Research/Publication/SC

Views

Current revision as of 06:42, 24 June 2010

System and Cognitive unit

Sang-Hun Lee, PhD, Dept. of Psychology, SNU HP

2009

* Asymmetric interaction between motion and stereopsis 23 revealed by concurrent adaptation.
[Article (PDF)]
Although contingent aftereffects between motion and stereopsis have been referred to as behavioral evidence for the joint processing of the two features, the reciprocal nature of encoding the two features has not been systematically studied. Using a novel form of concurrent adaptation, we probed the perception of direction- and disparity-de!ned coherent surfaces in parallel before and after adaptation to a stimulus that moved in a single direction at a particular binocular disparity. Contrary to earlier !ndings, we found a strong asymmetry between motion and stereopsis: the detection of disparity signal after adaptation was more impaired when the test stimulus was moving in the adapted direction than in the non-adapted direction, whereas the test disparity hardly affected the detection of coherent motion. However, motion adaptation became dependent on disparity when we added another surface that was moving in the opposite direction at the opposite sign of disparity to those of the original adaptor, as in previous studies of contingent aftereffects. The observed asymmetric contingency between motion and disparity adaptation urges the reinterpretation of previously reported contingent aftereffects and suggests a corresponding asymmetry between neural mechanisms devoted to processing of motion and stereopsis in human visual cortex.

2007

* Hierarchy of cortical responses underlying binocular rivalry.
[>Article (PDF)]
During binocular rivalry, physical stimulation is dissociated from conscious visual awareness. Human brain imaging reveals a tight linkage between the neural events in human primary visual cortex (V1) and the dynamics of perceptual waves during transitions in dominance during binocular rivalry. Here, we report results from experiments in which observers’ attention was diverted from the rival stimuli, implying that: competition between two rival stimuli involves neural circuits in V1, and attention is crucial for the consequences of this neural competition to advance to higher visual areas and promote perceptual waves.

2005

* Traveling waves of activity in primary visual cortex during binocular rivalry.
[Article (PDF)]
When the two eyes view large, dissimilar patterns that induce binocular rivalry, alternating waves of visibility arre experienced as one pattern sweeps the other out of conscious awaerness. Here we combine psychophysics with functional magnetic resonance imaging to show tight linkage between dynamics of perceptual waves during ribalry and neural events in human primary wisual cortex (V1).

Randolph Blake, PhD, Dept. of Psychology, Vanderbilt University HP

2010

[Publication list]

2009

* Periodic perturbations producing phase-locked fluctuations in visual perception. Journal of Vision, 9, 1 -12.
[Related articles]
This paper describes a novel psychophysical and analytical technique, called periodic perturbation, for creating and characterizing perceptual waves associated with transitions in visibility of a stimulus during binocular rivalry and during binocular fusion. Observers tracked rivalry within a small, central region of spatially extended rival targets while small, brief increments in contrast (“triggers”) were presented repetitively in antiphase within different regions of the two rival targets. Appropriately timed triggers produced entrainment of rivalry alternations within the central region, with the optimal timing dependent on an observer's native alternation rate. The latency between trigger and state switch increased with the distance between the location of the trigger and the central region being monitored, providing evidence for traveling waves of dominance. Traveling waves produced by periodic perturbation exhibited the same characteristics as those generated using a less efficient, more demanding discrete trial technique. We used periodic perturbation to reveal a novel relation between the dynamics associated with the spontaneous perceptual alternations and the speed of traveling waves across observers. In addition, we found evidence for traveling waves even when the events triggering them were initiated within regions of the visual field where binocular vision was stable, in the absence of binocular rivalry, implying that perceptual organization generally depends on spatio-temporal context.

* Spatial spread of interocular suppression is guided by stimulus configuration. Perception, 38, 215-231.
[PubMed]
When the two eyes view dissimilar monocular stimuli, the resulting interocular suppression can spread beyond the region of explicit stimulus conflict: portions of one rival target will disappear even though there is no competing stimulation at the corresponding location in the other eye’s view. In a series of experiments we examined whether this spread of suppression is spatially isotropic or governed by the configuration of the stimulus a portion of which is subject to suppression. Observers reported the incidence of stimulus disappearance at different locations along or nearby the contours of a large figure, part of which was suppressed by presentation of a continuous flash-suppression stimulus to a restricted region of the other eye. For all observers, suppression spread over several degrees along the contours of the figure, but tended not to spread to locations nearby but disconnected from the figure. Suppression spread effectively over a smoothly curved contour, and it spread around a sharp corner defined by two abutting contours, albeit less effectively. Suppression tended not to spread to features within the interior of a figure (a face), even if those features formed an integral part of the figure. A gap within a spatially extended stimulus arrested the spread of suppression, unless that gap appeared to arise from occlusion. Spread of suppression was unrelated to sensory eye dominance and was found with a more conventional binocular rivalry configuration, too. These findings implicate the involvement of neural circuitry in which inhibition propagates along paths of excitation beyond spatial regions of explicit interocular conflict.

Inah Lee, PhD, Dept. of Psychology, U of Iowa HP

2010

* Hippocampus is necessary for spatial discrimination using distal cue-configuration. Hippocampus.
[Article (PDF)]
The role of the hippocampus in processing contextual cues has been well recognized. Contextual manipulation often involves transferring animals between different rooms. Due to vague definition of context in such a paradigm, however, it has been difficult to study the role of the hippocampus parametrically in contextual information processing. We designed a novel task in which a different context can be parametrically defined by the spatial configuration of distal cues. In this task, rats were trained to associate two different configurations of distal cue-sets (standard contexts) with different food-well locations at the end of a radial arm. Experiment 1 tested the role of the dorsal hippocampus in retrieving well-learned associations between standard contexts and rewarding food-well locations by comparing rats with neurotoxic lesions in the dorsal hippocampus with controls. We found that the hippocampal-lesioned rats were unable to retrieve the context-place paired associations learned before surgery. To further test the role of the hippocampus in generalizing altered context, in Experiment 2, rats were trained in a task in which modified versions of the standard contexts (ambiguous contexts) were presented, intermixed with the standard contexts. Rats were able to process the ambiguous contexts immediately by using their similarities to the standard contexts, whereas muscimol inactivation of the dorsal hippocampus in the same animals reversibly deprived such capability. The results suggest that rats can effectively associate discrete spatial locations with spatial configuration of distal cues. More important, rats can generalize or orthogonalize modified contextual environments using learned contextual representation of the environment.

* Dentate gyrus is necessary for disambiguating similar object-place representations.
[Related articles] [PDF]
Objects are often remembered with their locations, which is an important aspect of event memory. Despite the well-known involvement of the hippocampus in event memory, detailed intrahippocampal mechanisms are poorly understood. In particular, no experimental evidence has been provided in support of the role of the dentate gyrus (DG) in disambiguating such events, even though computational models suggest otherwise. In the current study, rats encountered multiple objects in different locations and were required to discriminate the object-place paired associates for reward. Specifically, two different objects appeared in one of two locations (arms in a radial maze) that were relatively close to each other. Different objects were rewarded depending on the arm in which the objects appeared. The rats with colchicine-based, dorsal DG (dDG) lesions showed severe and sustained impairment in disambiguating the objects compared with controls (Experiment 1). The dDG-lesioned rats were normal, however, in discriminating four different objects presented (Experiment 2) in the same locations as in Experiment 1. Finally, when the two different objects used in Experiment 1 were presented at two remote locations (Experiment 3) involving less overlap between arm-associated contextual cues, the dDG-lesioned animals showed initial deficits in discriminating the objects, but gradually relearned the task, in contrast to the sustained deficits observed in Experiment 1. These results collectively suggest that the DG is necessary when the similarity is maximal between object-place paired associates due to overlapping object and/or spatial information, whereas its role becomes minimal as the overlap in either object or spatial information decreases.

*Perirhinal cortex is necessary for acquiring, but not for retrieving, object-place paired association.
[Related articles] [PDF]
Remembering events frequently involves associating objects and their associated locations in space, and it has been implicated that the areas associated with the hippocampus are important in this function. The current study examined the role of the perirhinal cortex in retrieving familiar object–place paired associates, as well as in acquiring novel ones. Rats were required to visit one of two locations of a radial-arm maze and choose one of the objects (from a pair of different toy objects) exclusively associated with a given arm. Excitotoxic lesions of the perirhinal cortex initially impaired the normal retrieval of object–place paired-associative memories that had been learned presurgically, but the animals relearned gradually to the level of controls. In contrast, when required to associate a novel pair of objects with the same locations of the maze, the same lesioned rats were severely impaired with minimal learning, if any, taking place throughout an extensive testing period. However, the lesioned rats were normal in discriminating two different objects presented in a fixed arm in the maze. The results suggest that the perirhinal cortex is indispensable to forming discrete representations for object–place paired associates. Its role, however, may be compensated for by other structures when familiar object–place paired associative memories need to be retrieved.

Marcus Kaiser, PhD, Complex Neural Systems, Newcastle Univ. HP

2010

* Optimal hierarchical modular topologies for producing limited sustained activation of neural networks.
[Article (PDF)]

Deviations from the average can provide valuable insights about the organization of natural systems. The present article extends this important principle to the systematic identification and analysis of singular motifs in complex networks. Six measurements quantifying different and complementary features of the connectivity around each node of a network were calculated, and multivariate statistical methods applied to identify singular nodes. The potential of the presented concepts and methodology was illustrated with respect to different types of complex real-world networks, namely the US air transportation network, the protein-protein interactions of the yeast Saccharomyces cerevisiae and the Roget thesaurus networks. The obtained singular motifs possessed unique functional roles in the networks. Three classic theoretical network models were also investigated, with the Barab´asi-Albert model resulting in singular motifs corresponding to hubs, confirming the potential of the approach. Interestingly, the number of different types of singular node motifs as well as the number of their instances were found to be considerably higher in the real-world networks than in any of the benchmark networks.

* A nonsynaptic mechanism underlying interictal discharges in human epileptic neocortex.
[Article (PDF)]

Neural connectivity at the cellular and mesoscopic level appears very specific and is presumed to arise from highly specific developmental mechanisms. However, there are general shared features of connectivity in systems as different as the networks formed by individual neurons in Caenorhabditis elegans or in rat visual cortex and the mesoscopic circuitry of cortical areas in the mouse, macaque, and human brain. In all these systems, connection length distributions have very similar shapes, with an initial large peak and a long flat tail representing the admixture of long-distance connections to mostly short-distance connections. Furthermore, not all potentially possible synapses are formed, and only a fraction of axons (called filling fraction) establish synapses with spatially neighboring neurons. We explored what aspects of these connectivity patterns can be explained simply by random axonal outgrowth. We found that random axonal growth away from the soma can already reproduce the known distance distribution of connections. We also observed that experimentally observed filling fractions can be generated by competition for available space at the target neurons—a model markedly different from previous explanations.

* Reducing influenza spreading over the airline network.
[Article (PDF)]

When calculating correlation networks from multi-electrode array (MEA) data, one works with extensive computations. Unfortunately, as the MEAs grow bigger, the time needed for the computation grows even more: calculating pair-wise correlations for current 60 channel systems can take hours on normal commodity computers whereas for future 1000 channel systems it would take almost 280 times as long, given that the number of pairs increases with the square of the number of channels. Even taking into account the increase of speed in processors, soon it can be unfeasible to compute correlations in a single computer. Parallel computing is a way to sustain reasonable calculation times in the future. We provide a general tool for rapid computation of correlation networks which was tested for: (a) a single computer cluster with 16 cores, (b) the Newcastle Condor System utilizing idle processors of university computers and (c) the inter-cluster, with 192 cores. Our reusable tool provides a simple interface for neuroscientists, automating data partition and job submission, and also allowing coding in any programming language. It is also sufficiently flexible to be used in other high-performance computing environments.

* Parallel calculation of multi-electrode array correlation networks.
[Article (PDF)]

Disease spreading through human travel networks has been a topic of great interest in recent years, such as with swine inﬂuenza or SARS pandemics. Most studies have proposed removing highly connected nodes (hubs) to control spreading. Here, we test alternative strategies using edge removal (ﬂight cancellation) for spreading over the airline network. Flight cancellation was more efﬁcient than shutting down whole airports: spreading took 81% longer if solely selected ﬂights were removed, compared to a 52% reduction when entire airports were shutdown, affecting the same number of ﬂights.

* Random outgrowth and spatial competition generate realistic connection length distributions and filling fractions.
[Article (PDF)]

Very fast oscillations (VFOs, >80 Hz) are important for physiological brain processes and, in excess, with certain epilepsies. Putative mechanisms for VFO include interneuron spiking and network activity in coupled pyramidal cell axons. It is not known whether either, or both, of these apply in pathophysiological conditions. Spontaneously occurring interictal discharges occur in human tissue in vitro, resected from neocortical epileptic foci.VFOassociated with these discharges was manifest in both field potential and, with phase delay, in excitatory synaptic inputs to fast spiking interneurons. Recruitment of somatic pyramidal cell and interneuron spiking was low, with no correlation between VFO power and synaptic inputs to principal cells. Reducing synaptic inhibition failed to affect VFO occurrence, but they were abolished by reduced gap junction conductance. These data suggest a lack of a causal role for interneurons, and favor a nonsynaptic pyramidal cell network origin for VFO in epileptic human neocortex.

* Beyond the average: detecting global singular nodes from local features in complex networks.
[Article (PDF)]

An essential requirement for the representation of functional patterns in complex neural networks, such as the mammalian cerebral cortex, is the existence of stable regimes of network activation, typically arising from a limited parameter range. In this range of limited sustained activity (LSA), the activity of neural populations in the network persists between the extremes of either quickly dying out or activating the whole network. Hierarchical modular networks were previously found to show a wider parameter range for LSA than random or small-world networks not possessing hierarchical organization or multiple modules. Here we explored how variation in the number of hierarchical levels and modules per level infl uenced network dynamics and occurrence of LSA. We tested hierarchical confi gurations of different network sizes, approximating the large-scale networks linking cortical columns in one hemisphere of the rat, cat, or macaque monkey brain. Scaling of the network size affected the number of hierarchical levels and modules in the optimal networks, also depending on whether global edge density or the numbers of connections per node were kept constant. For constant edge density, only few network confi gurations, possessing an intermediate number of levels and a large number of modules, led to a large range of LSA independent of brain size. For a constant number of node connections, there was a trend for optimal confi gurations in larger-size networks to possess a larger number of hierarchical levels or more modules. These results may help to explain the trend to greater network complexity apparent in larger brains and may indicate that this complexity is required for maintaining stable levels of neural activation.

Retrieved from "http://147.47.106.42/wiki/Research/Publication/SC"

Views

Current revision as of 06:42, 24 June 2010

System and Cognitive unit

Sang-Hun Lee, PhD, Dept. of Psychology, SNU HP

2009

2007

2005

Randolph Blake, PhD, Dept. of Psychology, Vanderbilt University HP

2010

2009

Inah Lee, PhD, Dept. of Psychology, U of Iowa HP

2010

Marcus Kaiser, PhD, Complex Neural Systems, Newcastle Univ. HP

2010

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@@ Line 63: / Line 63: @@
 perception. Journal of Vision, 9, 1 -12. </b><br>[<a
-href="http://journalofvision.org/9/2/8/" target="_blank">Related articles</a>]<br><br>
+href="http://journalofvision.org/9/2/8/" target="_blank">Related articles</a>]<br>
+This paper describes a novel psychophysical and analytical technique, called periodic perturbation, for creating and characterizing perceptual waves associated with transitions in visibility of a stimulus during binocular rivalry and during binocular fusion. Observers tracked rivalry within a small, central region of spatially extended rival targets while small, brief increments in contrast (“triggers”) were presented repetitively in antiphase within different regions of the two rival targets. Appropriately timed triggers produced entrainment of rivalry alternations within the central region, with the optimal timing dependent on an observer's native alternation rate. The latency between trigger and state switch increased with the distance between the location of the trigger and the central region being monitored, providing evidence for traveling waves of dominance. Traveling waves produced by periodic perturbation exhibited the same characteristics as those generated using a less efficient, more demanding discrete trial technique. We used periodic perturbation to reveal a novel relation between the dynamics associated with the spontaneous perceptual alternations and the speed of traveling waves across observers. In addition, we found evidence for traveling waves even when the events triggering them were initiated within regions of the visual field where binocular vision was stable, in the absence of binocular rivalry, implying that perceptual organization generally depends on spatio-temporal context. <br><br>
@@ Line 72: / Line 73: @@
 href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?
-artid=2720072" target="_blank">PubMed</a>]<br><br>
+artid=2720072" target="_blank">PubMed</a>]<br>
+When the two eyes view dissimilar monocular stimuli, the resulting interocular suppression can spread beyond the region of explicit stimulus conflict: portions of one rival target will disappear even though there is no competing stimulation at the corresponding location in the other eye’s view. In a series of experiments we examined whether this spread of suppression is spatially isotropic or governed by the configuration of the stimulus a portion of which is subject to suppression. Observers reported the incidence of stimulus disappearance at different locations along or nearby the contours of a large figure, part of which was suppressed by presentation of a continuous flash-suppression stimulus to a restricted region of the other eye. For all observers, suppression spread over several degrees along the contours of the figure, but tended not to spread to locations nearby but disconnected from the figure. Suppression spread effectively over a smoothly curved contour, and it spread around a sharp corner defined by two abutting contours, albeit less effectively. Suppression tended not to spread to features within the interior of a figure (a face), even if those features formed an integral part of the figure. A gap within a spatially extended stimulus arrested the spread of suppression, unless that gap appeared to arise from occlusion. Spread of suppression was unrelated to sensory eye dominance and was found with a more conventional binocular rivalry configuration, too. These findings implicate the involvement of neural circuitry in which inhibition propagates along paths of excitation beyond spatial regions of explicit interocular conflict.
+<br><br>
 </html>
@@ Line 88: / Line 91: @@
 cue-configuration. Hippocampus.</b><br>
-[<a href="http://bcs.snu.ac.kr/mediawiki/uploads/a/ab/Kim_Lee_HP_Text_Fig1-8.pdf" target="_blank">Article (PDF)</a>]<br><br>
+[<a href="http://bcs.snu.ac.kr/mediawiki/uploads/a/ab/Kim_Lee_HP_Text_Fig1-8.pdf" target="_blank">Article (PDF)</a>]<br>The role of the hippocampus in processing contextual cues has been well recognized. Contextual
+manipulation often involves transferring animals between different rooms. Due to vague
+definition of context in such a paradigm, however, it has been difficult to study the role of the
+hippocampus parametrically in contextual information processing. We designed a novel task in
+which a different context can be parametrically defined by the spatial configuration of distal cues.
+In this task, rats were trained to associate two different configurations of distal cue-sets (standard
+contexts) with different food-well locations at the end of a radial arm. Experiment 1 tested the
+role of the dorsal hippocampus in retrieving well-learned associations between standard contexts
+and rewarding food-well locations by comparing rats with neurotoxic lesions in the dorsal
+hippocampus with controls. We found that the hippocampal-lesioned rats were unable to retrieve
+the context-place paired associations learned before surgery. To further test the role of the
+hippocampus in generalizing altered context, in Experiment 2, rats were trained in a task in
+which modified versions of the standard contexts (ambiguous contexts) were presented,
+intermixed with the standard contexts. Rats were able to process the ambiguous contexts
+immediately by using their similarities to the standard contexts, whereas muscimol inactivation
+of the dorsal hippocampus in the same animals reversibly deprived such capability. The results
+suggest that rats can effectively associate discrete spatial locations with spatial configuration of
+distal cues. More important, rats can generalize or orthogonalize modified contextual
+environments using learned contextual representation of the environment.<br><br>
 * <b>Dentate gyrus is necessary for disambiguating similar object-place
@@ Line 95: / Line 116: @@
 [<a href="http://learnmem.cshlp.org/content/17/5/252.full.html#ref-list-1" target="_blank">Related articles</a>] [<a
-href="http://bcs.snu.ac.kr/mediawiki/uploads/6/6d/Learn._Mem.-2010-Lee-252-8%282%29.pdf" target="_blank">PDF</a>]<br><br>
+href="http://bcs.snu.ac.kr/mediawiki/uploads/6/6d/Learn._Mem.-2010-Lee-252-8%282%29.pdf" target="_blank">PDF</a>]<br>Objects are often remembered with their locations, which is an important aspect of event memory. Despite the well-known
+involvement of the hippocampus in event memory, detailed intrahippocampal mechanisms are poorly understood. In particular,
+no experimental evidence has been provided in support of the role of the dentate gyrus (DG) in disambiguating such
+events, even though computational models suggest otherwise. In the current study, rats encountered multiple objects in
+different locations and were required to discriminate the object-place paired associates for reward. Specifically, two different
+objects appeared in one of two locations (arms in a radial maze) that were relatively close to each other. Different objects
+were rewarded depending on the arm in which the objects appeared. The rats with colchicine-based, dorsal DG (dDG)
+lesions showed severe and sustained impairment in disambiguating the objects compared with controls (Experiment 1).
+The dDG-lesioned rats were normal, however, in discriminating four different objects presented (Experiment 2) in the
+same locations as in Experiment 1. Finally, when the two different objects used in Experiment 1 were presented at two
+remote locations (Experiment 3) involving less overlap between arm-associated contextual cues, the dDG-lesioned
+animals showed initial deficits in discriminating the objects, but gradually relearned the task, in contrast to the sustained
+deficits observed in Experiment 1. These results collectively suggest that the DG is necessary when the similarity is
+maximal between object-place paired associates due to overlapping object and/or spatial information, whereas its role
+becomes minimal as the overlap in either object or spatial information decreases.<br><br>
 *<b>Perirhinal cortex is necessary for acquiring, but not for retrieving,
@@ Line 102: / Line 137: @@
 [<a href="http://learnmem.cshlp.org/content/17/2/97.full.html#ref-list-1" target="_blank">Related articles</a>] [<a
-href="http://bcs.snu.ac.kr/mediawiki/uploads/1/10/Jo_%26_Lee_L%26M_2010.pdf" target="_blank">PDF</a>]<br><br>
+href="http://bcs.snu.ac.kr/mediawiki/uploads/1/10/Jo_%26_Lee_L%26M_2010.pdf" target="_blank">PDF</a>]<br>Remembering events frequently involves associating objects and their associated locations in space, and it has been implicated
+that the areas associated with the hippocampus are important in this function. The current study examined the role of the
+perirhinal cortex in retrieving familiar object–place paired associates, as well as in acquiring novel ones. Rats were required to
+visit one of two locations of a radial-arm maze and choose one of the objects (from a pair of different toy objects) exclusively
+associated with a given arm. Excitotoxic lesions of the perirhinal cortex initially impaired the normal retrieval of object–place
+paired-associative memories that had been learned presurgically, but the animals relearned gradually to the level of controls.
+In contrast, when required to associate a novel pair of objects with the same locations of the maze, the same lesioned rats were
+severely impaired with minimal learning, if any, taking place throughout an extensive testing period. However, the lesioned
+rats were normal in discriminating two different objects presented in a fixed arm in the maze. The results suggest that the
+perirhinal cortex is indispensable to forming discrete representations for object–place paired associates. Its role, however,
+may be compensated for by other structures when familiar object–place paired associative memories need to be retrieved.<br>  <br>
 </html>
@@ Line 121: / Line 166: @@
 ('pubs/Kaiser2010Frontiers.pdf');" href="http://www.biological-networks.org/pubs/Kaiser2010Frontiers.pdf"
-target="_blank">Article (PDF)</a>]</p><br><br>
+target="_blank">Article (PDF)</a>]</p><br>Deviations from the average can provide valuable insights about the organization
+of natural systems. The present article extends this important principle to the systematic
+identification and analysis of singular motifs in complex networks. Six measurements quantifying
+different and complementary features of the connectivity around each node of a network were
+calculated, and multivariate statistical methods applied to identify singular nodes. The potential of
+the presented concepts and methodology was illustrated with respect to different types of complex
+real-world networks, namely the US air transportation network, the protein-protein interactions
+of the yeast Saccharomyces cerevisiae and the Roget thesaurus networks. The obtained singular
+motifs possessed unique functional roles in the networks. Three classic theoretical network models
+were also investigated, with the Barab´asi-Albert model resulting in singular motifs corresponding
+to hubs, confirming the potential of the approach. Interestingly, the number of different types of
+singular node motifs as well as the number of their instances were found to be considerably higher
+in the real-world networks than in any of the benchmark networks.<br><br>
 * <b> A nonsynaptic mechanism underlying interictal discharges in
@@ Line 130: / Line 187: @@
 href="http://www.biological-networks.org/pubs/Roopun2010PNAS.pdf" target="_blank">Article (PDF)</a>]
-</p><br><br>
+</p><br>Neural connectivity at the cellular and mesoscopic level appears very
+specific and is presumed to arise from highly specific developmental
+mechanisms. However, there are general shared features of
+connectivity in systems as different as the networks formed by
+individual neurons in Caenorhabditis elegans or in rat visual cortex
+and the mesoscopic circuitry of cortical areas in the mouse,
+macaque, and human brain. In all these systems, connection length
+distributions have very similar shapes, with an initial large peak and
+a long flat tail representing the admixture of long-distance
+connections to mostly short-distance connections. Furthermore, not
+all potentially possible synapses are formed, and only a fraction of
+axons (called filling fraction) establish synapses with spatially
+neighboring neurons. We explored what aspects of these connectivity
+patterns can be explained simply by random axonal outgrowth.
+We found that random axonal growth away from the soma can
+already reproduce the known distance distribution of connections.
+We also observed that experimentally observed filling fractions
+can be generated by competition for available space at the
+target neurons—a model markedly different from previous explanations.
+<br><br>
 * <b>Reducing influenza spreading over the airline network.</b><br>
@@ Line 139: / Line 215: @@
 href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2762335/"
-target="_blank">Article (PDF)</a>]</p><br><br>
+target="_blank">Article (PDF)</a>]</p><br>When calculating correlation networks from multi-electrode array (MEA) data, one works with extensive
+computations. Unfortunately, as the MEAs grow bigger, the time needed for the computation grows
+even more: calculating pair-wise correlations for current 60 channel systems can take hours on normal
+commodity computers whereas for future 1000 channel systems it would take almost 280 times as long,
+given that the number of pairs increases with the square of the number of channels. Even taking into
+account the increase of speed in processors, soon it can be unfeasible to compute correlations in a single
+computer. Parallel computing is a way to sustain reasonable calculation times in the future. We provide
+a general tool for rapid computation of correlation networks which was tested for: (a) a single computer
+cluster with 16 cores, (b) the Newcastle Condor System utilizing idle processors of university computers
+and (c) the inter-cluster, with 192 cores. Our reusable tool provides a simple interface for neuroscientists,
+automating data partition and job submission, and also allowing coding in any programming language.
+It is also sufficiently flexible to be used in other high-performance computing environments.<br><br>
 * <b>Parallel calculation of multi-electrode array correlation networks.
@@ Line 146: / Line 233: @@
 ('pubs/Ribeiro2009.PDF');" href="http://www.biological-networks.org/pubs/Ribeiro2009.PDF"
-target="_blank">Article (PDF)</a>]</p><br><br>
+target="_blank">Article (PDF)</a>]</p><br>Disease spreading through human travel networks has been a topic of great interest in recent years, such as with swine inﬂuenza or SARS pandemics.
+Most studies have proposed removing highly connected nodes (hubs) to control spreading. Here, we test alternative strategies using edge removal (ﬂight cancellation) for spreading over the airline network. Flight cancellation was more efﬁcient than shutting down whole airports: spreading took 81% longer if solely selected ﬂights were removed, compared to a 52% reduction when entire airports were shutdown, affecting the same number of ﬂights.<br><br>
 * <b>Random outgrowth and spatial competition generate realistic
@@ Line 156: / Line 244: @@
 ('pubs/Kaiser2009CerCor.pdf');" href="http://www.biological-networks.org/pubs/Kaiser2009CerCor.pdf"
-target="_blank">Article (PDF)</a>]</p><br><br>
+target="_blank">Article (PDF)</a>]</p><br>Very fast oscillations (VFOs, >80 Hz) are important for physiological
+brain processes and, in excess, with certain epilepsies. Putative
+mechanisms for VFO include interneuron spiking and network activity
+in coupled pyramidal cell axons. It is not known whether either,
+or both, of these apply in pathophysiological conditions.
+Spontaneously occurring interictal discharges occur in human tissue
+in vitro, resected from neocortical epileptic foci.VFOassociated with
+these discharges was manifest in both field potential and, with
+phase delay, in excitatory synaptic inputs to fast spiking interneurons.
+Recruitment of somatic pyramidal cell and interneuron spiking
+was low, with no correlation between VFO power and synaptic inputs
+to principal cells. Reducing synaptic inhibition failed to affect
+VFO occurrence, but they were abolished by reduced gap junction
+conductance. These data suggest a lack of a causal role for interneurons,
+and favor a nonsynaptic pyramidal cell network origin for
+VFO in epileptic human neocortex.<br><br>
 * <b> Beyond the average: detecting global singular nodes from local
@@ Line 166: / Line 269: @@
 href="http://www.biological-networks.org/pubs/Costa2009EPL.PDF" target="_blank">Article (PDF)</a>]
-</p><br><br>
+</p><br>An essential requirement for the representation of functional patterns in complex neural
+networks, such as the mammalian cerebral cortex, is the existence of stable regimes of network
+activation, typically arising from a limited parameter range. In this range of limited sustained
+activity (LSA), the activity of neural populations in the network persists between the extremes
+of either quickly dying out or activating the whole network. Hierarchical modular networks
+were previously found to show a wider parameter range for LSA than random or small-world
+networks not possessing hierarchical organization or multiple modules. Here we explored
+how variation in the number of hierarchical levels and modules per level infl uenced network
+dynamics and occurrence of LSA. We tested hierarchical confi gurations of different network
+sizes, approximating the large-scale networks linking cortical columns in one hemisphere of
+the rat, cat, or macaque monkey brain. Scaling of the network size affected the number of
+hierarchical levels and modules in the optimal networks, also depending on whether global
+edge density or the numbers of connections per node were kept constant. For constant edge
+density, only few network confi gurations, possessing an intermediate number of levels and a
+large number of modules, led to a large range of LSA independent of brain size. For a constant
+number of node connections, there was a trend for optimal confi gurations in larger-size networks
+to possess a larger number of hierarchical levels or more modules. These results may help to
+explain the trend to greater network complexity apparent in larger brains and may indicate that
+this complexity is required for maintaining stable levels of neural activation.<br><br>
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