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April 18, 2014

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4:39 PM | Can Fruit Flies Glow in the Dark?
Question: How is a fruit fly like a firefly? No, this is not an obvious answer (their names start with the letter “f”) or the beginning of a bad entomology joke. These two organisms may both be winged insects, but as it turns out, what makes the firefly light show such a special treat on […]

Mofford D.M., Reddy G.R. & Miller S.C. (2014). Latent luciferase activity in the fruit fly revealed by a synthetic luciferin., Proceedings of the National Academy of Sciences of the United States of America, PMID:

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3:00 PM | 1 in 20 Misdiagnosed by Doctors: 10 things you can do about it
A new study out this week says that 1 in 20 adults will be misdiagnosed in outpatient clinics in the US. Thats roughly 12 million people each year, if that […]

Singh H., Meyer A.N.D. & Thomas E.J. The frequency of diagnostic errors in outpatient care: estimations from three large observational studies involving US adult populations, BMJ Quality & Safety, DOI:

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2:03 PM | Glucosidase I: Could targeting N-linked glycosylation of proteins help us fight viral infection?
Viruses are sneaky.  As you probably already know from your last bout with the common cold or the flu, for most viral infections doctors will simply prescribe plenty of water and […]

Sadat, M., Moir, S., Chun, T., Lusso, P., Kaplan, G., Wolfe, L., Memoli, M., He, M., Vega, H., Kim, L. & Huang, Y. (2014). Glycosylation, Hypogammaglobulinemia, and Resistance to Viral Infections, New England Journal of Medicine, 2147483647. DOI:

Herscovics, A. (1999). Importance of glycosidases in mammalian glycoprotein biosynthesis, Biochimica et Biophysica Acta (BBA) - General Subjects, 1473 (1) 96-107. DOI:

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2:00 PM | The Cournot model of oligopoly. A success story
Economic models of perfect competition and of monopoly only need to include individual behavior that takes the environment as given. In the case of […] Read more The post The Cournot model of oligopoly. A success story appeared first on Mapping Ignorance. Related posts:Experimenting with markets Modeling diversity in Macroeconomics Experiments in fairness

Ferreira J.L. (2014). Capacity precommitment, price competition and forward markets, Economics Letters, 122 (2) 362-364. DOI:

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2:40 AM | Dear CNRS: That mouse study did not "confirm" the neurobiological origin of ADHD in humans
Late last week the French National Centre for Scientific Research (CNRS - the acronym is based on the French translation) put out a press release describing a study conducted through a collaboration between several of its researchers and scientists from The University of Strasbourg. CNRS is a large (30,000+ employees), government-run research institution in France. It is the largest research organization in Europe, and is responsible for about 1/2 of the French scientific papers published […]

Mathis, C., Savier, E., Bott, J., Clesse, D., Bevins, N., Sage-Ciocca, D., Geiger, K., Gillet, A., Laux-Biehlmann, A., Goumon, Y. & Lacaud, A. (2014). Defective response inhibition and collicular noradrenaline enrichment in mice with duplicated retinotopic map in the superior colliculus, Brain Structure and Function, DOI:

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April 17, 2014

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7:29 PM | Research on flies suggests that lost stem cells are naturally replaced by non-stem cells
Erika MatunisCreditJohns Hopkins researchers have discovered an unexpected phenomenon in the organs that produce sperm in fruit flies, when a certain kind of stem cell is killed off experimentally, another group of non-stem cells can come out of retirement to replace them.The discovery sheds light on the tiny "environments" that stem cells occupy in animal bodies and may help explain how stem cells in tumors replenish themselves, the researchers report in the May 8 issue of the journal Cell […]

Phylis Hétié, Margaret de Cuevas, Erika Matunis (2014). Conversion of Quiescent Niche Cells to Somatic Stem Cells Causes Ectopic Niche Formation in the Drosophila Testis, Cell Reports, Other: http://dx.doi.org/10.1016/j.celrep.2014.03.058

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7:17 PM | Danish Project to Make Polymer Solar Cells More Profitable
Project Megawatt intends to make polymer solar cells profitable enough to allow power generation from polymer solar cells to compete on market terms with traditional coal-fired power plants. Read more »

Krebs, F., Espinosa, N., Hösel, M., Søndergaard, R. & Jørgensen, M. (2014). 25th Anniversary Article: Rise to Power - OPV-Based Solar Parks, Advanced Materials, 26 (1) 29-39. DOI:

Sommer-Larsen, P., Jørgensen, M., Søndergaard, R., Hösel, M. & Krebs, F. (2013). It is all in the Pattern-High-Efficiency Power Extraction from Polymer Solar Cells through High-Voltage Serial Connection, Energy Technology, 1 (1) 15-19. DOI:

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7:17 PM | Mesenchymal stem cells require hydrogen sulfide to function properly
Professor Songtao ShiMesenchymal stem cells need to produce hydrogen sulfide in order to properly multiply and form bone tissue, according to a new study from the Center for Craniofacial Molecular Biology at the Ostrow School of Dentistry.Professor Songtao Shi, principal investigator on the project, said the presence of hydrogen sulfide produced by the cells governs the flow of calcium ions. The essential ions activate a chain of cellular signals that results in osteogenesis, or the creation of […]

Liu, Y., Yang, R., Liu, X., Zhou, Y., Qu, C., Kikuiri, T., Wang, S., Zandi, E., Du, J., Ambudkar, I. & Shi, S. (2014). Hydrogen Sulfide Maintains Mesenchymal Stem Cell Function and Bone Homeostasis via Regulation of Ca2+ Channel Sulfhydration, Cell Stem Cell, DOI:

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5:44 PM | Li-Sulfur Batteries Last Longer With Metal-Organic Frameworks
Researchers at the PNNL added a kind of nanomaterial called a metal-organic framework, to the battery’s cathode to capture problematic polysulfides that usually cause lithium-sulfur batteries to fail after a few charges. Read more »

Zheng, J., Tian, J., Wu, D., Gu, M., Xu, W., Wang, C., Gao, F., Engelhard, M., Zhang, J., Liu, J. & Xiao, J. (2014). Lewis Acid–Base Interactions between Polysulfides and Metal Organic Framework in Lithium Sulfur Batteries, Nano Letters, 2147483647. DOI:

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2:00 PM | Is It Good For Kids To Have A Pet?
People overwhelmingly believe that having pets is overall a good thing for children. Indeed, a 2003 paper by developmental psychologist Gail F. Melson reports that most parents say that they acquired... -- Read more on ScientificAmerican.com

Mueller M.K. (2014). Is Human-Animal Interaction (HAI) Linked to Positive Youth Development? Initial Answers, Applied Developmental Science, 18 (1) 5-16. DOI:

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1:39 PM | What’s the Answer? (new Biostars interface)
BioStars 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 BioStars that are germane to our readers (end users of genomics resources). Every Thursday we will be highlighting one of those items or discussions here […]

Parnell L.D., Lindenbaum P., Shameer K., Dall'Olio G.M., Swan D.C., Jensen L.J., Cockell S.J., Pedersen B.S., Mangan M.E. & Miller C.A. & (2011). BioStar: An Online Question & Answer Resource for the Bioinformatics Community, PLoS Computational Biology, 7 (10) e1002216. DOI:

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11:32 AM | Cannabis use and structural changes in the brain
  “One or two spliffs a week could mess up your brain” – Metro, 16 April 2014 Spark your interest? This headline caught the eyes of the Antisense team, so […]

Gilman, J., Kuster, J., Lee, S., Lee, M., Kim, B., Makris, N., van der Kouwe, A., Blood, A. & Breiter, H. (2014). Cannabis Use Is Quantitatively Associated with Nucleus Accumbens and Amygdala Abnormalities in Young Adult Recreational Users, Journal of Neuroscience, 34 (16) 5529-5538. DOI:

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10:29 AM | Modified stem cells may offer treatment for Alzheimer's disease
Mathew Blurton-JonesUC Irvine neurobiologists have found that genetically modified neural stem cells show positive results when transplanted into the brains of mice with the symptoms and pathology of Alzheimer's disease. The pre-clinical trial is published in the journal Stem Cells Research and Therapy, and the approach has been shown to work in two different mouse models.Alzheimer's disease, one of the most common forms of dementia, is associated with accumulation of the protein amyloid-beta […]

Blurton-Jones, M., Spencer, B., Michael, S., Castello, N., Agazaryan, A., Davis, J., Müller, F., Loring, J., Masliah, E. & LaFerla, F. & (2014). Neural stem cells genetically-modified to express neprilysin reduce pathology in Alzheimer transgenic models, Stem Cell Research & Therapy, 5 (2) 46. DOI:

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8:31 AM | Mitochondrial dysfunction as a neurobiological subtype of autism
The paper by Suzanne Goh and colleagues [1] reporting on "a possible neurobiological subtype of mitochondrial dysfunction in ASD [autism spectrum disorder]" is a worthy addition to the research roll call which has graced this blog down the years. Based on the analysis of brain lactate levels - a potential marker of mitochondrial dysfunction - via the analysis of lactate doublets on brain magnetic resonance spectroscopic imaging (MRSI), authors picked up a significantly higher rate of […]

Goh, S., Dong, Z., Zhang, Y., DiMauro, S. & Peterson, B. (2014). Mitochondrial Dysfunction as a Neurobiological Subtype of Autism Spectrum Disorder, JAMA Psychiatry, DOI:

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April 16, 2014

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9:02 PM | What Do Preschoolers Learn from Fantastical Picture Books?
One of the new picture books making the bedtime rounds at our house is How Do Dinosaurs Say Goodnight?, which describes and depicts dinosaurs doing such un-dinosaurly things as tucking themselves into bed or kissing their human mothers good night. The book is whimsical, gorgeously illustrated, and includes a scientific angle, as the genus names […]

Ganea, P., Canfield, C., Simons Ghafari, K. & Chou, T. (2014). Do cavies talk? The effect of anthropomorphic picture books on children's knowledge about animals, Frontiers in Psychology, 5 DOI:

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Editor's Pick
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8:19 PM | Sex in (floral) advertising
Having a wingman can be helpful, but for many plants it’s absolutely crucial. Flowering plants don’t have smoky bars, speed dating or eHarmony. They have to rely entirely on their tiny wing—well, I guess “men” isn’t really appropriate. But unlike your witty friend who backs you up in the bar, pollinators don’t help plants with their … Continue reading →

Dötterl S, Glück U, Jürgens A, Woodring J & Aas G (2014). Floral Reward, Advertisement and Attractiveness to Honey Bees in Dioecious Salix caprea., PloS one, 9 (3) PMID:

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5:50 PM | L'universo spiegato a mia sorella
Non voglio fare concorrenza alla splendida spiegazione di Amedeo o a quella tecnica di Corrado, ma mia sorella, leggendo il post di pancia scritto nella sera dell'annuncio di BICEP2, ha candidamente confessato di non aver capito cosa era accaduto quel giorno. E allora proviamoci, a raccontarlo. (da The Cartoon History of the Universe #1 di Larry Gonick)C'era una volta un'idea di universo, che era la Terra al centro, quindi il Sole, la Luna e gli altri pianeti e sullo sfondo le stelle fisse, […]

Hubble E. (1929). A relation between distance and radial velocity among extra-galactic nebulae, Proceedings of the National Academy of Sciences, 15 (3) 168-173. DOI:

Gamow G. (1948). The Evolution of the Universe, Nature, 162 (4122) 680-682. DOI:

Alpher R.A. & Herman R. (1948). Evolution of the Universe, Nature, 162 (4124) 774-775. DOI:

Alpher R., Bethe H. & Gamow G. (1948). The Origin of Chemical Elements, Physical Review, 73 (7) 803-804. DOI:

Peebles P.J.E., Schramm D.N., Turner E.L. & Kron R.G. (1994). The Evolution of the Universe, Scientific American, 271 (4) 52-57. DOI:

McLeish T.C.B., Bower R.G., Tanner B.K., Smithson H.E., Panti C., Lewis N. & Gasper G.E.M. (2014). History: A medieval multiverse, Nature, 507 (7491) 161-163. DOI:

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2:00 PM | 2D brain mapping: gene expression and spatial location
Let’s try a little game. If I’d show you only parts of a famous building: a column, part of a wall, the ceiling…Would you be […] Read more The post 2D brain mapping: gene expression and spatial location appeared first on Mapping Ignorance. Related posts:The (energetical) cost of having a brain Mapping areas involved in voluntary forgetting is not simple... it is double! Reinforcement learning in the brain

Grange P., Bohland J.W., Okaty B.W., Sugino K., Bokil H., Nelson S.B., Ng L., Hawrylycz M. & Mitra P.P. (2014). Cell-type-based model explaining coexpression patterns of genes in the brain, Proceedings of the National Academy of Sciences, 111 (14) 5397-5402. DOI:

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2:00 PM | Self-Healing Composites- The Trick is Biology
Let’s face it, things wear out. Car tires go bye-bye, seals get worn, and Jets need constant upkeep to make sure that cracks in the fuselage [the main body of […]

Patrick J.F., Hart K.R., Krull B.P., Diesendruck C.E., Moore J.S., White S.R. & Sottos N.R. (2014). Continuous Self-Healing Life Cycle in Vascularized Structural Composites, Advanced Materials, n/a-n/a. DOI:

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1:37 PM | Video Tip of the Week: NaviCell for custom interaction maps for systems biology
The onslaught of sequence data from a whole range of species and tissues continues, and certainly will for a long time. But moving from there to the level of understanding the interactions among the genes that contribute to the structures, behaviors, and phenotypes of the systems requires other types of supporting software. NaviCell is a […]

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:

Funahashi A., Matsuoka Y., Jouraku A., Morohashi M., Kikuchi N. & Kitano H. (2008). CellDesigner 3.5: A Versatile Modeling Tool for Biochemical Networks, Proceedings of the IEEE, 96 (8) 1254-1265. DOI:

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1:17 PM | Journal Club: What’s old is new again: newly discovered songbird family is ancient
SUMMARY: Scientists analysing songbird DNA discovered that the spotted wren-babbler is neither a wren nor a wren-babbler, nor even a babbler. Instead, it represents an old evolutionary family that has no close living relatives. Spotted wren-babbler, Elachura formosa (previously Spelaeornis formosus). Image: Per Alström/SLU [doi:10.1098/rsbl.2013.1067]. A newly published study has uncovered a previously unknown family of songbirds that is represented by just one species. After analyzing one […]

Alström P., Hooper D.M., Liu Y., Olsson U., Mohan D., Gelang M., Hung L.M., Zhao J., Lei F. & Price T.D. & (2014). Discovery of a relict lineage and monotypic family of passerine birds, Biology Letters, 10 (3) DOI:

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1:17 PM | Journal Club: What’s old is new again: newly discovered songbird family is ancient
SUMMARY: Scientists analysing songbird DNA discovered that the spotted wren-babbler is neither a wren nor a wren-babbler, nor even a babbler. Instead, it represents an old evolutionary family that has no close living relatives. Spotted wren-babbler, Elachura formosa (previously Spelaeornis formosus). Image: Per Alström/SLU [doi:10.1098/rsbl.2013.1067]. A newly published study has uncovered a previously unknown family of songbirds that is represented by just one species. After analyzing one […]

Alström P., Hooper D.M., Liu Y., Olsson U., Mohan D., Gelang M., Hung L.M., Zhao J., Lei F. & Price T.D. & (2014). Discovery of a relict lineage and monotypic family of passerine birds, Biology Letters, 10 (3) DOI:

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12:30 PM | Does Animal-Assisted Therapy Help At-Risk Boys?
If existing behavioural programs aren’t working, can therapeutic sessions with a dog help boys who have problems at school?Photo: criben / ShutterstockA new paper by Abbey Schneider et al (2014) investigates the success of a program designed to help boys who are considered ‘at-risk’ – by matching them up with a specially trained dog and handler.In Colorado, a group of elementary schools take part in a program called the Human Animal Bond in Colorado (HABIC). It is […]

Schneider, A.A.,, Rosenberg, J., Baker, M., Melia, N., Granger, B. & Biringen, Z. (2014). Becoming relationally effective: High-risk boys in animal-assisted therapy, Human-Animal Interaction Bulletin, 2 (1) 1-18. Other: Link

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12:00 PM | Using Pain To Stop Pain
Biology concepts – desensitization, habituation, counter irritation, cautery, heat sensing, pain, chronic, acute, analgesiaGout usually attacks middle-aged men and the big toe joint is a favorite spot. But it can occur anywhere and in anyone. The accretions or urates build up and clog the joint, causng poor function and intense pain, painful enough that even the weight of a sheet on it at night is too much. Usually the acute attacks are far worse, and become less painful gouty arthritisas […]

Andreev YA, Kozlov SA, Korolkova YV, Dyachenko IA, Bondarenko DA, Skobtsov DI, Murashev AN, Kotova PD, Rogachevskaja OA, Kabanova NV & Kolesnikov SS (2013). Polypeptide modulators of TRPV1 produce analgesia without hyperthermia., Marine drugs, 11 (12) 5100-15. PMID:

Tobaldini G, de Siqueira BA, Lima MM, Tambeli CH & Fischer L (2014). Ascending nociceptive control contributes to the anti-nociceptive effect of acupuncture in a rat model of acute pain., The journal of pain : official journal of the American Pain Society, PMID:

Lee MG, Huh BK, Choi SS, Lee DK, Lim BG & Lee M (2012). The effect of epidural resiniferatoxin in the neuropathic pain rat model., Pain physician, 15 (4) 287-96. PMID:

Kelly S, Chapman RJ, Woodhams S, Sagar DR, Turner J, Burston JJ, Bullock C, Paton K, Huang J, Wong A & McWilliams DF (2013). Increased function of pronociceptive TRPV1 at the level of the joint in a rat model of osteoarthritis pain., Annals of the rheumatic diseases, PMID:

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10:13 AM | Tiger sharks: Each to their own diving depth
Despite some broad similarities, the diving behaviour of tiger sharks appears to vary greatly amongst individuals.  Tiger sharks (Galeocerdo cuvier) are one of the top predators in tropical and subtropical waters throughout the world. These large sharks are known to occupy both coastal and open seas, and can travel over both short and long distances. […]

Vaudo, J., Wetherbee, B., Harvey, G., Nemeth, R., Aming, C., Burnie, N., Howey-Jordan, L. & Shivji, M. (2014). Intraspecific variation in vertical habitat use by tiger sharks (Galeocerdo cuvier) in the western North Atlantic, Ecology and Evolution, DOI:

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5:54 AM | Joined by HDAC (inhibitors)
I'm treading quite carefully with this post which came about following my [non-expert] reading of the paper abstract from Anand Venkatraman and colleagues [1] on a potential downside to the use of HDAC (histone deacetylase) inhibitors for treating spinocerebellar ataxia type 1 (SCA1), a progressive disease affecting movement and other knock-on functions. This follows other work suggesting that certain HDAC inhibitors might offer some important new lines of investigation when it […]

Venkatraman A, Hu YS, Didonna A, Cvetanovic M, Krbanjevic A, Bilesimo P & Opal P (2014). The histone deacetylase HDAC3 is essential for Purkinje cell function, potentially complicating the use of HDAC inhibitors in SCA1., Human molecular genetics, PMID:

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1:36 AM | New Study Shows Surgical Checklists In Operating Rooms Are Less Effective Than Assumed
The patient has verified his or her identity, the surgical site, the type of procedure, and his or her consent. Check. The surgical site is marked on a patient if such marking is appropriate for the procedure. Check. The probe measuring blood oxygen content has been placed on the patient and is functioning. Check. All members of the surgical and anesthesia team are aware of whether the patient has a known allergy? Check. These were the first items on a... Read more

Urbach DR, Govindarajan A, Saskin R, Wilton AS & Baxter NN (2014). Introduction of surgical safety checklists in Ontario, Canada., The New England Journal of Medicine, 370 (11) 1029-38. PMID:

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1:36 AM | New Study Shows Surgical Checklists In Operating Rooms Are Less Effective Than Assumed
The patient has verified his or her identity, the surgical site, the type of procedure, and his or her consent. Check. The surgical site is marked on a patient if such marking is appropriate for the procedure. Check. The probe measuring blood oxygen content has been placed on the patient and is functioning. Check. All members of the surgical and anesthesia team are aware of whether the patient has a known allergy? Check. These were the first items on a... Read more

Urbach DR, Govindarajan A, Saskin R, Wilton AS & Baxter NN (2014). Introduction of surgical safety checklists in Ontario, Canada., The New England Journal of Medicine, 370 (11) 1029-38. PMID:

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1:32 AM | Stone Soup Eyes
Another installment from the Developmental Neurobiology Students at Reed College. Hope you enjoy! It’s not often that you get to recount the classic tale of Stone Soup when thinking about developmental biology, but that’s exactly what we did when discussing an almost classic 2011 Nature paper from Yoshiki Sasai’s group. In the story, a grumpy […]

Eiraku, M., Takata, N., Ishibashi, H., Kawada, M., Sakakura, E., Okuda, S., Sekiguchi, K., Adachi, T. & Sasai, Y. (2011). Self-organizing optic-cup morphogenesis in three-dimensional culture, Nature, 472 (7341) 51-56. DOI:

Fuhrmann, S. (2010). Eye Morphogenesis and Patterning of the Optic Vesicle, Current Topics in Developmental Biology, DOI:

Nakano, T., Ando, S., Takata, N., Kawada, M., Muguruma, K., Sekiguchi, K., Saito, K., Yonemura, S., Eiraku, M. & Sasai, Y. & (2012). Self-Formation of Optic Cups and Storable Stratified Neural Retina from Human ESCs, Cell Stem Cell, 10 (6) 771-785. DOI:

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April 15, 2014

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10:21 PM | Hold the drill! Fracking emitting more methane than previously thought
As politically divisive as hydraulic fracturing is, we still need much more data to determine its environmental effects before deciding if it can be major source of energy during our transition away from fossil fuels.  Unfortunately, this lack of data … Continue reading →

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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