Category Archives: Research

Ants, Ants, Ants

Ants really are amazing. The internet makes it easy to learn about these creatures. My Dad found them fascinating and I picked up that view. I had a flying one, flying around my house yesterday.

“Ants: The Invisible Majority” including Dr. Brian Fisher, chairman of the Department of Entomology at the Cal Academy of Sciences looking for ants in San Francisco. He created AntWeb, an online resource. The video discusses the Argentine Ant super colonies.

Are you ready for a world without antibiotics?

[Professor Tim Walsh] “This is potentially the end. There are no antibiotics in the pipeline that have activity against NDM 1-producing enterobacteriaceae. We have a bleak window of maybe 10 years, where we are going to have to use the antibiotics we have very wisely, but also grapple with the reality that we have nothing to treat these infections with.”

And this is the optimistic view – based on the assumption that drug companies can and will get moving on discovering new antibiotics to throw at the bacterial enemy. Since the 1990s, when pharma found itself twisting and turning down blind alleys, it has not shown a great deal of enthusiasm for difficult antibiotic research. And besides, because, unlike with heart medicines, people take the drugs for a week rather than life, and because resistance means the drugs become useless after a while, there is just not much money in it.
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“The emergence of antibiotic resistance is the most eloquent example of Darwin’s principle of evolution that there ever was,” says Livermore. “It is a war of attrition. It is naive to think we can win.”

I have been writing about the huge risks we are talking with our future for years. The careless misuse of antibiotics is very costly (in human lives, in the future). Bacteria pose great risks to us. We need to take antibiotics to fight serious threats. The misuse of antibiotics by doctors, patients, agri-business… is the problem. And we are all living a much riskier future because far to little is being done to reduce the misuse of antibiotics.

More and more antibiotic treatments are losing effectiveness as bacteria evolve resistance. The evolution is accelerated by misuse. This costs lives today, but is likely to costs many thousands and hundreds of thousands and possible more in the next 50 years.

The NDM-1-producing bacteria were highly resistant to all antibiotics except tigecycline and colistin. In some cases, isolates were resistant to all antibiotics. The emergence of NDM-1 positive bacteria is potentially a serious global public health problem as there are few new anti-Gram-negative antibiotics in development and none that are effective against NDM-1.

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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