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April 23, 2014

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6:27 PM | Biofuels From Crop Residue May Increase Greenhouse Gas Emissions
Using corn crop residue to make ethanol and other biofuels reduces soil carbon and can generate more greenhouse gases than gasoline, according to a study published in the journal Nature Climate Change (see footnote). Read more »

Liska, A., Yang, H., Milner, M., Goddard, S., Blanco-Canqui, H., Pelton, M., Fang, X., Zhu, H. & Suyker, A. (2014). Biofuels from crop residue can reduce soil carbon and increase CO2 emissions, Nature Climate Change, DOI:

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6:00 PM | Mantis Shrimp, is there anything you can’t teach us?
A big tenant for starting Loony Labs was an idea that nature provides us with answers to some of the biggest technical problems. So I am proud to announce some […]

Grunenfelder L.K., Suksangpanya N., Salinas C., Milliron G., Yaraghi N., Herrera S., Evans-Lutterodt K., Nutt S.R., Zavattieri P. & Kisailus D. & (2014). Bio-inspired impact-resistant composites, Acta Biomaterialia, DOI:

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4:49 PM | Scientists Use Airplane to Detect Methane From Fracking
Using an airplane to detect greenhouse gas emissions from freshly drilled shale gas wells in Pennsylvania’s Marcellus basin, Cornell and Purdue scientists have found that leaked methane from fracking is a tougher problem—between a hundred- and a thousandfold—than previously thought. Read more »

Caulton, D., Shepson, P., Santoro, R., Sparks, J., Howarth, R., Ingraffea, A., Cambaliza, M., Sweeney, C., Karion, A., Davis, K. & Stirm, B. (2014). Toward a better understanding and quantification of methane emissions from shale gas development, Proceedings of the National Academy of Sciences, DOI:

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4:00 PM | How To Do The Moonwalk
Walking around in the real world, as opposed to the uncluttered hallways of your school, requires flexible and adaptive fine-tuning of the basic alternating stepping pattern of our two legs. For animals to walk, central pattern generators (CPGs) must be modulated to allow different stride lengths in each leg or different swing heights to step … Continue reading →

Bidaye S.S., Machacek C., Wu Y. & Dickson B.J. (2014). Neuronal Control of Drosophila Walking Direction, Science, 344 (6179) 97-101. DOI:

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3:40 PM | Old champions get new help
Greetings     So often has been antibiotic resistance been talked about in this page, that it needs no introduction. There is a huge list of antibiotics that is currently in research. There are all sorts of chemicals, that has been investigated. It is now almost impossible to keep track of the growing list (I probably have even lost the count). The whole story of magic medicine bullet (Antibiotics I mean), has started from the discovery of penicillin (Not by Alexander Fleming, […]

Zhang J., Chen Y.P., Miller K.P., Ganewatta M.S., Bam M., Yan Y., Nagarkatti M., Decho A.W. & Tang C. (2014). Antimicrobial Metallopolymers and Their Bioconjugates with Conventional Antibiotics against Multidrug-Resistant Bacteria., Journal of the American Chemical Society, PMID:

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3:05 PM | Highest Efficiency Achieved for Small GaAs Solar Cells
Engineering researchers at the University of Arkansas have achieved the highest efficiency ever in a 9 mm2 solar cell made of gallium arsenide. Read more »

Makableh, Y., Vasan, R., Sarker, J., Nusir, A., Seal, S. & Manasreh, M. (2014). Enhancement of GaAs solar cell performance by using a ZnO sol–gel anti-reflection coating, Solar Energy Materials and Solar Cells, 123 178-182. DOI:

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2:00 PM | Je ne regrette rien (2): Consciuous decisions in the lab
Psychologists and neurologists have been interested in the problem of free will since the beginning of their specialities, though the first clearly devised and relevant […] Read more The post Je ne regrette rien (2): Consciuous decisions in the lab appeared first on Mapping Ignorance. Related posts:Je ne regrette rien (1): On the neuropsychology of free will Mapping areas involved in voluntary forgetting is not simple... it is double! Reinforcement learning in the brain

Filevich E., Kühn S., Haggard P. & Pourtois G. (2013). There Is No Free Won’t: Antecedent Brain Activity Predicts Decisions to Inhibit, PLoS ONE, 8 (2) e53053. DOI:

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1:36 PM | Video Tip of the Week: Atlas of Cancer Signaling Networks
Last week I highlighted a software tool that lets you customize maps of molecular interactions, and navigate around at various resolutions to explore. It’s called NaviCell, and it seems to offer a lot of opportunity for folks to develop helpful maps related to their research. This week I’m going to note that this same team […]

Kuperstein I., Cohen D.P., Pook S., Viara E., Calzone L., Barillot E. & Zinovyev A. (2013). NaviCell: a web-based environment for navigation, curation and maintenance of large molecular interaction maps, BMC Systems Biology, 7 (1) 100. DOI:

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12:30 PM | What Is A Typical Animal Hoarder?
Sometimes we hear their cases on the news – dozens of sick and frightened dogs or cats removed from the home of an animal hoarder. But is there a typical profile, and how big is the problem?A study by Calvo et al (2014) investigates 24 cases of animal hoarding in Spain between 2002 and 2011. Photo: schankz / ShutterstockAnimal hoarding is not simply having large numbers of pets; it also involves a lack of care for those pets, such that they are sick, not receiving veterinary care and […]

Calvo, P., Duarte, C., Bowen, J., Bulbena, A. & Fatjó, J. (2014). Characteristics of 24 cases of animal hoarding in Spain, Animal Welfare, 23 (2) 199-208. DOI:

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12:00 PM | Chili Peppers Run Hot And Cold
Biology concepts – obesity, brown adipose tissue, agonist/antagonist, protective hypothermia, hyperthermia, reactive oxygen species, ischemia, hypoxiaWhen The Wizard of Oz was released in 1939, it just barely turned a profit. The '39 version was the third attempt at filming the children’s classic, and the first two efforts had not fared much better. I don’t see how people didn’t take to the Wizard of Oz right away. It had new technology for the movies, a good villain, […]

Yoneshiro T, Aita S, Matsushita M, Kayahara T, Kameya T, Kawai Y, Iwanaga T & Saito M (2013). Recruited brown adipose tissue as an antiobesity agent in humans., The Journal of clinical investigation, 123 (8) 3404-8. PMID:

Feng Z, Hai-Ning Y, Xiao-Man C, Zun-Chen W, Sheng-Rong S & Das UN (2014). Effect of yellow capsicum extract on proliferation and differentiation of 3T3-L1 preadipocytes., Nutrition (Burbank, Los Angeles County, Calif.), 30 (3) 319-25. PMID:

Yoneshiro T & Saito M (2013). Transient receptor potential activated brown fat thermogenesis as a target of food ingredients for obesity management., Current opinion in clinical nutrition and metabolic care, 16 (6) 625-31. PMID:

Muzzi M, Felici R, Cavone L, Gerace E, Minassi A, Appendino G, Moroni F & Chiarugi A (2012). Ischemic neuroprotection by TRPV1 receptor-induced hypothermia., Journal of cerebral blood flow and metabolism : official journal of the International Society of Cerebral Blood Flow and Metabolism, 32 (6) 978-82. PMID:

Cao Z, Balasubramanian A & Marrelli SP (2014). Pharmacologically induced hypothermia via TRPV1 channel agonism provides neuroprotection following ischemic stroke when initiated 90 min after reperfusion., American journal of physiology. Regulatory, integrative and comparative physiology, 306 (2) 56. PMID:

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10:48 AM | Why are some syllables preferred?
 In a recent paper by Berent and others (citation below) they investigate language universals in syllable structure. Their argument goes: there is a preference for certain syllables over others across languages and even in people whose language does not include those syllables; a set of four syllables which do not occur in English shows this […]

Berent, I., Pan, H., Zhao, X., Epstein, J., Bennett, M., Deshpande, V., Seethamraju, R. & Stern, E. (2014). Language Universals Engage Broca's Area, PLoS ONE, 9 (4) DOI:

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8:25 AM | Phenylalanine and schizophrenia: new directions for intervention?
As regular readers might already have noticed, amino acids are a bit of a obsession of mine on this blog. Out of all of them - and there are quite a few - I'm particularly interested in the aromatic amino acids and the their various connections to health and wellbeing. I've talked at length about some of the proposed connections made between amino acids such as tryptophan, tyrosine and phenylalanine to all manner of conditions but specifically with the autism spectrum in mind (see here).The […]

Olaoluwa Okusaga, Olesja Muravitskaja, Dietmar Fuchs, Ayesha Ashraf, Sarah Hinman, Ina Giegling, Annette M. Hartmann, Bettina Konte, Marion Friedl, Jason Schiffman & Elliot Hong (2014). Elevated Levels of Plasma Phenylalanine in Schizophrenia: A Guanosine Triphosphate Cyclohydrolase-1 Metabolic Pathway Abnormality?, PLoS ONE, 9 DOI:

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2:23 AM | Autism, SSRIs, and Epidemiology 101
I can understand the eagerness with which science writers jump on stories that deal with new findings about autism spectrum disorders (ASDs). After all, the mystery surrounding the rapid increase in ASD rates over the past 20 years (see right) has made any ASD-related study that may offer some clues inherently interesting. Because people are anxiously awaiting some explanation of this medical enigma, it seems like science writers almost have an obligation to discuss new findings concerning the […]

Rebecca A. Harrington, Li-Ching Lee, Rosa M. Crum, Andrew W. Zimmerman, Irva Hertz-Picciotto (2014). Prenatal SSRI Use and Offspring With Autism Spectrum Disorder or Developmental Delay, PEDIATRICS, DOI:

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1:16 AM | Removal of crop residue for biofuels increases CO2 emissions
Back in 2007, Congress passed the US Energy Independence and Security Act, which was intended to be a mechanism towards removing our country’s dependence on petroleum and promote renewable energies.  The Senate opposed the original bill’s attempt to cut oil … Continue reading →

Liska, A., Yang, H., Milner, M., Goddard, S., Blanco-Canqui, H., Pelton, M., Fang, X., Zhu, H. & Suyker, A. (2014). Biofuels from crop residue can reduce soil carbon and increase CO2 emissions, Nature Climate Change, DOI:

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April 22, 2014

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6:56 PM | Polar Opposites? The Social Construction of Bulimia and Anorexia Nervosa
Some might argue that bulimia nervosa is more “hidden” than anorexia nervosa — it is not always obvious that someone is suffering from bulimia (though, I would argue, it is not always obvious that someone is suffering from any eating disorder). Even when it is “discovered,” BN is often placed in opposition with AN — as if the two were polar opposites. Indeed, attempts to define a phenotype (a set of observable traits or characteristics) for AN and BN tend to […]

Burns, M. (2004). Eating Like an Ox: Femininity and Dualistic Constructions of Bulimia and Anorexia, Feminism & Psychology, 14 (2) 269-295. DOI:

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6:27 PM | Plasmonic Metamaterials Could Improve Solar Cell Performance
New plasmonic metamaterials that operate at high temperatures could radically improve solar cell performance and bring advanced computer data storage technology that uses heat to record information on a magnetic disk. Read more »

Guler, U., Boltasseva, A. & Shalaev, V. (2014). Refractory Plasmonics, Science, 344 (6181) 263-264. DOI:

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4:00 PM | Alzheimer’s? Forget about it!
Let’s face it, diseases that affect the brain are some of the hardest to deal with. Anyone who’s lost someone to alzheimer’s knows exactly what I am talking about. Looking […]

Acharya S., Safaie B.M., Wongkongkathep P., Ivanova M.I., Attar A., Klarner F.G., Schrader T., Loo J.A., Bitan G. & Lapidus L.J. & (2014). Molecular Basis for Preventing  α-synuclein Aggregation by a Molecular Tweezer, Journal of Biological Chemistry, 289 (15) 10727-10737. DOI:

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2:22 PM | Frogs Survive Subzero Temperatures by Living as Ice Cubes
No matter how rough a winter you think you had, it was nothing compared to what a wood frog survives every year. Some of these little amphibians are still waiting for spring, when they’ll thaw out and turn from frog-shaped blocks of ice back into animals. Recently, scientists took a close look at wood frogs […]The post Frogs Survive Subzero Temperatures by Living as Ice Cubes appeared first on Inkfish.

Larson DJ, Middle L, Vu H, Zhang W, Serianni AS, Duman J & Barnes BM (2014). Wood frog adaptations to overwintering in Alaska: New limits to freezing tolerance., The Journal of experimental biology, PMID:

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1:54 PM | No link between STAP cells and acid reflux, except for paper’s authors
> If you’ve stayed current with the STAP cell fiasco you know it’s been a wild ride. STAP cells, or Stimulus-Triggered Acquisition of Pluripotency cells, caught the imagination of many in late January through their sheer simplicity: You hit cells with a shock of acidic conditions, and they become pluripotent. That’s it. No Yamanaka factors...Read more

Chen X., Qin R., Liu B., Ma Y., Su Y., Yang C., Glickman J., Odze R. & Shaheen N. Multilayered epithelium in a rat model and human Barrett's esophagus: similar expression patterns of transcription factors and differentiation markers, BMC Gastroentereology, 8 (1) DOI:

Wang X., Yang S., Zhao X., Guo H., Ling X., Wang L., Fan C., Yu J. & Zhou S. (2014). OCT3 and SOX2 promote the transformation of Barrett's esophagus to adenocarcinoma by regulating the formation of tumor stem cells., Oncology reports, PMID:

Wang X., Ouyang H., Yamamoto Y., Kumar P.A., Wei T.S., Dagher R., Vincent M., Lu X., Bellizzi A.M. & Ho K.Y. & Residual embryonic cells as precursors of a Barrett's-like metaplasia., Cell, PMID:

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April 21, 2014

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8:38 PM | Developing Gain Control in Single Cortical Neurons
If you are reading this sentence, it is quite likely that you have heard of “gain control” in a neuroscience context. You may notice that the picture provided above has very little to do with the context in which this blog post shall discuss “gain control”. You may also notice that this blog post has […]

Mease R.A., Famulare M., Gjorgjieva J., Moody W.J. & Fairhall A.L. (2013). Emergence of Adaptive Computation by Single Neurons in the Developing Cortex, Journal of Neuroscience, 33 (30) 12154-12170. DOI:

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6:56 PM | Easter Chocolate Cravings: The Power of Polyphenols
With the Easter weekend over for another year and the family festivities drawing to a close, we can sit and contemplate one thing…just how much chocolate have I eaten the […]

Katz, D., Doughty, K. & Ali, A. (2011). Cocoa and Chocolate in Human Health and Disease, Antioxidants & Redox Signaling, 15 (10) 2779-2811. DOI:

Franco R, Oñatibia-Astibia A & Martínez-Pinilla E (2013). Health benefits of methylxanthines in cacao and chocolate., Nutrients, 5 (10) 4159-73. PMID:

Selmi C, Cocchi CA, Lanfredini M, Keen CL & Gershwin ME (2008). Chocolate at heart: the anti-inflammatory impact of cocoa flavanols., Molecular nutrition & food research, 52 (11) 1340-8. PMID:

Ellam S & Williamson G (2013). Cocoa and human health., Annual review of nutrition, 33 105-28. PMID:

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6:49 PM | Most Efficient Thermoelectric Material Created
Northwestern University scientists have discovered a material—tin selenide—that is, according to a press release, “the best in the world at converting waste heat to useful electricity.” Read more »

Zhao, L., Lo, S., Zhang, Y., Sun, H., Tan, G., Uher, C., Wolverton, C., Dravid, V. & Kanatzidis, M. (2014). Ultralow thermal conductivity and high thermoelectric figure of merit in SnSe crystals, Nature, 508 (7496) 373-377. DOI:

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4:30 PM | Pyrolysis Biofuel Production Process Simplified
Innovations at the U.S. Department of Agriculture (USDA) are bringing researchers one step closer to developing “green” biofuel production systems farmers can use to meet on-farm energy needs, or to produce renewable fuels for commercial markets. Read more »

Pourhashem, G., Spatari, S., Boateng, A., McAloon, A. & Mullen, C. (2013). Life Cycle Environmental and Economic Tradeoffs of Using Fast Pyrolysis Products for Power Generation, Energy & Fuels, 27 (5) 2578-2587. DOI:

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4:01 PM | SIRT1 protein equired for integrity of induced pluripotent stem cells
This image shows chromosome abnormalities in reprogrammed cells in which SIRT1 protein has been removed (in red).Credit: Centro Nacional de Investigaciones OncologicasCell reprogramming converts specialised cells such as nerve cells or skin cells towards an embryonic stem cell state. This reversal in the evolutionary development of cells also requires a reversal in the biology of telomeres, the structures that protect the ends of chromosomes; whilst under normal conditions telomeres […]

De Bonis, M., Ortega, S. & Blasco, M. (2014). SIRT1 Is Necessary for Proficient Telomere Elongation and Genomic Stability of Induced Pluripotent Stem Cells, Stem Cell Reports, DOI:

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4:00 PM | Biofuels better for Nature? Maybe not!
Depending where you are in the world you might notice signs touting the 5% ethanol in the gasoline you are buying. The idea is that biofuels [currently primarily made from […]

Liska A.J., Yang H., Milner M., Goddard S., Blanco-Canqui H., Pelton M.P., Fang X.X., Zhu H. & Suyker A.E. (2014). Biofuels from crop residue can reduce soil carbon and increase CO2 emissions, Nature Climate Change, DOI:

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3:53 PM | Developing bulletproof vests using stem cells?
Stem cells demonstrate a bizarre property never before seen at a cellular level, according to a new study published today by researchers at the University of Cambridge. The property -- known as auxeticity -- is one which may have application as wide-ranging as soundproofing, super-absorbent sponges and bulletproof vests.Most materials when stretched will contract. For example, if one pulls on an elastic band, the elastic itself will get thinner. The opposite is also true: squeeze a material and […]

Pagliara, S., Franze, K., McClain, C., Wylde, G., Fisher, C., Franklin, R., Kabla, A., Keyser, U. & Chalut, K. (2014). Auxetic nuclei in embryonic stem cells exiting pluripotency, Nature Materials, DOI:

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3:43 PM | Researchers pinpoint the role of cancer stem cells in drug resistance
Credit: UC San Diego School of MedicineMost drugs used to treat lung, breast and pancreatic cancers also promote drug-resistance and ultimately spur tumor growth. Researchers at the University of California, San Diego School of Medicine have discovered a molecule, or biomarker, called CD61 on the surface of drug-resistant tumors that appears responsible for inducing tumor metastasis by enhancing the stem cell-like properties of cancer cells.The findings, published in the April 20, 2014 online […]

Seguin, L., Kato, S., Franovic, A., Camargo, M., Lesperance, J., Elliott, K., Yebra, M., Mielgo, A., Lowy, A., Husain, H. & Cascone, T. (2014). An integrin β3–KRAS–RalB complex drives tumour stemness and resistance to EGFR inhibition, Nature Cell Biology, DOI:

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2:00 PM | Parasites, chromosomes and the tree of life
Advances in the knowledge of the molecular basis of life have provided some of the most impressive and certain proofs to the notion that all […] Read more The post Parasites, chromosomes and the tree of life appeared first on Mapping Ignorance. Related posts:The flick of a switch controls the fate of human parasites Life and deeds of RNA (I): William Wallace and the fate of the cell Life and deeds of RNA (III): RNA processing, neurodegeneration and a rare disease

Akiyoshi B. & Gull K. (2014). Discovery of Unconventional Kinetochores in Kinetoplastids, Cell, 156 (6) 1247-1258. DOI:

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9:15 AM | Lathosterolosis, cholesterol and autism?
Although intrigued by the findings reported by Pier Luigi Calvo and colleagues [1] describing a "unique case" potentially linking liver functions and cognitive functions with a hat-tip to the presentation of autistic behaviours, I'll readily admit that I am way out of my comfort and competence zones when discussing this paper so please be ready with that pinch of salt.How do you like your eggs in the morning? @ Wikipedia As per what the paper and accompanying press release (see […]

Calvo, P., Brunati, A., Spada, M., Romagnoli, R., Corso, G., Parenti, G., Rossi, M., Baldi, M., Carbonaro, G., David, E. & Pucci, A. (2014). Liver Transplantation in Defects of Cholesterol Biosynthesis: The Case of Lathosterolosis, American Journal of Transplantation, DOI:

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3:45 AM | Cross-validation in finance, psychology, and political science
A large chunk of machine learning (although not all of it) is concerned with predictive modeling, usually in the form of designing an algorithm that takes in some data set and returns an algorithm (or sometimes, a description of an algorithm) for making predictions based on future data. In terminology more friendly to the philosophy […]

Bailey, D., Borwein, J., de Prado, M.L. & Zhu, Q. (2014). Pseudo-Mathematics and Financial Charlatanism: The Effects of Backtest Overfitting on Out-of-Sample Performance, Notices of the American Mathematical Society, 61 (5) 458. DOI:

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