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  • January 6, 2014
  • 06:38 PM

A Missing Genetic Link in Human Evolution

by Perikis Livas in Tracing Knowledge

Humans have multiple copies of a gene known as SRGAP2, which is thought to be involved in brain development. Chimps and orangutans have only one copy.

By: Emily Singer

Further reading... Read more »

Charrier C, Joshi K, Coutinho-Budd J, Kim JE, Lambert N, de Marchena J, Jin WL, Vanderhaeghen P, Ghosh A, Sassa T.... (2012) Inhibition of SRGAP2 function by its human-specific paralogs induces neoteny during spine maturation. Cell, 149(4), 923-35. PMID: 22559944  

Jiang Z, Tang H, Ventura M, Cardone MF, Marques-Bonet T, She X, Pevzner PA, & Eichler EE. (2007) Ancestral reconstruction of segmental duplications reveals punctuated cores of human genome evolution. Nature genetics, 39(11), 1361-8. PMID: 17922013  

Marques-Bonet T, & Eichler EE. (2009) The evolution of human segmental duplications and the core duplicon hypothesis. Cold Spring Harbor symposia on quantitative biology, 355-62. PMID: 19717539  

  • January 6, 2014
  • 05:00 PM

Synthetic Biology: Engineering Life To Examine It

by Jalees Rehman in The Next Regeneration

Two scientific papers that were published in the journal Nature in the year 2000 marked the beginning of engineering biological circuits in cells. The paper "Construction of a genetic toggle switch in Escherichia coli" by Timothy Gardner, Charles Cantor and James Collins created a genetic toggle switch by simultaneously introducing an artificial DNA plasmid into a bacterial cell. This DNA plasmid contained two promoters (DNA sequences which regulate the expression of genes) and two repressors (genes that encode for proteins which suppress the expression of genes) as well as a gene encoding for green fluorescent protein that served as a read-out for the system. ... Read more »

Daniel R, Rubens JR, Sarpeshkar R, & Lu TK. (2013) Synthetic analog computation in living cells. Nature, 497(7451), 619-23. PMID: 23676681  

  • January 4, 2014
  • 02:07 PM

Science Is Interpretation

by Neuroskeptic in Neuroskeptic_Discover

You don’t need new data to produce new science. A re-analysis or re-interpretation can be just as important and original as a new set of results. I say this because there’s an interesting discussion going on over at PubPeer. In brief, British physicists Julian Stirling and colleagues have released a draft paper using reanalysis to […]The post Science Is Interpretation appeared first on Neuroskeptic.... Read more »

Julian Stirling, Ioannis Lekkas, Adam Sweetman, Predrag Djuranovic, Quanmin Guo, Josef Granwehr, Raphaël Lévy, & Philip Moriarty. (2013) Critical assessment of the evidence for striped nanoparticles. arXiv. arXiv: 1312.6812v1

  • January 3, 2014
  • 09:03 AM

HZB Scientists Upgrade Chalcopyrite Solar Cells

by dailyfusion in The Daily Fusion

A team of scientists at the Helmholtz-Zentrum Berlin for Materials and Energy have developed a way to produce chalcopyrite solar cells without cadmium-based buffer layer. A single layer takes on the job of what used to be two layers, doing away with the wet chemical process. Despite a much simplified production method, efficiencies of greater than 18 percent are well within reach.... Read more »

Klenk, R., Steigert, A., Rissom, T., Greiner, D., Kaufmann, C. A., Unold, T. and Lux-Steiner, M. Ch. (2013) Junction formation by Zn(O,S) sputtering yields CIGSe-based cells with efficiencies exceeding 18%. Progress in Photovoltaics: Research and Applications. DOI: 10.1002/pip.2445  

  • December 19, 2013
  • 12:34 PM

When Roughly Is Good Enough: Approximate Computing Saves Energy

by dailyfusion in The Daily Fusion

Scientists are creating a new type of computers capable of “approximate computing”—performing calculations that are good enough for certain tasks that don’t require perfect accuracy—potentially doubling efficiency and reducing energy consumption.... Read more »

Swagath Venkataramani, Vinay K. Chippa, Srimat T. Chakradhar, Kaushik Roy, & Anand Raghunatha. (2013) Quality programmable vector processors for approximate computing. Proceedings of the 46th Annual IEEE/ACM International Symposium on Microarchitecture, 1-12. info:/10.1145/2540708.2540710

  • December 17, 2013
  • 11:34 AM

Do you know this song?

by Henkjan Honing in Music Matters

A challenging Citizen-Science Name-That-Tune game to study what makes a melody stick in our minds...... Read more »

J.A. Burgoyne et al. (2013) Hooked: A game for discovering what makes music catchy. Proceedings ISMIR. info:/

  • December 16, 2013
  • 11:15 PM

Lower bounds by negative adversary method

by Artem Kaznatcheev in Evolutionary Games Group

Are some questions harder than others? Last week I quantified hardness of answering a question with a quantum computer as the quantum query complexity. I promised that this model would allow us to develop techniques for proving lower bounds. In fact, in this model there are two popular tools: the polynomial method, and the (negative) […]... Read more »

Peter Hoyer, Troy Lee, & Robert Spalek. (2007) Negative weights make adversaries stronger. STOC. arXiv: quant-ph/0611054v2

  • December 16, 2013
  • 05:38 PM

New Method Predicts Power Grid Outages

by dailyfusion in The Daily Fusion

A method of assessing the stability of large-scale power grids in real time could bring the world closer to its goal of producing and utilizing a smart grid.... Read more »

  • December 16, 2013
  • 10:31 AM

New Geothermal Plant Design Uses Carbon Dioxide to Boost Output Tenfold

by dailyfusion in The Daily Fusion

Researchers are developing a new geothermal plant design that will lock away unwanted carbon dioxide (CO2) underground and use it as a tool to boost electric power generation by at least 10 times compared to conventional geothermal power.... Read more »

  • December 12, 2013
  • 07:09 PM

How You can Learn the Programming Basics in an Hour (Code Week 2013)

by Geoffrey Hannigan in Prophage

This probably would have best been posted a few days ago, but this week is computer science education week, or "code week" (coding just means writing computer programs). From December 9th to the 15th, over a million people all over the US are promoting computer science for students ranging from elementary school to college, as well as those of us finished with school. This is not only really cool because it is generating enthusiasm for computer science education, but it is also providing a lot of real educational resources (like online tutorials) for people of all ages to learn how to code (how cool is that?!).... Read more »

Libeskind-Hadas R, & Bush E. (2013) A first course in computing with applications to biology. Briefings in bioinformatics, 14(5), 610-7. PMID: 23449003  

  • December 11, 2013
  • 08:36 AM

New project to remove conflict among galaxy simulations

by Usman Paracha in SayPeople

Main Point:

In a new project dubbed AGORA, researchers are working to remove the discrepancies among different computer models of galaxy formation by comparing different codes against each other.

Published in:


Study Further:

The project AGORA is the short form for Assembling Galaxies of Resolved Anatomy. “We investigate galaxy formation with high-resolution numerical simulations and compare the results across different platforms, and with observation,” Project AGORA website noted.

Nine codes, nine galaxy formation scenarios: this is the sort of problem that AGORA is devoting itself to resolving by comparing different supercomputer simulations. (Credit: Simulations performed by Samuel Leitner (ART-II), Ji-hoon Kim (ENZO), Oliver Hahn (GADGET-2- CFS), Keita Todoroki (GADGET-3), Alexander Hobbs (GADGET-3-CFS and GADGET-3-AFS), Sijing Shen (GASOLINE), Michael Kuhlen (PKDGRAV-2), and Romain Teyssier (RAMSES))
Nine codes, nine galaxy formation scenarios: this is the sort of problem that AGORA is devoting itself to resolving by comparing different supercomputer simulations.
(Credit: Simulations performed by Samuel Leitner (ART-II), Ji-hoon Kim (ENZO), Oliver Hahn (GADGET-2- CFS), Keita Todoroki (GADGET-3), Alexander Hobbs (GADGET-3-CFS and GADGET-3-AFS), Sijing Shen (GASOLINE), Michael Kuhlen (PKDGRAV-2), and Romain Teyssier (RAMSES))

“The physics of galaxy formation is extremely complicated, and the range of lengths, masses, and timescales that need to be simulated is immense,” stated Piero Madau, professor of astronomy and astrophysics at the University of California, Santa Cruz and co-chair of the AGORA steering committee.

“You incorporate gravity, solve the equations of hydrodynamics, and include prescriptions for gas cooling, star formation, and energy injection from supernovae into the code. After months of number crunching on a powerful supercomputer, you look at the results and wonder if that is what nature is really doing or if some of the outcomes are actually artifacts of the particular numerical implementation you used.”

This project would increase our knowledge about the dark matter and its effects on universe as this object is hard to study physically at this time and such models are the best source to study them.


Project AGORA -

Worldwide collaboration announces project AGORA: Ambitious comparison of high-resolution computer simulations of galaxy formation and evolution - University of California (

Astrophysicists launch ambitious assessment of galaxy formation simulations - University of California (

Ji-hoon Kim, Tom Abel, Oscar Agertz, Greg L. Bryan, Daniel Ceverino, Charlotte Christensen, Charlie Conroy, Avishai Dekel, Nickolay Y. Gnedin, Nathan J. Goldbaum, Javiera Guedes, Oliver Hahn, Alexander Hobbs, Philip F. Hopkins, Cameron B. Hummels, Francesca Iannuzzi, Dusan Keres, Anatoly Klypin, Andrey V. Kravtsov, Mark R. Krumholz, Michael Kuhlen, Samuel N. Leitner, Piero Madau, Lucio Mayer, Christopher E. Moody, Kentaro Nagamine, Michael L. Norman, Jose Oñorbe, Brian W. O'Shea, Annalisa Pillepich, Joel R. Primack, Thomas Quinn, Justin I. Read, Brant E. Robertson, Miguel Rocha, Douglas H. Rudd, Sijing Shen, Britton D. Smith, Alexander S. Szalay, Romain Teyssier, Robert Thompson, Keita Todoroki, Matthew J. Turk, James W. Wadsley, John H. Wise, Adi Zolotov, & for the AGORA Collaboration (2013). The AGORA High-Resolution Galaxy Simulations Comparison Project arXiv arXiv: 1308.2669v4... Read more »

Ji-hoon Kim, Tom Abel, Oscar Agertz, Greg L. Bryan, Daniel Ceverino, Charlotte Christensen, Charlie Conroy, Avishai Dekel, Nickolay Y. Gnedin, Nathan J. Goldbaum.... (2013) The AGORA High-Resolution Galaxy Simulations Comparison Project. arXiv. arXiv: 1308.2669v4

  • December 10, 2013
  • 02:16 PM

Piezoelectric Material Plugs Leaks in Transistors, Saves Energy

by dailyfusion in The Daily Fusion

Tom van Hemert and Ray Hueting of the University of Twente’s MESA Institute for Nanotechnology have found a way to “plug” leakage current in transistors by “squeezing” the transistor with a piezoelectric material.... Read more »

van Hemert T., & Hueting R.J.E. (2013) Piezoelectric Strain Modulation in FETs. IEEE Transactions on Electron Devices, 60(10), 3265-3270. DOI: 10.1109/TED.2013.2274817  

  • December 9, 2013
  • 11:45 PM

Quantum query complexity

by Artem Kaznatcheev in Evolutionary Games Group

You probably noticed a few things about TheEGG: a recent decrease in blog post frequency and an overall focus on the algorithmic lens — especially its view of biology. You might also be surprised by the lack of discussion of quantum information processing: the most successful on-going application of the algorithmic lens. I actually first […]... Read more »

Simon, D.R. (1997) On the power of quantum computation. SIAM Journal on Computing, 1474. DOI: 10.1137/S0097539796298637  

  • December 9, 2013
  • 05:13 PM

Study: Some Companies Could Switch to Wood Power

by dailyfusion in The Daily Fusion

According to researchers at the Pennsylvania State University, it is possible for some companies to economically convert their operations to wood power.... Read more »

Biomass boiler conversion potential in the eastern United States. (2013) Biomass boiler conversion potential in the eastern United States. Renewable Energy, 439-453. DOI: 10.1016/j.renene.2013.07.019  

  • December 7, 2013
  • 10:33 AM

That strange behavior of supersymmetry…

by Marco Frasca in The Gauge Connection

I am a careful reader of scientific literature and an avid searcher for already published material in peer reviewed journals. Of course, arxiv is essential to accomplish this task and to satisfy my needs for reading. In these days, I am working on Dyson-Schwinger equations. I have written on this a paper (see here) a […]... Read more »

Marc Bellon, Gustavo S. Lozano, & Fidel A. Schaposnik. (2007) Higher loop renormalization of a supersymmetric field theory. Phys.Lett.B650:293-297,2007. arXiv: hep-th/0703185v1

Markus Q. Huber, & Jens Braun. (2011) Algorithmic derivation of functional renormalization group equations and Dyson-Schwinger equations. Computer Physics Communications, 183(6), 1290-1320. arXiv: 1102.5307v2

Markus Q. Huber, & Mario Mitter. (2011) CrasyDSE: A framework for solving Dyson-Schwinger equations. arXiv. arXiv: 1112.5622v2

  • December 7, 2013
  • 04:14 AM

Augmenting Memory With A Neuroprosthesis

by Neuroskeptic in Neuroskeptic_Discover

A new paper in the Journal of Neural Engineering describes Facilitation of memory encoding in primate hippocampus by a neuroprosthesis that promotes task-specific neural firing The research – from Sam Deadwyler’s team at Wake Forest University (and funded by DARPA) really is pretty amazing – if it pans out. Four Rhesus macaques were trained to […]The post Augmenting Memory With A Neuroprosthesis appeared first on Neuroskeptic.... Read more »

  • December 5, 2013
  • 12:40 PM

Virtual Invisible Wall Can Stop Oil Spills

by dailyfusion in The Daily Fusion

Researchers at the University of Missouri are working on a new technology to stop oil spills, using something they call a virtual wall. This technique has already allowed scientists to confine oily liquids to a certain area, aiding the study of these complex molecules.... Read more »

  • December 4, 2013
  • 10:27 PM

Recent Publication: The Skin Microbiome in Health and Disease

by Geoffrey Hannigan in Prophage

A couple of days ago, Elizabeth Grice (my research advisor) and I had a review published in this month's issue of Cold Spring Harbor Perspectives in Medicine...... Read more »

  • December 4, 2013
  • 04:04 PM

Exotic Drops May Help Create All-Liquid Battery

by dailyfusion in The Daily Fusion

Through the combination of water, oil and nanoparticle surfactants plus an external field water drops can be stabilized into non-equilibrium shapes that could find valuable uses as therapeutic delivery systems, biosensors, or possibly as the basis for an all-liquid battery.... Read more »

  • December 4, 2013
  • 12:13 PM

Tip of the Week: Creating an Electronic Informed Consent

by Trey in OpenHelix

Informed consent has been a foundation of research, and especially genetics research, in that last few decades though it’s taken quite some time to right past wrongs. And with genomics research and personal genomics generating huge amounts of data, informed consent becomes both more important and more complex. The National Human Genome Research Institute has […]... Read more »

Charles N Rotimi and Patricia A Marshall. (2010) Tailoring the process of informed consent in genetic and genomic research. Genome Medicine, 2(3). info:/doi:10.1186/gm141

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