for the original Axl – cueing the cancer cells to find a new home.

The decoy Axl worked wonders in mice. Mice with breast cancer given the treatment had 78 percent fewer new tumors, and mice with ovarian cancer had 90 percent fewer new tumors than mice with cancer not given the treatment.

Becky Bach is a former park ranger who now spends her time writing about science or practicing yoga. She’s a science-writing intern in the Office of Communications and Public Affairs.

Previously: Studying the drivers of metastasis to combat cancer, A computer kit could lead to a better way to design synthetic molecules, Common drug class targets breast cancer stem cells, may benefit more patients, says study
Photo by Rod Searcey

Applied Biotechnology, Bioengineering, Genetics, Research, Stanford News

A computer kit could lead to better way to design synthetic molecules

A computer kit could lead to better way to design synthetic molecules

SmolkeSlipping something small into cells to regulate gene expression has long been a goal of biomedical researchers. And there have been many efforts to do just that. Usually researchers concoct a teeny strip of microRNA, or miRNA, and hope it does the trick.

But now, researchers at Stanford’s Department of Bioengineering have developed a computer model to take the guesswork out of designing miRNA. The model determines how to assemble a molecule so it will measure the level of a certain compound in a cell and then use that information to regulate the expression of a gene.

The research is featured in the current edition of Nature Methods, and senior author Christina Smolke, PhD, describes the process in a release issued this week:

“You start with an idea of what you want to do in the cell, and then you build and iterate on a design over and over until you reach something close to what you want,” Smolke said. “As we design and build more sophisticated systems, we will want the ability to efficiently achieve precise quantitative behaviors, and being able to accurately predict relationships between the system inputs and outputs are important to achieving this goal.”

She and Smolke’s team — which includes former graduate student Ryan Bloom and former undergraduate Sally Winkler —tested the model on the well-known Wnt signaling pathway, which plays a key role in embryonic development, stem cell production and cancer. The synthesized miRNA correctly monitored the protein produced by the pathway, validating their model.

Becky Bach is a former park ranger who now spends her time writing about science or practicing yoga. She’s a science writing intern in the Office of Communications and Public Affairs. 

Previously: A non-surgical test for brain cancer?, From plant to pill: Bioengineers aim to produce opium-based medicines without using poppies, Researchers engineer biological “devices” to program cells
Photo of Smolke by L.A. Cicero

Applied Biotechnology, Bioengineering, Global Health, In the News, Stanford News

Stanford bioengineer among Popular Science magazine’s “Brilliant 10”

Stanford bioengineer among Popular Science magazine’s “Brilliant 10”

prakash-popsci

Manu Prakash, PhD, a prolific inventor of low-cost scientific tools, has been named one of Popular Science magazine’s “Brilliant 10” for 2014 – an award that recognizes the nation’s brightest young minds in science and engineering.

In the last year Prakash has introduced two novel science tools made from everyday materials.

The first was a fully functional paper microscope, which costs less than a dollar in materials, that can be used for diagnosing blood-borne diseases such as malaria, African sleeping sickness and Chagas. It can also be used by children — our future scientists — to explore and learn from the microscopic world.

The second was a $5 programmable kid’s chemistry set, inspired by hand-crank music boxes. Like a music box, users crank a wheel that feeds a strip of hole-punched paper through the mechanism. When a pin hits a hole, it activates a pump that releases a precise, time-sequenced drop of a liquid onto a surface. This low-cost device can be used to test water quality, to provide affordable medical diagnostic tests, or to design chemistry experiments in schools.

The inventions are brilliant in both their elegant simplicity and their use of emerging technologies, such as 3D printers, microfluidics, laser cutters and conductive-ink printing.

“In one part of our lab we’ve been focusing on frugal science and democratizing scientific tools to get them out to people around the world who will use them,” Prakash told Amy Adams in a recent Stanford News story. “I’d started thinking about this connection between science education and global health. The things that you make for kids to explore science are also exactly the kind of things that you need in the field because they need to be robust and they need to be highly versatile.”

Sometimes, just for the fun of it, I’ll wander over to the Prakash lab to check out the team’s new inventions. They never fail to impress.

I heartily agree with the Popular Science editors on this year’s choices for the Brilliant 10: “Remember their names: they are already changing the world as we know it.”

Previously: Manu Prakash on how growing up in India influenced his interests as a Maker and entrepreneur, Dr. Prakash goes to Washington, The pied piper of cool science tools, Music box inspires a chemistry set for kids and scientists in developing countries and Free DIY microscope kits to citizen scientists with inspiring project ideas
Illustration courtesy of Popular Science magazine

Bioengineering, Research, Stanford News, Technology

Proteins from pond scum revolutionize neuroscience

Proteins from pond scum revolutionize neuroscience

pond scum smallI wrote a story recently about a cool technique called optogenetics, developed by bioengineering professor Karl Deisseroth, MD, PhD. He won the Keio Prize in Medicine, and I thought it might be interesting to talk with some other neuroscientists at Stanford to get their take on the importance of the technology. You know something is truly groundbreaking when each and every person you interview uses the word “revolutionary” to describe it.

Optogenetics is a technique that allows scientists to use light to turn particular nerves on or off. In the process, they’re learning new things about how the brain works and about diseases and mental health conditions like Parkinson’s disease, addiction and depression.

In describing the award, the Keio Prize committee wrote:

By making optogenetics a reality and leading this new field, Dr. Deisseroth has made enormous contributions towards the fundamental understanding of brain functions in health and disease.

One of the things I found most interesting when writing the story came from a piece Deisseroth wrote several years ago in Scientific American in which he stressed the importance of basic research. Optogenetics would not have been a reality without discoveries made in the lowly algae that makes up pond scum.

“The more directed and targeted research becomes, the more likely we are to slow our progress, and the more certain it is that the distant and untraveled realms, where truly disruptive ideas can arise, will be utterly cut off from our common scientific journey,” Deisseroth wrote.

Deisseroth told me that we need to be funding basic, curiosity-driven research along with efforts to make those discoveries relevant. He said that kind of translation is part of the value of  programs like Stanford Bio-X – an interdisciplinary institute founded in 1998 – which puts diverse faculty members side by side to enable that translation from basic science to medical discovery.

Previously: They said “Yes”: The attitude that defines Stanford Bio-X, New York Times profiles Stanford’s Karl Deisseroth and his work in optogenetics, An in-depth look at the career of Stanford’s Karl Deisseroth, “a major name in science”, Lightning strikes twice: Optogenetics pioneer Karl Deisseroth’s newest technique renders tissues transparent, yet structurally intact, The “rock star” work of Stanford’s Karl Deisseroth and Nature Methods names optogenetics its “Method of the Year
Photo by Tim Elliott, Shutterstock photos

Bioengineering, Cardiovascular Medicine, Neuroscience, Research, Stanford News, Stroke

Targeted stimulation of specific brain cells boosts stroke recovery in mice

big blue brainThere are 525,949 minutes in a year. And every year, there are about 800,000 strokes in the United States – so, one stroke every 40 seconds. Aside from the infusion, within three or four hours of the stroke, of a costly biological substance called tissue plasminogen activator (whose benefit is less-than-perfectly established), no drugs have been shown to be effective in treating America’s largest single cause of neurologic disability and the world’s second-leading cause of death. (Even the workhorse post-stroke treatment, physical therapy, is far from a panacea.)

But a new study, led by Stanford neurosurgery pioneer Gary Steinberg and published in Proceedings of the National Academy of Sciences, may presage a better way to boost stroke recovery. In the study, Steinberg and his colleagues used a cutting-edge technology to directly stimulate movement-associated areas of the brains of mice that had suffered strokes.

Known as optogenetics – whose champion, Stanford psychiatrist and bioengineer Karl Deisseroth, co-authored the study – the light-driven method lets investigators pinpoint a specific set of nerve cells and stimulate only those cells. In contrast, the electrode-based brain stimulation devices now increasingly used for relieving symptoms of Parkinson’s disease, epilepsy and chronic pain also stimulate the cells’ near neighbors.

“We wanted to find out whether activating these nerve cells alone can contribute to recovery,” Steinberg told me.

As I wrote in a news release  about the study:

By several behavioral … and biochemical measures, the answer two weeks later was a strong yes. On one test of motor coordination, balance and muscular strength, the mice had to walk the length of a horizontal beam rotating on its axis, like a rotisserie spit. Stroke-impaired mice [in which the relevant brain region] was optogenetically stimulated did significantly better in how far they could walk along the beam without falling off and in the speed of their transit, compared with their unstimulated counterparts. The same treatment, applied to mice that had not suffered a stroke but whose brains had been … stimulated just as stroke-affected mice’s brains were, had no effect on either the distance they travelled along the rotating beam before falling off or how fast they walked. This suggests it was stimulation-induced repair of stroke damage, not the stimulation itself, yielding the improved motor ability.

Moreover, levels of some important natural substances called growth factors increased in a number of brain areas in  optogenetically stimulated but not unstimulated post-stroke mice. These factors are key to a number of nerve-cell repair processes. Interestingly, some of the increases occurred not only where stimulation took place but in equivalent areas on the opposite side of the brain, consistent with the idea that when we lose function on one side of the brain, the unaffected hemisphere can step in to help restore some of that lost function.

Translating these findings into human trials will mean not just brain surgery, but also gene therapy in order to introduce a critical light-sensitive protein into the targeted brain cells. Steinberg notes, though, that trials of gene therapy for other neurological disorders have already been conducted.

Previously: Brain sponge: Stroke treatment may extend time to prevent brain damage, BE FAST: Learn to recognize the signs of stroke and Light-switch seizure control? In a bright new study, researchers show how
Photo by Shutterstock.com

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