Post List

  • September 5, 2011
  • 04:20 PM

More than just calories

by Rebecca Nesbit in The birds, the bees and feeding the world

In today’s population of just over 7 billion people, more than 900 million are undernourished and over 2 billion have nutrient deficiencies, yet over 1 billion adults are overweight. Lots of work has gone on to address the problems of undernourishment and obesity, but the problem of nutrient deficiency has taken second place.

... Read more »

Remans R, Flynn DF, DeClerck F, Diru W, Fanzo J, Gaynor K, Lambrecht I, Mudiope J, Mutuo PK, Nkhoma P.... (2011) Assessing nutritional diversity of cropping systems in African villages. PloS one, 6(6). PMID: 21698127  

  • September 5, 2011
  • 01:53 PM

Cradle of Cholera’s Seventh Pandemic Found

by Michelle Ziegler in Contagions

Cholera is a disease of seemingly endless fascination to epidemiologists for good reason. Vibrio cholerae emerged on a global stage in the 19th century just in time for the beginnings of modern medicine to grapple with it and for its transmission to prove the worth of epidemiological work. Although we understand its treatment and transmission [...]... Read more »

Safa, A., Nair, G., & Kong, R. (2010) Evolution of new variants of Vibrio cholerae O1. Trends in Microbiology, 18(1), 46-54. DOI: 10.1016/j.tim.2009.10.003  

  • September 5, 2011
  • 01:24 PM

Can brain trauma cause cognitive enhancement?

by Bradley Voytek in Oscillatory Thoughts

Another post inspired by Quora. Someone asked the question: "Can brain trauma cause cognitive enhancement?".Obviously this topic is dear to me, so I felt compelled to answer.(Read previously on my TEDx talk, my Neuron paper on functional recovery after stroke, my PNAS paper on working memory network deficits after stroke, why we don't need a brain, and my discussion of Rep. Grabrielle Giffords' brain surgery).The full response to the Quora question is below.*****Maybe! But most likely only in very specific cases of brain damage, and only for very specific types of cognitive task.In 2005, Carlo Reverberi and colleagues published a really cool peer-reviewed paper in the journal Brain:Better without (lateral) frontal cortex? Insight problems solved by frontal patients. Reverberi C, Toraldo A, D'Agostini S, Skrap M. Brain. 2005 Dec; 128(Pt 12):2882-90.They studied patients with damage (lesions) to the prefrontal cortex:They had these patients perform an "insight"-based task. Very simply subjects were given a math problem arranged in toothpicks. The goal was to make the arithmetic work by only moving one toothpick. Visually:So for the very first problem, you can see it starts by saying "4 = 3 - 1" which is clearly wrong. But by moving one of the toothpicks in the equal sign over to the minus sign, you swap the two, making an arithmetically sound equation: "4 - 3 = 1".Without getting into a ton of details, it turns out that in some very specific cases, patients specifically with lateral prefrontal damage performed better than people without brain damage.The theory behind this sort of fits with what we know about decision making and expectation. Basically, because of these patients' lesions they have some deficits in using contextual information and internal cues to inform their decision-making. But in a difficult task such as this with a large "search space", rather than getting stuck in specific patterns, they're a bit more "freed up" from internal expectancies and thus can hit on the correct solution more quickly.Reverberi, C. (2005). Better without (lateral) frontal cortex? Insight problems solved by frontal patients Brain, 128 (12), 2882-2890 DOI: 10.1093/brain/awh577... Read more »

  • September 5, 2011
  • 10:21 AM

Walk Along the Paper Trail: Taste Hotsprings

by Michael Patterson in ...And You Will Know Me By The Trail of Papers

The Zuker lab recently reported the existence of taste hotspots in gustatory cortex. I go through the paper, and look at what that means.... Read more »

Chen X, Gabitto M, Peng Y, Ryba NJ, & Zuker CS. (2011) A gustotopic map of taste qualities in the mammalian brain. Science (New York, N.Y.), 333(6047), 1262-6. PMID: 21885776  

  • September 5, 2011
  • 08:00 AM

How much should we trust job applicant ratings of their own emotional intelligence?

by Alex Fradera in BPS Occupational Digest

Self-rating is a popular way to measure emotional intelligence in the workplace. Under lab conditions it's been shown that these ratings vary depending on what your (imaginary) objective is: to give a 'true' picture or to successfully win a job. A new study translates this lab finding to the workplace, finding that applicants for jobs really do rate themselves higher on EI than counterparts already working in that organisation.

The study compared scores for 109 job applicants with 239 volunteers, matched by department and managerial level. They rated themselves on four classic components of EI: self emotion appraisal, others emotion appraisal, use of emotion, and regulation of emotion. Applicants significantly outscored incumbents in all areas, on average rating themselves more than a standard deviation better. The areas of greatest divergence were in use of emotions and regulation of emotions, which have much in common with the Big Five personality traits conscientiousness and emotional stability, which we know job applicants have a higher tendency to inflate.

On all but one of the components, applicant scores were significantly more bunched together than incumbent scores, which could be seen as additional support that they were manufactured, with candidates homing in on scores that were solidly good, avoiding suspicious high or unhelpful low scores.

The study is important because in other areas of research, score discrepancies can be found in the lab, due to different explicit instructions, that don't seem to surface in the real world, suggesting the overt nature of lab conditions can exaggerate or even manufacture differences. Yet here the effect is found again, suggesting that if we do want to rely on self-report to assess EI we should recognise that this inflation may take place, and that relying on the normative data that accompanies these tests may lead us to unrealistically high appraisals of candidates.

Lievens, F., Klehe, U., & Libbrecht, N. (2011). Applicant Versus Employee Scores on Self-Report Emotional Intelligence Measures Journal of Personnel Psychology, 10 (2), 89-95 DOI: 10.1027/1866-5888/a000036
... Read more »

  • September 5, 2011
  • 08:00 AM

Walk Along the Paper Trail: Taste Hotsprings

by Michael Patterson in ...And You Will Know Me By The Trail of Papers

I haven't done many walkalongs about new papers, so let's review a new paper from Charles Zuker's lab.

Trail Prep

First, two pieces of background. There are two diametrically opposed theories of taste coding. The "labeled line" theory states that each taste quality (sweet, salty, bitter, etc.) is encoded by a single cell type, and individual cells respond to single taste qualities. In contrast,... Read more »

Chen X, Gabitto M, Peng Y, Ryba NJ, & Zuker CS. (2011) A gustotopic map of taste qualities in the mammalian brain. Science (New York, N.Y.), 333(6047), 1262-6. PMID: 21885776  

  • September 5, 2011
  • 07:02 AM

Hot hazy weather, violent behavior and the expert witness

by Doug Keene in The Jury Room

It’s really hot right now in Texas. We are in extreme drought. This weekend things became heated on my neighborhood email list when someone asked if our HOA had relaxed standards since so many lawns were brown. Multiple others took offense. Finally, someone recommended a cool glass of water for everyone. What’s amusing is that [...]

Related posts:When cross-examination [of the expert witness] offends
But, your honor! That witness was drunk!
The Jury Expert for May 2010 is uploaded
... Read more »

  • September 5, 2011
  • 07:00 AM

September 5, 2011

by Erin Campbell in HighMag Blog

When you hear the word “angiogenesis,” do you start hissing? Many of us associate angiogenesis with tumors on their way to becoming malignant cancer. Well, if it weren’t for angiogenesis, we’d all be in trouble. Angiogenesis is the formation of blood vessels from pre-existing ones, and is a key process during development.

Blood vessels are the tubular structures that transport all of the good stuff in our blood. The formation of blood vessels depends on angiogenesis, the process in which vessels are created from pre-existing ones. Angiogenesis is a tightly regulated process, as the blood vessels in many organs have a stereotypic organization, abundance, and shape. For example, zebrafish embryos have a regular pattern of blood vessels sprouting from the aorta, along the trunk of the fish. A recent paper describes the importance of Semaphorin-PlexinD1 signaling in the organization of these blood vessels. According to Zygmunt and colleagues, Semaphorin-PlexinD1 signaling ensures the correct spatial distribution and number of blood vessels along the embryo’s trunk. Without correct Semaphorin-PlexinD1 signaling, too many vessels sprout along the aorta, as seen in the images above. Normal embryos (left) have a very regular pattern of blood vessels (green, "SeA") sprouting up, while embryos lacking Semaphorin-PlexinD1 signaling (right) have too many sprouts, with incorrect positioning.

Zygmunt, T., Gay, C., Blondelle, J., Singh, M., Flaherty, K., Means, P., Herwig, L., Krudewig, A., Belting, H., Affolter, M., Epstein, J., & Torres-Vázquez, J. (2011). Semaphorin-PlexinD1 Signaling Limits Angiogenic Potential via the VEGF Decoy Receptor sFlt1 Developmental Cell DOI: 10.1016/j.devcel.2011.06.033
Copyright ©2011 Elsevier Ltd. All rights reserved.
... Read more »

Zygmunt, T., Gay, C., Blondelle, J., Singh, M., Flaherty, K., Means, P., Herwig, L., Krudewig, A., Belting, H., Affolter, M.... (2011) Semaphorin-PlexinD1 Signaling Limits Angiogenic Potential via the VEGF Decoy Receptor sFlt1. Developmental Cell. DOI: 10.1016/j.devcel.2011.06.033  

  • September 5, 2011
  • 01:56 AM

Why Is Facebook So Successful

by Dr Shock in Dr Shock MD PhD

Buffer Because Facebook use can evoke a positive emotional state. Researchers have esthablished these positive responses during an expirement in which they measured several psychophysiological measures. They recorded skin conductance, blood volume pulse, electroencephalogram, electromyography, respiratory activity, and pupil dilationstate. They measured these psychophysiological patterns in 30 healthy subjects during relaxation condition, showing slides of [...]

No related posts.... Read more »

  • September 4, 2011
  • 11:24 PM

Sulphur: Harbinger of life?

by Vivek Venkataraman in sciencebyte

Oldest fossilized cells ever found seem to be sulphur metabolizing bacteria... Read more »

  • September 4, 2011
  • 09:55 PM

Is It Possible to Not Judge A Book by Its Cover?

by Sam McNerney in Why We Reason

It’s an age-old aphorism preached to us by our parents, teachers, and coaches – Don’t Judge a Book By Its Cover. The lesson has manifested itself in a number of ways throughout history: Shakespeare said that all that glitters is not gold; MLK told us to judge a person not by the color of their [...]... Read more »

Darley, J., & Gross, P. (1983) A hypothesis-confirming bias in labeling effects. Journal of Personality and Social Psychology, 44(1), 20-33. DOI: 10.1037//0022-3514.44.1.20  

Rosenthal, R., & Jacobson, L. (1968) Pygmalion in the classroom. The Urban Review, 3(1), 16-20. DOI: 10.1007/BF02322211  

  • September 4, 2011
  • 09:11 AM

What explains HIV -induced pain syndrome?

by Connor Bamford in The Rule of 6ix

Does HIV-1 Tat protein induce pain in HIV/AIDS sufferers? Notice a Tat induced increase in activity when compared to control or inactivated protein. (Taken from: Chi, et al, 2011)

Pain is an extremely complicated symptom - just see the TED talk below on chronic pain, yet of the 33.4 million people currently living with HIV/AIDS worldwide, 90% will experience peripheral neuropathy - otherwise known as pain. This a general unrecognised and under-diagnosed (and under-treated) outcome of HIV infection, yet the reasons how and why the viral infection induces this are unknown, but probably are pretty complex.

Is it because of the inflammatory response? The antivirals being taken? Or, the direct effects of virus replication? While the importance of pain as a symptom of HIV/AIDS will only become more evident as this disease is further transformed into a chronic - yet manageable - illness.

HIV-1 genome organisation - one of these genes may be responsible for HIV/AIDS-associated pain. Notice Tat, expressed via splicing. (Wikipedia)

But HIV itself is not known to infect neurons (the major players in pain) during a natural infection, so how could it mess with their activity? One explanation for this is that the virus itself induces pain through interactions with the peripheral nervous system via the infection of a small number of cells associated with neurons (perivascular macrophages, microglia and astrocytes). And, maybe from this site, some effect of virus replication could damage the nearby neuronal cells, especially seeing as a number of HIV-encoded proteins have been shown to have a toxic effect on neurons. The role that these play in pain has not yet been explored.

A paper published this week in PLoS ONE (get paper here) explores the role of HIV-1 Tat protein - a protein released by infected cells and found in patients blood - on the activity of rat dorsal root ganglia neurons, which is a widely used model system for peripheral neurons and pain.

A rat dorsal root ganglion neuron - a model system for mammalian peripheral nervous system and pain. (Rick Stahl, NikonSmallWorld)

This group determined that addition of a recombinant form of tat specifically induced hyper-excitability in a dose dependent manor (independent of viral infection and other HIV proteins). It is believed that hyper-excitability or persistent firing of neurons may be experienced as pain in the sufferer. This effect was traced to a down-regulation of mRNA levels of cdk5 (a regulator of neuron activity) and its activator, p53 while knock-down of cdk5 appeared to induce the same kind of hyper-activity in these neurons. Tat may also induce greater levels of cell-death upon treatment.
The model put forward from this investigation appears to be that following HIV acquisition, the virus infects resident non-neuronal cells among the peripheral nervous system (lying close by to neurons). From here, tat is released into the space surrounding the cells and binds to - and interacts with - the neurons causing excitability and associated pain, and possibly cell death.
To further test if this hypothesis is correct, work will have to be completed with actual HIV and not just addition of tat protein. Cells could be pre-infected with the virus and then added alongside the neurons to see whether secreted, HIV tat functioned the same. Or an in vivo model of tat/neuron interaction could be used. This also gives us some clues as to a possible anti-pain treatment through blocking of Tat activity.
Chi, X., Amet, T., Byrd, D., Chang, K., Shah, K., Hu, N., Grantham, A., Hu, S., Duan, J., Tao, F., N... Read more »

  • September 3, 2011
  • 07:33 PM

Storms Inside Storms: How Hurricanes Spawn Tornadoes

by Paige Brown in From The Lab Bench

As Tropical Storm Lee makes landfall over the Louisiana coast and moves inland into southeast Louisiana, Mississippi, and Alabama, primary concerns include extensive flooding and damage from looming tornado weather. Tropical cyclones, or hurricanes, actually produce conditions amenable to tornado genesis.... Read more »

McCaul, E. W., Jr., D.E.Buechler, S.J.Goodman, and M.Cammarata. (2004) Doppler radar and lightning network observations of a severe outbreak of tropical cyclone tornadoes. Mon. Wea. Rev. info:/

  • September 3, 2011
  • 04:34 PM

DNA of the Black Death at East Smithfield, London

by Michelle Ziegler in Contagions

It seems as though every couple of months a new paper is published reporting Yersinia pestis DNA from ancient remains. This week brought the latest installment from London’s East Smithfield Black Death cemetery. This cemetery holds a special place in the scientific investigations of the Black Death because it is so well documented as being [...]... Read more »

Schuenemann, V., Bos, K., DeWitte, S., Schmedes, S., Jamieson, J., Mittnik, A., Forrest, S., Coombes, B., Wood, J., Earn, D.... (2011) PNAS Plus: Targeted enrichment of ancient pathogens yielding the pPCP1 plasmid of Yersinia pestis from victims of the Black Death. Proceedings of the National Academy of Sciences. DOI: 10.1073/pnas.1105107108  

  • September 3, 2011
  • 04:22 PM

Global Warming: Separating the noise from the signal

by Greg Laden in Greg Laden's Blog

A small "Signal-to-Noise Ratio" means that there is not enough real information (signal) compared to the background noise to make a definitive statement about something. With a sufficiently high Signal-to-Noise Ratio, it is possible to make statistically valid statements about some measure or observation. This applies to a lot of day to day decisions you make in life.

Climate change denialists understand this principle and they use it to try to fool people into thinking that "the jury is still out" on Global Warming, or that scientists are making up their data, and so on. Here, I want to explain very clearly what a Signal-to-Noise Ratio is and now it works in a totally understandable way; What this means for understanding Global Climate Change (in particular, warming); and to point you to an excellent paper ("Separating Signal and Noise in Atmospheric Temperature Changes: The Importance of Timescale") about to be published by Ben Santer and several other authors. Sander's paper effectively puts an end to Climate Change denialists misuse of data which has come to be known as "cherry picking" but that I prefer to call "dishonesty." Read the rest of this post... | Read the comments on this post...... Read more »

Santer, B., Karl, T., Lanzante, J., Meehl, G., Stott, P., Taylor, K., Thorne, P., Wehner, M., Wentz, F., Mears, C.... (2011) Separating Signal and Noise in Atmospheric Temperature Changes: The Importance of Timescale. Journal of Geophysical Research. DOI: 10.1029/2011JD016263  

  • September 3, 2011
  • 04:18 PM

Fruit and ketoacidosis

by Lucas Tafur in Ketotic

Ketoacidosis associated with fruitarianism.... Read more »

Causso C, Arrieta F, Hernández J, Botella-Carretero JI, Muro M, Puerta C, Balsa JA, Zamarron I, & Vázquez C. (2010) Severe ketoacidosis secondary to starvation in a frutarian patient. Nutricion hospitalaria : organo oficial de la Sociedad Espanola de Nutricion Parenteral y Enteral, 25(6), 1049-52. PMID: 21519781  

  • September 3, 2011
  • 12:56 PM

Do Cosmic Rays Cause Global Warming?

by Joel Rein in Moth Eyes

How do you make a cloud? Well, first you start with an aerosol particle, a small particle around which the much larger cloud condensation nuclei (CCNs) can condense. It takes a large CCN – at least 100 nanometres in size – for water vapour to be able to condense from water vapour. Clouds are made [...]... Read more »

Kirkby, J., Curtius, J., Almeida, J., Dunne, E., Duplissy, J., Ehrhart, S., Franchin, A., Gagné, S., Ickes, L., Kürten, A.... (2011) Role of sulphuric acid, ammonia and galactic cosmic rays in atmospheric aerosol nucleation. Nature, 476(7361), 429-433. DOI: 10.1038/nature10343  

  • September 3, 2011
  • 09:57 AM

Conservation and industry side by side

by Rebecca Nesbit in The birds, the bees and feeding the world

A paper published this month by researchers from the University of Alberta (Canada) looked at a trade-off between proposed industrial developments and protecting habitats the industry would destroy.

How you choose which areas of land to preserve is a much-debated issue. In this paper they worked on the premise that by protecting every ecosystem type in the area most species will have their needs met.
... Read more »

  • September 3, 2011
  • 08:19 AM

iPS and SMA

by Eva Amsen in Blogging for Science Online London

Intro/background: This is a post written as part of the Science Online London blogging workshop, which I am using to show how to embed media into a WordPress blog post and how to collaborate. The theme of the conference workshops is “spinal muscular atrophy”, and this post briefly explains how induced pluripotent stem cells can [...]... Read more »

Ebert, A., Yu, J., Rose, F., Mattis, V., Lorson, C., Thomson, J., & Svendsen, C. (2008) Induced pluripotent stem cells from a spinal muscular atrophy patient. Nature, 457(7227), 277-280. DOI: 10.1038/nature07677  

Makhortova, N., Hayhurst, M., Cerqueira, A., Sinor-Anderson, A., Zhao, W., Heiser, P., Arvanites, A., Davidow, L., Waldon, Z., Steen, J.... (2011) A screen for regulators of survival of motor neuron protein levels. Nature Chemical Biology, 7(8), 544-552. DOI: 10.1038/nchembio.595  

  • September 3, 2011
  • 08:00 AM

Antidepressants – Who’s Prescribing What

by Jennifer Gibson, PharmD in Brain Blogger

Antidepressant medications are among the most commonly prescribed drugs in the United States – one of the top three, depending on who is counting — owing to a dramatic rise in antidepressant use in the last 10 to 15 years. A new health policy report finds, however, that this increase in antidepressant use is driven [...]... Read more »

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