Distributed processing and temporal codes in neuronal networks

The cerebral cortex presents itself as a distributed dynamical system with the characteristics of a small world network. The neuronal correlates of cognitive and executive processes often appear to consist of the coordinated activity of large assemblies of widely distributed neurons. These features require mechanisms for the selective routing of signals across densely interconnected networks, the flexible and context dependent binding of neuronal groups into functionally coherent assemblies and the task and attention dependent integration of subsystems. In order to implement these mechanisms, it is proposed that neuronal responses should convey two orthogonal messages in parallel. They should indicate (1) the presence of the feature to which they are tuned and (2) with which other neurons (specific target cells or members of a coherent assembly) they are communicating. The first message is encoded in the discharge frequency of the neurons (rate code) and it is proposed that the second message is contained in the precise timing relationships between individual spikes of distributed neurons (temporal code). It is further proposed that these precise timing relations are established either by the timing of external events (stimulus locking) or by internal timing mechanisms. The latter are assumed to consist of an oscillatory modulation of neuronal responses in different frequency bands that cover a broad frequency range from <2 Hz (delta) to >40 Hz (gamma) and ripples. These oscillations limit the communication of cells to short temporal windows whereby the duration of these windows decreases with oscillation frequency. Thus, by varying the phase relationship between oscillating groups, networks of functionally cooperating neurons can be flexibly configurated within hard wired networks. Moreover, by synchronizing the spikes emitted by neuronal populations, the saliency of their responses can be enhanced due to the coincidence sensitivity of receiving neurons in very much the same way as can be achieved by increasing the discharge rate. Experimental evidence will be reviewed in support of the coexistence of rate and temporal codes. Evidence will also be provided that disturbances of temporal coding mechanisms are likely to be one of the pathophysiological mechanisms in schizophrenia. This article was part of LNCS 5286 (2008), Maria Marinaro, Silvia Scarpetta, Yoko Yamaguchi (eds.), “Dynamic Brain—from Neural Spikes to Behaviors, 12th International Summer School on Neural Networks Erice, Italy, December 2007 Revised Lectures” and summarized some of the putative functions of temporal codes resulting either from the timing of external events (feed forward/bottom up) or from internal timing mechanisms (top down). For comprehensive reviews of the theoretical prerequisites of synchronization in these processes see Yamaguchi and Shimizu (1994) and Shimizu et al. (1985).     

Robustness of neural codes and its implication on natural image processing

In this study, based on the view of statistical inference, we investigate the robustness of neural codes, i.e., the sensitivity of neural responses to noise, and its implication on the construction of neural coding. We first identify the key factors that influence the sensitivity of neural responses, and find that the overlap between neural receptive fields plays a critical role. We then construct a robust coding scheme, which enforces the neural responses not only to encode external inputs well, but also to have small variability. Based on this scheme, we find that the optimal basis functions for encoding natural images resemble the receptive fields of simple cells in the striate cortex. We also apply this scheme to identify the important features in the representation of face images and Chinese characters.

A neuronal network for the logic of Limax learning

We construct a neuronal network to model the logic of associative conditioning as revealed in experimental results using the terrestrial mollusk Limax maximus. We show, in particular, how blocking to a previously conditioned stimulus in the presence of the unconditional stimulus, can emerge as a dynamical property of the network. We also propose experiments to test the new model. Action Editor: G. Bard Ermentrout     

A model for the neuronal substrate of dead reckoning and memory in arthropods: a comparative computational and behavioral study

Returning to the point of departure after exploring the environment is a key capability for most animals. In the absence of landmarks, this task will be solved by integrating direction and distance traveled over time. This is referred to as path integration or dead reckoning. An important question is how the nervous systems of navigating animals such as the 1 mm³ brain of ants can integrate local information in order to make global decision. In this article we propose a neurobiologically plausible system of storing and retrieving direction and distance information. The path memory of our model builds on the well established concept of population codes, moreover our system does not rely on trigonometric functions or other complex non-linear operations such as multiplication, but only uses biologically plausible operations such as integration and thresholding. We test our model in two paradigms; in the first paradigm the system receives input from a simulated compass, in the second paradigm, the model is tested against behavioral data recorded from 17 ants. We were able to show that our path memory system was able to reliably encode and compute the angle of the vector pointing to the start location, and that the system stores the total length of the trajectory in a dependable way. From the structure and behavior of our model, we derive testable predictions both at the level of observable behavior as well as on the anatomy and physiology of its underlying neuronal substrate.     

Flexible and scalable genotyping-by-sequencing strategies for population studies

Background

Many areas critical to agricultural production and research, such as the breeding and trait mapping in plants and livestock, require robust and scalable genotyping platforms. Genotyping-by-sequencing (GBS) is a one such method highly suited to non-human organisms. In the GBS protocol, genomic DNA is fractionated via restriction digest, then reduced representation is achieved through size selection. Since many restriction sites are conserved across a species, the sequenced portion of the genome is highly consistent within a population. This makes the GBS protocol highly suited for experiments that require surveying large numbers of markers within a population, such as those involving genetic mapping, breeding, and population genomics. We have modified the GBS technology in a number of ways. Custom, enzyme specific adaptors have been replaced with standard Illumina adaptors compatible with blunt-end restriction enzymes. Multiplexing is achieved through a dual barcoding system, and bead-based library preparation protocols allows for in-solution size selection and eliminates the need for columns and gels.

Results

A panel of eight restriction enzymes was selected for testing on B73 maize and Nipponbare rice genomic DNA. Quality of the data was demonstrated by identifying that the vast majority of reads from each enzyme aligned to restriction sites predicted in silico. The link between enzyme parameters and experimental outcome was demonstrated by showing that the sequenced portion of the genome was adaptable by selecting enzymes based on motif length, complexity, and methylation sensitivity. The utility of the new GBS protocol was demonstrated by correctly mapping several in a maize F₂ population resulting from a B73 × Country Gentleman test cross.

Conclusions

This technology is readily adaptable to different genomes, highly amenable to multiplexing and compatible with over forty commercially available restriction enzymes. These advancements represent a major improvement in genotyping technology by providing a highly flexible and scalable GBS that is readily implemented for studies on genome-wide variation.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-979) contains supplementary material, which is available to authorized users.     

Temporal codes and sparse representations: A key to understanding rapid processing in the visual system

Where neural information processing is concerned, there is no debate about the fact that spikes are the basic currency for transmitting information between neurons. How the brain actually uses them to encode information remains more controversial. It is commonly assumed that neuronal firing rate is the key variable, but the speed with which images can be analysed by the visual system poses a major challenge for rate-based approaches. We will thus expose here the possibility that the brain makes use of the spatio-temporal structure of spike patterns to encode information. We then consider how such rapid selective neural responses can be generated rapidly through spike-timing-dependent plasticity (STDP) and how these selectivities can be used for visual representation and recognition. Finally, we show how temporal codes and sparse representations may very well arise one from another and explain some of the remarkable features of processing in the visual system.     

Neural population representation hypothesis of visual flow and its illusory after effect in the brain: psychophysics,neurophysiology and computational approaches

The neural representation of motion aftereffects induced by various visual flows (translational, rotational, motion-in-depth, and translational transparent flows) was studied under the hypothesis that the imbalances in discharge activities would occur in favor in the direction opposite to the adapting stimulation in the monkey MST cells (cells in the medial superior temporal area) which can discriminate the mode (i.e., translational, rotational, or motion-in-depth) of the given flow. In single-unit recording experiments conducted on anaesthetized monkeys, we found that the rate of spontaneous discharge and the sensitivity to a test stimulus moving in the preferred direction decreased after receiving an adapting stimulation moving in the preferred direction, whereas they increased after receiving an adapting stimulation moving in the null direction. To consistently explain the bidirectional perception of a transparent visual flow and its unidirectional motion aftereffect by the same hypothesis, we need to assume the existence of two subtypes of MST D cells which show directionally selective responses to a translational flow: component cells and integration cells. Our physiological investigation revealed that the MST D cells could be divided into two types: one responded to a transparent flow by two peaks at the instances when the direction of one of the component flow matched the preferred direction of the cell, and the other responded by a single peak at the instance when the direction of the integrated motion matched the preferred direction. In psychophysical experiments on human subjects, we found evidence for the existence of component and integration representations in the human brain. To explain the different motion perceptions, i.e., two transparent flows during presentation of the flows and a single flow in the opposite direction to the integrated flows after stopping the flow stimuli, we suggest that the pattern-discrimination system can select the motion representation that is consistent with the perception of the pattern from two motion representations. We discuss the computational aspects related to the integration of component motion fields.     

In vivo approach to the cellular mechanisms for sensory processing in sleep and wakefulness

1. The present review analyzes sensory processing during sleep and wakefulness from a single neuronal viewpoint. Our premises are that processing changes throughout the sleep–wakefulness cycle may be at least partially evidenced in single neurons by (a) changes in the phase locking of the response to the hippocampal theta rhythm, (b) changes in the discharge rate and firing pattern of the response to sound, and (c) changes in the effects of the neurotransmitters involved in the afferent and efferent pathways.2. The first part of our report is based on the hypothesis that the encoding of sensory information needs a timer in order to be processed and stored, and that the hippocampal theta rhythm could contribute to the temporal organization. We have demonstrated that the guinea pig's auditory and visual neuronal discharge exhibits a temporal relationship (phase locking) to the hippocampal theta waves during wakefulness and sleep phases.3. The concept that the neural network organization during sleep versus wakefulness is different and can be modulated by sensory signals and vice versa, and that the sensory input may be influenced by the CNS state, i.e., asleep or awake, is introduced. During sleep the evoked firing of auditory units increases, decreases, or remains similar to that observed during quiet wakefulness. However, there has been no auditory unit yet that stops firing as the guinea pig enters sleep. Approximately half of the cortical neurons studied did not change firing rate when passing into sleep while others increased or decreased. Thus, the system is continuously aware of the environment. We postulate that those neurons that changed their evoked firing during sleep are also related to still unknown sleep processes.4. Excitatory amino acid neurotransmitters participate in the synaptic transmission of the afferent and efferent pathways in the auditory system. In the inferior colliculus, however, the effects of glutamate's mediating the response to sound and the efferent excitation evoked by cortical stimulation failed to show differences in sleep and wakefulness.5. Considering that neonates and also infants spend most of the time asleep, the continuous arrival of sensory information to the brain during both sleep phases may serve to sculpt the brain by activity-dependent mechanisms of neural development, as has been postulated for wakefulness.     

Estimating prehistoric American Indian population size for united states area: Implications of the nineteenth century population decline and nadir

Implications of a revised United States American Indian nadir population and the pattern of decline leading to it are examined. Substituting the new nadir for that used by Dobyns (1966) lowers by several million his estimates of Indian population for the United States (and Canada) area. These estimates then become more compatible with ones currently being suggested by other scholars. The nineteenth century decline leading to this nadir is found to be remarkably linear. Assuming linearity in decline from initial European contact through the eighteenth century, an aboriginal population estimate of 1,845,183 for the United States area may be extrapolated, along with estimates for intervening years. The nineteenth century decline is then graphed with the data extrapolated to 1492. The resulting pattern of population decline is quite different from the ones suggested by Mooney (1928) and Dobyns (1966).     

Timing and structural consideration for the processing of mitochondrial matrix space proteins by the mitochondrial processing peptidase (MPP)

Most mitochondrial matrix space proteins are synthesized as a precursor protein, and the N-terminal extension of amino acids that served as the leader sequence is removed after import by the action of a metalloprotease called mitochondrial processing peptidase (MPP). The crystal structure of MPP has been solved very recently, and it has been shown that synthetic leader peptides bind with MPP in an extended conformation. However, it is not known how MPP recognizes hundreds of leader peptides with different primary and secondary structures or when during import the leader is removed. Here we took advantage of the fact that the structure of the leader from rat liver aldehyde dehydrogenase has been determined by 2D-NMR to possess two helical portions separated by a three amino acid (RGP) linker. When the linker was deleted, the leader formed one long continuous helix that can target a protein to the matrix space but is not removed by the action of MPP. Repeats of two and three leaders were fused to the precursor protein to determine the stage of import at which processing occurs, if MPP could function as an endo peptidase, and if it would process if the cleavage site was part of a helix. Native or linker deleted constructs were used. Import into isolated yeast mitochondria or processing with recombinantly expressed MPP was performed. It was concluded that processing did not occur as the precursor was just entering the matrix space, but most likely coincided with the folding of the protein. Further, finding that hydrolysis could not take place if the processing site was part of a stable helix is consistent with the crystal structure of MPP. Lastly, it was found that MPP could function at sites as far as 108 residues from the N terminus of the precursor protein, but its ability to process decreases exponentially as the distance increases.     

Influence of the interstimulus interval on temporal processing and learning: testing the state-dependent network model

The ability to determine the interval and duration of sensory events is fundamental to most forms of sensory processing, including speech and music perception. Recent experimental data support the notion that different mechanisms underlie temporal processing in the subsecond and suprasecond range. Here, we examine the predictions of one class of subsecond timing models: state-dependent networks. We establish that the interval between the comparison and the test interval, interstimulus interval (ISI), in a two-interval forced-choice discrimination task, alters the accuracy of interval discrimination but not the point of subjective equality—i.e. while timing was impaired, subjective time contraction or expansion was not observed. We also examined whether the deficit in temporal processing produced by short ISIs can be reduced by learning, and determined the generalization patterns. These results show that training subjects on a task using a short or long ISI produces dramatically different generalization patterns, suggesting different forms of perceptual learning are being engaged. Together, our results are consistent with the notion that timing in the range of hundreds of milliseconds is local as opposed to centralized, and that rapid stimulus presentation rates impair temporal discrimination. This interference is, however, decreased if the stimuli are presented to different sensory channels.     

Application of an image and environmental sensor network for automated greenhouse insect pest monitoring

This work presents an automated insect pest counting and environmental condition monitoring system using integrated camera modules and an embedded system as the sensor node in a wireless sensor network. The sensor node can be used to simultaneously acquire images of sticky paper traps and measure temperature, humidity, and light intensity levels in a greenhouse. An image processing algorithm was applied to automatically detect and count insect pests on an insect sticky trap with 93% average temporal detection accuracy compared with manual counting. The integrated monitoring system was implemented with multiple sensor nodes in a greenhouse and experiments were performed to test the system’s performance. Experimental results show that the automatic counting of the monitoring system is comparable with manual counting, and the insect pest count information can be continuously and effectively recorded. Information on insect pest concentrations were further analyzed temporally and spatially with environmental factors. Analyses of experimental data reveal that the normalized hourly increase in the insect pest count appears to be associated with the change in light intensity, temperature, and relative humidity. With the proposed system, laborious manual counting can be circumvented and timely assessment of insect pest and environmental information can be achieved. The system also offers an efficient tool for long-term insect pest behavior observations, as well as for practical applications in integrated pest management (IPM).     

Limit theorems for the population size of a birth and death process allowing catastrophes

The linear birth and death process with catastrophes is formulated as a right continuous random walk on the non-negative integers which evolves in continuous time with an instantaneous jump rate proportional to the current value of the process. It is shown that distributions of the population size can be represented in terms of those of a certain Markov branching process. The ergodic theory of Markov branching process transition probabilities is then used to develop a fairly complete understanding of the behaviour of the population size of the birth-death-catastrophe process.Research done while on leave at Colorado State University from the University of Western Australia and partially supported by N.S.F. grant DMS-8501763     

CCK processing by pituitary GH3 cells, human teratocarcinoma cells NT2 and hNT differentiated human neuronal cells evidence for a differentiation-induced change in enzyme expression and pro CCK processing

Human teratocarcinoma Ntera2/c 1.D1 (NT2) cells express very low levels of the prohormone convertase enzyme PC1, moderate levels of PC2 and significant levels of PC5. When infected with an adenovirus which expresses rat CCK mRNA, several glycine-extended forms were secreted that co-eluted with CCK 33, 22 and 12. Amidated CCK is not produced because these cells appear to lack the amidating enzyme. Pituitary GH3 cells express high levels of PC2 and PC5. CCK adenovirus-infected GH3 cells secrete amidated versions of the same peptides as NT2 cells. Differentiation of NT2 cells into hNT cells with retinoic acid and mitotic inhibitors increased expression of PC5 and decreased expression of PCI and PC2. CCK adenovirus-infected differentiated hNT cells also secrete glycine extended CCK products and the major molecular form produced co-eluted with CCK 8 Gly. These experiments demonstrate that the state of differentiation of this neuronal cell line influences its expression of PC 1,2, and 5 and its cleavage of pro CCK and suggests that these cells may make an interesting model to study how differentiation alters prohormone processing. These results also support the hypothesis that PC5 in differentiated neuronal cells is capable of processing pro CCK to glycine-extended CCK 8.     

Molecular and neuronal mechanisms for amino acid taste perception in the Drosophila labellum

1. Download : Download high-res image (179KB)
2. Download : Download full-size image

     

Extinction risk assessments at the population and species level: implications for amphibian conservation

Amphibian populations are declining worldwide and this is causing growing concern. High levels of population declines followed by the expansion of red lists are creating demands for effective strategies to maximize conservation efforts for amphibians. Ideally, integrated and comprehensive strategies should be based on complementary information of population and species extinction risk. Here we evaluate the congruence between amphibian extinction risk assessments at the population level (Declining Amphibian Database––DAPTF) and at species level (GAA––IUCN Red List). We used the Declining Amphibian Database––DAPTF that covers 967 time-series records of amphibian population declines assigned into four levels of declines. We assigned each of its corresponding species into GAA––IUCN red list status, discriminated each species developmental mode, and obtained their geographic range size as well. Extinction risk assessments at the population and species level do not fully coincide across geographic realms or countries. In Paleartic, Neartic and Indo-Malayan realms less than 25% of species with reported population declines are formally classified as threatened. In contrast, more than 60% of all species with reported population declines that occur in Australasia and the Neotropics are indeed threatened according to the GAA––IUCN Red List. Species with aquatic development presented proportionally higher extinction risks at both population and species level than those with terrestrial development, being this pattern more prominent at Australasia, Paleartic, and Neartic realms. Central American countries, Venezuela, Mexico and Australia presented the highest congruence between both population and species risk. We address that amphibian conservation strategies could be improved by using complementary information on time-series population trends and species threat. Whenever feasible, conservation assessments should also include life-history traits in order to improve its effectiveness.     

On the reproductive value and the spectrum of a population projection matrix with implications for dynamic population models

The eigenvalues of a population projection matrix-except for the Lotka coefficient-are uniquely determined by the reproductive values and the survival. This relation (proposed earlier, but not really well known in western literature) follows from another useful relation between fertility, reproductive values, survival, and Lotka’s coefficient. These results are applied to provide demographic interpretations to the intrinsically dynamic and metastable population models by Schoen and co-workers.     

Evaluating the effectiveness of overstory cover as a surrogate for bird community diversity and population trends

Landscape features are often used as surrogates for biodiversity. While landscape features may perform well as surrogates for coarse metrics of biodiversity such as species richness, their value for monitoring population trends in individual species is virtually unexplored. We compared the performance of a proposed habitat surrogate for birds, percentage cover of vegetation overstory, for two distinct aspects of bird assemblages: community diversity (i.e. species richness) and population trends. We used four different long-term studies of open woodland habitats to test the consistency of the relationship between overstory percentage cover and bird species richness across a large spatial extent (>1000 km) in Australia. We then identified twelve bird species with long-term time-series data to test the relationship between change in overstory cover and populations trends. We found percentage cover performed consistently as a surrogate for species richness in three of the four sites. However, there was no clear pattern in the performance of change in percentage cover as a surrogate for population trends. Four bird species exhibited a significant relationship with change in percentage overstory cover in one study, but this was not found across multiple studies. These results demonstrate a lack of consistency in the relationship between change in overstory cover and population trends among bird species, both within and between geographic regions. Our study demonstrates that biodiversity surrogates representing community-level metrics may be consistent across regions, but provide only limited information about individual species population trends. Understanding the limitations of the information provided by a biodiversity surrogate can inform the appropriate context for its application.     

An in situ probe for on-line monitoring of cell density and viability on the basis of dark field microscopy in conjunction with image processing and supervised machine learning

Fermentation industries would benefit from on-line monitoring of important parameters describing cell growth such as cell density and viability during fermentation processes. For this purpose, an in situ probe has been developed, which utilizes a dark field illumination unit to obtain high contrast images with an integrated CCD camera. To test the probe, brewer's yeast Saccharomyces cerevisiae is chosen as the target microorganism. Images of the yeast cells in the bioreactors are captured, processed, and analyzed automatically by means of mechatronics, image processing, and machine learning. Two support vector machine based classifiers are used for separating cells from background, and for distinguishing live from dead cells afterwards. The evaluation of the in situ experiments showed strong correlation between results obtained by the probe and those by widely accepted standard methods. Thus, the in situ probe has been proved to be a feasible device for on-line monitoring of both cell density and viability with high accuracy and stability.