Post List

  • December 23, 2010
  • 03:11 PM

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 prep........ Read more »

  • December 23, 2010
  • 11:56 AM

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

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

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

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 ........ 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

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

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

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

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 Resistanc........ Read more »

  • December 23, 2010
  • 06:24 AM

The paradigm is dead, long live the paradigm!

by Razib Khan in Gene Expression

Mitochondrial DNA and human evolution: Mitochondrial DNA from 147 people, drawn from five geographic populations have been analysed by restriction mapping. All these mitochondrial DMAs stem from one woman who is postulated to have lived ab7out 200,000 years ago, probably in Africa. All the populations examined except the African population have multiple origins, implying that [...]... Read more »

Reich, David, Green, Richard E., Kircher, Martin, Krause, Johannes, Patterson, Nick, Durand, Eric Y., Viola, Bence, Briggs, Adrian W., Stenzel, Udo, Johnson, Philip L. F.... (2010) Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature. info:/10.1038/nature09710

  • December 23, 2010
  • 06:00 AM

Vaccines are a pain: What to do about it

by Scott Gavura in Science-Based Medicine

As much as I support vaccines, I see the short term consequences. Vaccines can be painful. Kids don’t like them, and parents don’t like seeing their children suffer. That this transient pain is the most common consequence of gaining  protection from fatal illnesses seems like a fair trade-off to me. But that’s not the case [...]... Read more »

Taddio A, Appleton M, Bortolussi R, Chambers C, Dubey V, Halperin S, Hanrahan A, Ipp M, Lockett D, Macdonald N.... (2010) Reducing the pain of childhood vaccination: an evidence-based clinical practice guideline (summary). CMAJ : Canadian Medical Association journal , 182(18), 1989-95. PMID: 21098067  

  • December 23, 2010
  • 06:00 AM

Vaccines are a pain: What to do about it

by Scott in Science-Based Pharmacy

As much as I support vaccines, I see the short term consequences. Vaccines can be painful. Kids don’t like them, and parents don’t like seeing their children suffer. That this transient pain is the most common consequence of gaining protection from fatal illnesses seems like a fair trade-off to me. But that’s not the case [...]... Read more »

Taddio A, Appleton M, Bortolussi R, Chambers C, Dubey V, Halperin S, Hanrahan A, Ipp M, Lockett D, Macdonald N.... (2010) Reducing the pain of childhood vaccination: an evidence-based clinical practice guideline (summary). CMAJ : Canadian Medical Association journal , 182(18), 1989-95. PMID: 21098067  

  • December 23, 2010
  • 05:30 AM

Exercise 6hrs/wk for 20 years. Still gain weight. :(

by Yoni Freedhoff in Weighty Matters

I guess the good news is that you gained less weight. The bad news is if your motivation for exercising was weight loss, your 20 years of exercise not only didn't help you lose weight but your weight gain was only marginally less than your couch potato friends.What am I talking about?A study published last week in the Journal of the American Medical Association which using data from the CARDIA trial, sought to examine the relationship between exercise and weight gain over a 20 year period.3,554 ........ Read more »

Hankinson, A., Daviglus, M., Bouchard, C., Carnethon, M., Lewis, C., Schreiner, P., Liu, K., & Sidney, S. (2010) Maintaining a High Physical Activity Level Over 20 Years and Weight Gain. JAMA: The Journal of the American Medical Association, 304(23), 2603-2610. DOI: 10.1001/jama.2010.1843  

  • December 23, 2010
  • 05:24 AM

Better than sex! US college students value self-esteem boosts more than bodily pleasures

by BPS Research Digest in BPS Research Digest

'Because you're worth it!' L'Oreal's catchphrase taps into the narcissistic zeitgeist. But it also begs the question: Are we at risk of becoming obsessed with feeling good about ourselves? According to new research by Brad Bushman and his co-workers, not only do US college students have higher self-esteem than previous generations, they now value self-esteem boosts more than sex, food, receiving a salary payment, seeing a friend or having an alcoholic drink.

Bushman's team made their findi........ Read more »

  • December 23, 2010
  • 02:00 AM

Why people trying to quit smoking should avoid watching Mad Men: The influence of on-screen smoking cues

by SAGE Insight in SAGE Insight

Attentional bias in smokers: exposure to dynamic smoking cues in contemporary movies   From Journal of Psychopharmacology  Tobacco use is still prevalent in films, this study explores how people respond to on-screen smoking images by examining eye movement of smokers and non-smokers while watching a movie clip, using eye-tracking technology. This research reveals that smokers [...]... Read more »

  • December 23, 2010
  • 01:36 AM

4 Types of Internet Use among Children

by Dr Shock in Dr Shock MD PhD

Young people are high users of the Internet but we know very little about how they use the Internet, how they “are distributing their engagement across the various resources of the Internet”. This knowledge might be useful for learning and education.
Researchers collected data from a nationally representative face to face survey of young people (n=1069) [...]

Related posts:Elderly and Internet and Computer Skills, An Update
Four Types of Commonly Sought Health Information
Internet and Vid........ Read more »

  • December 23, 2010
  • 01:26 AM

The noisy brain

by Janet Kwasniak in Thoughts on thoughts

It is generally assumed, currently, that neural synchronization is the method of communication in networks of neurons involved in perception, cognition and action. In a recent paper Ward and others (citation below) have investigated the importance of stochastic resonance in this synchrony. So what is this thing called stochastic resonance?
You will eventually run into stochastic [...]... Read more »

  • December 22, 2010
  • 11:56 PM

Prehistoric Zoning

by teofilo in Gambler's House

When I was working at Chaco and would tell visitors that I was going to graduate school for city planning, most people would remark on what a difference that sounded like.  And, indeed, there are a lot of differences between my life when I was at Chaco and my life here at school in New [...]... Read more »

  • December 22, 2010
  • 11:40 PM

The ecology and geography of guppy speciation

by helikonios in The view from Helicon

And now for some more research blogging! Here’s a paper comparing the roles of geography and ecology in the early stages of speciation. I’m incredibly excited about this study because it begins to get around some of the major difficulties inherent in studying reinforcement and ecological speciation. But first let me back up and explain [...]... Read more »

  • December 22, 2010
  • 09:43 PM

Bad Metaphors Make for Bad Theories

by melodye in Child's Play

Imagine for a moment, that you have been thrown back into the Ellisonesque world of the 1980’s, with a delightful perm and even better trousers.  One fragile Monday morning, you are sitting innocently enough at your cubicle, when your boss comes to you with the summary of a report you have never read, on a [...]... Read more »

Ramscar, M.,, Yarlett, D.,, Dye, M.,, Denny, K.,, & Thorpe, K. (2010) The Effects of Feature-Label-Order and their implications for symbolic learning. Cognitive Science, 34(6), 909-957. info:/10.1111/j.1551-6709.2009.01092.x

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