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Big data, NIH, Research, Videos

Fly through the inside of a mouse lung

Fly through the inside of a mouse lung

Take a 50-second ride through the inside of an adult mouse lung in this video created by Rex Moats, PhD, scientific director at Children’s Hospital Los Angeles. A post published today on the NIH Director’s Blog describes the animation and points out that the video is a prime example of how scientists are using big data to make biomedical research more accessible to the public:

We begin at the top in the main pipeline, called the bronchus, just below the trachea and wind through a system of increasingly narrow tubes. As you zoom through the airways, take note of the cilia (seen as goldish streaks); these tiny, hair-like structures move dust, germs, and mucus from smaller air passages to larger ones. Our quick trip concludes with a look into the alveoli — the air sacs where oxygen is delivered to red blood cells and carbon dioxide is removed and exhaled.

… [Moats] created this virtual bronchoscopy from micro-computed tomography scans, which use X-rays to create a 3D image. The work demonstrates the power of converting Big Data (in this case, several billion data points) into an animation that makes the complex anatomy of a mammalian lung accessible to everyone.

Speaking of the power of big data, the Big Data in Biomedicine conference returns to Stanford May 20-22. For more information about the program or to register visit the conference website.

Previously: Big data = big finds: Clinical trial for deadly lung cancer launched by Stanford study and Peering deeply – and quite literally – into the intact brain: A video fly-through

Biomed Bites, Mental Health, Neuroscience, Research, Videos

A visual deluge may provide clues to ADHD treatment

A visual deluge may provide clues to ADHD treatment

It’s time for Biomed Bites, a weekly feature that introduces readers to some of Stanford’s most innovative researchers.

Looking out my window, I see a man dressed in red sweats on a bike. There’s my neighbor’s white truck parked in the street. A tree just starting to bud. A fire hydrant. A woman fertilizing roses. Closer, there’s my grey-and-white cat, Grizzly, bathing in the sun. My glass of ice water. My phone. Scattered papers.

And that’s probably only one-thousandth of the things I see right now. (I didn’t even mention the computer.) How do I make sense of that visual onslaught? How do I navigate, perceive threats, respond to changing conditions?

Well, that’s part of the puzzle Stanford neurobiologist Tirin Moore, PhD, is working to figure out.

“I’m a systems-level neurobiologist, which means I study how networks of neurons combine to either process sensory information or to control complex behaviors,” Moore explains in the video above.

How do we filter out what’s important – seeing the dog darting across the street in front of our car, but not focusing on the bird in the tree?

This process is most obvious when it breaks down, such as in patients with Attention Deficit Hyperactivity Disorder, or other attention disorders that affect from 3 to 8 percent of the population, Moore said:

At present, disorders such as ADHD are treatable, but their underlying neural basis is still very much a mystery… Our hope is that by understanding disorders of attention at the level of the neurocircuitry we will be able to arrive at more effective treatments…

Stay tuned to see what he, and his team, figures out.

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

Aging, Neuroscience, Stanford News, Stroke, Videos

Bio-X undergraduate student finds direction through research

Bio-X undergraduate student finds direction through research

Richie Sapp arrived to Stanford as an undergraduate already interested in studying neuroscience. After talking with several faculty members, he ended up working in the lab of Carla Shatz, PhD, director of Stanford Bio-X.

I interviewed Sapp recently for a series of stories I was working on about undergraduate research opportunities at Stanford. He had participated in a terrific summer program run by Bio-X. I was struck by a few things when we talked, one of which was Sapp’s sincere interest in helping people. He had grown up with a twin brother who had been born with hydrocephaly and as a result had learning delays and is on the autism spectrum. That experience shaped his interest in helping people with similar challenges.

Sapp said that through his experience in the lab he got more out of his undergraduate classes and learned a lot about where he wants to go with his life. He loves the research and discovery, but also wants to go the medical school before pursuing research. Without the experience provided by the Bio-X summer program he might not have known which direction to go.

“The experience of designing experiments and seeing a project through to the end is going to be important for me in whatever I do next,” he said.

Here is the full profile about Sapp, with more about his research experiences.

Previously: Drug helps old brains learn new tricks, and heal

Behavioral Science, Complementary Medicine, Neuroscience, Videos

This is your brain on meditation

This is your brain on meditation

For years, friends have been telling me I should try meditation. I’m embarrassed to admit it’s mostly because of (how can I put this delicately?) a temper that flares when I’m anxious or stressed out. But, as it is for many people, it’s one of those things I haven’t gotten around to. This video by AsapSCIENCE, though, describing the things scientists have discovered about meditators has me thinking about it again.

Meditation is linked to a decreased anxiety and depression, and increased pain tolerance. Your brain tunes out the outer world during meditation, and on brain scans of meditators, scientists can see increased activity in default mode network – which is associated with better memory, goal setting, and self-awareness. The part of the brain that controls empathy has also been shown to be more pronounced in monks who are long-time meditators. From the video:

“[Meditation] also literally changes your brain waves, and we can measure these frequencies. Medidators have higher levels of alpha waves, which have been shown to reduce feelings of negative mood, tension, sadness and anger.”

Much like hitting the gym can grow your muscles and increase your overall health, it seems that meditation may be a way of working out your brain—with extra health benefits.”

Other demonstrated benefits include better heart rate variability and immune system function. I’m glossing over a lot of the information that’s packed into this entertaining little video, but if you’re curious, check out this less-than-three-minute video yourself.

Previously: Study shows benefits of breathing meditation among veterans with PTSDResearch brings meditation’s health benefits into focusUsing meditation to train the brainCan exercise and meditation prevent cold and flu? and How meditation can influence gene activity
Video by AsapSCIENCE

Applied Biotechnology, Biomed Bites, Genetics, History, Research, Videos

Basic research underlies effort to thwart “greatest threat to face humanity”

Basic research underlies effort to thwart "greatest threat to face humanity"

Welcome to this week’s Biomed Bites, a weekly feature that introduces readers to Stanford’s most innovative researchers. 

Stanley Cohen, MD, isn’t a household name. But it probably should be. The Stanford geneticist was instrumental in the discovery of DNA cloning – the technology that underlies innumerable advances in biotechnology and medicine, and led to the founding of biotech giant Genentech.

It wasn’t always thought possible to snip out a gene, stitch it into a new stretch of DNA – often in a different organism – and have it produce a desired protein.

In the video above, Cohen emphasizes that striving to achieve a concrete – and profitable – goal didn’t enable the discovery of gene cloning. First, researchers had to work to understand the basic biological processes. “In order to apply knowledge, it’s necessary to get that knowledge somehow.”

These days, Cohen isn’t resting on his laurels. Instead, he’s striving to thwart what he considers perhaps the “greatest threat to humanity,” drug-resistent microbes.

“My lab is still interested in understanding microbial drug resistance and the way in which microbes exploit host genes to carry out microbial functions such as entering cells, reproducing in cells and exiting from cells,” he said. Scientists need that basic knowledge to develop strategies to thwart the process, he added.

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

Previously: The history of biotech in seven bite-sized chunks, The dawn of DNA cloning: Reflections on the 40th anniversary and Why basic research is the venture capital of the biomedical world

Mental Health, Neuroscience, Stanford News, Videos

Hope for the globby thing inside our skulls

Hope for the globby thing inside our skulls

While at the World Economic Forum annual meeting in Davos, neuroscientists Tony Wyss-Coray, PhD, and Amit Etkin, MD, PhD, had a webcast conversation with NPR correspondent Joe Palca as part of his series of conversations on brain science. During their conversation, Palca asked about the current state of treatment for mental health and neurodegenerative diseases (bad) and prospects for the future (better).

When asked the single most important thing people could do for their mental health, Etkin answered, “awareness”. He said people need to be aware of their mental health and know that help exists if they seek it out. Current treatments aren’t perfect, but they are better than no treatment at all.

They also discussed molecular tools for diagnosing degenerative diseases, and the goals of the Stanford Neurosciences Institute‘s Big Ideas in Neuroscience teams that the two co-lead to develop new diagnostics and treatments for mental health (Etkin) and neurodegenerative diseases (Wyss-Coray).

At the end, Palca summarized the wide-ranging conversation saying, “I think it’s a time of actually some hope. I feel quite positive that this globby thing that sits inside our skulls is being understood in enough detail to make some precise changes that can be helpful.”

Previously: Neurosciences get the limelight at DavosNeuroscientists dream big, come up with ideas for prosthetics, mental health, stroke and more

Applied Biotechnology, Bioengineering, Ophthalmology, Stanford News, Videos

A medical invention that brings tears to your eyes

A medical invention that brings tears to your eyes

dry-eye-implantMore than 20 million Americans suffer from dry eye, a painful condition where a personal’s lacrimal glands don’t create enough tears to lubricate the surface of the eye.

But relief is around the corner for these sufferers – a tiny implantable device that stimulates natural tear production on a long-term basis is currently in clinical trials. The device increases tear volume by delivering micro-electrical pulses to the lacrimal gland. It’s inserted into the mucus lining of the sinus cavity or under the skin beneath the eyebrow. Tear delivery rates can be adjusted manually with a wireless controller. (You can watch a video of this device producing tears, below.)

This clever invention is the brainchild of bioengineer and former Stanford Biodesign fellow Michael Ackermann, PhD, who says he spent a good part of his boyhood in Louisville, Kentucky, taking apart things like VCRs, radios and weed-whackers.

“My parents wanted me to be a doctor, but it was very clear from a young age that I was going to be an engineer,” said Ackermann.

He’s now at the helm of Oculeve, a 20-person startup dedicated to helping people with dry-eye. Ackermann’s tale of how he took one crazy idea and turned it into a product that has the potential to help millions of people is featured in the latest issue of Inside Stanford Medicine.

More than one person’s story, it’s another example of the efficacy of the Stanford Biodesign training program, whose fellows have started 36 medtech companies and filed more than 200 patents, all of which have reached 250,000-plus patients.

Previously: Crying without tears unlocks the mystery of a new genetic disease, Instagram for eyes: Stanford ophthalmologists develop low-cost device to ease image sharing and Stanford-developed eye implant could work with smartphone to improve glaucoma treatments
Photo and video by Michael Ackermann

Events, Medical Education, Medical Schools, Stanford News, Videos

What’s it like to be an internal medicine resident at Stanford?

What's it like to be an internal medicine resident at Stanford?

“I remember being in your shoes,” Ronald Witteles, MD, said to prospective residents during a recent Google+ Hangout sponsored by the Stanford Internal Medicine Residency program. “I really felt that Stanford was the best fit for me, so I crossed my fingers and came out here. It’s been everything I hoped it could be and more.”

Witteles is the resident program director, and he joined a panel of faculty, residents, and physicians to share stories and answer questions from prospective residents and the interested public about life at Stanford.

During the Hangout, department chair Robert Harrington, MD, spent time discussing Stanford’s tradition of innovation – highlighting the Biodesign program, a collaboration between the School of Medicine and the School of Engineering, and the Department of Medicine’s Clinical Excellence Research Center, which organizes research teams to discover and design new methods of health-care delivery. When asked to comment on the school’s innovative reputation, he replied: “There is a spirit of innovation across the residency, across the department, and across the university that I think is unique, and is one of our defining characteristics.”

Several programmatic changes were also addressed during the hour-long conversation. Witteles talked about a new initiative called Pathways of Distinction, or POD, which will allow residents to select one of seven individualized pathways that align with their academic and professional interests. Each POD, he explained, will provide residents with a unique opportunity for mentorship and development outside of their primary education in internal medicine.

Additional audience questions ranged from the level of autonomy afforded to residents (the answer: a significant amount, but you’re never left by yourself), to favorite things about Palo Alto, which garnered enthusiastic group consensus about the vibrant food scene and the close proximity to nature. Watch the full conversation above.

Previously: Stanford Internal Medicine Residency program to host Google+ Hangout

Applied Biotechnology, Bioengineering, Biomed Bites, Cancer, Imaging, Technology, Videos

Beam me up! Detecting disease with non-invasive technology

Beam me up! Detecting disease with non-invasive technology

Here’s this week’s Biomed Bites, a feature appearing each Thursday that introduces readers to Stanford’s most innovative biomedical researchers.

Star Trek fans rejoice! Stanford radiologist Sam Gambhir, MD, PhD, hopes that someday he’ll be able to scan patients using a handheld device — similar to the one used by Bones in the popular sci-fi series — to check their health.

“Our long-term goals are to be able to figure out what’s going on in each and every one of you cells anywhere in your body by essentially scanning you,” Gambhir said in the video above. “We’ve been working on this area for well over three decades.”

This is useful because it will help doctors diagnose diseases such as cancer months or even years before the symptoms become apparent, Gambhir said.

And these advances aren’t light-years away. “Many of the things we’re doing have already started to move into the hospital setting and are being tested in patients. Many others will come in the years to follow,” he said.

Gambhir is chair of the Department of Radiology. He also directs the Molecular Imaging Program and the Canary Center for Cancer Early Detection.

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

Previously: Stanford partnering with Google [x] and Duke to better understand the human body, Nano-hitchhikers ride stem cells into heart, let researchers watch in real time and weeks later and Developing a new molecular imaging system and technique for early disease detection

Biomed Bites, Genetics, Research, Videos

Gene regulation controls identity – and health

Gene regulation controls identity - and health

Welcome to the first Biomed Bites of 2015. We’ll be continuing this series this year — check each Thursday to meet more of Stanford’s most innovative biomedical researchers.

Push play and prepare to blow away many of your preconceptions about genetics. ‘Cause gene aren’t the thing these days. At least not for Michael Snyder, PhD. He leads Stanford’s genetics department and directs the Stanford Center for Genomics and Personalized Medicine. Here’s Snyder:

One of the things we’ve found is that our DNA has a lot more regulatory elements than people previously appreciated. In fact, there are more regulatory elements for genes than the genes themselves.

And that’s not all. What makes you you, is, in fact, your regulatory elements, not so much your genes, which really aren’t that different from those of a chimpanzee or that next-door neighbor you dislike.

Your health may also be governed by these regulatory elements, Snyder says:

This is going to be very, very powerful in a world where many people are getting their human genome sequences and trying to understand what diseases they might be at risk for or what diseases they have and what the underlying causes are.

This knowledge might lead to swifter diagnoses, or even prevent the disease from emerging at all.

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

Previously: Of mice and men: Stanford researchers compare mammals’ genomes to aid human clinical research, Personal molecular profiling detects diseases earlier and  You say “protein interactions,” I say “mosh pit”: New insights on the dynamics of gene expression

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