One of the fundamental problems in systems biology is that many important decisions get made at the level of individual cells, but most of the measurement techniques we have (mass spectroscopy, Western blots…) report data on the behavior of populations. And much of the time it’s hard to relate what you see on the single-cell [...]... Read more »
Pfeifer AC, Kaschek D, Bachmann J, Klingmüller U, & Timmer J. (2010) Model-based extension of high-throughput to high-content data. BMC systems biology, 4(1), 106. PMID: 20687942
Freakonomics and its successor Superfreakonomics are two books by the economist Steven Levitt and his partner in crime Stephen Dubner that have a common theme running through them (quote): “People respond to incentives, although not necessarily in ways that are predictable and manifest. Therefore, one of the most powerful laws in the universe is the [...]... Read more »
Bordetella pertussisIs your Emergency Department administering Tdap immunization boosters instead of dT boosters? Patients with wounds are getting updated not only for tetanus and diphtheria, but also now for pertussis. Apparently there has been sharp rise in the national incidence of pertussis in 2010. The infection has been documented in both infants (underimmunized less than 3 months old) and adolescents/adults (loss of immunity after 10 years). In fact, the CDC has issued an epidemic warning........ Read more »
Cornia PB, Hersh AL, Lipsky BA, Newman TB, & Gonzales R. (2010) Does this coughing adolescent or adult patient have pertussis?. JAMA : the journal of the American Medical Association, 304(8), 890-6. PMID: 20736473
David Woods was looking at the early Irish chronicles and he noticed something very odd. There are clusters of entries recording large mast crops. Mast? In Ireland, that would be mostly acorns.. In these sparse annals that normally only record battles, deaths, and other major events, why record large acorn falls? The only typical use [...]... Read more »
David Woods. (2003) Acorns, the Plague, and the 'Iona Chronicle'. Peritia, 495-502. info:/
I have seen many interesting sciencey things this week. Which makes sense, given that a large part of my job is to track new research. Sadly, and for the sake of brevity, I’ve had to pick but two for this post.
Starving to stay awake?
Another interesting factoid related to, well, taking in less calories than one [...]
[Click on the hyperlinked headline for more of the goodness]... Read more »
Matthew S. Thimgan, Yasuko Suzuki, Laurent Seugnet, Laura Gottschalk, Paul J. Shaw. (2010) The Perilipin Homologue, Lipid Storage Droplet 2, Regulates Sleep Homeostasis and Prevents Learning Impairments Following Sleep Loss. PLoS Biology. info:/10.1371/journal.pbio.1000466
Notter DA, Gauch M, Widmer R, Wäger P, Stamp A, Zah R, & Althaus HJ. (2010) Contribution of li-ion batteries to the environmental impact of electric vehicles. Environmental science , 44(17), 6550-6. PMID: 20695466
First off, Sci is sorry for two things: 1) Comments on this post are still disabled due to server issues. If you email me with something particularly witty and clever, perhaps I can tweet it. Or edit it on to the post. Or something. 2) Sci has a migraine of rather titanic proportions right now [...]... Read more »
(...) Although these adult sea squirts, or tunicates, don't consist of much more than translucent sacks with intestines, their larval "tadpole" stage exhibits all characteristics of the chordates. This means that they are actually more closely related to us chordate humans than this crab is!
In fact, transparent sea squirts are so similar to us that they may prove to be important for the development of more effective treatments for Alzheimer's disease.... Read more »
Michael J. Virata, & Robert W. Zeller. (2010) Ascidians: an invertebrate chordate model to study Alzheimer's disease pathogenesis. Disease Models , 377-385. DOI: 10.1242/dmm.003434
In this week's Journal of Neuroscience, researchers have shown that BDNF gates cocaine self-administration in rodents. These findings are comparable to those found with alcohol intake in rodents. Perhaps a BDNF pharmaceutical is the future, more efficacious therapeutic for the treatment of alcoholism... Read more »
Ghazaleh Sadri-Vakili,1 Vidhya Kumaresan,2 Heath D. Schmidt,3 Katie R. Famous,2 Prianka Chawla,2 Fair M. Vassoler,3, & Ryan P. Overland,1 Eva Xia,1 Caroline E. Bass,4 Ernest F. Terwilliger,5 R. Christopher Pierce,3 and Jang-Ho J. Cha1. (2010) Cocaine-Induced Chromatin Remodeling Increases Brain-Derived Neurotrophic Factor Transcription in the Rat Medial Prefrontal Cortex, Which Alters the Reinforcing Efficacy of Cocaine. Journal of Neuroscience. info:/10.1523/JNEUROSCI.2328-10.2010
Jerome Jeanblanc,1 Dao-Yao He,1 Sebastien Carnicella,1 Viktor Kharazia,1 Patricia H. Janak,1,2,3,4* and Dorit Ron1,2,3,4. (2009) Endogenous BDNF in the Dorsolateral Striatum Gates Alcohol Drinking. Journal of Neuroscience. DOI: 10.1523/JNEUROSCI.2243-09.2009
Rebecca A. Prosser1,*, Charles A. Mangrum1, and J. David Glass2. (2008) ACUTE ETHANOL MODULATES GLUTAMATERGIC AND SEROTONERGIC PHASE SHIFTS OF THE MOUSE CIRCADIAN CLOCK IN VITRO. Neuroscience. info:/
In this post, our heroine — spurred on by her godly pursuit of science and a bevy of caffeinated drinks — compares the standard approach to language to intelligent design. It might get noodly. Pick one : Does language “emerge” full-blown in children, guided by a hierarchy of inbuilt grammatical rules for sentence formation and comprehension? Or [...]... Read more »
Rescorla RA. (1988) Pavlovian conditioning. It's not what you think it is. American Psychologist, 43(3), 151-60. PMID: 3364852
Bannard C, Lieven E, & Tomasello M. (2009) Modeling children's early grammatical knowledge. Proceedings of the National Academy of Sciences of the United States of America, 106(41), 17284-9. PMID: 19805057
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(7), 909-957. info:/10.1111/j.1551-6709.2009.01092.x
Scholz, B., & Pullum, G. (2006) Irrational Nativist Exuberance. Contemporary Debates in Cognitive Science, 59-80. info:/
In summer and autumn, spiders become more noticeable. The tiny spiderlings born in the spring have now become adults and males are wandering in search of females. One of the most common spider species in the UK is the elegantly marked Linyphia triangularis (female above). This spider makes a sheet web with criss-crossing silk lines over it in low bushes and trees. The spider hangs belly up from the underneath the sheet. Flying insects colliding with the transversal lines fall onto the........ Read more »
S. Funke and B. A. Huber. (2005) Allometry of Genitalia and Fighting Structures in Linyphia triangularis (Araneae, Linyphiidae). Journal of Arachnology, 870-872. DOI: 10.1636/S04-16.1
Nielsen, N and Toft, S. (1990) Alternative male mating strategies in Linyphia triangularis (Araneae, Linyphiidae). Acta Zoologica Fennica. info:/
[Wherein our hero - having gone AWOL - is posting old thoughts that might still be relevant. They're interesting, at the very least.... one hopes] As I’ve mentioned previously I’ve already attained a degree. I mention this because the body of this post represents the strangest assignment I’ve received in a full 6 years of [...]... Read more »
Azaryahu, M. (1997) German Reunification and the Politics of Street Names. Political Geography. DOI: 10.1016/S0962-6298(96)00053-4
Schmidt HG, Peeck VH, Paas F, & van Breukelen GJ. (2000) Remembering the street names of one's childhood neighbourhood: a study of very long-term retention. Memory (Hove, England), 8(1), 37-49. PMID: 10820586
Ok, so you’re young, you’re surprisingly dusty, and you don’t match the models. No, not a picture of my geeky childhood, but the extrasolar planet HR 8799b. It orbits the star HR 8799 and, along with its two companions, is one of the two extrasolar planetary systems to be directly imaged, as shown above. Unsurprisingly [...]... Read more »
Brendan P. Bowler, Michael C. Liu, Trent J. Dupuy, Michael C. Cushing. (2010) Near-Infrared Spectroscopy of the Extrasolar Planet HR 8799 b. accepted by ApJ. info:/1008.4582
Knicole D. Colon, Eric B. Ford, Seth Redfield, Jonathan J. Fortney, Megan Shabram, Hans J. Deeg, & Suvrath Mahadevan. (2010) Probing potassium in the atmosphere of HD 80606b with tunable filter transit spectrophotometry from the Gran Telescopio Canarias. submitted to MNRAS. arXiv: 1008.4800v1
D. K. Sing, J.-M. Desert, J. J. Fortney, A. Lecavelier des Etangs, G. E. Ballester, J. Cepa, D. Ehrenreich, M. Lopez-Morales, F. Pont, M. Shabram, A. Vidal-Madjar. (2010) GTC OSIRIS Transiting Exoplanet Atmospheric Survey: Detection of potassium in XO-2b from spectrophotometry. submitted to A. info:/1008.4795
One of the big news stories from last year was the revelation that Americans are leaving their churches and religious institutions in droves. They are becoming "unaffiliated", although there was a lot of debate over what that meant. Are Americans losing religion, or is it simply that they are disillusioned with what they're being offered?
A new analysis, using data collected over the last three decades by the General Social Survey, sheds some light on this - and also tells us more about just wh........ Read more »
Flannelly KJ, Galek K, Kytle J, & Silton NR. (2010) Religion in America--1972-2006: religious affiliation, attendance, and strength of faith. Psychological reports, 106(3), 875-90. PMID: 20712176
Esophageal cancer is currently the eighth most common human cancer, with esophageal squamous cell carcinoma (ESCC) being the most common subtype. Tobacco and alcohol use are the most prevalent causes of ESCC; however, limited evidence suggests that infectious agents--in particular, human papillomavirus (HPV)--are linked to ESCC. Antonsson et al. recently analyzed HPV prevalence and lifestyle factors in ESCC patients. Archived tumor samples from a nationwide cohort of 222 ESCC patients in Austral........ Read more »
Antonsson, A. et al. (2010) High-Risk Human Papillomavirus in Esophageal Squamous Cell Carcinoma. Cancer Epidemiol Biomarkers Prev, 19(8), 2080-2087. DOI: 10.1158/1055-9965.EPI-10-0033
For all you soccer/football/fútbol/calcio fans out there, you may have been watching the 1997 Confederations Cup match between Brazil and France when Roberto Carlos lined up for a 35 meter (115 ft.), relatively long, free kick. Then you either screamed in unbridled joy or a crying disgust as Carlos appeared to botch the free kick [...]... Read more »
Guillaume Dupeux, Anne Le Goff, David Quéré and Christophe Clanet. (2010) The spinning ball spiral. New Journal of Physics. info:/
So it's done. I've accepted it. There will be no playoff entry for the Mets this year—something that was evident earlier in the year, but the motto of this team is "Ya gotta believe." So you know, I had to believe. Am I disappointed? Yes. What fan wouldn't be? Am I surprised? No. What Mets fan would be? Does it mean that I won't be there come spring anxiously awaiting the crack of the bat?
... Read more »
I haven’t done this before but I wanted to revisit the post I made last week about sub-optimal walking in the light of new information. You see, we had a journal club about the paper yesterday in which interesting discussions were had about the paper and the results – and the conclusions drawn from those results.If you recall, the central thesis of the paper is that we over-correct for deviations in our stride length and stride time that draw us away from the line of constant velocity (the G........ Read more »
Dingwell JB, John J, & Cusumano JP. (2010) Do humans optimally exploit redundancy to control step variability in walking?. PLoS computational biology, 6(7). PMID: 20657664
Carbon dioxide releases by hurricanes are significant, but offset by ocean cooling and phytoplankton growth
A hurricane’s passage over warm ocean waters can drive a significant amount of carbon dioxide from the waves to the sky. The violent winds associated with a passing storm can dramatically increase the gas exchange between the ocean and [...]... Read more »
P. Huang, & J. Imberger. (2010) Variation of pCO2 in ocean surface water in response to the passage of a hurricane. J. Geophys. Res. info:/10.1029/2010JC006185
An information-saturated society is going to notice plenty of weird correlations, like the Blade Runner curse or the unfortunate fate of American presidents elected in years that ended in a zero (for a long time beginning in 1860, all died in office). The more data we collect, the more patterns we see. Iran leads the world in nose-jobs per capita. Major wars have been preceded by stock-market plunges on the other side of the world. It's increasingly easy to find unexpected alignments betw........ Read more »
The latest stop in the #PDEx tour is being hosted by The Intersection at Discover magazine.Despite the advances our society has made for women’s rights and sexual equality during the last century this example is just one more sign of how far we still have to go. It’s not an isolated incident. According to statistics compiled by the US Equal Employment Opportunity Commission there were 12,696 workplace sexual harassment cases filed in 2009 (which would be a fraction of the number that actuall........ Read more »
Martin N. Muller and Richard W. Wrangham. (2009) Sexual Coercion in Primates and Humans: An Evolutionary Perspective on Male Aggression Against Females. Harvard University Press. info:/
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