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  • October 5, 2012
  • 12:42 AM

Technology Is Rapidly Lowering the Cost of Testing

by Eric Horowitz in peer-reviewed by my neurons

People may view this as something for the good news/bad news file, but technology has quietly made it significantly easier to grade tests electronically. For example, a new paper in the Journal of Science Education and Technology highlights a system called “Eyegrade” : While most current solutions are based on expensive scanners, Eyegrade offers a [...]... Read more »

  • October 4, 2012
  • 03:50 PM

A Microsyringe to Take the Pain out of Shots

by Hector Munoz in Microfluidic Future

Back when I was in sixth grade, I remember reading a little blurb in some science magazine at school that in the future we could receive shots via a method that would feel as soft as a banana peel. Although I’m now a champ at taking shots, it’s still not a bad idea. We’ve had transdermal patches (think nicotine and birth control) for some time now, but those release their medicine over a period of time. A syringe is capable of delivering a dose at once, and can take a biological sample too. Researchers from the University of Pisa have developed this ‘syringe of the future’ within ‘A minimally invasive microchip for transdermal injection/sampling applications’ in Lab on a Chip.... Read more »

  • October 1, 2012
  • 01:11 PM

Does playing Solo or Vs make a Difference in Kinect or Wii? (Study)

by Stephen Yang in ExerGame Lab

If you thought yes, "you are correct Sir!" According to the current study, playing Xbox Kinect™ Reflex Ridge resulted in a 1 MET higher rating than Wii Sports Boxing, and playing multiplayer...

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... Read more »

  • October 1, 2012
  • 01:10 AM

Does playing Solo or Vs make a Difference in Kinect or Wii? (Study)

by Stephen P. Yang, Ph.D. in ExerGame Lab

According to the current study, playing Xbox Kinect™ Reflex Ridge resulted in a 1 MET higher rating than Wii Sports Boxing, and playing multiplayer yielded a 0.5 MET increase compared to solo play... Read more »

  • September 26, 2012
  • 08:50 AM

Fellows of the Wiki Society? The Royal Society in London experiments with Wikipedia

by Duncan Hull in O'Really?

Venerable and learned society experiments with wikipedia... Read more »

Wodak Shoshana J., Mietchen Daniel, Collings Andrew M., Russell Robert B., & Bourne Philip E. (2012) Topic Pages: PLoS Computational Biology Meets Wikipedia. PLoS Computational Biology, 8(3). DOI: 10.1371/journal.pcbi.1002446  

  • September 26, 2012
  • 01:38 AM

Mirror, Mirror on the wall, Am I healthy after all?

by Aurametrix team in Health Technologies

Health gadgets continue to evolve in many forms and shapes - from something that fits in your pocket to something that is wearable or walkable. Everyday objects are turning into "Smart objects", building the foundation for the next version of the Internet. And it's not all smoke and mirrors. So let's talk about mirrors. Fairy tales and science fiction stories often pave the way to real world technology. Magic mirrors have been used in Snow White and Harry Potter's world. Now you can get one, too - manufactured by a Hong Kong company James Law Cybertecture International. Cybertecture mirror can tell you about the weather or your last weight readings reported by the scales. It can show you a TV channel, let you browse Facebook or twitter and help you to exercise. Impressive, yet so much more is yet to come.Could a mirror tell us how healthy we are? For example, could it measure our heart rate at a distance? Sure, it could. And it has already been demonstrated as a concept prototype (Cardiocam, MIT media labs, Poh et al. 2010), although the designer is now focusing on mobile devices (check his company Cardiio).What other health metrics could be performed by the mirror during your regular morning hygiene routine? If a camera can measure minute changes in the color of your face to determine your heart rate, it could also measure your facial expressions and emotions or perform observational analysis  - the first of four methods of diagnosis performed by traditional Chinese medicine. Prototypes for computerized facial diagnostic systems already have been developed. One recent study, for example, (Li et al 2012) analyzes lips. The software segments lips from the rest of the face and extracts color, texture and shape features. Special supervised learning algorithms are then able to classify lips as deep-red, purple, red or pale and make inferences related to energy levels and circulation. Health management applications will not be limited to smartphones or smart homes. All objects in our lives will gradually become "smarter." Mobile phones can already manage vacuum cleaners and thermostats. Refrigerators can tweet, check Google calendars, download recipes, play tunes and alert us about food spoilage. Mirrors can monitor our weight and exercise. There is still more emphasis these days on technological wizardry than on actual benefits, but systems like Aurametrix are bringing it all together and generating valuable insights. And perhaps, one day, we won't regard the mirror on the wall nagging us about losing weight or commenting on the bags under eyes is an invasion of privacy. Let's build the future piece by piece - and they will come.REFERENCESPoh MZ, McDuff DJ, & Picard RW (2010). Non-contact, automated cardiac pulse measurements using video imaging and blind source separation. Optics express, 18 (10), 10762-74 PMID: 20588929Li F, Zhao C, Xia Z, Wang Y, Zhou X, & Li GZ (2012). Computer-assisted lip diagnosis on traditional Chinese medicine using multi-class support vector machines. BMC complementary and alternative medicine, 12 (1) PMID: 22898352Littlewort, G., Whitehill, J., Wu, T., Fasel, I.R., Frank, M., Movellan, J.R., Bartlett, M.S. (2011) The Computer Expression Recognition Toolbox (CERT). Proceedings of the 9th IEEE Conference on Automatic Face and Gesture Recognition. ... Read more »

  • September 22, 2012
  • 07:11 PM

Quantum computers | Κβαντικοί υπολογιστές

by Perikis Livas in Chilon

A research team led by Australian engineers has created the first working quantum bit based on a single atom in silicon, opening the way to ultra-powerful quantum computers of the future.

In a landmark paper published today in the journal Nature, the team describes how it was able to both read and write information using the spin, or magnetic orientation, of an electron bound to a single phosphorus atom embedded in a silicon chip.... Read more »

UNSW News, NATURE, Physics4u, Physicsgg, & Γούσια Πολυξένη. (2012) Quantum computers | Κβαντικοί υπολογιστές . Tracing Knowledge. info:/

  • September 22, 2012
  • 01:26 PM

Can Video Games Teach Kids “Grit”?

by Eric Horowitz in peer-reviewed by my neurons

KIPP’s character report card and Paul Tough’s new book have laudably placed an emphasis on how emotional skills and character traits (e.g. persistence, curiosity, optimism, etc.) influence a child’s academic trajectory. Yet the question remains, will our education system make a real effort to emphasize these new ideas, or will they join things like Carol [...]... Read more »

  • September 22, 2012
  • 11:02 AM

OMG! An Open Molecule Generator!

by egonw in Chem-bla-ics

Earlier this week an important cheminformatics paper appeared in the Journal of Cheminformatics. It is about the Open Molecule Generator (see below for the paper). This was one important piece of functionality still missing from Open Source cheminformatics. This works uses the Chemistry Development Kit, and was written by Julio Peironcely.

The Analytical Biosciences' group of Prof. Hankemeier (and many others, including also Theo Reijmers) and funded by the Netherlands Metabolomics Centre has been using the CDK for metabolomics for a while now, with Miguel Rojas-Chertó as other principle user (and of course CDK developer!). I congratulate them all with this piece of work, and particularly with their choice of license!

Julio (with the other authors) have picked up a difficult algorithm, based in mathematics, but not the straightforward graph theory either. Others have tried to implement structure generation in the CDK, and I looked into this too, when working in Christoph Steinbeck's group back in Cologne. What the OMG team has achieved is significant.

The paper compares their results with MolGen, resulting in results like those in this table (from the CC-SA-BY paper):

It shows that the results are identical, when you consider the atom types it uses. And the use the CDK atom type framework I initiated, which is way cool! Julio found the tables I constructed from earlier CDK code incomplete (as did others) and extended them, to match their needs.

One "problem" with their current code base is that it is quite slow compared to OMG. This is easily compensated by the added functionality of OMG, such as restricting the structure generation with multiple fragments. Now, the CDK data classes are know to be somewhat sluggish, as compared to competition, but the community is increasingly improving this.

But I also think that the OMG use of Naughty via JNI is not helping performance either, and I hope someone will soon jump in and convert that C code into Java code, which should speed up performance too. Another side to this is that removing the dependency on C code will also make it easier to integrate into other tools, like Bioclipse, Taverna, and KNIME.

Julio E Peironcely, Miguel Rojas-Chertó, Davide Fichera, Theo Reijmers, Leon Coulier, Jean-Loup Faulon, & Thomas Hankemeier (2012). OMG: open molecule generator Journal of Cheminformatics, 4 DOI: 10.1186/1758-2946-4-21... Read more »

Julio E Peironcely, Miguel Rojas-Chertó, Davide Fichera, Theo Reijmers, Leon Coulier, Jean-Loup Faulon, & Thomas Hankemeier. (2012) OMG: open molecule generator. Journal of Cheminformatics, 21. DOI: 10.1186/1758-2946-4-21  

  • September 22, 2012
  • 08:00 AM

New Caledonian crows reason about hidden causal agents

by Rogue Medic in Rogue Medic

We have generally believed that animals are not capable of very complex thought, even though many species use tools and engage in other complex behaviors.

Even a bird brain appears to be capable of understanding things that are not visible may be affecting their environment.

This study looks at whether New Caledonian crows, that were caught just for this experiment, are capable of attributing actions to a hidden cause, when they see that possible cause come and go.... Read more »

  • September 17, 2012
  • 10:30 PM

How to Build a Neuron: Shortcuts

by TheCellularScale in The Cellular Scale

So you want to build a neuron, but don't have the time to fill and stain it, digitally reconstruct it, or even to knit one. Knitting Neuroscience from Knit a Neuron Well you are in luck because a lot of scientists have collected a lot of data already and some of them are even willing to openly share their work.  While it is great that people are willing to share their data, that willingness alone is not enough to actually make the data widely accessible (or searchable for that matter). To bridge the chasm, other scientists have developed databases and repositories.  These databases and repositories store large datasets and organize them in a searchable way.  The first shortcut to building a neuron I will discuss is the Cell Centered Database (CCDB).Sounds a little like "self-centered" but represents just the opposite: scientists willing to share their data with everyoneIn 2003, Martone and colleagues created the CCDB as a repository for 2D, 3D, and 4D images of cells that could be downloaded and used by researchers around the globe. There is a ton of data here, protein stains, electron microscopy, and fluorescent confocal images just to name a few.  While you could do a lot with this kind of information, I am just going to give you one example of how it can be used as a major short cut in the process of building a neuron. So say you want to make a model of a cerebellum purkinje cell, but you don't have the time or lab facilities to fill and stain your own neuron.  You could go to CCDB, type in 'purkinje neuron' in the search box and download whichever 3D image stack suits your fancy.  example Purkinje neuron that I just got from CCDBWith this data you could go straight to step 2: reconstructing the neuron.  But what if you don't have the time to digitally reconstruct the neuron?  We have already discussed how much time reconstructing a neuron can take, so it's pretty easy to see why you would want to bypass that step too. And in fact, there is a database for that! Halavi et al (2008) developed as a repository for neural reconstructions. has almost 8,000 downloadable digital reconstructions of neurons, which as they say on the website represents over 200,000 hours of manual reconstruction time., for all your neural needs.Similar to CCDB, Neuromorpho offers much more than just a shortcut for lazy computational modelers. It has such detailed information about each neuron that a whole project could be done simply by comparing neural characteristics of different cell classes or different species.  But my job here is to tell you how you can use it as a shortcut to building a neuron.Say you want to build a computational model of a CA1 Hippocampal Pyramidal Cell, but you don't want to stain it and you don't want to reconstruct it.  Well, just go to and click 'browse by brain region' and then on 'hippocampus'. Then look through the 1,000 hippocampal cells (organized by class) that have already been reconstructed for you...Pyramidal cell in the Hippocampus from ...and pick your favorite.  Then you can jump right on through to step 3. (coming soon)Halavi M, Polavaram S, Donohue DE, Hamilton G, Hoyt J, Smith KP, & Ascoli GA (2008). NeuroMorpho.Org implementation of digital neuroscience: dense coverage and integration with the NIF. Neuroinformatics, 6 (3), 241-52 PMID: 18949582Martone ME, Tran J, Wong WW, Sargis J, Fong L, Larson S, Lamont SP, Gupta A, & Ellisman MH (2008). The cell centered database project: an update on building community resources for managing and sharing 3D imaging data. Journal of structural biology, 161 (3), 220-31 PMID: 18054501... Read more »

  • September 13, 2012
  • 08:59 PM

This is your brain on implants (spoiler: it’s better)

by aimee in misc.ience

Today, the Journal of Neural Engineering published rather an interesting paper. In it, they showed that they had been able to restore (and in some cases, improve) decision-making ability in primates through the use of an implanted prosthetic. Sounds like something out of science fiction, doesn’t it?     The region of the brain responsible [...]

[Click on the hyperlinked headline for more of the goodness]... Read more »

  • September 11, 2012
  • 05:28 PM

A tougher and more stretchable hydrogel

by Cath in Basal Science (BS) Clarified

Why settle for good enough, when there can be improvements?  “Conventional hydrogels are very weak and brittle—imagine a spoon breaking through jelly,” says lead author Jeong-Yun Sun, a postdoctoral fellow [...]... Read more »

S. Khetan, C. Chung, & JA. Burdick. (2009) Tuning hydrogel properties for applications in tissue engineering. Conference proceedings : .. Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Conference, 2094-6. PMID: 19963530  

O. Wichterle, & D. Lim. (1960) Hydrophilic Gels for Biological Use. Nature, 117. DOI: 10.1038/185117a0  

Jeong-Yun Sun, Xuanhe Zhao, Widusha R. K. Illeperuma Ovijit Chaudhuri, Kyu Hwan Oh, David J. Mooney, Joost J. Vlassak, & Zhigang Suo. (2012) Highly stretchable and tough hydrogels. Nature, 133. DOI: 10.1038/nature11409  

  • September 10, 2012
  • 06:33 AM

Coming Soon: New Species of Metals

by Andrew Porterfield in United Academics

Most metallic things around us—bridges, microchip wires, buildings—are made of arrays of tiny crystals that owe their strength to an orderly, repeating pattern of grains. However, these mixtures, or alloys, of different metals are unstable; under heat or stress they tend to meld together and become larger and weaker. But the right mix can produce a metal that’s stronger, more heat-resistant and capable of creating structures never thought possible.... Read more »

Tongjai Chookajorn, Heather A. Murdoch, Christopher A. Schuh. (2012) Design of Stable Nanocrystalline Alloys. Science. DOI: 10.1126/science.1224737  

  • September 6, 2012
  • 11:00 AM

L-systems and algorithmic sound experiments

by Alejandro Mosquera in amsqr

New user-generated content music genres such as the "Bytebeat", that is a new genre of electronic music where a piece of rhythmic and/or somewhat melodic music is generated in real-time using just a relatively short formula. In this experiment I combine both approaches, generative L-systems and executable formulae.... Read more »

  • August 31, 2012
  • 08:28 AM

Here Come The Cyborgs

by gunnardw in The Beast, the Bard and the Bot

Cyborgs, or cybernetic organisms, are creatures in which biological tissues and artificial additions are closely intertwined. Well-known recent examples include moths and beetles that can be controlled through the use of electronic steering mechanisms attached to their brains. But, the … Continue reading →... Read more »

Tian, B., Liu, J., Dvir, T., Jin, L., Tsui, J.H., Qing, Q., Suo, Z., Langer, R., Kohane, D.S., & Lieber, C.M. (2012) Macroporous nanowire nanoelectronic scaffolds for synthetic tissues. Nature Materials. DOI: 10.1038/nmat3404  

  • August 30, 2012
  • 09:00 PM

How to Build a Neuron: Step 2

by TheCellularScale in The Cellular Scale

Recently we've discussed the first step in how to build a neuron. Today we will discuss step 2: reconstructing that stained cell.Hippocampus CA1 Pyramidal neuron (from are a couple of ways that you turn an image (or image stack) of a neuron into a digital neuron file like the one pictured above.  Basically there is an easy way and a hard way.  The hard way is to reconstruct the neuron manually, where you literally trace the neuron by hand.  The easy way is to auto-trace the neuron.In a recent Frontier's in Neuroinformatics article, Myatt et al. (2012) explain the hard to easy gradient in reconstruction methods."Manual (Camera lucida). Prisms are employed to visually overlay the microscope image onto a piece of paper, and the neuron is then traced by hand. Although primarily used for 2D tracings, 3D reconstructions can be derived from these with time consuming post-processing (Ropireddy et al., 2011).Semi-manual (e.g., Neuron_Morpho, Neurolucida). Digital segments are added by hand through a software interface, typically sequentially, beginning at the soma, and working down the dendritic tree.Semi-automatic [e.g., NeuronJ (Meijering et al., 2004; 2D reconstruction only) and Imaris (3D reconstruction)]. User interaction defines the basic morphology, such as identifying the tree root and terminations, but branch paths are traced by the computerFully automatic (e.g., Imaris, NeuronStudio; Rodriguez et al., 2003, AutoNeuron add-on for Neurolucida). The entire morphology is extracted with minimal user-input. " (Myatt et al., 2012)You may ask: "Why not just do it the easy way?" Good question.  It is actually surprisingly difficult to make a versatile program that can accurately reconstruct neurons.  So difficult in fact that in 2010 an open challenge was issued with a monetary prize for the best automatic reconstruction algorithm. Five teams competed in this DIADEM challenge and the results and process are explained in detail in a special issue of Neuroinformatics. (And in less detail in this HHMI press release)automatic reconstructions of neurons (source)Advances in automatic reconstruction are being made at an astounding pace, but most neural reconstructions are still being done in a semi-manual or semi-automatic way.  If you are interested in reconstructing some neurons, you can download Neuromantic for free or Neurolucida for money. There is other reconstruction software available, summarized nicely in Myatt et al. 2012, but these are the two I am most familiar with.  In the next edition of "How to Build a Neuron" I will tell you how you can completely skip step 1 (the staining of the neuron) and step 2 (the reconstruction of the neuron).  For ease of access, the whole "How to Build a Neuron" series is archived. © TheCellularScaleMyatt DR, Hadlington T, Ascoli GA, & Nasuto SJ (2012). Neuromantic - from semi-manual to semi-automatic reconstruction of neuron morphology. Frontiers in neuroinformatics, 6 PMID: 22438842... Read more »

  • August 29, 2012
  • 10:53 PM

What are we really recycling?

by Cath in Basal Science (BS) Clarified

Having grown up with reduce, reuse, recycle campaigns (Tweety’s Global Patrol circa 1990), recycling is part of my daily routine. In fact, I’ve even spent time at a Japanese university lab [...]... Read more »

Reck BK, & Graedel TE. (2012) Challenges in metal recycling. Science (New York, N.Y.), 337(6095), 690-5. PMID: 22879508  

  • August 29, 2012
  • 05:30 PM

how to weave machinery into biology

by Greg Fish in weird things

As we’re starting to test artificially grown organs, scientists are wondering how to make sure that their methods result in viable tissues. One of the first steps was to take organ growth into three dimensions, letting the cells grow on a scaffold and self-organize into the right muscles, valves, and other soft tissue. Usually these scaffolds are derived from existing organs purified of all their old cells and many are designed to break down into [...]... Read more »

Bozhi Tian,, Jia Liu,, Tal Dvir,, Lihua Jin,, Jonathan H. Tsui,, Quan Qing,, Zhigang Suo,, Robert Langer,, Daniel S. Kohane,, & Charles M. Lieber. (2012) Macroporous nanowire nanoelectronic scaffolds for synthetic tissues. Nature Materials. DOI: 10.1038/nmat3404  

  • August 29, 2012
  • 09:08 AM

Video Tip of the Week: GenoCAD for Synthetic Biology

by Mary in OpenHelix

The field of synthetic biology has been simmering for quite a while. It occasionally takes a big leap, such as when Venter’s team published about their work on M. genitalium, and it took a big leap recently with the paper about modeling a lot of the cellular processes in a simple cell that I talked [...]... Read more »

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