Post List

  • August 5, 2010
  • 11:21 AM

Inevitability and oil, Pt. 2: the “end of oil” and human empathy

by Hannah Waters in Culturing Science – biology as relevant to us earthly beings

Never thought I’d actually get around to a Pt. 2, eh?  Well, I’ve shown you!  Here’s the first part: Inevitability and Oil, Pt. 1: the inherent risk for accidents in complex technology For decades now economists and scientists have predicted the “end of oil:” the day when we use up our oil reserves, potentially resulting [...]... Read more »

  • August 5, 2010
  • 10:13 AM

Publication Bias: Not Dead Yet

by Neuroskeptic in Neuroskeptic

Suppose you do two clinical trials of a drug, and only one of them shows it to work. It would be entirely misleading to only tell people about that one, and sweep the negative result under the carpet - but it happens.That's publication bias. A simple but powerful remedy is to require everyone to publically announce their trials before the data comes in. The USA has led the way in this, with the public database, and for several years it's been a legal requirement that all clini........ Read more »

Bourgeois FT, Murthy S, & Mandl KD. (2010) Outcome Reporting Among Drug Trials Registered in Annals of internal medicine, 153(3), 158-66. PMID: 20679560  

  • August 5, 2010
  • 10:04 AM

Humans beat computers in predicting protein structures

by The Curious Wavefunction in The Curious Wavefunction

I was going to first describe Rosetta in a post, but a rather cool paper related to the program which appeared in Nature yesterday makes me jump the gun.In a nutshell, Rosetta tries to predict the structure of proteins from amino acid sequence by inserting fragments from known protein structures and doing many rounds of side chain torsional angle and rigid-body energy optimization. It uses a scoring function to rank the resulting structures that uses empirically derived hydrogen bonding, hydroph........ Read more »

Cooper, S., Khatib, F., Treuille, A., Barbero, J., Lee, J., Beenen, M., Leaver-Fay, A., Baker, D., Popović, Z., & players, F. (2010) Predicting protein structures with a multiplayer online game. Nature, 466(7307), 756-760. DOI: 10.1038/nature09304  

  • August 5, 2010
  • 10:00 AM

Fructose and pancreatic cancer

by Orac in Respectful Insolence

I hate science press releases.

Well, not exactly. I hate science press releases that hype a study beyond its importance. I hate it even more when the investigators who published the study make statements not justified by the study and use the study as a jumping off point to speculate wildly. True, it's not always the fault of the investigators, particularly if they don't have much experience dealing with the press, but all too often scientists fall prey to the tendency to gab glibly and give th........ Read more »

Liu, H., Huang, D., McArthur, D., Boros, L., Nissen, N., & Heaney, A. (2010) Fructose Induces Transketolase Flux to Promote Pancreatic Cancer Growth. Cancer Research, 70(15), 6368-6376. DOI: 10.1158/0008-5472.CAN-09-4615  

  • August 5, 2010
  • 08:42 AM

‘Personalising’ autoimmune disease treatments

by Wellcome Trust in Wellcome Trust Blog

Researchers have identified biomarkers that could save patients with severe autoimmune disease from having to take potentially toxic drug treatments for too long. The biomarkers predict how different patients will react following initial treatment – opening the door to more personalised therapies. Researchers from the University of Cambridge and colleagues found a pattern of gene [...]... Read more »

McKinney EF, Lyons PA, Carr EJ, Hollis JL, Jayne DR, Willcocks LC, Koukoulaki M, Brazma A, Jovanovic V, Kemeny DM.... (2010) A CD8 T cell transcription signature predicts prognosis in autoimmune disease. Nature medicine, 16(5), 586. PMID: 20400961  

  • August 5, 2010
  • 08:24 AM

Foldit: Innovative Biology for Gamers

by GrrlScientist in This Scientific Life

Guessing how a protein will fold up based on its DNA sequence is often too difficult for even the most advanced computer programs. Now biochemists and computer scientists at my alma mater, the University of Washington, have collaborated to create Foldit, an online computer game where computer players do the work. ... Read more »

Cooper, S., Khatib, F., Treuille, A., Barbero, J., Lee, J., Beenen, M., Leaver-Fay, A., Baker, D., Popović, Z., & players, F. (2010) Predicting protein structures with a multiplayer online game. Nature, 466(7307), 756-760. DOI: 10.1038/nature09304  

  • August 5, 2010
  • 08:00 AM

Do Fitness Tax Credits Only Make The Rich Richer?

by Arya M. Sharma in Dr. Sharma's Obesity Notes

Yesterday, University of Alberta’s John Spence (on faculty of the annual Canadian Obesity Network’s Student Boot Camp) together with Valerie Carson (former Bootcamper) and coworkers, published a most interesting article in BMC Public Health.
The paper looks at the uptake and effectiveness of the Children’s Fitness Tax Credit (CFTC) on Canadians. This tax credit was introduced [...]... Read more »

  • August 5, 2010
  • 08:00 AM

Eyes on the edge: How archerfish see in and out of water

by Zen Faulkes in NeuroDojo

Archerfish rock.

These little sharpshooters are famous for being able to spit water at an insect, not on the surface of the water, but a good ways above it. And these insects are often camouflaged to boot. Then, they have to catch the insect when it hits the water before other fish get it, or it gets swept away by any water currents.

In other words, archerfish have to calculate, perform precision maneuvers, and anticipate the outcomes of their actions.

This paper, though, looks mainly at the ........ Read more »

  • August 5, 2010
  • 06:56 AM

A Practical Approach to MIQE for the Bench Scientist

by aviwener in Canadian Biotechnologist 2.0

In a groundbreaking review published in February 2009, Bustin et al bemoaned the lack of standardization in Quantitative Real-Time PCR (qPCR) experimentation and data analysis. In their critique the authors cite the use of diverse reagents, protocols, analysis methods and reporting formats which has negatively impacted on the acceptance of qPCR as a robust quantitative [...]... Read more »

Bustin SA, Benes V, Garson JA, Hellemans J, Huggett J, Kubista M, Mueller R, Nolan T, Pfaffl MW, Shipley GL.... (2009) The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. Clinical chemistry, 55(4), 611-22. PMID: 19246619  

  • August 5, 2010
  • 06:14 AM

The good old days, revisited

by iayork in Mystery Rays from Outer Space

As a general remark, the Measles were mild, while on the contrary, the Mumps were almost invariably severe, and frequently attended with metastasis to the testicles. Some cases of the latter were attended with enormous swelling and high inflammatory excitement, requiring the lancet and other antiphlogistic remedies. … As a local application to the scrotum none appeared to afford [...]... Read more »

Quinlisk, M. (2010) Mumps Control Today. The Journal of Infectious Diseases, 2147483647. DOI: 10.1086/655395  

  • August 5, 2010
  • 03:38 AM

1 in 200 men direct descendants of Genghis Khan

by Razib Khan in Gene Expression

In 2003 a groundbreaking historical genetics paper reported results which indicated that a substantial proportion of men in the world are direct line descendants of Genghis Khan. By direct line, I mean that they carry Y chromosomes which seem to have come down from an individual who lived approximately 1,000 years ago. As Y chromosomes [...]... Read more »

ZERJAL, T. (2003) The Genetic Legacy of the Mongols. The American Journal of Human Genetics, 72(3), 717-721. DOI: 10.1086/367774  

  • August 5, 2010
  • 12:16 AM

Language and inflation

by Ingrid Piller in Language on the Move

Some Language-on-the-Movers based here in Sydney had the opportunity to attend Professor Masaki Oda’s lecture about the current state of the English language in Japan yesterday. With major Japanese companies announcing a switch to English as their official company language … Continue reading →... Read more »

  • August 5, 2010
  • 12:00 AM

Close encounters with outer shells

by Joerg Heber in All That Matters

If you look at the image of an atom in a text book, it looks rather quiet and peaceful. There is a nucleus in the center made from a number of protons and neutrons. Around the nucleus the electrons typically are shown to orbit the core like planets around the sun. The reality, however, is far more complicated. First of all, the electrons don’t look like small planets, but are smeared out in complex shapes known as orbitals. The energy states of the different orbitals correspond to the electron........ Read more »

Goulielmakis, E., Loh, Z., Wirth, A., Santra, R., Rohringer, N., Yakovlev, V., Zherebtsov, S., Pfeifer, T., Azzeer, A., Kling, M.... (2010) Real-time observation of valence electron motion. Nature, 466(7307), 739-743. DOI: 10.1038/nature09212  

  • August 4, 2010
  • 10:55 PM

A Clinically Useful Fluorescence Microscope for $240 USD

by Michael Long in Phased

Andrew Miller (Rice University, United States) and coworkers have developed a remarkably cheap microscope with both the portability and imaging capabilites required for routine slide-based medical diagnostics, an extremely useful development for health professionals in remote regions of the world. This news feature was written on August 4, 2010.... Read more »

Miller, A. R., Davis, G. L., Oden, Z. M., Razavi, M. R., Fateh, A., Ghazanfari, M., Abdolrahimi, F., Poorazar, S., Sakhaie, F., Olsen, R. J.... (2010) Portable, Battery-Operated, Low-Cost, Bright Field and Fluorescence Microscope. PLoS ONE, 5(8). DOI: 10.1371/journal.pone.0011890  

  • August 4, 2010
  • 09:51 PM

Pharmacy Customers Perception of Complementary and Alternative Medicine in Pharmacies

by Darcy Cowan in Skepticon

Going through the papers cluttering my inbox I found this survey of Australian pharmacy customers relating to their use of CAM and their impressions of how pharmacists should approach the subject. Regular readers of Sciblogs may remember a kerfuffle earlier in the year regarding the sale of homeopathic remedies in pharmacies, I and others were [...]... Read more »

Braun, L., Tiralongo, E., Wilkinson, J., Spitzer, O., Bailey, M., Poole, S., & Dooley, M. (2010) Perceptions, use and attitudes of pharmacy customers on complementary medicines and pharmacy practice. BMC Complementary and Alternative Medicine, 10(1), 38. DOI: 10.1186/1472-6882-10-38  

  • August 4, 2010
  • 09:25 PM

Don’t Bite: The Defenestration of Cookie

by Jason Goldman in Child's Play

III. Whither the Cookie Task? WARNING: What you are about to read may contain graphic statistical content.  Side effects may include: contagious yawning, inappropriate arousal, and / or spontaneous combustion, depending on how you like your math cooked… darling. Psychologists often think about the cookie task as a test of cognitive control, and in keeping [...]... Read more »

Eigsti, I., Zayas, V., Mischel, W., Shoda, Y., Ayduk, O., Dadlani, M., Davidson, M., Aber, J., & Casey, B. (2006) Predicting Cognitive Control From Preschool to Late Adolescence and Young Adulthood. Psychological Science, 17(6), 478-484. DOI: 10.1111/j.1467-9280.2006.01732.x  

Mischel, W., Shoda, Y., & Rodriguez, M. (1989) Delay of gratification in children. Science, 244(4907), 933-938. DOI: 10.1126/science.2658056  

  • August 4, 2010
  • 06:05 PM

More on maternal spiders

by Africa Gomez in BugBlog

I posted recently on maternal behaviour in spiders, but I when I came across this I knew another post was in order. The photo above shows what is is most likely a Gnaphosidae spider with her eggs in her nest on the 19th of July. The spider has wrapped herself inside a silken nest she has made for her eggs, and she will remain there until they hatch and the spiderlings disperse. This behaviour, called 'egg guarding' is present in many spiders. Why would a spider do this? Do the eggs benefit ........ Read more »

Pollard, S.D. (1984) Egg guarding by Clubiona cambridgei (Araneae, Clubionidae) against conspecific predators. Journal of Arachnology, 323-326. info:/

Nyffeler, M., Breene, R., Dean, D., & Sterling, W. (1990) Spiders as predators of arthropod eggs. Journal of Applied Entomology, 109(1-5), 490-501. DOI: 10.1111/j.1439-0418.1990.tb00080.x  

  • August 4, 2010
  • 05:12 PM

The Palin Effect

by Bob O'Hara in This Scientific Life

As attentive readers of the New York Times are aware, science bloggers are all about being noisy and shouting at people we don’t like. As most of us have liberal leanings, that means we can be obnoxious towards people on the political right. And this week we’ve got great fodder, in the shape of a [...]... Read more »

  • August 4, 2010
  • 03:51 PM

The genetics of dystonia in CRPS – not what we were expecting

by Lorimer Moseley in BodyInMind

The genetics of dystonia in CRPS - genes don't seem to predispose or cause dystonia in CRPS. This doesn’t mean that there is no genetic contribution, but it does mean that the genes that underpin familial dystonia are not important in CRPS-dystonia.... Read more »

[1] Fahn S. (1988) Concept and classification of dystonia. Advances in neurology, 1-8. PMID: 3041755  

[2] van Rijn MA, Marinus J, Putter H, & van Hilten JJ. (2007) Onset and progression of dystonia in complex regional pain syndrome. Pain, 130(3), 287-93. PMID: 17499924  

  • August 4, 2010
  • 03:44 PM

Real Time fMRI

by Neuroskeptic in Neuroskeptic

Wouldn't it be cool if you could measure brain activation with fMRI... right as it happens?You could lie there in the scanner and watch your brain light up. Then you could watch your brain light up some more in response to seeing your brain light up, and watch it light up even more upon seeing your brain light up in response to seeing itself light up... like putting your brain between two mirrors and getting an infinite tunnel of activations.Ok, that would probably get boring, eventually. But th........ Read more »

Hinds, O., Ghosh, S., Thompson, T., Yoo, J., Whitfield-Gabrieli, S., Triantafyllou, C., & Gabrieli, J. (2010) Computing moment to moment BOLD activation for real-time neurofeedback. NeuroImage. DOI: 10.1016/j.neuroimage.2010.07.060  

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