Publish or Perish sums up the urgency for scientists to publish in top journals. Scientists work in competitive environments in which publishing is essential to their careers, reputation and research funding. Journal editors and peer reviewers are the ones to judge the manuscripts for quality and safeguard the interests of the readership of the journal.
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Drazen, J., Van Der Weyden, M., Sahni, P., Rosenberg, J., Marusic, A., Laine, C., Kotzin, S., Horton, R., Hebert, P., Haug, C.... (2009) Uniform Format for Disclosure of Competing Interests in ICMJE Journals. New England Journal of Medicine. DOI: 10.1056/nejme0909052
Jefferson, T. (2002) Effects of Editorial Peer Review: A Systematic Review. JAMA: The Journal of the American Medical Association, 287(21), 2784-2786. DOI: 10.1001/jama.287.21.2784
DeMaria, A. (2003) Duplicate publication: insights into the essence of a medical journal. Journal of the American College of Cardiology, 41(3), 516-517. DOI: 10.1016/S0735-1097(03)00002-0
Red may be the literary color of love, but for psychologists red is emerging as the color of male sexual desire, as a recent study finds that the mere presence of red color increases men's perception of women's attractiveness.... Read more »
Elliot, A., & Niesta, D. (2008) Romantic red: Red enhances men's attraction to women. Journal of Personality and Social Psychology, 95(5), 1150-1164. DOI: 10.1037/0022-35220.127.116.110
Recently we took our hybrid car into the shop for its annual emissions test. In our state, the test is conducted while the car is idling. A hybrid doesn't actually idle -- it shuts the engine off completely. So our car's emissions were tested at 0 RPM. It may be time to rethink our state's emissions laws.
There's another law that might need rethinking in the age of hybrids. Our car's internal combustion engine often doesn't start up even when the car is moving at low speeds -- it uses electric motors, running nearly silently. This can potentially be dangerous for pedestrians in parking lots and crosswalks: if they can't hear us, they might not notice us at all, and if we don't see them, someone could get hurt. Now some states are actually considering legislation requiring cars to make noise even while idling or moving at low speeds.
But how much does noise help us spot objects? Aren't pedestrians supposed to look for cars, not just listen for them? Aren't drivers supposed to look for hazards, not hear them? Indeed, there has been some research suggesting that sounds do help us locate objects. However, most of this research has been on directional sounds -- a sound from the right helps us spot an object on the right side of the computer screen (for an exception, see this post). Does a sound that's not from a particular direction still help us notice a change?
A team led by Toemme Noesselt flashed images using an extra fast-response computer display to flash images at 16 volunteers. The displays looked something like
this movie (click on the image to play):
For each trial, viewers had to say whether the top or the bottom ring of dots disappeared. It's easy in this version because your computer display is probably not fast enough to show the actual flashes. In the actual experiment, viewers were first tested to determine how quick a flash they could spot. Usually this was around 15 milliseconds (the flash in my movie, for comparison, was 100 milliseconds). Then they were shown movies like mine, where either the central cross changed to a circle to cue viewers that one of the rings of dots were disappearing, or a tone was played while the ring disappeared, or nothing cued them. Read the rest of this post... | Read the comments on this post...... Read more »
What’s grosser than gross? How ‘bout a 100-mile long wad of E. Coli-infested mucus?
(Oh, sorry, did that make you gag? We said it was grosser than gross…)
Mucus wads—also known as mucilages—have been reported in the Mediterranean Sea since at least 1729, but recent research found that the loogies are getting bigger, lasting longer and harboring [...]... Read more »
Danovaro, R., Fonda Umani, S., & Pusceddu, A. (2009) Climate Change and the Potential Spreading of Marine Mucilage and Microbial Pathogens in the Mediterranean Sea. PLoS ONE, 4(9). DOI: 10.1371/journal.pone.0007006
Meralgia Paresthetica like most other neuropathies can purpose a dilemma in diagnosing. Nerves often project arbitrary findings in the examination process. This article discusses a new valid test manual therapist can finally use to help in their diagnosis.... Read more »
A recent paper in PLoS One finds hundreds of new putative transcription start sites (TSS): PLoS ONE: Genome-Wide Identification of Transcription Start Sites, Promoters and Transcription Factor Binding Sites in E. coli. I found the paper interesting, and a good example of how high-throughput studies and genomics can advance our understanding of biology and work in concert with experimental biology, while at the same time dumping a whole lot of new data in our laps.
I’d like to point out some of the databases and resources that are mentioned and used in this paper. In fact, this is the first semi-weekly installment of ‘what did they use?’ post. I’d like to start citing papers that I find interesting and pull out the software, databases and genomics resources used in them. Might help our readers get an understanding of what is being used out there.
First and foremost, this paper has added a large set of new data to RegulonDB, or to paraphrase their about page:
RegulonDB is a computational model of mechanisms of transcriptional regulation including the complex regulation of transcription initiation or regulatory network of the cell and of the organization of the genes in transcription units, operons and simple and complex regulons.
So, if you have used RegulonDB in the past, or might find use of it, you’ll see there is a large set of new data.
Additionally, the paper does it’s analysis using several programs (some of which have web interfaces) including WConsensus (from the same lab that brings you Consensus, tutorial, for those subscribed) and Patser (ftp link to download, also from the Stormo lab) to predict promotors. The authors also use Matrix-Scan, to predict transcription factor binding sites.
As with many papers, I had to go to the citation of the paper about the resource, find the paper and then determine where the database or software resided. As I’ve said before, there needs to be a better way to reference work done using databases.
Mendoza-Vargas, A., Olvera, L., Olvera, M., Grande, R., Vega-Alvarado, L., Taboada, B., Jimenez-Jacinto, V., Salgado, H., Juárez, K., Contreras-Moreira, B., Huerta, A., Collado-Vides, J., & Morett, E. (2009). Genome-Wide Identification of Transcription Start Sites, Promoters and Transcription Factor Binding Sites in E. coli PLoS ONE, 4 (10) DOI: 10.1371/journal.pone.0007526
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Mendoza-Vargas, A., Olvera, L., Olvera, M., Grande, R., Vega-Alvarado, L., Taboada, B., Jimenez-Jacinto, V., Salgado, H., Juárez, K., Contreras-Moreira, B.... (2009) Genome-Wide Identification of Transcription Start Sites, Promoters and Transcription Factor Binding Sites in E. coli. PLoS ONE, 4(10). DOI: 10.1371/journal.pone.0007526
THE humble fruit fly (Drosophila melanogaster) has the ability to learn and remember, and to make predictions about the outcome of its behaviours on the basis of past experience. Compared to a human brain, that of the fruit fly is relatively simple, containing approximately 250,000 cells. Even so, little is known about the anatomical basis of memory formation. The neural circuitry underlying memories in these insects has now been dissected. In an elegant new study published in the journal Cell, researchers from the University of Oxford show that aversive memories are dependent on a tiny cluster of neurons, and also demonstrate that such memories can be implanted in the fruit fly's brain by using light to manipulate the cells' activity. Read the rest of this post... | Read the comments on this post...... Read more »
Claridge-Chang, A., Roorda, R., Vrontou, E., Sjulson, L., Li, H., Hirsh, J., & Miesenböck, G. (2009) Writing Memories with Light-Addressable Reinforcement Circuitry. Cell, 139(2), 405-415. DOI: 10.1016/j.cell.2009.08.034
Ecosystems can provide nuisances as well as benefits
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Lyytimäki, J., & Sipilä, M. (2009) Hopping on one leg – The challenge of ecosystem disservices for urban green management. Urban Forestry . DOI: 10.1016/j.ufug.2009.09.003
Just as I was in the process of finishing my doctorate in August, I found out that my first first-author paper had been accepted for publication by The EMBO Journal. This was good news, because we were reporting some pretty fundamental findings in a relatively saturated field, and one of our competitors had managed to successfully stall the acceptance of this paper since March. Up until that point, witnessing this happen firsthand had been a somewhat frustrating and disillusioning experience for a young scientist, but I think that we were vindicated in the end. Anyway, this paper--and another paper that I contributed to--were published online earlier this month.
These studies both explore the important biological process of integrin activation. The first paper (Anthis et al.) provides some new basic molecular details for how this process is carried out in the cell. Cells in humans and other higher organisms exist in a dynamic environment, alternately grasping and disengaging from the three-dimensional web of their surroundings (i.e. the extracellular matrix). Many of these tasks involve a family of proteins called integrins, which act as the "hands" of the cell. The cell internally controls whether an integrin is adhesive by signals from within the cell, using another protein called talin. By exploring the detailed three-dimensional structure of a talin/integrin complex, we showed how key interactions between talin, the integrin, and the inner surface of the cell membrane can elegantly promote the structural changes outside the cell that modulate adhesion strength.
The following figure (from my thesis) illustrates the process of integrin activation: Read the rest of this post... | Read the comments on this post...... Read more »
Anthis NJ, Wegener KL, Ye F, Kim C, Goult BT, Lowe ED, Vakonakis I, Bate N, Critchley DR, Ginsberg MH.... (2009) The structure of an integrin/talin complex reveals the basis of inside-out signal transduction. The EMBO journal. PMID: 19798053
Goult BT, Bouaouina M, Harburger DS, Bate N, Patel B, Anthis NJ, Campbell ID, Calderwood DA, Barsukov IL, Roberts GC.... (2009) The Structure of the N-Terminus of Kindlin-1: A Domain Important for alphaIIbbeta3 Integrin Activation. Journal of molecular biology. PMID: 19804783
Some invasive plants only become a big problem when they reach a certain abundance. Scientists search for that magic threshold...read more... Read more »
Gooden, B., French, K., Turner, P., & Downey, P. (2009) Impact threshold for an alien plant invader, Lantana camara L., on native plant communities. Biological Conservation, 142(11), 2631-2641. DOI: 10.1016/j.biocon.2009.06.012
You can never accuse cosmologists of thinking small. To them even galaxies are like tiny little molecules and complex formulas govern the behavior of manifolds measuring hundreds of millions of light years. And if you thought that one universe was complicated and difficult enough, some cosmologists are actually tackling the idea of multiple universes branching [...]... Read more »
In a recent online publication about another form of brain stimulation in treatment resistant depression showed promising results. The electrodes are placed on the brain instead of in the brain as with Deep Brain Stimulation (DBS):
A new neurosurgical procedure may prove helpful for patients with treatment-resistant depression. Bilateral epidural prefrontal cortical stimulation (EpCS) was found [...]
Related posts:Deep Brain Stimulation for Treatment Resistant depression New data are being published about deep brain stimulation...Hands on Experience with Deep Brain Stimulation for Depression Recently I found a hands on experience blog for...New Innovations in Deep Brain Stimulation Surgery A great step forward, patients don’t have to be...
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Nahas, Z., Anderson, B., Borckardt, J., Arana, A., George, M., Reeves, S., & Takacs, I. (2009) Bilateral Epidural Prefrontal Cortical Stimulation for Treatment-Resistant Depression. Biological Psychiatry. DOI: 10.1016/j.biopsych.2009.08.021
Late last week, I received emails from two journals (The Journal of Biological Chemistry (JBC) and PLoS ONE) indicating that they are now incorporating interactive 3D images of molecular structures in their papers. The atomic coordinates of all published biomolecular structures have been available for some time at the Protein Data Bank. However, making sense of something as complex as a protein structure can require quite a bit of analysis. So, scientists go through great pains to represent important features of their structures in 2D images for publication. Ostensibly, this new functionality will save readers time and enhance their understanding by letting them explore these structures, but starting with the important features already highlighted.
After a quick look at these new interactive 3D images, though, I have to admit that I'm finding the experience slightly cumbersome. Still, this is a good idea, and I imagine that the experience will be improved over time. You can check out the first JBC paper incorporating the interactive images here, and a collection of papers in PLos ONE incorporating the images here. Below is the press release on the subject from PLoS ONE: Read the rest of this post... | Read the comments on this post...... Read more »
Kumar, P., Vahedi-Faridi, A., Saenger, W., Merino, E., Lopez de Castro, J., Uchanska-Ziegler, B., & Ziegler, A. (2009) Structural Basis for T Cell Alloreactivity among Three HLA-B14 and HLA-B27 Antigens. Journal of Biological Chemistry, 284(43), 29784-29797. DOI: 10.1074/jbc.M109.038497
Raush, E., Totrov, M., Marsden, B., & Abagyan, R. (2009) A New Method for Publishing Three-Dimensional Content. PLoS ONE, 4(10). DOI: 10.1371/journal.pone.0007394
Scientists love to group things. We also like to name things. We also like to plot data on bivariate graphs. On really crazy nights, we let our hair down, well not me per se but other scientists with hair, and do all three. 90% of science is grouping, naming, and plotting.
If you don’t know already [...]... Read more »
Tyler, P., Marsh, L., Baco-Taylor, A., & Smith, C. (2009) Protandric hermaphroditism in the whale-fall bivalve mollusc Idas washingtonia. Deep Sea Research Part II: Topical Studies in Oceanography, 56(19-20), 1689-1699. DOI: 10.1016/j.dsr2.2009.05.014
Cytomegalovirus (CMV) is one of the herpesvirus group, viruses that are extremely hard or impossible for the body to clear. They lurk and return time after time. CMV doesn't cause immediate issues in healthy people, but over time it becomes one of the principle causes of the characteristic failure of the immune system with aging: Your immune system is capped in its use of resources; it can only have a set number of T cells in operation at one time. ... chronic infections by the likes of cytomegalovirus (CMV) cause too many of your immune cells to be - uselessly - specialized. ... because you cannot clear it from your system, its presence chews up more and more of your limited immune resources with time. Immune cells dedicated to remembering and attacking the many biochemical signatures of CMV are not available to fight new threats - and that starts to be a real issue in later life. Your immune system simply cannot mount an effective response when so much of it is tied up in uselessly awaiting the next emergence of CMV. Many research groups are investigating ways to effectively destroy herpesviruses like CMV, and thus clear them from the...... Read more »
Duan QJ, Tao R, Hu MF, & Shang SQ. (2009) Efficient inhibition of human cytomegalovirus UL122 gene expression in cell by small interfering RNAs. Journal of basic microbiology. PMID: 19810036
Crudely speaking, our actions can be divided into those that are automatic and driven by the environment and those that are initiated volitionally, as an act of will. In an intriguing new study, Todd Horowitz and colleagues claim to have recorded the relatively sluggish time taken for free will to be enacted. Their finding could help explain our natural tendency to search visual scenes via apparently random, haphazard attentional shifts, rather than using our conscious will to search more strategically. The fact is, our volitional control is simply too slow, rendering a deliberate, ordered approach ineffective. In one experiment, Horowitz's team presented ten participants with a display rather like a clock face, but with capital letters in the positions where numbers would usually be. The display was visible for just a brief flash (53ms) before disappearing and re-appearing again, which it did twelve times.In the condition that tested the speed of free will, the participants' task was to shift their gaze in time with the flashes of the display, so that they focused on each successive letter position on the clock face, starting at the 12 o'clock position and going clockwise.The participants' aim was to look out for the letter "Y" and note its colour. Crucially, the letters changed each time the clock face returned and the "Y" only appeared during one flash of the display, in a specific position. If a participant hadn't shifted their attention around the display in time with the clock face flashes, they wouldn't be attending in the right place at the right time to see the "Y".By varying the duration of the lulls between each flash of the clock face, the researchers were able to test the top speed at which participants were able to volitionally shift their attention from one letter position to the next. It turned out the participants needed an average of about 274ms (about quarter of a second) to make these attentional shifts successfully. This volitional condition was contrasted with a control task in which participants could attend to any letter position on the clock face that they wanted. As before, the clock face flashed on and off and the participants had to spot the "Y" and note its colour. However, if the lulls between each flash were too quick, there wouldn't be time for the participants' automatic attentional system to shift between letter positions in search of the "Y". In this mode, with their attentional system free to operate on auto (the researchers dubbed this the "anarchy" condition), the participants needed just 85ms to shift attention from one letter position to another. Four further experiments with different parameters supported this finding. Past research in this field has tended to use symbolic cues, such as arrows, to direct participants' volitional shifts of attention. A short-coming of these studies is that the time taken to interpret and process these cues likely contaminated estimates of the time taken to wilfully shift attention. The current research avoids this problem."It is substantially faster to 'delegate authority'" when searching a visual scene the researchers said. "If you tell yourself to find the letter 'P' or red verticals or your coffee mug, selective attention will shift around the visual world at a rate at least four times faster, in our estimation, than it would if you insisted on commanding each deployment of attention with an individual act of will." _________________________________Horowitz TS, Wolfe JM, Alvarez GA, Cohen MA, & Kuzmova YI (2009). The speed of free will. Quarterly journal of experimental psychology (2006), 62 (11), 2262-88 PMID: 19255946
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by Rita Tojeiro in we are all in the gutter
In our first post exploring galaxy evolution, we saw how observing galaxies at different distances from us is crucial for our understanding of how galaxies form and evolve. It also naturally follows that the larger the range of distances we can study, the better we can constrain our theories. So it’s only natural that astronomers [...]... Read more »
M. Bradač, T. Treu, D. Applegate, A. H. Gonzalez, D. Clowe, W. Forman, C. Jones, P. Marshall, P. Schneider, & D. Zaritsky. (2009) Focusing Cosmic Telescopes: Exploring Redshift z~5-6 Galaxies with the Bullet Cluster 1E0657-56. Accepted for publication in ApJL. arXiv: 0910.2708v1
P. A. Oesch, R. J. Bouwens, G. D. Illingworth, C. M. Carollo, M. Franx, I. Labbe, D. Magee, M. Stiavelli, M. Trenti, & P. G. van Dokkum. (2009) z~7 Galaxies in the HUDF: First Epoch WFC3/IR Results. submitted to ApJL. arXiv: 0909.1806v1
Andrew Bunker, Stephen Wilkins, Richard Ellis, Daniel Stark, Silvio Lorenzoni, Kuenley Chiu, Mark Lacy, Matt Jarvis, & Samantha Hickey. (2009) The Contribution of High Redshift Galaxies to Cosmic Reionization: New Results from Deep WFC3 Imaging of the Hubble Ultra Deep Field. Submitted to MNRAS. arXiv: 0909.2255v2
Sexual activities at work have become a modern taboo. Everything from sexual jokes and innuendo to overt touching and sex acts have become absolutely forbidden in the workplace. Some sexual behaviors (jokes, banter, flirting) might be seen as innocent and a natural part of being human, but the current trend is one of zero tolerance [...]... Read more »
Dysphagia among stroke patients is suggested by the following test:
First check the patient for “swallowing complaints, abnormalities of voice quality, facial asymmetry, or either expressive or receptive aphasia.” If none is detected then go to step 2.
Have the patient drink 10 mL of water from a cup without a straw while seated upright [...]... Read more »
Turner-Lawrence DE, Peebles M, Price MF, Singh SJ, & Asimos AW. (2009) A feasibility study of the sensitivity of emergency physician Dysphagia screening in acute stroke patients. Annals of emergency medicine, 54(3), 344. PMID: 19362752
Everyday in the news we see stories decrying the use of cell phones while driving. Research reports aplenty have been released estimating the percentage of one’s attention siphoned by mobile jabber and how little is left to focus on the highway.
This is great and I’m glad the discussion is happening, but it might be useful to ask whether cell phone use in other (non-driving) venues has a similar effect on attention. What better way to make the point that cell phone use is dangerous when driving than showing its effect on someone doing something not nearly as focus intensive — like walking, for instance.
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Hyman, I., Boss, S., Wise, B., McKenzie, K., & Caggiano, J. (2009) Did you see the unicycling clown? Inattentional blindness while walking and talking on a cell phone. Applied Cognitive Psychology. DOI: 10.1002/acp.1638
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