By Chelsea Conaboy, Globe Staff

A look at the morning's top health industry news.

Pyramid out. Plate in: Daily Dose blogger Deborah Kotz wrote about the new plate icon that has replaced the food pyramid. The design is meant to make it easier for us to decide what to put on our own plates. The Wall Street Journal posted a video here of First Lady Michelle Obama helping the US Department of Agriculture to unveil the new tool. Also check out the early coverage from the New York Times, which included this quote from Dr. Walter C. Willett, chairman of the nutrition department at the Harvard School of Public Health: “It’s going to be hard not to do better than the current pyramid, which basically conveys no useful information.”

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By Carolyn Y. Johnson, Globe Staff

Through research ranging from brute force genome sequencing to the painstaking study of thousands of zebrafish tumors, local scientists announced today new insights into blood and skin cancers that could lead to clinical trials with existing drugs.

In three papers published in the journal Nature, separate teams of researchers used different genetic approaches that highlight the strategies scientists are using to reveal the biological underpinnings of cancer.

One team, led by researchers at the Broad Institute in Cambridge and Dana-Farber Cancer Institute in Boston, reported they had sequenced the full genomes of tumors removed from 38 patients with multiple myeloma, a rare and incurable form of cancer. The research provides the deepest and most comprehensive look at a cancer yet, according to Dr. Bert Vogelstein, a professor of oncology and pathology at Johns Hopkins University, who was not involved in the research.

The study highlighted several new genes involved in the disease, for example, genes that are involved in blood clotting or the way genetic material is translated into proteins. Researchers also found that a small subset -- an estimated 4 percent of patients --

carry a mutation in a gene called BRAF. Already, treatments that target the BRAF gene have been clinically tested in melanoma patients, so the finding suggests an immediate trial that could be done in a subset of multiple myeloma patients using a drug already in late-stage development.

"There had been some speculation that maybe we've discovered all the cancer-causing genes and there's nothing left," said Dr. Todd Golub, a core faculty member at the Broad and senior author of

Dr. Todd Golub. Photo credit: Len Rubenstein.

the new research. "The ability to look broadly in this way is showing us that we haven't discovered everything."

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By Carolyn Y. Johnson, Globe Staff

Mining the complete text of 4 percent of the world's books, Harvard University and Google scientists used a powerful new research tool unveiled today to glean surprising insights into language, culture, and history.

Books already tell stories, but when their words are combined and analyzed with computational tools, they tell bigger stories. By studying billions of words that appeared in books published over the last 200 years, the researchers found that references to God have been dropping off since about 1850. People are becoming celebrities earlier in life now than in the past, but their fifteen minutes of fame are passing more quickly as their names drop out of the lexicon. References to past years are becoming less present in culture. Censorship leaves a discernible pattern that may be useful to identify propaganda or suppression of victims.

The findings, the fruits of the ambitious Google project to digitize every book in existence, were published today in the journal Science. They are a tantalizing first glimpse at what researchers think may become a transformative new tool for humanities researchers.

Google is publicly launching the new tool, Google Books Ngram Viewer, to allow scholars or the simply curious to ask questions – such as when references to “The Great War,” which peaks between 1915 and 1941 was replaced by the term “World War I.” The tool currently allows people to look up words or phrases that range from one to five words, and see their frequency over time -- the number of times a word is mentioned divided by the total number of words written that year.

"This is really the largest data release in the history of the humanities -- a fantastic wealth of data,” said Jean-Baptiste Michel, a postdoctoral researcher in the program for evolutionary dynamics at Harvard. “In our paper we present our initial investigation -- we explore this new terrain, we dig a little bit. It is a very cool feeling to have, but what people will be able to do will far exceed everything we have done.”

The study, led by Michel and senior author Erez Lieberman Aiden, who runs the multidisciplinary Laboratory-at-Large at Harvard’s engineering school, drew on a wide and unusual array of collaborators -- not only from Harvard and Google, but also from Encyclopaedia Britannica and the American Heritage Dictionary.

Michel and Lieberman Aiden had previously worked together on a 2007 study in the journal Nature that tracked the evolution of language through a much more painstaking process – hunting down obscure old books and reading them to discover the linguistic heritage of modern verbs. As they were wrapping up their study, they began to notice obscure books becoming available through Google Books, the initiative that has now scanned 15 million books, or more than 10 percent of published books, according to Jon Orwant, engineering manager of Google books, which has a large presence in Cambridge.

Michel and Lieberman Aiden, realizing that their research techniques would soon be antiquated, approached Google and began a collaboration with the goal of creating a tool that could be broadly useful to humanities researchers.

“As we’ve amassed more and more information that isn’t available elsewhere, I started to realize we’re sitting on these troves of data that are very useful,” Orwant said -- not just for web users searching for the answers to specific questions, but to the scholarly community, too.

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By Stephen Smith, Globe Staff

For decades, they harbored a secret: Why were they living with the AIDS virus, free of symptoms and the need for potent drugs, while so many others infected with the same germ turned deathly ill?

Their innate ability to keep HIV infections in check intrigued researchers, who suspected these people, known as "controllers," might carry clues to designing effective vaccines after nearly 30 years of frustration.

Now, an international team of researchers, led by specialists in Boston, has cracked these HIV-survivors' genetic code, sifting through almost 1.4 million pieces of DNA to discover five amino acids that separate the small cadre of controllers from the vast majority who must take medication or face death.

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By Carolyn Y. Johnson, Globe Staff

Eric S. Lander, founding director of the Broad Institute of MIT and Harvard, is one of three winners of the Albany Medical Center Prize in Biomedical Research, a $500,000 prize awarded this year for advances that led to mapping the human genome.

Lander heads the Broad, a Cambridge genetics research center and is co-chair of the President's Council of Advisors on Science and Technology. He shares the prize with Dr. Francis Collins, director of the National Institutes of Health, and David Botstein, director of the Lewis-Sigler Institute for Integrative Genomics at Princeton University.

James J. Barba, president and chief executive of the Albany Medical Center said the scientists were being honored as "initiators of a genuine revolution" in understanding the nature and origins of human disease.

In the 1980s, Botstein, a geneticist at the Massachusetts Institute of Technology, proposed creating a genetic map of the human being. He worked with Eric Lander, who was then on sabbatical from MIT at Harvard Business School, to craft a plan to map the human genome. Lander's laboratory later played a key role in sequencing the genome.

At the University of Michigan, Dr. Collins was developing techniques to identify disease-related genes, and in 1989 discovered the gene that causes cystic fibrosis. He later headed the National Human Genome Research Institute at the NIH.

"What's so powerful about genetics is that it is a spotlight that can illuminate the molecular mechanism of disease -- genetic mapping is an incredibly powerful way to figure out what's wrong under the hood and, from there, to begin to figure out how to fix it," Lander said in a press release.

Carolyn Y. Johnson can be reached at cjohnson@globe.com

Up to a quarter of strokes are second strokes, and people who suffer two strokes in quick succession are more likely to die or be severely disabled. It is a serious problem affecting about 5 percent of stroke patients, but because doctors don't know which of their patients are at highest risk of recurrence, they typically prescribe medications -- some with troubling side effects -- for all patients. In a study published online today in Neurology,  Boston researchers report they have developed a free, Web-based tool designed to predict which people will go on to have a second stroke within 90 days, based on information gathered when they had their first stroke.

Dr. A. Gregory Sorensen and colleagues from Massachusetts General Hospital, the Broad Institute, and the National Institute of Neurological Disorders and Stroke analyzed the medical records of almost 1,500 patients who were admitted to the hospital within 72 hours of suffering ischemic strokes, which are caused by a blockage of blood flow in the brain. After 90 days, 806 patients were reached by phone. Of those patients, 60 had suffered second strokes, and half of those happened in the first two weeks. The researchers calculated the risk of recurrence among these 806 patients to be 2.6 percent at two weeks and 6 percent at 90 days.

After reviewing clinical records and brain scans from these patients' first strokes, the researchers developed a tool that took into account a number of risk factors, including a history of many small strokes in the month before the first major stroke; multiple areas of brain tissue death that occurred at different ages; obstructed small arteries; and large-artery
atherosclerosis. People who had four or more risk factors had a risk of a second stroke that was 40 times higher than people with no risk factors. More than 96 percent of second-stroke patients had at least one risk factor.

"We've suspected some patients are much more likely to have stroke, but ... to treat all 100 percent to benefit those 5 percent sometimes has a downside," Sorensen said in an interview. "This is a group of patients who have already been seen once by a doctor. It's kind of a shame we haven't figured out how to stop strokes once they've had that first stroke."

Long-term risk factors for stroke such as smoking, diabetes, or high blood pressure were not associated with a higher risk of stroke recurrence within 90 days, confirming previous research. Sorensen compared the person who continues to have many small strokes, also called transient ischemic attacks, to a person with chest pain that may signal an impending heart attack. These are the patients who need to be followed closely and urged to take their medications, including blood thinners that may limit activities, he said.

The study's results need to be validated in a larger, multi-center trial, both the researchers and the authors of an accompanying editorial said. Dr. Tobias Kurth and Dr. Christian Stapf of the Institut National de la Sante et de la Recherche Medicale in Paris also noted that follow-up information was available for only about half of the patients and that the number of strokes was relatively small, possibly limiting the power of the prediction tool.

Despite these methodological considerations, they write, "A refined forecast may guide stroke physicians to the good weather zones, allow early identification of high-risk patients, lead to adjusted treatment  plans in the postacute period, and help improve stroke recurrence in specific patient subgroups at risk."

Massachusetts remains second in the number of grants awarded through federal stimulus funding for biomedical research, after a new batch of grants were announced today by the White House.

With 1,148 grants made through the American Recovery and Reinvestment Act of 2009 to date, the state trails only California's 1,604, in keeping with earlier grant totals tallied in this Sept. 4 Globe story.

Among the newly funded projects is a $4.5 million joint effort by scientists at Children's Hospital Boston, the Cambridge-based Broad Institute, and Harvard Medical School to sequence whole genomes of people with autism. Dr. Christopher Walsh of Children's, Michael Greenberg of Harvard, and Stacey Gabriel and Dr. David Altshuler of the Broad are the co-investigators.

Their work will build on Walsh's earlier studies of 85 Middle Eastern patients who share ancestors and recessive forms of autism. The researchers will sequence their DNA to pinpoint disease-causing genes and also study parts of their genome that don't code for proteins -- sometimes called "junk DNA" -- but might influence gene activity related to autism. Gene activity in brain cells will also be examined.

Part of the federal Grand Opportunity program to spur research activity, the grant must be spent within 18 months.

Massachusetts has made a strong showing in a $348 million federal grant program that encourages biomedical researchers to engage in high-risk projects with the potential to accelerate the translation of research discoveries into treatments.

Eleven of 42 Transformational R01 grants are flowing to scientists in the state and 12 of 55 New Innovator award winners are based here. One of 18 Pioneer Award recipients is from Massachusetts. All three programs from the National Institutes of Health are designed to spur exploration that may have been deemed too risky in past rounds.

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A research collaboration based in Boston has won a five-year, $15 million grant to study how the hepatitis C virus defies immune system efforts to defeat it.

The Cooperative Center for Translational Research in Human Immunology, which will be based at Massachusetts General Hospital, won the grant from the National Institute of Allergy and Infectious Diseases, the hospital said. Dr. Raymond Chung, director of hepatology in the MGH Gastrointestinal Unit, will co-direct the new center with Dr. Paul Klenerman of Oxford University.

The center also includes researchers from MIT, Harvard, the Broad Institute of MIT and Harvard, Dana-Farber Cancer Institute, and the Wistar Institute, in Philadelphia.

Hepatitis C is a viral, blood-borne disease that can cause a life-threatening liver infection. Some people recover from the infection, but for most people the illness is chronic. The center will explore how the immune system fails to suppress and remove the virus.

Massachusetts ranks first in the number of early-career scientists to win prestigious grants in a national program designed to encourage innovation when research dollars are scarce.

Ten researchers -- from Harvard, Massachusetts General Hospital, MIT, and University of Massachusetts Medical School -- are among 50 scientists who have won six-year appointments to the Howard Hughes Medical Institute. California ranked second, with eight winners.

The $200 million Early Career Scientist program pays the salaries of the scientists and gives them each $1.5 million to fund their research.

The program was created last year to help scientists establish their own research programs amid a tighter funding climate that was harsh for people at the start of their independent careers. Candidates must have led their own laboratories for two to six years. A total of 2,000 applicants sought the appointments, which support the scientists at their home institutions.

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