Post List

  • September 27, 2010
  • 11:44 AM

Diagnosing Gout

by Robert Badgett in ClinDx

Even if using the prediction rule developed in this study, physicians should consider aspirating most all joints with monoarthritis as value even in joints suggestive of gout had a one in 20 chance of an alternative diagnosis. Also, the label of gout may affect future decision making and life-long medications.... Read more »

Janssens HJ, Fransen J, van de Lisdonk EH, van Riel PL, van Weel C, & Janssen M. (2010) A diagnostic rule for acute gouty arthritis in primary care without joint fluid analysis. Archives of internal medicine, 170(13), 1120-6. PMID: 20625017  

  • September 27, 2010
  • 11:41 AM

Sub-angstrom modeling of complexes between flexible peptides and globular proteins

by Nir London in Macromolecular Modeling Blog

We present Rosetta FlexPepDock, a novel tool for refining coarse peptide–protein models that allows significant changes in both peptide backbone and side chains. We obtain high resolution models, often of sub-angstrom backbone quality, over an extensive and general benchmark of 89 peptide–protein interactions.

... Read more »

  • September 27, 2010
  • 11:30 AM

Children and Their Pets

by Jason Goldman in The Thoughtful Animal

Your humble narrator finds himself sick with a cold, so here's a post from the archives.

There is considerable research on how children interact with other children and with adults, and how child development can be influenced by those interactions. But research on children's interactions with non-human animals seem to be limited. Given how ubiquitous pets are in the homes of children (at least, in WEIRD cultures), it is somewhat surprising that there hasn't been more work on the way pet ownership might affect child development.

According to the US Humane Society:

There are approximately 77.5 million owned dogs in the United States
Thirty-nine percent of U.S. households own at least one dog
Most owners (67 percent) own one dog
Twenty-four percent of owners own two dogs
Nine percent of owners own three or more dogs
On average, dog owners spent $225 on veterinary visits (vaccine, well visits) annually

There are approximately 93.6 million owned cats in the United States
Thirty-three percent of U.S. households (or 38.2 million) own at least one cat
Fifty-six percent of owners own more than one cat
On average, owners have two cats (2.45)
Cat owners spent an average of $203 on routine veterinary visits

Developmental scientist Gail F. Melson noted this paucity in research in a 2003 review paper in The American Behavioral Scientist. Melson points out that most parents report that they acquired their family pets "for the children," and given the ubiquity of child-pet bonding and interaction, she suggests that it is an important area for child development research to investigate. She goes through several topic areas in child development and examines what has been learned, or could be learned, by investigating human-animal bonding.
Read the rest of this post... | Read the comments on this post...... Read more »

  • September 27, 2010
  • 11:27 AM

This (Long) Week in the Universe: September 16th – September 27th

by S.C. Kavassalis in The Language of Bad Physics

I know, I know, I switched back to writing these on Mondays again without telling anyone.  It turns out, Wednesdays were a terrible choice of day for me. I swear I asked someone to fill in for me last week…
...but I guess she wasn't all that interested in the job.
Astrophysics and Gravitation:
Taking a Swim in the Lagoon Nebula
Credit: NASA/ESA Hubble Space Telescope
NASA and the ESA Hubble Space Telescope, via the Advanced Camera for Surveys, have provided us with a gorgeous picture of the Lagoon Nebula.  This nebula is of particular interest to amateur astronomers because it is one of only a few of its kind actually visible with the naked eye from Earth.  While it may be a blurry oval to the unassisted human viewer, to Hubble, this gas cloud is a giant, dynamic, home to new stars.  Okay, so there isn’t any new physics here, but they did get a great image.
For more, see Breaking Waves in the Stellar Lagoon.
AGILE on Gamma Rays
Marisaldi, M., et al. (2010). Gamma-Ray Localization of Terrestrial Gamma-Ray Flashes Physical Review Letters, 105 (12) DOI: 10.1103/PhysRevLett.105.128501
A team using satellite data to watch thunderstorms has figured out to to locate gamma rays (sometimes produced in said thunderstorms) with exceptional accuracy.  These models are helping physicists understand gamma rays and how they relate to electrical storms (which most theories wouldn’t actually anticipate).
For more, see Pinpointing Earthly Gamma Rays.
ANITA on Cosmic Rays
S. Hoover, & et al. (2010). Observation of Ultra-high-energy Cosmic Rays with the ANITA Balloon-borne Radio Interferometer Physical Review Letters arXiv: 1005.0035v2
A team using airborne radio detectors has noticed a characteristic radio wave signal produced by ultrahigh energy cosmic rays as they hit the ice in the Antarctic.  Since we still don’t know where these ultrahigh energy particles come from, being able to track them once they hit the earth will be a useful tool in figuring out where they originated from.
For more, see Tuning In to Highest Energy Cosmic Rays.
So Long S-Process
A. J. Gallagher, S. G. Ryan, A. E. García Pérez, & W. Aoki (2010). The barium isotopic mixture for the metal-poor subgiant star HD140283 Astronomy and Astrophysics arXiv: 1008.3541v1
Snipet from the abstract:
Current theory regarding heavy element nucleosynthesis in metal-poor environments states that the r-process would be dominant. The star HD140283 has been the subject of debate after it appeared in some studies to be dominated by the s-process. We provide an independent measure… that observations and analysis do not validate currently accepted theory.
It’s another one of these fun astrophysics mysteries.  We have a reasonable idea how stars work, but every now and then an observation comes along and tells us that our theoretical mechanisms can not be the end all be all of star dynamics and formation.  Star HD140283 is another fun piece to contradictory puzzle.  Because of the suspected age of HD140283 (ie. that it’s very, very old), it should have formed in its galaxy before the first red giants/barium producing stars formed, meaning that it shouldn’t (and according to current theory, couldn’t) have inherited any barium from its neighbours (and thus undergo r-process nucleosynthesis).  However, Gallagher et al.’s team’s observations say otherwise (that instead, we see s-process nucleosynthesis).  Is the current model of star formation incorrect, ie. do we need to rethink this late production of s-process isotope issue? Could there have been barium somehow to kick off this stars life? Could it be something else? Could that star have somehow been pulled in from an older galaxy? At this point, it seems pretty open.
For more, see Ancient star poses galactic puzzle.
High Energy Physics and Particles:
Good news, everyone! We might have been way off about quarks and gluons!
... Read more »

Marisaldi, M., Argan, A., Trois, A., Giuliani, A., Tavani, M., Labanti, C., Fuschino, F., Bulgarelli, A., Longo, F., Barbiellini, G.... (2010) Gamma-Ray Localization of Terrestrial Gamma-Ray Flashes. Physical Review Letters, 105(12). DOI: 10.1103/PhysRevLett.105.128501  

A. J. Gallagher, S. G. Ryan, A. E. García Pérez, & W. Aoki. (2010) The barium isotopic mixture for the metal-poor subgiant star HD140283. Astronomy and Astrophysics. arXiv: 1008.3541v1

Chou, C., Hume, D., Rosenband, T., & Wineland, D. (2010) Optical Clocks and Relativity. Science, 329(5999), 1630-1633. DOI: 10.1126/science.1192720  

  • September 27, 2010
  • 09:59 AM

Innate Immune Memory in Mosquitoes: The Latest Buzz in the Fight against Malaria

by Kelly Grooms in Promega Connections

For many of us mosquitoes are an itchy aggravation. They come in the evenings in the warmer months. They disrupt hikes, camping trips and picnics, leaving behind itching reminders that have us reaching for antihistamines and no-itch creams. For people in some areas of the world however, mosquitoes are more than just a pest with [...]... Read more »

Rodrigues J, Brayner FA, Alves LC, Dixit R, & Barillas-Mury C. (2010) Hemocyte differentiation mediates innate immune memory in Anopheles gambiae mosquitoes. Science (New York, N.Y.), 329(5997), 1353-5. PMID: 20829487  

  • September 27, 2010
  • 09:33 AM

How to put the quantum into silicon computers

by Joerg Heber in All That Matters

Quantum computers are so highly sought after because they can solve complex mathematical problems and parallel computer operations such as code breaking really fast. Attempts to build quantum computers come in many flavours and use different kinds of quantum states, ranging from trapped atoms, superconductors to semiconductors such as gallium arsenide or diamond. The approach [...]... Read more »

Andrea Morello, Jarryd J. Pla, Floris A. Zwanenburg, Kok W. Chan, Kuan Y. Tan, Hans Huebl, Mikko Mottonen, Christopher D. Nugroho, Changyi Yang, Jessica A. van Donkelaar.... (2010) Single-shot readout of an electron spin in silicon. Nature. DOI: 10.1038/nature09392  

  • September 27, 2010
  • 09:22 AM

Quit Yakking on Your Phone in Public

by APS Daily Observations in Daily Observations

You’re on the bus after a long day at work when you hear…“Yeah, I’m on my way home.” “That’s funny.” “Uh-huh.” “What? No! I thought you were.” The lady next... Read more »

Emberson L.L., Lupyan G., Goldstein M.H., & Spivey M.J. (2010) Overheard Cell-Phone Conversations: When Less Speech Is More Distracting. Psychological science : a journal of the Association for Psychological Science/ APS. PMID: 20817912  

  • September 27, 2010
  • 09:00 AM

Spanking in the USA: A sad state of affairs and why spanking is never ok.

by Nestor Lopez-Duran PhD in Child-Psych

MONDAY BRIEFS: Quick mussing on child related research. Editor’s note: Monday’s briefs are usually brief posts, but the topic today resulted in a longer than usual philosophical discussion of corporal punishment. The most recent issue of the journal of the American Academy of Pediatrics included a report on the use of physical violence as a form of discipline [...]... Read more »

  • September 27, 2010
  • 08:42 AM

News about the Integrated Microbial Genomes (IMG) resource

by Jennifer in OpenHelix

I’ve got a few news items regarding IMG, or Integrated Microbial Genomes, from the DOE Joint Genome Institute. The first item is that their Sept 2010 release occurred this week. IMG is now on version 3.2, has updated features and a bunch of new/revised genomes. I’ve begun updating our tutorial & will let you know when that is released. It’s not the craziest level of tool changes that I’ve seen from this group, but dang, they SURE don’t rest on their laurels! They are constantly changing and improving their interface and database.
If you are involved in microbial research and haven’t already checked out this powerful resource, I strongly suggest that you do. We’ve been training on this resource since 2006 and really believe in its value, which seems to increase with each of their releases. Mary & Trey presented an IMG workshop at NIH recently and it was surprising how many of their researchers were not aware of IMG. We hear that pretty often and it is too bad, it has so much to offer the microbial community and others as well.
The second item is that IMG has an annotation tool specifically designed for undergraduate education. Iddo Friedberg  describes this as ‘Way cool’ in a recent tweet. The program/interface is named the “Integrated Microbial Genomes Annotation Collaboration Toolkit (IMG-ACT)“, and is somewhat associated with the “Interpret a GEBA Genome for Education” project from JGI. “GEBA” stands for Genomic Encyclopedia of Bacteria and Archaea.  Both efforts are aimed at encouraging undergraduate research in microbial genome annotation, which might lead to the ‘alternative science career’ as a biocurator!
You can read all about the tool in their PLoS Biology article “Incorporating Genomics and Bioinformatics across the Life Sciences Curriculum“, or see a tour of the program/interface here. The tour makes the interface seem a bit clunky to me, but well thought out with lots of solutions to problems/issues often associated with undergraduate classes. The paper really provides a nice overview of the concept, collaborations, and initial outcomes of the 2008-2009 program.
Sign-ups are occurring for the 2011-2012 version of the program. The time frame is as follows:
Timeline to Participate:
1. Apply to be part of the 2011-2012 team by Monday, November 5, 2010 (download the application)
2. After acceptance, attend the workshop at the JGI (January 2011)
3. Implement in 2011-2012 academic year
as can be seen at the bottom of this page.
IMG-ACT Reference:
Ditty, J., Kvaal, C., Goodner, B., Freyermuth, S., Bailey, C., Britton, R., Gordon, S., Heinhorst, S., Reed, K., Xu, Z., Sanders-Lorenz, E., Axen, S., Kim, E., Johns, M., Scott, K., & Kerfeld, C. (2010). Incorporating Genomics and Bioinformatics across the Life Sciences Curriculum PLoS Biology, 8 (8) DOI: 10.1371/journal.pbio.1000448

... Read more »

Ditty, J., Kvaal, C., Goodner, B., Freyermuth, S., Bailey, C., Britton, R., Gordon, S., Heinhorst, S., Reed, K., Xu, Z.... (2010) Incorporating Genomics and Bioinformatics across the Life Sciences Curriculum. PLoS Biology, 8(8). DOI: 10.1371/journal.pbio.1000448  

  • September 27, 2010
  • 07:33 AM

can language affect blood flow?

by Chris in The Lousy Linguist

Do languages affect blood flow in the brain differently? Apparently, yes! In a recent fMRI study, researchers showed that Cantonese verbs and nouns are processed in (slightly) different parts of the brain than English nouns and verbs in bilinguals. The researchers used a lexical decision task to contrast the processing of English and Cantonese verbs and nouns in the brains of bilingual speakers.Chinese nouns and verbs showed a largely overlapping pattern of cortical activity. In contrast, English verbs activated more brain regions compared to English nouns. Specifically, the processing of English verbs evoked stronger activities of left putamen, left fusiform gyrus, cerebellum, right cuneus, right middle occipital areas, and supplementary motor area. The cognition of English nouns did not evoke stronger activities in any cortical regions.This is truly language affecting thought, no? The point of general interest to linguist is that bilingual speakers seem to process words in their two languages differently. Cantonese words are processed using diffuse brain regions and English words are processed using localized regions (this is a simplified explanation of course).Now, I have to admit that this is not my specialty so I am not familiar with the background literature. However, as interesting as this is, I must say I have some serious questions about their methodology and underlying assumptions. IFirst, they use orthography as their base for determining the "similarity" and "complexity" of languages. That is, if two languages use an alphabet, they are considered similar. While they give some passing references to other linguist measures, ultimately it is orthography that they use to compare "complexity" of stimuli (their word, not mine). So, they compared the mean number of strokes in a Chinese character with the number of letters in an English word to determine which was "more complex" than the other. I found this weird.Then they made an assumption that Cantonese words are more ambiguous with respect to parts of speech. I do not klnow if this is true, but it certainly is true that English has plenty of POS ambiguity (just ask Eric Brill), so it's not obvious to me that this is a fair assumption. Furthermore, they provider no evidence for this. Unfortunately, they do not publish their actual sets of stimuli, so it's not possible (this morning while googling around) to look at which words they actually use, but I suspect there's plenty of ambiguity to be found in the English words.Based on earlier work, they conjecture that morphological simplicity leads the brain to distribute where words are processed in the brain:...a recent fMRI study examining monolingual Chinese adults in our own laboratory indicated that Chinese nouns and verbs activate a wide range of overlapping brain areas (without a significantly different network) than those reported in the English studies cited above (Li et al., 2004). Relatively fewer distinctive  grammatical features of nouns and verbs at the lexical level are likely to be responsible for this finding, but the question may be addressed more directly by employing bilingual individuals.And the corollary should be true: the fact that English has tense and number markings means English verbs and nouns are processed ion more isolated parts of the brain. This is my wording of their conjecture. I may be oversimplifying just a bit, but I'm trying to wrap my head around the underlying claim. It's not clear to me why this would be true.Next (and this may be a bit nit-picky), they judged the level of bilingual proficiency using a self-assessment questionnaire. Call me a cynic, but I just don't trust people's perceptions of their own language skills. Then, the researches used frequency data from really dated sources including Francis and Kuceras 1982. I love F&K as much as the next guy, but in the age of the BNC, Davies's freely available 400 million word COCA, and the redonkulous Web 1T corpus of 1 trillion words (yes, 1 Trillion!), I see no reason to use resources so old.Their basic conclusions are a tad confusing too. They never clearly explained the connection between bilingualism and morphological complexity, imho. The interplay is complicated and requires thorough discussion, which they simply did not provide. When I used to teach writing to college freshmen, I always told them that their job when writing a paper was to make my job as a reader easy. Explain things clearly so I don't have to work too hard to figure out what you mean. These authors failed to make my job easy. I had to figure things out too much for myself.Ultimately, they found something interesting, I'm just not sure what it means and without more thorough linguistic vetting of their underlying assumptions, their results remain a head scratcher.Chan, A., Luke, K.K., Li, G., Li, P., Weekes, B., Yip, V., & Tan, L.H. (2008). Neural correlates of nouns and verbs in early bilinguals. Annals of the New York Academy of Sciences, 1145, 30–40. (pdf)Chan, A., Luke, K., Li, P., Yip, V., Li, G., Weekes, B., & Tan, L. (2008). Neural Correlates of Nouns and Verbs in Early Bilinguals Annals of the New York Academy of Sciences, 1145 (1), 30-40 DOI: 10.1196/annals.1416.000... Read more »

Chan, A., Luke, K., Li, P., Yip, V., Li, G., Weekes, B., & Tan, L. (2008) Neural Correlates of Nouns and Verbs in Early Bilinguals. Annals of the New York Academy of Sciences, 1145(1), 30-40. DOI: 10.1196/annals.1416.000  

  • September 27, 2010
  • 07:12 AM

Dizziness, Dix-Hallpike and the Epley manoeuvre

by Euan in Dr Euan Lawson| Doctor Writer

This article is a brief review of the evidence surrounding the diagnosis of benign paroxysmal positional vertigo (BPPV) and the use of the Epley manoeuvre to treat BPPV. The process couldn’t be more straightforward – do a Dix-Hallpike test and if this is positive move on to the Epley manoeuvre. Yet, it doesn’t get done. [...]... Read more »

  • September 27, 2010
  • 07:11 AM

How do miRNAs affect protein production?

by Becky in It Takes 30

A recent paper from the Bartel and Weissman groups (Guo et al. Mammalian microRNAs predominantly act to decrease target mRNA levels, Nature 466 835-40, PMID: 20703300) provides an interesting snapshot of the journey of a field from consensus to controversy to (one day?) consensus again. At issue is the question of how microRNAs — small [...]... Read more »

  • September 27, 2010
  • 06:00 AM

Correcting Hubble images

by Emma in we are all in the gutter

I’m going to be upfront here: this post is about CCDs and readout electronics. Wait, come back, it’s going to be interesting I promise*. It involves the Hubble Space Telescope. Everyone likes that, don’t they? Many astronomical instruments, including the ones on Hubble, use Charge Coupled Devices or CCDs. These detectors are like containers for [...]... Read more »

Massey, R., Stoughton, C., Leauthaud, A., Rhodes, J., Koekemoer, A., Ellis, R., & Shaghoulian, E. (2010) Pixel-based correction for Charge Transfer Inefficiency in the Advanced Camera for Surveys . Monthly Notices of the Royal Astronomical Society, 401(1), 371-384. DOI: 10.1111/j.1365-2966.2009.15638.x  

  • September 27, 2010
  • 05:08 AM

You've discovered a whacky wood-eating catfish? So what's new? | GrrlScientist

by GrrlScientist in GrrlScientist

The press has recently been abuzz with news of a newly discovered species of catfish that eats wood, of all things... Read more »

  • September 27, 2010
  • 04:52 AM

Power leads us to dehumanise others

by BPS Research Digest in BPS Research Digest

'How can you not feel sorry about people who have died? I mean you would be inhuman if you didn't think that,' former UK Prime Minister Tony Blair speaking to Andrew Marr on the BBC.Think how terrible you'd feel if a decision you made led to the death of another person. How then does a political leader cope with the burden of making decisions which lead to the deaths of hundreds of thousands? According to a new journal article, they cope through dehumanising those over whom they have power. By this account, dehumanising - seeing others as less than human - isn't always a bad thing. It serves a function, allowing leaders and certain professionals, such as doctors, to cope with the decisions they have to make.

Joris Lammers and Diederik Stapel had 102 student participants complete a measure of their sense of power (including items like 'to what degree does your opinion typically affect other people's opinions?'). Afterwards they were asked to read about a fictional, poor, South-American-sounding country called Aurelia and rate its inhabitants. Those who scored more highly on the power scale subsequently showed more evidence of dehumanising the inhabitants of Aurelia - for example, rating them as less civilised and more childish.

Next, the researchers primed some student participants to feel more powerful by having them write about an occasion when they had had power over an another person or persons. Those primed this way were subsequently more likely than controls (who wrote about a supermarket visit) to say they would back a plan to move Aurelians living in slums to an undeveloped part of their country, against their will if necessary. What's more, the participants primed to feel powerful were were more likely to show evidence of dehumanising the Aurelians when asked to rate them on factors like civility and childishness - an association largely mediated by their decision about the planned eviction.

In a final study, Lammers and Stapel had 50 student participants role-play the position of senior surgeon, junior surgeon or nurse before making a treatment decision about their fictional patient - a 56-year-old man with an abdominal growth. Those participants role-playing a more powerful position were more likely to opt for the painful but more effective of two treatment options. Moreover, the participants role-playing the senior surgeon role were more likely to show evidence of dehumanising the patient in a 'mechanistic' fashion - that is, rating him as more passive and less sensitive. The association between seniority of role and dehumanising was largely mediated by the decision to opt for the more painful treatment.

'By treating other people as objects or tools, the emotional consequences of the powerful people's actions are downplayed and become irrelevant,' the researchers said. 'Although this can lead people to abuse others, it may also facilitate the powerful in making tough decisions. ... Without dehumanising they would be overcome by the pain and suffering that result from their decisions.'

Lammeres and Stapel acknowledge, however, that the link between power and dehumanising wasn't entirely mediated by the making of tough decisions. 'We interpret this as evidence that power can also increase dehumanisation for reasons other than to justify decisions,' they said, before adding that more research is needed to explore what these other factors are.

Lammers, J., and Stapel, D. (2010). Power increases dehumanization. Group Processes and Intergroup Relations DOI: 10.1177/1368430210370042

... Read more »

Lammers, J., & Stapel, D. (2010) Power increases dehumanization. Group Processes . DOI: 10.1177/1368430210370042  

  • September 27, 2010
  • 03:35 AM

Memory as a resource

by Janet Kwasniak in Thoughts on thoughts

p { margin-bottom: 0.08in; }
Some people are surprised, even disturbed, by the idea that our vision does not give us an accurate picture of what we look at. For example, the colours we experience are not a measure of the wavelength of the light entering our eyes. But accuracy is not the point of vision; [...]... Read more »

  • September 27, 2010
  • 03:35 AM

Story of X

by Razib Khan in Gene Expression

A month ago I pointed to a short communication in Nature Genetics which highlighted differences in the patterns of variation between the X chromosome and the autosome. I thought it would be of interest to revisit this, because it’s a relatively short piece with precise and crisp results which we can ruminate upon.
Sometimes there is [...]... Read more »

  • September 27, 2010
  • 01:35 AM

Fear/Anxiety/Avoidance – and some treatments!

by Bronwyn Thompson in Healthskills: Skills for Healthy Living

I’ve been pondering the post by Neil O’Connell on Body in Mind in which he comments on a paper by Foster, Thomas, Bishop, Dunne and Main (2010) in which he makes the point that “There is a huge emphasis on psychological variables in research and current care for low back pain. My experience (the usual … Read more... Read more »

  • September 26, 2010
  • 10:59 PM

Humans 1, Environment 0

by CJA Bradshaw in ConservationBytes

While travelling to our Supercharge Your Science workshop in Cairns and Townsville last week (which, by the way, went off really well and the punters gave us the thumbs up – stay tuned for more Supercharge activities at a university near you…), I stumbled across an article in the Sydney Morning Herald about the state [...]... Read more »

Australian Bureau of Statistics. (2010) Measures of Australia's Progress. Report. info:other/

Raudsepp-Hearne, C., Peterson, G., Tengö, M., Bennett, E., Holland, T., Benessaiah, K., MacDonald, G., & Pfeifer, L. (2010) Untangling the Environmentalist's Paradox: Why Is Human Well-being Increasing as Ecosystem Services Degrade?. BioScience, 60(8), 576-589. DOI: 10.1525/bio.2010.60.8.4  

  • September 26, 2010
  • 08:14 PM

Cold start of Life: Ice as a protocellular medium for RNA replication

by Olexandr Isayev in

The hot spot for life on early Earth may have been a very cold place. Tiny pockets and channels that form inside ice can contain and protect replicating molecules, researchers report September 21 in Nature Communications. The paper suggests that life could have sprung from icy slush covering a freshwater lake, rather than a broiling [...]... Read more »

Attwater, J., Wochner, A., Pinheiro, V., Coulson, A., & Holliger, P. (2010) Ice as a protocellular medium for RNA replication. Nature Communications, 1(6), 1-8. DOI: 10.1038/ncomms1076  

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