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Feb 04, 2010

Evidence for grid cells in a human memory network

Evidence for grid cells in a human memory network.

Nature. 2010 Jan 20;

Authors: Doeller CF, Barry C, Burgess N

Grid cells in the entorhinal cortex of freely moving rats provide a strikingly periodic representation of self-location which is indicative of very specific computational mechanisms. However, the existence of grid cells in humans and their distribution throughout the brain are unknown. Here we show that the preferred firing directions of directionally modulated grid cells in rat entorhinal cortex are aligned with the grids, and that the spatial organization of grid-cell firing is more strongly apparent at faster than slower running speeds. Because the grids are also aligned with each other, we predicted a macroscopic signal visible to functional magnetic resonance imaging (fMRI) in humans. We then looked for this signal as participants explored a virtual reality environment, mimicking the rats' foraging task: fMRI activation and adaptation showing a speed-modulated six-fold rotational symmetry in running direction. The signal was found in a network of entorhinal/subicular, posterior and medial parietal, lateral temporal and medial prefrontal areas. The effect was strongest in right entorhinal cortex, and the coherence of the directional signal across entorhinal cortex correlated with spatial memory performance. Our study illustrates the potential power of combining single-unit electrophysiology with fMRI in systems neuroscience. Our results provide evidence for grid-cell-like representations in humans, and implicate a specific type of neural representation in a network of regions which supports spatial cognition and also autobiographical memory.

May 06, 2009

Open Source Eye-Tracker

Via Mauro Cherubini's blog

The Gaze Group at the IT University of Copenhagen is developing an open-source eye-tracking application that will provide a low-cost alternative to commercial gaze tracking systems. The ITU Gaze Tracker is video-based and works with any videocamera or a webcam equipped with infrared nightvision

More to explore: San Agustin, J., Skovsgaard, H., Hansen, J. P., and Hansen, D. W. 2009. Low-cost gaze interaction: ready to deliver the promises. In Proceedings of the 27th international Conference Extended Abstracts on Human Factors in Computing Systems (Boston, MA, USA, April 04 - 09, 2009). CHI EA ‘09. ACM, New York, NY, 4453-4458.



Apr 20, 2009

New Science 2.0 group on Linkedin

Science 2.0 member

I have created a new group on Science 2.0 on Linkedin. The goal of the community is to connect researchers, consultants and companies and institutions interested in the impact of social media and web 2.0 tools on science and technology.

The community is growing beyond my expectations, with more than 50 professionals and researchers subscribed. I see it as a great opportunity to share news, opinions and tools in this exciting field.

If you are interested and already subscribed to Linkedin, you can join this group here

Mar 29, 2008

Nature Precedings

Nature Precedings is a place for researchers to share pre-publication research, unpublished manuscripts, presentations, posters, white papers, technical papers, supplementary findings, and other scientific documents. Submissions are screened by our professional curation team for relevance and quality, but are not subjected to peer review. Contributions range from biology and medicine (except clinical trials) to chemistry and the earth sciences.

13:08 Posted in Research tools | Permalink | Comments (0) | Tags: research tools

Mar 03, 2008

Google: Free Database Storage for Scientists

Via Medgadget

The storage will be free to scientists and access to the data will be free for all. The project, known as Palimpsest and first previewed to the scientific community at the Science Foo camp at the Googleplex last August, missed its original launch date this week, but will debut soon.

Building on the company's acquisition of the data visualization technology, Trendalyzer, from the oft-lauded, TED presenting Gapminder team, Google will also be offering algorithms for the examination and probing of the information. The new site will have YouTube-style annotating and commenting features.

The storage would fill a major need for scientists who want to openly share their data, and would allow citizen scientists access to an unprecedented amount of data to explore. For example, two planned datasets are all 120 terabytes of Hubble Space Telescope data and the images from the Archimedes Palimpsest, the 10th century manuscript that inspired the Google dataset storage project.

23:39 Posted in Research tools | Permalink | Comments (0) | Tags: research tools

Jan 14, 2008

The neuroscience of collecting

My friend and science journalist Pierangelo Garzia has written an interesting piece on the neuroscientific basis of collecting that will appear soon in the Cartier Art Magazine, "Collectors".

Here is the abstract:

Recent studies in neuroscience have demonstrated that collecting is a biological necessity even more than a psychological one. For early man collecting was a means of providing for his vital needs. For contemporary man is an important way of providing for psychological well-being.

Prehistoric man set aside the fundamental elements he needed for his survival and so do we. The refrigerator and the supermarket are the modern equivalents of cold cellars and food caches of earlier times.

Collecting is born of a basic need: survival, not only physical, but psychical well. There's not a great deal of difference between prehistoric man and urbanized third millennium beings like ourselves.


Cartier 19, 2008, Cartier Art Magazine, "Collectors" (monographic issue).

12:54 Posted in Research tools | Permalink | Comments (0) | Tags: research tools

Jul 23, 2007

Novel brain-scanning technology invented

Researchers from Siemens have developed a prototype MRI scanner that uses a lattice of small coils positioned around the head rather than large coils you lie inside. As noted in this Technology Review article, the device is likely to have important applications in functional magnetic resonance imaging (fMRI), a variation of standard MRI that tracks blood flow in the brain as an indirect measure of activity.

The technique is often used to locate the parts of the brain that control specific functions, such as speech and movement. The first clinical application for the device will likely be fMRI for neurosurgery planning, says [Siemens MR vice president] Bundy. "Surgeons want to know where speech and motor areas are when they take a tumor out- the more precise, the better."


18:50 Posted in Research tools | Permalink | Comments (0) | Tags: research tools

Jun 14, 2007

IQR simulator for large scale neural systems

Via Neurobot 

Ulysses Bernardet from the Institute of Neuroinformatics University ETH Zurich has developed IQR, an efficient graphical environment to design large-scale multi-level neuronal systems that can control real-world devices - robots in the broader sense - in real-time.

IQR has been released as open-source under GNU General Public License (GPL)

IQR neuronal simulator


16:01 Posted in Research tools | Permalink | Comments (0) | Tags: research tools

Mar 10, 2007

Scientists claim first in using brain scans to predict intentions

Via kurzweilAI.net

Researchers at Berlin's Bernstein Center for Computational Neuroscience claim they have identified people's decisions about how they would later do a high-level mental activity - in this case, adding versus subtracting. 

Read the full story 



20:13 Posted in Research tools | Permalink | Comments (0) | Tags: research tools

Feb 17, 2007

Action Video Games Sharpen Vision 20 Percent

From Medgadget

According to researchers at University of Rochester, video games that contain high levels of action, such as Unreal Tournament, can actually improve your vision:

Researchers at the University of Rochester have shown that people who played action video games for a few hours a day over the course of a month improved by about 20 percent in their ability to identify letters presented in clutter--a visual acuity test similar to ones used in regular ophthalmology clinics.

In essence, playing video game improves your bottom line on a standard eye chart...

Bavelier [Daphne Bavelier is Professor of brain and cognitive sciences at the University of Rochester --ed.] and graduate student Shawn Green tested college students who had played few, if any, video games in the last year. "That alone was pretty tough," says Green. "Nearly everybody on a campus plays video games."

At the outset, the students were given a crowding test, which measured how well they could discern the orientation of a "T" within a crowd of other distracting symbols--a sort of electronic eye chart. Students were then divided into two groups. The experimental group played Unreal Tournament, a first-person shoot-'em-up action game, for roughly an hour a day. The control group played Tetris, a game equally demanding in terms of motor control, but visually less complex.

After about a month of near-daily gaming, the Tetris players showed no improvement on the test, but the Unreal Tournament players could tell which way the "T" was pointing much more easily than they had just a month earlier.

"When people play action games, they're changing the brain's pathway responsible for visual processing," says Bavelier. "These games push the human visual system to the limits and the brain adapts to it. That learning carries over into other activities and possibly everyday life."

The improvement was seen both in the part of the visual field where video game players typically play, but also beyond--the part of your vision beyond the monitor. The students' vision improved in the center and at the periphery where they had not been "trained." That suggests that people with visual deficits, such as amblyopic patients, may also be able to gain an increase in their visual acuity with special rehabilitation software that reproduces an action game's need to identify objects very quickly.

20:58 Posted in Research tools | Permalink | Comments (0) | Tags: research tools

Brain Scan Mind Reading 70% Accurate

Via NeuroGuy 

brain-fmri 1


Researchers are making progresses in predicting the intention of subjects with reasonable accuracy:

Now researchers have been able to decode these secret intentions from patterns of their brain activity. They let subjects freely and covertly choose between two possible tasks - to either add or subtract two numbers. They were then asked to hold in mind their intention for a while until the relevant numbers were presented on a screen. The researchers were able to recognize the subjects intentions with 70% accuracy based alone on their brain activity - even before the participants had seen the numbers and had started to perform the calculation.


That quote is from a press release from the Max Planck Institute, Revealing secret intentions in the brain

20:23 Posted in Research tools | Permalink | Comments (0) | Tags: research tools

Jan 22, 2007

The mystery of consciousness

Steven Pinker, professor of psychology at Harvard University, has an article in Time magazine about the current state of understanding of consciousness.

From the article:

So neuroscientists are well on the way to identifying the neural correlates of consciousness, a part of the Easy Problem. But what about explaining how these events actually cause consciousness in the sense of inner experience--the Hard Problem?

TO APPRECIATE THE HARDNESS OF THE HARD PROBLEM, CONSIDER how you could ever know whether you see colors the same way that I do. Sure, you and I both call grass green, but perhaps you see grass as having the color that I would describe, if I were in your shoes, as purple. Or ponder whether there could be a true zombie--a being who acts just like you or me but in whom there is no self actually feeling anything. This was the crux of a Star Trek plot in which officials wanted to reverse-engineer Lieut. Commander Data, and a furious debate erupted as to whether this was merely dismantling a machine or snuffing out a sentient life.

No one knows what to do with the Hard Problem. Some people may see it as an opening to sneak the soul back in, but this just relabels the mystery of "consciousness" as the mystery of "the soul"--a word game that provides no insight.

Many philosophers, like Daniel Dennett, deny that the Hard Problem exists at all. Speculating about zombies and inverted colors is a waste of time, they say, because nothing could ever settle the issue one way or another. Anything you could do to understand consciousness--like finding out what wavelengths make people see green or how similar they say it is to blue, or what emotions they associate with it--boils down to information processing in the brain and thus gets sucked back into the Easy Problem, leaving nothing else to explain. Most people react to this argument with incredulity because it seems to deny the ultimate undeniable fact: our own experience.

The most popular attitude to the Hard Problem among neuroscientists is that it remains unsolved for now but will eventually succumb to research that chips away at the Easy Problem. Others are skeptical about this cheery optimism because none of the inroads into the Easy Problem brings a solution to the Hard Problem even a bit closer. Identifying awareness with brain physiology, they say, is a kind of "meat chauvinism" that would dogmatically deny consciousness to Lieut. Commander Data just because he doesn't have the soft tissue of a human brain. Identifying it with information processing would go too far in the other direction and grant a simple consciousness to thermostats and calculators--a leap that most people find hard to stomach. Some mavericks, like the mathematician Roger Penrose, suggest the answer might someday be found in quantum mechanics. But to my ear, this amounts to the feeling that quantum mechanics sure is weird, and consciousness sure is weird, so maybe quantum mechanics can explain consciousness.

And then there is the theory put forward by philosopher Colin McGinn that our vertigo when pondering the Hard Problem is itself a quirk of our brains. The brain is a product of evolution, and just as animal brains have their limitations, we have ours. Our brains can't hold a hundred numbers in memory, can't visualize seven-dimensional space and perhaps can't intuitively grasp why neural information processing observed from the outside should give rise to subjective experience on the inside. This is where I place my bet, though I admit that the theory could be demolished when an unborn genius--a Darwin or Einstein of consciousness--comes up with a flabbergasting new idea that suddenly makes it all clear to us.

21:55 Posted in Research tools | Permalink | Comments (0) | Tags: research tools

Jan 15, 2007

Neglect and prism adaptation: a new therapeutic tool for spatial cognition disorders

Neglect and prism adaptation: a new therapeutic tool for spatial cognition disorders.

Restor Neurol Neurosci. 2006;24(4-6):347-56

Authors: Rode G, Klos T, Courtois-Jacquin S, Rossetti Y, Pisella L

PURPOSE: A large proportion of right-hemisphere stroke patients show unilateral neglect, a neurological deficit of perception, attention, representation, and/or performing actions within their left-sided space, inducing many functional debilitating effects on everyday life, and responsible for poor functional recovery and ability to benefit from treatment. This spatial cognition disorder affects the orientation of behaviour with a shift of proprioceptive representations toward the lesion side. METHODS: This shift can be reduced after a prism adaptation period to a right lateral displacement of visual field (induced by a simple target-pointing task with base-left wedge prisms). The modification of visuo-motor or sensory-motor correspondences induced by prism adaptation involves improvement of different symptoms of neglect. RESULTS: Classical visuo-motor tests could be improved for at least 2h after adaptation, but also non-motor and non-visual tasks. In addition, cross-modal effects have been described (tactile extinction and dichotic listening), mental imagery tasks (geographic map, number bisection) and even visuo-constructive disorders. These cognitive effects are shown to result from indirect bottom-up effects of the deeper, adaptive realignment component of the reaction to prisms. Lesion studies and functional imaging data evoke a cerebello-cortical network in which each structure plays a specific role and not all structures are crucial for adaptation ability. CONCLUSIONS: These cognitive effects of prism adaptation suggest that prism adaptation does not act specifically on the ipsilesional bias characteristic of unilateral neglect but rehabilitates more generally the visuo-spatial functions attributed to the right cortical hemisphere. These results reinforce the idea that the process of prism adaptation may activate brain functions related to multisensory integration and higher spatial representations and show a generalization at a functional level. Prism adaptation therefore appears as a new powerful therapeutic tool for spatial cognition disorders.

22:55 Posted in Research tools | Permalink | Comments (0) | Tags: research tools

Jan 11, 2007

The euCognition network

thx to Giuseppe Riva

The principal goal of the euCognition network is to leverage added-value from existing work through interaction and to use this to encourage further contributions from new participants. A key objective of the network is to foster interaction between all the many different scientific sectors involved in this multi-disciplinary area and to help create truly inter-disciplinary perspectives. The network activities will cover the four key issues of:

  • Outreach

  • Scientific Outlook

  • Education

  • On-line Resources for the Community

You can get a good idea of the goals of the network and the way it works from the euCognition website

Dec 28, 2006


Via the Neuronerd 

Diigo is a social annotation service that turns the web writable allowing users to privately or publicly annotate any website they visit, thereby making a “participatory and interactive media” for its users. When you highlight a word on any page a drop down menu automatically appears (see image below) that lets you:

  • search for the highlighted words on the web with any of four search engines
  • search for highlighted terms in four social bookmarking systems
  • do a blog search for highlighted terms
  • search for your terms in the entire site you are on (Google, Yahoo, Ask site: search)
  • search for inbound links to the URL you are on in four different search engines (including Technorati and Google)
  • search for your highlighted terms in seven different verticals from local to TV to stocks.


19:48 Posted in Research tools | Permalink | Comments (0) | Tags: research tools

Dec 23, 2006

The future of research journals and peer-review

Via Medgadget

PLoS ONE - the newest journal of the Public Library of Science - is looking to completely shift the way peer-reviewed literature works:


PLoS ONE features reports of primary research from all disciplines within science and medicine. By not excluding papers on the basis of subject area, PLoS ONE facilitates the discovery of the connections between papers whether within or between disciplines.

Peer Review:

Each submission will be assessed by a member of the PLoS ONE Editorial Board before publication. This pre-publication peer review will concentrate on technical rather than subjective concerns and may involve discussion with other members of the Editorial Board and/or the solicitation of formal reports from independent referees. If published, papers will be made available for community-based open peer review involving online annotation, discussion, and rating.

Open Access:

All works published in PLoS journals are open access, licensed under the Creative Commons Attribution License. Everything is immediately available online without cost to anyone, anywhere--to read, download, redistribute, include in databases, and otherwise use--subject only to the condition that the original authorship is properly attributed. Copyright is retained by the author.


Read more

13:45 Posted in Research tools | Permalink | Comments (0) | Tags: research tools

Dec 15, 2006

The future of research journals and peer-review

via Langreiter

a commentary at the Journal of Neuroscience speculates on the future of research journals and peer-review:

Research studies appear on databases, not in journals

First, I don't think that it makes any sense to continue with paper copies of research articles. Instead of the "quasi-legal" document that is the current scientific article, we should be moving to full data being available on the web together with the software that might have been used to manipulate the data, as well as multimedia presentations to back up the data. Research papers are primarily of interest to other researchers in the same area, and they usually don't need the introduction and certainly not the discussion, which mostly degenerates to hype anyway
If an absence of peer review (or post-publication review, as I call it) is a step too far, then we should have an author (or rather funder) pays model. These fees could support a peer review mechanism, which should be open in that both authors and readers would know who was reviewing studies. It's ethically unacceptable that such important judgements should be made an unidentified judge. Like it or not, we live in a world where what is not transparent is deemed to be biased, corrupt, or incompetent until proved otherwise. Plus I believe that peer review should be a scientific discourse rather than an arbitrary judgment. This is far from radical: it's simply science returning to its roots when science was presented and discussed at meetings rather than published in journals.

Perhaps we will invent new forms of peer review by learning from innovations like Wikipedia. It is in some ways a form of peer review, only reviewers make changes directly rather than simply commenting.
Another worry from the conservative about such a system is to wonder how credit would be allocated. At present credit comes from publishing in prestigious journals. Often the impact factor of the journal (a dubious and manipulated statistic) is allocated to the paper, which is wholly unscientific because there is little correlation between the citations to studies and the impact factor of the journals in which they are published, because the impact factor of a journal is driven by a small number of highly cited studies (Seglen, 1997). In the new world I'm imagining, credit would come from the buzz from researchers and hits on the study. These hits can be disclosed in real time, unlike citations, which come years after studies are published.

00:25 Posted in Research tools | Permalink | Comments (0) | Tags: research tools

Nov 29, 2006

3D - Computer Based Pain Visualisation Tool

Via Medgadget


Researchers from Brunel University in the UK have developed a PDA-based pain recording and monitoring system:

Brunel University today unveils the World's first computer based, three-dimensional (3D) solution for pain visualisation. The tool will help patients record their own pain, as well as providing practitioners with a way to collect information on patient experience of pain and allows greater insight into the way pain travels around the body...

The innovative pain visualisation tool is displayed via a web browser as a 3D body. Users can log pain data on an easy-to-use PDA monitor at regular intervals. Pain can be classified as: burning, aching, stabbing, pins and needles and numbness with each pain type allocated a colour, which is represented on the 3D rotating tool.

The data is collected and the pain entries can be stored and replayed over an extended period as a rotating multimedia image, providing physicians with more detailed understanding of surface pain journeys.

Brunel University today unveils the World's first computer based, three-dimensional (3D) solution for pain visualisation. The tool will help patients record their own pain, as well as providing practitioners with a way to collect information on patient experience of pain and allows greater insight into the way pain travels around the body...

The innovative pain visualisation tool is displayed via a web browser as a 3D body. Users can log pain data on an easy-to-use PDA monitor at regular intervals. Pain can be classified as: burning, aching, stabbing, pins and needles and numbness with each pain type allocated a colour, which is represented on the 3D rotating tool.

The data is collected and the pain entries can be stored and replayed over an extended period as a rotating multimedia image, providing physicians with more detailed understanding of surface pain journeys.



Nov 22, 2006

Test yourself for synaesthesia

Via Mind Hacks

Synesthete.org is a website where you can test yourself for synaesthesia - the condition where senses are crossed so, for example, you might be able to taste shapes or see colours associated with specific numbers. The site is run by the Eagleman Lab at the Baylor College of Medicine.

09:26 Posted in Research tools | Permalink | Comments (0) | Tags: research tools

Nov 11, 2006

Artificial gut

Via Frontal Cortex


The New York Times reports that British scientists have built an apparatus that simulates human digestion.

From the article:

Constructed from sophisticated plastics and metals able to withstand the corrosive acids and enzymes found in the human gut, the device may ultimately help in the development of super-nutrients, such as obesity-fighting foods that could fool the stomach into thinking it is full.

''There have been lots of jam-jar models of digestion before,'' said Dr. Martin Wickham of Norwich's Institute of Food Research, the artificial gut's chief designer, referring to the beakers of enzymes typically used to approximate the chemical reactions in the stomach.

Wickham's patented artificial gut is a two-part model that is slightly larger than a desktop computer. The top half consists of a funnel in which food, stomach acids and digestive enzymes are mixed. Once this hydration process is finished, the food gets ground down in a silver metal tube encased in a dark, transparent box.

Software sets the parameters of the artificial gut - how long food remains in a particular part of the stomach, predicted hormone responses at various stages, and whether it is an infant or adult gut.


With a capacity about half the size of an actual stomach, the artificial gut can ''eat'' roughly 24 ounces of food. To date, the most substantial meal it's enjoyed is vegetable soup.

''It's so realistic that it can even vomit,'' adds Wickham.


Read the full story here

14:15 Posted in Research tools | Permalink | Comments (0) | Tags: research tools

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