In May, 2010 a truly international and collaborative genomic diagnostic tool was launched. MutaDATABASE is a publicly available, open access, free, online database that provides standardised information on human disease genes, including disease-causing variations. According to a recently published article in Nature Biotechnology: The unprecedented speed and scale with which human sequence variants are being [...]... Read more »
Sherri Bale, Martijn Devisscher, Wim Van Criekinge, Heidi L Rehm, Frederik Decouttere, Robert Nussbaum, Johan T Den Dunnen, & Patrick Willems. (2011) MutaDATABASE: a centralized and standardized DNA variation database. Nature Biotechnology, 117-118. info:/doi:10.1038/nbt.1772
Wish I had know this before when starting in Academia. Really starting your career after all the training you’ve been through, a real challenge. How to start of on the new job.
Important strategies from the medical literature, management practices and hands on experience for “on-boarding”:
Start early, meaning getting toknow your organisation before your start date. [...]
No related posts.... Read more »
Gustin, J., & Tulsky, J. (2010) Effective “On-Boarding”: Transitioning from Trainee to Faculty. Journal of Palliative Medicine, 13(10), 1279-1283. DOI: 10.1089/jpm.2010.0123
The readers of Antony's blog know enough about the problem. And many in the QSAR community know it too (and many other do not). Chemical structure data is noisy. I haven't recently created a new local data set for analysis, so I have not taken time to blog about it much, but the ambiguity in chemical databases is enormous. Just yesterday, Antony and I had a good discussion about tautomers and in particular how things are linked together.
If we are in the field of property prediction, knowing wh........ Read more »
Be where the conversations are: the critical importance of social media From Business Information Review It has become clear that the website is no longer the most important single online source of information. It is now vital that we pay attention to social media conversations. People and companies have a presence in a wider variety [...]... Read more »
Bradley, P. (2011) Be where the conversations are: The critical importance of social media. Business Information Review, 27(4), 248-252. DOI: 10.1177/0266382110390976
The study of speciation—the formation of new species—has had a long history in evolutionary biology, but the past few decades have seen leaps in how we think about the process that creates biodiversity. We now know that natural selection is almost always heavily involved in the process, and that new species can form even when [...]... Read more »
Rova, E., & Björklund, M. (2011) Can Preference for Oviposition Sites Initiate Reproductive Isolation in Callosobruchus maculatus?. PLoS ONE, 6(1). DOI: 10.1371/journal.pone.0014628
Dieting doesn’t work. No really, it doesn’t. Much as people like to talk about how the things they are sticking to are “lifestyle changes”, etc, a lot of them (but not all) are still diets, still ways of restricting your eating, and over 80% of them will fail. By fail, scientists mean that you will [...]... Read more »
Pankevich, D., Teegarden, S., Hedin, A., Jensen, C., & Bale, T. (2010) Caloric Restriction Experience Reprograms Stress and Orexigenic Pathways and Promotes Binge Eating. Journal of Neuroscience, 30(48), 16399-16407. DOI: 10.1523/JNEUROSCI.1955-10.2010
This is sort of a random post, but I remember coming across this paper from 2007 awhile back titled “The quercetin paradox” that shows how quercetin protects against some oxidative damage in a lung cell line but the oxidation product … Continue reading →... Read more »
Jacobs H, Moalin M, Bast A, van der Vijgh WJ, & Haenen GR. (2010) An essential difference between the flavonoids monoHER and quercetin in their interplay with the endogenous antioxidant network. PloS one, 5(11). PMID: 21079733
by PsychBusyBee in ionpsych
Do you take business trips? If so, do you rent a car or take the train, bus, or taxi into town?
What if you are interviewing for a new job? What's the best way to learn where the closest shopping or best pizza place is?
It turns out renting that car might give you a better idea for the city's spatial layout. Continue reading →... Read more »
by Janus in ionpsych
Did you take a foreign language, like Spanish, in high school or college? You might still be able to understand a little Spanish, but you wouldn’t be able to say a whole sentence if your life dependend on it. Even … Continue reading →... Read more »
Warker JA, Xu Y, Dell GS, & Fisher C. (2009) Speech errors reflect the phonotactic constraints in recently spoken syllables, but not in recently heard syllables. Cognition, 112(1), 81-96. PMID: 19398099
A Better Grip: T Cells Strengthen Our Hand against Influenza Clinical Infectious Diseases, 52 (1), 8-9 DOI: 10.1093/cid/ciq018Flu vaccines are important and useful, but also relatively ineffective compared to many other vaccines. Immunity is imperfect, there are many 'strains' of influenza in a given year only some of which are addressed by the available vaccine (though often the most common ones) and one year's vaccine does not provide immunity to subsequent years' influenza because the virus ........ Read more »
Berthoud, T., Hamill, M., Lillie, P., Hwenda, L., Collins, K., Ewer, K., Milicic, A., Poyntz, H., Lambe, T., Fletcher, H.... (2011) Potent CD8 T-Cell Immunogenicity in Humans of a Novel Heterosubtypic Influenza A Vaccine, MVA-NP M1. Clinical Infectious Diseases, 52(1), 1-7. DOI: 10.1093/cid/ciq015
Hambleton, S. (2011) A Better Grip: T Cells Strengthen Our Hand against Influenza. Clinical Infectious Diseases, 52(1), 8-9. DOI: 10.1093/cid/ciq018
Trying to capture the movement of a colony of leaf-cutter ants in a single photo is nearly impossible in my (amateur) experience. The queues of ants follow a worn-down trail in the ground that they themselves made with the impact of their little ant feet. There are ants moving in both directions, between the food [...]... Read more »
Currie, C., Scott, J., Summerbell, R., & Malloch, D. (1999) Fungus-growing ants use antibiotic-producing bacteria to control garden parasites. Nature, 398(6729), 701-704. DOI: 10.1038/19519
Schoenian, I., Spiteller, M., Ghaste, M., Wirth, R., Herz, H., & Spiteller, D. (2011) Chemical basis of the synergism and antagonism in microbial communities in the nests of leaf-cutting ants. Proceedings of the National Academy of Sciences, 108(5), 1955-1960. DOI: 10.1073/pnas.1008441108
The reliability of science is increasingly under fire. We all know that media often gives a distorted picture of scientific findings (i.e. Hot news: Curry, Curcumin, Cancer & cure). But there is also an ever growing number of scientific misreports or even fraud (see bmj editorial announcing retraction of the Wakefield paper about causal relation beteen MMR vaccination [...]... Read more »
Gonon, F., Bezard, E., & Boraud, T. (2011) Misrepresentation of Neuroscience Data Might Give Rise to Misleading Conclusions in the Media: The Case of Attention Deficit Hyperactivity Disorder. PLoS ONE, 6(1). DOI: 10.1371/journal.pone.0014618
Barbaresi, W., Katusic, S., Colligan, R., Weaver, A., & Jacobsen, S. (2007) Modifiers of Long-Term School Outcomes for Children with Attention-Deficit/Hyperactivity Disorder: Does Treatment with Stimulant Medication Make a Difference? Results from a Population-Based Study. Journal of Developmental , 28(4), 274-287. DOI: 10.1097/DBP.0b013e3180cabc28
GONON, F. (2009) The dopaminergic hypothesis of attention-deficit/hyperactivity disorder needs re-examining. Trends in Neurosciences, 32(1), 2-8. DOI: 10.1016/j.tins.2008.09.010
What I love about developmental biology is the collaborative nature of the field. The vast majority of biologists feel that by sharing ideas, data, and reagents, we can learn more than if we were all to work alone with blinders on our heads. A recent paper in Development puts forth a hypothesis about embryonic stem [...]... Read more »
The King of herrings (Regalecus glesne) is the world's longest bony fish. Also known as the giant oarfish, this gentle giant commonly reaches lengths of 7 meters, with its maximum length estimated to be 17 m!
Click the link and see photos and videos of these marvelous creatures.... Read more »
Benfield MC, Cook S, Sharuga S, & Valentine MM. (2013) Five in situ observations of live oarfish Regalecus glesne (Regalecidae) by remotely operated vehicles in the oceanic waters of the northern Gulf of Mexico. Journal of fish biology, 83(1), 28-38. PMID: 23808690
Dragičević, B., Pallaoro, A., Grgičević, R., Lipej, L., & Dulčić, J. (2011) On the Occurrence of Early Life Stage of the King of Herrings, Regalecus Glesne (Actinopterygii: Lampriformes: Regalecidae), in the Adriatic Sea. Acta Ichthyologica Et Piscatoria, 41(3), 251-253. DOI: 10.3750/AIP2011.41.3.13
Taylor, J., & Saloman, C. (1968) The Oarfish, Regalecus glesne: A New Occurrence and Previous Records from the Gulf of Mexico. Copeia, 1968(2), 404. DOI: 10.2307/1441770
Can you take away the feelings of guilt through self harm? Well, here's one way to find out.
Take 59 Australian students, and split them into three groups. Get two groups to write about something they did that they feel guilty about.
Then get one of those groups to stick their arms into iced water - if you've ever tried to do that for a long time, it hurts! The other group gets nice warm water. The third group writes about just some everyday interaction, but then they get the ice bath too.
W........ Read more »
Bastian B, Jetten J, & Fasoli F. (2011) Cleansing the Soul by Hurting the Flesh: The Guilt-Reducing Effect of Pain. Psychological science : a journal of the American Psychological Society / APS. PMID: 21245493
Could social networks be more important than the media in the spread of eating disorders?There's a story about eating disorders roughly like this: eating disorders (ED) are about wanting to be thin. The idea that thinness is desireable is something that's spread by Western media, especially visual media i.e. TV and magazines. Therefore, Western media exposure causes eating disorders.It's a nice simple theory. And it seems to fit with the fact that eating disorders, hitherto very rare, start to a........ Read more »
Becker, A., Fay, K., Agnew-Blais, J., Khan, A., Striegel-Moore, R., & Gilman, S. (2011) Social network media exposure and adolescent eating pathology in Fiji. The British Journal of Psychiatry, 198(1), 43-50. DOI: 10.1192/bjp.bp.110.078675
All quantum physicists know that observation itself changes the object of observation. We will never know what things are actually doing when we are not looking, just because if in order to figure out what they do, we need to look; it's catch-22. But that's quantum physics, you say. How about molecular biology?Well, here is an example. Mitochondria, as you know, have their own genome, and they translate it, and they do so in a very funky way. Ever translation termination........ Read more »
Neubauer C, Gao YG, Andersen KR, Dunham CM, Kelley AC, Hentschel J, Gerdes K, Ramakrishnan V, & Brodersen DE. (2009) The structural basis for mRNA recognition and cleavage by the ribosome-dependent endonuclease RelE. Cell, 139(6), 1084-95. PMID: 20005802
Andreev D, Hauryliuk V, Terenin I, Dmitriev S, Ehrenberg M, & Shatsky I. (2008) The bacterial toxin RelE induces specific mRNA cleavage in the A site of the eukaryote ribosome. RNA (New York, N.Y.), 14(2), 233-9. PMID: 18083838
Pedersen K, Zavialov AV, Pavlov MY, Elf J, Gerdes K, & Ehrenberg M. (2003) The bacterial toxin RelE displays codon-specific cleavage of mRNAs in the ribosomal A site. Cell, 112(1), 131-40. PMID: 12526800
Young DJ, Edgar CD, Murphy J, Fredebohm J, Poole ES, & Tate WP. (2010) Bioinformatic, structural, and functional analyses support release factor-like MTRF1 as a protein able to decode nonstandard stop codons beginning with adenine in vertebrate mitochondria. RNA (New York, N.Y.), 16(6), 1146-55. PMID: 20421313
Soleimanpour-Lichaei HR, Kühl I, Gaisne M, Passos JF, Wydro M, Rorbach J, Temperley R, Bonnefoy N, Tate W, Lightowlers R.... (2007) mtRF1a is a human mitochondrial translation release factor decoding the major termination codons UAA and UAG. Molecular cell, 27(5), 745-57. PMID: 17803939
Temperley R, Richter R, Dennerlein S, Lightowlers RN, & Chrzanowska-Lightowlers ZM. (2010) Hungry codons promote frameshifting in human mitochondrial ribosomes. Science (New York, N.Y.), 327(5963), 301. PMID: 20075246
Who you tawkin' to?
Yuh caen't pahk yuh cah heah.
Who drank da last o'da cawfee?
Whatsa matta wid you?
Ah, the sounds of New York City! I can identify a New Yorker in conversation in a heartbeat. And it's likely that the rest of the country can as well. Residents of New York City and western Long Island (or Lung Guylan as I am apt to pronounce it—a good friend of mine from the Midwest once told me that I was the only person she knew who could produce such a hard /g/ in front ........ Read more »
MUEHLMANN, S. (2008) “Spread your ass cheeks”: And other things that should not be said in indigenous languages. American Ethnologist, 35(1), 34-48. DOI: 10.1111/j.1548-1425.2008.00004.x
Yoga is a practice almost as old as time itself. It combines mental and physical elements that people today use to enhance spirituality, exercise, decrease stress, and increase well-being. While many practitioners of yoga seem almost mystical and more philosophical than the average bear, a new study proves that you need not be a yogi [...]... Read more »
Smith BW, Shelley BM, Dalen J, Wiggins K, Tooley E, & Bernard J. (2008) A pilot study comparing the effects of mindfulness-based and cognitive-behavioral stress reduction. Journal of alternative and complementary medicine (New York, N.Y.), 14(3), 251-8. PMID: 18370583
Streeter CC, Whitfield TH, Owen L, Rein T, Karri SK, Yakhkind A, Perlmutter R, Prescot A, Renshaw PF, Ciraulo DA.... (2010) Effects of yoga versus walking on mood, anxiety, and brain GABA levels: a randomized controlled MRS study. Journal of alternative and complementary medicine (New York, N.Y.), 16(11), 1145-52. PMID: 20722471
In my last post I started to discuss the questionnaire domains that can be used in a battery of questionnaires for chronic pain. Today it’s time to turn to the specific measures that we’ve chosen as part of a set that a group working across the public health system in New Zealand have selected. It’s … Read more... Read more »
McCracken LM, & Dhingra L. (2002) A short version of the Pain Anxiety Symptoms Scale (PASS-20): preliminary development and validity. Pain research , 7(1), 45-50. PMID: 16231066
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