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  • February 27, 2013
  • 09:48 AM

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

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

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:/

  • February 21, 2013
  • 08:55 PM

Neuro-mechanical control using differential stochastic operators - Likelihood calculus paper series review part 2

by Travis DeWolf in studywolf

The second paper put out by Dr. Terence Sanger in the likelihood calculus paper series is Neuro-mechanical control using differential stochastic operators. Building on the probabalistic representation of systems through differential stochastic operators presented in the last paper (Controlling variability, which I review here) Dr. Sanger starts exploring how one could effect control over a system whose dynamics are described in terms of these operators. Here, he specifically looks at driving a population of neurons described by differential stochastic operators to generate the desired system dynamics. Neural control of a system requires that several phenomena outside the realm of classical control theory be addressed, including the effects of variability in control due to stochastic firing, large partially unlabeled cooperative controllers, bandlimited control due to finite neural resources, and variation in the number of available neurons.... Read more »

Sanger TD. (2010) Neuro-mechanical control using differential stochastic operators. Conference proceedings : .. Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Conference, 4494-7. PMID: 21095779  

  • February 21, 2013
  • 03:00 PM

Tracking Immune Responses to Food with a Gut on a Chip

by Hector Munoz in Microfluidic Future

In an effort to model the complex processes occurring in human bodies, Donald Ingber has pioneered the development of ‘organs-on-chips,’ reproducing the lung and the gut on microfluidic devices. These systems allow researchers to replicate and study organs without the use of human test subjects. While this is one of the best options, there are too many variables to control, understand, and more importantly, manipulate. At the other end of the spectrum is an in vitro study with a cell line and few variables that hardly resemble the real environment. Researchers in Switzerland have developed their own gut-on-a-chip that imitates a human gastrointestinal tract called the Nutrichip. They hope to use this microfluidic device to study the immune-modulatory function of food (with a strong focus on dairy food). This work is detailed in the article “NutriChip: Nutrition Analysis Meets Microfluidics,” which appears in Lab on a Chip.... Read more »

Ramadan, Q., Jafarpoorchekab, H., Huang, C., Silacci, P., Carrara, S., Koklü, G., Ghaye, J., Ramsden, J., Ruffert, C., Vergeres, G.... (2013) NutriChip: nutrition analysis meets microfluidics. Lab on a Chip, 13(2), 196. DOI: 10.1039/c2lc40845g  

  • February 21, 2013
  • 09:36 AM

The Sobering Reality of Orbital Weapons Platforms

by Jason Carr in Wired Cosmos

Space warfare is quickly becoming a reality. Though people might often imagine that wars fought in space would be against some sort of extraterrestrial power, this might not be the case. It’s far more likely than human beings will someday war with one another. As with every other major venture, international law is involved with [...]... Read more »

  • February 20, 2013
  • 08:59 AM

New targets for HIV therapy

by sedeer in Inspiring Science

In a pair of studies published last year, researchers across Europe used computer simulations to make major advances in our …Continue reading »... Read more »

Sadiq SK, Noé F, & De Fabritiis G. (2012) Kinetic characterization of the critical step in HIV-1 protease maturation. Proceedings of the National Academy of Sciences of the United States of America, 109(50), 20449-54. PMID: 23184967  

  • February 18, 2013
  • 10:06 AM

Editorial Crisis: you won't read all this

by Eugenio Maria Battaglia in Science to Grok

In many field beyond Science we could see a huge editorial crisis. A comprehensive study by the University of Bristol and the journalism school of Cardiff University shows that Politics, Economy, Science, Environmental issues and Religion, are some of the topics that general audience have difficulties to understand.[1]

The research - by means of special algorithms - was made by examining two and a half million articles from nearly 500 different sources in the English language, and comparing them between the major U.S. newspapers (printed and online).

The results disassemble part of the myth of "quality journalism" that alone would be enough to survive in the newspapers in this time of transition. It's not surprising the confirmation of the more readability of online newspapers rather than the one of tabloid journals, at least it's worrying to discover that the hottest issues are even less comprehensible to the average reader.... Read more »

Flaounas, I., Ali, O., Lansdall-Welfare, T., De Bie, T., Mosdell, N., Lewis, J., & Cristianini, N. (2013) RESEARCH METHODS IN THE AGE OF DIGITAL JOURNALISM. Digital Journalism, 1(1), 102-116. DOI: 10.1080/21670811.2012.714928  

  • February 13, 2013
  • 12:07 PM

Microsoft’s Kinect game controller could save $30 billion of U.S. healthcare

by Usman Paracha in SayPeople

Researchers have estimated that the Microsoft Kinect game controller could save $30 billion of U.S. healthcare by increasing the remote interaction of the physicians and other healthcare staff with the patients.

This report has been published in the International Journal of Electronic Finance.

In the study, researchers noted that the patients’ transport costs living at considerable distances from suitable hospitals and health centers could be reduced by using their proposed Kinect system. Moreover, the chances of hospital-acquired infections could also be reduced.

Researchers proposed that a laptop, a $150 Kinect, an Azure connection, and an Office 365 account, all costing a few hundred dollars could easily become the good substitute of the present telemedicine system costing tens of thousands of dollars. "The Kinect allows doctors to control the system without breaking the sterile field via hand gestures and voice commands with a goal of reducing the direct cost of healthcare associated infections to hospitals and patients," the research team explained.

This proposed system has an additional benefit of the availability even in low-bandwidth and unreliable connectivity. Researchers Kinect system, referred to as Collaboration and Annotation of Medical Images (CAMI) is, the team said, "Not anticipated to be a panacea to the telemedicine environment but it is a powerful tool that can be affordable in virtually any community that has existing technology and communication infrastructure."


Bailey, J., & Jensen, B. (2013). Telementoring: using the Kinect and Microsoft Azure to save lives International Journal of Electronic Finance, 7 (1) DOI: 10.1504/IJEF.2013.051755... Read more »

  • February 12, 2013
  • 03:31 PM

Online Goal Babbling - motor learning paper review

by Travis DeWolf in studywolf

Diving into that title, online means that we're using information from every movement as it's gathered to improve our control, as opposed to 'batch' where learning only occurs every so-many trials. Bootstrapping is the process of bringing a system up to a functionally useful level. High dimensions then refers to the complexity of the system being controlled, where every component that requires a control signal is another dimension. Humans, for example, require extremely high dimensional control signals. Inverse models refer to a type of internal model, which 'describe relations between motor commands and their consequences'. Forward models predict the results of a movement, and inverse models allow suggest a motor command that can be used to achieve a desired consequence, such as 'the ball falls on the floor' or 'my hand touches the red balloon'.... Read more »

  • February 11, 2013
  • 11:36 AM

Cell Circuits Remember Their History

by Jason Carr in Wired Cosmos

MIT engineers have created genetic circuits in bacterial cells that not only perform logic functions, but also remember the results, which are encoded in the cell’s DNA and passed on for dozens of generations. The circuits, described in the Feb. 10 online edition of Nature Biotechnology (citation below), could be used as long-term environmental sensors, efficient controls [...]... Read more »

  • February 7, 2013
  • 06:07 PM

The difference between the RF and the NNI distance

by Leonardo Martins in bioMCMC

Just to complement my answer to a blog post, where I maintain that the Nearest-Neighbor Interchange (NNI) distance is not equivalent to the Robinson-Foulds (RF) distance, a simple example:Where we can see that trees T1 and T2 differ only in the location of nodes A and B -- on these trees, we can naturally think of the nodes A, B, 1,..., 6 as representing leaves, but they might also be large subtrees.The RF distance is the number of edges (=branches) that are unique to each tree (that's why it's also called the symmetric difference), and it may be normalized to one. If we highlight the unique edges on trees T1 and T2We see that the (unnormalized) RF distance is 10. For dichotomic trees, the number of unique edges is the same on both trees.The NNI distance is the minimum number of NNIs that must be applied to one tree such that it becomes equal to the other. One NNI branch swap will change exactly one edge, thus is very tempting to assume that the NNI distance can be found by looking at the distinct edges.But the problem is when the same branch is involved in more than one path of the "NNI walk". The RF distance (divided by two, for fully resolved trees) is then a lower bound on the minimum number of NNIs. In our example:The NNI distance between T1 and T2 is 6, one more than the RF distance since the edge splitting (1,2,3) and (4,5,6) is used twice in the NNI computation. The problem, as explained by Liam, is that simulating trees with a specified distance is hard, and the solution of using very large trees masks the cases where the distances disagree...Reference:Bryant D. (2004). The Splits in the Neighborhood of a Tree, Annals of Combinatorics, 8 (1) 1-11. DOI: 10.1007/s00026-004-0200-z (Crossposted from Bioinformatics News and Reviews, my personal blog)... Read more »

Bryant David. (2004) The Splits in the Neighborhood of a Tree. Annals of Combinatorics, 8(1), 1-11. DOI: 10.1007/s00026-004-0200-z  

  • January 29, 2013
  • 07:31 PM

Microstructure of Film Coated Tablets

by Axel Zeitler in Pharmaceutical Solid State Research Cluster (PSSRC)

Since 2007 when terahertz pulsed imaging (TPI) was first developed to non-destructively measure the coating thickness of pharmaceutical tablets there has been intense research in the PSSRC into how this technique can help improve the quality of pharmaceutical coatings and thus make controlled release technology based on coatings of single dosage forms attractive to industry.... Read more »

Brock, D., Zeitler, J., Funke, A., Knop, K., & Kleinebudde, P. (2012) A comparison of quality control methods for active coating processes. International Journal of Pharmaceutics, 439(1-2), 289-295. DOI: 10.1016/j.ijpharm.2012.09.021  

  • January 24, 2013
  • 04:45 AM

Storage and successful retrieval of a huge amount of data utilizing DNA strands

by Usman Paracha in SayPeople

Researchers have converted the dream of a huge amount of DNA storage and its accurate retrieval into reality.

This research has been published online in the journal Nature.

In this research, scientists have successfully stored an audio file of 26 seconds from the Martin Luther King's 1963 "I have a dream" speech on the adenine, thymine, cytosine and guanine components of synthesized DNA. Not only had this but they also stored all 154 of Shakespeare's sonnets, a digital photo of their laboratory and the famous paper of James Watson and Francis Crick about the description of double-stranded DNA on DNA. This research presented the storage of huge amount of 2.2 petabytes of data per gram of DNA.

"We already know that DNA is a robust way to store information because we can extract it from wooly mammoth bones, which date back tens of thousands of years, and make sense of it,” Dr Nick Goldman of EMBL-European Bioinformatics Institute (EMBL-EBI), said in a statement. “It’s also incredibly small, dense and does not need any power for storage, so shipping and keeping it is easy.”

Previously scientists from Harvard University reported the storage of 704 terabytes of data in a gram of DNA and the research was published in the journal Science.

Scientists, in this study, also corrected the errors on previous DNA-encoding techniques and accurately regained 100% information. In order to do this, scientists reserved one of the letters to break up the long runs of any of the other three bases.

Generalized approach to the storage of the data on DNA (Credit: Goldman et al., Nature)
DNA storage is highly anticipated because memory in DNA could be stored for thousands of years without special storage requirements such as cold, dark and/or dry. It is proposed that one gram of single-stranded DNA can store nearly 100 billion DVDs of data that can help to store a huge amount of data by large organizations such as CERN in a small place.

“We’ve created a code that's error tolerant using a molecular form we know will last in the right conditions for 10 000 years, or possibly longer,” Nick said. “As long as someone knows what the code is, you will be able to read it back if you have a machine that can read DNA.”

Although, this storage technique is highly efficient but is also very much costly.


Goldman, N., Bertone, P., Chen, S., Dessimoz, C., LeProust, E., Sipos, B., & Birney, E. (2013). Towards practical, high-capacity, low-maintenance information storage in synthesized DNA Nature DOI: 10.1038/nature11875... Read more »

  • January 23, 2013
  • 07:38 AM

Sending Odors and Tastes as an Email Attachment

by Jason Carr in Wired Cosmos

Research into cybernetic organs has been largely focused on replacements for disabled individuals who have lost a limb. Electronic noses and tongues are designed for a radically different purpose. Humans perceive different chemicals as various tastes and odors. Many types of additives are industrially manufactured to replicate certain flavors or scents. Electronic noses and tongues [...]... Read more »

  • January 22, 2013
  • 03:54 PM

These dudes figured out how to identify supposedly anonymous people whose genomes are publically available

by Sick Papes in Sick Papes

Super nasty genome hacking I CANT BELIEVE IT!!... Read more »

Gymrek M, McGuire AL, Golan D, Halperin E, & Erlich Y. (2013) Identifying personal genomes by surname inference. Science (New York, N.Y.), 339(6117), 321-4. PMID: 23329047  

  • January 22, 2013
  • 04:09 AM

ToxBank: the next generation toxicology

by egonw in Chem-bla-ics

Before I moved to my current position in Maastricht, I had the great pleasure to work with Prof. Roland Grafström (check his pathway bioinformatics done with his then PhD Rebecca) and Prof. Bengt Fadeel at the Karolinska Institutet. During this year I part-time worked on ToxBank and part-time on nano-QSAR, and worked on semantics, predictive toxicology, and Open Data. This blog post is about the ToxBank work.

I promised firework, and the first rockets are heading upwards: a key ToxBank paper has now been published in Molecular Informatics. Pekka Kohonen wrote up a nice overview of the ToxBank project, the current platform (based on RDF, REST, ISATab, and OpenTox (my archives)), and the test compounds that the SEURAT-1 cluster identified. Various bioinformatics approaches were used to visualize the diversity of the selected compounds. The idea is that the all EU FP7 projects in the SEURAT-1 cluster (consisting of six consortia) will test at least these compounds, creating a rich data set of toxicology-related data for these compounds.

As a temporary, quick solution I proposed the Semantic MediaWiki to create a semantic knowledge base, which was extensively and very productively continued by David from Leadscope. This way, we could easily list all compounds, by doing a search, rather than manually adding them:

Each compound has extensive information on the mode of action, physicochemical properties and more (such as here for acetaminophen):

All this information is available as semantic data. For example, check this link. Network and Gene Ontology analyses on these compounds have been performed, and presented in the paper, further confirming the diversity of the compound set. This leads to possible integration of their work with WikPathways and PathVisio, and I will do my best to get the right people talking to each other.

The ToxBank project further develops Open Source software for an online data warehouse for hosting experimental data on these compounds. A mix of approaches is used here to base their warehouse on, including OpenTox (RDF and REST(-like)-based), ISATab, and various ontologies.

In designing their software, they use a pretty unique approach for EU projects, based on formal requirement analyses protocols, resulting in a user-oriented platform. Now, there is much to say about who the user is, and in fact, there are multiple user types, called personas, and ToxBank takes that idea into account.

Therefore, in many ways, ToxBank is, in my humble but somewhat biased opinion, a project that leads the (predictive) toxicology community into a new era. Congratulations to the full ToxBank consortium! It was great being part of it!

Kohonen, P., Benfenati, E., Bower, D., Ceder, R., Crump, M., Cross, K., Grafström, R., Healy, L., Helma, C., Jeliazkova, N., Jeliazkov, V., Maggioni, S., Miller, S., Myatt, G., Rautenberg, M., Stacey, G., Willighagen, E., Wiseman, J., & Hardy, B. (2013). The ToxBank Data Warehouse: Supporting the Replacement of In Vivo Repeated Dose Systemic Toxicity Testing Molecular Informatics DOI: 10.1002/minf.201200114... Read more »

Kohonen, P., Benfenati, E., Bower, D., Ceder, R., Crump, M., Cross, K., Grafström, R., Healy, L., Helma, C., Jeliazkova, N.... (2013) The ToxBank Data Warehouse: Supporting the Replacement of In Vivo Repeated Dose Systemic Toxicity Testing. Molecular Informatics. DOI: 10.1002/minf.201200114  

  • January 20, 2013
  • 12:00 PM

New nanotech fiber: Robust handling, shocking performance

by Perikis Livas in Chilon

Rice University’s latest nanotechnology breakthrough was more than 10 years in the making, but it still came with a shock. Scientists from Rice, the Dutch firm Teijin Aramid, the U.S. Air Force and Israel’s Technion Institute this week unveiled a new carbon nanotube (CNT) fiber that looks and acts like textile thread and conducts electricity and heat like a metal wire. In this week’s issue of Science, the researchers describe an industrially scalable process for making the threadlike fibers, which outperform commercially available high-performance materials in a number of ways.... Read more »

Jade Boyd. (2013) New nanotech fiber: Robust handling, shocking performance. Rice University News. info:/

  • January 18, 2013
  • 09:47 AM

On "Join Papester Collective 1.0: How to reply to #icanhazpdf in 3 seconds"

by Eugenio Maria Battaglia in Science to Grok

I'm totally supporting this potential system theorized some days ago by Micah Allen and his friend Hauke on Allen's Neuroconscience blog . They discuss a quick and reliable strategy to share papers behind a paywall.
The proposed system is really easy and accessible by everyone, since it uses particular twitter's #hashtags for query and response.
I strongly believe that what started after Aaron Swartz's dead with #pdftribute, and continued with #sharecredentials (unfortunately and strangely still not so shared on twitter), and now followed by #icanhazpdf / #papester will quickly lead to a massive weaken of paywall systems. Therefore, this will push people to understand and to propose alternative ways that are more ethically correct and also apt to current science needs.... Read more »

Cook, J., & Attari, S. (2012) Paying for What Was Free: Lessons from the Paywall . Cyberpsychology, Behavior, and Social Networking, 15(12), 682-687. DOI: 10.1089/cyber.2012.0251  

  • January 17, 2013
  • 01:54 PM

How to export, delete and replace your Mendeley account and library

by Duncan Hull in O'Really?

News that Reed Elsevier is in talks to buy will have many scientists reaching for their “delete account” button. Mendeley has built an impressive user-base of scientists and other academics since they started, but the possibility of an Elsevier takeover has worried some of its users. Elsevier has a strained relationship with some groups in the scientific community [1], so it will be interesting to see how this plays out.

If you’ve built a personal library of scientific papers in Mendeley, you won’t just want to delete all the data, you’ll need to export your library first, delete your account and then import it into a different tool.

Disclaimer: I’m not advocating that you delete your account, just that if you do decide to, here’s how to do it, and some alternatives to consider.... Read more »

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