As I mentioned last week, I am watching a lot of farmers on twitter talk about this year’s North American growing season. To get a taste of that yourself, have a look at #Plant16 + wheat as a search. This is where the rubber of tractor tires and plant genomics hits the…well…rows. And just coincidentally […]... Read more »
Philippa Borrill, Ricardo Ramirez-Gonzalez, & Cristobal Uauy. (2016) expVIP: a customisable RNA-seq data analysis and visualisation platform. Plant Physiology, 2172-2186. info:/10.1104/pp.15.01667
Can I just get it out of the way? May the 4th be with you.OK. The results from Mark Strom & Jonathan Silverberg  caught my eye recently and further evidence of a 'correlation' between asthma and developmental and/or behavioural outcomes. This time around it was "caregiver-reported speech disorders in US children" and how the appearance of asthma, hay fever and/or food allergy might show some important relationships with something like speech disorder. This follows other, similar work from........ Read more »
Strom MA, & Silverberg JI. (2016) Asthma, hay fever and food allergy are associated with caregiver-reported speech disorders in US children. Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology. PMID: 27091599
Is anybody out there? Where are all the alien civilizations? Even if (intelligent) life is very unlikely, the sheer size and age of the universe means that even long odds might have produced space faring civilizations. Yet, so far, nada. When people are considering the (im)probability of non-human space travellers, one thing always comes up: […]... Read more »
Frank A, & Sullivan WT 3rd. (2016) A New Empirical Constraint on the Prevalence of Technological Species in the Universe. Astrobiology. PMID: 27105054
Machine learning, when machines, er.. learn, is of growing interest to the autism research field. The names Wall and Duda have filled quite a few posts on this blog (see here and see here for example) on this topic and their suggesting that applying machine learning algorithms to something like autism screening and detection could cut down on time taken and resources used.As per the publication of the paper by Daniel Bone and colleagues  it appears that others working in autism research are a........ Read more »
Bone D, Bishop S, Black MP, Goodwin MS, Lord C, & Narayanan SS. (2016) Use of machine learning to improve autism screening and diagnostic instruments: effectiveness, efficiency, and multi-instrument fusion. Journal of child psychology and psychiatry, and allied disciplines. PMID: 27090613
Vaccines don't cause autism, but because the brain is so complex, we still don't know how much of it works so figuring out the real causes (as in more than one) of autism has been slow going. Well, researchers have identified a brain receptor that appears to initiate adolescent synaptic pruning, a process believed necessary for learning, but in this case it is one that appears to go awry in both autism and schizophrenia.... Read more »
Sonia Afroz, Julie Parato, Hui Shen Sheryl, & Sue Smith. (2016) Synaptic pruning in the female hippocampus is triggered at puberty by extrasynaptic GABAA receptors on dendritic spines . eLife. info:/
Psychiatric drugs come in many kinds: there are antidepressants, antipsychotics, anti-anxiety medications, and more. But what all of these categories have in common is that they're anti- something. This is how we classify these drugs - by what they treat.
Except there's a problem - very few psychiatric drugs are only used to treat one thing. Take "antipsychotics". They're used in psychosis, but they're also a key tool in the treatment of mania, a different disorder entirely. Many of these dru... Read more »
Zohar J, Stahl S, Moller HJ, Blier P, Kupfer D, Yamawaki S, Uchida H, Spedding M, Goodwin GM, & Nutt D. (2015) A review of the current nomenclature for psychotropic agents and an introduction to the Neuroscience-based Nomenclature. European neuropsychopharmacology : the journal of the European College of Neuropsychopharmacology, 25(12), 2318-25. PMID: 26527055
Most people who know a little bit about chronic fatigue syndrome / myalgic encephalomyelitis (CFS/ME) will probably understand the potential importance of the findings reported by Leonard Jason and colleagues  (open-access available here). Suggesting that there may be "four groupings of patients" when it comes to how we "name and define the illnesses", this research group who surveyed over 500 people "in the United States, Great Britain, and Norway" report on one of the biggest challenge........ Read more »
Jason LA, McManimen S, Sunnquist M, Brown A, Furst J, Newton JL, & Strand EB. (2016) Case definitions integrating empiric and consensus perspectives. Fatigue : biomedicine, health , 4(1), 1-23. PMID: 27088059
Generally seen as antithetical to one another, evolution and religion can hardly fit in a scientific discourse simultaneously. However, in a new article, a biology researcher delves into observations on the influences a few major religions have had on evolutionists and their scientific thinking over the centuries.
... Read more »
Romero Jr., A. (2016) The influence of religion on science: the case of the idea of predestination in biospeleology. Research Ideas and Outcomes. DOI: 10.3897/rio.2.e9015
Insomnia, fun fact those of us who have served or are serving in the military have a much higher incidence of sleep problems. So if you are like me and have ever been prescribed something to help you sleep, you know that there are some unwanted side effects. For instance the time I lost memory of a whole day of interacting with people to the ambien I had taken the night before, not fun. Thankfully Danish researchers found that the level of salts in the brain plays a critical role in whether we a........ Read more »
Ding, F., ODonnell, J., Xu, Q., Kang, N., Goldman, N., & Nedergaard, M. (2016) Changes in the composition of brain interstitial ions control the sleep-wake cycle. Science, 352(6285), 550-555. DOI: 10.1126/science.aad4821
In a new Nature paper, Berkely neuroscientists Alexander G. Huth and colleagues present a 'semantic atlas' of the human brain. Huth et al. have mapped which brain areas respond to words, according to the semantics (meanings) of each word. It turns out that these maps are highly similar across individuals - which could have implications for 'mind reading' technology.
Huth et al. recorded brain activity with fMRI while seven volunteers listened to over two hours of audio narrative (taken fr... Read more »
Huth AG, de Heer WA, Griffiths TL, Theunissen FE, & Gallant JL. (2016) Natural speech reveals the semantic maps that tile human cerebral cortex. Nature, 532(7600), 453-8. PMID: 27121839
Whilst the package inserts of the various drugs that modern medicine has at its disposal provides important information on potential mode of action, there is a growing realisation that drugs generally have quite a few more molecular targets than are perhaps listed. Take for example the quite commonly used (in some parts of the world anyway) compound called melatonin that in some instances can provide almost miraculous relief when it comes to sleeping issues under certain circumstances. A d........ Read more »
Yuan L, Liu S, Bai X, Gao Y, Liu G, Wang X, Liu D, Li T, Hao A, & Wang Z. (2016) Oxytocin inhibits lipopolysaccharide-induced inflammation in microglial cells and attenuates microglial activation in lipopolysaccharide-treated mice. Journal of neuroinflammation, 13(1), 77. PMID: 27075756
The whole of human intelligence, right at your fingertips. Sure it might not make the layman an engineer or physicist, but if we want to learn about a particular topic the internet can give us that information. But you better hold on tight before you lose it. New research finds retweeting or otherwise sharing information creates a “cognitive overload” that interferes with learning and retaining what you’ve just seen.
... Read more »
Jiang, T., Hou, Y., & Wang, Q. (2016) Does micro-blogging make us “shallow”? Sharing information online interferes with information comprehension. Computers in Human Behavior, 210-214. DOI: 10.1016/j.chb.2016.02.008
Treating immune disorders might have gotten easier with a new mouse model.... Read more »
Beura, L., Hamilton, S., Bi, K., Schenkel, J., Odumade, O., Casey, K., Thompson, E., Fraser, K., Rosato, P., Filali-Mouhim, A.... (2016) Normalizing the environment recapitulates adult human immune traits in laboratory mice. Nature, 532(7600), 512-516. DOI: 10.1038/nature17655
Mestas, J., & Hughes, C. (2004) Of Mice and Not Men: Differences between Mouse and Human Immunology. The Journal of Immunology, 172(5), 2731-2738. DOI: 10.4049/jimmunol.172.5.2731
Signatures of Mutational Processes Extracted from the Mutational Catalogs of 21 Breast Cancer Genomes. Credit:http://dx.doi.org/10.1016/j.celrep.2012.12.008Cancer is the second leading cause of death worldwide, with approximately 14 million new cases and 8.2 million cancer related deaths each year (Source: WHO). A family history of cancer typically increases a person's risk of developing the disease, yet most cancer cases have no family history at all. This suggests that a combination of both ge........ Read more »
Alexandrov LB, Nik-Zainal S, Wedge DC, Aparicio SA, Behjati S, Biankin AV, Bignell GR, Bolli N, Borg A, Børresen-Dale AL.... (2013) Signatures of mutational processes in human cancer. Nature, 500(7463), 415-21. PMID: 23945592
Alexandrov LB, Nik-Zainal S, Siu HC, Leung SY, & Stratton MR. (2015) A mutational signature in gastric cancer suggests therapeutic strategies. Nature communications, 8683. PMID: 26511885
"Children with higher urinary DMP [dimethylphosphate] concentrations may have a twofold to threefold increased risk of being diagnosed with ADHD [attention-deficit hyperactivity disorder]."So said the results presented in the paper by Yu and colleagues  who looking at "97 doctor-diagnosed ADHD cases and 110 non-ADHD controls who were 4-15 years of age" examined urine and blood samples for various factors including "biomarkers of OP [organophosphate] pesticide exposure." Th........ Read more »
Yu CJ, Du JC, Chiou HC, Chung MY, Yang W, Chen YS, Fuh MR, Chien LC, Hwang B, & Chen ML. (2016) Increased risk of attention-deficit/hyperactivity disorder associated with exposure to organophosphate pesticide in Taiwanese children. Andrology. PMID: 27070915
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
Han HJ, Yu H, & Yu XJ. (2016) Evidence for zoonotic origins of Middle East respiratory syndrome coronavirus. The Journal of general virology, 97(2), 274-80. PMID: 26572912
Han, H., Wen, H., Zhou, C., Chen, F., Luo, L., Liu, J., & Yu, X. (2015) Bats as reservoirs of severe emerging infectious diseases. Virus Research, 1-6. DOI: 10.1016/j.virusres.2015.05.006
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
Lin R, Heylbroeck C, Pitha PM, & Hiscott J. (1998) Virus-dependent phosphorylation of the IRF-3 transcription factor regulates nuclear translocation, transactivation potential, and proteasome-mediated degradation. Molecular and cellular biology, 18(5), 2986-96. PMID: 9566918
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
Yang Y, Ye F, Zhu N, Wang W, Deng Y, Zhao Z, & Tan W. (2015) Middle East respiratory syndrome coronavirus ORF4b protein inhibits type I interferon production through both cytoplasmic and nuclear targets. Scientific reports, 17554. PMID: 26631542
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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
Matthews KL, Coleman CM, van der Meer Y, Snijder EJ, & Frieman MB. (2014) The ORF4b-encoded accessory proteins of Middle East respiratory syndrome coronavirus and two related bat coronaviruses localize to the nucleus and inhibit innate immune signalling. The Journal of general virology, 95(Pt 4), 874-82. PMID: 24443473
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Li Y, Banerjee S, Wang Y, Goldstein SA, Dong B, Gaughan C, Silverman RH, & Weiss SR. (2016) Activation of RNase L is dependent on OAS3 expression during infection with diverse human viruses. Proceedings of the National Academy of Sciences of the United States of America, 113(8), 2241-6. PMID: 26858407
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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
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