Research

Rape of high-school-aged girls is shockingly common in Kenya, where a new Stanford study found that one in four girls had been raped in the previous year, usually by someone they knew, such as a boyfriend, relative or neighbor. But a six-week class of verbal and physical self-defense skills sharply reduced the rate at which girls were raped, the study also found.

The self-defense program was developed by No Means No Worldwide, a non-governmental organization that has developed sexual-assault prevention curricula for several groups in Kenya, including young girls, elderly women and boys. The NGO teamed up with adolescent medicine researchers at Stanford and Lucile Packard Children’s Hospital to test the program for high-school girls.

The research team found that in the 10-month period after receiving training, nine percent of girls were raped, down from nearly 25 percent in the year prior to training. Even more encouraging, during the follow-up period, more than half of the girls had used their self-defense skills to fend off a would-be attacker. And, instead of complying with the ingrained culture of silence about rape, those who experienced rape were much more likely to seek help following an attack than they were before receiving training.

From our press release on the study:

“We were pretty stunned that the self-defense training was so effective,” [study author and No Means No Worldwide co-founder Jake] Sinclair, [MD,] said. “From the testimonials we collected, we saw that even a small girl could disable an attacker and get away, again and again.”

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“Often, people focus on women as victims,” said Cynthia Kapphahn, MD, a clinical associate professor of pediatrics at Stanford and an adolescent medicine specialist at Packard Children’s who was also an author of the study. “This work shows that it’s also important to focus on them as empowered beings; that approach can have an important role in a woman’s ability to protect herself.”

The data from this study are impressive – in addition to reducing assaults, the program was also very cost-effective, at $1.75 per girl, compared to $86 for after-care following rape. But the numbers tell only part of the story. The other aspect, the emotional power of the girls’ new empowerment, is eloquently conveyed in the short video above, in which Kenyan girls talk about how they used their new self-defense skills to stop attacks.

Previously: More reaction to the Supreme Court’s health-care decision: Are women the big winners? and Stanford ob-gyn Paul Blumenthal discusses advancing women’s health in developing countries
Video courtesy of No Means No Worldwide

On Thursday, Stanford pediatric gastroenterologist KT Park, MD, will participate in a Twitter chat about his latest research on celiac disease. The chat will be hosted by the American Gastroenterological Association and begins at 12 noon Pacific Time. Follow the conversation and ask questions using the hashtag #CeliacChat.

Park and colleagues at Stanford published findings (subscription required) in the latest issue of Clinical Gastroenterology and Hepatology showing that screening adolescents who are either symptomatic or at high-risk for celiac disease is more cost-effective than universal screening. Researchers compared both approaches in an effort to determine if one method would prove better at preventing bone loss and non-traumatic hip and vertebral fractures in celiac patients. Park, co-lead study author, discussed the team’s findings in a American Gastroenterological Association release:

Our study showed that conducting systematic screening of patients at risk of celiac disease is more cost effective than screening all adolescents for the disease. We determined that adopting a universal screening strategy fails to increase the long-term quality of life of the population as a whole, and introduces potential harm from unnecessary endoscopic evaluations of healthy individuals.

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There is an ongoing clinical concern in the GI community that the current practice of celiac disease screening misses a considerable proportion of asymptomatic patients due to the frequency of silent or inactive disease. However, implementing universal screening to prevent bone disease and subsequent non-traumatic fractures alone in undiagnosed or untreated celiac disease patients does not appear to be a viable health policy alternative to the standard of care.

Screening only those at risk was more cost effective, by a margin of $60, in preventing bone loss and fractures among patients with undiagnosed or subclinical disease. However, researchers noted that future analysis of risk and cost of other potential consequences of undiagnosed patients, such as anemia, infertility and malignancy, could alter the cost-effectiveness of universal screening for celiac disease.

Previously: Living the gluten-free life, From frustration to foundation: Embracing a diagnosis of celiac disease and Gluten: The “new diet villain?”
Photo by Wellcome Images

The growth of hair on your head (and elsewhere on your body, for that matter) is a tightly regulated and fascinating biological activity. Researchers are particularly interested in understanding how the stem cells in the hair follicles, which are called bulge cells, know how and when to cycle in and out of dormancy. Learning more about this process, they believe, may provide the insight necessary to harness the regenerative capacity of many types of stem cells for tissue repair and renewal.

This week, Stanford dermatologist Anthony Oro, MD, PhD, and colleagues published a study (subscription required) in Genes and Development of a mouse model they developed of a human condition called Timothy syndrome. Patients with Timothy syndrome are born bald and often take months or years to develop any hair. They also suffer from cardiac abnormalities and physical malformations and usually die at a tragically young age. But they have a very interesting genetic mutation. As Oro explained to me:

Stem cells exhibit the ability to cyclically regenerate organs, but what controls the timing of activation remains a puzzle. Timothy syndrome (TS) patients carry mutations in a calcium channel called Cav1.2 that controls the timing of the heartbeat. TS patients exhibit both cardiac arrhythmia and a significant delay in the activation of the hair cycle.

Oro and his colleagues, including Stanford postdoctoral scholar and the study’s first author Gozde Yucel, PhD, were puzzled as to why bulge cells, which (they showed in their study) don’t respond to or rely on the electrical and molecular pulses that drive cardiac cells, would even have a calcium channel. They used mouse genetics and pharmacology to investigate the abnormality in hair stem cell timing in the animals with a similar mutation. They found that, in the mice, the channel functions to control the levels of stem cell regulators responsible for tissue regeneration. According to Oro:

These surprising results demonstrate a wider function for pacemaker channels in tissue stem cells, and suggest the existence of channel ligands that have therapeutic applications in regenerative medicine.

Previously New skin cancer target identified by Stanford researchers, The secret life of hair follicles, revealed by Stanford researchers and Examining the role of genetics in hair loss

For researchers still on the fence about using social media tools to engage with colleagues and the public, a recent post on Active Scientist offers a short primer on ways Twitter can prove useful in monitoring relevant content about developments in your field.

Among the guidance on using Twitter to filter science news, the piece offers tips on who to follow, topics to tweet and lists the following benefits for researchers:

• Keep track of developments in your field and in touch with distant colleagues.
• Alert the media when you are about to publish or have made significant progress toward a scientific goal.
• Develop an online presence as someone who cares about scientific progress in your field.
• Present your scientific ideas and interests to a general audience. Twitter is a great tool for public outreach.
• Join campaigns to increase government funding of science, make scientific publishing open access, or whatever your interests are.

In a Q&A published this week on Scope, Stanford physician Leah Millheiser, MD, discussed her motivation for using social media to raise awareness and foster discussion about issues relating to women’s sexual health. Millheiser recently launched her own blog and Twitter feed.

Additionally, the School of Medicine  feed (@SUMedicine) currently maintains Twitter lists of organizations affiliated with the medical center and Stanford physicians and biomedical researchers.

Previously: Social media advice from a physician-blogger, Advice for physicians when interacting with patients online, 33Charts’ Bryan Vartabedian talks about physician blogging and How can physicians manage their online persona? KevinMD offers guidance
Photo by Steve Garfield

Interesting stem cell news today. A blog post from the California Institute for Regenerative Medicine describes research published in Cell Stem Cell by researchers at Stanford and the VA Palo Alto Health Care System. The study investigates the relative difficulty reprogramming adult cells from fully developed tissues like skin into what are known as induced pluripotent stem cells, or iPS cells. The technique was first described in 2006 by Nobel Prize recipient Shinya Yamanaka, MD, PhD (now at the Gladstone Institutes in San Francisco). As the blog post describes:

And yet seven years after the initial breakthrough, reprogramming is still very inefficient: less than 99 percent of treated cells actually get reprogrammed into embryonic-like stem cells. Many researchers are trying to better understand what goes on inside cells during the reprogramming process to help increase this efficiency and ultimately help accelerate disease research.

The researchers, including CIRM grant recipient Ji-Fan Hu, MD, PhD, and Stanford endocrinologist Andrew Hoffman, MD, found that chromosomal looping is a critical step in reprogramming. And not all would-be-iPS cells do it. From CIRM’s blog post:

During the reprogramming process, scientists activate a handful of genes that act as master control switches: they produce proteins that bind to specific spots on the cell’s DNA. This DNA binding then activates a cascading set of genes that ultimately re-sets the skin cells’ properties to the stem cell-like state of iPSC. It turns out that those cascading events only happen if the string-like DNA loops around, bringing proteins bound to distant parts of the DNA together (see the simplified illustration above).

Hu and his colleagues showed that those loops were only present in the cells that did get reprogrammed. The other 99% that don’t get reprogrammed into stem cells lacked the DNA loops.

Previously: Nobel Prize-netting iPS-cell discovery was initially a tough sell (for me, anyway) and The end of iPS? Stanford scientists directly convert mouse skin cells to neural precursors

Thanks to a public outcry that included objections from bioethics experts from across the country, the federal Office for Human Research Protections (OHRP) has decided to suspend sanctions it imposed earlier this year on a study of blood oxygen levels used to treat premature infants. The OHRP’s sanctions, issued in March, sharply criticized the study’s leaders for not providing the infants’ parents with adequate information about the risks of the trial. But many bioethics experts disagreed with the OHRP’s assessment of the situation.

Last week, a group of more than 40 of the country’s top bioethicists, including two at Stanford, sent a letter to OHRP stating that the sanctions could have a chilling effect on much-needed clinical research. In a highly unusual action, Francis Collins, MD, PhD, the director of the National Institutes of Health, worked with two colleagues to write a similarly critical letter that said, in part:

This controversy has alarmed some of the parents of infants who were in the study, confused the biomedical research community, and befuddled IRBs. Several other studies seeking new insights to improve care for these vulnerable infants have been put on hold as the field tries to understand the OHRP findings.

The two letters appear online today in the New England Journal of Medicine (NEJM), and constitute a remarkably intense criticism of the OHRP, the agency within the U.S. Department of Health and Human Services responsible for overseeing the safety and well-being of human research subjects.

I’ve been following the developing story with the help of Stanford bioethicist David Magnus, PhD, who was one of the writers of the bioethicists’ letter. Last week, before the agency revised its stance, Magnus summarized what the bioethics community found objectionable about the OHRP’s sanctions: “They believe in an absolute interpretation of risk,” he said. The agency’s risk assessment was based “not [on] what kids who are actually sick would be exposed to, but what a healthy child would be exposed to.” Healthy babies born at term face much lower risks of severe eye disease, neurological damage and death than the babies in the study – but the tiny preemies in the study weren’t healthy term infants, and were not placed at additional risk, the bioethicists assert, because of their participation in the study.

The tussle has a complex back story that involves 1,300 fragile premature infants, their parents, 23 academic medical centers and an important piece of paperwork.

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The cost of genome sequencing has fallen dramatically in the last decade, ushering in a new era of personalized medicine and promising to yield more effective treatments for cancers and other serious diseases. As a result, an increasing number of people are opting to make their genetic data available for research, clinical and personal use. But as biological databases continue to grow with the influx of patients’ personal health information, meeting the challenge of interpreting this data in a way that’s useful in a clinical setting while protecting individuals’ privacy becomes imperative.

To confront this challenge, nearly 70 leading health-care, research and disease-advocacy organizations, including Stanford, have joined forces and created an international alliance dedicated to enabling secure sharing of genomic and clinical data. Members of the global non-profit announced this morning that they have each signed a letter of intent and committed to creating “an organization with responsible and transparent governance that will develop both technical and ethical standards for data sharing,” according to a release.

Stanford geneticist Carlos Bustamante, PhD, who is involved with the initiative, commented on the importance of the global alliance in accelerating biomedical research, saying:

A major goal of genomic medicine is understanding how common and rare genetic changes may contribute to health and disease. In order to assess the impact of a given change, we often need to aggregate data across many tens of thousands of genomes. A major goal of this initiative is building the data standards for securely sharing these genetic data in a way that enables patient-powered medicine while protecting privacy. Today, much of the data is in silos, be they individual universities, hospitals or research centers. We want to work together to aggregate these data in a way that enables new and powerful analyses while preserving privacy of research participants.

A strong advocate for increased representation of underserved populations in genetics studies, Bustamante added that he is “particularly keen to work on ways that engage minority communities and international partners.”

Formation of the alliance originated in January, when group of 50 colleagues from eight countries met to assess the current challenges and opportunities in genomic research and medicine and how to work together to foster medical progress. A white paper was circulated in June prompting organizations from Africa, Asia, Australia, Europe and North and South America to join the effort. Michael Stratton, director of the Britain-based Wellcome Trust Sanger Institute, explained in the release:

In recent years, many groups around the world have recognized the need for improved approaches to bring together genomic and clinical data, and some have made progress addressing this. But in coming together, and studying the challenges, we recognized that something was missing: an international body that spanned diseases and institutions, committed to furthering progress in an innovative and responsible fashion.

Looking toward the future, the alliance is now inviting others, including for-profit organizations, to join its ranks and develop a “common framework, enabling learning from data while protecting participant autonomy and privacy.”

Stanford bioethicist and law professor Hank Greely, JD, who participated in the January meeting, noted that although the initiative is just launching, it offers the best approach for sharing genomic and clinical data, while protecting privacy of participants. He said:

The global alliance holds the promise of an effective way to share genomic and clinical data that is critically important for medicine, while respecting the interests of the men and women that data describes. Both with respect to data sharing and to participant interests, the global alliance is a huge advance over our current “system,” which is, at best, a bedraggled patchwork of often inconsistent pieces. The global alliance is still being born; it will, no doubt, be a work in progress for a long time. But at least it offers the hope of real progress, in genomic medicine and in research participants’ rights.

Previously: Stanford researchers use data mining to show safety of peripheral artery disease treatment, Atul Butte discusses why big data is a big deal in biomedicine, Transforming personalized medicine into the new standard of care, Stanford geneticist talks tracking biological data points and personalized medicine and Scientists announce the completion of the ENCODE project, a massive genome encyclopedia

For Mother’s Day, my husband gifted me with an iPad mini. I can’t tell you how much I love my new little toy, but I have noticed that I am going to be bed much later – even after I’ve put away the device.

The light being emitted from smartphones and tablets has long been suspected of suppressing levels of the hormone melatonin, which helps regulate our bodies’ sleep and wake cycles. Now, researchers from the Mayo Clinic suggest you should adjust your device’s screen brightness to the lowest setting and keep it at a certain distance to avoid disrupting sleep. The results were presented this week during the SLEEP 2013 conference in Baltimore.

According to a Medical Daily article:

The researchers investigated how levels of light emitted from mobile devices at different distances from a user’s face compared to the threshold of light that suppresses the secretion of melatonin, 30 lux.

In a dark room, they used a sensitive light meter to measure the light coming from two Apple tablets and a smartphone: an iPad 1, an iPad 3 with retinal display, and an iPhone 4. The emitted light was measured at 0 inches and 14 inches from a user’s face.

The measurements showed that when the brightness was lowered to the minimal setting, the LED lights of all three devices were well below the 30 lux melatonin-suppressing threshold.

“We found that only at the highest setting was the light over a conservative threshold that might affect melatonin levels,” said Dr. Krahn. “If it’s at the mid setting or at a low setting it’s bright enough to use.”

This seems simple enough. Perhaps I’ll give it a try before going to bed tonight.

Photo by ianmunroe

Recently, I traveled on the train to the far corner of northeastern Montana to attend a family funeral. Although the event was sad, I had the privilege of a personalized tour by my elderly father of the homestead where my grandparents settled and farmed in the 1920s. The experience piqued my interest in my ancestors, several of whom came from Norway to the United States in the late 1800s, and how their experiences and the genetic background affect me and my children. In fact, much of that part of the country was settled by Scandinavians, and many of my immediate family share the fair skin and light eyes of that northern European region.

Stanford geneticist Carlos Bustamante, PhD, studies this type of gene flow across geographic regions, and its result on the genetic diversity of current populations, on a much larger scale. In research published online today in the Proceedings of the National Academy of Sciences (subscription required), he and former postdoctoral scholar Brenna Henn, PhD, describe a similar phenomenon in southern Europe, which tends to — for reasons not well understood — be more genetically diverse than northern Europe.

They’ve discovered that many southern Europeans, particularly in Spain, Portugal and other parts of Iberia, share genetic traits of northwestern Africans found in a geographic region called Maghreb. (This was somewhat surprising because previous research comparing Southern Europeans with a benchmark sub-Saharan African population had found little genetic flow between the two groups.) The findings suggest that at least some of the genetic diversity seen in southern European populations is due to gene flow from North Africa that occurred during the past few centuries.

Bustamante and Henn described their results to me in an email exchange. According to Henn:

For me, it was most surprising that we were really able to pinpoint the source of the gene flow to the Maghreb (or northwestern Africa). Populations in the Western Sahara, Morocco and the Tunisian Berbers clearly showed a strong signal of genetic ancestry with Iberian populations. It is this connection to the Maghreb and Berbers which is both consistent with historical records and highlights the heterogeneity of populations across North Africa as well.

But the researchers, who studied small genetic differences called single nucleotide polymorphisms, or SNPs, in more than 2000 individuals from 43 populations to conduct the study, also found differences among the southern Europeans themselves. According to Bustamante:

To me, the differences among Southern European populations were really interesting. Populations in southwestern Europe, such as Spain and Portugal, showed clear evidence of North African gene flow, but there was little in south-central regions such as Italy, or in the southeastern populations of Greece or Turkey. We attribute this to relatively recent gene flow in historical times (most likely during the period of Moorish inhabitation in Iberia) that differentially impacted European regions.

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Maryland high school student Jack Andraka burst into the international scientific scene last year after winning the Gordon E. Moore Award at the 2012 Intel International Science and Engineering Fair. He was awarded the top honor for developing a novel paper sensor that detects pancreatic, ovarian, and lung cancers in five minutes and costs as little as 3 cents. The rapid diagnostic test is 168 times faster, 26,000 times less expensive and more than 400 times more sensitive than the current test.

Andraka was inspired to create a better way to detect pancreatic cancer after a close family friend, who Andraka often says was like an uncle to him, was diagnosed with the disease and passed away shortly afterwards. After conducting research and learning that the current test for detecting the disease is 60 years old, and that the majority of pancreatic cancer cases are diagnosed at a late stage, he set out to invent a better method and hopefully save lives.

This fall, Andraka will deliver the opening keynote at the Stanford Medicine X conference, where he’ll talk about curiosity, open source research and the new scientist. I recently had the chance to ask him a few questions about his work.

At what point did your quest to learn more about pancreatic cancer transform into a research project to create a faster, cheaper and more accurate diagnostic test?

When my uncle was first diagnosed I really didn’t understand the gravity of the disease. I didn’t even know what a pancreas was! When he died so quickly after his initial diagnosis I was so surprised. I spent a lot of time on the Internet learning about the pancreas, pancreatitis and pancreatic cancer. I learned about how the disease was often discovered when it was advanced and how the lack of a reliable early detection screening method led to so many deaths. I thought there had to be a better way and started sketching out criteria for what an early detection method would need. At the same time, I was still reading about nanotubes, a subject that fascinated me and that I had done a project on the year before. When I sneaked a paper on nanotubes into biology class one day, the teacher was lecturing us on antibodies. I wondered what if I combined what I was reading about (single walled carbon nanotubes) with what I was supposed to be learning about (antibodies) and made a sensor to detect pancreatic cancer. Of course I had a lot of research to do to even begin making an experimental design!

You contacted more than 200 scientists involved in research on pancreatic cancer requesting space in their lab to test your experiment and only received one response. How did you overcome this challenge and find the motivation to move forward without losing hope?

I spent a lot of time preparing my proposal and I was quite excited about it. I used the Internet to find professors in my area who were working on the subject. I figured I would send some e-mails out and then sit back and wait for the acceptances to roll in! Of course these are busy and successful professionals and many didn’t even take the time to respond to a 14-year-old. Those who did either replied that they had no room, or that they were working on something a bit different or even that my idea was impossible. Many times I was dejected and discouraged and my mom would tell me that maybe in a few years when I was 16 I could try again, or that maybe I could change my research topic. Then she’d tell me that if I believed in my topic I should keep trying. So I’d head back to the Internet and look up some more names. Actually all the rejections helped me because I refined and improved my project and bolstered it with even more detailed material lists, even including catalog numbers. When [Johns Hopkins researcher Anirban Maitra, MBBS,] said “maybe’ and invited me in for a discussion, I knew this was my big chance and came prepared with binders of journal articles and a really well-prepared grant proposal. It only takes one ‘yes’ for a door to open and then it’s up to you to take advantage of the opportunity.

What was it like to be a high school student working in a lab at Johns Hopkins?

I was so focused on convincing a professor to give me an interview to work in a lab that I didn’t think ahead to imagine what it would be like being a freshman high school student working with very experienced researchers in a lab like Johns Hopkins! Again my lack of experience helped me because I was more excited than intimidated. I first realized what I had got myself into when I arrived for my initial interview. There were so many researchers asking me serious questions and they were all much older than me. I wasn’t intimidated though because I was well prepared and enjoyed the discussion. In the lab everyone was helpful. If I asked a question, they took the time to answer. It helped that I tried to be as self-sufficient and prepared as possible and to not have the need to be “babysat.”

Medicine X explores the potential of information technologies to advance the practice of medicine, improve health and empower patients to be active participants in their own care. How have you used information technologies in your own research?

I had no access to any information that wasn’t on the Internet. I was able to educate myself using Google and Wikipedia. These resources can empower not only patients, but researchers like me who do not have access to university libraries or classrooms. I was able to learn the basics and then dig deeper as questions arose. I was able to access research from many fields and then connect the dots to create my new sensor. My mentor, Dr, Maitra, mentioned a colleague who regularly brought home journals from different fields to read and think about. I did not have access to many of these journal articles due to paywall barriers, but the articles I was able to access from many different fields served the same purpose for me. I was able to download journal articles and connect the dots to create my pancreatic cancer sensor.

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