Science-- there's something for everyone

Monday, December 31, 2012

Why do we blink?

Obviously, people blink in order to lubricate their eyes. But that can’t be the only reason. We blink far more often than simple moistening obligations would require. Plus, we seem to blink most at attention break points—at the ends of written sentences or during pauses in speech. This makes sense if you consider that each blink causes a momentary black-out of our visual system. We’re blinking at times when we’ll miss the least amount of information. Or are we looking at things the wrong way around? Researchers led by Tamami Nakano of Osaka University showed that eyeblinks actually cause attention disengagement rather than occurring after we’ve already briefly disengaged.

In particular, the researchers were interested in two regions of the brain: the dorsal attention network, which controls where we focus our attention, and the default-mode network (DMN), which counteracts the dorsal attention network and is involved in introspection. They placed ten healthy volunteers in an fMRI while the subjects watched scenes from a TV show (Mr. Bean). The subjects blinked an average of 17.4 times per minute. They compared brain activity during the spontaneous blinks to activity when the subjects were not blinking and to moments when the screen was physically blacked out for the same duration and frequency as normal eyeblinks.

The scientists found that spontaneous eyeblinks activated the DMN and deactivated the dorsal attention network. This was not true for screen blackouts, which affected the visual areas of the brain, but not the attention allocating areas. This suggests that we blink not because there’s been a break in our attention, but in order to cause that break. Blinking may help us push forward to the next image or line of dialogue.

Nakano T, Kato M, Morito Y, Itoi S, & Kitazawa S (2012). Blink-related momentary activation of the default mode network while viewing videos. Proceedings of the National Academy of Sciences of the United States of America PMID: 23267078.

Friday, December 28, 2012

Using dogs to detect C. difficile

Researchers from the Netherlands have been testing the diagnostic powers of dogs. At least, they’ve been testing whether a two-year old beagle named Cliff can detect which hospital patients are infected with Clostridium difficile. Not surprisingly, it turns out that he can.

C. difficile often arises as a secondary infection in patients whose internal flora has been decimated by antimicrobials. Unfortunately, it’s also extremely contagious, requiring strict infection control. For this reason, the sooner patients with this illness are identified the better. Patients with a C. difficile infection often have diarrhea with a distinctive smell that even humans can detect well over half the time. The researchers suspected that dogs could do much better than that. To that end, they had professional detection dog instructor Hotsche Luik teach Cliff to alert to the scent of C. difficile in stool samples. This process took two months, and can be seen in the video at the bottom of the post.

Cliff, preparing for rounds.
DOI: 10.1136/bmj.e7396

For the testing phase, Cliff was presented with 100 stool samples, half of which had come from C. difficile patients. The dog successfully identified all 50 C. difficile samples. He gave an inconclusive response to three of the negative samples.

Next, Cliff was walked through thirty ten-bed wards, each of which contained one C. difficile patient and nine controls without that illness. Cliff’s trainer, who accompanied him, did not know which person out of the ten had C. difficile. The dog correctly identified 25 out of the 30 C. difficile patients and 261 out of the 270 controls. In many of the cases in which Cliff gave an inconclusive or incorrect response, he’d been distracted. For example, even though the dog wasn’t supposed to interact with or touch the patients, some of them offered him food or beckoned to him.

This leads me to a large caveat about using detection dogs: their eagerness to please their humans makes them susceptible to fudging the results (see my prior post about sniffer dogs). It’s not hard to envision that in a real hospital setting, the nursing staff would have strong suspicions about which patients have C. difficile, and this knowledge could very well influence the dogs into providing the answers they think their humans want. That said, it only took Cliff about ten minutes per ward. That’s a pretty quick and completely noninvasive way to screen patients even if dogs do have a small error rate.

You can see Cliff in action below.

Bomers, M., van Agtmael, M., Luik, H., van Veen, M., Vandenbroucke-Grauls, C., & Smulders, Y. (2012). Using a dog's superior olfactory sensitivity to identify Clostridium difficile in stools and patients: proof of principle study BMJ, 345 (dec13 8) DOI: 10.1136/bmj.e7396

Thursday, December 27, 2012

Monkeys can’t hear the beat

Only a few animals have been shown to have ‘beat induction’, that is the ability to perceive a regular beat or pulse. Interestingly, this list has included birds, but not non-human primates. However, this deficit could merely represent a lack of response to rhythms rather than an inability to perceive those rhythms. In other words, just because an animal doesn’t bob its head or tap its feet doesn’t mean that it hasn’t noticed the beat.

Researchers from the University of Amsterdam and from the Universidad Nacional Autonoma de México decided to bypass physical manifestations of beat induction and study actual brain activity in two rhesus monkeys (Macaca mulatta). They played a drum pattern either in its entirety or with specific notes omitted. Human adults and even newborn babies will notice those missing elements. Was that true for the monkeys?

To find out, the researchers looked for mismatch negativity in the monkeys’ brains. This occurs when something unexpected occurs, such as when the incoming stimuli don’t match expectations. For example, if you’re listening to a sound pattern and the music skips a beat, this will activate mismatch negativity in your brain. It turns out that while monkeys can detect rhythms based on the duration of sounds, they can’t pick out the regularity, or beat, of those sounds the way humans and some birds can.

The authors speculate that beat induction emerged by convergent evolution in creatures that are able to mimic sounds. If so, the ability to copy not only sounds but specific rhythms may have been one of the factors involved in the acquisition of human language.

Honing H, Merchant H, Háden GP, Prado L, & Bartolo R (2012). Rhesus Monkeys (Macaca mulatta) Detect Rhythmic Groups in Music, but Not the Beat. PloS one, 7 (12) PMID: 23251509.

Wednesday, December 26, 2012

Just for fun: The home of the future

The U.S. Commerce Department's National Institute of Standards and Technology (NIST) has been experimenting with energy-efficient home design. They believe their model home 'Net Zero Energy Residential Test Facility', or NZERTF, will produce as much energy as it uses over the course of a year.

Credit: NIST

I would volunteer to test whether this house is as energy efficient as the researchers predict. How about you?

Monday, December 24, 2012

Are you fit for space travel?

Despite the mothballing of the space shuttle program, public and private funding for space travel is ongoing. Over the coming decades, space tourism as well as jobs requiring work in space are expected to climb. Both spaceports and new spacecrafts are in the planning or even construction phases. However, there is one major deficiency. Apparently, there’s currently no consensus on how to approve people for space travel. Researchers, led by Marlene Grenon from the University of California, San Francisco, think we need to remedy that lack.

Today, people who travel in space are almost uniformly fit and healthy and most are in the first half of their lives. That won’t always be the case. Grenon and her colleagues predict that doctors will one day be fielding questions about whether heart patients can withstand liftoff forces or about how long osteoporosis patients can safely live with low or no gravity. Zero gravity can cause a host of problems even in healthy people, how will it affect people who already have one or more infirmity?

So far, the evidence suggests that most people can tolerate the forces (or lack of forces) associated with space travel, even if they have pre-existing conditions. That said, we’re obviously far from knowing all there is to know about the medical effects of space travel. At present, the FAA is putting the onus of ensuring medical safety on the spacecraft operators, asking only for informed consent. This in turn means that prospective travelers will be seeking advice from their own doctors. For this reason, the researchers suggest that physicians begin to compile data and resources to share with their patients. The scientists have put together the following helpful chart as a starting point.

Hypothetical spaceflight considerations for common medical entities

Medical condition
Influence of spaceflight
Preflight intervention
Coronary artery disease
May increase the risk for cardiac dysrhythmias or myocardial ischaemia
If patient decides to fly, ensure that blood pressure and cardiac rhythm are properly controlled
Cerebrovascular disease
Possible altered flow patterns in a carotid lesion
Optimise medical treatment and consider repair as per current guidelines
Peripheral arterial disease
Volume shifts may exacerbate symptoms
Optimise medical management; consider treatment of critical limb ischaemia and claudication
Abdominal/thoracic aortic aneurysm
Impact of linear acceleration during launch could increase the risk of rupture
Consider treating (endovascular or open)
Aortic dissection (type B)
Impact of linear acceleration during launch could worsen the extent of the dissection
Consider treating (endovascular or open)
Chronic obstructive pulmonary disease/asthma
Symptoms may increase with the stress of flight
Optimise medical management
Increase in bone loss during spaceflight
Consider bisphosphonate treatments for longer duration flights (probably no effect for suborbital flights)
Possibility that immune suppression (and exposure to radiation) may exacerbate condition
Consider postponing flight
History of deep venous thrombosis
Theoretical increased risk of thrombosis with stasis and decreased use of lower extremities
Prophylactic low molecular weight heparin injections during flight
Gastrointestinal reflux
May exacerbate with the lack of gravity
Ensure that patients symptoms are well controlled with appropriate medical therapy
Transient infections (urinary tract infection, pneumonia, ears, skin infection)
Could exacerbate with effects on the immune system, increased growth of bacteria in space, unknown efficacy of common antibiotics with changes in pharmacokinetics and pharmacodynamics
Consider postponing flight until the acute process is resolved
Psychiatric problems
May exacerbate (or possibly improve) state
Ensure that the patient is not a threat to himself/herself or others

Unknown data on effects
Consider postponing the flight until after pregnancy

Elizabeth Preston has more on this over at Inkfish.

Grenon, S., Saary, J., Gray, G., Vanderploeg, J., & Hughes-Fulford, M. (2012). Can I take a space flight? Considerations for doctors BMJ, 345 (dec13 8) DOI: 10.1136/bmj.e8124

Friday, December 21, 2012

Cave art is more accurate than modern art

In the 1880’s, Eadweard Muybridge (and no, that’s not his original name. He was born Edward Muggeridge) pioneered photography of animals in motion. He’s most famous for having solved the age-old riddle of whether all four of a horse’s hooves ever leave the ground at once (answer: yes--see below).

Muybridge’s photographs put together into a film.

Since his experiments, we’ve had a better understanding of animal locomotion, and this knowledge shows in post-Muybridge art work. The error rate for correctly depicting animals in motion fell from 84% before his studies came to light to 58% afterwards. Now, would you like to know how good prehistoric people were at depicting moving animals? The error rate in cave art is 46%.

This interesting comparison is courtesy of some Hungarian researchers led by Gabor Horvath of Eotvos University. They collected 1000 examples of art containing quadrupeds in motion. Their samples included both 2D (paintings, drawings, reliefs) and 3D (statues) art pieces. Because the authors assume that there are 60 possible combinations for placement of all four feet (right forefoot in front and on the ground, right forefoot forward but raised in the air, etc.), 16 of which occur in nature, they come up with an error rate for random foot placement of 73%. That is, before Muybridge’s studies, people did worse than chance at depicting moving animals.

To see what the authors meant, let's look at a couple of examples. First, here's a drawing of a horse from the Lascaux Caves in France.

Even if you're not sure where the ground would be in this drawing (is the left forefoot lifted?) this animal is anatomically correct. Score one for cavemen. 

On the other hand, look at this pre-Muybridge modern drawing:

A horse would only assume this posture with the left forefoot raised in front of the animal if the right hindfoot was behind the left hindfoot. Showing the animal with the right hind foot placed forward is incorrect. Sorry Da Vinci.

Horvath G, Farkas E, Boncz I, Blaho M, & Kriska G (2012). Cavemen were better at depicting quadruped walking than modern artists: erroneous walking illustrations in the fine arts from prehistory to today. PloS one, 7 (12) PMID: 23227149.

Thursday, December 20, 2012

Dishwashing doesn’t kill norovirus

The leading cause of food borne illness is not Escherichia coli or Salmonella. No, that honor goes to the norovirus, a group of viruses named for the Norwalk virus. Transmission of noroviruses can be via direct contact or contaminated food or water. In general though, if you got sick with a norovirus, you probably ate someone’s poo.

Most restaurants do their best to make sure their food is safe. They use techniques known to kill bacteria such as E. coli. But how well do these food safety practices work against a virus like the norovirus? To test this, researchers led by Lizanel Feliciano from the Ohio State University allowed cream cheese contaminated with either E. coli or norovirus stock to harden onto ceramic plates and stainless steel forks. Contaminated milk was left to dry in drinking glasses. The tableware was then washed with detergent and sanitized with either chlorine-bleach or quaternary ammonium compounds. Titers of bacteria or virus were taken both before and after air-drying and washing.

Not surprisingly, the bacteria and viruses did fine on the air-dried surfaces prior to cleaning. If a surface has been contaminated, the bugs on it can survive for an extended period of time, up to a month in the case of norovirus. Bacteria are more sensitive but can still last quite some time.

Washing the tableware dropped the bacterial load significantly. Unfortunately, that wasn’t the case for norovirus. There was a reduction in the viral titer after washing, but not nearly enough to prevent disease transmission. This was true for both mechanical and manual dishwashing methods, though mechanical washing was slightly better at killing bacteria. Interestingly, sanitization did not improve the outcomes for either bacteria or virus. The greatest drop in microbe levels was achieved solely by washing, subsequent sanitization was no better than spraying with tap water.

I should point out that it only takes a handful of norovirus particles to cause an infection. In other words, you have to eliminate all trace of the virus from tableware to ensure food safety. Standard washing methods simply can’t achieve this goal, though vigilance on the part of restaurant management to ensure that sick people stay out of the kitchen may do so. Bon appétit.

Lizanel Feliciano, Jianrong Li, Jaesung Lee, & Melvin A. Pascall (2012). Efficacies of Sodium Hypochlorite and Quaternary Ammonium Sanitizers for Reduction of Norovirus and Selected Bacteria during Ware-Washing Operations PloS ONE : doi:10.1371/journal.pone.0050273.

Wednesday, December 19, 2012

Just for fun: 2012 Infographics

The Visual-ly Blog has a collection of 20 of the best infographics of 2012.  They range from the beautiful to the fascinating. You can see the list here, but below are two of my favorites.

Here are the color palettes for 10 artists over 10 years.

10 Artists, 10 Years: Color Palettes

And KVSStudio takes a look at what the world would be like...

If the World were 100 People

Tuesday, December 18, 2012

Lose weight by remembering meals

Does the memory of a large meal affect future hungriness? According to researchers from the University of Bristol, led by Jeffrey Brunstrom, yes, it can.

What I love most about this study is the self-filling soup bowl used by the researchers. 100 participants were shown bowls containing either 300 or 500 ml of soup. They proceeded to eat the soup. Unbeknownst to the diners, the bowls had a secret filling/emptying system that covertly changed the amount of soup in the bowls. Thus, the people who saw 300 ml in their bowls were actually eating either 300 or 500 ml of soup. In the same way, the people who were presented with 500 ml of soup actually ate either 300 or 500 ml. There were 25 people in each of these four groups.

You can see a diagram of the soup-filling apparatus below. Volunteers were instructed to stop eating when the soup reached a certain line in the bowl to ensure that they didn’t discover the filling apparatus at the bottom (the total amount of soup was adjusted to account for this).



Only six people out of hundred noticed that the volume of soup in their bowls was being manipulated. Those people were replaced with another six volunteers.

The subjects had been asked to abstain from eating for at least three hours before the test. After eating their soup, they were sent home with a buzzer to remind them to rate their level of hunger every hour for the next three hours. People who thought they had eaten 500 ml of soup but really had only consumed 300 ml reported more satiety than people who consumed 500 ml of soup but thought they had eaten 300 ml. In other words, the perception of having eaten a large meal had a great effect than the actual amount ingested.

This data suggests that if you wish to help a dieting friend, trick him into thinking he’s consuming a larger portion than he really is. I can see a market for a line of bowls with false bottoms that appear larger than they really are.

Brunstrom JM, Burn JF, Sell NR, Collingwood JM, Rogers PJ, Wilkinson LL, Hinton EC, Maynard OM, & Ferriday D (2012). Episodic memory and appetite regulation in humans. PloS one, 7 (12) PMID: 23227200.

Monday, December 17, 2012

Antibiotic resistant soil

You know that not taking all your antibiotics can lead to the evolution of drug resistant bacteria. You even know that a much larger problem is the amount of antibiotics given to livestock. But what you may not have realized is that the problem isn’t just that the bugs living in animals will become drug resistant and then infect humans. No, a bigger problem may be that bacteria living in soil can become resistant to drugs pooped out of medicated animals. Yes, antibiotic resistance is being spread throughout our agricultural fields.

Researchers from Agriculture and Agri-Food Canada applied a mix of sulfamethazine (SMZ), tylosin (TYL), and chlortetracycline (CTC), three kinds of antibiotics common in livestock management, to fields annually for ten years. At the end of that time, soil samples were taken and compared to similar fields that had not been treated. 

When the scientists added SMZ or TYL to the samples, they found that the drugs biodegraded much more quickly from fields that had previously been exposed to those drugs. In other words, the bacteria in the virgin soils were far less equipped to deal with the influx of antibiotics. In contrast, bacteria that had spent the last ten years in soil containing antibiotics had adapted to those drugs. The scientists even discovered at least one type of bacteria that was not only resistant but appeared to actually use SMZ as a nutrient source.

This news isn’t necessarily bad. As long as the soil bacteria don’t affect human health (and I realize that’s a big if), we might be able to employ them to clean up fields before the drugs deposited there by livestock can leach into water sources. Of course, we have little hope of cataloguing, let alone managing, all the kinds of bacteria living in the dirt. So we’re all probably better off if fewer drugs get deposited in those fields going forward.

Add caption
Edward Topp, Ralph Chapman, Marion Devers-Lamrani, Alain Hartmann, Romain Marti, Fabrice Martin-Laurent, Lyne Sabourin, Andrew Scott, & Mark Sumarah (2012). Accelerated Biodegradation of Veterinary Antibiotics in Agricultural Soil following Long-Term Exposure, and Isolation of a Sulfamethazine-degrading Microbacterium Journal of Environmental Quality : doi: 10.2134/jeq2012.0162.

Friday, December 14, 2012

Dogs don't generalize words like humans do

When humans learn the names of objects, they generally associate that name with the overall shape of the object. Thus, if they are taught that a U-shaped object is called a ‘DAX’ and asked to identify another DAX, they’ll pick an object with the same shape, but not necessarily the same size or texture. In other words, when it comes to nomenclature, we generalize in a specific way with a bias toward shape. Is this true for dogs as well?

There are a handful of dogs with a large enough vocabulary to test this feature of language. I’ve written before about Chaser, who knows as many words as a human toddler (over a thousand). This time, the test subject was a Border Collie named Gable, who reliably knows the names of over 40 different objects.

Emile van der Zee, Helen Zulch and Daniel Mills from the University of Lincoln and Gable's trainer taught the dog specific nonsense names for some novel objects. For example, in one set of experiments, he was taught that the L-shaped object shown as (1) in the figure below was a GNARK. When asked to retrieve another GNARK from amongst pairs of the objects shown, he invariably chose something the same size (2 or 3) rather than the same shape (4 or 7). Apparently, Gable was not making the same mental associations that humans do.

I don’t know about you, but I’d say that if object 1 was presented to me as a GNARK, then objects 4 and 7 are definitely GNARKS as well. This may be because, as a human, I rely heavily on my eyesight to interpret the world. Dogs no doubt rely on other cues, perhaps weight or mouth-feel. As you can see below, Gable does mouth each object before deciding which is the GNARK. Since word generalization is a critical feature in language, these data may mean that the way humans developed language is not the only road to that achievement. 

Below, a test session in which Gable is asked to retrieve a u-shaped DAX. Between trials, the trainer lets Gable play with the DAX prototype. As the test begins, the researcher pretends to make that prototype one of the choices.

Test session in which Gable is asked to retrieve a u-shaped DAX. Between trials, the trainer lets Gable play with the DAX prototype. As the test begins, the researcher pretends to make that prototype one of the choices.

Emile van der Zee, Helen Zulch, & Daniel Mills (2012). Word Generalization by a Dog (Canis familiaris): Is Shape Important? PloS ONE : doi:10.1371/journal.pone.0049382

Thursday, December 13, 2012

The secret of the porcupine’s quill

North American porcupine quills are notoriously easy to stick into something but hard to pull back out. A dozen researchers from MIT, Harvard, Xi’an Jiaotong University and Trinity College have now cracked the puzzle as to why this is so. And in case you’re wondering why you should care, consider that there are a lot of medical devices that also function by being stuck into people.

Porcupine quills are composed of a black tip, typically a few millimeters long, and a much longer white shaft. The tip contains microscopic backward-facing barbs, each less than 50 microns (millionths of a meter) across. The researchers compared normal porcupine quills to quills that had been carefully sanded down to remove those tiny barbs without altering the overall shape of the quill. The barbed quills required 54% less penetration force than the sanded quills. Interestingly, it’s the region 2-4 mm from the tip that’s critical for reducing penetration force, and not the very tip. Quills with the barbs sanded down only in this region required significantly more force to penetrate flesh regardless of whether the barbs in the first 2 mm were intact.

It turns out that a barbed porcupine quill requires less penetration force than an 18 gauge hypodermic needle. Though, to be fair, you’ll rarely need to be stuck with such a large needle unless you’re giving blood. So, I don’t think you’ll be seeing your doctor pull out a porcupine quill the next time you get your flu shot. On the other hand, the backward facing barbs somewhat counterintuitively result in a cleaner cut with less tissue damage. This is despite the fact that the quills with barbs penetrate deeper into flesh and are harder to remove. This characteristic may prove useful for implanting medical devices.

And now, a random porcupine.

Woo Kyung Cho, James A. Ankrum, Dagang Guoa, Shawn A. Chester, & et al (2012). Microstructured barbs on the North American porcupine quill enable easy tissue penetration and difficult removal Proceedings of the National Academy of Sciences of the United States of America : doi: 10.1073/pnas.1216441109.