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  • October 24, 2013
  • 05:58 PM

Scientists Build ‘Impossible’ Silicon Supercapacitor

by dailyfusion in The Daily Fusion

Researchers at the Vanderbilt University in Nashville propose a novel silicon supercapacitor design. Such supercapacitor can be, theoretically, integrated into a silicon chip, opening some interesting options for energy storage.... Read more »

Oakes L, Westover A, Mares JW, Chatterjee S, Erwin WR, Bardhan R, Weiss SM, & Pint CL. (2013) Surface engineered porous silicon for stable, high performance electrochemical supercapacitors. Scientific Reports, 3020. PMID: 24145684  

  • October 20, 2013
  • 10:07 AM
  • 448 views calls for help

by egonw in Chem-bla-ics

I don't think I mentioned this JISC project by David Shotton et al. yet, and should perhaps have done so earlier. But it is not too late, as Shotton is calling out for help in a Nature Comment this week (doi:10.1038/502295a). Now, I have been tracking what is citing the CDK literature using CiteUlike since 2010, and just asked the project developers how I can contribute this data.

Interestingly, the visualization from is interesting as it also shows papers citing papers that cite the CDK:

This image shows that the corpus is yet small: this CDK paper is cited more then 250 times. In the comment, Shotton writes that "[i]deally, references will come directly from publishers at the time of article publication." I do hope that publishers soon start providing APIs to extract such data. But I like to complement the call out, by inviting everyone to start annotating their old papers with this information, e.g. using CiTO and CiteULike as I did. Importantly, the authors must type their citation, something that will greatly improve the paper itself, anyway.

Now, my own use case, is to get an idea on how the CDK is used. Reason: people are not paying us, so I am limited to reports in the public that write up how they use the CDK. Direct citation is important, but I am even more interested in papers that do not cite the CDK, but cite a paper that describes a tool that depends on the CDK, like PaDEL (doi:10.1002/jcc.21707) which is cited already 73 times. Such papers are traditionally not counted as measure of the impact of the CDK, but surely are. This work, combined with CiTO allows just that.

D. Shotton (2013). Publishing: Open citations Nature, 502 (7471), 295-297 : 10.1038/502295a... Read more »

D. Shotton. (2013) Publishing: Open citations. Nature, 502(7471), 295-297. info:/10.1038/502295a

  • October 19, 2013
  • 11:30 PM

Software through the lens of evolutionary biology

by Artem Kaznatcheev in Evolutionary Games Group

My preferred job title is ‘theorist’, but that is often too ambiguous in casual and non-academic conversation, so I often settle for ‘computer scientist’. Unfortunately, it seems that the overwhelming majority of people equate computer scientists to programmers or some general ‘tech person’, forgetting M.R. Fellows rallying cry: “Computer science is not about machines, in […]... Read more »

Schulte, E., Fry, Z. P., Fast, E., Weimer, W., & Forrest, S. (2013) Software Mutational Robustness. Journ. Genetic Programming and Evolvable Machines. DOI: 10.1007/s10710-013-9195-8  

  • October 19, 2013
  • 06:29 AM

The Selective Clearance of Senescent Cells – a Promising Target for Ageing

by Robert Seymour in NeuroFractal

When cells are put under stress (e.g. UV light, ionising radiation, reactive oxygen species) they undergo a process known as cellular senescence in which cell division (mitosis) is arrested. This is thought to contribute to ageing. In their 2013 paper Naylor and colleagues outline a strategy to selectively remove in vivo senescent cells expressing p16Ink4A .... Read more »

  • October 16, 2013
  • 05:08 AM

New insight into the Earth’s deep interior

by Perikis Livas in Tracing Knowledge

For 300 years we have known that the Earth’s magnetic field moves gradually westward. Computer simulations on the CSCS super-computer “Monte Rosa” by researchers at ETH Zurich and the University of Leeds explain why this happens.... Read more »

Livermore PW, Hollerbach R, & Jackson A. (2013) Electromagnetically driven westward drift and inner-core superrotation in Earth's core. Proceedings of the National Academy of Sciences of the United States of America, 110(40), 15914-15918. PMID: 24043841  

  • October 15, 2013
  • 08:00 AM

Philippine language relations in a map

by nath in Imprints of Philippine Science

“The number of individual languages listed for Philippines is 185. Of these, 181 are living and 4 are extinct. Of …Continue reading »... Read more »

Bouchard-Côté A, Hall D, Griffiths TL, & Klein D. (2013) Automated reconstruction of ancient languages using probabilistic models of sound change. Proceedings of the National Academy of Sciences of the United States of America, 110(11), 4224-9. PMID: 23401532  

  • October 13, 2013
  • 11:45 PM

Mathematics in finance and hiding lies in complexity

by Artem Kaznatcheev in Evolutionary Games Group

Mathematics has a deep and rich history, extending well beyond the 16th century start of the scientific revolution. Much like literature, mathematics has a timeless quality; although its trends wax and wane, no part of it becomes out-dated or wrong. What Diophantus of Alexandria wrote on solving algebraic equations in the 3rd century was still […]... Read more »

  • October 12, 2013
  • 05:24 PM

Stochastic Optimization in R by Parallel Tempering

by Lindon in Lindon's Log

I’ve written a few posts now about using parallel tempering to sample from complicated multi-modal target distributions but there are also other benefits and uses to this algorithm. There is a nice post on Darren Wilkinson’s blog about using tempered posteriors for marginal likelihood calculations. There is also another area where parallel tempering finds application, […]The post Stochastic Optimization in R by Parallel Tempering appeared first on Lindons Log.... Read more »

Li Yaohang, Protopopescu Vladimir A., Arnold Nikita, Zhang Xinyu, & Gorin Andrey. (2009) Hybrid parallel tempering and simulated annealing method. Applied Mathematics and Computation, 212(1), 216-228. DOI: 10.1016/j.amc.2009.02.023  

  • October 11, 2013
  • 08:44 AM

Bone-Crack Detection, Targeting, and Repair Using Ion Gradients

by Perikis Livas in Tracing Knowledge

Bone cracks can be detected by utilizing the damaged matrix itself as both the trigger and the fuel. A crack in a material with a high mineral content such as bone generates ion gradients, which can be utilized for active targeting and treatment. This approach to targeting a biological structure augments current methods, which are focused on biomacromolecular interactions involving proteins and nucleic acids.... Read more »

Yadav V, Freedman JD, Grinstaff M, & Sen A. (2013) Bone-Crack Detection, Targeting, and Repair Using Ion Gradients. Angewandte Chemie (International ed. in English). PMID: 24039057  

  • October 10, 2013
  • 07:33 AM

3-D Printing Good For The Environment

by Qdragon in United Academics

Have you always wanted a 3-D printer but never really had a justification for the investment? Well, a study done by Michigan technological University has your back. It shows that in many cases 3-D printing products are more environmentally friendly than mass production.... Read more »

Christian Baechler, Matthew DeVuono, Joshua M. Pearce. (2013) Distributed recycling of waste polymer into RepRap feedstock. Rapid Prototyping Journal. DOI: 10.1108/13552541311302978  

  • October 10, 2013
  • 04:30 AM

Computational complexity of evolutionary stable strategies

by Artem Kaznatcheev in Evolutionary Games Group

Yesterday, I shared a video of John Maynard Smith introducing evolutionary game theory (EGT) to the London Mathematical Society. I suggested that at its foundation, EGT was just like classical game theory, and based on equilibrium analysis — the evolutionary stable strategy (Maynard Smith & Price, 1973). Given a utility function that gives the expected […]... Read more »

Conitzer, V. (2013) The exact computational complexity of evolutionarily stable strategies. The 9th Conference on Web and Internet Economics (WINE). info:/

  • October 9, 2013
  • 10:43 AM

Honeybees Can Avoid Deadlock When Making Group Decisions, So Why Can't We?

by Miss Behavior in The Scorpion and the Frog

This honeybee swarm has precious little time to make a democratic decision as to where they will move to. A decision deadlock could have fatal consequences. Image by Nino Barbieri at Wikimedia Commons.In case you've been living in a cave lately, the U.S. Government has been shut down since October 1st. Not because of a terrorist attack or a bank system meltdown or a natural disaster, but because Congress cannot agree on a spending bill to determine our government's funding plan for the next year. The government shutdown has its consequences (such as closed national parks, postponed federal research funding, the halting of the CDC's flu vaccine program, and unpaid federal employees), but these will seem like a slap on the wrist if Congress can't agree to raise the debt ceiling by October 17. If we are still in a government deadlock at that point, we will default on our national loans and suffer disastrous consequences (such as the devaluation of the dollar, social security payments not being made, spiking interest rates, and devaluation and forced selling off of bonds). Congress is up against a deadline to make a group decision, and the consequences of not making one in time are much higher than the consequences of making an inperfect one. It's hard to come to a consensus when so many individuals in the group have a strong opinion one way or another, but the fact of the matter is: honeybees can do it. So why can't we? This week at Accumulating Glitches I tell the story of how honeybees democratically decide on what new home to move to, all while avoiding a deadlock at indecision. Check it out here.And to learn more, check these out: Seeley, T.D., Visscher, P.K., Schlegel, T., Hogan, P.M., Franks, N.R., & Marshall, J.A.R. (2012). Stop signals provide cross inhibition in collective decision-making by honeybee swarms Science, 335, 108-111 DOI: 10.1126/science.1210361Seeley, T.D. Honeybee Democracy, Princeton University Press (2010). And learn more about group decision-making in animals at Can a Horde of Idiots Be a Genius? and Why This Horde of Idiots Is No Genius ... Read more »

  • October 7, 2013
  • 07:35 PM

Python package essentially with astronomy related functionality

by Usman Paracha in SayPeople

Main Point:

Researchers have presented the first public version (v0.2) of the open-source and community-developed Python package, Astropy, that is able to provide core astronomy-related functionality to the community.

Published in:

Astronomy & Astrophysics

Study Further:

Python is a portable, interpreted, object-oriented programming language developed and freely distributed by its developer. Python runs on many platforms, including UNIX, Windows, OS/2 and Macintosh and is used for writing TCP/IP applications.

Python is one of the largest growing languages in the astronomy community in the last decade.

Astropy project:

The Astropy project was started in 2011 with the desire to bring the astronomy related developers together to make progress in the development of Python tools for astronomers.

Present Research:

Researchers have presented the first public release of the Astropy package (v0.2) i.e., a Python package for astronomers. Researchers have described the main functionality of the package in the present research.

This main functionality includes “the support for domain-specific file formats such as flexible image transport system (FITS) files, Virtual Observatory (VO) tables, and common ASCII table formats, unit and physical quantity conversions, physical constants specific to astronomy, celestial coordinate and time transformations, world coordinate system (WCS) support, generalized containers for representing gridded as well as tabular data, and a framework for cosmological transformations and conversions.”

To study the further details of presentation or to check the package, you can see the reference.


Astropy - A community Python Library for Astronomy (

The Astropy Collaboration, & Thomas P. Robitaille et al. (2013). Astropy: A community Python package for astronomy Astronomy & Astrophysics DOI: 10.1051/0004-6361/201322068... Read more »

The Astropy Collaboration, & Thomas P. Robitaille et al.,. (2013) Astropy: A community Python package for astronomy. Astronomy . DOI: 10.1051/0004-6361/201322068  

  • October 7, 2013
  • 04:14 PM

Gene activity and transcript patterns visualized for the first time in thousands of single human cells

by Perikis Livas in Tracing Knowledge

Biologists of the University of Zurich have developed a method to visualize the activity of genes in single cells. The method is so efficient that, for the first time, a thousand genes can be studied in parallel in ten thousand single human cells. Applications lie in fields of basic research and medical diagnostics. The new method shows that the activity of genes, and the spatial organization of the resulting transcript molecules, strongly vary between single cells.... Read more »

  • October 7, 2013
  • 01:00 AM

Parallel Tempering in R with Rmpi

by Lindon in Lindon's Log

My office computer recently got a really nice upgrade and now I have 8 cores on my desktop to play with. I also at the same time received some code for a Gibbs sampler written in R from my adviser. I wanted to try a metropolis-coupled markov chain monte carlo, , algorithm on it to […]The post Parallel Tempering in R with Rmpi appeared first on Lindons Log.... Read more »

Earl David J., & Deem Michael W. (2005) Parallel tempering: Theory, applications, and new perspectives. Physical Chemistry Chemical Physics, 7(23), 3910. DOI: 10.1039/b509983h  

  • October 4, 2013
  • 08:13 AM

Why PLOS ONE is no longer my default journal

by Juan Nunez-Iglesias in I Love Symposia!

Time-to-publication at the world’s biggest scientific journal has grown dramatically, but the nail in the coffin was its poor production policies. When PLOS ONE was announced in 2006, its charter immediately resonated with me. This would be the first journal where only scientific accuracy mattered. Judgments of “impact” and “interest” would be left to posterity, […]... Read more »

  • October 3, 2013
  • 02:02 PM

Lithium-Ion Batteries Improved With Germanium Nanowires

by dailyfusion in The Daily Fusion

New research led by an electrical engineer at the University of California, San Diego is aimed at improving lithium-ion batteries through possible new electrode architectures with precise nano-scale designs.... Read more »

  • October 2, 2013
  • 04:14 PM

New Metabolic Pathway Could Lead to 50% Increase In Biofuel Production

by dailyfusion in The Daily Fusion

UCLA chemical engineering researchers have created a new synthetic metabolic pathway for breaking down glucose that could lead to a 50 percent increase in the production of biofuels.... Read more »

  • October 2, 2013
  • 10:21 AM

We Have the Technology…

by Roli Roberts in PLOS Biologue

“Gentlemen, we can rebuild him. We have the technology. We have the capability to make the world’s first bionic man. Steve Austin will be that man. Better than he was before. Better…stronger…faster.”

Readers of a certain age will tingle with recognition at those words, intoned over the intro to ’70s TV series “The Six Million Dollar Man“, promising the bodily reconstruction of a seriously injured astronaut. Back then it was distant science fiction, but fast-forward 30 years to 2003, and a very shiny new PLOS Biology published a paper in its second ever issue that did indeed “have the technology”...... Read more »

Carmena JM, Lebedev MA, Crist RE, O'Doherty JE, Santucci DM, Dimitrov DF, Patil PG, Henriquez CS, & Nicolelis MA. (2003) Learning to control a brain-machine interface for reaching and grasping by primates. PLoS biology, 1(2). PMID: 14624244  

  • October 2, 2013
  • 08:45 AM

Programming language for biochemistry

by Artem Kaznatcheev in Evolutionary Games Group

Computer scientists that think of nature as literally computing, often take the stance that biological organisms are nothing more than protein interaction networks. For example, this is the stance that Leslie Valiant (2009) takes when defining ecorithms: biology is just a specialization of computer science focused on evolvable circuits. User @exploderator summarized the realist computational […]... Read more »

Chen, Y.J., Dalchau, N., Srinivas, N., Phillips, A., Cardelli, L., Soloveichik, D., & Seelig, G. (2013) Programmable chemical controllers made from DNA. Nature nanotechnology. PMID: 24077029  

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