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  • December 24, 2010
  • 07:47 AM
  • 747 views

Fried food may cause diabetes in thin people too.

by ABK in Environment and Health

A Taiwanese research group published on the effects of high oxidized frying oil on insulin secretion (reduces insulin secretion)in 2007. In this study they (Chiang et al. 2010) attempt to determine the cause by experimenting with mice. They used three treatment groups: Low Fat DietHigh Fat DietHigh Oxidized Frying Oil Diet. The mice fed high oxidized frying oil exhibited reduced insulin secretion and high blood glucose levels. Very important here: their islets of langerhans (the tissue that produces insulin, as well as glucagon) showed evidence of oxidative damage. Glucagon and insulin work together to keep blood sugar stable. It seems likely that oxidative damage would occur throughout the body, so its probably best to avoid fried food even if diabetes or metabolic syndrome is not one of your concerns. The High Fat diet mice did not show such changes. This implies that a diet high in fried food may put people at risk of diabetes or metabolic disorder by interfering with production of hormones regulating blood sugar, while a high fat diet of unoxidized oil might be just fine. Vitamin E is an important anti-oxidant and is protective against the effects of High Oxidized Frying Oil. Chiang et al. found that adding Vitamin E to the diet reduced the effects of the Oxidized Fat diet. Thanks to all for their hard work.Ya-Fan Chiang, Huey-Mei Shaw, Mei-Fang Yang, Chih-Yang Huang, Cheng-Hsien Hsieh and Pei-Min Chao (2010). Dietary oxidised frying oil causes oxidative damage of pancreatic islets and impairment of insulin secretion, effects associated with vitamin E deficiency British Journal of Nutrition : 10.1017/S0007114510005039Chao, P., Huang, H., Liao, C., Huang, S., & Huang, C. (2007). A high oxidised frying oil content diet is less adipogenic, but induces glucose intolerance in rodents British Journal of Nutrition, 98 (01) DOI: 10.1017/S000711450769000X... Read more »

Ya-Fan Chiang, Huey-Mei Shaw, Mei-Fang Yang, Chih-Yang Huang, Cheng-Hsien Hsieh and Pei-Min Chao. (2010) Dietary oxidised frying oil causes oxidative damage of pancreatic islets and impairment of insulin secretion, effects associated with vitamin E deficiency. British Journal of Nutrition. info:/10.1017/S0007114510005039

  • December 24, 2010
  • 07:34 AM
  • 1,227 views

Levels of evolution

by Lab Rat in Lab Rat

Eukaryotes - animals, plants, and other creatures with a nucleus, evolve relatively slowely. Genetic variation occurs through changes in the DNA between generations; each offspring will be a genetic product of their parents and nothing else. Genetic changes happen down the generations. In bacteria, however, everything is a little more insane. Because bacteria can change DNA with almost any other bacteria they come accross, there is less of a conserved genetic record. Genes are flying around all over the place which can make it very difficult to seperate bacteria into neat taxonomic groups.It's helped by the fact that bacterial genomes aren't completely random, and can usually be seperated into 'core' genes and 'accessory' genes. Core genes are most useful to taxonomists as they show what the bacterial species actually is, and where it sits within molecular phylogeny. The accessory genes are more interesting to bacteriologists as the play a more significant role in phenotypic differences and determin what the bacteria do. Paradoxically, the accessory genes are also the ones used most in adaption (think of antibiotic resistance) and are therefore more likely to be evolutionarily selected for or against. These accessory genes are often found in specific 'hypervariable' regions of the genome called genomic islands.Cartoon by Nick Kim, www.nearingzero.netThe increase in second-generation sequencing technologies opened up the ability for large scale comparitive-genomics studies; essentially sequencing huge numbers of bacterial genomes and then comparing them all to each other. Back in the day, population studies were done using an approach known as MultiLocus Sequence Typing (MLST) - which took seven core genes and sequenced those for each bacteria. Nowadays you can sequences all the parts of the genome you need in hundreds of different strains.As with most new microbiology technologies, these new techniques are initially being applied to human pathogens, as human pathogen research is (rightly) where most of the money is. Using wholescale sequencing technologies on pathogens such as Clostridium difficile which has high levels of antibiotic resistance. The grand aim is to try and understand both the extent and the distribution of natural genomic variation between one bacterial species. This could help to understand what roles are played by bacterial migrations, recombinations (switching DNA around), active selection and drift in the spread of antibiotic resistance.C. difficile is a very genetically diverse species which has been evolving for the last 1.8 million years. As each bacteria is likely to replicate at least once a day, this allows for a huge amount of change and genetic variation. It might be suspected that the virulent species is formed from a single offshoot, one bacteria that became virulent and then passed that ability onto its offspring but instead it looks like virulence arose in many different lineages, most likely through horizontal gene transfer. This means that each different virulent strain is likely to show a relatively large amount of variation in the rest of its genome.It isn't just small bits of DNA on separate plasmids that C. difficile can exchange, they can also carry out homologous recombination, a process by which whole sections of the bacterial genome can be cut out and shared between related species. This process is aided by the presence of 'mobile elements' within the genome, i.e pieces of DNA which are particularly good at jumping around and splicing themselves in and out of bacterial chromosomes. It turns out that the C. difficile genome contains lots of mobile elements.From a bacteriologists point of view this is a fascinating example of just how variable a single strain of bacterial species can be. From a medical viewpoint it's more worrying. The ability of highly virulent bacteria to chop out large portions of their genome and pass them onto other, potentially non-virulent strains could help to spread not just antibiotic resistance, but also other tricks like biofilm formation and different enzymes which help the bacteria to cope with antibiotic challenges.Not only that but it means that every gene in the genome has been tried and tested by many different strains in many different conditions. They aren't just good genes for the bacteria to be hanging onto. They're the best.---He, M., Sebaihia, M., Lawley, T., Stabler, R., Dawson, L., Martin, M., Holt, K., Seth-Smith, H., Quail, M., Rance, R., Brooks, K., Churcher, C., Harris, D., Bentley, S., Burrows, C., Clark, L., Corton, C., Murray, V., Rose, G., Thurston, S., van Tonder, A., Walker, D., Wren, B., Dougan, G., & Parkhill, J. (2010). Evolutionary dynamics of Clostridium difficile over short and long time scales Proceedings of the National Academy of Sciences, 107 (16), 7527-7532 DOI: 10.1073/pnas.0914322107... Read more »

He, M., Sebaihia, M., Lawley, T., Stabler, R., Dawson, L., Martin, M., Holt, K., Seth-Smith, H., Quail, M., Rance, R.... (2010) Evolutionary dynamics of Clostridium difficile over short and long time scales. Proceedings of the National Academy of Sciences, 107(16), 7527-7532. DOI: 10.1073/pnas.0914322107  

  • December 24, 2010
  • 07:07 AM
  • 1,698 views

Simple Jury Persuasion: Are those folks in the jury box thinkers or feelers?

by Rita Handrich in The Jury Room

Here’s a nice and very simple persuasion tactic first presented at PsyBlog in their ongoing series on 10 forms of persuasion. They cite the recent work of Nicole Mayer & Zakary Tormala (2010) and discuss the natural tendency we have to see the world (and thus describe it) via either thinking (useless or useful) or [...]


Related posts:Simple Jury Persuasion: I’m too smart to fall for that!
Simple Jury Persuasion: You may want to disagree with this post
Simple Jury Persuasion: Don’t confuse argument with persuasion
... Read more »

Mayer ND, & Tormala ZL. (2010) "Think" versus "feel" framing effects in persuasion. Personality and social psychology bulletin, 36(4), 443-54. PMID: 20363901  

  • December 24, 2010
  • 07:00 AM
  • 722 views

Love Can Alleviate Pain

by Shaheen Lakhan in Brain Blogger

The early stages of a new, romantic relationship are associated with feelings of euphoria, which likely arise from brain mechanisms responsible for sensations of pleasure or reward. Imaging studies have shown that viewing pictures of a new, romantic partner elicits brain activity in multiple reward processing centers in the brain. Interestingly, these findings have now [...]... Read more »

Kelley AE, & Berridge KC. (2002) The neuroscience of natural rewards: relevance to addictive drugs. The Journal of neuroscience : the official journal of the Society for Neuroscience, 22(9), 3306-11. PMID: 11978804  

Master SL, Eisenberger NI, Taylor SE, Naliboff BD, Shirinyan D, & Lieberman MD. (2009) A picture's worth: partner photographs reduce experimentally induced pain. Psychological science : a journal of the American Psychological Society / APS, 20(11), 1316-8. PMID: 19788531  

  • December 24, 2010
  • 06:15 AM
  • 1,007 views

Dark energy as theoretical entity

by Jörg Friedrich in Reading Nature

Dark matter and dark energy are typical examples of what is known in the philosophy of science as “theoretical entity”: elements of theories, whose existence is hypothesized and their assumed properties and behaviours can be used for explanation of the … Continue reading →... Read more »

  • December 24, 2010
  • 05:47 AM
  • 426 views

Placebos - now with added ethics!

by Richard Morrisroe in DisgruntledPhD

Placebo effects can be induced in patients without deception, according to a new study in PLoS One. The study was an open label (no blinding for patients) single blind (the investigators did not know which treatment participants were given) controlled trial in 80 people suffering from Irritable Bowel Syndrome. The patients were followed for one month, with a baseline, end and midpoint assessment. According to validated self report measures for the syndrome, the patients who were given the pill improved much more than the patients who received no treatment. Its important to note that the groups were randomised, and they were also matched in the amount of interaction they had with the medical providers.An interesting point in the study (which doesn't appear to have been picked up by other science bloggers) is that some of the patients (N=17) also received counterbalanced provider interaction - they saw a male doctor once, and and also a female nurse. Contrary to some conceptions of the authority of the provider having an impact on the response to treatment, there were no differences in outcome which could be attributed to this difference. Given the small number of patients in this group, thats not very surprising. I really wish this trial had gone the whole hog and randomised everyone to see both practitioners, as that might have provided some very useful data. Open-label placebo produced significantly higher mean (±SD) global improvement scores (IBS-GIS) at both 11-day midpoint (5.2±1.0 vs. 4.0±1.1, p<.001) and at 21-day endpoint (5.0±1.5 vs. 3.9±1.3, p = .002). Significant results were also observed at both time points for reduced symptom severity (IBS-SSS, p = .008 and p = .03) and adequate relief (IBS-AR, p = .02 and p = .03); and a trend favoring open-label placebo was observed for quality of life (IBS-QoL) at the 21-day endpoint (p = .08). The above is from the finding section of the abstract, but it cogently sums up the major findings of the study. Now, there are a number of important caveats to the straightforward interpretation of the study. There are also a number of interesting implications arising from both the study, and the reactions of some of the better known science bloggers. My first issue with this study is the number of statistical analyses which were carried out, with only 80 participants and at least ten significance tests reported in the article (and probably more which were not reported), the authors probably should have corrected for multiple tests (the most popular approach is to divided the required p value by the number of tests). That being said, this was a pilot study, so the results will require replication in a larger trial which would ideally have a protocol with details of analyses to be carried out published beforehand (what can i say, I'm an optimist). Orac, (of respectful insolence fame) critiqued this study on a number of grounds. The first was (he claimed) a failure of randomisation. He based this on the numbers with each type of IBS (diarrhea or constipation primary) and argued that this could be responsible for the observed improvement. While i do take his point, i would suggest to my readers (all three of you) to look at the Table itself published in the article. Now, it can be seen from the table that indeed the groups did not appear matched on type of IBS.However, if you look a little more closely in the table, it can be seen that the open label group had a longer mean duration of IBS,  a higher initial mean symptom severity score, and a lower initial quality of life. If anything, if there was no change over the course of the trial, then the no treatment group should have come out superior.  Given that only stable IBS patients were admitted into the study (look at the confidence intervals for the lenght of time with IBS) it seems unlikely that regression to the mean could account for these results.The effect size for the mean difference between groups at the end of the study was d=.79, which is a large effect by anyone's standards (see the pun? you're a nerd if you do). To explain the effect size measure, its a difference in standard deviations, and one standard deviation is the difference between your high school teacher and Einstein, as measured by IQ (assuming an IQ for the teacher of 115 and giving Einstein 130).This is not a small difference, and yet Ed Yong reports that Edward Ernst claims this is too small to be clinically significant, which makes me wonder what effect sizes he sees in everyday practice, cos thats a large effect to me (I'd kill for an effect size that large, i'd get t-shirts printed and everything). Orac also takes the research to task for deception, as the placebo pills were described as empty sigar pills which have been proven in rigorous clinical testing to have an impact on self healing processes. He claims that this is the worst deception of all, far nastier than those involved in ordinary Randomised trials. Frankly, i don't agree. There have been a number of meta-analyses  conducted on the placebo, as well as re-analyses of data from many, many clinical trials, and what participants were told was not a deception, unless telling people about what clinical trials have shown about any medical treatment is a deception. So, i really dont see why this bothers him. Orac also uses guilt by association as he notes that the study was funded by the National Council for Complementary and Alternative Medicine, but i believe that argument is beneath any self respecting scientist so I'll ignore it.PaiMD also takes note of the study, and claims that what was compared here was one non biological treatment against another. I would disagree, what this trial shows is that care and some kind of medical ritual (take these pills two times daily) are much better in combination than they are apart. That, to me, is perhaps the most interesting finding of this study.Something which may also interests students of the placebo was the theoretical implications of this study. I've talked elsewhere about theories of placebo, and briefly i think that this study shows that the effects of expectancies are subservient to those of ritual. This is a clear mark in favour of Hyland's theory of motivational concordance, which basically holds that placebo effects arise from what we do that we find meaningful, rather than what we think (or expect) about a treatment. See the link to my previous post on theories if you'd like a more in depth discussion of the theoretical approaches in the field.One brief detail that i would like to know more about in the study is how many pills the open label group took, and whether those who overdosed got more benefit. The authors note that a pill count was taken, but they do not report the results of this measure, which is a shame. This measure would have been especially great as it could be modelled as a Poisson variable (for count data) and then demographics and other measures collected could have been regressed against it to understand the causes and correlates of this interesting variable a little better.Now, my own thoughts on the future of this line of research are as follows: it will be difficult to replicate this effect when a drug is being used in the study. This seems intuitive to me, given that the meaning of getting placebo or drug is very different from the meaning of getting placebo or no treatment. Mind you, I hope I'm wrong here. An interesting line of research which bears upon this study is the work using the balanced placebo design. Essentially, this work combines the drug and placebo arms of your standard clinical trial with two deceptive conditions, where the participant is told they get a drug but get placebo and vice versa.I personally would find a replication of this study using that design to be far more interesting (though ethically challenging) as the effects of placebo-placebo condition could be contrasted with the others. Again, this is probably just a pipe dream, but if ever have enough funding, i'd like to make this happen.One way in which these findings can be explained is as follows. I've spoken before about the effects of self monitoring of internal processes on the placebo effect (essentially, it increases them). It may be that the open label group, while taking the pills paid more attention to their bodies, and this attention increased their self healing processes (which is all the placebo effect really is). This work on somatic awareness also ties into the results of a recent meta-analysis on in what conditions the placebo is effective Just a thought, probably needs a little more refining into a useful predictive theory.Anyway, thanks for reading. You may have noted that I haven't really talked that much about the paper itself. Its is PLos One, which is free to everyone, and its very clearly and engagingly written, so... Read more »

Kaptchuk, T., Friedlander, E., Kelley, J., Sanchez, M., Kokkotou, E., Singer, J., Kowalczykowski, M., Miller, F., Kirsch, I., & Lembo, A. (2010) Placebos without Deception: A Randomized Controlled Trial in Irritable Bowel Syndrome. PLoS ONE, 5(12). DOI: 10.1371/journal.pone.0015591  

  • December 23, 2010
  • 11:12 PM
  • 558 views

Walls

by teofilo in Gambler's House

Sand Canyon Pueblo, which I discussed in the previous post, is one of the best-known prehistoric communities in the Southwest due to the multi-year research program conducted there by Crow Canyon Archaeological Center in the 1980s and 1990s.  Crow Canyon selected it for this research for a variety of reasons, including its short period of [...]... Read more »

  • December 23, 2010
  • 09:08 PM
  • 1,201 views

Three Cheers for Failure!

by David Berreby in Mind Matters


Last week I vowed to pay more attention to replication in psychology experiments. Repeated experiments are an important test of whether a finding is "really out there" or an accident, so, as a number of psychologists have been saying lately to the public, it is kind of a problem that many ...Read More
... Read more »

Jennifer V. Fayard, Amandeep K. Bassi, Daniel M. Bernstein, & Brent W. Roberts. (2009) Is cleanliness next to godliness? Dispelling old wives’ tales: Failure to replicate Zhong and Liljenquist (2006). Journal of Articles in Support of the Null Hypothesis, 6(2), 21-29. info:other/1539-8714

  • December 23, 2010
  • 08:34 PM
  • 1,231 views

You wouldn’t lie to me, would you?

by PalMD in White Coat Underground

“Fake Pills Can Work, Even If Patients Know It” “Irritable Bowel Syndrome: Placebo Works Even if Patients Know” “Knowingly taking a placebo helps, study finds” “Sugar Pills Work Even When People Know They Are Fake” That’s just a sample of the headlines accompanying a new study on placebos published in PLoS ONE.  The study attempts [...]... Read more »

Kaptchuk, T., Friedlander, E., Kelley, J., Sanchez, M., Kokkotou, E., Singer, J., Kowalczykowski, M., Miller, F., Kirsch, I., & Lembo, A. (2010) Placebos without Deception: A Randomized Controlled Trial in Irritable Bowel Syndrome. PLoS ONE, 5(12). DOI: 10.1371/journal.pone.0015591  

  • December 23, 2010
  • 07:18 PM
  • 1,192 views

How to make a transistor based on electron spin

by Joerg Heber in All That Matters

Last week I blogged about the potential of using the magnetic properties of an electron, its spin, for novel electronics. And already this week we have come a step further towards spin electronics through the demonstration of a spin-based transistor device! In spin electronics, it is the spin of the electron and not its electrical [...]... Read more »

Datta, S., & Das, B. (1990) Electronic analog of the electro-optic modulator. Applied Physics Letters, 56(7), 665. DOI: 10.1063/1.102730  

Wunderlich, J., Park, B., Irvine, A., Zarbo, L., Rozkotova, E., Nemec, P., Novak, V., Sinova, J., & Jungwirth, T. (2010) Spin Hall Effect Transistor. Science, 330(6012), 1801-1804. DOI: 10.1126/science.1195816  

  • December 23, 2010
  • 05:13 PM
  • 869 views

Magical thinking enhances creativity

by Tom Rees in Epiphenom

It's tough being an atheist dad at Christmas. I mean, the kids love the all the stories, the sense of drama, the sense of community and of being part of something big. They also love to think they have a magical friend who cares about them and watches over them.

But I still feel awkward looking them in the eyes and telling them that Santa is real. I guess it's the incorrigible rationalist in me. Arty types probably have it easier.

Well, here's a study that I was hoping would salve my conscience over all the porkies I've told my kids over the years. Unfortunately it doesn't quite do that. Let me explain...

Eugene Subbotsky, a psychologist at the University of Lancaster in the UK, wanted to know whether encouraging kids to think about magic would actually help them to be more creative. We know that kids are often delighted by magical thoughts, but we don't know if they are just a byproduct (an, ahem, epiphenomenon) or if they are actually contribute to their mental development in some way.

Basically, he set groups of kids down to watch clips from Harry Potter film (the first one). These clips either contained magical elements, or they did not. Before and after, they tested the kids creative powers using some standard setups (problem solving, drawing creatively, etc).

Subbotsky found that kids who watched magical scenes did actually think more creatively. The effect was quite marked. Although both groups improved, the improvement in the 'no magic' group was around 50%, whereas it doubled in the 'magical scenes' group.

Unfortunately, the results are complicated by the fact that the groups weren't matched at the start of the experiment. The kids were put into groups at random - which is the gold standard method, and is supposed to ensure that the groups are similar. For this experiment, it didn't work out. The kids in the 'magical scenes' group were actually less creative than the kids in the other group.

Although you can control for that statistically (and he did), you're left wondering if whether what you're seeing here is simply regression to the mean.

Subbotsky also showed that, although creativity increased, magical beliefs didn't. Well, actually, they did - by the end of the experiment the kids in the 'magical scenes' group were averaging around 50% higher on the magical beliefs scoring. It's just that the difference was not statistically significant.

Subbotsky concludes that watching magical scenes can increase children's creativity without increasing their magical beliefs. I'm not so convinced, based on the evidence shown.

But go ahead, bring the magic of Christmas to your kids, even if you are a stoney-hearted rationalist. It may, after all, boost their creativity!

Oh, and Merry Christmas everyone!

Subbotsky E, Hysted C, & Jones N (2010). Watching films with magical content facilitates creativity in children. Perceptual and motor skills, 111 (1), 261-77 PMID: 21058605

This article by Tom Rees was first published on Epiphenom. It is licensed under Creative Commons.

... Read more »

Subbotsky E, Hysted C, & Jones N. (2010) Watching films with magical content facilitates creativity in children. Perceptual and motor skills, 111(1), 261-77. PMID: 21058605  

  • December 23, 2010
  • 03:11 PM
  • 1,355 views

Comparison of various DNA-Seq library prep methods

by epibio in EpiCentral

Adey et al. (in the laboratory of Jay Shendure, University of Washington) recently published a methods paper characterizing various library prep technologies for high-throughput DNA sequencing, including Epicentre’s Nextera™ technology. The publication highlights recent advances in DNA library preparation for next-generation sequencing, in order to overcome the bottleneck posed by earlier methods, i.e., labor, time, and lack of automation.

With Nextera technology, it is now possible to prepare literally hundreds of libraries in a day.  With respect to bias, the authors state: 
Comparison to conventional methods of library preparation, relying on mechanical or endonuclease fragmentation, finds that although transposase-catalyzed adaptor insertion demonstrates a slightly greater insertion bias, this has little impact at the level of genomic coverage, and is offset by large advantages with respect to speed, simplicity, and low input requirements. As described in the paper, the Nextera system is highly versatile, and can be adapted to multiple applications. These include library preparation from as little as 10 pg DNA, exome capture, PCR-free and colony PCR library preparation, and sample prep automation.

Adey, A. et al. (2010). Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition Genome Biology, 11 (12) DOI: 10.1186/gb-2010-11-12-r119... Read more »

  • December 23, 2010
  • 11:56 AM
  • 2,371 views

I’m Bringing Home my Baby Bumble-Bee!

by John Carroll in Chronicles of Zostera


Won’t my mommy be so proud of me?
For a group of 8-10 year olds from an English elementary school, a group of parents are proud.  Why? Because their sons and daughters produced a science project whose results were published in the most recent issue of Biological Bulletin, a fairly prestigious accomplishment even for scientists who do . . . → Read More: I’m Bringing Home my Baby Bumble-Bee!... Read more »

Blackawton, P., Airzee, S., Allen, A., Baker, S., Berrow, A., Blair, C., Churchill, M., Coles, J., Cumming, R., Fraquelli, L.... (2010) Blackawton bees. Biology Letters. DOI: 10.1098/rsbl.2010.1056  

  • December 23, 2010
  • 11:24 AM
  • 638 views

What Killed Alaska’s Dinosaurs?

by Brian Switek in Dinosaur Tracking

In northern Alaska, along the banks of the Colville River, a series of fossil bonebeds preserve remnants of the Late Cretaceous world. These ancient environments were quite different from those found farther south. Even though the climate of Cretaceous Alaska was warmer than that of today, areas near the Colville River deposits were cold enough [...]... Read more »

  • December 23, 2010
  • 11:11 AM
  • 1,719 views

Presents for the holidays – Plant pathogen genomes

by stajich in The Hyphal Tip

Though a bit cliche, I think the metaphor of “presents under the tree” of some new plant pathogen genomes summarized in 4 recent publications is still too good to resist.  There are 4 papers in this week’s Science that will certainly make a collection of plant pathogen biologists very happy. There are also treats for the [...]... Read more »

Baxter, L., Tripathy, S., Ishaque, N., Boot, N., Cabral, A., Kemen, E., Thines, M., Ah-Fong, A., Anderson, R., Badejoko, W.... (2010) Signatures of Adaptation to Obligate Biotrophy in the Hyaloperonospora arabidopsidis Genome. Science, 330(6010), 1549-1551. DOI: 10.1126/science.1195203  

Spanu, P., Abbott, J., Amselem, J., Burgis, T., Soanes, D., Stuber, K., Loren van Themaat, E., Brown, J., Butcher, S., Gurr, S.... (2010) Genome Expansion and Gene Loss in Powdery Mildew Fungi Reveal Tradeoffs in Extreme Parasitism. Science, 330(6010), 1543-1546. DOI: 10.1126/science.1194573  

Raffaele, S., Farrer, R., Cano, L., Studholme, D., MacLean, D., Thines, M., Jiang, R., Zody, M., Kunjeti, S., Donofrio, N.... (2010) Genome Evolution Following Host Jumps in the Irish Potato Famine Pathogen Lineage. Science, 330(6010), 1540-1543. DOI: 10.1126/science.1193070  

Schirawski, J., Mannhaupt, G., Munch, K., Brefort, T., Schipper, K., Doehlemann, G., Di Stasio, M., Rossel, N., Mendoza-Mendoza, A., Pester, D.... (2010) Pathogenicity Determinants in Smut Fungi Revealed by Genome Comparison. Science, 330(6010), 1546-1548. DOI: 10.1126/science.1195330  

  • December 23, 2010
  • 10:59 AM
  • 884 views

Depression Treatment Increased From 1998 to 2007

by Neuroskeptic in Neuroskeptic

A paper just out reports on the changing patterns of treatment for depression in the USA, over the period from 1998 to 2007.The headline news is that increased: the overall rate of people treated for some form of "depression" went from 2.37% to 2.88% per year. That's an increase of 21%, which is not trivial, but it's much less than the increase in the previous decade: it was just 0.73% in 1987.But the increase was concentrated in some groups of people.Americans over 50 accounted for the bulk of the rise. Their use went up by about 50%, while rates in younger people stayed almost steady. In '98 the peak age band was 35-49, now it's 50-64, with almost 5% of those people getting treated in any given year.Men's rates of treatment went up by over 40% while women's only increased by 10%. Women are still more likely to get treated for depression than men, though, with a ratio of 1.7 women for each 1 man. But that ratio is a lot closer than it used to be.Black people's rates increased hugely, by 120%. Rates in black people now stand at 2.2% which is close behind whites at 3.2%. Hispanics are now the least treated major ethnic group at 1.9%: in previous studies, blacks were the least treated. (There was no data on Asians or others).So the increase wasn't an across the board rise, as we saw from 1985 to 1995. Rather the '98-'07 increase was more of a "catching up" by people who've historically had low levels of treatment, closing in on the level of the historically highest group: middle-aged white women.In terms of what treatments people got, out of everyone treated for depression, 80% got some kind of drugs, and that didn't change much. But use of psychotherapy declined a bit from 54% to 43% (some people got both).What's also interesting is that the same authors reported last year that, over pretty much the same time period ('96 to '05), the number of Americans who used antidepressants in any given year sky-rocketed from 5% to 10% - that is to say, much faster than the rate of depression treatment rose! And the data are comparable, because they came from the same national MEPS surveys.In other words, the decade must have seen antidepressants increasingly being used to treat stuff other than depression. What stuff? Well, all kinds of things. SSRIs are popular in everything from anxiety and OCD to premature ejaculation. Several of the "other new" drugs, like mirtazapine and trazodone, are very good at putting you to sleep (rather too good, some users would say...)Marcus SC, & Olfson M (2010). National trends in the treatment for depression from 1998 to 2007. Archives of general psychiatry, 67 (12), 1265-73 PMID: 21135326... Read more »

Marcus SC, & Olfson M. (2010) National trends in the treatment for depression from 1998 to 2007. Archives of general psychiatry, 67(12), 1265-73. PMID: 21135326  

  • December 23, 2010
  • 09:43 AM
  • 832 views

What Makes a Face Look Alive? Video

by APS Daily Observations in Daily Observations

No matter how good technology is, we can often tell the difference between a human face and an animated face. Being able to tell the difference allows us to pay ... Read more »

  • December 23, 2010
  • 09:43 AM
  • 967 views

Top-down vs bottom-up approaches to cognition: Griffiths vs McClelland

by Sean Roberts in A Replicated Typo 2.0

Two articles to be published in Trends in Cognitive Sciences debate the merits of approaching cognition from different ends of the microscope. The central issue is which approach is the most productive for explaining phenomena in cognition. Structured probabilistic takes a 'top-down' approach while Emergentism takes a 'bottom-up' approach.... Read more »

Griffiths, T., Chater, N., Kemp, C., Perfors, A., & Tenenbaum, J. (2010) Probabilistic models of cognition: exploring representations and inductive biases. Trends in Cognitive Sciences, 14(8), 357-364. DOI: 10.1016/j.tics.2010.05.004  

McClelland, J., Botvinick, M., Noelle, D., Plaut, D., Rogers, T., Seidenberg, M., & Smith, L. (2010) Letting structure emerge: connectionist and dynamical systems approaches to cognition. Trends in Cognitive Sciences, 14(8), 348-356. DOI: 10.1016/j.tics.2010.06.002  

Zeil J, Hofmann MI, & Chahl JS. (2003) Catchment areas of panoramic snapshots in outdoor scenes. Journal of the Optical Society of America. A, Optics, image science, and vision, 20(3), 450-69. PMID: 12630831  

  • December 23, 2010
  • 08:54 AM
  • 656 views

an instance of misconstrued media reporting: placebos

by Ragamuffin in How We Are Hungry

A most recent example of the media mis-representing scientific findings is the recent NPR report on placebos being equally effective in IBS patients as "the strongest prescription drugs", even when the patients knew that they were being given the placebo. This coverage was a translation of a study out of Harvard Medical, and published in PLoS ONE.... Read more »

Ted J. Kaptchuk, Elizabeth Friedlander, John M. Kelley, M. Norma Sanchez, Efi Kokkotou, Joyce P. Singer, Magda Kowalczykowski, Franklin G. Miller, Irving Kirsch, Anthony J. Lembo. (2010) Placebos without Deception: A Randomized Controlled Trial in Irritable Bowel Syndrome. PLoS. info:/

  • December 23, 2010
  • 08:10 AM
  • 756 views

Autoimmune disease and inhalation of particulates

by ABK in Environment and Health

Airborne particulate matter appears to increase risk of diabetes, as discussed a few posts down and diabetics appear to have altered immune function according to a number of parameters. Diabetics have now been observed to have stronger indicators of immune response when air pollution levels (particulate matter in this case) are high. Schneider and Alexis (2010 . . . two first authors, congratulations all) observed increased blood levels of endogenous promotors of Activated Protein C Resistance. Diabetics who were also obese, or who did not express GSTm1, (not having this, by the way, increases risk of a wide array of cancers) or who already had elevated HbA1C (this is an indicator of longer-term blood glucose levels) had the strongest response to particulate matter. So, are diabetics more vulnerable to challenges to the immune system? Do these challenges contribute to development of diabetes? Or is there an interplay in each (diabetes and immune response)alters the pattern of the other. Lets hope they don't progressively spiral over time and continued exposure. The cohort was small with only 20 subjects, but it would be interesting to look at response to particulate matter by age, or time since diagnosis of type II diabetes. Schneider A, Alexis NE, Diaz-Sanchez D, Neas LM, Harder S, Herbst MC, Cascio WE, Buse JB, Peters A, & Devlin RB (2010). Ambient PM2.5-Exposure Up-regulates the Expression of Co-Stimulatory Receptors on Circulating Monocytes in Diabetic Individuals. Environmental health perspectives PMID: 21169129... Read more »

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