Post List

  • January 10, 2011
  • 04:40 PM

Brain training – it happens all the time

by Bronwyn Thompson in Healthskills: Skills for Healthy Living

At the risk of seeming untrendy, the trend to rave on about neuroplasticity can be a bit overdone.  Not, I add quickly, because it doesn’t happen, or it’s not important – in fact, quite the opposite – but because it happens all the time.  And at the back of our minds, I think we’ve known … Read more... Read more »

Iannetti, G., & Mouraux, A. (2010) From the neuromatrix to the pain matrix (and back). Experimental Brain Research, 205(1), 1-12. DOI: 10.1007/s00221-010-2340-1  

Neugebauer, V., Galhardo, V., Maione, S., & Mackey, S. (2009) Forebrain pain mechanisms. Brain Research Reviews, 60(1), 226-242. DOI: 10.1016/j.brainresrev.2008.12.014  

  • January 10, 2011
  • 03:50 PM

Measles, Papua New Guinea and the brain

by Connor Bamford in The Rule of 6ix

You may not have realised that – since most people nowadays have been vaccinated against it and have never seen it – but measles is a very serious illness. Generally an acute disease of children, measles is spread by the measles virus where it infects the body via the respiratory route and establishes a systemic [...]... Read more »

Rima, B., & Duprex, W. (2006) Morbilliviruses and human disease. The Journal of Pathology, 208(2), 199-214. DOI: 10.1002/path.1873  

  • January 10, 2011
  • 03:00 PM

The Lone Wolf or the Support Group Enthusiast?

by Lorimer Moseley in BodyInMind

What type of person are you?? When tough times come around – whether it is stress at work, a painful injury, or forced participation in Secret Santa – what do you do? Some people, those lone wolf types, find relief in being alone, taking some time to regroup, and dealing with the problem themselves. Others, [...]... Read more »

  • January 10, 2011
  • 01:53 PM

Can a Font Make You Smarter?

by Kari Kenefick in Promega Connections

Today is the second Monday of the New Year, January 10, 2011 and we are returning to work, school and normal life, you know, the one without endless shopping, cooking and preparing. Hopefully most of your holiday 2010 remembrances are fond ones…the greetings, baked goods, travel, gifts…all good. Hold on. The greetings; was there was [...]... Read more »

  • January 10, 2011
  • 01:43 PM

Crowdsourcing Science with TOPSAN

by Sanford- Burnham in Beaker

New advances in technology are allowing scientists to sequence genomes and determine the structures of the proteins they encode at a faster rate and lower cost than ever before. The NIH’s Protein Structure Initiative centers, such as the Joint Center for Structural Genomics (JCSG), have been instrumental in establishing the structures of hundreds of proteins [...]... Read more »

Ellrott K, Zmasek CM, Weekes D, Sri Krishna S, Bakolitsa C, Godzik A, & Wooley J. (2011) TOPSAN: a dynamic web database for structural genomics. Nucleic acids research, 39(Database issue). PMID: 20961957  

Krishna SS, Weekes D, Bakolitsa C, Elsliger MA, Wilson IA, Godzik A, & Wooley J. (2010) TOPSAN: use of a collaborative environment for annotating, analyzing and disseminating data on JCSG and PSI structures. Acta crystallographica. Section F, Structural biology and crystallization communications, 66(Pt 10), 1143-7. PMID: 20944203  

Weekes D, Krishna SS, Bakolitsa C, Wilson IA, Godzik A, & Wooley J. (2010) TOPSAN: a collaborative annotation environment for structural genomics. BMC bioinformatics, 426. PMID: 20716366  

  • January 10, 2011
  • 01:23 PM

This Week in the Universe: January 4th – January 10th

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

Astrophysics and Gravitation:
Supermassive Black Hole Surprise?
CREDIT: Reines, et al., David Nidever, NRAO/AUI/NSF, NASA
The dwarf galaxy Henize 2-10, seen in visible light by the Hubble Space Telescope. The central, light-pink region shows an area of radio emission, seen with the Very Large Array. This area indicates the presence of a supermassive black hole drawing in material from its surroundings. This also is indicated by strong X-ray emission from this region detected by the Chandra X-Ray Observatory.
Astronomers have identified a supermassive black hole candidate at the centre of the dwarf galaxy Henize 2-10.  Amy Reines, one of the members of the discovery team, on why this is important:
This galaxy gives us important clues about a very early phase of galaxy evolution that has not been observed before.
For more, see Surprise: Dwarf Galaxy Harbors Supermassive Black Hole.
High Energy Physics and Particles:
Good-Bye to the Tevatron?
Obviously the big news of today is the rumour that the Tevatron will cease operations at the end of 2011.  We’re still waiting on the official announcement though.
New in Nuclear Fission
Andreyev, A., et al., (2010). New Type of Asymmetric Fission in Proton-Rich Nuclei Physical Review Letters, 105 (25) DOI: 10.1103/PhysRevLett.105.252502
An exotic fission process is studied and an exciting and anomalous asymmetry in the daughter masses is discussed.
As Abhishek Agarwal writes:
The ISOLDE team’s puzzling result hints that a very subtle interplay between macroscopic and microscopic interactions plays a deeper role in the fission process than expected and is likely to inspire detailed theoretical studies and further experiment.
For more, see Unequal Parts.

General Relativity, Quantum Gravity, et al.:
Projective flatness in the quantisation of bosons and fermions
Siye Wu (2010). Projective flatness in the quantisation of bosons and fermions arXiv arXiv: 1008.5333v2
The abstract:
We compare the quantisation of linear systems of bosons and fermions. We recall the appearance of projectively flat connection and results on parallel transport in the quantisation of bosons. We then discuss pre-quantisation and quantisation of fermions using the calculus of fermionic variables. We then define a natural connection on the bundle of Hilbert spaces and show that it is projectively flat. This identifies, up to a phase, equivalent spinor representations constructed by various polarisations. We introduce the concept of metaplectic correction for fermions and show that the bundle of corrected Hilbert spaces is naturally flat. We then show that the parallel transport in the bundle of Hilbert spaces along a geodesic is the rescaled projection or the Bogoliubov transformation provided that the geodesic lies within the complement of a cut locus. Finally, we study the bundle of Hilbert spaces when there is a symmetry.
So I’m a sucker for nice math, and this paper has got that in spades.  If you want some beautiful geometry, and some quantum mechanics (which together, I firmly believe are critical to good quantum gravity), then this is well worth the read.
... Read more »

Andreyev, A., Elseviers, J., Huyse, M., Van Duppen, P., Antalic, S., Barzakh, A., Bree, N., Cocolios, T., Comas, V., Diriken, J.... (2010) New Type of Asymmetric Fission in Proton-Rich Nuclei. Physical Review Letters, 105(25). DOI: 10.1103/PhysRevLett.105.252502  

  • January 10, 2011
  • 12:40 PM

Count Your Plaintiffs Before Certification Hatches: Class Size Matters in Some Unexpected Ways

by Dr. Ken Broda-Bahm in Persuasive Litigator

By: Dr. Ken Broda-Bahm - When dealing with the number of plaintiffs in a class action, mass tort, or other large scale litigation, is "Super-Size Me" the plaintiff's best choice? At a legal level, the U.S. Supreme Court will get a chance to weigh in, after the decision last week to determine whether as many as 1.5 million female Wal-Mart workers claiming gender discrimination can be certified as a class (Dukes v. Wal-Mart). The common belief is that a large number of plaintiffs serves to maximize the degree of harm that a jury is likely to perceive and amplify the...... Read more »

Loran F. Nordgren and Mary-Hunter Morris McDonnell. (2010) The Scope-Severity Paradox: Why Doing More Harm Is Judged to be Less Harmful. Social Psychological and. info:/

  • January 10, 2011
  • 12:09 PM

Barnacle Evolution I: Phylogeny Served Without Plates

by Kevin Zelnio in Deep Sea News

Lepas anatifera from Washington state, USA. Photo credit: David Cowles 1997.
Barnacle evolution was recently rewritten by a large effort of Perez-Losada and colleagues in 2008. Using a combination of genes and morphological traits they rejected some of the ideas that were foundational to barnacle biology and taxonomy, while giving new support for other ideas.
Though . . . → Read More: Barnacle Evolution I: Phylogeny Served Without Plates... Read more »

Pérez-Losada M, Harp M, Høeg JT, Achituv Y, Jones D, Watanabe H, & Crandall KA. (2008) The tempo and mode of barnacle evolution. Molecular phylogenetics and evolution, 46(1), 328-46. PMID: 18032070  

  • January 10, 2011
  • 12:00 PM

Endless Forms Most Viral

by Moselio Schaechter in Small Things Considered

by Welkin E. Johnson

Perhaps more than any other biological discipline, the study of animal viruses is confined to the present. Virions are simply not the stuff of which robust fossils are made. Phylogenetic analysis can help by revealing deep relationships between extant viral lineages, yet such reconstructions lack detail (telling us nothing about transitional or extinct viral forms, the movement of viruses between species, or the timing of major events in viral evolution), and molecular clock estimates are notoriously imprecise when applied to viruses [1]. Until recently, ancient endogenous retroviruses (ERVs) were the closest thing to a fossil record available to scientists with a proclivity for combining virology and natural history. Happily, a trio of recent studies appearing in PLoS Genetics [2], PLoS Biology [3], and PLoS Pathogens [4] reveal an unexpected wealth of non-retroviral virus sequences embedded in the genome sequence databases, a virtual equivalent of the Burgess Shale, ripe for excavation by eager paleovirologists.... Read more »

  • January 10, 2011
  • 11:55 AM

Environmentally Friendly Alkyl Halide Synthesis from Alcohols

by Michael Long in Phased

A very common chemical conversion (important to pharmaceutical and other syntheses), which in its most gentle application generates much waste, has now been rendered far more environmentally friendly.... Read more »

Dai, C., Narayanam, J. M. R., & Stephenson, C. R. J. (2011) Visible-light-mediated conversion of alcohols to halides. Nature Chemistry. DOI: 10.1038/NCHEM.949  

  • January 10, 2011
  • 11:14 AM

tau zero tries to read kardashev’s tea leaves

by Greg Fish in weird things

According to a study by the founder of the Tau Zero Foundation, a collective of space enthusiasts focused on the potential for interstellar travel, which last year published a paper on what it might take to reach a nearby star, we won’t be ready to launch anything outside the solar system by 2196 or so. [...]... Read more »

  • January 10, 2011
  • 11:02 AM

Care and equality in volunteer tourism: the perspective of locals

by Émilie Crossley in Journeys through the psychosocial

Advocates of volunteer tourism are keen to stress that the relationship between hosts and guests it engenders is one of responsibility, equality and reciprocity. It is a model of tourism that supposedly brings benefits to all parties involved, especially to host communities in developing countries, and which stands in firm opposition to the insensitive and [...]... Read more »

Sin, H.L. (2010) Who are we responsible to? Locals’ tales of volunteer tourism. Geoforum, 983-992. info:/

  • January 10, 2011
  • 10:55 AM

Rifaximin in IBS: A Quick Fix?

by Pranab Chatterjee in Scepticemia

This study published in the NEJM seems to have tackled the really dicey issue of unearthing a pharmacotherapeutic agent to deal with the rather ubiquitous, though poorly understood, and more often than not, even less poorly managed problem of irritable … Continue reading →... Read more »

Pimentel M, Lembo A, Chey WD, Zakko S, Ringel Y, Yu J, Mareya SM, Shaw AL, Bortey E, Forbes WP.... (2011) Rifaximin therapy for patients with irritable bowel syndrome without constipation. The New England journal of medicine, 364(1), 22-32. PMID: 21208106  

  • January 10, 2011
  • 10:55 AM

Learning the passive

by gameswithwords in Games with Words

If Microsoft Word had its way, passive verbs would be excised from the language. That would solve children some problems, because passive verbs are more difficult to learn than one might think, because not all verbs passivize. Consider:

*The bicycle was resembled by John.
*Three bicycles are had by John.
*Many people are escaped by the argument.

The bicycle was resembled by John: A how-to guide.
So children must learn which verbs have passives and which don't. I recently sat down to read Pinker, Lebeaux and Frost (1987), a landmark study of how children learn to passivize verbs. This is not a work undertaken lightly. At 73 pages, Pinker et al. (1987) is not Steve Pinker's longest paper -- that honor goes to his 120-page take-down of Connectionist theories of language, Pinker and Pinker (1988) -- but it is long, even for psycholinguistics. It's worth the read, both for the data and because it lays out the core of what become Learnability and Cognition, one of the books that has had the most influence on my own work and thinking.

The Data

The authors were primarily interested in testing the following claim: that children are conservative learners and only passivize verbs that they have previously heard in the passive. This would prevent them from over-generating passives that don't exist in the adult language.

First, the authors looked at a database of transcriptions of child speech. A large percentage of the passive verbs they found were passives the children couldn't possibly have heard before because they aren't legal passives in the adult language:

It's broked? (i.e., is it broken?)
When I get hurts, I put dose one of does bandage on.
He all tieded up, Mommy.

Of course, when we say that the child couldn't have heard such passives before, you can't really be sure what the child heard. It just seems unlikely. To more carefully control what the child had heard, the authors taught children of various ages (the youngest group was 4 years old) made-up verbs. For instance, they might demonstrate a stuffed frog jumping on top of a stuffed elephant and say, "Look, the frog gorped the elephant." Then they would show the elephant jumping on top of a mouse and ask the child, "What happened to the mouse?"

If you think "gorp" has a passive form, the natural thing to do would be to say "The mouse was gorped by the elephant." But a child who only uses passive verbs she has heard before would refuse to utter such a sentence. However, across a range of different made-up verbs and across four different experiments, the authors found that children were willing -- at least some of the time -- to produce these new passive verbs. (In addition to production tests, there were also comprehension tests where the children had to interpret a passivization of an already-learned verb.)

Some Considerations

These data conclusively proved that children are not completely conservative, at least not by 4 years of age (there has been a lot of debate more recently about younger children). With what we know now, we know that the conservative child theory had to be wrong -- again, at least for 4 yos -- but it's worth remembering that at the time, this was a serious hypothesis.

There is a lot of other data in the paper. Children are more likely to produce new passive forms as they get older (higher rates for 5 year-olds than 4 year-olds). They taught children verbs where the agent is the object and the patient is the subject (that is, where The frog gorped the elephant means "the elephant jumped on top of the frog"). Children had more difficulty passivizing those verbs. However, a lot of these additional analyses are difficult to interpret because of the small sample sizes (16 children and only a handful of verbs per experiment or sub-experiment).


Fair warning: the rest of this post is pretty technical.

What excites me about this paper is the theoretical work. For instance, the authors propose a theory of linking rules that have strong innate constraints and yet still some language-by-language variation.
The linkages between individual thematic roles in thematic cores and individual grammatical functions in predicate-argument structures is in turn mediated by a set of unmarked universal linking rules: agents are mapped onto subjects; patients are mapped onto objects; locations and paths are mapped onto oblique objects. Themes are mapped onto any unique grammatical function but can be expressed as oblique, object or subject; specifically, as the 'highest' function on that list that has not already been claimed by some other argument of the verb.With respect to passivization, what is important is that only verbs which have agents as subjects are going to be easily passivized. The trick is that what counts as an 'agent' can vary from language to language.
It is common for languages to restrict passivized subjects to patients affect by an action ... The English verbal passive, of course, is far more permissive; most classes of transitive verbs, even those that do not involve physical actions, have the privilege of passivizability assigned to them. We suggest this latitude is possible because what counts as the patient of an action is not self-evident ... Languages have the option of defining classes in which thematic labels are assigned to arguments whose roles abstractly resemble those of physical thematic relations...This last passage sets up the core of the theory to be developed in Learnability and Cognition. Children are born knowing that certain canonical verbs -- ones that very clearly have agents and patients, like break -- must passivize, and that a much larger group of verbs in theory might passivize, because they could be conceived of as metaphorically having agents and patients. What they have to learn is which verbs from that broader set actually do passivize. Importantly, verbs come in classes of verbs with similar meanings. If any verb from that set passivizes, they all will.

This last prediction is the one I am particularly interested in. A later paper (Gropen, Pinker, Hollander, Goldberg & Wilson, 1989) explored this hypothesis with regards to the dative alternation, but I don't know of much other work. In general, Learnability and Cognition go less attention than it should have, perhaps because by the time it was published, the Great Past Tense Debate had already begun. I've often thought of continuing this work, but teaching novel verbs to children in the course of an experiment is damn hard. Ben Ambridge has recently run a number of great studies on the acquisition of verb alternations (like the passive), so perhaps he will eventually tackle this hypothesis directly.

Pinker S, Lebeaux DS, and Frost LA (1987). Productivity and constraints in the acquisition of the passive. Cognition, 26 (3), 195-267 PMID: 3677572

... Read more »

  • January 10, 2011
  • 10:51 AM

The Source of Levodopa’s Unwanted Dance

by Rob Mitchum in ScienceLife

The motor symptoms of Parkinson’s disease - tremor, inability to initiate movement, rigidity - result from the loss of neurons that secrete the neurotransmitter dopamine. It therefore follows that the best way to treat these symptoms is by replacing a person’s lost dopamine, the strategy behind the drug levodopa. For the first few years, levodopa [...]... Read more »

Ding Y, Won L, Britt JP, Lim SA, McGehee DS, & Kang UJ. (2010) Enhanced striatal cholinergic neuronal activity mediates L-DOPA-induced dyskinesia in parkinsonian mice. Proceedings of the National Academy of Sciences of the United States of America. PMID: 21187382  

  • January 10, 2011
  • 10:42 AM

Managing Supply Chains with multiple Pipelines

by Daniel Dumke in SCRM Blog - Supply Chain Risk Management

Companies offer a smaller or larger range of products serving different markets, depending on their history and primarily the respective business model.

From a supply chain management point of view this poses the question if it is ok just to use the same supply chain strategy for all those products.

Pipelines vs. Supply Chains
Aitken et al. (2005) make a convincing argument against this approach and instead suggest the "pipeline" to describe the specific operational mechanisms and procedures that are employed to service specific product/market contexts within one supply chain.
So one supply chain usually contains several different pipelines.

Continue reading "Managing Supply Chains with multiple Pipelines"
... Read more »

Aitken, J., Childerhouse, P., Christopher, M.G., & Towill, D.R. (2005) Designing and Managing multiple Pipelines. Journal of Business Logistics, 26(2), 73-95. info:/

  • January 10, 2011
  • 10:39 AM

Velociraptor Table Scraps

by Brian Switek in Dinosaur Tracking

What did Velociraptor eat? Despite what the Jurassic Park franchise might suggest, the answer is not “tourists and hapless scientists.” Those were in rather short supply during the Mesozoic. Instead, as reported in Palaeogeography, Palaeoclimatology, Palaeoecology last year, recently found fossils confirm that this famous, sickle-clawed dinosaur fed upon the horned dinosaur Protoceratops. In 1971, [...]... Read more »

Hone, D., Choiniere, J., Sullivan, C., Xu, X., Pittman, M., & Tan, Q. (2010) New evidence for a trophic relationship between the dinosaurs Velociraptor and Protoceratops. Palaeogeography, Palaeoclimatology, Palaeoecology, 291(3-4), 488-492. DOI: 10.1016/j.palaeo.2010.03.028  

  • January 10, 2011
  • 10:00 AM

Lemur Week: Ringtailed Lemurs Look Where You're Looking

by Jason Goldman in The Thoughtful Animal

In honor of Science Online, which begins on Thursday night, I will be writing about lemurs this week. Why lemurs? Because on Friday morning, as a part of Science Online, I will be taking a tour of the Duke Lemur Center.

It is common among animals - especially primates - to orient their gaze preferentially towards other individuals, as well as to follow the gaze of others. Lots of attention has been paid to gaze-following, in part because the ability to recognize and orient to the behavior of others is missing or impaired in various developmental disorders, such as autism. It is well known that, at least in highly-controlled laboratory studies, human and nonhuman primates pay special attention to the faces and eyes of their conspecifics, and evidence has been found for gaze-following in other animals as well, ranging from horses to tortoises. The problem is that different experiments in different laboratories yield inconsistent results, partly as a result of different measurement techniques, and partly as a result of the different ways that researchers have operationalized the term gaze-following itself. In addition, there are contextual variables that need to be taken into account in order to fully understand the way that gaze-following works. For example, gaze-following in rhesus macaques is dependent upon the social status of the observer as well as the observed individual. Some studies of gaze-following in non-human animals have used humans as the attentional cue, which clearly places the animal in a non-natural social context.

Stephen V. Shepherd and Michael L. Platt of the Departments of Neurobiology and Cognitive Neuroscience, respectively, at Duke University in Durham, North Carolina think that they have a solution to the methodological problems that have riddled the study of gaze-following in animals. They decided to investigate social orienting in ringtailed lemurs (Lemur catta) continuously in a semi-natural enriched environment. Instead of subjecting each of a group of lemurs to a set of experimental tests using human social cues (as would fit well within the established methodology), they simply observed lemurs behaving naturally with each other. But how could they record that kind of data in a non-intrusive way?

Wireless infrared optical gaze-tracking dual-camera backpacks.
Read the rest of this post... | Read the comments on this post...... Read more »

  • January 10, 2011
  • 09:56 AM

Gabrielle Giffords' brain surgery: Decompressive hemicraniectomy

by Bradley Voytek in Oscillatory Thoughts

Description of Congresswoman Giffords' neurosurgery... Read more »

Voytek B, Secundo L, Bidet-Caulet A, Scabini D, Stiver SI, Gean AD, Manley GT, & Knight RT. (2010) Hemicraniectomy: a new model for human electrophysiology with high spatio-temporal resolution. Journal of Cognitive Neuroscience, 22(11), 2491-502. PMID: 19925193  

  • January 10, 2011
  • 09:05 AM

New advances in triple negative breast cancer

by Sally Church in Pharma Strategy Blog

Phase 2 study showing the use of gemcitabine and carboplatin plus iniparib, as compared with gemcitabine and carboplatin alone, resulted in a significantly higher rate of response and increased the progression-free survival. Continue reading →... Read more »

O'Shaughnessy, J., Osborne, C., Pippen, J., Yoffe, M., Patt, D., Rocha, C., Koo, I., Sherman, B., & Bradley, C. (2011) Iniparib plus Chemotherapy in Metastatic Triple-Negative Breast Cancer. New England Journal of Medicine, 2147483647. DOI: 10.1056/NEJMoa1011418  

Carey, L., & Sharpless, N. (2011) PARP and Cancer — If It's Broke, Don't Fix It. New England Journal of Medicine, 2147483647. DOI: 10.1056/NEJMe1012546  

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