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  • March 27, 2013
  • 09:45 AM
  • 774 views

Video Tip of the Week: Enzyme Portal and User-Centered Design

by Mary in OpenHelix

This week’s video tip of the week introduces you to Enzyme Portal, an interface to explore data about these important proteins, from the EBI. In the video, Jenny Cham–one of the authors of the paper below–takes you through the main features of their newly designed resource. I learned about the new effort from this blog [...]... Read more »

de Matos, P., Cham, J., Cao, H., Alcántara, R., Rowland, F., Lopez, R., & Steinbeck, C. (2013) The Enzyme Portal: A case study in applying user-centred design methods in bioinformatics. BMC Bioinformatics, 14(1), 103. DOI: 10.1186/1471-2105-14-103  

  • March 27, 2013
  • 08:27 AM
  • 323 views

Modern Privacy: More Access to Cells than Toilets

by Katja Keuchenius in United Academics

Most people in the world now live in a city, feeling pretty anonymous. An even bigger number of people don’t have to defocate out in the open anymore, but have access to a toilet. And then there’s this growing amount of people that can talk in private on their cells. But beware, these are false senses of privacy.... Read more »

de Montjoye YA, Hidalgo CA, Verleysen M, & Blondel VD. (2013) Unique in the Crowd: The privacy bounds of human mobility. Scientific reports, 1376. PMID: 23524645  

  • March 26, 2013
  • 08:48 AM
  • 773 views

Breakthrough Research Shows Chemical Reaction in Real Time

by Perikis Livas in Chilon

The ultrafast, ultrabright X-ray pulses of the Linac Coherent Light Source (LCLS) have enabled unprecedented views of a catalyst in action, an important step in the effort to develop cleaner and more efficient energy sources.

Scientists at the U.S. Department of Energy’s (DOE) SLAC National Accelerator Laboratory used LCLS, together with computerized simulations, to reveal surprising details of a short-lived early state in a chemical reaction occurring at the surface of a catalyst sample. The study offers important clues about how catalysts work and launches a new era in probing surface chemistry as it happens.... Read more »

Andy Freeberg. (2013) Breakthrough Research Shows Chemical Reaction in Real Time. SLAC National Accelerator Laboratory News. info:/

  • March 26, 2013
  • 06:01 AM
  • 456 views

X-ray Laser Explores How to Write Data with Light

by Perikis Livas in Chilon

Using laser light to read and write magnetic data by quickly flipping tiny magnetic domains could help keep pace with the demand for faster computing devices.

Now experiments with SLAC’s Linac Coherent Light Source (LCLS) X-ray laser have given scientists their first detailed look at how light controls the first trillionth of a second of this process, known as all-optical magnetic switching.... Read more »

Glenn Roberts Jr. (2013) X-ray Laser Explores How to Write Data with Light. SLAC National Accelerator Laboratory News. info:/

  • March 22, 2013
  • 06:50 PM
  • 911 views

A great role model for collaborative science: meet the OpenWorm

by Eugenio Maria Battaglia in Science to Grok

Sometimes even big project could start from a tweet.

Matteo Cantarelli - member of the OpenWorm team - says: "It was 2007 when Giovanni Idili and I started - naively - talking about simulating the worm. We were approaching the problem after having hit common limits of artificial intelligence. We never got to write any code for the worm at that time, we just had lengthy conversations and paper reading sessions together."
... Read more »

  • March 18, 2013
  • 04:04 AM
  • 806 views

Internet Bad Neighborhoods

by Rense in Curving Normality

ResearchBlogging.org

Don’t venture too far on the internet: bad neighborhoods were located! Internet bad neighborhoods are those geographical areas where the majority of spam and phishing mails originate from. Interestingly, some regions specialize in spam, while others focus on phishing for your bank account. ... Read more »

Giovane C. M. Moura, Anna Sperotto, Ramin Sadre, & Aiko Pras. (2013) Evaluating Third-Party Bad Neighborhood Blacklists for Spam Detection. IFIP/IEEE International Symposium on Integrated Network Management. info:/

  • March 15, 2013
  • 11:38 AM
  • 715 views

Surprising Control over Photoelectrons from a Topological Insulator

by Perikis Livas in Chilon

Plain-looking but inherently strange crystalline materials called 3D topological insulators (TIs) are all the rage in materials science. Even at room temperature, a single chunk of TI is a good insulator in the bulk, yet behaves like a metal on its surface.

Researchers find TIs exciting partly because the electrons that flow swiftly across their surfaces are “spin polarized”: the electron’s spin is locked to its momentum, perpendicular to the direction of travel. These interesting electronic states promise many uses – some exotic, like observing never-before-seen fundamental particles, but many practical, including building more versatile and efficient high-tech gadgets, or, further into the future, platforms for quantum computing.... Read more »

Paul Preuss. (2013) Surprising Control over Photoelectrons from a Topological Insulator. Berkeley Lab News Center. info:/

  • March 13, 2013
  • 08:46 AM
  • 760 views

Predicting Technological Progress: Putting Moore’s Law to the Test

by GDW in The Beast, the Bard and the Bot

Being able to predict the pace of technological development could be quite useful for a lot of people. No surprise then, that several models (or ‘laws’) have been posited that aim to describe how technological progress will unfurl (the most famous one probably being Moore’s law, for those interested: original article here). However, these laws [...]... Read more »

  • March 12, 2013
  • 10:38 AM
  • 715 views

New Ultra-Efficient HPC Data Center Debuts

by Perikis Livas in Chilon

Scientists and researchers at the U.S. Department of Energy’s National Renewable Energy Laboratory (NREL) are constantly innovating, integrating novel technologies, and “walking the talk.” Since 1982, NREL has won 52 R&D 100 Awards — known in the research and development community as “the Oscars of Innovation” — for its groundbreaking work.... Read more »

Heather Lammers. (2013) New Ultra-Efficient HPC Data Center Debuts. NREL Newsroom. info:/

  • March 11, 2013
  • 02:04 PM
  • 1,197 views

Let’s Explore Quantum Computing

by Jason Carr in Wired Cosmos

It’s fairly easy to surmise how quantum computing will evolve in the future if/when it becomes a reality. Devices that are currently based around a system of electronic circuits would eventually die off. Quantum devices would ultimately become the new standard in computing. While Peter Shor’s research showed how quantum algorithms would speed up advanced [...]... Read more »

Benningshof OW, Mohebbi HR, Taminiau IA, Miao GX, & Cory DG. (2013) Superconducting microstrip resonator for pulsed ESR of thin films. Journal of magnetic resonance (San Diego, Calif. : 1997), 84-87. PMID: 23454577  

Petersson KD, McFaul LW, Schroer MD, Jung M, Taylor JM, Houck AA, & Petta JR. (2012) Circuit quantum electrodynamics with a spin qubit. Nature, 490(7420), 380-3. PMID: 23075988  

  • March 7, 2013
  • 06:30 AM
  • 687 views

Games, culture, and the Turing test (Part I)

by Artem Kaznatcheev in Evolutionary Games Group

Intelligence is one of the most loaded terms that I encounter. A common association is the popular psychometric definition — IQ. For many psychologists, this definition is too restrictive and the g factor is preferred for getting at the ‘core’ of intelligence tests. Even geneticists have latched on to g for looking at heritability of [...]... Read more »

Strannegård, C., Amirghasemi, M., & Ulfsbäcker, S. (2013) An anthropomorphic method for number sequence problems. Cognitive Systems Research, 27-34. DOI: 10.1016/j.cogsys.2012.05.003  

  • March 6, 2013
  • 10:03 AM
  • 1,213 views

Dead Sparrow Turned into Robot to Study Bird Behavior

by Jason Carr in Wired Cosmos

Researchers at Duke University recently took a major step toward better understanding how swamp sparrows use a combination of song and visual displays to communicate with one another. How they came about making this discovery, though, is what makes this story particularly newsworthy — they stuffed a deceased swamp sparrow with a miniature computer and some [...]... Read more »

  • March 5, 2013
  • 04:00 PM
  • 696 views

Continuously Sorting Particles According to Shape

by Hector Munoz in Microfluidic Future

There are numerous filters to separate particles in liquid based on their size, which can be enough to isolate them; however, particle shape can be more important, as it distinguishes healthy red blood cells from those affected by sickle-cell disease or malaria. Shape can also be used to determine what stage a cell is in of the cell cycle, which would benefit researchers looking for dividing cells. Recent research by Dino Di Carlo of UCLA looks to separate particles of differing aspect ratios continuously, using inertial fluid-dynamics. His work, “Continuous Inertial Focusing and Separation of Particles by Shape,” featured in Physical Review X reminds me of his previous work to use inertial fluid-dynamics to continuously filter particles according to size.... Read more »

  • March 4, 2013
  • 01:50 PM
  • 1,090 views

Distributed control of uncertain systems using superpositions of linear operators - Likelihood calculus paper series review part 3

by Travis DeWolf in studywolf

The third (and final, at the moment) paper in the likelihood calculus series from Dr. Terrence Sanger is Distributed control of uncertain systems using superpositions of linear operators. Carrying the torch for the series right along, here Dr. Sanger continues investigating the development of an effective, general method of controlling systems operating under uncertainty. This is the paper that delivers on all the promises of building a controller out of a system described by the stochastic differential operators we’ve been learning about in the previous papers. In addition to describing the theory, there are examples of system simulation with code provided! Which is a wonderful, and sadly uncommon, thing in academic papers, so I’m excited. We’ll go through a comparison of Bayes’ rule and Markov processes (described by our stochastic differential equations), go quickly over the stochastic differential operator description, and then dive into the control of systems. The examples and code run-through I’m going to have to save for another post, though, just to keep the size of this post reasonable.... Read more »

  • March 4, 2013
  • 05:37 AM
  • 589 views

The models vs. patterns problem

by Peter Kraker in Science and the Web

Update: Sebastian Dennerlein and I have written a paper entitled “Towards a Model of Interdisciplinary Teamwork for Web Science: What can Social Theory Contribute?” which includes the patterns vs. models problem. The paper has been accepted for the Web Science 2013 Workshop: “Harnessing the Power of Social Theory for Web Science”. You can download it …Read More... Read more »

Peter Kraker, & Sebastian Dennerlein. (2013) Towards a Model of Interdisciplinary Teamwork for Web Science: What can Social Theory Contribute?. Web Science 2013 Workshop: Harnessing the Power of Social Theory for Web Science. info:/

  • February 27, 2013
  • 01:16 PM
  • 845 views

#ifihadglass I Would Build an Augmented Biomed Browser

by Eugenio Maria Battaglia in Science to Grok

In the previous post, I’ve described the relationship between environmental factors and the public’s insights. Moreover, what would happen if we have more than an ideal “physical” environment? Will people embrace a brand new world in which virtual components are added to the physical ones?


We all know that more research should be carried out to create software which supports the most complex and time-consuming portions of the analytical process, so that analysts can respond to increasingly more complex questions.... Read more »

Gershon Dublon, & Joseph A. Paradiso. (2012) Tongueduino: hackable, high-bandwidth sensory augmentation. Proceeding CHI EA '12 CHI '12 Extended Abstracts on Human Factors in Computing Systems, 1453-1454. DOI: 10.1145/2212776.2212482  

  • February 27, 2013
  • 10:47 AM
  • 849 views

Let’s Explore Flywheel Energy Storage Devices

by Jason Carr in Wired Cosmos

Flywheel energy storage devices could be looked at as a radical application of very traditional technology. They work by maintaining rotational energy by moving a flywheel. This same idea is used to keep a mechanical watch ticking. A majority of modern FES devices use electricity to put the flywheel in motion, but some researchers are [...]... Read more »

MacIntosh BR, Rishaug P, & Svedahl K. (2003) Assessment of peak power and short-term work capacity. European journal of applied physiology, 88(6), 572-9. PMID: 12560957  

  • February 27, 2013
  • 09:48 AM
  • 1,254 views

GABA, how exciting!

by TheCellularScale in The Cellular Scale

I would like to thank my good friend Anonymous for asking me a great question on a previous post. Anonymous asks: "Are there any known transmitters in the NS that activate both inhibitory receptor subtypes AND excitatory receptor subtypes? Or does every known transmitter activate EITHER a bunch of excitatory subtypes OR a bunch of inhibitory subtypes?" (btw. This doesn't qualify as a LMAYQ post because it's a real true question that someone directly asked, not a search term)While I don't know of any instances of glutamate (excitatory) activating GABA (inhibitory) receptors or of GABA activating glutamate receptors, there is an interesting little way that GABA can activate an inhibitory receptor, but actually help excite the cell.  GABA receptor (source) Here's how that works: GABA(A) receptors are permeable to chloride ions, and as the picture above shows, chloride ions (Cl-) are negatively charged. When GABA binds to the receptor, the receptor opens and chloride ions rush in, bringing their negative charge with them. This hyperpolarizes the cell, meaning it brings it lower and lower in total charge (membrane potential), which brings it further and further away from the threshold where it will fire an action potential.BUT.... if there is a lot of chloride inside the cell already (or if the cell is resting more negatively than the chloride reversal potential), chloride will actually flow out of the cell, bringing its negative charge with it. Negative ions flowing out of the cell will depolarize the neuron increasing its total charge (membrane potential), which brings it closer and closer to the threshold where it will fire an action potential.GABA reversing at -62mV (source)A paper published last year in the Journal of Neuroscience shows that in a model of a hippocampal neuron, when a strong excitatory (glutamate) stimulation happens right after a GABA stimulation close by on the dendrite, the cell is actually more likely to fire than when the glutamate stimulation occurs on its own. This effect is dependent on the location of the GABA stimulation along the dendrite.Chiang et al., 2012 Figure 4E (GPSP in the dendrite)This figure shows that a GABA stimuation (first dotted line, blue trace) can push the glutamate (excitatory) stimulation (second dotted line, red trace) up to the point of firing an action potential (green trace). This paper also showed that GABA can still inhibit the action potential in these cells, it just has to be at the soma and almost the same time as the glutamatergic input.Chiang et al., 2012 Figure 4G (GPSP in the soma) So there you have it, GABA enhancing the likelihood of an action potential and acting excitatory sometimes, and acting inhibitory other times.   © TheCellularScaleChiang PH, Wu PY, Kuo TW, Liu YC, Chan CF, Chien TC, Cheng JK, Huang YY, Chiu CD, & Lien CC (2012). GABA is depolarizing in hippocampal dentate granule cells of the adolescent and adult rats. The Journal of neuroscience : the official journal of the Society for Neuroscience, 32 (1), 62-7 PMID: 22219270... Read more »

Chiang PH, Wu PY, Kuo TW, Liu YC, Chan CF, Chien TC, Cheng JK, Huang YY, Chiu CD, & Lien CC. (2012) GABA is depolarizing in hippocampal dentate granule cells of the adolescent and adult rats. The Journal of neuroscience : the official journal of the Society for Neuroscience, 32(1), 62-7. PMID: 22219270  

  • February 27, 2013
  • 09:30 AM
  • 375 views

Training Robots As Members of Human Team

by Katja Keuchenius in United Academics

For those of you who think robots always act according to a programmed plan and therefore aren’t flexible: read on. Robots, already working alongside humans in factories or hazardous locations, are constantly adapting their behavior to their environment. Human colleagues actively train them, literally saying: ‘good robot’ or ‘bad robot’.... Read more »

  • February 23, 2013
  • 03:39 PM
  • 570 views

The brain race: can giant computers map the mind?

by Perikis Livas in Chilon

The fact the Blue Brain project has not produced any significant breakthroughs in recent years does not seem to have worried the European funding agencies. Apparently they like the idea of Markram building a monster computer to lead Europe into the future of brain research.... Read more »

Charles Watson. (2013) The brain race: can giant computers map the mind?. The Conversation. info:/

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