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  • June 5, 2013
  • 08:30 PM

Machine learning and prediction without understanding

by Artem Kaznatcheev in Evolutionary Games Group

Big data is the buzzword du jour, permuting from machine learning to hadoop powered distributed computing, from giant scientific projects to individual social science studies, and from careful statistics to the witchcraft of web-analytics. As we are overcome by petabytes of data and as more of it becomes public, it is tempting for a would-be […]... Read more »

Chattopadhyay, Ishanu, Wen, Yicheng, & Ray, Asok. (2010) Pattern Classification In Symbolic Streams via Semantic Annihilation of Information. American Control Conference. arXiv: 1008.3667v1

  • June 5, 2013
  • 01:06 PM

Using Existing Data to Assess Tidal Power Potential

by dailyfusion in The Daily Fusion

In a new thesis on marine current power at Uppsala University, Emilia Lalander shows that currently available water data are valuable for estimating the movement speed of water and thereby the potential energy resource available in a particular area.... Read more »

  • June 5, 2013
  • 10:25 AM

Better IQ Testing for Animals: There's an App for That

by Elizabeth Preston in Inkfish

It's 2013, and laboratory pigeons are demanding an upgrade. Well, maybe they aren't demanding so much as continuing to do whatever tasks get them their pigeon pellets. Nevertheless, switching from analog to digital testing could mean more rigorous studies, better statistics, and a chance for previously ignored animals to try their paws at cognition research.

One of the classic cognitive tests that psychologists like to give animals involves two or more strings. At the far end of one string, there's a treat. The animal has to figure out that tugging on the near end of this string will gradually bring the reward close enough to eat.

How classic is the string test? In a recent Animal Cognition paper, Edward Wasserman of the University of Iowa and his coauthors list 74 different papers involving this experiment. Animals subjected to string-pulling tasks have includes apes, monkeys, birds, cats, rats, and Asian elephants. The experiments have been limited, though, to animals that can grasp and pull on a string or rope. Another constraint is the time it takes an experimenter to physically set up the strings and refill the food dishes over and over again.

Wasserman and his colleagues used a pigeon focus group to try out a new kind of string test with no string at all. The whole thing took place on a touchscreen, which you can see above. When pigeons pecked at the square on the near end of a "string," the "dish" on the other end moved a little closer. One dish was an empty black box; the other was a photo of pigeon feed. When a pigeon reeled the food dish all the way in, a tasty (non-virtual) pellet dropped out of a dispenser.

The four pigeons in the study quickly got the gist of things, learning to peck the end of the string attached to the food. They started off with simple tasks, in which the strings were short and didn't cross over each other. Then the strings got longer, appeared at various angles, and eventually crossed. These tasks were increasingly challenging to the pigeons. But even for the hardest tasks, the first string they pecked was usually the correct one.

Unlike in a real string test, there was no pulling—no physical weight of food to focus on dragging closer. Still, Wasserman thinks the touchscreen experiment is an accurate substitute for the real thing. In videos like this one, you can see the pigeons bobbing their heads along the strings as they work, seeming to understand the logic of the puzzle. The authors compare the experiment to a game of Angry Birds, which also simulates real physics (albeit with slingshotted cartoon animals).

Also unlike a real string test, the researchers were able to instantly change the length or placement of the strings. They put their pigeons through tens of thousands of trials without much trouble. All of this means better statistical analyses and more reliable results are possible. Using a touchscreen "allows us to conduct experiments with much greater rigor than would otherwise be the case," Wasserman says.

The new method could also let researchers try this kind of testing on any animal that can work a touchscreen, Wasserman says—"even those without dextrous appendages." For example, fish. He also suggests mammals such as dogs, horses, or cows, as well as birds that can't use their claws like hands. One aquarium has already demonstrated that its penguins can play an iPad game. From the aquarium's video, though, it's unclear whether the penguin is truly enjoying the app for cats, or if trying to nab an onscreen mouse is turning it into an Angry Bird.

Wasserman, E., Nagasaka, Y., Castro, L., & Brzykcy, S. (2013). Pigeons learn virtual patterned-string problems in a computerized touch screen environment Animal Cognition DOI: 10.1007/s10071-013-0608-0

Image: Wasserman et al.

... Read more »

  • June 5, 2013
  • 07:22 AM

Mind over mechanics

by Perikis Livas in Chilon

It’s a staple of science fiction: people who can control objects with their minds.

At the University of Minnesota, a new technology is turning that fiction into reality.

In the lab of biomedical engineering professor Bin He, several young people have learned to use their thoughts to steer a flying robot around a gym, making it turn, rise, dip, and even sail through a ring.

The technology, pioneered by He, may someday allow people robbed of speech and mobility by neurodegenerative diseases to regain function by controlling artificial limbs, wheelchairs, or other devices. And it’s completely noninvasive: Brain waves (EEG) are picked up by the electrodes of an EEG cap on the scalp, not a chip implanted in the brain.... Read more »

University of Minnesota. (2013) Mind over mechanics. UM News. info:/

  • June 4, 2013
  • 11:35 AM

New Graphene Applications in Energy Review

by dailyfusion in The Daily Fusion

Like diamond or graphite, graphene is a structural modification (an allotrope) of carbon, that has many special properties that make it a very useful material with great potential for application in technology. In essence, graphene is an isolated atomic plane of graphite, which is very light (1-square-meter sheet weighing only 0.77 milligrams) and at the same time very strong (graphene has a breaking strength over 100 times greater than a hypothetical steel film of the same thickness). The electrical properties of this novel material are being extensively researched for the wide range of potential graphene applications.... Read more »

Connolly, M., Chiu, K., Giblin, S., Kataoka, M., Fletcher, J., Chua, C., Griffiths, J., Jones, G., Fal'ko, V., Smith, C.... (2013) Gigahertz quantized charge pumping in graphene quantum dots. Nature Nanotechnology. DOI: 10.1038/nnano.2013.73  

Britnell, L., Ribeiro, R., Eckmann, A., Jalil, R., Belle, B., Mishchenko, A., Kim, Y., Gorbachev, R., Georgiou, T., Morozov, S.... (2013) Strong Light-Matter Interactions in Heterostructures of Atomically Thin Films. Science. DOI: 10.1126/science.1235547  

  • June 4, 2013
  • 08:56 AM

Are You Racist? Maybe Change Your Avatar

by Michael Kasumovic in United Academics

A new study in Consciousness and Cognition demonstrates technology may be able to offer part of the solution: donning the skin of a dark-skinned avatar significantly decreased an individual’s racial biases.... Read more »

  • June 2, 2013
  • 08:58 AM

Procrastination to find the most cited paper in the field of MRI

by Know Your Images in Know Your Images

I have posted recently about the most cited (important?) papers in Medical Imaging in the last ten/five/two years here. Today I look for the most cited papers in the field of MRI. Interesting to note that these 3 papers were published in Neuroimage.Most cited paper in Radiology, Nuclear Science and Medical Imaging Field about MRI:- of the last 10 years with 1346 citations:Ashburner, J., & Friston, K. (2005). Unified segmentation NeuroImage, 26 (3), 839-851 DOI: 10.1016/j.neuroimage.2005.02.018 This paper is the basis for the SPM framework, one of the most important in the field of MRI. Thus, it is understandable that this paper has a lot of citations, because most researchers who use this framework (and there are a lot, myself included) use this paper in their citations.- of the last 5 years with 250 citations:Klein, A., Andersson, J., Ardekani, B., Ashburner, J., Avants, B., Chiang, M., Christensen, G., Collins, D., Gee, J., Hellier, P., Song, J., Jenkinson, M., Lepage, C., Rueckert, D., Thompson, P., Vercauteren, T., Woods, R., Mann, J., & Parsey, R. (2009). Evaluation of 14 nonlinear deformation algorithms applied to human brain MRI registration NeuroImage, 46 (3), 786-802 DOI: 10.1016/j.neuroimage.2008.12.037I have to say that I am quite surprised by finding this paper on top. Brain MRI registration is nowadays considered almost a solved problem and I don't think there are many people looking into this anymore. However, it is always nice to put in your own paper: "I used this registration, because this paper says it is the best".- of the last 2 years with 106 citations:Smith, S., Miller, K., Salimi-Khorshidi, G., Webster, M., Beckmann, C., Nichols, T., Ramsey, J., & Woolrich, M. (2011). Network modelling methods for FMRI NeuroImage, 54 (2), 875-891 DOI: 10.1016/j.neuroimage.2010.08.063 I have talked about brain networks some times in this blog and this paper shows me that this topic has been hot in the last two years. This papers discusses different methods to obtain networks with fMRI data: "Many different methods are being used in the literature, but almost none has been carefully validated or compared for use on FMRI timeseries data."... Read more »

Ashburner, J., & Friston, K. (2005) Unified segmentation. NeuroImage, 26(3), 839-851. DOI: 10.1016/j.neuroimage.2005.02.018  

Klein, A., Andersson, J., Ardekani, B., Ashburner, J., Avants, B., Chiang, M., Christensen, G., Collins, D., Gee, J., Hellier, P.... (2009) Evaluation of 14 nonlinear deformation algorithms applied to human brain MRI registration. NeuroImage, 46(3), 786-802. DOI: 10.1016/j.neuroimage.2008.12.037  

Smith, S., Miller, K., Salimi-Khorshidi, G., Webster, M., Beckmann, C., Nichols, T., Ramsey, J., & Woolrich, M. (2011) Network modelling methods for FMRI. NeuroImage, 54(2), 875-891. DOI: 10.1016/j.neuroimage.2010.08.063  

  • May 31, 2013
  • 06:01 PM

Electron Microscopy Imaging Solves LED Efficiency Mystery

by dailyfusion in The Daily Fusion

Ending a long-time controversy concerning the reason behind indium gallium nitride semiconductor efficiency, MIT and Brookhaven Lab scientists have concluded that it definitely has nothing to do with indium-rich clusters.... Read more »

  • May 30, 2013
  • 10:11 AM

Atom-trapping laser gratings : A technological quantum leap for space

by Perikis Livas in Chilon

New micro-fabricated grating chips developed through ESA-led research enable the laser-based cooling and capture of atoms on a more compact basis than ever before, potentially delivering laboratory-standard performance for precision environmental sensing and timekeeping from devices portable enough to be flown into space.... Read more »

ESA Space Engineering. (2013) Atom-trapping laser gratings : A technological quantum leap for space. ESA. info:/

  • May 29, 2013
  • 11:30 PM

Microscopic computing in cells and with self-assembling DNA tiles

by Artem Kaznatcheev in Evolutionary Games Group

One of the three goals of natural algorithms is to implement computers in non-electronic media. In cases like quantum computing, the goal is to achieve a qualitatively different form of computing, but other times (as with most biological computing) the goal is just to recreate normal computation (or a subset of it) at a different […]... Read more »

Cardelli L, & Csikász-Nagy A. (2012) The cell cycle switch computes approximate majority. Scientific Reports, 656. PMID: 22977731  

  • May 29, 2013
  • 12:41 PM

New Catalysts Will Get Cellphones Running on Acid

by dailyfusion in The Daily Fusion

Physicist Florian Nitze at the Umeå University, Sweden, has developed several new catalysts that improve the capacity of the fuel cells, making it possible to use relatively environmentally friendly formic acid in fuel cell powering your mobile phone or laptop.... Read more »

  • May 29, 2013
  • 08:13 AM

Angelina Jolie doesn't trust medical imaging

by Know Your Images in Know Your Images

Angelina Jolie shocked us all with her decision to remove both her breasts in order to prevent breast cancer. Her breast cancer risk was calculated based on genetics and was 87%. Now it is 5%. I have to agree that this woman is brave! However, I think a very intense screening could have been done with very good results. There are several methods to detect breast cancer: (digital) mammography, tomosynthesis, breast MRI, ultrasound, positron emission tomography and even microwave imaging. Some without any risk, besides the huge amount of money that they cost if we would perform them on every woman. I think money is not a problem for Angelina Jolie and she could get checked out as many times as she wanted...The following article "Warner, E. (2004). Surveillance of BRCA1 and BRCA2 Mutation Carriers With Magnetic Resonance Imaging, Ultrasound, Mammography, and Clinical Breast Examination JAMA: The Journal of the American Medical Association, 292 (11), 1317-1325 DOI: 10.1001/jama.292.11.1317" refers all these important points:- "Women with BRCA1 and BRCA2 mutations who do not undergo prophylactic surgery have a lifetime risk of breast cancer of up to 85%, with a significantly higher risk of breast cancer than the general population from age 25 years onward." - This is the case of Angelina Jolie.- "The combination of MRI, ultrasound, and mammography had a sensitivity of 95%." - great numbers!- "To date, the reluctance to use breast MRI for surveillance of high-risk women outside the context of a clinical trial relates, to a large extent, to its high cost and relatively low specificity compared with mammography." - This would not be a problem for Angelina Jolie.- "In conclusion, our results support the position that MRI-based screening is likely to become the cornerstone of breast cancer surveillance for BRCA1 and BRCA2 mutation carriers, but it is necessary to demonstrate that this surveillance tool lowers breast cancer mortality before it can be recommended for general use." - A public figure like Angelina Jolie could help this matter.And another article "Kriege M, Brekelmans CT, Boetes C, Besnard PE, Zonderland HM, Obdeijn IM, Manoliu RA, Kok T, Peterse H, Tilanus-Linthorst MM, Muller SH, Meijer S, Oosterwijk JC, Beex LV, Tollenaar RA, de Koning HJ, Rutgers EJ, Klijn JG, & Magnetic Resonance Imaging Screening Study Group (2004). Efficacy of MRI and mammography for breast-cancer screening in women with a familial or genetic predisposition. The New England journal of medicine, 351 (5), 427-37 PMID: 15282350" states: "In conclusion, our study shows that the screening program we used, especially MRI screening, can detect breast cancer at an early stage in women at risk for breast cancer."... Read more »

  • May 28, 2013
  • 04:31 PM

Shape-shifting Nanoparticles Flip from Sphere to Net in Response to Tumor Signal

by Perikis Livas in Chilon

Scientists at the University of California, San Diego, have designed tiny spherical particles to float easily through the bloodstream after injection, then assemble into a durable scaffold within diseased tissue. An enzyme produced by a specific type of tumor can trigger the transformation of the spheres into netlike structures that accumulate at the site of a cancer, the team reports in the journal Advanced Materials this week.... Read more »

Susan Brown. (2013) Shape-shifting Nanoparticles Flip from Sphere to Net in Response to Tumor Signal. UC San Diego News Center. info:/

  • May 27, 2013
  • 04:55 PM

Transparent Graphene Electrode Makes Flexible Solar Cells Possible

by dailyfusion in The Daily Fusion

In a recent article published in journal Advanced Functional Materials, researchers describe a new graphene-coated transparent electrode made of silver nanowires. Because of its ability to bend without breaking, the new invention can be used to create flexible solar cells, computer and consumer electronics displays and future “optoelectronic” circuits for sensors and information processing.... Read more »

  • May 26, 2013
  • 11:30 PM

Distributed computation in foraging desert ants

by Artem Kaznatcheev in Evolutionary Games Group

For computer scientists, ants are most familiar from ant colony optimization. These algorithms rely on simulating how ants lay, follow, and modify pheromone trails to find efficient paths from their hives to food sources. Hence, it might come as a surprise that this is not a universal feature of ants. The cataglyphis niger desert ant […]... Read more »

  • May 24, 2013
  • 11:30 PM

Computer science on prediction and the edge of chaos

by Artem Kaznatcheev in Evolutionary Games Group

With the development of statistical mechanics, physicists became the first agent-based modellers. Since the scientists of the 19th century didn’t have super-computers, they couldn’t succumb to the curse of computing and had to come up with analytic treatments of their “agent-based models”. These analytic treatments were often not rigorous, and only a heuristic correspondence was […]... Read more »

Chazelle, B. (2012) Natural algorithms and influence systems. Communications of the ACM, 55(12), 101. DOI: 10.1145/2380656.2380679  

  • May 24, 2013
  • 10:07 AM

Ants Reveal How to Build a Tunnel You Can't Fall Down

by Elizabeth Preston in Inkfish

It's hard to keep your footing in a steep tunnel made of loose dirt while others are scrambling around and over your body. Harder still in pitch blackness. That's why fire ants build tunnels that will catch them when they fall—a strategy human engineers might want to steal.

"Slips and missteps are likely a constant, recurring feature of life underground," says Nick Gravish, a graduate student in Daniel Goldman's rheology and biomechanics lab at Georgia Tech. Yet ants have to traverse their tunnels quickly, especially when there's a colony emergency like a flood or destruction by a gardener's spade.

To study how ants engineer their tunnels, Gravish brought the fire ant Solenopsis invicta into the lab. Invasive to countries around the world and packing a nasty sting, these South American ants deal out plenty of hardship. But Gravish was interested in how they handle adversity themselves.

First, the ants were put into "laboratory soil" (actually tiny glass balls) to dig. Researchers took x-ray CT scans of the resulting tunnels and found that no matter the moisture of the "soil" or the size of the glass beads, ants dug circular tunnels of approximately the same diameter. That diameter was just a little bit more than the length of their bodies, not counting legs or antennae.

This suggested that the diameter of the tunnel was crucial to the fire ants. To see how well the ants moved within these tunnels, the researchers recorded video of them climbing as fast as they could. ("We startled them into climbing at high speed by exhaling gently into the nest," Gravish says.) They saw that ants were able to navigate their tunnels quickly, reaching speeds of more than 9 body lengths per second. They also saw that sometimes the ants slipped and had to recover their footing.

In addition to their tunnels, the researchers recorded ants climbing in vertical glass tubes. To get a better idea of how ants corrected their falls, the scientists jolted the tubes to knock the ants off the walls while they were climbing. (If you enjoy videos in the falling-bugs genre, this study generated several new additions. Here's one video of several ants falling and stopping themselves.)

Now the reason ants build tunnels so close in diameter to their own body length became clear. Ants responded to a fall by spreading all their appendages wide and waiting until they jammed to a stop. "One of the coolest things we found was that fire ants used their antennae to brace themselves," Gravish says. While falling, the ants turned these delicate sensors into extra load-bearing limbs.

When the glass tube width increased to 1.3 times the ants' body length, the strategy began to fail. The tunnels ants built themselves had an average diameter of just 1.06 times their body length, the authors report in PNAS. It seems fire ants put most of the responsibility for stopping falls on the tunnels themselves. After that, all a plummeting insect has to do is stretch out its limbs.

Gravish likens this strategy to the way humans build stairs. Steps are engineered to fit our bodies. If they're too tall or short, we struggle to use them (or maybe just fall down them). But with the right design, our environment works with us to get us where we're going.

This strategy could inspire how we design robots for confined spaces such as search-and-rescue zones, Gravish says. For instance, "falling is usually considered a failure mode for a robot." But fire ants seem to use little falls to descend more quickly through their tunnels. If engineers knew the size of the cracks and crevices in a disaster area, they might be able to send in many inexpensive robots designed to tumble through those spaces—rather than one very expensive robot built to keep its footing.

What about humans ourselves: would we benefit from building tunnels that were only as wide as our head-plus-torso length, like the ants? Gravish points out that fire ants often fall many body lengths before catching themselves, making this not such a great strategy for people. "Ants have a robust exoskeleton," he says. "We humans are quite soft in comparison."

Images: ant in tunnel by Laura Danielle Wagner; ants falling by Gravish et al.

Gravish, N., Monaenkova, D., Goodisman, M., & Goldman, D. (2013). Climbing, falling, and jamming during ant locomotion in confined environments Proceedings of the National Academy of Sciences DOI: 10.1073/pnas.1302428110

... Read more »

Gravish, N., Monaenkova, D., Goodisman, M., & Goldman, D. (2013) Climbing, falling, and jamming during ant locomotion in confined environments. Proceedings of the National Academy of Sciences. DOI: 10.1073/pnas.1302428110  

  • May 23, 2013
  • 03:37 PM

Researchers Turn a Smartphone into a Biosensor

by Jason Carr in Wired Cosmos

University of Illinois at Urbana-Champaign researchers have developed a cradle and app for the iPhone that uses the phone’s built-in camera and processing power as a biosensor to detect toxins, proteins, bacteria, viruses and other molecules. Having such sensitive biosensing capabilities in the field could enable on-the-spot tracking of groundwater contamination, combine the phone’s GPS … Read More →... Read more »

Gallegos, D., Long, K., Yu, H., Clark, P., Lin, Y., George, S., Nath, P., & Cunningham, B. (2013) Label-free biodetection using a smartphone. Lab on a Chip, 13(11), 2124. DOI: 10.1039/C3LC40991K  

  • May 23, 2013
  • 11:58 AM

New Method for Clean and Safe Hydrogen Production Proposed

by dailyfusion in The Daily Fusion

Duke University engineers have developed a new safer method for catalytic hydrogen production. According to the authors of the study, it does not require high temperatures and produces smaller amounts of toxic chemicals than other industrial hydrogen production technologies.... Read more »

  • May 21, 2013
  • 10:15 AM

Algorithmic view of historicity and separation of scales in biology

by Artem Kaznatcheev in Evolutionary Games Group

A Science publications is one of the best ways to launch your career, especially if it is based on your undergraduate work, part of which you carried out with makeshift equipment in your dorm! That is the story of Thomas M.S. Chang, who in 1956 started experiments (partially carried out in his residence room in […]... Read more »

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