At the Edge of Chaos: How Cerebellar Granular Layer Network Dynamics Can Provide the Basis for Temporal Filters

Models of the cerebellar microcircuit often assume that input signals from the mossy-fibers are expanded and recoded to provide a foundation from which the Purkinje cells can synthesize output filters to implement specific input-signal transformations. Details of this process are however unclear. While previous work has shown that recurrent granule cell inhibition could in principle generate a wide variety of random outputs suitable for coding signal onsets, the more general application for temporally varying signals has yet to be demonstrated. Here we show for the first time that using a mechanism very similar to reservoir computing enables random neuronal networks in the granule cell layer to provide the necessary signal separation and extension from which Purkinje cells could construct basis filters of various time-constants. The main requirement for this is that the network operates in a state of criticality close to the edge of random chaotic behavior. We further show that the lack of recurrent excitation in the granular layer as commonly required in traditional reservoir networks can be circumvented by considering other inherent granular layer features such as inverted input signals or mGluR2 inhibition of Golgi cells. Other properties that facilitate filter construction are direct mossy fiber excitation of Golgi cells, variability of synaptic weights or input signals and output-feedback via the nucleocortical pathway. Our findings are well supported by previous experimental and theoretical work and will help to bridge the gap between system-level models and detailed models of the granular layer network.     

Polarized signal classification by complex and quaternionic multi-layer perceptrons

For polarized signals, which arise in many application fields, a statistical framework in terms of quaternionic random processes is proposed. Based on it, the ability of real-, complex- and quaternionic-valued multi-layer perceptrons (MLPs) of performing classification tasks for such signals is evaluated. For the multi-dimensional neural networks the relevance of class label representations is discussed. For signal to noise separation it is shown that the quaternionic MLP yields an optimal solution. Results on the classification of two different polarized signals are also reported.     

A fast fixed-point algorithm for independent component analysis of complex valued signals

Separation of complex valued signals is a frequently arising problem in signal processing. For example, separation of convolutively mixed source signals involves computations on complex valued signals. In this article, it is assumed that the original, complex valued source signals are mutually statistically independent, and the problem is solved by the independent component analysis (ICA) model. ICA is a statistical method for transforming an observed multidimensional random vector into components that are mutually as independent as possible. In this article, a fast fixed-point type algorithm that is capable of separating complex valued, linearly mixed source signals is presented and its computational efficiency is shown by simulations. Also, the local consistency of the estimator given by the algorithm is proved.     

Differential coding of humoral stimuli by timing and amplitude of intracellular calcium spike trains

The ubiquitous Ca2(+)-phosphoinositide pathway transduces extracellular signals to cellular effectors. Using a mathematical model, we simulated intracellular Ca2+ fluctuations in hepatocytes upon humoral stimulation. We estimated the information encoded about random humoral stimuli in these Ca2+ spike trains using an information-theoretic approach based on stimulus estimation methods. We demonstrate accurate transfer of information about random humoral signals with low temporal cutoff frequencies. In contrast, our results suggest that high-frequency stimuli are poorly transduced by the transmembrane machinery. We found that humoral signals are encoded in both the timing and amplitude of intracellular Ca2+ spikes. The information transmitted per spike is similar to that of sensory neuronal systems, in spite of several orders of magnitude difference in firing rate.     

Closed-loop control of muscle length through motor unit recruitment in load-moving conditions

Neuroprostheses aimed at restoring lost movement in the limbs of spinal cord injured individuals are being developed in this laboratory. As part of this program, we have designed a digital proportional-integral-derivative controller integrated with a stimulation system which effects recruitment of motor units according to the size principle. This system is intended to control muscle length while shortening against fixed loads. Feline sciatic nerves were exposed and stimulated with ramp, triangular, sinusoidal, staircase and random signals as test inputs. Changes in muscle length and effective time delay under different conditions were measured and analyzed. Differences of tracking quality between open- and closed-loop conditions were examined through analysis of variance as well as the differences between small (250g) and large (1kg) loads. The results showed that parameters used to compare muscle length output to the input signals were dramatically improved in the closed-loop trials as compared to the open-loop condition. Mean squared correlation coefficients between input and output signals for ramp signals increased by 0.019, and for triangular signals by 0.12. Mean peak cross correlation between input and output signals for sinusoidal waveforms increased by 0.06, with decreases in time to peak cross correlation (effective time delay) from 195 to 38ms. In slow random signals (power up to 0.5Hz), peak cross correlation went from 0.74 to 0.89, and time-to-peak cross correlation decreased from 205 to 55ms. In fast random signals (power up to 1Hz), peak cross correlation went from 0.82 to 0.89, and time-to-peak cross correlation from 200 to 65ms. For staircase signals, both rise times and mean steady-state errors decreased. It was found that, once the length range was set, the load weight had no effect on tracking performance. Analysis of mean square error demonstrated that for all signals tested, the feedback decreased the tracking error significantly, whereas, again, load had no effect. The results suggest that tracking is vastly improved by using a closed-loop system to control muscle length, and that load does not affect the quality of signal tracking as measured by standard control system analysis methods.     

A family of quasi-white random signals and its optimal use in biological system identification

A new family of random test signals that can be used in biological system identification is introduced. These signals approximate the statistical properties of white noise. Their use in connection with the crosscorrelation technique provides several advantages over the quasi-white test signals that have been used so far. The most important advantages are their easy generation and their effective error analysis that allows the optimal determination of the test parameters.     

A Flattest Constrained Envelope Approach for Empirical Mode Decomposition

Empirical mode decomposition (EMD) is an adaptive method for nonlinear, non-stationary signal analysis. However, the upper and lower envelopes fitted by cubic spline interpolation (CSI) may often occur overshoots. In this paper, a new envelope fitting method based on the flattest constrained interpolation is proposed. The proposed method effectively integrates the difference between extremes into the cost function, and applies a chaos particle swarm optimization method to optimize the derivatives of the interpolation nodes. The proposed method was tested on three different types of data: ascertain signal, random signals and real electrocardiogram signals. The experimental results show that: (1) The proposed flattest envelope effectively solves the overshoots caused by CSI method and the artificial bends caused by piecewise parabola interpolation (PPI) method. (2) The index of orthogonality of the intrinsic mode functions (IMFs) based on the proposed method is 0.04054, 0.02222±0.01468 and 0.04013±0.03953 for the ascertain signal, random signals and electrocardiogram signals, respectively, which is lower than the CSI method and the PPI method, and means the IMFs are more orthogonal. (3) The index of energy conversation of the IMFs based on the proposed method is 0.96193, 0.93501±0.03290 and 0.93041±0.00429 for the ascertain signal, random signals and electrocardiogram signals, respectively, which is closer to 1 than the other two methods and indicates the total energy deviation amongst the components is smaller. (4) The comparisons of the Hilbert spectrums show that the proposed method overcomes the mode mixing problems very well, and make the instantaneous frequency more physically meaningful.     

The distributed representation of vestibulo-oculomotor signals by brain-stem neurons

The vestibuloocular reflex and other oculomotor functions are subserved by populations of neurons operating in parallel. This distributed aspect of the system's organization has been largely ignored in previous block diagram models. Neurons that transmit oculomotor signals, such as those in the vestibular nucleus (VN), actually combine the different types of signals in a diverse, seemingly random way that could not be predicted from a block diagram. We used the backpropagation learning algorithm to program distributed neural-network models of the vestibulo-oculomotor system. Networks were trained to combine vestibular, pursuit and saccadic eye velocity command signals. The model neurons in these neural networks have diverse combinations of vestibulo-oculomotor signals that are qualitatively similar to those reported for actual VN neurons in the monkey. This similarity implicates a learning mechanism as an organizing influence on the vestibulo-oculomotor system and demonstrates how VN neurons can encode vestibulo-oculomotor signals in a diverse, distributed manner.     

Temporally fluctuating selection of sex-limited signaling traits in the Texas field cricket,Gryllus texensis

Abstract.— Gryllus texensis males produce acoustic mating signals and display extensive heritable variation in when and how much time they spend signaling throughout the night. The goal of this research is to elucidate the potential mechanism responsible for maintaining this heritable variation. Mating signals attract female crickets. In low-density spring populations females select males that signal most often; in high-density fall populations mating appears random with respect to signaling time. Mating signals also inadvertently attract acoustically orienting parasitoid flies; parasitoids are prevalent during the first half of the evening in the fall mating season. I hypothesized that mating signals are influenced by sex-limited temporally fluctuating selection. I predicted how mating signals would respond to this pattern of cyclical selection a priori, and then measured the sexual characters over four successive generations. I provide correlative evidence that mating signals appear to respond to sex-limited temporally fluctuating selection. These results indicate that sex-limited temporally fluctuating selection may play a role in the maintenance of variation in these sexual characters.     

Autonomous DNA replication in human cells is affected by the size and the source of the DNA.

We previously developed short-term and long-term assays for autonomous replication of DNA in human cells. This study addresses the requirements for replication in these assays. Sixty-two random human genomic fragments ranging in size from 1 to 21 kb were cloned in a prokaryotic vector and tested for their replication ability in the short-term assay. We found a positive correlation between replication strength and fragment length, indicating that large size is favored for efficient autonomous replication in human cells. All large fragments replicated efficiently, suggesting that signals which can direct the initiation of DNA replication in human cells are either very abundant or have a low degree of sequence specificity. Similar results were obtained in the long-term assay. We also used the same assays to test in human cells a random series of fragments derived from Escherichia coli chromosomal DNA. The bacterial fragments supported replication less efficiently than the human fragments in the short-term and long-term assays. This result suggests that while the sequence signals involved in replication in human cells are found frequently in human DNA, they are uncommon in bacterial DNA.     

Fluid mechanosensory stimulation of behaviour from a planktonic marine copepod, Euchaeta rimana Bradford

This research provides the first reported thresholds for thebehavioural response of an individual planktonic copepod. Usinga novel technique to create near-field fluid disturbances, wedirected microlitre volumes of water towards the antennularysetae. In response to an increasing strength of this purelymechanical signal, the animal varied its behaviour from a rapidflick to a capture response and finally an escape reaction.This work provides a basis for addressing the criteria copepodsuse to interpret biologically generated signals to elicit anappropriate behavioural response and offers insight into howthese signals are differentiated from the random fluid motionin their environment.     

A new method for evaluation of cavitation near mechanical heart valves

Evaluation of cavitation in vivo is often based on recordings of high-pass filtered random high-frequency pressure fluctuations. We hypothesized that cavitation signal components are more appropriately assessed by a new method for extraction of random signal components of the pressure signals. We investigated three different valve types and found a high correlation between the two methods (r2: 0.8806-0.9887). The new method showed that the cavitation signal could be extracted without a priori knowledge needed for setting the high-pass filter cut off frequency, nor did it introduce bandwidth limitation of the cavitation signal.     

A screen of random sequences for those that alter the trafficking of the influenza virus hemagglutinin in vivo

In order to determine if the sequence patterns known to specify internalization represent the majority of possible internalization signals, we identified random sequences capable of causing a reporter protein to be internalized at least several-fold faster than the rate of non-selective internalization of membrane by clathrin-coated pits. A library of influenza hemagglutinin (HA) proteins, bearing short random sequences in place of the wild-type cytoplasmic domain, was prepared in recombinant SV40 virus. The library was expressed and screened for HAs that could internalize anti-HA antibody from the medium. The cytoplasmic sequences of the selected proteins were determined. From a small sample of sequences, we detected several that did not resemble those previously identified. The known internalization signals must represent only a subset of the sequences that can serve as internalization signals.     

Probabilistic reinforcement and neurotic breakdown in unrestrained dogs]

The substitution of a constant reinforcement for a random one with a probability of 0.5 in experiments on two dogs with a simple motor stereotype was attended with nervous breakdowns with motor excitation, inadequate orienting reactions or passive-defensive behaviour. The change in the probability of reinforcement from 0.5 to 0.3 had a positive effect in experiments on one dog, while in the other it developed drowsiness. In two other dogs with a complicated stereotype, the change in the mode of reinforcement was attended with a peculiar preventive effect of probabilistic, but ordered reinforcement in experimental surroundings, including signals with a probabilistic random reinforcement as well. In this case the dogs displayed primarily signs of emotional stress only. Behaviour was somewhat disturbed in one animal only when testing signals with a probabilistic random reinforcement.     

Automatic computer control of fermentation processes

The application of an optimization algorithm to fermentation processes is described, which is based on information received by means of cascading the input quantities with pseudo random binary signals. The results in optimization of temperature, pH-value as well as productivity are presented and discussed.     

Optimization of phage-immobilized ELISA for autoantibody profiling in human sera

Phage libraries displaying cDNA or random peptides have been used for profiling autoantibodies in cancer. The detection of autoantibodies in human sera using phages displaying specific epitopes is usually performed by phage-immobilized ELISAs which can detect specific antibodies without identification of whole antigens. However, these ELISAs can give feeble detection signals that are indistinguishable from background signals which are caused by human sera. To improve the usefulness of phage ELISA for human sera, the conditions for each step in phage ELISA were optimized. The antigenicity of phage antigens was maximal when using coating buffer of neutral pH. By using protein-free blocking buffer and pre-adsorbing human sera with phage host cell ER2738 extracts significantly decreased non-specific signals. Finally, when these conditions were applied to phage ELISA using K10P1, the values of the negative controls were concentrated near cutoff values, which made the assay more reliable. The optimized phage ELISA conditions described here would increase the efficacy of detection specific autoantibodies in human sera.     

The uniqueness of protein sequences: molecular territoriality

The number of tripeptides which do not occur and which occur only a small number of times in the existing data bank of protein sequences is much larger than that expected on the basis of random selection (from Monte Carlo analyses). Forty tripeptides are not found in the data bank of 289 500 amino acids while the value expected on the basis of random selection is 8.0 +/- 3.1. Seventy-one tripeptides occur only once with an expected value of 37.1 +/- 6.1. These results suggest that some peptides not found in certain species are reserved for use only in other species. The proposal is made that small peptides serve as species specific markers and function as signals in the recognition process for activation of the immune response.     

LOMA: A fast method to generate efficient tagged-random primers despite amplification bias of random PCR on pathogens

Background  

Pathogen detection using DNA microarrays has the potential to become a fast and comprehensive diagnostics tool. However, since pathogen detection chips currently utilize random primers rather than specific primers for the RT-PCR step, bias inherent in random PCR amplification becomes a serious problem that causes large inaccuracies in hybridization signals.