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  • 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

  • December 3, 2013
  • 10:38 AM

Shapes of Things to Come

by Perikis Livas in Tracing Knowledge

Featured article
Shapes of Things to Come: Exotic Shapes for Liquid Drops Have Many Possible Uses
Berkeley Lab

Reference paper
Stabilizing Liquid Drops in Nonequilibrium Shapes by the Interfacial Jamming of Nanoparticles

Further reading
Polymer Scientists Jam Nanoparticles, Trapping Liquids into Useful Shapes
University of Massachusetts Amherst... Read more »

  • December 2, 2013
  • 11:56 AM

Learning to see through semantics

by neuroecology in Neuroecology

Humans have a visual bias: everything in vision seems easy and natural to us, and it can seem a bit of a mystery why computers are so bad at it. But there is a reason such a massive chunk (about 30%) of cortex is devoted to it. It’s really hard! To do everything that it […]... Read more »

Frome A, Corrado GS, Shlens J, Bengio S, Dean J, Ranzato M, & Mikolov T. (2013) DeViSE: A Deep Visual-Semantic Embedding Model. NIPS. info:/

Dean T, Ruzon MA, Segal M, Shlens J, Vijayanarasimhan S, & Yagnik J. (2013) Fast, Accurate Detection of 100,000 Object Classes on a Single Machine. Proceedings of IEEE Conference on Computer Vision and Pattern Recognition. DOI: 10.1109/CVPR.2013.237  

  • November 30, 2013
  • 05:00 AM

A baby porcupine and her apple | video | @GrrlScientist

by GrrlScientist in GrrlScientist

To celebrate caturday today, we check in with a baby pincushion, erm, porcupine, and her apple.... Read more »

Cho W. K., Ankrum J. A., Guo D., Chester S. A., Yang S. Y., Kashyap A., Campbell G. A., Wood R. J., Rijal R. K., & Karnik R. (2012) Microstructured barbs on the North American porcupine quill enable easy tissue penetration and difficult removal. Proceedings of the National Academy of Sciences, 109(52), 21289-21294. DOI: 10.1073/pnas.1216441109  

  • November 21, 2013
  • 05:13 AM

New Deep Brain Stimulation System Measures Neurotransmitter Release

by The Neurocritic in The Neurocritic

Wireless Instantaneous Neurotransmitter Concentration Sensing System (WINCS) Patient Module printed circuit board & sterilizable case. (Fig. 1, Kimble et al. 2009). Last month, the New York Times reported that the Defense Advanced Research Projects Agency (DARPA) will spend $70 million to further the development of technologies that use deep brain stimulation (DBS), which has been highly successful in treating Parkinson's Disease (PD). The SUBNETS program (Systems-Based Neurotechnology for Emerging Therapies) is part of the BRAIN Initiative that aims to "revolutionize our understanding of the human mind."DARPA issued their call for proposals on October 25. My original take was that the goals were overly ambitious and nearly impossible to achieve within the specified time frame:To elaborate, over a 5 year period, the successful applicants must conduct clinical trials in human patients with 7 specified psychiatric and neurological disorders (not including PD), some of which have never been treated with DBS. The successful teams will use devices that both stimulate and record neural activity, and provide real-time data that can be decoded as reflecting a particular behavioral state... basically, a futuristic implant that can adjust its own stimulation parameters based on how the patient is doing. At least, that's how I interpret it.  How close are we to seeing a DBS implant that not only stimulates neural tissue, but also records electrical or chemical signals and then uses this information to adjust the stimulation parameters? Closer than I originally suspected. A recent Nature News article reported on the Mayo Clinic's efforts to develop a DARPAesque, state-of-the-art implant that aims to track brain signals in real time:Researchers hope that the device will identify the electrical and chemical signals in the brain that correlate in real time with the presence and severity of symptoms, including the tremors experienced by people with Parkinson’s disease. This information could help to uncover where and how DBS exerts its therapeutic effects on the brain, and why it sometimes fails, says Kendall Lee, a neurosurgeon at the Mayo Clinic in Rochester, Minnesota, who is leading the project.. . ....Using a method called fast-scan cyclic voltammetry, the device applies a localized voltage change in the brain. This transiently pulls electrons off certain neurotransmitters — the brain chemicals that activate or inhibit neurons — giving rise to electrical currents that can be measured. Each neurotransmitter molecule produces a different electrochemical signature, which can be used to identify it and estimate its concentration every 10 milliseconds.Studies in awake behaving rats have used fast-scan cyclic voltammetry to measure phasic dopamine release associated with burst firing (Robinson et al., 2003).Fig, 3 (Robinson et al., 2003). Heterogeneity of electrically evoked dopamine release in the nucleus accumbens of a freely moving rat.Further information about the device is provided in this article from the Mayo Clinic, which indicates that the WINCS has already been tested in 15 human patients with Parkinson's disease or essential tremor. The study registered in is described as an Efficacy Study whose primary purpose is basic science:Neurotransmitter Measurements Using Wireless Instantaneous Neurotransmitter Concentration System (WINCS) During Deep Brain Stimulation NeurosurgeryIn this study, the investigators will monitor extracellular neurotransmitter levels using a probe that is able to perform real time electrochemical detection during deep brain stimulation surgery. The overall question this study is designed to answer is: Are there neurotransmitters released during deep brain stimulation? Interestingly, the primary outcome measure is adenosine1 release recorded by WINCS, and the secondary outcome measure is dopamine release (pre-, during, and post-DBS, over a time frame of 30 min). Adenosine A2A antagonists may extend the duration of action of L-dopa, a primary treatment for PD. Preliminary studies in rats were able to detect subsecond dopamine and adenosine release at an implanted sensor in the striatum during high-frequency stimulation of ascending fibers (Kimble et al., 2009). It seems the early results in patients were also successful in measuring neurotransmitter release.The WINCS will be integrated with another device, the MINCS (Mayo Investigational Neuromodulation Control System), which is optically linked to WINCS. The entire system is being tested in animal models to deliver brain stimulation wirelessly. Fig 1B (Chang et al., 2013). Photograph of the MINCS-WINCS hardware showing relative size, optical connection, and recording and stimulating electrode leads. ADC = analog-to-digital converter; DAC = digital-to-analog converter; LPF = low-pass filter; MC = microcontroller; TIA = transimpedance amplifier; V/I Sense = voltage/current sense. Numbers 1 and 4 indicate the microcontrollers; 2 and 3 are the Bluetooth modules.These developments in DBS devices for Parkinson's disease are very impressive indeed, but DARPA wants to go 7 steps further by developing similar clos... Read more »

Kimble CJ, Johnson DM, Winter BA, Whitlock SV, Kressin KR, Horne AE, Robinson JC, Bledsoe JM, Tye SJ, Chang SY.... (2009) Wireless Instantaneous Neurotransmitter Concentration Sensing System (WINCS) for intraoperative neurochemical monitoring. Conference proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society., 4856-9. PMID: 19963865  

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