Coronaviruses (CoV) are positive sense RNA viruses with a genome size of 29-32 kb with four genera (Alpha-, Beta-, Gamma- and Delta CoV) belonging to the family of the Coronaviridae within the order of Nidovirales, with the Betacoronaviruses further divided into four lineages (A-D).
Most CoV identified until now are causing severe disease only in animals including agricultural important animals such as chicken, cattle, and pigs. To date only six human CoV (HCoV) have been identified, namely ........ Read more »
Chan JF, Lau SK, To KK, Cheng VC, Woo PC, & Yuen KY. (2015) Middle East respiratory syndrome coronavirus: another zoonotic betacoronavirus causing SARS-like disease. Clinical microbiology reviews, 28(2), 465-522. PMID: 25810418
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Wong LY, Lui PY, & Jin DY. (2016) A molecular arms race between host innate antiviral response and emerging human coronaviruses. Virologica Sinica, 31(1), 12-23. PMID: 26786772
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Yang XL, Hu B, Wang B, Wang MN, Zhang Q, Zhang W, Wu LJ, Ge XY, Zhang YZ, Daszak P.... (2015) Isolation and Characterization of a Novel Bat Coronavirus Closely Related to the Direct Progenitor of Severe Acute Respiratory Syndrome Coronavirus. Journal of virology, 90(6), 3253-6. PMID: 26719272
Menachery VD, Yount BL Jr, Sims AC, Debbink K, Agnihothram SS, Gralinski LE, Graham RL, Scobey T, Plante JA, Royal SR.... (2016) SARS-like WIV1-CoV poised for human emergence. Proceedings of the National Academy of Sciences of the United States of America. PMID: 26976607
Munster, V., Adney, D., van Doremalen, N., Brown, V., Miazgowicz, K., Milne-Price, S., Bushmaker, T., Rosenke, R., Scott, D., Hawkinson, A.... (2016) Replication and shedding of MERS-CoV in Jamaican fruit bats (Artibeus jamaicensis). Scientific Reports, 21878. DOI: 10.1038/srep21878
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Siu, K., Yeung, M., Kok, K., Yuen, K., Kew, C., Lui, P., Chan, C., Tse, H., Woo, P., Yuen, K.... (2014) Middle East Respiratory Syndrome Coronavirus 4a Protein Is a Double-Stranded RNA-Binding Protein That Suppresses PACT-Induced Activation of RIG-I and MDA5 in the Innate Antiviral Response. Journal of Virology, 88(9), 4866-4876. DOI: 10.1128/JVI.03649-13
Lui PY, Wong LY, Fung CL, Siu KL, Yeung ML, Yuen KS, Chan CP, Woo PC, Yuen KY, & Jin DY. (2016) Middle East respiratory syndrome coronavirus M protein suppresses type I interferon expression through the inhibition of TBK1-dependent phosphorylation of IRF3. Emerging microbes . PMID: 27094905
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Xu W, Shao Q, Zang Y, Guo Q, Zhang Y, & Li Z. (2015) Pigeon RIG-I Function in Innate Immunity against H9N2 IAV and IBDV. Viruses, 7(7), 4131-51. PMID: 26205406
The paper introducing our new tree visualisation tool Phylo.io was just published in MBE.
Yet another tool to display trees, you might say, and indeed, so it is. But for all the tools that have been developed over the years, there are very few that scale to large trees, make it easy to compare trees side-by-side, and simply run in a browser on any computer or mobile device.
To fill this gap, we created Phylo.io.
Story behind the paper
The project started as a student summer internshi........ Read more »
Robinson, O., Dylus, D., & Dessimoz, C. (2016) Phyla.io: interactive viewing and comparison of large phylogenetic trees on the web . Molecular Biology and Evolution. DOI: 10.1093/molbev/msw080
It was the summer of 1882, and grape farmers in the Médoc region of southwest France (north of Bordeaux, on the Atlantic coast) had a problem.Schoolchildren (or university students, or just anyone travelling the roads along which the grapevines grew, depending on what source you're reading) were pilfering their grapes. To try and ward them off, some farmers decided to dissolve some slaked lime and copper sulfate in water and spray it on their grapevines closest to the roads. The idea was... Read more »
Pimentel J, & Marques F. (1969) 'Vineyard sprayer's lung': A new occupational disease. Thorax, 24(6), 678-688. DOI: 10.1136/thx.24.6.678
Back in 2013, I wondered if we would ever discover the neural basis of spontaneous thoughts. Why, I asked, do certain ideas just "pop" into our minds at particular times? Now a new paper published in Neuroimage, Canadian neuroscientists Melissa Ellamil and colleagues reports on the neural basis of spontaneous thoughts.
Ellamil et al. recruited a group of 18 volunteers, all of whom were highly experienced practitioners of mindfulness meditation. These individuals were selected, the authors... Read more »
Ellamil M, Fox KC, Dixon ML, Pritchard S, Todd RM, Thompson E, & Christoff K. (2016) Dynamics of neural recruitment surrounding the spontaneous arising of thoughts in experienced mindfulness practitioners. NeuroImage. PMID: 27114056
"Parents ultimately wanted therapists to produce positive outcomes for their children and were willing to sacrifice other desired qualities, as long as the therapy program was effective."and"The SLPs [Speech-Language Pathologists] expressed strong support for evidence-based practice (EBP) and indicated that they thought parents expected their children would be provided with evidence-based interventions."Those quotes come from two papers recently published in the same journal; the first........ Read more »
Edwards, A., Brebner, C., Mccormack, P., & Macdougall, C. (2016) “More than blowing bubbles”: What parents want from therapists working with children with autism spectrum disorder. International Journal of Speech-Language Pathology, 1-13. DOI: 10.3109/17549507.2015.1112835
Trembath, D., Hawtree, R., Arciuli, J., & Caithness, T. (2016) What do speech-language pathologists think parents expect when treating their children with autism spectrum disorder?. International Journal of Speech-Language Pathology, 1-9. DOI: 10.3109/17549507.2016.1139625
Why does one person who tries cocaine get addicted, while another might use it and then leave it alone? Why do some people who kick a drug habit manage to stay clean, while others relapse? And why do some families seem more prone to addiction than others? According to a new study, the road to answering these questions may have a lot to do with specific genetic factors that vary from individual to individual.
... Read more »
Flagel, S., Chaudhury, S., Waselus, M., Kelly, R., Sewani, S., Clinton, S., Thompson, R., Watson, S., & Akil, H. (2016) Genetic background and epigenetic modifications in the core of the nucleus accumbens predict addiction-like behavior in a rat model. Proceedings of the National Academy of Sciences, 201520491. DOI: 10.1073/pnas.1520491113
Sometimes at the climax of a Star Trek episode, the captain would yell out "Battle stations!" and send the crew scurrying frantically through the corridors. It wasn't really clear what those battle stations were. Presumably, crew members headed to posts they'd been previously assigned, and this let the whole ship react to the crisis efficiently.
Certain ants respond to a crisis by binding their bodies together into floating rafts. And like the Star Trek crew, they seem to have designat........ Read more »
Avril, A., Purcell, J., & Chapuisat, M. (2016) Ant workers exhibit specialization and memory during raft formation. The Science of Nature, 103(5-6). DOI: 10.1007/s00114-016-1360-5
Over the years I’ve started to follow a lot of farmers on twitter. It might sound odd to folks who are immersed in human genomics and disease. But I actually find the plant and animal genomics communities to be pushing tech faster and further to the hands of end-users than a lot of the clinical […]... Read more »
Grant, D., Nelson, R., Cannon, S., & Shoemaker, R. (2009) SoyBase, the USDA-ARS soybean genetics and genomics database. Nucleic Acids Research, 38(Database). DOI: 10.1093/nar/gkp798
For the first time anywhere - an easy explanation of your immune system in 1500 words! For the low, low price of zero dollars you can find out how your body protects you better the second time you are exposed to a disease. Special bonus offer – we’ll throw in how vaccines work and why you need one every year for the flu, although your old flu vaccines might still be helping you. ... Read more »
Mathews, J., McBryde, E., McVernon, J., Pallaghy, P., & McCaw, J. (2010) Prior immunity helps to explain wave-like behaviour of pandemic influenza in 1918-9. BMC Infectious Diseases, 10(1), 128. DOI: 10.1186/1471-2334-10-128
Kash, J., Qi, L., Dugan, V., Jagger, B., Hrabal, R., Memoli, M., Morens, D., & Taubenberger, J. (2010) Prior infection with classical swine H1N1 influenza viruses is associated with protective immunity to the 2009 pandemic H1N1 virus. Influenza and Other Respiratory Viruses, 4(3), 121-127. DOI: 10.1111/j.1750-2659.2010.00132.x
Cowling, B., Ng, S., Ma, E., Cheng, C., Wai, W., Fang, V., Chan, K., Ip, D., Chiu, S., Peiris, J.... (2010) Protective Efficacy of Seasonal Influenza Vaccination against Seasonal and Pandemic Influenza Virus Infection during 2009 in Hong Kong. Clinical Infectious Diseases, 51(12), 1370-1379. DOI: 10.1086/657311
The A WordI'm not typically inclined to talk about TV programmes on this blog (well, not usually) but today I'm making an exception based on the conclusion of the BBC drama series 'The A Word' last evening.For those who might not know, this [fictional] series charts the ups and downs of a family living in the Lake District whose lives are in one way or another touched by autism as a function of a 5-year old boy diagnosed with the condition. The show had a notable addition to the cast with a very........ Read more »
Singh K, & Zimmerman AW. (2016) Sulforaphane treatment of young men with Autism Spectrum Disorder. CNS . PMID: 27071786
Human sacrifice to preserve inequality Statistically speaking (wait, wait, don’t click away, I know this is not the most enticing opening, but bear with me), you and me, we are not part of the 1%, or the 0.01%, that in most Western societies holds a disproportionate amount of influence and resources. Secretly, though, we want […]... Read more »
Watts J, Sheehan O, Atkinson QD, Bulbulia J, & Gray RD. (2016) Ritual human sacrifice promoted and sustained the evolution of stratified societies. Nature, 532(7598), 228-31. PMID: 27042932
The paper by Zheng and colleagues  caught my eye recently and the interesting ideas that "dysbiosis of the gut microbiome may have a causal role in the development of depressive-like behaviors" and "transplantation of GF [germ-free] mice with ‘depression microbiota’ derived from MDD [major depressive disorder] patients resulted in depression-like behaviors compared with colonization with ‘healthy microbiota’ derived from healthy control individuals."Bearing in........ Read more »
Zheng, P., Zeng, B., Zhou, C., Liu, M., Fang, Z., Xu, X., Zeng, L., Chen, J., Fan, S., Du, X.... (2016) Gut microbiome remodeling induces depressive-like behaviors through a pathway mediated by the host’s metabolism. Molecular Psychiatry. DOI: 10.1038/mp.2016.44
The replicability of psychological research is surprisingly low. Why? In this blog post I present new evidence showing that questionable research practices are at the heart of failures to replicate psychological effects. Quick recap. A recent publication in Science claims that only around 40% of psychological findings are replicable, based on 100 replication attempts in […]... Read more »
Asendorpf, J., Conner, M., De Fruyt, F., De Houwer, J., Denissen, J., Fiedler, K., Fiedler, S., Funder, D., Kliegl, R., Nosek, B.... (2013) Recommendations for Increasing Replicability in Psychology. European Journal of Personality, 27(2), 108-119. DOI: 10.1002/per.1919
Gerber, A., & Malhotra, N. (2008) Publication Bias in Empirical Sociological Research: Do Arbitrary Significance Levels Distort Published Results?. Sociological Methods , 37(1), 3-30. DOI: 10.1177/0049124108318973
Gerber, A., Malhotra, N., Dowling, C., & Doherty, D. (2010) Publication Bias in Two Political Behavior Literatures. American Politics Research, 38(4), 591-613. DOI: 10.1177/1532673X09350979
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
Head ML, Holman L, Lanfear R, Kahn AT, & Jennions MD. (2015) The extent and consequences of p-hacking in science. PLoS biology, 13(3). PMID: 25768323
Ioannidis JP, Munafò MR, Fusar-Poli P, Nosek BA, & David SP. (2014) Publication and other reporting biases in cognitive sciences: detection, prevalence, and prevention. Trends in cognitive sciences, 18(5), 235-41. PMID: 24656991
Kühberger A, Fritz A, & Scherndl T. (2014) Publication bias in psychology: a diagnosis based on the correlation between effect size and sample size. PloS one, 9(9). PMID: 25192357
Kunert R. (2016) Internal conceptual replications do not increase independent replication success. Psychonomic bulletin . PMID: 27068542
Open Science Collaboration. (2015) Estimating the reproducibility of psychological science. Science, 349(6251). DOI: 10.1126/science.aac4716
I'm talking about parenting again today. Two papers are served up for your reading interest today, providing an important 'science-based' perspective on the general experience of parenting a child who is also diagnosed with an autism spectrum disorder (ASD) or attention-deficit hyperactivity disorder (ADHD).The first paper by Britt Laugesen and colleagues  "aimed to identify and synthesize the best available evidence on parenting experiences of living with a child with attention-deficit hyper........ Read more »
Laugesen B, Lauritsen MB, Jørgensen R, Sørensen EE, Rasmussen P, & Grønkjær M. (2016) Living with a child with attention deficit hyperactivity disorder: a systematic review. International journal of evidence-based healthcare. PMID: 27058250
Physical attractiveness influences mate selection across cultures, and youthfulness of women is associated with their future reproductive value and fertility. Men attribute importance to youthful features in females such as large eyes, small nose, higher pitched voice, and full lips and perceive these neotenous features as attractive. More feminine women report more frequently being guarded […]... Read more »
Pazhoohi, F., Jahromi, A., & Doyle, J. (2016) Mate Retention Tactics Decline with Age of Iranian Men. Evolutionary Psychological Science. DOI: 10.1007/s40806-016-0046-8
A Lyme disease study published a few weeks ago in the New England Journal of Medicine has received a lot of coverage in the press. According to the abstract of the study, Berende and colleagues conducted a randomized placebo-controlled clinical trial to test the effectiveness of long-term antibiotics in treating "longer-term" symptoms "attributed" to Lyme disease.As many readers of this blog know, treatment of Lyme disease is a controversial topic. Antibiotics are effective in treati........ Read more »
Berende A, ter Hofstede HJ, Vos FJ, van Middendorp H, Vogelaar ML, Tromp M, van den Hoogen FH, Donders AR, Evers AW, & Kullberg BJ. (2016) Randomized Trial of Longer-Term Therapy for Symptoms Attributed to Lyme Disease. The New England Journal of Medicine, 374(13), 1209-20. PMID: 27028911
Melia MT, & Auwaerter PG. (2016) Time for a Different Approach to Lyme Disease and Long-Term Symptoms. The New England Journal of Medicine, 374(13), 1277-8. PMID: 27028918
There are some aspects of the autism research landscape that make for uncomfortable reading. I've covered a few of them on this blog (see here and see here for example) simply because of my belief that science should not be afraid to ask about and try and answer difficult questions.I'd place the paper by Winnie Yu Pow Lau and colleagues  in that uncomfortable reading zone as a consequence of their findings related to parenting efficacy as a function of parents who themselves have been di........ Read more »
Lau, W., Peterson, C., Attwood, T., Garnett, M., & Kelly, A. (2016) Parents on the autism continuum: Links with parenting efficacy. Research in Autism Spectrum Disorders, 57-64. DOI: 10.1016/j.rasd.2016.02.007
Guest post by Rebecca McDonald, science writerPhoto Credit: LeRoy N. Sanchez While many scientists who study climate change look up to the sky for clues about the Earth’s future, one researcher has spent her career looking down—at the abundance of life in the soil below. Innumerable microorganisms such as bacteria and fungi live in harmony with plant roots, decomposing fallen leaves and dead animals. In addition to acting as the ultimate recyclers, they also stabilize the soil and help to re........ Read more »
Steven B, Kuske CR, Gallegos-Graves LV, Reed SC, & Belnap J. (2015) Climate change and physical disturbance manipulations result in distinct biological soil crust communities. Applied and environmental microbiology, 81(21), 7448-59. PMID: 26276111
Sinsabaugh RL, Belnap J, Rudgers J, Kuske CR, Martinez N, & Sandquist D. (2015) Soil microbial responses to nitrogen addition in arid ecosystems. Frontiers in microbiology, 819. PMID: 26322030
Mueller RC, Belnap J, & Kuske CR. (2015) Soil bacterial and fungal community responses to nitrogen addition across soil depth and microhabitat in an arid shrubland. Frontiers in microbiology, 891. PMID: 26388845
In today's short post I'd like to bring the findings reported by Lotta Höglund Carlsson and colleagues  to your attention and a reminder that developmental regression accompanying autism onset is an important feature for quite a few people.With the aim of looking at the "national, routine 18-month developmental surveillance at Child Healthcare Centres (CHC) on children later diagnosed with autism spectrum disorder (ASD)" in Stockholm County, Sweden, authors reported on the results of sa........ Read more »
Höglund Carlsson, L., Westerlund, J., Barnevik Olsson, M., Eriksson, M., Hedvall, �., Gillberg, C., & Fernell, E. (2016) Autism spectrum disorders before diagnosis: results from routine developmental surveillance at 18 months. Acta Paediatrica. DOI: 10.1111/apa.13418
"Short IPIs [interpregnancy intervals] are associated with a significantly increased risk of ASD [autism spectrum disorder]. Long IPIs also appear to increase the risk of ASD.So said the results of the systematic review undertaken by Agustín Conde-Agudelo and colleagues  into how birth spacing might impact on the risk of a child developing an ASD. Drawing on data from 7 studies that "reported an association between short IPIs and increased risk of ASD" including over 1.1 ........ Read more »
Conde-Agudelo, A., Rosas-Bermudez, A., & Norton, M. (2016) Birth Spacing and Risk of Autism and Other Neurodevelopmental Disabilities: A Systematic Review. PEDIATRICS. DOI: 10.1542/peds.2015-3482
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