by United Academics in United Academics
Researchers from the Oxford University have found that people consuming a common heart disease drug, propranolol (40 mg), show less implicit racism than those who don’t consume the medicine. The drug acts on the mechanisms that activate fear, which, according to the scientists, is the main cause of racism.... Read more »
Terbeck, S., Kahane, G., McTavish, S., Savulescu, J., Cowen, P., & Hewstone, M. (2012) Propranolol reduces implicit negative racial bias. Psychopharmacology. DOI: 10.1007/s00213-012-2657-5
by Clay Clark in Biochem Blogs
sciseekclaimtoken-4f580c3179515 Rapid bioorthogonal labeling of proteins By Clay Clark, @biochemprof There are a number of current methods for labeling proteins for imaging either in vitro and/or in live cells and organisms, including fusions with fluorescent proteins, dyes, tags (such as SNAP, … Continue reading →... Read more »
Lang, K., Davis, L., Torres-Kolbus, J., Chou, C., Deiters, A., & Chin, J. (2012) Genetically encoded norbornene directs site-specific cellular protein labelling via a rapid bioorthogonal reaction. Nature Chemistry. DOI: 10.1038/NCHEM.1250
Chen, I., & Ting, A. (2005) Site-specific labeling of proteins with small molecules in live cells. Current Opinion in Biotechnology, 16(1), 35-40. DOI: 10.1016/j.copbio.2004.12.003
Best, M. (2009) Click Chemistry and Bioorthogonal Reactions: Unprecedented Selectivity in the Labeling of Biological Molecules. Biochemistry, 48(28), 6571-6584. DOI: 10.1021/bi9007726
by Colin Beale in Safari Ecology
15 times more toxic than cobra venom, you really shouldn't eat a Nairobi beetle! Nairobi bugs (also known around East Africa as Nairobi Eye, Nairobi Fly, Nairobi beetles, Blister Beetles and a whole range of other names) are not the best loved creatures out here. This year they've come out in greater number than the last few years, presumably thanks to some relatively good rains, and whilst they're not loved, they're certainly fascinating wee beasties. But before we go into the details, let's start with some identification preliminaries.There are actually at least two species of beetle known as Nairobi bugs around here, but they're so similar that most people won't notice them. Similarly marked relatives of these two are pretty widely distributed across the world, mainly in the tropics, and for now I don't think we need to bother about the precise identification. They're all small (7mm-1cm ish) and well marked with typical warning (aposematic) colours of black and red. In fact, despite the variety of names these are beetles (Coleopterans) of the family Staphylinidae, the rove beetles. If you don't know the Nairobi beetle, you might well know the Devil's Coach-horse and similar species - much larger and all black, but of a similar basic structure. The beetles we're interested in are of the genus Paederus and are carnivorous beetles that live mostly in long grass and anywhere with rotting leaves. And the most interesting things about them, as anyone will tell you, is that whilst they neither bite nor sting, they're still seriously nasty.All you have to do is brush against or slightly squash a Nairobi but, and you'll likely end up with chemical burns wherever you came in contact with the beast. It's a pretty remarkable defence (and fairly effective at dissuading the main predator - wolf spiders - from eating them too, though not other insects) and whilst looking things up for this post I was amazed to discover the the British, Canadian and US armed forces all take the beetles very seriously: I particularly like the US paper on "Entomological terrorism", suggesting that Paederus beetles could be used by an enemy in a direct attack. And the Indian Armed Forces investigated the use of the beetles in chemical warfare back in 2002! Indeed, there's even a suggestion that two of the 10 plagues that the Ancient Egyptian suffered we caused by mass emergence of these beetles that was brough on by the first two (Nile and frogs): Number four (flies), followed a few days later by number 6 (incurable boils). Paederus crebinpunctatus or P. sabaeus? Anyone know? Arusha, March 2012That actually leads nicely into what started me puzzling over these beasts in the first place: a beetle crawls on you, you damage it as you brush it away and nothing happens. Huh? Then a day or two later, your skin turns red and soon it starts to blister nastily, the sores lasting (I can say from personal experience!) for 10 days to two weeks. A pretty seriously long time for such a nasty experience. So I set out to research what makes these beetles quite so nasty. As ever, the more I learnt, the more fascinating it becomes. It turns out that the toxin involved is highly toxic - about 15 times more toxic than Cobra venom, (which means that the dose you have to give a group of 100 rats to kill 50 of them is about 1/15th that of cobra venom) so it's just as well they don't bite! And trust me, you really, really don't want to eat one of these beetles. But it's action is far from normal - this isn't an acid burn as some would have you think (in fact, the active ingredient is an amide, so probably slightly alkaline), but something far more interesting. It turns out that whilst we still don't know exactly how it does it, the active ingredient (called pedarin, as it comes from Paederus beetles) has the almost instant effect of stopping the cells making protein and DNA. That might not sound too bad, but over a day or two it's pretty serious (hence the interesting delay in the action) as cells that stop doing these things die (in fact, the cells kill themselves, in a process known as apoptosis).Now, stopping protein and DNA synthesis (but, curiously, not RNA synthesis) is a pretty remarkable activity for a biological toxin, and like a lot of defence chemicals it's attracted a bit of attention from the pharmaceutical world. One property in particular is very interesting: it stops cell division (mitosis). Now, if you know anything about cancer, you'll know that a cancer is simply a bunch of cells that have forgotten to stop dividing. So a chemical that stops cell division, and can even induce cells to kill themselves is going to attract a lot of interest. And sure enough, pedarin has been shown to slow the growth of a cancerous tumour in mice. I've not found any research yet that takes this further into humans, but watch this space...Interestingly too, it turns out that pedarin isn't actually produced by the beetles themselves. Only females can produce it themselves (though males can have some from the egg), and only some females at that. In fact, it's produced by symbiotic bacteria living within the insect, a species of bacteria that is fairly closely related to Pseudomonas aeruginosa, a fairly well-known disease causing bug. It turns out that females with the bacteria lay eggs that are also infected with the bacteria, allowing their offspring to be pre-infected with it (though males can't keep it and must make use of the tiny quantities of chemical in the egg). Females without the bacteria can't do this, but they can be infected with it if they eat the eggs or larvae of a female that is infected, and then they, too, can lay eggs pre-infected with the bacteria. Neat! And there's even a theory that squashing the beetle releases not only the beetle juices (technically called haemolymph), but also the bacteria too, which can keep living in the skin for a while, producing yet more nasty pedarin - and explaining quite why it might take so long to heal. As I say, they're really, really nasty bugs!Main references:... Read more »
Kellner, R. (2002) Molecular identification of an endosymbiotic bacterium associated with pederin biosynthesis in Paederus sabaeus (Coleoptera: Staphylinidae). Insect Biochemistry and Molecular Biology, 32(4), 389-395. DOI: 10.1016/S0965-1748(01)00115-1
Jewett, J., & Rawal, V. (2007) Total Synthesis of Pederin. Angewandte Chemie, 119(34), 6622-6624. DOI: 10.1002/ange.200701677
Brega, A. (1968) STUDIES ON THE MECHANISM OF ACTION OF PEDERINE. The Journal of Cell Biology, 36(3), 485-496. DOI: 10.1083/jcb.36.3.485
by Clay Clark in Biochem Blogs
Let there be { if (RhoGTP + Effector == ProteinComplex) { Luc1 + Luc2 = ActiveLuciferase; LIGHT = 1; } else if (RhoGTP + GAP == RhoGDP) { RhoGDP + Effector = NoProteinComplex; LIGHT = 0; } else if (RhoGDP … Continue reading →... Read more »
Anderson, E., & Hamann, M. (2012) Detection of Rho GEF and GAP activity through a sensitive split luciferase assay system. Biochemical Journal, 441(3), 869-879. DOI: 10.1042/BJ20111111
Jaiswal M, Dubey BN, Koessmeier KT, Gremer L, & Ahmadian MR. (2012) Biochemical assays to characterize Rho GTPases. Methods in molecular biology (Clifton, N.J.), 37-58. PMID: 22144266
Massoud, T., Paulmurugan, R., De, A., Ray, P., & Gambhir, S. (2007) Reporter gene imaging of protein–protein interactions in living subjects. Current Opinion in Biotechnology, 18(1), 31-37. DOI: 10.1016/j.copbio.2007.01.007
by Clay Clark in Biochem Blogs
When nano first met biology by Xun Lu Lysozyme is an enzyme that helps to protect us from getting bacterial infections because it can degrade and utilize the sugars in the bacterial cell wall. A good source of lysozyme … Continue reading →... Read more »
Choi, Y., Moody, I., Sims, P., Hunt, S., Corso, B., Perez, I., Weiss, G., & Collins, P. (2012) Single-Molecule Lysozyme Dynamics Monitored by an Electronic Circuit. Science, 335(6066), 319-324. DOI: 10.1126/science.1214824
by David Steen in Living Alongside Wildlife
A New York Snapping Turtle
Protecting Snapping Turtles in Canada. The distribution and range of a species is often heavily influenced by climate and habitat. If an area does not have suitable climate or habitat for a species, they cannot occur there. It's that simple. Polar Bears would not be comfortable in tropical jungles and you will not find Green Iguanas basking on icecaps. It gets a ... Read more »
Cedervall, T., Hansson, L., Lard, M, Frohm, B, & Linse, S. (2012) Food Chain Transport of Nanoparticles Affects Behaviour and Fat Metabolism in Fish. PLoS ONE, 7(2). info:/
de Solla SR, Bishop CA, Lickers H, & Jock K. (2001) Organochlorine pesticides, PCBs, dibenzodioxin, and furan concentrations in common snapping turtle eggs (Chelydra serpentina serpentina) in Akwesasne, Mohawk Territory, Ontario, Canada. Archives of environmental contamination and toxicology, 40(3), 410-7. PMID: 11443374
Allender MC, Dreslik M, Wylie S, Phillips C, Wylie DB, Maddox C, Delaney MA, & Kinsel MJ. (2011) Chrysosporium sp. infection in eastern massasauga rattlesnakes. Emerging infectious diseases, 17(12), 2383-4. PMID: 22172594
by Elizabeth Preston in Inkfish
Infinitesimal particles inside our cosmetics, drugs, and processed foods are making their way into streams and oceans. There, they become a whole new food group for fish and other aquatic life. Although we treat them as harmless, the nanoparticles added to fish's diets may put them off their lunch altogether.
Manmade nanoparticles--bits of material built to be 300 microns across or smaller--have been booming over the last 10 to 15 years. In pharmaceuticals, they carry tiny doses of drugs into our bodies. In sunscreen, they protect our skin without creating an opaque white coating. Eddie Bauer uses them to make stain-repellent "Nano-Care" khakis.
But once these products have passed through our bodies or been washed off our skin, nanoparticles can journey out into the world, perhaps to be ingested by other organisms. And they don't travel alone. Like staticky socks, nanoparticles collect a coating of hangers-on as they pass through the hallways of an animal's body. Instead of dust and hair, though, they like to gather proteins. For example, several types of nanoparticles are known to trap molecules called apolipoproteins. These proteins are crucial to animals: they help us process the fat that we eat.
Researchers in Sweden set out to discover whether nanoparticles in a fish's environment would affect its metabolism. Would nanoparticles travel up the food chain and into the bodies of predatory fish? And after they'd ingested nanoparticles, would fish have trouble breaking down fats?
Inside the lab, the scientists set up a simple food chain. On the first day of their study, they added plastic nanoparticles to bottles of growing green algae. After 24 hours, they filtered out the algae and fed it to speck-sized crustaceans called daphnia, or water fleas. After another 24 hours, these tiny animals were removed and rinsed off. (The filtering and rinsing steps ensured that only nanoparticles that had actually been consumed would travel up the food chain.)
On the third day, the daphnia were fed to tanks of carp. The researchers observed the fish's feeding behavior, and timed how long it took the fish to gobble up 95% of the hapless water fleas. Then the cycle started over: new nanoparticles were given to new algae, which was fed to new daphnia, which were fed to the same tanks of carp. This went on for 30 days, with the fish fed every 3 days and weighed periodically.
The effects of the fish's new diet didn't show up right away. But after a couple weeks of eating water fleas infused with plastic nanoparticles--and accumulating those nanoparticles inside their own bodies--the carp behaved strangely.
Fish fed a nanoparticle-free diet consistently munched through their food in about five minutes. But the nanoparticle-eating fish slowed way, way down. It took these fish more than twice as long as the others to eat their meal. They moved sluggishly, not actively hunting for the tiny food animals that had been freed in their tank. Bizarrely, the researchers write, "test fish let daphnia swim in and out of their mouth without trying to eat them."
Because they expected nanoparticles to screw up the fish's fat processing, the researchers intentionally gave the fish too little to eat. This made all the fish lose weight as they began to burn up their fat reserves, just like any animal on a diet.
But as time went on, the nanoparticle-fed fish stopped losing weight. By the end of the month, they'd even gained a little.
The authors think that because nanoparticles had sucked up more and more of the carp's apolipoproteins as they ate the contaminated food, the fish couldn't use those proteins to process fat. When starved, they were unable to burn up their stored fat. And somewhere in the complex system of feedback loops that control eating and energy, the fish actually stopped losing weight--even as they lost nearly all interest in their food.
The plastic nanoparticles used in this study are a type that's handy for research, but not especially common outside of the lab. The nanoparticles in sunscreen, for example, are made of zinc oxide or titanium dioxide. Nanoparticles can have various shapes and surface charges, which determine what proteins they'll cling to as they pass through the world. But previous research has shown that the types of metal nanoparticles found in sunscreen can bind to lipoproteins, just as the plastic particles in this study did.
The authors don't address how the concentration of nanoparticles used in their study compares to the concentration that might be found in, say, a contaminated pond--or in your body. But it wouldn't hurt to look into how nanoparticles affect our own metabolisms. And the effect on the fish in this study intensified over time, as nanoparticles seemed to accumulate in their systems.
Every bit of nanoparticle-containing material we add to the waterways, then, might be contributing to some effect on fish. Maybe in the future we'll have to medicate them with nanodrugs.
Cedervall, T., Hansson, L., Lard, M., Frohm, B., & Linse, S. (2012). Food Chain Transport of Nanoparticles Affects Behaviour and Fat Metabolism in Fish PLoS ONE, 7 (2) DOI: 10.1371/journal.pone.0032254
Photo: Benson Kua/Flickr
Thanks to Michael Shuler at Cornell University for talking to me about nanoparticles. He published a paper earlier this month on the effect of dietary nanoparticles on chickens.
... Read more »
Cedervall, T., Hansson, L., Lard, M., Frohm, B., & Linse, S. (2012) Food Chain Transport of Nanoparticles Affects Behaviour and Fat Metabolism in Fish. PLoS ONE, 7(2). DOI: 10.1371/journal.pone.0032254
This post is part of OpenHelix's "Tip of the Week" blog feature. For today’s tip I am offering our full introductory tutorial on the RCSB PDB, which we completely updated to cover their Top Search Bar, PDB 101 education feature, and more. ... Read more »
Berman, H., & et al. (2000) The Protein Data Bank. Nucleic Acids Research, 28(1), 235-242. DOI: 10.1093/nar/28.1.235
Rose, P., Beran, B., Bi, C., Bluhm, W., Dimitropoulos, D., Goodsell, D., Prlic, A., Quesada, M., Quinn, G., Westbrook, J.... (2010) The RCSB Protein Data Bank: redesigned web site and web services. Nucleic Acids Research, 39(Database). DOI: 10.1093/nar/gkq1021
by Mutant Dragon in Puff the Mutant Dragon
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Centers for Disease Control and Prevention (CDC). (2012) Severe Methemoglobinemia and Hemolytic Anemia from Aniline Purchased as 2C-E (4-ethyl-2,5-dimethoxyphenethylamine), a Recreational Drug, on the Internet - Oregon, 2011. MMWR. Morbidity and mortality weekly report, 85-8. PMID: 22318470
by Neurobonkers in Neurobonkers
A detailed analysis of a new infographic dealing with the issue of falsification in scientific research.... Read more »
Ioannidis, J. (2005) Why Most Published Research Findings Are False. PLoS Medicine, 2(8). DOI: 10.1371/journal.pmed.0020124
Moonesinghe, R., Khoury, M., & Janssens, A. (2007) Most Published Research Findings Are False—But a Little Replication Goes a Long Way. PLoS Medicine, 4(2). DOI: 10.1371/journal.pmed.0040028
Young NS, Ioannidis JP, & Al-Ubaydli O. (2008) Why current publication practices may distort science. PLoS medicine, 5(10). PMID: 18844432
Fanelli D. (2009) How many scientists fabricate and falsify research? A systematic review and meta-analysis of survey data. PloS one, 4(5). PMID: 19478950
by Dan Bailey in Smells Like Science
There aren’t many foods that are as closely tied to American identity as apple pie. And Americans love apple pie so much that, at times, we’ve felt compelled to make it even when we don’t have any apples. I’ve heard about a recipe for apple-less apple pie from a number of people over the years, but I’ve never talked to anyone who’s actually eaten it. So this past weekend, I decided to give it a try.
... Read more »
Spence, C., Levitan, C., Shankar, M., & Zampini, M. (2010) Does Food Color Influence Taste and Flavor Perception in Humans?. Chemosensory Perception, 3(1), 68-84. DOI: 10.1007/s12078-010-9067-z
by Cris Campbell in Genealogy of Religion
If we think deeply about evolution, we eventually will ask questions not about the origin of species but about the origin of life. For some theistic evolutionists, this is the point of Designer intervention. They find it hard to imagine that chemicals could combine in way that gives rise to life. For those less inclined [...]... Read more »
Urey, Harold. (1952) On the Early Chemical History of the Earth and the Origin of Life. Proceedings of the National Academy of Sciences, 38(4), 351-363. DOI: 10.1073/pnas.38.4.351
Peretó J. (2005) Controversies on the origin of life. International microbiology : the official journal of the Spanish Society for Microbiology, 8(1), 23-31. PMID: 15906258
Joyce, G. (1989) RNA evolution and the origins of life. Nature, 338(6212), 217-224. DOI: 10.1038/338217a0
Orgel LE. (1998) The origin of life--a review of facts and speculations. Trends in biochemical sciences, 23(12), 491-5. PMID: 9868373
by Mutant Dragon in Puff the Mutant Dragon
For those unfortunate enough to inherit it, sickle cell anemia is a devastating disease. Victims suffer from symptoms like frequent infections, persistent fatigue and bouts of crippling pain. It’s a little surprising to realize all this havoc stems from a single and seemingly minor change in the hemoglobin protein — exchanging one amino acid called glutamate for another called valine. That swap creates a pocket on the surface of the protein that can bind other hemoglobin molecules when oxygen is in short supply.... Read more »
Tackett, A. (2002) Non-Watson-Crick interactions between PNA and DNA inhibit the ATPase activity of bacteriophage T4 Dda helicase. Nucleic Acids Research, 30(4), 950-957. DOI: 10.1093/nar/30.4.950
by DundeePhysics in Dundee Physics
One of the things that we are working on in the lab is the study of ice nucleation making use of optically trapped droplets. Nucleation is in the starting point for processes such as freezing and crystallization, and so obviously is of great scientific and industrial importance. Another of the things that my group is [...]... Read more »
Ward, M., McHugh, S., & Alexander, A. (2012) Non-photochemical laser-induced nucleation of supercooled glacial acetic acid. Physical Chemistry Chemical Physics, 14(1), 90. DOI: 10.1039/c1cp22774b
by Joerg Heber in All That Matters
We are all familiar with the basic ways in which light interacts with matter, when light absorption causes atoms to move and creates heat, or when light gets absorbed by the outer electrons of atoms so that they move into energetically excited states, which is how electricity in solar cells is created. Common to both [...]... Read more »
Schwartz, T., Hutchison, J., Genet, C., & Ebbesen, T. (2011) Reversible Switching of Ultrastrong Light-Molecule Coupling. Physical Review Letters, 106(19). DOI: 10.1103/PhysRevLett.106.196405
Hutchison, J., Schwartz, T., Genet, C., Devaux, E., & Ebbesen, T. (2012) Modifying Chemical Landscapes by Coupling to Vacuum Fields. Angewandte Chemie International Edition. DOI: 10.1002/anie.201107033
by Mutant Dragon in Puff the Mutant Dragon
In the movies, lab chemicals are usually blue, green or some other startling color. In reality, most of the chemicals you encounter in a lab are colorless or have fairly boring colors. There are exceptions, however, and this is one of them.... Read more »
Benner, S., Ricardo, A., & Carrigan, M. (2004) Is there a common chemical model for life in the universe?. Current Opinion in Chemical Biology, 8(6), 672-689. DOI: 10.1016/j.cbpa.2004.10.003
by Neurobonkers in Neurobonkers
Watch the full video of the lecture and uncover what was in the slides censored for "copyright reasons"... Read more »
Nutt, D., King, L., & Phillips, L. (2010) Drug harms in the UK: a multicriteria decision analysis. The Lancet, 376(9752), 1558-1565. DOI: 10.1016/S0140-6736(10)61462-6
Nutt, D. (2009) Estimating drug harms: a risky business?. Centre for Crime and Justice Studies. info:/
Halpern JH, Sherwood AR, Hudson JI, Gruber S, Kozin D, & Pope HG Jr. (2011) Residual neurocognitive features of long-term ecstasy users with minimal exposure to other drugs. Addiction (Abingdon, England), 106(4), 777-86. PMID: 21205042
Carhart-Harris, R., Erritzoe, D., Williams, T., Stone, J., Reed, L., Colasanti, A., Tyacke, R., Leech, R., Malizia, A., Murphy, K.... (2012) Neural correlates of the psychedelic state as determined by fMRI studies with psilocybin. Proceedings of the National Academy of Sciences. DOI: 10.1073/pnas.1119598109
Editorial team. (2010) The EMCDDA annual report 2010: the state of the drugs problem in Europe. The European Monitoring Centre for Drugs and Drug Addiction, also published in Euro surveillance :European communicable disease bulletin, 15(46). PMID: 21144426
by Aaron Sterling in Nanoexplanations
I’ve posted twice about Anonymous hacking into Stratfor — and, more generally, their hacktivism has been making bigger and bigger waves. CNN recently ran a fairly positive story on the support hacktivists are providing the Occupy movement. Many of these … Continue reading →... Read more »
Joachim J. Eggers, W.D. Ihlenfeldt, & Bern Girod. (2001) Digital Watermarking of Chemical Structure Sets. Information Hiding, 200-214. DOI: 10.1007/3-540-45496-9_15
by Hector Munoz in Microfluidic Future
Biomimetics. I love that word. Well, probably not as much as microfluidics, but it’s a close second. If you’re unfamiliar with the word, it basically refers to design that mimics biology. Biological systems have evolved into finely tuned machines, why not mimic them in order to synthesize what we need? Biomimetics isn’t new, it’s been around in one form or another for a long time (my favorite instance is Velcro), but our capabilities are broadening as we are able to manufacture at smaller, micro and nano levels. If you want to learn more about this topic, you should check out the Biomimetic Microsystems Platform at the Wyss Institute. Today I’d like to share biomimetic microfluidic research that mimics the silk-spinning process of spiders from Korea University.... Read more »
Kang, E., Jeong, G., Choi, Y., Lee, K., Khademhosseini, A., & Lee, S. (2011) Digitally tunable physicochemical coding of material composition and topography in continuous microfibres. Nature Materials, 10(11), 877-883. DOI: 10.1038/nmat3108
by Michelle Clement in Crude Matter
Many of us, especially the current or former graduate students among us, are addicted to our breakfast caffeinated beverage of choice. Mine is tea, but if I had to guess, I’d wager that the most popular option is coffee. We chug it down in the morning to get ready for our day, we sip it thoughtfully at work, and we seek it out in the wee hours when we should be sleeping but instead we’re at the lab or at our desks, telling ourselves that we’ll run just one more gel or write just one more page. The ritual of coffee (or tea!) is deeply ingrained in our daily lives for many of us, but aside from keeping us alert, what else does it do for us? A recent study suggests that certain polyphenolic compounds in tea and coffee may offer protective effects against type 2 diabetes mellitus (T2 diabetes) by interfering with the formation of amyloid fibrils in the pancreas. Wow, that sounds great, doesn’t it? Another excuse to drink more of the stuff! But what the heck does it mean? In order to understand how this might work, we first need to understand some concepts. Specifically, what is an amyloid fibril, and what does it have to do with T2 diabetes?... Read more »
Cheng, B., Liu, X., Gong, H., Huang, L., Chen, H., Zhang, X., Li, C., Yang, M., Ma, B., Jiao, L.... (2011) Coffee Components Inhibit Amyloid Formation of Human Islet Amyloid Polypeptide in Vitro: Possible Link between Coffee Consumption and Diabetes Mellitus. Journal of Agricultural and Food Chemistry, 59(24), 13147-13155. DOI: 10.1021/jf201702h
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