Post List

  • June 2, 2010
  • 12:56 AM

Metagenome Sequence Simulators

by Daemios in Rudimenthos

Richter DC, Ott F, Auch AF, Schmid R, & Huson DH (2008). MetaSim: a sequencing simulator for genomics and metagenomics. PloS one, 3 (10) PMID: 18841204An article from the Huson's Group at Tübingen University has just came out in the Open Access (and scientific publishing innovator) journal PLoS ONE, describing MetaSim, a software to produce artificial or syntetic or in silico metagenomes out of a selection of completely sequenced genomes.This is just "heaven-sent" for me since I've been wor........ Read more »

Richter DC, Ott F, Auch AF, Schmid R, & Huson DH. (2008) MetaSim: a sequencing simulator for genomics and metagenomics. PloS one, 3(10). PMID: 18841204  

Mavromatis K, Ivanova N, Barry K, Shapiro H, Goltsman E, McHardy AC, Rigoutsos I, Salamov A, Korzeniewski F, Land M.... (2007) Use of simulated data sets to evaluate the fidelity of metagenomic processing methods. Nature methods, 4(6), 495-500. PMID: 17468765  

  • June 2, 2010
  • 12:56 AM

To Metagenome or not to Metagenome

by Daemios in Rudimenthos

A masterpiece of science blogging was posted here (, addressing the finding of primate sequences in the GOS dataset, just one of the unassesed ambiguities in metagenomics.The post is beautifully written and made me laugh really loud. The point is that metagenomics is sometimes being overselled just in the very same way as genomics has been (see Eisen's blog for just some examples) and this leads to an skeptic counterwave........ Read more »

Rusch DB, Halpern AL, Sutton G, Heidelberg KB, Williamson S, Yooseph S, Wu D, Eisen JA, Hoffman JM, Remington K.... (2007) The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific. PLoS biology, 5(3). PMID: 17355176  

  • June 1, 2010
  • 10:07 PM

Pesticides Linked to ADHD: Salad with a Side of Suspected Toxins

by Polly Palumbo in Momma Data

I try to buy organic fruits and veggies, at least the dirty dozen.  Organic milk too. Pasta, once or twice. Pajamas, never.  So you may not be surprised to learn I read the new study linking ADHD to pesticides as my children gobbled up grapes that were not organic, this being New Jersey and not the West Coast where I imagine pesticide-free is an achievable if not cost-effect lifestyle.  After finishing the article published in the curre........ Read more »

  • June 1, 2010
  • 10:00 PM

Experimental test of Darwin's naturalization hypothesis

by Marc Cadotte in The EEB and flow

Among the numerous and still informative ecological predictions made by Darwin, one posits that when species are introduced into regions where they were not formerly found, the most successful tend to not have close relatives already occupying the region. This is known as Darwin's Naturalization Hypothesis, and his logic was that among close relatives, where ecological requirements should be most similar, the struggle for existence is most severe. Thus the modern formulation is that invader succ........ Read more »

Jiang, L., Tan, J., & Pu, Z. (2010) An Experimental Test of Darwin’s Naturalization Hypothesis. The American Naturalist, 175(4), 415-423. DOI: 10.1086/650720  

  • June 1, 2010
  • 08:42 PM

Seafood poisoning

by sandnsurf in Life in the Fast Lane

A couple present to the ED with vomiting and paraesthesiae after eating at a seafood restaurant. Can you help them by solving the seafood poisoning conundrum?... Read more »

  • June 1, 2010
  • 04:13 PM

The fine line between Hype and Hope in breast cancer

by Sally Church in Pharma Strategy Blog

While on the road here in San Francisco at the American Urology Association, I received an email from someone about latest news surrounding the breast cancer vaccine published in Nature Medicine. Expecting to find some snippets on how this vaccine...... Read more »

Jaini, R., Kesaraju, P., Johnson, J., Altuntas, C., Jane-wit, D., & Tuohy, V. (2010) An autoimmune-mediated strategy for prophylactic breast cancer vaccination. Nature Medicine. DOI: 10.1038/nm.2161  

  • June 1, 2010
  • 03:57 PM

Humpback whales realize the importance of girl power!

by Dr. Carin Bondar in Dr. Carin Bondar - Biologist With a Twist

The bulk of research done on the evolution of sociality has focused on sexual pairings (aka interactions between males and females).  While such interactions directly affect the reproductive success of the individuals involved, they are certainly not the only kind of interaction that matters.  Female alliances have been shown to increase infant survival in a [...]... Read more »

  • June 1, 2010
  • 03:47 PM

RNA Journal Club 5/13/10

by YPAA in You'd Prefer An Argonaute

Cooperation Between Translating Ribosomes and RNA Polymerase in Transcription Elongation Sergey Proshkin, A. Rachid Rahmouni, Alexander Mironov, Evgeny Nudler Science, Vol. 328. no. 5977: pp. 504 – 508, 23 April 2010. DOI: 10.1126/science.1184939 This week’s smart summary and analysis by Pavan Vaidyanathan: In this paper, the authors propose a mechanism for active physical cooperation between [...]... Read more »

  • June 1, 2010
  • 01:03 PM

Experimental virus treatment is still in development

by Cancer Research UK in Cancer Research UK - Science Update

Over the last week or so, we’ve received a lot of enquiries to our helpline and email service about a new experimental cancer drug called reolysin. This followed several reports in the national press the week previously. Reolysin is a relatively new drug developed from a fairly harmless type of virus called a reovirus. Most [...]... Read more »

  • June 1, 2010
  • 12:06 PM

Ethical Debate: Killing sharks for science?

by WhySharksMatter in Southern Fried Science

While attending last year’s American Elasmobranch Society conference, I was asked to fill out a survey concerning my views on lethal shark research. My response, along with those of many other participants, has now been analyzed and written up into a new essay in the Journal of Conservation Biology. Michelle Heupel and Colin Simpendorfer argue [...]... Read more »

  • June 1, 2010
  • 11:59 AM

Autism, Psychosis and circadian clock

by sandygautam in The Mouse Trap

Image via Wikipedia

I recently came across this post by Michelle Dawson that states the thesis that one of the abnormalities in Autism spectrum disorders is due to abnormal circadian clock functioning. More specifically, the clock is internally driven and has a greeter ‘free running’ period and does not entrain readily to environmental and social clues.
Autistics More >Rating: 0.0/10 (0 votes cast)

Related posts:Tick, Tick, Tock: The Mouse without the C........ Read more »

  • June 1, 2010
  • 11:52 AM

SSRIs and Suicide

by Neuroskeptic in Neuroskeptic

Prozac and suicide: what's going on?Many people think that SSRI antidepressants do indeed cause suicide, and in recent years this idea has gained a huge amount of attention. My opinion is that, well, it's all rather complicated...At first glance, it seems as though it should be easy to discover the truth. SSRIs are some of the most studied drugs in the world. We have data from several hundred randomized placebo-controlled trials, totaling tens of thousands of patients. Let's just look and see wh........ Read more »

  • June 1, 2010
  • 11:43 AM

Niches of Sunlight

by Lab Rat in Lab Rat

In every environment there will be competition for resources, and there are generally two ways organisms deal with this; generalise or specialise. To generalise, you try to cope with as many different conditions as possible, so that if you get out-competed in one area you can try to cope with the conditions elsewhere. To specialise, you get damn good at using the conditions in your little niche, in the hope that you'll be better than anyone else who comes along, and be able to out-compete them.T........ Read more »

Rocap G, Larimer FW, Lamerdin J, Malfatti S, Chain P, Ahlgren NA, Arellano A, Coleman M, Hauser L, Hess WR.... (2003) Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation. Nature, 424(6952), 1042-7. PMID: 12917642  

  • June 1, 2010
  • 11:35 AM

Relativity on a Human Scale

by Chad Orzel in Uncertain Principles

While I mostly restricted myself to watching invited talks at DAMOP last week, I did check out a few ten-minute talks, one of which ended up being just about the coolest thing I saw at the meeting. Specifically, the Friday afternoon talk on observing relativity with atomic clocks by Chin-Wen Chou of the Time and Frequency Division at NIST in Boulder.

The real technical advance is in a recent paper in Physical Review Letters (available for free via the Time and Frequency Publications Database, b........ Read more »

Chou, C., Hume, D., Koelemeij, J., Wineland, D., & Rosenband, T. (2010) Frequency Comparison of Two High-Accuracy Al^{ } Optical Clocks. Physical Review Letters, 104(7). DOI: 10.1103/PhysRevLett.104.070802  

Schmidt, P. (2005) Spectroscopy Using Quantum Logic. Science, 309(5735), 749-752. DOI: 10.1126/science.1114375  

  • June 1, 2010
  • 10:45 AM

Is air pollution responsible for rising rates of diabetes?

by Yoni Freedhoff in Weighty Matters

A recent study says so.The study, Traffic-related Air Pollution and Incident Type 2 Diabetes: Results from the SALIA Cohort Study set out to look at 1,775 non-diabetic middle aged women and their incidence of developing type 2 diabetes over a 16 year period as a function of their exposure to traffic-related air pollution. The study was conducted in Germany and the authors hypothesized that particulate matter air pollution may promote the development of type 2 diabetes with the proposed mechanism........ Read more »

Krämer, U., Herder, C., Sugiri, D., Strassburger, K., Schikowski, T., Ranft, U., & Rathmann, W. (2010) Traffic-related Air Pollution and Incident Type 2 Diabetes: Results from the SALIA Cohort Study. Environmental Health Perspectives. DOI: 10.1289/ehp.0901689  

  • June 1, 2010
  • 10:00 AM

Predicting Dropout Rates for Students Completing Online Surveys

by Richard Landers in NeoAcademic

An upcoming paper in Cyberpsychology, Behavior and Social Networking examines participant drop out rates in online surveys. I even made a handy chart!... Read more »

Hoerger, M. (2010) Participant dropout as a function of survey length in Internet-mediated university studies: Implications for study design and voluntary participation in psychological research. Cyberpsychology, Behavior and Social Networking. info:/10.1089/cyber.2009.0445

  • June 1, 2010
  • 09:00 AM

When what an acupuncture study shows is much more interesting than what acupuncture believers think it shows

by Orac in Respectful Insolence

Of all the "alternative" therapies out there, arguably the most studied is the modality known as acupuncture. Perhaps the reason is that, unlike homeopathy, which based on physics, chemistry, and biology alone is so implausible that, for it to "work," huge swaths of well-established physics and chemistry would have to be shown to be not just wrong but extravagantly and outrageously wrong (making homeopathy far more akin to magic than science), or reiki, which, when you come right down to it, is ........ Read more »

Goldman, N., Chen, M., Fujita, T., Xu, Q., Peng, W., Liu, W., Jensen, T., Pei, Y., Wang, F., Han, X.... (2010) Adenosine A1 receptors mediate local anti-nociceptive effects of acupuncture. Nature Neuroscience. DOI: 10.1038/nn.2562  

  • June 1, 2010
  • 08:59 AM

Web4All Conference 2010

by Simon Harper in Thinking Out Loud

This years conference focused on Developing Regions wishing to investigate accessibilities Common Goals and Common Problems. The rationale was that the community thought that a revolution in the information society was starting, based on the use of mobile phones in developing countries. The hyper-growth of mobile phone penetration was deeply changing the lives of people in most of the world; their ways of communicating, working, learning, and structuring their societies. The promising next step ........ Read more »

Andy Brown, Caroline Jay, and Simon Harper. (2010) Audio access to calendars. W4A '10: Proceedings of the 2010 International Cross Disciplinary Conference on Web Accessibility (W4A), 1(1), 1-10. info:/10.1145/1805986.1806028

Brian Kelly, Sarah Lewthwaite, and David Sloan. (2010) Developing countries; developing experiences: approaches to accessibility for the real world. W4A '10: Proceedings of the 2010 International Cross Disciplinary Conference on Web Accessibility (W4A), 1(1), 1-4. info:/10.1145/1805986.1805992

  • June 1, 2010
  • 08:00 AM

Will the Public Accept Laws that Prohibit Weight Discrimination?

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

Regular readers of these pages will be well aware of the very real problems caused by weight-bias and discrimination.
As noted previously, anti-fat prejudice has direct implications for the health of those struggling with excess weight as it can increase vulnerability for depression, low self-esteem, anxiety, suicidality, maladaptive eating behaviors, avoidance of physical activity, poorer outcomes [...]... Read more »

  • June 1, 2010
  • 08:00 AM

The impact of off-road vehicles on beach-dwelling wildlife

by Rob Goldstein in Conservation Maven

... Read more »

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