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# Posts

### April 12, 2014

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Imagine you are offered a package full of delicious chocolates. Would the size of the pieces of chocolate influences how much you eat? Yes, the size of your piece of chocolate matters. This so-called unit size of food refers to the number of units in which a portion of food is divided. Earlier studies have shown that smaller units typically lead people to eat less. For example, Wansink and colleagues found that people being given four 100-calorie packs of crackers ate about 25% […]

van Kleef E., Kavvouris C. & van Trijp H.C.M. (2014). The unit size effect of indulgent food: How eating smaller-sized items signals impulsivity and makes consumers eat less, Psychology & Health, 1-41. DOI:

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In Portugal and Spain climate change has already driven over 2°C of warming in summer, and new findings from Sergio Vicente-Serrano from the Pyrenean Institute of Ecology are dispelling uncertainties that the temperatures are making drought more severe and widespread.

Vicente-Serrano, S., Lopez-Moreno, J., Beguería, S., Lorenzo-Lacruz, J., Sanchez-Lorenzo, A., García-Ruiz, J., Azorin-Molina, C., Morán-Tejeda, E., Revuelto, J., Trigo, R. & Coelho, F. (2014). Evidence of increasing drought severity caused by temperature rise in southern Europe, Environmental Research Letters, 9 (4) 44001. DOI:

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### April 11, 2014

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In this post I'm talking about the paper by Pål Surén and colleagues [1] and their suggestion that "paternal obesity is an independent risk factor for ASDs [autism spectrum disorders] in children". I do so not with the intent of stigmatising parents and specifically parents with weight issues, which tend to be present for many more reasons than just food and exercise (see here), but merely to highlight how parental physical health may show some relationship to […]

Suren, P., Gunnes, N., Roth, C., Bresnahan, M., Hornig, M., Hirtz, D., Lie, K., Lipkin, W., Magnus, P., Reichborn-Kjennerud, T. & Schjolberg, S. (2014). Parental Obesity and Risk of Autism Spectrum Disorder, PEDIATRICS, DOI:

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Un triangolo aureo è un triangolo isoscele in cui il rapporto tra uno dei lati uguali con la base è pari alla sezione aurea $\varphi$. Utilizzando un triangolo aureo di lato 1, è possibile dimostrare che $1 + \frac{1}{\varphi^2} + \frac{1}{\varphi^4} + \cdots = \varphi$ $\frac{1}{\varphi} + \frac{1}{\varphi^3} + \cdots = 1$ $\frac{1}{\varphi} + \frac{1}{\varphi^2} + \frac{1}{\varphi^3} + \cdots = \varphi$ Il triangolo aureo qui sopra è lo screenshot della […]

Edwards S. (2014). Proof Without Words: An Infinite Series Using Golden Triangles, The College Mathematics Journal, 45 (2) 120-120. DOI:

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David Newman, a physicist at the University of Alaska, believes that smaller grids would reduce the likelihood of severe outages, such as the 2003 Northeast blackout that cut power to 50 million people in the United States and Canada for up to two days. Read more »

Carreras, B., Newman, D. & Dobson, I. (2014). Does size matter?, Chaos: An Interdisciplinary Journal of Nonlinear Science, 24 (2) 23104. DOI:

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A new model for solar farms that “co-locates” biofuel crops and solar panels could result in a harvest of valuable plants along with solar energy. Read more »

Ravi, S., Lobell, D. & Field, C. (2014). Tradeoffs and Synergies between Biofuel Production and Large Solar Infrastructure in Deserts, Environmental Science & Technology, 48 (5) 3021-3030. DOI:

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Credit: Michael HelfenbeinNewborns whose mothers were exposed during pregnancy to any one of a variety of environmental stressors -- such as trauma, illness, and alcohol or drug abuse -- become susceptible to various psychiatric disorders that frequently arise later in life. However, it has been unclear how these stressors affect the cells of the developing brain prenatally and give rise to conditions such as schizophrenia, post-traumatic stress disorder, and some forms of autism and bipolar […]

Hashimoto-Torii, K., Torii, M., Fujimoto, M., Nakai, A., El Fatimy, R., Mezger, V., Ju, M., Ishii, S., Chao, S., Brennand, K. & Gage, F. (2014). Roles of Heat Shock Factor 1 in Neuronal Response to Fetal Environmental Risks and Its Relevance to Brain Disorders, Neuron, DOI:

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The activity of four transcription factors – proteins that regulate the expression of other genes – appears to distinguish the small proportion of glioblastoma cells responsible for the aggressiveness and treatment resistance of the deadly brain tumor. The findings by a team of Massachusetts General Hospital (MGH) investigators, which will be published in the April 24 issue of Cell and are receiving advance online release, support the importance of epigenetics – processes […]

Suvà, M., Rheinbay, E., Gillespie, S., Patel, A., Wakimoto, H., Rabkin, S., Riggi, N., Chi, A., Cahill, D., Nahed, B. & Curry, W. (2014). Reconstructing and Reprogramming the Tumor-Propagating Potential of Glioblastoma Stem-like Cells, Cell, DOI:

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New research from North Carolina State University and UNC-Chapel Hill reveals that energy is transferred more efficiently inside of complex, three-dimensional organic solar cells when the donor molecules align face-on, rather than edge-on, relative to the acceptor. This finding may aid in the design and manufacture of more efficient and economically viable organic solar cell technology. Read more »

Tumbleston, J., Collins, B., Yang, L., Stuart, A., Gann, E., Ma, W., You, W. & Ade, H. (2014). The influence of molecular orientation on organic bulk heterojunction solar cells, Nature Photonics, DOI:

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You’re sitting there, reading this post, and your skin should be crawling. Well it practically is, along with your nostrils, lungs, gut and any of your mucus-covered surfaces. You’re crawling with […]

Kotula JW, Kerns SJ, Shaket LA, Siraj L, Collins JJ, Way JC & Silver PA (2014). Programmable bacteria detect and record an environmental signal in the mammalian gut., Proceedings of the National Academy of Sciences of the United States of America, 111 (13) 4838-43. PMID:

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Many theories of humanness rely on a simple idea that the cerebral cortex is enlarged in humans relative to other primates and in primates relative to other mammals. So it must be the cerebral cortex that is the important part of the brain, giving us our smarts and our skills. What is often overlooked is […]

Baizer, J. (2014). Unique Features of the Human Brainstem and Cerebellum, Frontiers in Human Neuroscience, 8 DOI:

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Is neuro-skepticism in danger of going too far? Is it time to take a critical look at critiques of neuroscience? Martha Farah of the University of Pennsylvania says yes, in a Hastings Center Report just published: Brain Images, Babies, and Bathwater: Critiquing Critiques of Functional Neuroimaging Farah covers a broad spectrum of criticisms, ranging from […]The post Brain Scans: Don’t Throw Out The Baby With The Dead Salmon appeared first on Neuroskeptic.

Farah MJ (2014). Brain images, babies, and bathwater: critiquing critiques of functional neuroimaging., The Hastings Center report, 44 Suppl 2 30. PMID:

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Editor's Pick
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Does Tamiflu have any meaningful effects on the prevention or treatment of influenza? Considering the drug’s been on the market for almost 15 years, and is widely used, you should expect this question has been answered after 15 flu seasons. Answering this question from a science-based perspective requires three steps: Consider prior probability, be systematic […]

Jefferson T., Jones M., Doshi P., Spencer E.A., Onakpoya I. & Heneghan C.J. (2014). Oseltamivir for influenza in adults and children: systematic review of clinical study reports and summary of regulatory comments, BMJ, 348 (apr09 2) g2545-g2545. DOI:

Freemantle N., Shallcross L.J., Kyte D., Rader T. & Calvert M.J. (2014). Oseltamivir: the real world data, BMJ, 348 (apr09 2) g2371-g2371. DOI:

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Editor's Pick

### April 10, 2014

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Conventional wisdom is that you can get your best time in a race by starting off a little slower than your goal pace: “Negative splits” are the ideal — times for each mile run should decrease over the course of the race. So, for example, if you were running a 10k and had a goal […]

Reardon J. (2013). Optimal pacing for running 400- and 800-m track races, American Journal of Physics, 81 (6) 428. DOI:

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Multnomah Falls, © EEGDisclaimer: I work on HIV vaccine design and I'm quite proud of it. I know that for three million HIV-positive kids in Africa, a vaccine is the only hope they have to grow into adulthood. So, when people tell me that vaccines are bad I cringe. Infant mortality rates have dropped since vaccinations have been introduced. We live longer, healthier lives thanks to vaccines. Diseases like polio can paralyze and kill, yet they are no longer a concern for children in the […]

Hogenesch H (2012). Mechanism of immunopotentiation and safety of aluminum adjuvants., Frontiers in immunology, 3 406. PMID:

Tomljenovic L & Shaw CA (2011). Do aluminum vaccine adjuvants contribute to the rising prevalence of autism?, Journal of inorganic biochemistry, 105 (11) 1489-99. PMID:

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Kui Yao and co-workers from the A*STAR Institute of Materials Research and Engineering in Singapore have discovered a way to give lightweight polymer vibration harvesters a hundredfold boost in energy output—a finding that may help to eliminate manual battery recharging in microsensors and mobile devices. Read more »

Lei Zhang, ., Oh, S., Ting Chong Wong, ., Chin Yaw Tan, . & Kui Yao, . (2013). Piezoelectric polymer multilayer on flexible substrate for energy harvesting, IEEE Transactions on Ultrasonics, Ferroelectrics and Frequency Control, 60 (9) 2013-2020. DOI:

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BioStar is a site for asking, answering and discussing bioinformatics questions and issues. We are members of the community and find it very useful. Often questions and answers arise at BioStar that are germane to our readers (end users of genomics resources). Every Thursday we will be highlighting one of those items or discussions here […]

Pybus M., Dall'Olio G.M., Luisi P., Uzkudun M., Carreno-Torres A., Pavlidis P., Laayouni H., Bertranpetit J. & Engelken J. (2013). 1000 Genomes Selection Browser 1.0: a genome browser dedicated to signatures of natural selection in modern humans, Nucleic Acids Research, 42 (D1) D903-D909. DOI:

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Could exposure to dietary gluten affect a person's moods or emotional state?Well, if the paper by Simone Peters and colleagues [1] (open-access here) is to be believed the answer may very well be yes, at least in some cases, as they report a link between gluten consumption and feelings of depression under [short-term] experimental conditions. If replicated, such a finding may have profound consequences for how we view our relationship between food and mental health and wellbeing.Bread […]

Peters SL, Biesiekierski JR, Yelland GW, Muir JG & Gibson PR (2014). Randomised clinical trial: gluten may cause depression in subjects with non-coeliac gluten sensitivity - an exploratory randomised clinical study., Alimentary pharmacology & therapeutics, PMID:

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Just Wow. Photo: Chris Sembrot PhotographyHi Julie,Yes, but WHY? I loved Claudia Fugazza's guest post about drawing on dogs' social imitation capacities to learn as copy-cats in the Do as I do training technique. Good stuff! A few things collided this week that resulted in me deciding to look into why dogs lick people. The first was the Huffington Post 'This Is What Happens When You Ask People To Kiss Their Dogs In Front Of A Camera' (example above from Chris Sembrot's 'For the love […]

Bradshaw J.W.S., Blackwell E.J. & Casey R.A. (2009). Dominance in domestic dogs—useful construct or bad habit?, Journal of Veterinary Behavior: Clinical Applications and Research, 4 (3) 135-144. DOI:

Bonanni R., Cafazzo S., Valsecchi P. & Natoli E. (2010). Effect of affiliative and agonistic relationships on leadership behaviour in free-ranging dogs, Animal Behaviour, 79 (5) 981-991. DOI:

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I often get questions related to Blastocystis epidemiology research, and many of these are 'how-to' questions.And as announced, I've chosen to dedicate a separate post listing some easy-to-use tools for subtyping Blastocystis from humans and animals.First, I want to guide your attention to the YouTube video that I made; it takes you through various important steps of subtyping and introduces you to the online database that can be used to call subtypes by BLASTing batches of fasta files - […]

Stensvold CR (2013). Comparison of sequencing (barcode region) and sequence-tagged-site PCR for Blastocystis subtyping., Journal of clinical microbiology, 51 (1) 190-4. PMID:

Alfellani MA, Taner-Mulla D, Jacob AS, Imeede CA, Yoshikawa H, Stensvold CR & Clark CG (2013). Genetic Diversity of Blastocystis in Livestock and Zoo Animals., Protist, 164 (4) 497-509. PMID:

Stensvold CR (2013). Blastocystis: Genetic diversity and molecular methods for diagnosis and epidemiology., Tropical parasitology, 3 (1) 26-34. PMID:

Alfellani MA, Stensvold CR, Vidal-Lapiedra A, Onuoha ES, Fagbenro-Beyioku AF & Clark CG (2013). Variable geographic distribution of Blastocystis subtypes and its potential implications., Acta tropica, 126 (1) 11-8. PMID:

Clark CG, van der Giezen M, Alfellani MA & Stensvold CR (2013). Recent developments in blastocystis research., Advances in parasitology, 82 1-32. PMID:

Stensvold CR, Ahmed UN, Andersen LO & Nielsen HV (2012). Development and Evaluation of a Genus-Specific, Probe-Based, Internal-Process-Controlled Real-Time PCR Assay for Sensitive and Specific Detection of Blastocystis spp., Journal of clinical microbiology, 50 (6) 1847-51. PMID:

Stensvold CR, Suresh GK, Tan KS, Thompson RC, Traub RJ, Viscogliosi E, Yoshikawa H & Clark CG (2007). Terminology for Blastocystis subtypes--a consensus., Trends in parasitology, 23 (3) 93-6. PMID:

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The emotion of awe is a self-transcendent one, in the sense that the experience of awe entails a feeling of being confronted with something much greater than oneself. Many people think of awe as a particularly religious emotion and therefore seem to assume that people with no religious beliefs at all, e.g. atheists are closed to the experience of awe. This assumption is quite false and reflects a wider prejudice against atheists. An illustrative example of this particular prejudice occurred […]

Caldwell-Harris, C., Wilson, A., LoTempio, E. & Beit-Hallahmi, B. (2011). Exploring the atheist personality: well-being, awe, and magical thinking in atheists, Buddhists, and Christians, Mental Health, Religion & Culture, 14 (7) 659-672. DOI:

Rudd M, Vohs KD & Aaker J (2012). Awe expands people's perception of time, alters decision making, and enhances well-being., Psychological science, 23 (10) 1130-6. PMID:

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If you are a chronic procrastinator, you're not alone. Habitual procrastination plagues around 15-20% of adults and 50% of college students. In a chronic procrastinator, repeated failure to efficiently complete important tasks can lead to lower feelings of self-worth. In certain contexts, it can also result in very tangible penalties. For example, a survey in 2002 found that 29% of American tax-payers procrastinated on their taxes, resulting in errors due to rushed filing that cost an average […]

Gustavson, D., Miyake, A., Hewitt, J. & Friedman, N. (2014). Genetic Relations Among Procrastination, Impulsivity, and Goal-Management Ability: Implications for the Evolutionary Origin of Procrastination, Psychological Science, DOI:

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### April 09, 2014

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SUMMARY: Two independent studies find a positive relationship between social environment and telomere length. The first study -- that nearly everyone has heard about -- is in children. The second study -- that few have heard about -- is in pet grey parrots. The second study raises the question: might telomere length be developed as a new way to measure chronic stress -- in animals? Telomere caps (white) on the ends of human chromosomes (grey). Image: U.S. Department of Energy... Read more

Aydinonat D., Penn D.J., Smith S., Moodley Y., Hoelzl F., Knauer F., Schwarzenberger F. & Saretzki G. (2014). Social Isolation Shortens Telomeres in African Grey Parrots (Psittacus erithacus erithacus), PLoS ONE, 9 (4) e93839. DOI:

Shalev I., Entringer S., Wadhwa P.D., Wolkowitz O.M., Puterman E., Lin J. & Epel E.S. (2013). Stress and telomere biology: A lifespan perspective, Psychoneuroendocrinology, 38 (9) 1835-1842. DOI:

Mitchell C., Hobcraft J., McLanahan S.S., Siegel S.R., Berg A., Brooks-Gunn J., Garfinkel I. & Notterman D. Social disadvantage, genetic sensitivity, and children's telomere length, Proceedings of the National Academy of Sciences, DOI:

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Neurologist Dr. Steven CramerIn an analysis of published research, neurologist Dr. Steven Cramer and biomedical engineer Weian Zhao identified 46 studies that examined the use of mesenchymal stromal cells -- a type of multipotent adult stem cells mostly processed from bone marrow -- in animal models of stroke. They found mesenchymal stem cells (MSCs) to be significantly better than control therapy in 44 of the studies.Importantly, the effects of these cells on functional recovery were robust […]

Vu Q, Xie K, Eckert M, Zhao W & Cramer SC (2014). Meta-analysis of preclinical studies of mesenchymal stromal cells for ischemic stroke., Neurology, 82 (14) 1277-86. PMID:

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Based on a chemical discovery by scientists at Oregon State University (OSU), it appears that trees may soon play a major role in making high-tech supercapacitors for energy storage. Read more »

Luo, W., Wang, B., Heron, C., Allen, M., Morre, J., Maier, C., Stickle, W. & Ji, X. (2014). Pyrolysis of Cellulose under Ammonia Leads to Nitrogen-Doped Nanoporous Carbon Generated through Methane Formation, Nano Letters, 2147483647. DOI:

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Dr Ashley Ng Melbourne researchers have solved a puzzle as to how an essential blood-making hormone stimulates production of the blood clotting cells known as platelets.Platelets are small, disc shaped clear cell fragments which are essential for stopping bleeding. They are produced by their ‘parent’ cells, called megakaryocytes.The discovery, made by scientists at the Walter and Eliza Hall Institute, identified how bone marrow cells could become overstimulated and produce too […]

Ng, A., Kauppi, M., Metcalf, D., Hyland, C., Josefsson, E., Lebois, M., Zhang, J., Baldwin, T., Di Rago, L., Hilton, D. & Alexander, W. (2014). Mpl expression on megakaryocytes and platelets is dispensable for thrombopoiesis but essential to prevent myeloproliferation, Proceedings of the National Academy of Sciences, DOI:

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Nearly every cell in your body is releasing microscopic bubbles that contain tiny messages to other cells in your body. The bubbles are so small that if a cell were the size of the Empire State Building, the vesicles would be the size of teenage couriers, running to deliver messages to neighboring buildings in the organism of Manhattan. But now there's evidence that at least in worms, these little bubbles, called extracellular vesicles (ECVs), can leave the cells of the Manhattan Island worm to […]

Wang J, Silva M, Haas LA, Morsci NS, Nguyen KC, Hall DH & Barr MM (2014). C. elegans Ciliated Sensory Neurons Release Extracellular Vesicles that Function in Animal Communication., Current biology : CB, 24 (5) 519-25. PMID:

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Nanostructures could enable more light to be directed into the active layer of solar cells, increasing their efficiency. Read more »

Schmid, M., Grandidier, J. & Atwater, H. (2013). Scanning near-field optical microscopy on dense random assemblies of metal nanoparticles, Journal of Optics, 15 (12) 125001. DOI:

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Two independent studies find a positive relationship between social environment and telomere length. The first study -- that nearly everyone has heard about -- is in children. The second study -- that few have heard about -- is in pet grey parrots. The second study raises the question: might telomere length be developed a new way to measure chronic stress -- in animals? Telomeres, the DNA-protein caps that prevent chromosomal fraying, are positively affected by social stress, according to two […]

Mitchell C., Hobcraft J., McLanahan S.S., Siegel S.R., Berg A., Brooks-Gunn J., Garfinkel I. & Notterman D. Social disadvantage, genetic sensitivity, and children's telomere length, Proceedings of the National Academy of Sciences, DOI:

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I am currently in Puerto Varas, Chile at an EMBO genomics workshop. The workshop is mainly for grad students and the instructors are, for the most part, alumni of the Bork group. I gave a tutorial on genomics databases. Anyway, the last two days of the workshop is a challenge, in teams of 3-4 advised […]

Laulederkind S.J.F., Hayman G.T., Wang S.J., Smith J.R., Lowry T.F., Nigam R., Petri V., de Pons J., Dwinell M.R. & Shimoyama M. & (2013). The Rat Genome Database 2013--data, tools and users, Briefings in Bioinformatics, 14 (4) 520-526. DOI:

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