NOTE: Orac is on semi-vacation this week, trying very hard to recharge his Tarial cells. Actually, although he is at home, he is spending much of his time in his Sanctum Sanctorum (i.e., his home office) working on an R01 for the February submission cycle. Given that the week between Christmas and New Years Day tends to be pretty boring, both from a blogging and blog traffic standpoint, he's scaling back the new, original stuff and mixing in some "best of" reruns, as well as some more recent stu........ Read more »
Berrington de Gonzalez, A., Mahesh, M., Kim, K., Bhargavan, M., Lewis, R., Mettler, F., & Land, C. (2009) Projected Cancer Risks From Computed Tomographic Scans Performed in the United States in 2007. Archives of Internal Medicine_id, 169(22), 2071-2077. http://archinte.ama-assn.org/cgi/doi/10.1001/archinternmed.2009.440
Smith-Bindman, R., Lipson, J., Marcus, R., Kim, K., Mahesh, M., Gould, R., Berrington de Gonzalez, A., & Miglioretti, D. (2009) Radiation Dose Associated With Common Computed Tomography Examinations and the Associated Lifetime Attributable Risk of Cancer. Archives of Internal Medicine, 169(22), 2078-2086. DOI: 10.1001/archinternmed.2009.427
Redberg RF. (2009) Cancer risks and radiation exposure from computed tomographic scans: how can we be sure that the benefits outweigh the risks?. Archives of internal medicine, 169(22), 2049-50. PMID: 20008685
Brenner DJ, & Hall EJ. (2007) Computed tomography--an increasing source of radiation exposure. The New England journal of medicine, 357(22), 2277-84. PMID: 18046031
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Santos, M., & Whitham, T. (2009) Predictors of Ips confusus Outbreaks During a Record Drought in Southwestern USA: Implications for Monitoring and Management. Environmental Management. DOI: 10.1007/s00267-009-9413-6
If a patient with a complicated psychiatric history suffers a traumatic brain injury and then develops new psychological problems, how do you know whether the new problems are related to the head injury or the prior psychiatric diagnoses? This dilemma forms the latest 'complex case' to appear in the journal Personality and Mental Health where it is accompanied by five expert commentaries. The complex case is described by psychiatrist Kathleen Diehl at the University of Michigan. She undertook se........ Read more »
Diehl, K. (2009) Head trauma, dissociation and possible development of multiple personalities. Personality and Mental Health, 3(4), 295-301. DOI: 10.1002/pmh.95
Jinbo Hu (Shanghai Institute of Organic Chemistry) and coworkers have synthesized the Z isomer of monofluoroalkenes in high yield, which will be useful towards designing protein-based drugs that resist degradation within the body. This news feature was written on December 30, 2009.... Read more »
Zhang, W., Huang, W., & Hu, J. (2009) Highly Stereoselective Synthesis of Monofluoroalkenes from alpha-Fluorosulfoximines and Nitrones. Angewandte Chemie International Edition, 48(52), 9858-9861. DOI: 10.1002/anie.200905077
Death elasticity and the estate tax.... Read more »
Kopczuk, W., & Slemrod, J. (2003) Dying to Save Taxes: Evidence from Estate-Tax Returns on the Death Elasticity. Review of Economics and Statistics, 85(2), 256-265. DOI: 10.1162/003465303765299783
Gans, J., & Leigh, A. (2006) Did the Death of Australian Inheritance Taxes Affect Deaths?. Topics in Economic Analysis , 6(1). DOI: 10.2202/1538-0653.1654
I often get questions about bioinformatics, bioinformatics jobs and career paths. Most of the questions reflect a general sense of confusion between creating bioinformatics resources and using them. Bioinformatics is unique in this sense. No one confuses writing a package like Photoshop with being a photographer, yet for some odd reason, people seem to expect this of biologists. In the same respect, even the programmers and database administrators who work in bioinformatics, are unfairly ass........ Read more »
Dudley, J., & Butte, A. (2009) A Quick Guide for Developing Effective Bioinformatics Programming Skills. PLoS Computational Biology, 5(12). DOI: 10.1371/journal.pcbi.1000589
Demand from aquarium enthusiasts may fuel invertebrate fishery collapse
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Rhyne, A., Rotjan, R., Bruckner, A., & Tlusty, M. (2009) Crawling to Collapse: Ecologically Unsound Ornamental Invertebrate Fisheries. PLoS ONE, 4(12). DOI: 10.1371/journal.pone.0008413
While my Christmas post was of the gloomy kind, most blogs I follow had more heart-warming stories. Sociolingo Africa picked up a press release coming out of Orlando, Florida issued by who-I-don’t-know, about new translations of the Christmas story becoming available just in time for this year’s event. According to the press release, the Wycliffe [...]... Read more »
Errington, Joseph. (2008) Linguistics in a colonial world: a story of language, meaning, and power. Blackwell Publishing. info:/
James Hansen (NASA Goddard Institute for Space Studies, New York) and coworkers have determined why glaciers on the Tibetan Plateau are quickly melting, and offer possible solutions for preserving this essential water source for future generations. This news feature was written on December 30, 2009.... Read more »
So let’s continue the theme of the AWESOME papers I ran across this semester and didn’t get to blog about. I find every aspect of this paper to be simply cool. There’s also something which kind of ground my gears a bit, but I’ll get to that later if I have time this week.
Controlling mosquitoes [...]... Read more »
Devine, G., Perea, E., Killeen, G., Stancil, J., Clark, S., & Morrison, A. (2009) Using adult mosquitoes to transfer insecticides to Aedes aegypti larval habitats. Proceedings of the National Academy of Sciences, 106(28), 11530-11534. DOI: 10.1073/pnas.0901369106
Whiptails and fencers scurry and make haste,
cross White Sands their paths converge and pace.
Tho' differing by both origin and type,
their causal genotypes follow trace.
Independent mutations had aligned,
and were by adaptation refined.
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Rosenblum, E., Rompler, H., Schoneberg, T., & Hoekstra, H. (2009) Molecular and functional basis of phenotypic convergence in white lizards at White Sands. Proceedings of the National Academy of Sciences. DOI: 10.1073/pnas.0911042107
I have a diverse set of research interests - high-end microscopy, immunology, infectious disease, cancer, etc. Its rare that a paper hits the "awesome" end of the scale in most of those categories, but this week Nature Immunology published a paper that got the nerd senses tingling. In this tour-de-force, Mark Davis's group uses a new form of microscopy to analyse how T-cells work.As usual, a bit of background first.T-cells are the major regulatory cell of our immune system. The........ Read more »
Lillemeier, B., Mörtelmaier, M., Forstner, M., Huppa, J., Groves, J., & Davis, M. (2009) TCR and Lat are expressed on separate protein islands on T cell membranes and concatenate during activation. Nature Immunology, 11(1), 90-96. DOI: 10.1038/ni.1832
Over the past decade it has become evident that many proteins have disordered regions, even in their native states. Moreover, entire proteins were found to be intrinsically disordered. We present here 17 webservers intended to predict disordered regions from protein sequence. Is your protein folded ?
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Linding R, Jensen LJ, Diella F, Bork P, Gibson TJ, & Russell RB. (2003) Protein disorder prediction: implications for structural proteomics. Structure (London, England : 1993), 11(11), 1453-9. PMID: 14604535
Ward, J., Sodhi, J., McGuffin, L., Buxton, B., & Jones, D. (2004) Prediction and Functional Analysis of Native Disorder in Proteins from the Three Kingdoms of Life. Journal of Molecular Biology, 337(3), 635-645. DOI: 10.1016/j.jmb.2004.02.002
Cheng, J., Sweredoski, M., & Baldi, P. (2005) Accurate Prediction of Protein Disordered Regions by Mining Protein Structure Data. Data Mining and Knowledge Discovery, 11(3), 213-222. DOI: 10.1007/s10618-005-0001-y
Prilusky, J. (2005) FoldIndex(C): a simple tool to predict whether a given protein sequence is intrinsically unfolded. Bioinformatics, 21(16), 3435-3438. DOI: 10.1093/bioinformatics/bti537
Linding, R. (2003) GlobPlot: exploring protein sequences for globularity and disorder. Nucleic Acids Research, 31(13), 3701-3708. DOI: 10.1093/nar/gkg519
Dosztanyi, Z. (2005) IUPred: web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content. Bioinformatics, 21(16), 3433-3434. DOI: 10.1093/bioinformatics/bti541
Yang, Z. (2005) RONN: the bio-basis function neural network technique applied to the detection of natively disordered regions in proteins. Bioinformatics, 21(16), 3369-3376. DOI: 10.1093/bioinformatics/bti534
Vullo A, Bortolami O, Pollastri G, & Tosatto SC. (2006) Spritz: a server for the prediction of intrinsically disordered regions in protein sequences using kernel machines. Nucleic acids research, 34(Web Server issue). PMID: 16844983
Galzitskaya OV, Garbuzynskiy SO, & Lobanov MY. (2006) FoldUnfold: web server for the prediction of disordered regions in protein chain. Bioinformatics (Oxford, England), 22(23), 2948-9. PMID: 17021161
Deng X, Eickholt J, & Cheng J. (2009) PreDisorder: ab initio sequence-based prediction of protein disordered regions. BMC bioinformatics, 10(1), 436. PMID: 20025768
Ishida T, & Kinoshita K. (2008) Prediction of disordered regions in proteins based on the meta approach. Bioinformatics (Oxford, England), 24(11), 1344-8. PMID: 18426805
Ishida, T., & Kinoshita, K. (2007) PrDOS: prediction of disordered protein regions from amino acid sequence. Nucleic Acids Research, 35(Web Server). DOI: 10.1093/nar/gkm363
McGuffin LJ. (2008) Intrinsic disorder prediction from the analysis of multiple protein fold recognition models. Bioinformatics (Oxford, England), 24(16), 1798-804. PMID: 18579567
Even in the twenty-first century, infectious diseases such as malaria, dengue fever, cholera, and AIDS remain widespread in much of the developing world, at tremendous cost to human life and economic productivity. Poorer nations lack the resources for more effective public health measures; but widespread infectious disease may slow or prevent the economic development that can provide those resources. A new paper in Proceedings of the Royal Society tries to sort out this chicken-and-egg problem, ........ Read more »
Bonds, M., Keenan, D., Rohani, P., & Sachs, J. (2009) Poverty trap formed by the ecology of infectious diseases. Proc. R. Soc. B. DOI: 10.1098/rspb.2009.1778
As many of us once again rouse ourselves from festivities filled with an overabundance of food, it might be sombering to ponder that a recent PLoS ONE study suggests that nearly 40 percent of food in the United States is wasted. As noted in a recent ScienceNOW article, physiologist Kevin Hall and mathematician Carson Chow, [...]
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Hall, K., Guo, J., Dore, M., & Chow, C. (2009) The Progressive Increase of Food Waste in America and Its Environmental Impact. PLoS ONE, 4(11). DOI: 10.1371/journal.pone.0007940
When do you throw in the towel and concede that a rare species has gone extinct? A new study presents a methodology for helping conservationists answer this difficult question...... Read more »
Elphick, C., Roberts, D., & Michael Reed, J. (2009) Estimated dates of recent extinctions for North American and Hawaiian birds. Biological Conservation. DOI: 10.1016/j.biocon.2009.11.026
Businesses and the economy as a whole rely increasingly on computing, but many potential users are not entirely confident of the technology. A research study published in January suggests that an individual’s computer self-efficacy is influenced by their competence in mathematics. I asked the author Assistant Professor of Management Information Systems Franklin Morris of The [...]Post from: David Bradley's Sciencetext Tech TalkComputer skills linked to math talent
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R. Franklin Morris, Jr., & Evelyn H. Thrasher. (2010) Implications for e-commerce: the influence of math and computer confidence on computer self-efficacy. International Journal of Electronic Marketing and Retailing, 3(1), 15-37. info:/
The promise of perfect "20/10" vision for everybody appeared to be a real possibility in the early 2000's. 2010 is already here and your doctor cannot offer you yet supervision...... Read more »
Santamaria, Artal, Bescos. (1987) Determination of the point spread function of human eyes using a hybrid optical-digital method. J.Opt.Soc.Am.A., 1109. info:/
Egan & Cordan (2008) digitally altered the faces of 17-year-old girls (n=10) to look either younger (morphed to appear similar to the prototype of 10-year-old girls – top row) or older (similar to the prototype of 20-year-old women – bottom row). Additionally, some stimuli were altered by adding digital make-up (right column). The authors had [...]... Read more »
Egan, V., & Cordan, G. (2009) Barely legal: Is attraction and estimated age of young female faces disrupted by alcohol use, make up, and the sex of the observer?. British Journal of Psychology, 100(2), 415-427. DOI: 10.1348/000712608X357858
... Read more »
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