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Evolution, Global Health, In the News, Microbiology, Nutrition, Research

A key bacteria from hunter gatherers’ guts is missing in industrial societies, study shows

392924423_860dafa0a4_oTrends like the paleo diet and probiotic supplements attest to the popular idea that in industrial societies, our digestion has taken a turn for the worse. The scientific community is gathering evidence on how the overuse of antibiotics affects our microbiome, and on what might be causing the increasing incidence gastrointestinal inflammatory disorders like Crohn’s disease and colitis. Scientists are now one step closer to knowing exactly what has changed since the majority of humans were hunter-gatherers.

Yesterday, a paper published in Nature Communications found that an entire genus of bacteria has gone missing from industrialized guts. Treponema are common in all hunter-gatherer societies that have been studied, as well as in non-human primates and other mammals. Treponema have primarily been known as pathogens responsible for diseases like syphilis, but the numerous strains found in the study are non-pathenogenic and closely resemble carbohydrate-digesting bacteria in pigs, whose digestive system is notably similar to that of humans. The genus is undetectable in humans from urban-industrial societies.

The study, led by anthropologists from the University of Oklahoma and the Universidad Científica del Sur in Peru, used genomic reconstruction to compare microbes in stool samples from two groups in Peru, one of hunter-gatherers and one of traditional farmers, with samples from people in Oklahoma. Each group comprised around 25 people. This is the first comprehensive study of the full-spectrum of microbial diversity in the guts of a group of hunter-gatherers – in this case, the Amazonian Matses people.

The researchers also sought to understand how diet affects gut health: The hunter-gatherers ate game and wild tubers, the traditional farmers ate potatoes and domestic mammals, and the Oklahomans ate primarily processed, canned, and pre-packaged food, with some additional meat and cheese.

Science published a news report discussing the findings, in which co-author Christina Warinner, PhD, an anthropologist at the University of Oklahoma, is quoted as saying:

Suddenly a picture is emerging that Treponema was part of core ancestral biome. What’s really striking is it is absolutely absent, not detectable in industrialized human populations… What’s starting to come into focus is that having a diverse gut microbiome is critical to maintaining versatility and resiliency in the gut. Once you start to lose the diversity, it may be a risk factor of inflammation and other problems.

Further research is needed to answer the next question: Is there a direct link between the absence of Treponema and the digestive health and prevalence of certain diseases (like colitis and Crohn’s) in industrialized humans? If so, this could be a valuable key to increasing our digestive health. It would also indicate that imitating a paleo diet is not enough to achieve a real “paleo gut.”

Previously: Drugs for bugs: industry seeks small molecules to target, tweak, and tune-up our gut microbes, Tiny hitchhikers, big impact: studying the microbiome to learn about disease, Civilization and its dietary (dis)contents: Do modern diets starve our gut-microbial community?, Stanford team awarded NIH Human Microbiome Project grant, and Contemplating how our human microbiome influences personal health
Photo by AJC1

Global Health, In the News, Mental Health, Public Health, Research

Study links air pollution with anxiety; calls it a “leading global health concern”

Study links air pollution with anxiety;  calls it a "leading global health concern"

3280739522_c1f8001000_zI often find that natural spaces and fresh air have a calming, balancing effect, and judging by the cultural association between relaxation and the outdoors, I’m not alone. Now some new research backs up the connection. Yesterday, the British Medical Journal published an article linking air pollution with anxiety, as well as an editorial on air pollution’s health effects and another study elaborating on a previously-noted connection between pollution and stroke.

The anxiety study, conducted by researchers at Harvard and Johns Hopkins University, showed a significant connection between exposure to fine particulate pollution and symptoms of anxiety for more than 70,000 older women (mean age of 70 years) in the contiguous United States. Bigger particles appeared to have no effects, interestingly, nor did living close to a major road. The connection was present over a variety of time periods from one month to fifteen years, but was stronger in the short term. This evidence shows a clear need for studies to be done in other demographic groups, and to elaborate on the biological plausibility of the connection.

The stroke article, meanwhile, is a meta-analysis of 103 studies conducted in 28 countries and including 6.2 million events. Researchers found that both gaseous and particulate air pollution had a “marked and close temporal association” with strokes resulting in hospital admissions or death.

As stated in the editorial, particulate air pollution has already been shown to be a contributing factor in a variety of serious health conditions, including a well-supported link to cardiopulmonary diseases, but also diabetes, low birth weight, and pre-term birth. In fact, the World Health Organization estimates that one of every eight deaths is caused by air pollution. The body of research on the topic suggests that pollution may initiate systemic inflammation, thereby affecting multiple organ systems.

With such a broad range of detrimental effects, and because it affects such a significant percentage of the population, air pollution is becoming a top public health concern. As the University of British Columbia’s Michael Brauer, ScD, wrote in the editorial:

The findings of these two studies support a sharper focus on air pollution as a leading global health concern… One of the unique features of air pollution as a risk factor for disease is that exposure to air pollution is almost universal. While this is a primary reason for the large disease burden attributable to outdoor air pollution, it also follows that even modest reductions in pollution could have widespread benefits throughout populations. The two linked papers in this issue confirm the urgent need to manage air pollution globally as a cause of ill health and offer the promise that reducing pollution could be a cost effective way to reduce the large burden of disease from both stroke and poor mental health.

Photo by Billy Wilson

In the News, Medical Education, Medical Schools, Research, SMS Unplugged

Research in medical school: The need to align incentives with value

Research in medical school: The need to align incentives with value

SMS (“Stanford Medical School”) Unplugged is a forum for students to chronicle their experiences in medical school. The student-penned entries appear on Scope once a week; the entire blog series can be found in the SMS Unplugged category.

7336836234_05b7e59045_zIt is a truism of American medical education that students should do research. Stanford medical school’s website espouses a “strong commitment to student research,” because it makes us “valued members of any medical field.” A similar message can be found at almost any other institution. It’s not just medical school either. Many undergraduate programs tout their research offerings for pre-medstudents, while residencies and fellowships often encourage their trainees to pursue investigatory projects.

There are several reasons for the emphasis on research in medical training. One obvious explanation is that schools want to prepare students for a career in academic medicine, through which physicians can combine scientific discovery with clinical insight to drive medicine forward. More broadly speaking, research is a way to develop analytic and critical thinking skills. These abilities not only help students better understand disease – they teach us how to read and interpret scientific literature to keep up to date with the latest advances in the field.

I believe in the value of engaging in research, but I recently came across the work of two prominent academic physicians who question whether it accomplishes these goals. The first is Ezekiel Emanuel. While he may be best known for his work on the Affordable Care Act as a special advisor to the White House, Emanuel’s background is in academics. After completing an MD/PhD at Harvard, he stayed on as an associate professor; he’s now a vice provost and professor at the University of Pennsylvania.

In his book, Reinventing American Health Care, Emanuel discusses how to make medical education more effective, and he specifically targets the research paradigm as an inefficiency. Whether or not it is explicitly stated, many top-tier programs require their students to do research in addition to their clinical training. To Emanuel, this constitutes “exploitation of trainees for no improvement in clinical skills.” He argues that eliminating such requirements can streamline medical education and boost the physician workforce. The physician shortage is one of the most discussed problems in health care. Trimming the length and cost of training can help address it. Reducing research requirements would allow students to prioritize their clinical work or other relevant interests.

“Exploitation” is perhaps an overstatement, but Emanuel addresses a legitimate concern about whether students’ time is best spent on research. And findings from researchers like Stanford’s John Ioannidis, MD, amplify the concern.

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Cancer, Genetics, In the News, Women's Health

Angelina Jolie Pitt’s New York Times essay praised by Stanford cancer expert

Angelina Jolie Pitt's New York Times essay praised by Stanford cancer expert

4294641229_c78b406658_zYou’ve likely heard today about Angelina Jolie Pitt’s New York Times essay regarding her decision to have her ovaries and fallopian tubes removed. Women who carry mutations in the BRCA1 or BRCA2 genes have a significantly increased risk for breast and ovarian cancer; Jolie carries such a mutation, and in 2013 she shared publicly her decision to have her breasts removed to reduce her risk of cancer.

Jolie Pitt shares her decision-making process and notes that though she won’t be able to have any more children and though she still remains prone to cancer, she feels “at ease with whatever will come.” She closes her latest essay by writing, “It is not easy to make these decisions. But it is possible to take control and tackle head-on any health issue. You can seek advice, learn about the options and make choices that are right for you.”

After reading the piece I reached out to Stanford cancer geneticist Allison Kurian, MD, who told me:

Angelina Jolie made a very courageous decision to share her experience publicly.  The surgery she chose is strongly recommended for all women with BRCA1/2 mutations by age 40, since it’s the only way to prevent an ovarian cancer in these high-risk women, and early detection doesn’t work. This is a life-saving intervention for high-risk women.

Kurian is associate director of the Stanford Program in Clinical Cancer Genetics and a member of the Stanford Cancer Institute. In 2012 she published on online tool to help women with BRCA mutations understand their treatment options.

Previously: Helping inform tough cancer-related decisions, NIH Director highlights Stanford research on breast cancer surgery choices and Breast cancer patients are getting more bilateral mastectomies – but not any survival benefit
Photo by Marco Musso

Cardiovascular Medicine, In the News, Pediatrics, Surgery

Marathon surgery at Stanford gives 6-year-old boy a chance to thrive

Marathon surgery at Stanford gives 6-year-old boy a chance to thrive

image.img.320.highA rare chromosomal disorder called Williams syndrome left 6-year-old Jordan Ervin with a host of medical problems, including severe heart defects. But it also gave him a gregarious personality and an infectious smile, one that made the multiple medical appointments and hospitalizations much easier to handle, according to his mother, Seville Spearman.

“Jordan is such a champ,’’  Spearman said in a recent Inside Stanford Medicine article. “He’s always been just a really happy kid.”

And in December, he became a much healthier one thanks to the skillful work of Stanford cardiothoracic surgeon Frank Hanley, MD. More from the piece:

It was a complicated case. The stenotic arteries caused severe pulmonary hypertension. In less-severe cases, in which there is only one area of stenosis near or at the pulmonary valve, doctors can perform a fairly simple surgical catheter procedure that uses a tiny balloon to expand the artery. But Jordan had multiple narrowings: 12 in his left lung and 14 in the right lung. The balloon technique is much less effective in this scenario, and no other surgical techniques have been developed to treat these stenoses. So Jordan would need a different approach.

That approach was developed by Hanley, who receives referrals from all over the world. He’s the pioneer of a one-stage, fix-all-the-defects surgery called unifocalization.

“We’re definitely on the leading edge of this kind of surgery,’’ said Hanley, who holds the Lawrence Crowley, MD, Endowed Professorship in Child Health. “Jordan is going to have perfectly normal life expectancy.”

Ervin is back in school in Illinois, where his parents are delighted with the outcome. His mother said in the story, “Everything is back to normal, but I will never take anything for granted again.”

Previously: How better understanding Williams syndrome could advance autism research, Pediatric surgeon fixes “heart that can’t be fixed” and Patient is “living to live instead of living to survive,” thanks to heart repair surgery
Photo by Norbert von der Groeben

Health Costs, Health Policy, In the News, Patient Care, Public Health

Health-care policy expert Arnold Milstein weighs in on Medicare’s plan to prioritize “value over volume”

Health-care policy expert Arnold Milstein weighs in on Medicare's plan to prioritize "value over volume"

8266476742_4967a82707_zAmerican health-care spending is the highest in the world, yet some question whether that money really leads to improved patient outcomes. But significant reforms taking place within Medicare, the US’s biggest healthcare payer, over the next few years aim to quell these concerns and reduce costs while improving quality of care.

Health policy experts explained the context of these changes last week in a webinar hosted by Reporting on Health and supported by the NIH’s Health Care Management Foundation. The panel featured Stanford’s Arnold Milstein, MD, MPH, director of the Clinical Excellence Research Center, as well as health economist Austin Frakt, PhD, professor at Boston University School of Medicine, and Jordan Rau, a correspondent for Kaiser Health News.

Health-care’s dominant “fee for service” (FFS) model has been around “since doctors were getting paid in chickens,” said Rau in the webinar, but it has no link whatsoever to quality. Many think this model needs to be changed because it incentivizes physicians to do more (and more expensive) procedures, regardless of the effect they have on patient outcomes. “Better, less expensive care is a national imperative,” said Milstein. “The cost to society of inefficiently delivered care is creating enormous opportunity cost.”

Starting in 2011, Medicare began to tie payments to quality: Doctors get paid 2 percent more if quality goes up, and 6 percent less when it goes down, based on patient ratings and rates of readmission and infection. In 2014, quality-linked FFS accounted for around 80 percent of care, of which around 20 percent featured some more radical change. The new plan is that 50 percent of payments will be non-FFS by 2018.

Options to reform this model could include bundled fees (a flat rate per “episode” that includes all complications and follow-up care), accountable care organizations (ACOs) that take responsibility for all patient needs and costs, incentives for cross-provider cooperation, and population-based payment in which doctors receive a set fee for any patient (currently being pioneered in Maryland).

How will we know which changes to push? Milstein used a graph to indicate “positive value outliers,” institutions with high quality and low cost, whose strategies and techniques will be emulated to see if they can be effective elsewhere. He explained what researchers found makes them different:

[Positive value outliers] tended to have deeper, more personal relationship with their patients; their patients trusted that if they called these doctors on nights and weekends, someone who knew something about them would be rapidly responsive. Doctors’ vision of their responsibility to their patients extended far beyond producing a perfect office visit; it really meant being a steward for their patients’ best interests as their patients traversed emergency room doctors, hospitalists and medical specialists. And lastly, these doctors were not trying to be solo heroes – they did a wonderful job hiring and training medical assistants and taking advantage of a team… and it was associated with a substantial improvement in value. Our next step is to splice this DNA into average performing primary care practices and verify that this is indeed the right stuff.

Some other ideas for achieving the targets were mentioned, such as sending physicians to homes so patients don’t get admitted, or in the longer term, having an intensive-care unit (ICU) “airline control tower” with more perspective than those on the “frontline” of critical care, an idea Milstein said was studied across 56 American ICUs and resulted in a 25 percent mortality reduction.

Milstein said such approaches could lower baseline health-care costs by 30 percent, but moreover could slow the rate at which health-care spending outgrows the economy, which is the real measure of success. Innovators in this area, he said, will need to draw from behavioral and computer science to think about problems differently.

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Events, In the News, Medical Education, Medical Schools, Stanford News

Match Day at Stanford sizzles with successful matches & good cheer

Match Day at Stanford sizzles with successful matches & good cheer

Rowza Rumma, hugs Jennifer DeCoste-Lopez, at Match Day 2015 at Stanford School of Medicine on March 20, 2015. ( Norbert von der Groeben/Stanford School of Medicine )Across the country at the exact same time — 9 AM in California — on the third Friday in March, graduating medical students assemble for Match Day, the day they receive their assignments to residencies.

It’s a spectacle — a cross between a graduation celebration replete with champagne and balloons and a theater audition with tears and heartbreak. The Stanford students, no surprise, are top-notch, so there were more grins than groans and plenty of congratulations and good cheer for all.

The stats themselves stand out: 77 students were matched Friday and they’re heading to 14 states, with California and Massachusetts leading the list. (A map showing where everyone is headed is below.) General medicine is the most popular specialty, followed by anesthesia, neurosurgery and pediatrics. No Stanford students were matched in urology, radiology and psychiatry.

Before the event, I checked in with two graduating students, Mia Kanak and Rowza Tur Rumma. Both are accomplished health professionals with interesting backgrounds and plans to make the world a better place. Kanak is a Tokyo native who hopes to help impoverished children. Rumma wants to translate the success of the world’s best operating rooms into practices that work in the poorest nations.

As I wrote in a story:

For [Rumma], the day was both exciting and nerve-wracking. “I think it’s hard to not have the jambalaya of those issues in our minds,” she said. Clutching the red envelope and a cell phone, she was dialing repeatedly, trying to get in touch with her parents in Bangladesh to share the moment with them.

Finally, her father on the phone, Rumma slit open the envelope, a relieved grin spreading across her face. “It’s Brigham,” she said, her first choice. Brigham and Women’s Hospital offers opportunities for its surgical residents to specialize in global health, just the program Tur Rumma was hoping for. For the residency, she was interviewed by Atul Gawande, the well-known author and surgeon, and was able to discuss her work during a summer program in Bangladesh, where she worked to implement — and adapt — a checklist of steps to reduce surgical complications adopted by the World Health Organization.

Kanak also secured her first choice, a berth in the Boston Children’s Hospital‘s pediatrics program.

“I want to say how proud all of us at Stanford Medicine are of your accomplishments today,” Dean Lloyd Minor, MD, told the group after envelopes had been torn open. “And now, on behalf of everyone, a toast to your success, to the impact you’re going to have on the lives of so many people moving forward: Best wishes!”

View Stanford Residency Match Day 2015 in a full screen map

Previously: Stanford Medicine’s Match Day, in pictures, It’s Match Day: Good luck, medical students!, At Match Day 2014, Stanford med students take first steps as residents and Image of the Week: Match Day 2012
Photo of Rowza Tur Rumma by Norbert von der Groeben; map by Kris Newby

Clinical Trials, In the News, Research, Stanford News, Technology

Lights, camera, action: Stanford cardiologist discusses MyHeart Counts on ABC’s Nightline

Lights, camera, action: Stanford cardiologist discusses MyHeart Counts on ABC's Nightline

GMA shoot - 560

Apple’s new ResearchKit, and Stanford Medicine’s MyHeart Counts iPhone app, were highlighted on ABC’s Nightline on Friday. Michael McConnell, MD, professor of cardiovascular medicine and principal investigator for the MyHeart Counts study, was interviewed, telling business correspondent Rebecca Jarvis around the 4-minute mark that the app will “definitely” change the way his job works. “It gives us a whole new way to do research,” he explained. “Traditionally reaching many people to participate in research studies is quite challenging. The ability to reach people through their phone is one major advance.”

Previously: Build it (an easy way to join research studies) and the volunteers will comeMyHeart Counts app debuts with a splash and Stanford launches iPhone app to study heart health
Photo by Margarita Gallardo

In the News, Pain, Patient Care, Research

More benefit than bite: Potential therapies from “pest” animals

More benefit than bite: Potential therapies from "pest" animals

512px-Scary_scorpionA painful spider bite can make you question why such creatures exist. Yet just because “pests” like spiders, scorpions, and snakes lack the appeal that kittens and puppies possess, it doesn’t mean they aren’t important or useful.

Yesterday, an article from Medical News Today drove this message home by highlighting some of the medical benefits we derive from six of the creatures we tend to complain the most about. As writer Honor Whiteman explains in the story, scientists are exploring ways to use toxins and substances produced by so-called pest animals, such as spiders scorpions, and reptiles, to treat chronic pain, repair nerves, and develop new ways to kill the human immunodeficiency virus.

From the piece:

In 2013, MNT [Medical News Today] reported on a study published in Antiviral Therapy, in which researchers revealed how a toxin found in bee venom – melittin – has the potential to destroy human immunodeficiency virus (HIV).

The investigators, from the Washington University School of Medicine, explained that melittin is able to make holes in the protective, double-layered membrane that surrounds the HIV virus. Delivering high levels of the toxin to the virus via nanoparticles could be an effective way to kill it.

A more recent study published in September 2014 claims bees may also be useful for creating a new class of antibiotics. Researchers from the Lund University in Sweden discovered lactic acid bacteria in fresh honey found in the stomachs of bees that has antimicrobial properties.

The story cites several other potential uses for venoms and animal-derived substances, such as my favorite example, Gila monster spit:

In 2007, a study by researchers from the University of North Carolina at Chapel Hill School of Medicine revealed how exenatide – a synthetic form of a compound found in the saliva of the Gila monster, called exendin-4 – may help people with diabetes control their condition and lose weight.

The compound works by causing the pancreas to produce more insulin when blood sugar is too high. In the study, 46% of patients who were given exenatide in combination with diabetes drug metformin had good control of their blood sugar, compared with only 13% of control participants.

As Whiteman explains in the article, many of these potential medical treatments are still in the early stages of development. Yet some therapies, such as the synthetic version of the compound found in Gila monster saliva, exenatide, are already in use, offering hope that other animal-derived medical treatments may be available in the future.

Previously: Tiny fruit flies as powerful diabetes modelFruit flies headed to the International Space Station to study the effects of weightlessness on the heartBiomedical Indiana Jones travels the world collecting venom for medical research and Tarantula venom peptide shows promise as a drug
Photo by H Dragon

Ethics, Genetics, History, In the News, Medicine and Society, Microbiology, Stanford News

Stanford faculty lend voices to call for “genome editing” guidelines

Stanford faculty lend voices to call for "genome editing" guidelines

baby feetStanford law professor Hank Greely, JD, and biochemist Paul Berg, PhD, are two of 20 scientists who have signed a letter in today’s issue of Science Express discussing the need to develop guidelines to regulate genome editing tools like the recently discovered Crispr/Cas9. Researchers are particularly concerned that the technology could be used to alter human embryos. From the commentary:

The simplicity of the CRISPR-Cas9 system enables any researcher with knowledge of molecular biology to modify genomes, making feasible many experiments that were previously difficult or impossible to conduct. […]

We recommend taking immediate steps toward ensuring that the application of genome engineering technology is performed safely and ethically.

We’ve written a bit here before about the Crispr system, which essentially lets researchers swap one section of DNA for another with high specificity. The potential uses, for both research or therapy, are touted as nearly endless. But, as Greely pointed out in an email to me: “Making babies using genomic engineering right now would be reckless – it would be unknowably risky to the lives of those babies, none of whom consented to the procedure. For me, those safety issues are paramount in human germ line modification, but there are also other issues that have sparked social concern. It would be prudent for science to slow down while society as a whole discusses all the issues – safety and beyond.”

The list of others who signed the commentary reads like a veritable who’s who of biology and bioethics. It includes Caltech’s David Baltimore, PhD; U.C. Berkeley’s Michael Botchan, PhD; Harvard’s George Church, PhD; and George Q. Daley, MD, PhD; University of Wisconsin bioethicist R. Alta Charo, JD; and Crispr/Cas9 developer Jennifer Doudna, PhD. (Another group of scientists published a similar letter in Nature last Friday.)

The call to action echos one in the 1970s in response to the discovery of the DNA snipping ability of restriction endonucleases, which launched the era of DNA cloning. Berg, who shared the 1980 Nobel Prize in Chemistry for this discovery, organized a historic meeting at Asilomar in 1975 known as the International Congress on Recombinant DNA Molecules to discuss concerns and establish guidelines for the use of the powerful enzymes.

Berg was prescient in an article in Nature in 2008 discussing the Asilomar meeting:

That said, there is a lesson in Asilomar for all of science: the best way to respond to concerns created by emerging knowledge or early-stage technologies is for scientists from publicly-funded institutions to find common cause with the wider public about the best way to regulate — as early as possible. Once scientists from corporations begin to dominate the research enterprise, it will simply be too late.

Previously: Policing the editor: Stanford scientists devise way to monitor CRISPR effectiveness and The challenge – and opportunity – of regulating new ideas in science and technology
Photo by gabi manashe

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