Category Archives: Research

Being sociable is good for your health

With a little help from your friends you can live longer

A circle of close friends and strong family ties can boost a person’s health more than exercise, losing weight or quitting cigarettes and alcohol, psychologists say.
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Holt-Lunstad’s team reviewed 148 studies that tracked the social interactions and health of 308,849 people over an average of 7.5 years. From these they worked out how death rates varied depending on how sociable a person was.

Being lonely and isolated was as bad for a person’s health as smoking 15 cigarettes a day or being an alcoholic. It was as harmful as not exercising and twice as bad for the health as being obese.

Open access paper: Social Relationships and Mortality Risk: A Meta-analytic Review.

Monarch Migration Research

Monarch Butterfly

Monarch butterflies – renowned for their lengthy annual migration to and from Mexico – complete an even more spectacular journey home than previously thought.

New research from the University of Guelph reveals that some North American monarchs born in the Midwest and Great Lakes fly directly east over the Appalachians and settle along the eastern seaboard. Previously, scientists believed the majority of monarchs migrated north directly from the Gulf Coast.

Unfortunately the press release doesn’t provide a link to the study – maybe it is not open science. Often organization focused on closed science don’t do well providing web links (though even open science organizations fall down on this more than they should).

“It solves the long-standing mystery of why monarchs always show up later on the east coast compared to the interior,” he said. “Importantly, it means that the viability of east coast populations is highly dependent upon productivity on the other side of the mountains.”

Monarchs travel thousands of kilometres each year from wintering sites in central Mexico back to North America’s eastern coast, a journey that requires multiple generations (in the same year) produced at various breeding regions.

Biologists had suspected that monarchs fly back from Mexico west-to-east over the Appalachians, but no evidence existed to support the theory. “Ours is the first proof of longitudinal migration,” Miller said.

For the study, the researchers collected 90 monarch samples from 17 sites between Maine and Virginia in June and July of 2009. They also collected 180 samples of milkweed (the only plant monarch larvae can eat) from 36 sites along the eastern coast between May and July of that year.

They then used hydrogen and carbon isotope measurements to determine when and where the monarchs were born. Isotope values in milkweed vary longitudinally and can be measured in monarch wings, Miller said. The researchers discovered that 88 per cent of the monarchs sampled originated in the Midwest and Great Lakes regions.

“This means that the recolonization of the east coast is by second-generation monarchs that hatched around the Great Lakes and then migrated eastward over the Appalachians,” Miller said. “We must target the Great Lakes region to conserve the east coast monarch populations.”

Full press release

Google Research Awards

Google Faculty Research Awards, support full-time faculty pursuing research. The most recent quarterly funding totals over $4 million in 75 awards across 18 different areas. The areas that received the highest level of funding for this round were systems and infrastructure, human computer interaction, multimedia and security. In this round, 26 percent of the funding was awarded to universities outside the U.S.

Some examples

Erik Brynjolfsson, Massachusetts Institute of Technology. The Future of Prediction – How Google Searches Foreshadow Housing Prices and Quantities (Economics and market algortihms): How data from search engines like Google provide a highly accurate but simple way to predict future business activities.
John Quinn, Makerere University, Uganda. Mobile Crop Surveillance in the Developing World (Multimedia search and audio/video processing): A computer vision system using camera-enabled mobile devices to monitor the spread of viral disease among staple crops.
Ronojoy Adhikari, The Institute of Mathematical Sciences, India (probably this is the person, why doesn’t google include a link to these people’s sites?). Machine Learning of Syntax in Undeciphered Scripts (Machine learning): Devise algorithms that would learn to search for evidence of semantics in datasets such as the Indus script.
Jennifer Rexford, Princeton. Rethinking Wide-Area Traffic Management (Software and hardware systems infrastructure): Drawing on mature techniques from optimization theory, design new traffic-management solutions where the hosts, routers, and management system cooperate in a more effective way.

Smart companies realize great research is done in universities that should be adlopted by companies. Many companies listen to fools that talk of academic research as not “real world.” Companies like Google do well for many reasons but one is they pay more attention to scientific research than wall street research. More companies would benefit from adopting this leadership style from Google. Google also continues to fund and support research.

Students Will Spend Year Doing Career-Changing Research Thanks to HHMI

This year, 116 medical, dental, and veterinary students from 47 schools across the country will take a break from memorizing molecular metabolism and studying drug interactions to spend a year in a lab doing hands-on research. The break from regular coursework, funded through a $4 million Howard Hughes Medical Institute (HHMI) initiative, is intended to give students an opportunity to immerse themselves in science and consider whether they want to pursue a career as a physician-scientist.

Nearly 500 medical students applied for the research year through the HHMI-National Institutes of Health (NIH) Medical Research Scholars and HHMI Medical Research Fellows programs. Both efforts seek to strengthen and expand the pool of medically-trained researchers. The funding HHMI provides is a great resource.

“We want medical, dental, and veterinary students to become immersed in the life of academic science for at least a year. And we hope they get so engaged in the process and life of scientific research that they will decide to continue it for the rest of their lives,” says Peter Bruns, HHMI’s vice president for grants and special programs. “We need more doctors who do basic research to improve human health.”

As part of its commitment to fostering the translation of basic research discoveries into improved diagnoses and treatments, HHMI has developed a range of programs to nurture the careers of researchers who bridge the gap between clinical medicine and basic science. In addition to the programs for medical students, the Institute supports medical training for Ph.D. students in the basic sciences and has made specific efforts to fund top physician-scientists as HHMI investigators.

The medical research scholars and fellows programs are open to medical, dental, and veterinary students enrolled in U.S. schools. Most have completed the second or third year of their professional program when they spend a year working in a lab either at the NIH or at an academic medical center or research university they select. During the last 25 years, more than 2,100 students have participated.

The HHMI Medical Research Fellowships program allows medical, dental, and veterinary students to pursue biomedical research at a laboratory anywhere in the United States except the NIH campus in Bethesda. Each student submits a research plan to work in a specific lab with a mentor they have identified. Since 1989, about 1,200 students have participated.

This year, 74 students from 26 medical schools and two veterinary schools were chosen as fellows from a pool of 274. While most students elect to stay at their home institution to do their research, this year 17 fellows will work in labs at a different school. Their research topics include schizophrenia, wound healing, organ development, and many other important biological questions.

The HHMI-NIH Research Scholars program was established in 1985 to encourage medical students to pursue research by allowing them to take a year off from their medical studies. The program has since been expanded to include dental and veterinary students. It has enabled about 1,000 students to work in NIH labs.

Students selected as research scholars often enter the program with only a general idea of what type of research they would like to do. As soon as they are accepted, they begin researching the more than 1,100 laboratories at NIH. They meet with a number potential mentors before finalizing which project to pursue under the guidance of their NIH advisor and HHMI’s staff. The students are sometimes called “cloister scholars” because they live in apartments or dorm-style rooms in a refurbished cloister on the NIH campus in Bethesda.

This year, 42 students from 28 medical schools and one veterinary school were chosen as research scholars. More than 200 students from 93 schools applied.

Variation in Human DNA

Variation on the order of thousands to hundreds of thousands of DNA’s smallest pieces – large swaths varying in length or location or even showing up in reverse order – appeared 4,205 times in a comparison of DNA from just four people.

Those structural differences popped into clear view through computer analysis of more than 500 linear feet of DNA molecules analyzed by the powerful genome mapping system developed over nearly two decades by David C. Schwartz, professor of chemistry and genetics at UW-Madison.

“We probably have the most comprehensive view of the human genome ever,” Schwartz says. “And the variation we’re seeing in the human genome is something we’ve known was there and important for many years, but we haven’t been able to fully study it.”

To get a better picture of those structural variations, Schwartz and his team developed the Optical Mapping System, a wholly new type of genome analysis that directly examines millions of individual DNA molecules.

“Our newer genome analysis systems, if commercialized, promise genome analysis in one hour, at under $1,000,” Schwartz says. “And we require that high speed and low cost to power the new field of personal genomics.”

Read full press release

NASA to Launch GM Co-Developed Robot to International Space Station

NASA will launch the first human-like robot to space later this year to become a permanent resident of the International Space Station. Robonaut 2, or R2, was developed jointly by NASA and General Motors under a cooperative agreement to develop a robotic assistant that can work alongside humans, whether they be astronauts in space or workers at GM manufacturing plants on Earth.

The 300-pound R2 consists of a head and a torso with two arms and two hands and will launch on space shuttle Discovery as part of the STS-133 mission planned for September. Once aboard the station, engineers will monitor how the robot operates in weightlessness. R2 joins another station robot, known as Dextre. That robot, built by the Canadian Space Agency, consists of two, long arms to perform tasks that normally require spacewalking astronauts to complete.

While Dextre is located on the station’s exterior, R2 will be confined to operations in the station’s Destiny laboratory. However, future enhancements could allow it to move more freely around the station’s interior, and it could one day be modified to operate outside the complex.

“The use of R2 on the space station is just the beginning of a quickening pace between human and robotic exploration of space,” said John Olson, director of NASA’s Exploration Systems Integration Office. “The partnership of humans and robots will be critical to opening up the solar system and will allow us to go farther and achieve more than we can probably even imagine today.”

The dexterous humanoid robot not only looks like a human, it is designed to work like one. With human-like hands and arms, R2 is able to use the same tools that station crew members use. In the future, the greatest benefit of humanoid robots in space may be as an assistant or stand-in for astronauts during spacewalks or for tasks too difficult or dangerous for humans. For now, R2 is still a prototype and lacks adequate protection needed to exist outside the space station in the extreme temperatures of space.

A Breakthrough Cure for Ebola

A breakthrough cure for Ebola By Steven Salzberg

Last week, in what may be the biggest medical breakthrough of its kind in years, a group of scientists published results in The Lancet describing a completely new type of anti-viral treatment that appears to cure Ebola. They report a 100% success rate, although admittedly the test group was very small, just 4 rhesus monkeys.

This is a breakthrough not only because it may give us a cure for an uncurable, incredibly nasty virus, but also because the same method might work for other viruses, and because we have woefully few effective antiviral treatments. We can treat bacterial infections with antibiotics, but for most viruses, we have either a vaccine or nothing. And a vaccine, wonderful as it is, doesn’t help you after you’re already infected.

The scientists, led by Thomas Geisbert at Boston University, used a relatively new genomics technique called RNA interference to defeat the virus. Here’s how it works.
First, a little background: the Ebola virus is made of RNA, just like the influenza virus. And just like influenza, Ebola has very few genes – only 8. One of its genes, called L protein, is responsible for copying the virus itself. Two others, called VP24 and VP35, interfere with the human immune response, making it difficult for our immune system to defeat the virus.

Geisbert and his colleagues (including scientists from Tekmira Pharmaceuticals and USAMRIID) designed and synthesized RNA sequences that would stick to these 3 genes like glue. How did they do that? We know the Ebola genome’s sequence – it was sequenced way back in 1993. And we know that RNA sticks to itself using the same rules that DNA uses. This knowledge allowed Geisbert and colleagues to design a total of 10 pieces of RNA (called “small interfering RNA” or siRNA) that they knew would stick to the 3 Ebola genes. They also took care to make sure that their sticky RNA would not stick to any human genes, which might be harmful. They packaged these RNAs for delivery by inserting them into nanoparticles that were only 81-85 nanometers across.
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Google Prediction API

This looks very cool.

The Prediction API enables access to Google’s machine learning algorithms to analyze your historic data and predict likely future outcomes. Upload your data to Google Storage for Developers, then use the Prediction API to make real-time decisions in your applications. The Prediction API implements supervised learning algorithms as a RESTful web service to let you leverage patterns in your data, providing more relevant information to your users. Run your predictions on Google’s infrastructure and scale effortlessly as your data grows in size and complexity.

Accessible from many platforms: Google App Engine, Apps Script (Google Spreadsheets), web & desktop apps, and command line.

The Prediction API supports CSV formatted training data, up to 100M in size. Numeric or unstructured text can be sent as input features, and discrete categories (up to a few hundred different ones) can be provided as output labels.

Uses:
Language identification
Customer sentiment analysis
Product recommendations & upsell opportunities
Diagnostics
Document and email classification
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Evidence that Refined Carbohydrates Threaten the Heart

More Evidence that Refined Carbohydrates, not Fats, Threaten the Heart

Eat less saturated fat: that has been the take-home message from the U.S. government for the past 30 years. But while Americans have dutifully reduced the percentage of daily calories from saturated fat since 1970, the obesity rate during that time has more than doubled, diabetes has tripled, and heart disease is still the country’s biggest killer. Now a spate of new research, including a meta-analysis of nearly two dozen studies, suggests a reason why: investigators may have picked the wrong culprit. Processed carbohydrates, which many Americans eat today in place of fat, may increase the risk of obesity, diabetes and heart disease more than fat does – a finding that has serious implications for new dietary guidelines expected this year.
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Right now, Post explains, the agency’s main message to Americans is to limit overall calorie intake, irrespective of the source. “We’re finding that messages to consumers need to be short and simple and to the point,” he says. Another issue facing regulatory agencies, notes Harvard’s Stampfer, is that “the sugared beverage industry is lobbying very hard and trying to cast doubt on all these studies.”

The medical studies about what food to eat to remain healthy can be confusing but some details are not really in doubt. So while the exact dangers of processed carbohydrates, fat, excess calories and high fructose corn syrup may be in question their is no doubt we, in the USA, are not as healthy as we should be. And food is a significant part of the problem. Eat food, not too much, mostly plants and get enough exercise is good advice.

A single Liter of Seawater Can Hold More Than One Billion Microorganisms

Mat of microbes the size of Greece discovered on seafloor

mighty microbes, which constitute 50 to 90 percent of the oceans’ total biomass, according to newly released data.

These tiny creatures can join together to create some of the largest masses of life on the planet, and researchers working on the decade-long Census of Marine Life project found one such seafloor mat off the Pacific coast of South America that is roughly the size of Greece.

A single liter of seawater, once thought to contain about 100,000 microbes, can actually hold more than one billion microorganisms, the census scientists reported. But these small creatures don’t just live in the water column or on the seafloor. Large communities of microscopic animals have even been discovered more than one thousand meters beneath the seafloor. Some of these deep burrowers, such as loriciferans, are only a quarter of a millimeter long.

“Far from being a lifeless desert, the deep sea rivals such highly diverse ecosystems as tropical rainforests and coral reefs,”
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Microbes help to turn atmospheric carbon dioxide into usable carbon, completing about 95 percent of all respiration in the Earth’s oceans…