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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

Imaging, Mental Health, Neuroscience, NIH, Research, Stanford News

Study: Major psychiatric disorders share common deficits in brain’s executive-function network

Study: Major psychiatric disorders share common deficits in brain's executive-function network

marble brainPsychiatric disorders, traditionally distinguished from one another based on symptoms, may in reality not be as discrete as we think.

In a huge meta-analysis just published in JAMA Psychiatry, Stanford neuroscientist and psychiatrist Amit Etkin, MD, PhD, and his colleagues pooled the results from 193 different studies. This allowed them to compare brain images from 7,381 patients diagnosed with any of six conditions – schizophrenia, bipolar disorder, major depression, addiction, obsessive-compulsive disorder, and a cluster of anxiety syndromes – to one another, as well as to brain images from 8,511 healthy patients.

Compared with healthy brains, patients in all six psychiatric categories showed a loss of gray matter in each of three separate brain structures. These three areas, along with others, tend to fire in synchrony and are known to participate in the brain’s so-called “executive-function network,” which is associated with high-level functions including planning, decision-making, task-switching, concentrating in the face of distractions, and damping counterproductive impulses.

The findings call into question a longstanding tendency to distinguish psychiatric disorders chiefly by their symptoms

(“Gray matter” refers to information-processing nerve-cell concentrations in the brain, as opposed to the “white matter” tracts that, like connecting cables, shuttle information from one part of the brain to another.)

As Etkin told me when I interviewed him for the news release we issued on this study, “these three structures can be viewed as the alarm system for the brain.” More from our release:

“They work together, signaling to other brain regions when reality deviates from expectations – that something important and unpredicted has happened, or something important has failed to happen.” That signaling guides future behavior in directions more likely to obtain desired results.

The studies of psychiatric patients that Etkin’s team employed all used a technique that yields high-resolution images of the brain’s component structures but can say nothing about how or when these structures work or interact with one another. However, that kind of imaging data was available for the healthy subjects. And, on analysis, those healthy peoples’ performance on classic tests of executive-function (such as  asking the test-taker to note the color of the word “blue,” displayed in a color other than blue, after seeing it briefly flashed on a screen) correlated strongly with the volume of gray matter in the three suspect brain areas, supporting the idea that the anatomical loss in psychiatric patients was physiologically meaningful.

The findings call into question a longstanding tendency to distinguish psychiatric disorders chiefly by their symptoms rather than their underlying brain pathology – and, by implication, suggest that disparate conditions may be amenable to some common remedy.

As National Institute of Mental Health Director Thomas Insel, MD, told me in an interview about the study, the Stanford investigators “have stepped back from the trees to look at the forest and see a pattern in that forest that wasn’t apparent when you just look at the trees.”

Previously: Hope for the globby thing inside our skulls, Brain study offers intriguing clues toward new therapies for psychiatric disorders and Study shows abnormalities in brains of anxiety-disorder patients
Photo by Philippe Put

Big data, Clinical Trials, FDA, NIH, Research, Science

Transparency in clinical trials: The importance of getting the whole picture

Transparency in clinical trials: The importance of getting the whole picture

New rules for clinical trials Scope blog 2015.02.02Last week, the Journal of the American Medical Association ran a Viewpoint article from Francis Collins, MD, PhD, director of the National Institutes of Health and Kathy Hudson, PhD, deputy director of NIH, about the U.S. Health and Human Services’s plans to beef up transparency of clinical trials of FDA-regulated drugs and devices.

As they write, the rate of results-sharing for clinical trials is fairly dismal. Some of the reasons for this go beyond researchers; for example, it’s extremely difficult to get negative results published in scientific journals. Collins and Hudson point out that another avenue exists for sharing summary results: NIH’s website. But even there, less than one-third of researchers had shared results within four years of the end of their studies. Collins and Hudson are critical of this lapse in data sharing:

Without access to complete information about a particular scientific question, including negative or inconclusive data, duplicative studies may be initiated that unnecessarily put patients at risk or expose them to interventions that are known to be ineffective for specific uses. If multiple related studies are conducted but only positive results are reported, publication bias can distort the evidence base. Incomplete knowledge can then be incorporated into clinical guidelines and patient care. However, one of the greatest harms from nondisclosure of results may be the erosion of the trust accorded to researchers by trial participants and, when public funds are used, by taxpayers.

The new rules make the expectations to report some summary details about clinical trials, including adverse events, explicit. Although NIH has always encouraged sharing of summary results, the rules haven’t always been explicit. Now that there will be detailed guidance, the penalty for not complying will be harsher:

Thus, with the implementation of clearer requirements, augmented support materials and resources, and facilitated reporting, the NIH expects that investigators and sponsoring organizations will have the necessary tools to provide accurate, complete, and timely trial results submissions. However, for grantees who are subject to the amendments act and fail to comply after sufficient notification, the law is clear that NIH and other federal funders of clinical trials must then withhold further funding for the grant and any future grant to the grantee. In addition, the timely reporting of clinical trials will be taken into consideration during review of subsequent applications for funding.

The proposed changes to the regulations are currently in the public comment period, which will end in a few weeks, on February 19. After a review of the comments (and possible revisions), a final rule will likely be issued in a few months time. Once the rule goes into effect, it will be interesting to watch how this changes the research process for new NIH and FDA-regulated studies.

Previously: Shake up research rewards to improve accuracy, says Stanford’s John IoannidisRe-analyses of clinical trial results rare, but necessary, say Stanford researchersHow important is it to publish negative results?Researchers call for “democratization” of clinical trials data and A critical look at the difficulty of publishing “negative” results
Photo by U.S. Department of Defense

Genetics, In the News, NIH, Public Health, Research

The genomics revolution and the rise of the “molecular stethoscope”

The genomics revolution and the rise of the “molecular stethoscope”

ATCGBack in 2012, Stanford bioengineer Stephan Quake, PhD, and colleagues sequenced the genome of a fetus using only a maternal blood sample for the first time. Technology Review later recognized the work as one of the “10 Breakthrough Technologies 2013.”

In a recently published opinion piece (subscription required) in the Wall Street Journal, Quake and Eric Topol, MD, a professor of genomics at the Scripps Research Institute, discuss the method and how it exemplifies the potential of the genomics revolution to provide scientists and clinicians with a new type of stethoscope that allows one to see “inside the body at the molecular level.” They write:

The prenatal molecular stethoscope is the first truly widespread clinical application to result from the human-genome project. The National Institutes of Health has an opportunity to build on this new knowledge of “alien” DNA in healthy individuals, and determine whether it may change their clinical course—the molecular-stethoscope approach. Meanwhile, whole genome sequencing of the germ-line, or native, DNA from populations is under way, with seven ongoing world-wide projects, each sequencing the native DNA from 100,000 or more individuals. It’s projected that nearly two million people will be sequenced by 2017.

Already, the scientific literature is brimming with new applications of the molecular stethoscope. Two studies in the New England Journal of Medicine in December showed that more than 10% of healthy people over age 65 carried so-called somatic mutations in their blood cells, and that these individuals had more than a tenfold increased risk of subsequently developing a blood-based cancer.

Previously: Stanford-developed eye implant could work with smartphone to improve glaucoma treatmentsA simple blood test may unearth the earliest signs of heart transplant rejection and Step away from the DNA? Circulating *RNA* in blood gives dynamic information about pregnancy, health
Photo by Stefano

Genetics, NIH, Research, Videos

DNA origami: How our genomes fold

DNA origami: How our genomes fold

Here’s an interesting factoid about our genomes: If you stretched out the DNA in a single cell, which is only a few millionths of an inch wide, it would span more than six feet. And another: DNA folding is a dynamic process that changes over time. Scientists have been trying to understand how DNA folds itself up so efficiently, and a recent post on the NIH Director’s Blog highlights new research illustrating how the human genome folds inside the cell’s nucleus, as well as how DNA folding affects gene regulation. The research team created this delightful video that demonstrates the principles involved using origami art.

Researchers have been working to determine how cells regulate gene expression for nearly as long as we’ve known about DNA. How, for example, do nerve cells know to turn off only nerve cell genes and turn off bone cell genes? DNA folding loops are part of the answer. This research team, which published their findings in a paper in Cell yesterday, found that the number of loops is much lower than expected. There are only 10,000 loops instead of the predicted millions, and they form on/off switches in DNA. As explained in the blog post:

[The] paper in Cell adds fascinating details to that map, and it confirms that DNA loops appear to play a crucial role in gene regulation. The researchers found that many stretches of DNA with the potential to fold into loops have genes located at one end and, at the other end, novel genetic switches. When a loop forms, placing a hidden switch in contact with a once-distant gene, the gene is turned on or off. In fact, the mapping work uncovered thousands of these “secret” switches within the genome—information that may provide valuable new clues for understanding cancer and many other complex, common diseases.

Previously: DNA architecture fascinates Stanford researcher – and dictates biological outcomes

Genetics, NIH, Research, Science, Stanford News, Technology

Of mice and men: Stanford researchers compare mammals' genomes to aid human clinical research

Of mice and men: Stanford researchers compare mammals' genomes to aid human clinical research

Scientists have long considered the laboratory mouse one of the best stand-ins for researching human disease because of the animals’ genetic similarity to humans. Now Stanford researchers, as part of a consortium of more than 30 institutions, have confirmed the mouse’s utility in clinical research by showing that the basic principles controlling genes are similar between the two species. However, they also found some important differences.

From our press release on the work:

“At the end of the day, a lot of the genes are identical between a mouse and a human, but we would argue how they’re regulated is quite different,” said Michael Snyder, PhD, professor and chair of genetics at Stanford. “We are interested in what makes a mouse a mouse and a human a human.”

The research effort, Mouse ENCODE, complements a project called the Encyclopedia of DNA Elements, or ENCODE, both funded by the National Human Genome Research Institute. ENCODE studied specific components in the human genome that guide genes to code for proteins that carry out a cell’s function, a process known as gene expression. Surrounding the protein-coding genes are noncoding regulatory elements, molecules that regulate gene expression by attaching proteins, called transcription factors, to specific regions of DNA.

The Mouse ENCODE consortium annotated the regulatory elements of the mouse genome to make comparisons between the two species. Because many clinical studies and drug discovery use mice as model organisms, understanding the similarities and differences in gene regulation can help researchers understand whether their mouse study applies to humans.

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Aging, NIH, Public Health, Research, Science, Stanford News

Tick tock goes the clock – is aging the biggest illness of all?

Tick tock goes the clock - is aging the biggest illness of all?

3821120232_d1452b4109_zIt’s an uncomfortable truth that aging is the single biggest risk factor for many chronic diseases. It’s also completely out of our control. (The alternative is, well, not so fun to contemplate.) But although we all think we’d like to live longer, longevity in and of itself is not necessarily a good thing. Living longer rapidly loses its appeal if you’re too sick or feeble to really enjoy your extra “golden” years.

But researchers from many scientific disciplines are now working to understand how and why our bodies tend to break down as time passes. The Trans-NIH Geroscience Interest Group (a group of researchers from numerous NIH institutes) interested in aging held a summit in 2013 to explore mechanisms of aging and identify common themes that could serve as research targets. The thought is that understanding, and slowing, aging may be an efficient way to tackle many chronic diseases simultaneously.

Now the group, which includes Stanford geneticist Anne Brunet, PhD; neurologist Tony Wyss-Coray, PhD; and Thomas Rando, MD, PhD, has released the conclusions of the summit and outlined a plan for the work that lies ahead. (Rando is the director of the Glenn Center for the Biology of Aging at Stanford.) Many of the findings focus  on a concept called “healthspan,” which designates the portion of a person’s lifespan in which he or she is relatively healthy and fully functional. From the Cell article:

While life expectancy continues to rise, healthspan is not keeping pace because current disease treatment often decreases mortality without preventing or reversing the decline in overall health.  Elders are sick longer, often coping with multiple chronic diseases simultaneously.  Thus, there is an urgent need to extend healthspan.

The researchers identified seven intertwined “pillars of aging” for targeted research, including adaptation to stress, stem cells and regeneration, metabolism, macromolecular damage, inflammation, epigenetics and a concept called proteostasis, which describes the intricate dance in which proteins are made, transported and degraded within a cell. They suggest the creation of an Aging Research Initiative that works to merge the emerging field of geroscience with research on chronic disease and to search for therapeutic interventions that could extend both lifespan and healthspan.

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Clinical Trials, Health Policy, NIH, Women's Health

A look at NIH’s new rules for gender balance in biomedical studies

A look at NIH’s new rules for gender balance in biomedical studies

In May, Francis Collins, MD, PhD, director of the National Institutes of Health, co-authored a Comment piece in Nature, outlining new requirements for biomedical researchers that made balancing the sex of animals and cell lines in studies much more important than they have been in the past. The first changes were set to be implemented this month. But, as Scientific American reported earlier this week,  the NIH isn’t likely to implement the changes as quickly as previously thought:

Funding rules, however, have yet to change, with only one week left in the month. Instead, the agency is gathering comments from researchers about which research areas need sex balance the most and the challenges scientists face in including male and female subjects in their studies. Officials have set aside $10.1 million in grants for scientists who want to add animals of the opposite sex to their existing experiments. The NIH is also making videos and online tutorials to teach scientists who are new to studying both sexes how to design such studies. Meanwhile, [Janine A. Clayton, director of the NIH’s Office of Research on Women’s Health] “can’t say” when new funding rules will take effect. “Details about the policy and implementation plans will roll out during the next year,” she says.

Scientists rely heavily on male animals, rarely using females, and the changes would require some drastic changes for researchers seeking funds from NIH. More from Scientific American:

Once in place and codified, the requirement would be a major shift for the nation’s biomedical labs, many of which study mostly or exclusively male animals. One estimate found that pharmacology studies include five times as many male animals as female ones, while neuroscience studies are skewed 5.5:1 male-to-female.

Scientists assumed biology findings that held in males would apply just as well to females, but a growing body of research has discovered this is not always true. Female and male mice’s bodies make different amounts of many proteins, for example. Men and women have differing risks for many health conditions that are not obviously sex-based, including anxiety, depression, hypertension and strokes. Yet those diseases are still predominantly studied in male animals. Scientists who study sex differences think the mismatch might be the reason women suffer more side effects than men do from drugs approved by the U.S. Food and Drug Administration. Pharmaceuticals that researchers test mainly on male animals may work better for men than for women.

When the NIH does begin to implement these changes, the first steps will be training staff and grantees on what these changes mean for experimental design. And it should be noted that this isn’t the first time that NIH has encouraged sex balance. In 2013, its Office of Research on Women’s Health started a program of supplemental grants for currently funded researchers to add enough animals for gender-balanced study results.

Previously: Why it’s critical to study the impact of gender differences on diseases and treatments, Large federal analysis: Hormone therapy shouldn’t be used for chronic-disease prevention and A call to advance research on women’s health issues
Photo by Mycroyance

NIH, Research, Science Policy, Stanford News

Shake up research rewards to improve accuracy, says Stanford's John Ioannidis

Shake up research rewards to improve accuracy, says Stanford's John Ioannidis

currencyLab animals such as mice and rats can be trained to press a particular lever or to exhibit a certain behavior to get a coveted food treat. Ironically the research scientists who carefully record the animals’ behavior really aren’t all that different. Like mice in a maze, researchers in this country are rewarded for specific achievements, such as authoring highly cited papers in big name journals or overseeing large labs pursuing multiple projects. These rewards come in the form of promotions, government grants and prestige among a researcher’s peers.

Unfortunately, the achievements do little to ensure that the resulting research findings are accurate. Stanford study-design expert John Ioannidis, MD, DSci, has repeatedly pointed out serious flaws in much published research (in 2005 he published what was to be one of the most highly-accessed and most highly-cited papers ever in the biomedical field “Why most published research findings are false”).”

Today, Ioannidis published another paper in PLoS Medicine titled “How to make more published research true.” He explores many topics that could be addressed to improve the reproducibility and accuracy of research. But the section that I found most interesting was one in which he argues for innovative, perhaps even disruptive changes to the scientific reward system. He writes:

 The current system does not reward replication—it often even penalizes people who want to rigorously replicate previous work, and it pushes investigators to claim that their work is highly novel and significant. Sharing (data, protocols, analysis codes, etc.) is not incentivized or requested, with some notable exceptions. With lack of supportive resources and with competition (‘‘competitors will steal my data, my ideas, and eventually my funding”) sharing becomes even disincentivized. Other aspects of scientific citizenship, such as high-quality peer review, are not valued.

Instead he proposes a system in which simply publishing a paper has no merit unless the study’s findings are subsequently replicated by other groups. If the results of the paper are successfully translated into clinical applications that benefit patients, additional “currency” units would be awarded. (In the example of the mice in the maze, the currency would be given in the form of yummy food pellets. For researchers, it would be the tangible and intangible benefits accrued by those considered to be successful researchers). In contrast, the publication of a paper that was subsequently refuted or retracted would result in a reduction of currency units for the authors. Peer review and contributions to the training and education of others would also be rewarded.

The concept is really intriguing, and some ideas would really turn the research enterprise in this country on its head. What if a researcher were penalized (fewer pellets for you!) for achieving an administrative position of power… UNLESS he or she also increased the flow of reliable, reproducible research? As described in the manuscript:

[In this case] obtaining grants, awards, or other powers are considered negatively unless one delivers more good-quality science in proportion. Resources and power are seen as opportunities, and researchers need to match their output to the opportunities that they have been offered—the more opportunities, the more the expected (replicated and, hopefully, even translated) output. Academic ranks have no value in this model and may even be eliminated: researchers simply have to maintain a non-negative balance of output versus opportunities. In this deliberately provocative scenario, investigators would be loath to obtain grants or become powerful (in the current sense), because this would be seen as a burden. The potential side effects might be to discourage ambitious grant applications and leadership.

Ioannidis, who co-directs with Steven Goodman, MD, MHS, PhD, the new  Meta-Research Innovation Center at Stanford, or METRICS, is quick to acknowledge that these types of changes would take time, and that the side effects of at least some of them would likely make them impractical or even harmful to the research process. But, he argues, this type of radical thinking might be just what’s needed to shake up the status quo and allow new, useful ideas to rise to the surface.

Previously: Scientists preferentially cite successful studies, new research shows, Re-analyses of clinical trial results rare, but necessary, say Stanford researchers  and John Ioannidis discusses the popularity of his paper examining the reliability of scientific research
Photo by Images Money

History, Medicine and Society, NIH, Public Health

"Don't go to bed with a malaria mosquito:" exploring World War II medical posters

"Don't go to bed with a malaria mosquito:" exploring World War II medical posters

After exploring Stanford’s collection of historical medical images last week after a tour of the School of Medicine, I got hooked. Hooked on historical medical images — a quirky interest tailor-made for the internet. Turns out the National Institutes of Health’s U.S. National Library of Medicine maintains a massive image library, one that includes some fabulous propaganda posters from World War II, including the lady mosquito with the alluring proboscis (above).

Others in the World War II poster collection focus on venereal diseases, recruiting nurses and doctors, encouraging blood donations and even curbing noise or visiting the dentist.

And that’s just World War II posters. Its Flickr collection is tantalizing, kicking off with a series of medical oddities reminiscent of Philadelphia’s Mütter Museum. It’s quite addictive – just warning you.

Previously: A trip down memory lane: Stories from the early days of the School of Medicine, #ACT4NIH seeks stories to spur research investment and Examining the impact of psychological distress on soldiers’ spinal injuries
Images courtesy of U.S National Library of Medicine

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