Posts

November 12, 2014

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1:08 PM | Video Tip of the Week: UpSet about genomics Venn Diagrams?
Who can forget the Banana Venn? It was one of the most talked-about visualizations in genomics that I’m aware of. A new concept in data visualization: the Venn/banana diagram. MT @phylogenomics http://t.co/xjitNDNl — Iddo Friedberg (@iddux) July 19, 2012 Banana? RT @phylogenomics: Perhaps the best genomics Venn diagram ever #Bananas #NotSureWhatItMeansButDontCare http://t.co/xMV25GBG — Brian Kent […]

D’Hont A., Jean-Marc Aury, Franc-Christophe Baurens, Françoise Carreel, Olivier Garsmeur, Benjamin Noel, Stéphanie Bocs, Gaëtan Droc, Mathieu Rouard & Corinne Da Silva & (2012). The banana (Musa acuminata) genome and the evolution of monocotyledonous plants, Nature, 488 (7410) 213-217. DOI: http://dx.doi.org/10.1038/nature11241

Lex A., Gehlenborg N., Strobelt H., Vuillemot R.V. & Pfister H. (2014). UpSet: Visualization of Intersecting Sets, IEEE Transactions on Visualization and Computer Graphics (InfoVis '14), Other:

Lex A. (2014). Points of view: Sets and intersections, Nature Methods, 11 (8) 779-779. DOI: http://dx.doi.org/10.1038/nmeth.3033

Gibbs R.A., Michael L. Metzker, Donna M. Muzny, Erica J. Sodergren, Steven Scherer, Graham Scott, David Steffen, Kim C. Worley, Paula E. Burch & Geoffrey Okwuonu & (2004). Genome sequence of the Brown Norway rat yields insights into mammalian evolution, Nature, 428 (6982) 493-521. DOI: http://dx.doi.org/10.1038/nature02426

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9:49 AM | Loneliness is a disease that changes the brain's structure and function
Loneliness increases the risk of poor sleep, higher blood pressure, cognitive and immune decline, depression, and ultimately an earlier death. Why? The traditional explanation is that lonely people lack life’s advisors: people who encourage healthy behaviours and curb unhealthy ones. If so, we should invest in pamphlets, adverts and GP advice: ignorance is the true disease, loneliness just a symptom.But this can’t be the full story. Introverts with small networks aren’t at […]

Cacioppo, S., Capitanio, J. & Cacioppo, J. (2014). Toward a neurology of loneliness., Psychological Bulletin, 140 (6) 1464-1504. DOI: 10.1037/a0037618

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1:44 AM | Video Gaming and Internet Addiction : Harmful or Harmless?
The more the addiction to video games, Internet and social media is increased among teenagers and young adults, the more concerned the parents become. It is where family therapists play an important role. Are video games really bad for children? How to counter addiction to social media? Researchers explored the impact for these new forms […] The post Video Gaming and Internet Addiction : Harmful or Harmless? appeared first on Wiley Asia Blog.

Jordan, N. (2014). Video games: support for the evolving family therapist, Journal of Family Therapy, 36 (4) 359-370. DOI: 10.1111/j.1467-6427.2012.00593.x

Park, T., Kim, S. & Lee, J. (2014). Family therapy for an Internet-addicted young adult with interpersonal problems, Journal of Family Therapy, 36 (4) 394-419. DOI: 10.1111/1467-6427.12060

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12:46 AM | Organic solar cells are heating up!
Imagine you want to buy a new car, so you travel out to the closest dealer to see what they offer.  When you arrive, you notice that, strangely, all the cars in the lot look exactly the same.  The car salesman approaches … Continue reading →

Liu Y., Zhao J., Li Z., Mu C., Ma W., Hu H., Jiang K., Lin H., Ade H. & Yan H. & (2014). Aggregation and morphology control enables multiple cases of high-efficiency polymer solar cells., Nature communications, PMID: http://www.ncbi.nlm.nih.gov/pubmed/25382026

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November 11, 2014

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7:03 PM | Some Plants can regenerate by DNA duplication
When munched by grazing animals (or mauled by scientists in the lab), some herbaceous plants overcompensate – producing more plant matter and becoming more fertile than they otherwise would. Scientists […]

Scholes DR & Paige KN (2014). Plasticity in ploidy underlies plant fitness compensation to herbivore damage., Molecular ecology, 23 (19) 4862-70. PMID: http://www.ncbi.nlm.nih.gov/pubmed/25145792

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4:55 PM | Recovering from an Eating Disorder in a Society that Loves Fat Shaming (and Dieting)
Is ED recovery easier when your body is “normative or stereotypically desirable”? The anon asking the question implied that recovery could be more difficult because “an obese person … will never stop hearing hearing extremely triggering stuff about their body type.” Anon asked, “Have there been any studies on this?” Andrea tackled this question in her last post (it might be helpful to read it first if you […]

Berner, L.A., Shaw, J.A., Witt, A.A. & Lowe, M.R. (2013). The relation of weight suppression and body mass index to symptomatology and treatment response in anorexia nervosa., Journal of Abnormal Psychology, 122 (3) 694-708. PMID: http://www.ncbi.nlm.nih.gov/pubmed/24016010

Bulik, C.M., Marcus, M.D., Zerwas, S., Levine, M.D. & La Via, M. (2012). The changing "weightscape" of bulimia nervosa., The American Journal of Psychiatry, 169 (10) 1031-6. PMID: http://www.ncbi.nlm.nih.gov/pubmed/23032383

Lebow, J., Sim, L.A. & Kransdorf, L.N. (2014). Prevalence of a History of Overweight and Obesity in Adolescents With Restrictive Eating Disorders., The Journal of Adolescent Health, PMID: http://www.ncbi.nlm.nih.gov/pubmed/25049202

McKisack, C. & Waller, G. (1997). Factors influencing the of group psychotherapy for bulimia nervosa., The International Journal of Eating Disorders, 22 (1) 1-13. PMID: http://www.ncbi.nlm.nih.gov/pubmed/9140730

Sim, L., Lebow, J. & Billings, M. (2013). Eating Disorders in Adolescents With a History of Obesity, PEDIATRICS, 132 (4) DOI: 10.1542/peds.2012-3940

Wildes, J.E. & Marcus, M.D. (2012). Weight suppression as a predictor of weight gain and response to intensive behavioral treatment in patients with anorexia nervosa., Behaviour Research and Therapy, 50 (4) 266-74. PMID: http://www.ncbi.nlm.nih.gov/pubmed/22398152

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3:24 PM | Found: The Ideal Fatness for Elephant Seals
Like many new mothers, a female elephant seal puts herself on a strict diet after giving birth. She dives into the Pacific and spends two months eating everything she can find. It’s only by working hard at building up her blubber stores that she can get back her ideal body. Northern elephant seals (Mirounga angustirostris) […]The post Found: The Ideal Fatness for Elephant Seals appeared first on Inkfish.

Adachi, T., Maresh, J., Robinson, P., Peterson, S., Costa, D., Naito, Y., Watanabe, Y. & Takahashi, A. (2014). The foraging benefits of being fat in a highly migratory marine mammal., Proceedings of the Royal Society B: Biological Sciences, 281 (1797) 20142120-20142120. DOI: 10.1098/rspb.2014.2120

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9:50 AM | Psychiatric comorbidity in post H1N1 vaccination narcolespy?
I can imagine that the paper by Atilla Szakács and colleagues [1] is likely to draw some rather differing opinions about potential importance based on their subject matter and methods/participant numbers looking at the frequency of psychiatric comorbidity among those with narcolepsy including narcolepsy post H1N1 vaccination. The fact that autism - "pervasive developmental disorder not otherwise specified (i.e., atypical autism)" - is mentioned as one of the comorbidity in the […]

Szakács A, Hallböök T, Tideman P, Darin N & Wentz E (2014). Psychiatric Comorbidity and Cognitive Profile in Children With Narcolepsy With or Without Association to the H1N1 Influenza Vaccination., Sleep, PMID: http://www.ncbi.nlm.nih.gov/pubmed/25325473

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9:39 AM | Who are the most eminent psychologists of the modern era?
A new paper identifies Albert Bandura as themost eminent psychologist of the modern era.Twelve years ago the behaviourist B.F. Skinner topped a list of the 100 most eminent psychologists of the twentieth century, followed by Jean Piaget and Sigmund Freud. Now a team led by Ed Diener has used their own criteria to compile a list of the 200 most eminent psychologists of the modern era (i.e. people whose careers occurred primarily after 1956).Here is the top 10: Albert Bandura in first place, […]

Diener, E., Oishi, S. & Park, J. (2014). An incomplete list of eminent psychologists of the modern era., Archives of Scientific Psychology, 2 (1) 20-31. DOI: 10.1037/arc0000006

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November 10, 2014

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8:57 PM | A new way to look at Global Warming
Global warming, nothing new with that and it’s here to stay for now. But while computer models churn out bleak forecasts for the planet’s future, we also have a more […]

Donohoe A., Armour K.C., Pendergrass A.G. & Battisti D.S. (2014). Shortwave and longwave radiative contributions to global warming under increasing CO2 , PNAS, DOI: 10.1073/pnas.1412190111

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6:17 PM | The Dancing Kiwa Puravida (Yeti Crab)
Kiwa PuravidaCredit: Andrew ThurberKingdom: AnimaliaPhylum: ArthropodaSubphylum: CrustaceaClass: MalacostracaOrder: DecapodaInfraorder: AnomuraFamily: KiwaidaeGenus: KiwaSpecies: Kiwa puravidaConservation Status: Not assessedCommon Name: Yeti crabMeet Kiwa puravida, a recently discovered deep-sea dwelling decapod and one of three species informally known as "yeti crabs". The other two are kiwa hirsuta and a creature commonly known as the "Hoff […]

Thurber, A., Jones, W. & Schnabel, K. (2011). Dancing for Food in the Deep Sea: Bacterial Farming by a New Species of Yeti Crab, PLoS ONE, 6 (11) DOI: 10.1371/journal.pone.0026243

Roterman CN, Copley JT, Linse KT, Tyler PA & Rogers AD (2013). The biogeography of the yeti crabs (Kiwaidae) with notes on the phylogeny of the Chirostyloidea (Decapoda: Anomura)., Proceedings. Biological sciences / The Royal Society, 280 (1764) 20130718. PMID: http://www.ncbi.nlm.nih.gov/pubmed/23782878

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2:48 PM | Genome Editing with CRISPR-Cas9, nifty animation
I saw this come across my twitter feed the other day, and as a nice Friday afternoon diversion I posted it to Google+. I was surprised how popular it was. So I thought–hey, I have a blog too. Let’s put it there…. So grab some coffee and watch, a nice gentle way to get your […]

Platt R., Sidi Chen, Yang Zhou, Michael J. Yim, Lukasz Swiech, Hannah R. Kempton, James E. Dahlman, Oren Parnas, Thomas M. Eisenhaure, Marko Jovanovic & Daniel B. Graham (2014). CRISPR-Cas9 Knockin Mice for Genome Editing and Cancer Modeling, Cell, 159 (2) 440-455. DOI: http://dx.doi.org/10.1016/j.cell.2014.09.014

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2:26 PM | Rhythm and Blue: Plant Circadian Rhythms
Anyone who's suffered from jet lag will know that circadian rhythms are an important process. But perhaps what you didn't know is that plants are also regulated by a circadian clock - and - that the same receptor is used in both plants and animals.Read more »

McClung, C. (2006). Plant Circadian Rhythms, THE PLANT CELL ONLINE, 18 (4) 792-803. DOI: 10.1105/tpc.106.040980

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9:59 AM | When we lie to children, are we teaching them to be dishonest?
Cookie Monster - one ofthe characters featuredin this research.Most parents lie to their children, often as a way to control their behaviour. A new study asks whether lying to the little ones increases the likelihood that they too will lie. The authors, Chelsea Hays and Leslie Carver, say theirs is the first attempt to investigate this possibility.Nearly two hundred children aged three to seven were each put through a similar scenario, one at a time. First, they were invited to go through to […]

Hays, C. & Carver, L. (2014). Follow the liar: the effects of adult lies on children's honesty, Developmental Science, 17 (6) 977-983. DOI: 10.1111/desc.12171

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9:10 AM | Water-Use Advantage for Lianas over Trees in Tropical Seasonal Forests
Lianas exhibit peak abundance in tropical forests with strong seasonal droughts, the eco-physiological mechanisms associated with lianas coping with water deficits are poorly understood. Researchers examined soil water partitioning, sap flow, and canopy eco-physiological properties for 99 individuals of 15 liana and 34 co-occurring tree species in three tropical forests that differed in soil water […] The post Water-Use Advantage for Lianas over Trees in Tropical Seasonal Forests […]

Chen, Y., Cao, K., Schnitzer, S., Fan, Z., Zhang, J. & Bongers, F. (2014). Water-use advantage for lianas over trees in tropical seasonal forests, New Phytologist, DOI: 10.1111/nph.13036

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8:01 AM | Metabolomics and autism: the continuing search for biomarkers
I'm always a happy bunny when some of my own research findings receive something like independent replication. So it was when I read the monster paper from Paul West and colleagues [1] (open-access) reporting results based on not one, not two, not three, not even four, but five mass spectrometric methods looking for potential biomarkers for autism. Metabolomics in action (see here for an introduction to this topic).Rosina @ Wikipedia The particular reason for my excitement was […]

West, P., Amaral, D., Bais, P., Smith, A., Egnash, L., Ross, M., Palmer, J., Fontaine, B., Conard, K., Corbett, B. & Cezar, G. (2014). Metabolomics as a Tool for Discovery of Biomarkers of Autism Spectrum Disorder in the Blood Plasma of Children, PLoS ONE, 9 (11) DOI: 10.1371/journal.pone.0112445

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November 09, 2014

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5:48 PM | If being sad is “bad”, then why is there sad music?
We tell children not to look so sad. We tell adults to wipe that sad look off their face and smile. We even worry that if you are sad too long, […]

Taruffi L & Koelsch S (2014). The paradox of music-evoked sadness: an online survey., PloS one, 9 (10) PMID: http://www.ncbi.nlm.nih.gov/pubmed/25330315

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5:43 PM | Will anyone follow this route to low emission, low cost farming?
Can we stop cheap, climate-friendly fertiliser via the STEP process being like transport by jetpack – a promise destined to remain unkept?

Licht, S., Cui, B., Wang, B., Li, F., Lau, J. & Liu, S. (2014). Ammonia synthesis by N2 and steam electrolysis in molten hydroxide suspensions of nanoscale Fe2O3, Science, 345 (6197) 637-640. DOI: 10.1126/science.1254234

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11:12 AM | Sunday's Nudibranch: Jorunna funebris
 Jorunna funebrisPhoto by © Mark Rosenstein  [CC BY-NC-SA 3.0]Kingdom: AnimaliaPhylum: MolluscaClass: GastropodaSuperfamily: DoridoideaFamily: DiscodorididaeGenus: JorunnaSpecies: Jorunna funebrisCommon Name: Dotted nudibranch, Polka DotWhen I was writing my "14 Most Amazing Nudibranchs" post I had a really hard time choosing which species to include and which not.This animal group is very diverse and full of beautiful, alien-like or simply […]

Pattira Kasamesiri, Shettapong Meksumpun, and Charumas Meksumpun (2012). Observations on Embryonic Development of Black-Spot Jorunna, Jorunna Funebris (Kelaart, 1859) (Gastropoda: Nudibranchia) , Journal of Shellfish Research, 33 (2) 111-117. Other:

Camacho-Garcia, Y. & Gosliner, T. (2008). Systematic revision of Jorunna Bergh, 1876 (Nudibranchia: Discodorididae) with a morphological phylogenetic analysis, Journal of Molluscan Studies, 74 (2) 143-181. DOI: 10.1093/mollus/eyn002

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10:29 AM | Subduction is not the end
Subduction is just the beginning. Stuck on the surface of the earth as we are, it’s easy to think that when oceanic lithosphere is destroyed when it vanishes into the mantle. But this is wrong. The more we manage to peer … Continue reading →

Dobson D.P. (2005). Subducted banded iron formations as a source of ultralow-velocity zones at the core–mantle boundary, Nature, 434 (7031) 371-374. DOI: http://dx.doi.org/10.1038/nature03430

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November 08, 2014

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5:55 PM | When it comes to sleep recommendations, what about the children?
Sleep is a hot topic lately, are we getting too much, too little, how much is enough? However, most of these questions are for adults, so what about children? Well […]

Crowley SJ, Van Reen E, LeBourgeois MK, Acebo C, Tarokh L, Seifer R, Barker DH & Carskadon MA (2014). A Longitudinal Assessment of Sleep Timing, Circadian Phase, and Phase Angle of Entrainment across Human Adolescence., PloS one, 9 (11) PMID: http://www.ncbi.nlm.nih.gov/pubmed/25380248

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3:59 PM | Are we really evolving into super-humans?
© EEGI came across an article on the Popular Science website, which, turns out, is the excerpt of a new book on evolution by Science Guy Bill Nye. From the reviews I gather that Bill Nye is an excellent writer and, being also an entertainer, he knows how to not only expose well but also infuse some good humor to what he says. That's all fantastic. But while the article starts off with some rigor, his conclusion had me roll my eyes. Because, even though he does include some […]

Salih NA, Hussain AA, Almugtaba IA, Elzein AM, Elhassan IM, Khalil EA, Ishag HB, Mohammed HS, Kwiatkowski D & Ibrahim ME & (2010). Loss of balancing selection in the betaS globin locus., BMC medical genetics, 11 21. PMID: http://www.ncbi.nlm.nih.gov/pubmed/20128890

Hafid Laayounia,1, Marije Oostingb,c,1, Pierre Luisia, Mihai Ioanab,d, Santos Alonsoe, Isis Ricaño-Poncef, Gosia Trynkaf,2, Alexandra Zhernakovaf, Theo S. Plantingab, Shih-Chin Chengb, Jos W. M. van der Meerb, Radu Poppg, Ajit Soodh, B. K. Thelmai, Cisca (2014). Convergent evolution in European and Rroma populations reveals pressure exerted by plague on Toll-like receptors, PNAS, DOI: 10.1073/pnas.1317723111

Coop G, Pickrell JK, Novembre J, Kudaravalli S, Li J, Absher D, Myers RM, Cavalli-Sforza LL, Feldman MW & Pritchard JK & (2009). The role of geography in human adaptation., PLoS genetics, 5 (6) PMID: http://www.ncbi.nlm.nih.gov/pubmed/19503611

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9:51 AM | UK Millennium Cohort Study: School and the disabled child
Quite recently the BBC News online ran with the headline: "Disabled children's behaviour 'deteriorates at school'". The story revolved around the findings reported by Rebecca Fauth and colleagues [1] (open-access) looking at "the extent to which the associations between disability and behaviour are linked to children’s developmental stage and thus may be ‘grown out of’ as children enter school and move out of the early years". I should add that, at the time of writing, the […]

Connelly R & Platt L (2014). Cohort Profile: UK Millennium Cohort Study (MCS)., International journal of epidemiology, PMID: http://www.ncbi.nlm.nih.gov/pubmed/24550246

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4:45 AM | Bernstein polynomials and non-linear public goods in tumours
By analogy, or maybe homage, to standard game theory, when we discuss the payoffs of an evolutionary game, we usually tell the story of two prototype agents representing their respective strategies meeting at random and interacting. For my stories of yarn, knitting needles, and clandestine meetings in the dark of night, I even give these […]

Archetti, M. (2014). Evolutionary dynamics of the Warburg effect: glycolysis as a collective action problem among cancer cells., Journal of theoretical biology, 341 1-8. PMID: http://www.ncbi.nlm.nih.gov/pubmed/24075895

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November 07, 2014

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3:37 PM | Breaking Research: A method by which invading bacteria avoid detection could also be our key to defeating them
Have you ever wondered how our body recognizes when it’s being invaded by harmful bacteria? Nearly all forms of life—from single-celled organisms all the way to humans—have an “innate” immune system, which has evolved to recognize cellular components shared by broad groups of pathogens. One such example is peptidoglycan, a molecule found on the cell […]

Atilano M.L., Filipa Vaz, Maria João Catalão, Patricia Reed, Inês Ramos Grilo, Rita Gonçalves Sobral, Petros Ligoxygakis, Mariana Gomes Pinho & Sérgio Raposo Filipe (2014). Bacterial autolysins trim cell surface peptidoglycan to prevent detection by the Drosophila innate immune system, eLife, 3 DOI: http://dx.doi.org/10.7554/elife.02277

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3:01 PM | Powerful Ravens Sabotage Others’ Relationships
  If we’re lucky, this is behavior we haven’t seen since high school. The coolest individuals can’t stand to see others gaining social status, so they cut down any peers who are starting to elevate themselves. Ravens have to live with this behavior all the time. When the top-dog birds see others building new relationships, […]The post Powerful Ravens Sabotage Others’ Relationships appeared first on Inkfish.

Massen, J., Szipl, G., Spreafico, M. & Bugnyar, T. (2014). Ravens Intervene in Others’ Bonding Attempts, Current Biology, DOI: 10.1016/j.cub.2014.09.073

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9:11 AM | Treating depression: exercise or anti-inflammatory meds?
Reiterating my primary caveat on this blog about not giving anything that looks, sounds or smells like medical and/or clinical advice, I'm bringing three papers to the research blogging table today, all published in the JAMA journal family and all talking about depression / depressive symptoms.See my hat... @ Wikipedia First up is the paper by Ole Köhler and colleagues [1] reviewing "the antidepressant and possible adverse effects of anti-inflammatory interventions". Some […]

Ole Köhler, Michael E. Benros, Merete Nordentoft, Michael E. Farkouh, Rupa L. Iyengar, Ole Mors & Jesper Krogh (2014). Effect of Anti-inflammatory Treatment on Depression, Depressive Symptoms, and Adverse Effects, JAMA Psychiatry, Other:

Snehal M. Pinto Pereira, Marie-Claude Geoffroy & Christine Power (2014). Depressive Symptoms and Physical Activity During 3 Decades in Adult Life, JAMA Psychiatry, Other:

Toseeb, U., Brage, S., Corder, K., Dunn, V., Jones, P., Owens, M., St Clair, M., van Sluijs, E. & Goodyer, I. (2014). Exercise and Depressive Symptoms in Adolescents, JAMA Pediatrics, DOI: 10.1001/jamapediatrics.2014.1794

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2:40 AM | Diving into Energy Drinks
How much do you know about energy drinks? We always consume energy drinks to boost our mood in general and to enhance our physical endurance. Being consumed since 1960s in Europe and Asia, we are uncertain about the side effects that energy drinks could produce. While energy drinks are consumed by general consumers, teenagers and […] The post Diving into Energy Drinks appeared first on Wiley Asia Blog.

Heckman, M., Sherry, K. & De Mejia, E. (2010). Energy Drinks: An Assessment of Their Market Size, Consumer Demographics, Ingredient Profile, Functionality, and Regulations in the United States, Comprehensive Reviews in Food Science and Food Safety, 9 (3) 303-317. DOI: 10.1111/j.1541-4337.2010.00111.x

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November 06, 2014

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10:53 PM | A Possible Genetic “Cure” for HIV… Maybe
Let’s face it, a cure for HIV probably won’t be coming around for awhile. That slippery little virus manages to avoid everything we throw at it. Well researchers at Massachusetts General […]

Mandal, P., Ferreira, L., Collins, R., Meissner, T., Boutwell, C., Friesen, M., Vrbanac, V., Garrison, B., Stortchevoi, A., Bryder, D. & Musunuru, K. (2014). Efficient Ablation of Genes in Human Hematopoietic Stem and Effector Cells using CRISPR/Cas9, Cell Stem Cell, 15 (5) 643-652. DOI: 10.1016/j.stem.2014.10.004

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10:39 PM | The Inherent Limits of MRI Tractography?
A popular neuroscience tool, diffusion MRI tractography, may fundamentally have limited accuracy. That’s according to a paper just published in PNAS: Anatomical accuracy of brain connections derived from diffusion MRI tractography is inherently limited The authors, Cibu Thomas and colleagues of Bethesda, Maryland, begin by explaining why diffusion MRI is so widely used The creation […]The post The Inherent Limits of MRI Tractography? appeared first on Neuroskeptic.

Thomas C, Ye FQ, Irfanoglu MO, Modi P, Saleem KS, Leopold DA & Pierpaoli C (2014). Anatomical accuracy of brain connections derived from diffusion MRI tractography is inherently limited., Proceedings of the National Academy of Sciences of the United States of America, PMID: http://www.ncbi.nlm.nih.gov/pubmed/25368179

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