The hottest buzz-word in biology today is CRISPR: an adaptive immune system in bacteria and archea. At its basis is a nuclease, named Cas9, which is targeted to DNA by a short single-guide RNA (sgRNA). This turned out to be … Continue reading →... Read more »
Deng W, Shi X, Tjian R, Lionnet T, & Singer RH. (2015) CASFISH: CRISPR/Cas9-mediated in situ labeling of genomic loci in fixed cells. Proceedings of the National Academy of Sciences of the United States of America, 112(38), 11870-5. PMID: 26324940
Nelles DA, Fang MY, O'Connell MR, Xu JL, Markmiller SJ, Doudna JA, & Yeo GW. (2016) Programmable RNA Tracking in Live Cells with CRISPR/Cas9. Cell, 1-9. PMID: 26997482
To prepare our children to meet the goals of a complex world, we should pull them out of their managed world and plop them in the mermaid’s court. That’s the verdict of a randomised control trial published recently in the Journal of Experimental Child Psychology that found American pre-schoolers who engaged in fantastical pretend play showed improvements to their executive function – the suite of cognitive abilities that organises thought and actions to achieve goals.The study involved dai........ Read more »
Thibodeau, R., Gilpin, A., Brown, M., & Meyer, B. (2016) The effects of fantastical pretend-play on the development of executive functions: An intervention study. Journal of Experimental Child Psychology, 120-138. DOI: 10.1016/j.jecp.2016.01.001
"ADHD children may just be immature, research suggests".So went the recent BBC headline with reference to the findings reported by Mu-Hong Chen and colleagues  (open-access) and the idea that: "Relative age, as an indicator of neurocognitive maturity, is crucial in the risk of being diagnosed with ADHD [attention-deficit hyperactivity disorder] and receiving ADHD medication among children and adolescents."Chen et al are not unfamiliar names discussed on this blog (see here........ Read more »
Chen, M., Lan, W., Bai, Y., Huang, K., Su, T., Tsai, S., Li, C., Lin, W., Chang, W., Pan, T.... (2016) Influence of Relative Age on Diagnosis and Treatment of Attention-Deficit Hyperactivity Disorder in Taiwanese Children. The Journal of Pediatrics. DOI: 10.1016/j.jpeds.2016.02.012
Microbiology, and especially microbial ecology, has become increasingly dependent on advanced DNA and RNA sequencing technologies. This is most evident with the increasing popularity of the human microbiome and its various impacts on human health...... Read more »
Schirmer, M., Ijaz, U., D'Amore, R., Hall, N., Sloan, W., & Quince, C. (2015) Insight into biases and sequencing errors for amplicon sequencing with the Illumina MiSeq platform. Nucleic Acids Research, 43(6). DOI: 10.1093/nar/gku1341
Schirmer, M., D’Amore, R., Ijaz, U., Hall, N., & Quince, C. (2016) Illumina error profiles: resolving fine-scale variation in metagenomic sequencing data. BMC Bioinformatics, 17(1). DOI: 10.1186/s12859-016-0976-y
Innovations don’t require heroic geniuses any more than your thoughts hinge on a particular neuron.... Read more »
If Parkinson’s disease wasn’t bad enough for families to have to learn to deal with, about 80% of patients also develop dementia. That’s the problem with the brain; while it has the amazing ability to adapt to just about anything, it can’t fix everything. There are no particularly good solutions to Parkinson’s or dementia, however, early detection of dementia is key to keeping it at bay and a new study may have a way to do just that.
... Read more »
Bertrand, J., McIntosh, A., Postuma, R., Kovacevic, N., Latreille, V., Panisset, M., Chouinard, S., & Gagnon, J. (2016) Brain Connectivity Alterations Are Associated with the Development of Dementia in Parkinson's Disease. Brain Connectivity, 6(3), 216-224. DOI: 10.1089/brain.2015.0390
If you see me on the street and I am running, there is a good chance you should be running as well, because something dangerous is coming. I don’t run, I hate to run, I loathe running, did I mention I don’t like to run? Maybe it’s all the running I did in the military, or if a new study is correct, it may have to do with my mother. Which is good, because now I can blame someone else for my hatred of running.
... Read more »
Eclarinal, J., Zhu, S., Baker, M., Piyarathna, D., Coarfa, C., Fiorotto, M., & Waterland, R. (2016) Maternal exercise during pregnancy promotes physical activity in adult offspring. The FASEB Journal. DOI: 10.1096/fj.201500018R
Does ice cream cause drownings? Let's think about this statistically. Consider that, in any given city, daily sales of ice cream are, most likely, positively correlated with daily rates of drownings.
Now, no matter how strong this correlation is, it doesn't really mean that ice cream is dangerous. Rather, the association exists because of a 'confound' variable. In this case it's temperature: on sunny days, people tend to eat more ice cream and they also tend to go swimming more often, thu... Read more »
Westfall J, & Yarkoni T. (2016) Statistically Controlling for Confounding Constructs Is Harder than You Think. PloS one, 11(3). PMID: 27031707
Today (April 2nd) is World Autism Awareness Day. The theme this year is on inclusion and as the United Nations note: "Mainstreaming disability" insofar as recognising that: "Autism and other forms of disability are part of the human experience that contributes to human diversity." A noble cause indeed; not forgetting that for many on the autism spectrum, long-term outcome remains poor (see here) and awareness about human diversity really needs to go hand-in-hand with real action to change prospe........ Read more »
Murza KA, Schwartz JB, Hahs-Vaughn DL, & Nye C. (2016) Joint attention interventions for children with autism spectrum disorder: a systematic review and meta-analysis. International journal of language . PMID: 26952136
At least once per year, and more is likely better, laughter is the best medicine. On April Fool's Day, everybody from school-age kids to technology companies tries to trick people into believing into jokes. Yet, as Sigmund Freud suggested, jokes often expose unconscious desires. Perhaps the technologies listed below, too, have a grain of our desires wrapped in a smile?
Here are a few announcements made on April 1 2016.... Read more »
[No authors listed]. (2000) April Fool's Day and the Medicinal Value of Humor. The virtual mentor : VM, 2(4). PMID: 23270623
If you’re a transplant recipient you know that transplant organs are a veritable ticking time bomb waiting to be rejected by your well-meaning (but stupid) body. Not only can you do everything right and still have the organs rejected, you have to take a steady stream of expensive pills to inhibit the immune system and stop the body from launching its attack. Don’t throw your pill organizers away just yet, but soon.
... Read more »
MacDonald, K., Hoeppli, R., Huang, Q., Gillies, J., Luciani, D., Orban, P., Broady, R., & Levings, M. (2016) Alloantigen-specific regulatory T cells generated with a chimeric antigen receptor. Journal of Clinical Investigation, 126(4), 1413-1424. DOI: 10.1172/JCI82771
It may sound superficial, but you can judge a lot about an animal from its schnoz. Plant-eaters have evolved the perfect snout shapes to nibble, chomp, or tear up the foods they love. And by decoding those shapes, scientists hope they can learn more about plant-eaters that are more mysterious—namely, dinosaurs.
"When you see cows in a field, their faces almost look like they're glued to the ground as they nibble away," says Jon Tennant, a PhD student at Imperial College London. Cows are ........ Read more »
It's that time of the year again. You step out of the house and your eyes itch, your nose starts running and your head feels like an empty balloon. Yes, it's allergy season again. Even the resilient ones, give them enough time and eventually they will develop some form of allergic reaction. But what are allergies and why do so many people suffer from them?Allergies are a glitch in our immune system. The immune system is built to recognize and destroy pathogens -- potential threats like viruses........ Read more »
Ziska, L., Knowlton, K., Rogers, C., Dalan, D., Tierney, N., Elder, M., Filley, W., Shropshire, J., Ford, L., Hedberg, C.... (2011) Recent warming by latitude associated with increased length of ragweed pollen season in central North America. Proceedings of the National Academy of Sciences, 108(10), 4248-4251. DOI: 10.1073/pnas.1014107108
Li, Q., & Zhou, J. (2016) The microbiota–gut–brain axis and its potential therapeutic role in autism spectrum disorder. Neuroscience. DOI: 10.1016/j.neuroscience.2016.03.013
Molloy, J., Allen, K., Collier, F., Tang, M., Ward, A., & Vuillermin, P. (2013) The Potential Link between Gut Microbiota and IgE-Mediated Food Allergy in Early Life. International Journal of Environmental Research and Public Health, 10(12), 7235-7256. DOI: 10.3390/ijerph10127235
"In conclusion, [the] present meta-analysis strongly suggested a significant association of the MTHFR C677T polymorphism with autism."So said the findings reported by Vandana Rai  as yet more discussion emerges on the possible role of issues with the methylenetetrahydrofolate reductase (MTHFR) gene in relation to at least some autism. The reason I've titled this post as a 'meta-meta-analysis' is because we've previously seen meta-analysis done on this polymorphism (SNP) in rela........ Read more »
Rai, V. (2016) Association of methylenetetrahydrofolate reductase (MTHFR) gene C677T polymorphism with autism: evidence of genetic susceptibility. Metabolic Brain Disease. DOI: 10.1007/s11011-016-9815-0
Currently, neuroscientists think our brain has about enough storage space to hold the entire internet. That’s a lot of space, about a petabyte in fact — if we are to believe this estimate. So, what did you read in the news this day 5 years ago? Don’t worry, I don’t even remember what I had for breakfast this morning and my long-term memory doesn’t fair much better. However, vital information about how the brain erases long-term memories has been uncovered by researchers.
... Read more »
Migues, P., Liu, L., Archbold, G., Einarsson, E., Wong, J., Bonasia, K., Ko, S., Wang, Y., & Hardt, O. (2016) Blocking Synaptic Removal of GluA2-Containing AMPA Receptors Prevents the Natural Forgetting of Long-Term Memories. Journal of Neuroscience, 36(12), 3481-3494. DOI: 10.1523/JNEUROSCI.3333-15.2016
"For 2012, the combined estimated prevalence of ASD [autism spectrum disorder] among the 11 ADDM [Autism and Developmental Disabilities Monitoring] Network sites was 14.6 per 1,000 (one in 68) children aged 8 years."So said the report by Deborah Christensen and colleagues  continuing a research theme as the CDC map the estimated prevalence of autism in the United States over the years (see here and see here). This time around, as last time covering 2010, the figure se........ Read more »
Christensen, D., Baio, J., Braun, K., Bilder, D., Charles, J., Constantino, J., Daniels, J., Durkin, M., Fitzgerald, R., Kurzius-Spencer, M.... (2016) Prevalence and Characteristics of Autism Spectrum Disorder Among Children Aged 8 Years — Autism and Developmental Disabilities Monitoring Network, 11 Sites, United States, 2012. MMWR. Surveillance Summaries, 65(3), 1-23. DOI: 10.15585/mmwr.ss6503a1
Recently projects have been developed with the aim to reproduce published research results in psychology, biology and economics to verify their reliability. The results indicate different degrees of reproducibility in each area, however, they served to alert the scientific community about how fragile results considered irrefutable can be and reflect on the role of science in self-correcting. … Read More →... Read more »
Fanelli, D. (2010) “Positive” Results Increase Down the Hierarchy of the Sciences. PLoS ONE, 5(4). DOI: 10.1371/journal.pone.0010068
, . (2015) Estimating the reproducibility of psychological science. Science, 349(6251). DOI: 10.1126/science.aac4716
Baker, M. (2015) First results from psychology’s largest reproducibility test. Nature. DOI: 10.1038/nature.2015.17433
Baker, M. (2015) Over half of psychology studies fail reproducibility test. Nature. DOI: 10.1038/nature.2015.18248
Gilbert, D., King, G., Pettigrew, S., & Wilson, T. (2016) Comment on "Estimating the reproducibility of psychological science". Science, 351(6277), 1037-1037. DOI: 10.1126/science.aad7243
Anderson, C., Bahnik, �., Barnett-Cowan, M., Bosco, F., Chandler, J., Chartier, C., Cheung, F., Christopherson, C., Cordes, A., Cremata, E.... (2016) Response to Comment on "Estimating the reproducibility of psychological science". Science, 351(6277), 1037-1037. DOI: 10.1126/science.aad9163
Etz, A., & Vandekerckhove, J. (2016) A Bayesian Perspective on the Reproducibility Project: Psychology. PLOS ONE, 11(2). DOI: 10.1371/journal.pone.0149794
Camerer, C., Dreber, A., Forsell, E., Ho, T., Huber, J., Johannesson, M., Kirchler, M., Almenberg, J., Altmejd, A., Chan, T.... (2016) Evaluating replicability of laboratory experiments in economics. Science, 351(6280), 1433-1436. DOI: 10.1126/science.aaf0918
Bohannon, J. (2016) About 40% of economics experiments fail replication survey. Science. DOI: 10.1126/science.aaf4141
Begley, C., & Ellis, L. (2012) Drug development: Raise standards for preclinical cancer research. Nature, 483(7391), 531-533. DOI: 10.1038/483531a
Prinz, F., Schlange, T., & Asadullah, K. (2011) Believe it or not: how much can we rely on published data on potential drug targets?. Nature Reviews Drug Discovery, 10(9), 712-712. DOI: 10.1038/nrd3439-c1
Van Noorden, R. (2015) Sluggish data sharing hampers reproducibility effort. Nature. DOI: 10.1038/nature.2015.17694
We should not ignore that researchers – in general but also in supply chain management – are not always as properly trained to perform data analysis as they should be. A highly visible discussion is currently going on regarding the prevalent misuses of p-values. For example, too often research has been considered as “good” research, […]... Read more »
Wasserstein, R., & Lazar, N. (2016) The ASA's Statement on p-values: Context, Process, and Purpose. The American Statistician. DOI: 10.1080/00031305.2016.1154108
It's goo week here at Rosin Cerate. So far we've looked at forms of natural springtime goo. For today's post, it's on to a much darker and less life-affirming goo. We're going to take a peek at the viscous fluids you can extract from a corpse to determine where/when/how it became a corpse and other useful forensic information.... Read more »
Bévalot F, Cartiser N, Bottinelli C, Fanton L, & Guitton J. (2015) Vitreous humor analysis for the detection of xenobiotics in forensic toxicology: A review. Forensic Toxicology, 34(1), 12-40. DOI: 10.1007/s11419-015-0294-5
Deking J, Hargrove VM, & Molina DK. (2014) Synovial fluid: An alternative toxicologic specimen?. The American Journal of Forensic Medicine and Pathology, 35(2), 154-6. PMID: 24781403
A few months ago, we published a paper that spent four years in peer-review (story behind the paper). Because of this, I feel entitled to an opinion on the pre- vs post-publication review debate.
Background on preprints and their effect on peer-review
If you have been living under a rock, or if you are not on Twitter, you may not have noticed that preprints are becoming more widely accepted in biology—supported by initiatives such as Haldane’s Sieve and bioRxiv. This is particularly tr........ Read more »
Tan G, Muffato M, Ledergerber C, Herrero J, Goldman N, Gil M, & Dessimoz C. (2015) Current Methods for Automated Filtering of Multiple Sequence Alignments Frequently Worsen Single-Gene Phylogenetic Inference. Systematic biology, 64(5), 778-91. PMID: 26031838
Do you write about peer-reviewed research in your blog? Use ResearchBlogging.org to make it easy for your readers — and others from around the world — to find your serious posts about academic research.
If you don't have a blog, you can still use our site to learn about fascinating developments in cutting-edge research from around the world.
Research Blogging is powered by SMG Technology.
To learn more, visit seedmediagroup.com.