Post List

  • October 20, 2011
  • 06:15 PM
  • 1,378 views

Sleep quality and fatigue among prehospital providers

by Rogue Medic in Rogue Medic

Even though many in EMS will tell you that EMS stands not for Emergency Medical Services, but for Earn Money Sleeping, sleep deprivation is a problem for many in EMS, many in medicine, and many in other fields. I am a night person, much more awake and alert at 2 AM, than at 8 AM. ... Read more »

Patterson PD, Suffoletto BP, Kupas DF, Weaver MD, & Hostler D. (2010) Sleep quality and fatigue among prehospital providers. Prehospital emergency care : official journal of the National Association of EMS Physicians and the National Association of State EMS Directors, 14(2), 187-93. PMID: 20199233  

  • October 20, 2011
  • 05:57 PM
  • 750 views

Tracking your colony: SAPling

by Zen Faulkes in Marmorkrebs



Where was this when I started my Marmorkrebs colony?

A new article in The Journal of Experimental Biology describes a software package called SAPling that is intended to track the pedigree of entire colonies of asexually reproducing animals. You can find the software at: http://genomics.princeton.edu/schoetzlab/software.html.

I’ve downloaded the software, which is written in Java. I have not quite figured out how to run the program yet, though. There’s no standard *.exe file to run. If anyone knows how to get Java *.class files going, I would be most appreciative of any pointers!

Reference

Thomas MA, Schötz E-M. 2011. SAPling: a Scan-Add-Print barcoding database system to label and track asexual organisms. The Journal of Experimental Biology 214(21): 3518-3523. DOI: 10.1242/jeb.059048... Read more »

  • October 20, 2011
  • 03:41 PM
  • 1,498 views

Urban Heat Islands as Explanation for Hockey Stick Global Warming Curve

by Greg Laden in Greg Laden's Blog

Urban areas can be warmer than surrounding non-urban areas because there is a lot of combustion, pavement and other structure can collect solar heat and retain it for a while, and other factors. It is not uncommon to look at a weather map where conditions for precipitation are marginal, and everywhere but the urban zone, or only the urban zone and nothing else, is showing a weather phenomenon. Because people and airports (where weather is very important) are located in or very near urban areas, it stands to reason that a lot of the data used to estimate global temperatures would be affected by any urban effects, and if urban areas are a) warmer than surrounding areas and b) increasingly warm over time then "global warming" may well be an artifact of the urban heat island effect. That wouldn't necessarily make it a hoax, but it would make it wrong. We would then have to revise our understanding of certain aspects of physics because we expect global warming to occur in CO2 levels go up, but physics has been revised before. Kepler was wrong, Newton was wrong, maybe the climate change scientists are wrong too.

Some time ago a study was funded by a number of organizations and individuals, including some who are famously skeptical of global warming (such as the Charles G. Koch foundation) in order to see if urban heat island effects could explain the famous "Hockey Stick" curve. The study was supposed to be non-biased, and it may well be, but if there are any biases they would likely be in favor off anti-Global Warming thinking, or perhaps "pro-denialist" or "anti-warmist" ... pick your term.

Well, just moments ago, the study was released and the findings are quite interesting. I have to admit, I was not expecting these findings at all, and they have caused me to change my mind about certain things. Which is fine, because that is how science works, but still, I was rather shocked. Read the rest of this post... | Read the comments on this post...... Read more »

Wickham, C., Curry, J., Groom, D., Jacobson, R., Muller, R., Perlmutter, S., Rohde, R., Rosenfeld, A., & Wurtele, J. (2011) Influence of urban heating on the global temperature land average using rural sites identified from MODIS classifications. Unknown. info:/

  • October 20, 2011
  • 01:42 PM
  • 674 views

Remember Herman Cain's "9-9-9" Plan, and Don't Forget the Power of a Good Mnemonic

by Persuasion Strategies in Persuasive Litigator

By Dr. Ken Broda-Bahm: Whatever you think of Republican Presidential contender and former pizza magnate Herman Cain, you've got to give him credit for creating a theme using only three digits... and a theme about tax policy, no less. Mr. Cain has been ascendant recently in the race for the GOP nomination, largely based on the strength of a simple idea: a 9 percent business flat tax, a 9 percent individual flat tax, and a 9 percent national sales tax. Even voters who wouldn't otherwise favor the candidate can see a certain appeal in its simplicity and apparent fairness, with...

... Read more »

Lim MS, Hocking JS, Aitken CK, Fairley CK, Jordan L, Lewis JA, & Hellard ME. (2011) Impact of text and email messaging on the sexual health of young people: a randomised controlled trial. Journal of epidemiology and community health. PMID: 21415232  

  • October 20, 2011
  • 12:45 PM
  • 496 views

The elusive mystery of KRAS and EGFR inhibitors in colorectal cancer

by Sally Church in Pharma Strategy Blog

The other week during a conversation with Dr Gordon Mills (MDACC) at the European Multidisciplinary Meeting (EMCC) in Stockholm, he mentioned the conundrum of variable responses to EGFR inhibitors in colorectal cancers and the impact of RAS.  Originally, it was thought … Continue reading →... Read more »

  • October 20, 2011
  • 12:11 PM
  • 1,388 views

Actionable evidence: Injectable contraceptives increase the risk of HIV infection

by Debajyoti Datta in Medicine...Life

I was thinking of a new categoryof posts which I would be calling actionable evidence. Actionable evidence isthat evidence which you can immediately put into practice; these are of directclinical relevance. So to start this off I have selected a very important studythat came out in the Lancet Infectious Diseases titled “Use of hormonal contraceptives and risk of HIV-1 transmission: a prospective cohort study”... Read more »

Heffron R, Donnell D, Rees H, Celum C, Mugo N, Were E, de Bruyn G, Nakku-Joloba E, Ngure K, Kiarie J.... (2011) Use of hormonal contraceptives and risk of HIV-1 transmission: a prospective cohort study. The Lancet infectious diseases. PMID: 21975269  

  • October 20, 2011
  • 11:23 AM
  • 1,332 views

Everything the Movies Taught You About Sororities is True

by Eric Horowitz in peer-reviewed by my neurons

Everybody knows the stereotypes about sororities. They exemplify the worst kind of set-feminism-back-25-years popularity and attractiveness contests that put no weight on the quality of your personality or character. Well, a new study by researchers at Tufts and Dartmouth provides some support for the stereotype, especially for “high status” (i.e. more desirable) sororities. [...]... Read more »

  • October 20, 2011
  • 09:29 AM
  • 1,117 views

October 20, 2011

by Erin Campbell in HighMag Blog

One man’s trash is another man’s treasure. Photobleaching is an unavoidable side effect of imaging that leads to weakened fluorescent signals. Most of us pooh-pooh photobleaching, but some clever cell biologists use photobleaching as a fantastic tool instead. Today’s image is my new favorite use of photobleaching. Glial cells function in the nervous system to support neurons and their signal transmission. Schwann cells are glial cells found at the neuromuscular junction (where neurons signal to muscles), and monitor the neurotransmission exchanged. Schwann cells can even function to form and regenerate the neuromuscular junction. A recent paper describes how Schwann cells establish their arrangement around the neuromuscular junction. In this paper, Brill and colleagues labeled individual Schwann cells and used live imaging to monitor their positioning. Schwann cells are dynamic during development, finding their appropriate position by competing for space with other Schwann cells. Schwann cells in adult animals, however, are much more static. In the images above, individual Schwann cells (pseudo-colored yellow, blue, white, and purple) were labeled by sequentially photobleaching one cell at a time, leading to distinct levels of fluorescence in each cell. The axon of the neuromuscular junction is in green. The Schwann cells are very dynamic in young mice (left) compared with adult mice (right), seen as the frequent formation and retraction of cell protrusions (arrowheads in the images of the boxed regions).Brill, M., Lichtman, J., Thompson, W., Zuo, Y., & Misgeld, T. (2011). Spatial constraints dictate glial territories at murine neuromuscular junctions originally published in The Journal of Cell Biology, 195 (2), 293-305 DOI: 10.1083/jcb.201108005... Read more »

Brill, M., Lichtman, J., Thompson, W., Zuo, Y., & Misgeld, T. (2011) Spatial constraints dictate glial territories at murine neuromuscular junctions. originally published in The Journal of Cell Biology, 195(2), 293-305. DOI: 10.1083/jcb.201108005  

  • October 20, 2011
  • 08:00 AM
  • 904 views

A Mocha for Your Mood

by Jennifer Gibson, PharmD in Brain Blogger

The smell of coffee can rouse you out of bed; the taste of coffee can warm your soul. And, the caffeine in coffee can lower the risk of depression. In fact, a new study reports that the more coffee one drinks, the lower the risk. The study, conducted by Harvard University nutritionists and epidemiologists, was [...]... Read more »

  • October 20, 2011
  • 05:35 AM
  • 1,037 views

The Secret Journal Club: Vitamins Are For Death Panels

by John Cmar in The Secret Lair

Last week during my usual work commute traffic/weather check-in with WTOP radio, I repeatedly heard a soundbyte about how a freshly published study demonstrated that many vitamin supplements were found to be associated with increased death in elderly people who take them.1 Calcium alone, they reported, was shown to increase lifespan in the elderly. The segment was only 30 seconds long, and offered no further comment or critique.

A sterling example of excellent medical reporting? Somehow, I suspect not. Let’s take a look.... Read more »

  • October 20, 2011
  • 05:13 AM
  • 1,867 views

Solving broomcorn millet

by Jeremy in Agricultural Biodiversity Weblog

Broomcorn millet is a bit of a puzzle. You start to get archaeobotanical evidence for cultivated Panicum miliaceum in both China and Europe at about the same time before 7000 BP. Independent domestication or movement along the fabled Silk Road (like wheat)? And if the latter, in which direction? You can hear the conundrum set [...]... Read more »

  • October 20, 2011
  • 02:53 AM
  • 825 views

The Facebook Brain

by Neuroskeptic in Neuroskeptic

Facebook friend tally is associated with differences in brain structurePeople with lots of Facebook friends have denser grey matter in three regions of the brain, a study suggestsWhen I heard about this, my heart sank. The Facebook area of the brain? It had all the hallmarks of a piece of media neuro-nonsense: a hook (Facebook!), a simplistic neo-phrenological story (bigger brains are better!)... so I was expecting to discover that the fuss was all about some tiny, statistically questionable study, which wasn't really about what the newspapers said it was, as is so often the case. So I was very surprised to find that it's actually an extremely good paper.Kanai et al from London took 125 young Facebookers (mostly students) and correlated their friend count with grey matter density across the brain. They found some correlations:The numbers seem solid. It was a large study. They used whole-brain correction for multiple comparisons (a=0.05 FWE corrected), controlling for age, gender and overall brain grey matter. Most importantly, they included a replication sample, something that very few neuroscience papers do. After having done the first 125 people, they got another 40, and looked in the areas where they'd previously found results. They found the same correlation in all three cases - in fact, it was even stronger.They even made sure to only display the scatterplots from the replication sample, thus avoiding the dreaded voodoo correlations problem that so often plagues such graphs. Note that the correlations are actually with the square root of the number of friends.As if this wasn't enough, they confirmed a previously reported correlation between amygdala size and social network size, in both of their samples. And to cap it all, they show that Facebook friends are correlated (albeit not hugely) with other measures of number of friends.So, as unlikely as it sounds, this Facebook finding is stronger than a good 90% of similar papers.What does it mean that the size of the amygdala, left MTG, right STS and right entorhinal cortex are correlated with your Friend count? Good question. The authors discuss the result in terms of the known functions of these areas, e.g. the entorhinal cortex is involved in learning to associate pairs of stimuli, such as matching names to faces, which might be related to keeping track of your friends... but frankly this is just a post-hoc story.You could tell an equally convincing tale about almost any part of the brain, if you found a correlation there. And as the authors point out, they didn't find correlations with other "social" areas you might expect like the mirror neuron system. But that doesn't change the fact that the results of the study seem rock solid. So what's going on? It could be that having lots of friends makes your brain bigger. Or it could be the reverse, that having a certain kind of brain wins you friends, or at least Facebook ones. Or it could be that there's some third factor underlying the correlation, although who knows what that is.Kanai, R., Bahrami, B., Roylance, R., & Rees, G. (2011). Online social network size is reflected in human brain structure Proceedings of the Royal Society B: Biological Sciences DOI: 10.1098/rspb.2011.1959... Read more »

Kanai, R., Bahrami, B., Roylance, R., & Rees, G. (2011) Online social network size is reflected in human brain structure. Proceedings of the Royal Society B: Biological Sciences. DOI: 10.1098/rspb.2011.1959  

  • October 20, 2011
  • 12:39 AM
  • 2,067 views

Does plate tectonics control magnetic reversals?

by Chris Rowan in Highly Allochthonous

Possibly, but this paper will not convince you. Continue reading →... Read more »

Pétrélis, F., Besse, J., & Valet, J. (2011) Plate tectonics may control geomagnetic reversal frequency. Geophysical Research Letters, 38(19). DOI: 10.1029/2011GL048784  

  • October 20, 2011
  • 12:03 AM
  • 1,048 views

Lack of Awareness of Fluid Needs Among Participants at a Midwest Marathon

by Jeffrey B. Driban in Sports Medicine Research (SMR): In the Lab & In the Field

Participation in marathons has increased from 25,000 runners in 1976 to 425,000 runners in 2008. This growth in popularity has attracted runners with various levels of experience, fitness, and knowledge about potential complications of marathon running. Brown et al. examined the experience of the typical marathon participant in the 2007 Chicago Marathon regarding the potential complications of running a marathon and hydration status.... Read more »

Brown S, Chiampas G, Jaworski C, & Passe D. (2011) Lack of Awareness of Fluid Needs Among Participants at a Midwest Marathon. Sports Health: A Multidisciplinary Approach, 3(5), 451-454. info:/

  • October 19, 2011
  • 09:00 PM
  • 1,426 views

Back to the Future – Mental Time Travel in Tropical Birds?

by Paul Norris in AnimalWise

I may not have a nuclear-powered DeLorean parked in my driveway, but I can travel in my own personal time machine anytime I want, and so can you. Through what’s known as mental time travel, or MTT, you can move backwards and forwards through time – visiting the past when you remember a specific event [...]... Read more »

  • October 19, 2011
  • 07:13 PM
  • 1,191 views

Göbekli Tepe: Houses of the Holy?

by Cris Campbell in Genealogy of Religion

In the series introduction, I asked whether Göbekli Tepe was (as the excavator Klaus Schmidt suggests) an archaeological or metaphorical Stairway to Heaven. Continuing the Led Zeppelin riff, a better question for today might be whether Göbekli’s megalithic structures were Houses of the Holy.

E.B. Banning suggests something along these lines in “So Fair a House: [...]... Read more »

Banning, E.B. (2011) So Fair a House: Gobekli Tepe and the Identification of Temples in the Pre-Pottery Neolithic. Current Anthropology, 52(5), 619-660. info:/10.1086/661207

  • October 19, 2011
  • 06:45 PM
  • 1,304 views

Bumpy nipples explained: smell directs babies to milk

by NerdyOne in Try Nerdy

The aesthetics of the human female nipple can be a touchy subject; that’s all I’ll say on that. The fact remains, though, that the areola (the pigmented ring of skin surrounding the nipple) often has little raised bumps on it. These bumps are at times a source of self-consciousness for women, and the butt of jokes for comedians. However, new research on these areolar glands could potentially put all humility and humor aside. It turns out that these nipple nodules may serve a critical role in guiding babies to much-needed breast milk.

At times it seems there are no mistakes in biology….... Read more »

  • October 19, 2011
  • 05:20 PM
  • 1,437 views

Space cleaner wanted: must have own laser

by Emma in we are all in the gutter

Since the launch of Sputnik in 1957 we’ve launched tonnes of stuff (literally) into space. We’ve not kept things very tidy up there either, so we now have hundreds of thousands of pieces of junk orbiting around us, threatening to crash into important things like the International Space Station. Or the satellite that handles your [...]... Read more »

Claude R. Phipps, Kevin L. Baker, Brian Bradford, E. Victor George, Stephen B. Libby, Duane A. Liedahl, Bogdan Marcovici, Scot S. Olivier, Lyn D. Pleasance, James P. Reilly.... (2011) Removing Orbital Debris with Lasers. Advances in Space Research. arXiv: 1110.3835v1

  • October 19, 2011
  • 04:35 PM
  • 1,224 views

Shift Work Linked to Multiple Sclerosis Risk

by William Yates, M.D. in Brain Posts

Fiery Skipper ButterflyMultiple sclerosis (MS) is a neurological disorder characterized by t cell-mediated inflammation involving the myelin sheath that covers neurons.  The inflammation can occur in the brain or peripheral nervous system.When inflammation damages the myelin sheath, the axons become less efficient in function.  Since the inflammation associated with MS can occur nearly anywhere axons are found, the variety of types of neurological symptoms is diverse.The rates of MS vary across geographical locations and across racial and cultural groups.  A common estimate of the prevalence of MS is one per thousand individuals .  But a variety of risk factors appear to increase risk.Some of the important risk factors associated with MS include:Age between 20 and 40Female genderFirst degree relative with MS (increases risk 10 to 30 fold)Other autoimmune disorder, i.e. thyroiditis, type 1 diabetes mellitus, inflammatory bowel disease (Crohns disease, ulcerative colitis)Caucasian raceObesityLiving in a temperate climateNorthern European family of origin, i.e. ScandanavianHistory of viral infections, i.e. Ebstein-Barr (mononucleosis) virusCigarette smokingVitamin D deficiencyNow a epidemiological study from Sweden has reported that doing shift work early in life may also increase risk for later development of MS.  The authors of this study report that shift work has been implicated in several other conditions including immune thyroid problems, heart disease and cancer.Shift work was defined this research as "permanent or alternating working hours other than ordinary day work".  This would include evening and night shift workers and workers beginning work before 7 am.  The researchers looked at two independent Swedish study samples and examine age of performing shift work and as well as duration/intensity of shift work.Potential confounding variables controlled in the analysis included: gender, ancestry, smoking status, sun exposure habits and serum vitamin D levels.Using a case-control design, the research team found both samples demonstrated a link between early age shift work and risk of later development of MS.  There did appear to also be a duration effect---those beginning shift work as a teenager and working three or more years in shift work by age 20 showed the largest effect with a two-fold increase in rates of MSThe authors propose this shift work association may be due to interaction between circadian rhythms and immunological system function.  Proinflammatory cytokines peak during the night when cortisol is typically low and melatonin levels high.  Additionally, shift workers may have impairment in sleep.  Sleep deprivation appears to have significant negative effects on immune function via changes in "number of circulating lymphocytes, natural killer cells and antibody titers".This is an important study that needs replication.  It does support further study of the potential role of shift work on sleep and immune function and a variety of clinical neuroscience disorders.  The study suggests if shift work is necessary, it may be best to delay it until individuals pass through the adolescent developmental period.Photo of Fiery Skipper butterfly from the author's collection.Risk factor list from factors listed in manuscript as well as from the Mayo Clinic website on MS.Hedström, A., Åkerstedt, T., Hillert, J., Olsson, T., & Alfredsson, L. (2011). Shift work at young age is associated with increased risk for multiple sclerosis Annals of Neurology DOI: 10.1002/ana.22597... Read more »

  • October 19, 2011
  • 02:56 PM
  • 818 views

Elmer & Meyer 2011: Adaptation in the age of ecological genomics: insights from parallelism and convergence

by UNIL_student in genome ecology evolution etc

Natural selection is one of the two major forces which drive evolution of species, morphs and phenotypes. However, due to the confounding effects of environmental stochasticity, replication at the taxon level is needed for better understanding the influence and importance of natural selection in evolutionary biology. Parallel evolution events, in which related taxons independently evolve similar traits, provide a useful framework to investigate the mechanisms of adaptation using powerful new genomic and transcriptomic tools.In the paper “Adaptation in the age of ecological genomics: insights from parallelism and convergence”, Kathryn Elmer and Axel Meyer reviewed examples of parallel evolution in natural populations of non-model species and compared the genetic bases of their adaptive traits. Inspired by the hypotheses that parallel phenotypes share homologous genetic bases, they investigated the advances allowed by new genomic technique in the field of adaptive evolution. Understanding genetic origins and mechanisms of phenotypic changes will raise insights into the opportunities for species to adapt under ecological pressure.The authors proposed a classification for the nature of genetic variations leading to similar phenotypes among three levels: homologous mutation at the same nucleotides, homologous mutation in the same gene at different nucleotide and non-homologous mutation in different genes. Mutations participating to any of these categories can be part of the genetic standing variation, the pool of old mutations already present in ancestral population or may have appeared de novo after parallel evolution begun.The new emerging genomic methods will be very useful in identifying variation responsible for adaptation because they allow broad analyses at the population level without a priori hypotheses, unlike the older but reliable methods focusing on candidate genes. Efficient mapping of phenotypes now permits identification of genome parts involved, and loci under selection can be tracked through genome scans.The compilation of studies using molecular and geographical wide methods on different species or complexes revealed that parallel evolution of phenotypes is driven by all categories of mutations, at same or different genes. A representative example is provided by studies of coat coloration in mice species of genus Peromyscus. Unless these first results need to be supported by other studies, it suggests that a broad variety of genetic mechanisms may are responsible for parallel evolution and a clear pattern is still to emerge. Despite this large evolutionary potential, the phenotypic response seems limited by morphological and developmental constraints, suggesting there is no tight couple between genetic bases and phenotypes. Until now, the focus on this king of mapping between genotypes and phenotypes may have clouded the genetic variability newly emphasised by genomics methods.Accordingly with authors’ view, our discussion firstly focused on the absence of clear pattern revealed by the review. New genomic methods are emerging and have been only applied a few times in studies of parallel adaptation. In fact, nearly all studies carried so far are reviewed here, laying the basis for future research. The conclusions, emphasizing the complexity of mechanisms, raised questions about the pertinence of knowing precisely which genes are responsible for adaptation. However, the main question the authors set does not much concern the proximal mechanisms, but the complexity of these mechanisms: a constant pattern in the causes driving adaptation may be interpreted as a determined strategy of Nature allowing for the evolution of parallel phenotypes. On the other hand, random mechanisms would reflect an important role of stochasticity in this process of evolution.The proposed classification for nucleotides changes discriminates between mutations happening in same or different genes. This last option potentially affects phenotypes through an extensive amount of mechanistic patterns of expression and/or regulation, in contrast to the other categories. We thus discussed the relevance of splitting it in two according that the mutated genes have similar functions or not. Also debated was the relevance of grouping the two categories of mutations happening on the same gene, considered as unlikely to happen in parallel evolution. However, homologous mutation at the same nucleotide would be more likely to be due to standing genetic variation than to de novo mutation, and it is worth making the difference.The possibilities of building tests for the basis of parallel adaption were discussed, in light of the experiment about foxes’ domestication conducted in Siberia during the last 50 years. Such long lasting experiment reveals that evolution may be relatively quick under stringent selective conditions in evolved animals. However, more realistic tests would preferentially use bacteria to produce results quicker.I am personally not familiar with new genomics methods, having a more traditional background of searching for candidate genes. The main impact of the review is thus emphasizing on the power of these democratizing methods. I believe it is important to focus researchers’ attention on emerging new methodologies as soon as possible in order to boost advances in comprehension of evolution.Elmer, K., & Meyer, A. (2011). Adaptation in the age of ecological genomics: insights from parallelism and convergence Trends in Ecology & Evolution, 26 (6), 298-306 DOI: 10.1016/j.tree.2011.02.008... Read more »

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