Parsimony,Exhaustivity and Balanced Detection in Neocortex

The layout of sensory brain areas is thought to subtend perception. The principles shaping these architectures and their role in information processing are still poorly understood. We investigate mathematically and computationally the representation of orientation and spatial frequency in cat primary visual cortex. We prove that two natural principles, local exhaustivity and parsimony of representation, would constrain the orientation and spatial frequency maps to display a very specific pinwheel-dipole singularity. This is particularly interesting since recent experimental evidences show a dipolar structures of the spatial frequency map co-localized with pinwheels in cat. These structures have important properties on information processing capabilities. In particular, we show using a computational model of visual information processing that this architecture allows a trade-off in the local detection of orientation and spatial frequency, but this property occurs for spatial frequency selectivity sharper than reported in the literature. We validated this sharpening on high-resolution optical imaging experimental data. These results shed new light on the principles at play in the emergence of functional architecture of cortical maps, as well as their potential role in processing information.     

The effect of chronic deafferentation on mental imagery: a case study

Visual- and motor imagery rely primarily on perceptual and motor processes, respectively. In healthy controls, the type of imagery used to solve a task depends on personal preference, task instruction, and task properties. But how does the chronic loss of proprioceptive and tactile sensory inputs from the body periphery influence mental imagery? In a unique case study, we investigated the imagery capabilities of the chronically deafferented patient IW when he was performing a mental rotation task. We found that IW''s motor imagery processes were impaired and that visual imagery processes were enhanced compared to controls. These results suggest that kinaesthetic afferent signals from the body periphery play a crucial role in enabling and maintaining central sensorimotor representations and hence the ability to incorporate kinaesthetic information into the imagery processes.     

Effects of shear rate and suspending viscosity on deformation and frequency of red blood cells tank-treading in shear flows

The tank-treading rotation of red blood cells (RBCs) in shear flows has been studied extensively with experimental, analytical, and numerical methods. Even for this relatively simple system, complicated motion and deformation behaviors have been observed, and some of the underlying mechanisms are still not well understood. In this study, we attempt to advance our knowledge of the relationship among cell motion, deformation, and flow situations with a numerical model. Our simulation results agree well with experimental data, and confirm the experimental finding of the decrease in frequency/shear-rate ratio with shear rate and the increase of frequency with suspending viscosity. Moreover, based on the detailed information from our simulations, we are able to interpret the frequency dependency on shear rate and suspending viscosity using a simple two-fluid shear model. The information obtained in this study thus is useful for understanding experimental observations of RBCs in shear and other flow situations; the good agreement to experimental measurements also shows the potential usefulness of our model for providing reliable results for microscopic blood flows.     

Biophysical models of ciliary activity: Gaussian frequency distributions

A model of a freely rotating exended scatterer is proposed to describe light scattering from beating cilia. Gaussian rotation frequency distributions, characterized by a mean angular frequency and a standard deviation, are introduced in order to simulate intensity autocorrelation functions and to fit the model to experimental data. Thus the ciliary beats are characterized by a mean beat frequency and a standard deviation of the beat frequency distribution. The standard deviation influences the damping of the intensity autocorrelation function of light scattered from cilia. The calculated intensity autocorrelation function shows a more prominent oscillating behaviour the smaller the standard deviation of the beat frequency. The validity of the model is supported by experimental data in two ways: 1) The model fits very well to experimental data in computer evaluations, 2) Neither the model nor information obtained from measurements are dependent on the measuring angle.The contents were presented in part at the 9th International Biophysics Congress in Jerusalem, Israel, August 23–28, 1987 Offprint requests to: P. Thyberg     

Learning to produce predicted static handgrip forces

The objective of this study was to prove the hypothesis that kinaesthetic sensations, without visual or verbal guidance, give sufficient information to produce predictive handgrip forces. The ability of 70 girls and 70 boys aged 11 to 17 years to produce predicted static handgrip force was examined. The subjects were requested to produce 50% of their individual maximum handgrip force and maintain it for 2 seconds without visual control. Ten trials were done first by the right-hand and then by the left-hand. The maximum grip strength increased parallel with age, but significant differences were found between both the right and the left-hand, and the genders. Close correlations were found between the desired and the exerted forces. The differences between the desired forces and the exerted forces produced by the fifth trials were significantly smaller than that of the first trials. The verbal information about each exerted force contributed to the learning with right-hand since it caused a further decrease in the difference between the desired force and the exerted force. In contrast, the learning with left-hand was not enhanced by verbal feedback. These results suggest that kinaesthetic feedback information from the hand plays an effective role in learning to produce predicted grip strengths without visual and verbal information.     

Increasing confidence in vergence as a cue to distance

Multiple cues contribute to the visual perception of an object's distance from the observer. The manner in which the nervous system combines these various cues is of considerable interest. Although it is accepted that image cues play a significant role in distance perception, controversy exists regarding the use of kinaesthetic information about the eyes' state of convergence. We used a perturbation technique to explore the contribution of vergence to visually based distance estimates as a function of both fixation distance and the availability of retinal information. Our results show that the nervous system increases the weighting given to vergence as (i) fixation distance becomes closer; and (ii) the available retinal image cues decrease. We also identified the presence of a strong contraction bias when distance cues were studied in isolation, but we argue that such biases do not suggest that vergence provides an ineffectual signal for near-space perception.     

A lock-and-key model for protein-protein interactions

MOTIVATION: Protein-protein interaction networks are one of the major post-genomic data sources available to molecular biologists. They provide a comprehensive view of the global interaction structure of an organism's proteome, as well as detailed information on specific interactions. Here we suggest a physical model of protein interactions that can be used to extract additional information at an intermediate level: It enables us to identify proteins which share biological interaction motifs, and also to identify potentially missing or spurious interactions. RESULTS: Our new graph model explains observed interactions between proteins by an underlying interaction of complementary binding domains (lock-and-key model). This leads to a novel graph-theoretical algorithm to identify bipartite subgraphs within protein-protein interaction networks where the underlying data are taken from yeast two-hybrid experimental results. By testing on synthetic data, we demonstrate that under certain modelling assumptions, the algorithm will return correct domain information about each protein in the network. Tests on data from various model organisms show that the local and global patterns predicted by the model are indeed found in experimental data. Using functional and protein structure annotations, we show that bipartite subnetworks can be identified that correspond to biologically relevant interaction motifs. Some of these are novel and we discuss an example involving SH3 domains from the Saccharomyces cerevisiae interactome. AVAILABILITY: The algorithm (in Matlab format) is available (see http://www.maths.strath.ac.uk/~aas96106/lock_key.html).     

An NMR-based scoring function improves the accuracy of binding pose predictions by docking by two orders of magnitude

Low-affinity ligands can be efficiently optimized into high-affinity drug leads by structure based drug design when atomic-resolution structural information on the protein/ligand complexes is available. In this work we show that the use of a few, easily obtainable, experimental restraints improves the accuracy of the docking experiments by two orders of magnitude. The experimental data are measured in nuclear magnetic resonance spectra and consist of protein-mediated NOEs between two competitively binding ligands. The methodology can be widely applied as the data are readily obtained for low-affinity ligands in the presence of non-labelled receptor at low concentration. The experimental inter-ligand NOEs are efficiently used to filter and rank complex model structures that have been pre-selected by docking protocols. This approach dramatically reduces the degeneracy and inaccuracy of the chosen model in docking experiments, is robust with respect to inaccuracy of the structural model used to represent the free receptor and is suitable for high-throughput docking campaigns.     

The role of kinaesthetic feedback in goal-directed movements

The purpose of this study was to investigate the role of kinaesthetic feedback in the control of goal-directed movements. The subjects were qualified basketball and handball players compared to weightlifters as controls. The body measures and the general motor tests verified fit physical condition of the subjects, and detected no sign that would disturb the execution of special motor tests. The special motor tests were free-throw shootings with basketball to the basket, free shootings with handball to a rectangular frame, zigzag dribbling with basketball to 14 m among traffic cones 2 m apart, and stopping at a mark after running to 10 m. These tests were performed both with open eyes and closed eyes. The results of all special motor tests decreased significantly in the lack of visual information. Furthermore, in contrast to the significantly different results obtained from the three different groups with open eyes, these groups produced equally minor results with closed eyes. It is concluded that the practice of goal-directed movement, learned under visual guidance, does not make the kinaesthetic feedback able to compensate the lack of visual input.     

Simulation of the hippocampal theta rhythm

Centre of Theoretical and Computational Neuroscience, University of Plymouth, UK Basing on the hypothesis about the mechanisms of the theta rhythm generation, the article presents mathematical and computational models of theta activity in the hippocampus. The problem of the theta rhythm modeling is nontrivial because the slow theta oscillations (about 5 Hz) should be generated by a neural system composed of frequently firing neural populations. We studied a model of neural pacemakers in the septum. In this model, the pacemaker follows the frequency of the external signal if this frequency does not deviate too far from the natural frequency of the pacemaker, otherwise the pacemaker returns to the frequency of its own oscillations. These results are in agreement with the experimental records of medial septum neurons. Our model of the septal pacemaker of the theta rhythm is based on the hypothesis that the hippocampal theta appears as a result of the influence of the assemblies of neurons in the medial septum which are under control of pacemaker neurons. Though the model of the pacemaker satisfies many experimental facts, the synchronization of activity in different neural assemblies of the model is not as strong as it should be. Another model of the theta generation is based on the anatomical data about the existence of the inhibitory GABAergic loop between the medial septum and the hippocampus. This model shows stable oscillations at the frequency of the theta rhythm in a broad range of parameter values. It also provides explanation to the experimental data about the variation of the frequency and the amplitude of the theta rhythm under different external stimulations of the system. The role of the theta rhythm for information processing in the hippocampus is discussed.     

Methodology for predicting oxygen transport on an intravenous membrane oxygenator combining computational and analytical models

A computational methodology for accurately predicting flow and oxygen-transport characteristics and performance of an intravenous membrane oxygenator (IMO) device is developed, tested, and validated. This methodology uses extensive numerical simulations of three-dimensional computational models to determine flow-mixing characteristics and oxygen-transfer performance, and analytical models to indirectly validate numerical predictions with experimental data, using both blood and water as working fluids. Direct numerical simulations for IMO stationary and pulsating balloons predict flow field and oxygen transport performance in response to changes in the device length, number of and balloon pulsation frequency. Multifiber models are used to investigate interfiber interference and length effects for a stationary balloon whereas a single fiber model is used to analyze the effect of balloon pulsations on velocity and oxygen concentration fields and to evaluate oxygen transfer rates. An analytical lumped model is developed and validated by comparing its numerical predictions with experimental data. Numerical results demonstrate that oxygen transfer rates for a stationary balloon regime decrease with increasing number of fibers, independent of the fluid type. The oxygen transfer rate ratio obtained with blood and water is approximately two. Balloon pulsations show an effective and enhanced flow mixing, with time-dependent recirculating flows around the fibers regions which induce higher oxygen transfer rates. The mass transfer rates increase approximately 100% and 80%, with water and blood, respectively, compared with stationary balloon operation. Calculations with combinations of frequency, number of fibers, fiber length and diameter, and inlet volumetric flow rates, agree well with the reported experimental results, and provide a solid comparative base for analysis, predictions, and comparisons with numerical and experimental data.     

面孔分类中空间高低频表征的神经机制：一个颅内脑电研究

来自多方面的研究表明,面孔的分类和识别位于特定脑区．同时,已有行为实验研究表明,图像的空间高低频特征在面孔分类的不同范畴中起不同的贡献,例如身份更多被低频信号传递,性别被高低频共同传递,而表情更多被高频传递．然而,空间频率在面孔分类中的贡献,其表征和神经机制目前相关研究很少．利用特定癫痫患者植入颅内电极的监控期,呈现不同类型面孔图像,同时记录其颅内脑电,用事件相关电位方法考察了据认为是面孔特定成分的相关电位的潜伏期在170 ms的波形(N170波形)的变化;用电极反应显著性分析考察了空间频率在不同分类特征上的贡献．结果表明,空间高频(HSF)图像的N170潜伏期显著延迟．只呈现空间低频(LSF)图像,N170的潜伏期对普通人面孔会延迟,而对熟悉的名人则没有这个差异．女性面孔诱发的N170在HSF条件下潜伏期明显晚于LSF条件,而男性面孔诱发的波形则不存在这个差异．表情在N170上没有体现出任何差异．但是基于电极的显著性分析表明,有更多的额叶电极参与了表情的加工;身份特征加工有更多电极在空间低频上表现出差异,而性别加工则空间高低频比较平衡．与以往行为结果不同的是,表情加工也有更多低频贡献,而且表情的差异可以在早达114 ms的时候就发生．这符合表情信息在颞枕区域有一个快速基本加工,再传递到其他脑区的认知模型．因此,空间高低频信息在身份和性别上的贡献,可能发生在经典的面孔加工脑区,由N170表达,表情信息不由N170表达,而是在颞枕较广泛的范围内快速加工再传递到别的脑区,如额叶．这是首次利用颅内脑电就空间频率在面孔分类中的贡献的神经机制进行研究,为深入理解脑内面孔各种特征加工的动态过程提供了一个新的切入点．     

Allele frequency‐free inference of close familial relationships from genotypes or low‐depth sequencing data

Knowledge of how individuals are related is important in many areas of research, and numerous methods for inferring pairwise relatedness from genetic data have been developed. However, the majority of these methods were not developed for situations where data are limited. Specifically, most methods rely on the availability of population allele frequencies, the relative genomic position of variants and accurate genotype data. But in studies of non‐model organisms or ancient samples, such data are not always available. Motivated by this, we present a new method for pairwise relatedness inference, which requires neither allele frequency information nor information on genomic position. Furthermore, it can be applied not only to accurate genotype data but also to low‐depth sequencing data from which genotypes cannot be accurately called. We evaluate it using data from a range of human populations and show that it can be used to infer close familial relationships with a similar accuracy as a widely used method that relies on population allele frequencies. Additionally, we show that our method is robust to SNP ascertainment and applicable to low‐depth sequencing data generated using different strategies, including resequencing and RADseq, which is important for application to a diverse range of populations and species.     

Motility analysis of circularly swimming bull spermatozoa by quasi-elastic light scattering and cinematography.

The Rayleigh-Gans-Debye approximation is used to predict the electric field autocorrelation functions of light scattered from circularly swimming bull spermatozoa. Using parameters determined from cinematography and modeling the cells as coated ellipsoids of semiaxes a = 0.5 micrometers, b = 2.3 micrometers, and c = 9.0 micrometers, we were able to obtain model spectra that mimic the data exactly. A coat is found to be a necessary attribute of the particle. It is also clear that these model functions at 15 degrees may be represented by the relatively simple function used before by Hallett et al. (1978) to fit data from circularly swimming cells, thus giving some physical meaning to these functional shapes. Because of this agreement the half-widths of experimental functions can now be interpreted in terms of an oscillatory frequency for the movement of the circularly swimming cell. The cinematographic results show a trend to chaotic behavior as the temperature of the sample is increased, with concomitant decrease in overall efficiency. This is manifested by a decrease in oscillatory frequency and translational speed.     

Parameter estimation from experimental laboratory data of HSV-1 by using alternative regression method

In this paper, an estimation of model parameters is performed by using the Alternative Regression (AR) approach on an experimental data set of Herpes Simplex Virus type-1 (HSV-1) infection with innate immune response. Throughout the specified course of time, the measurements of monocytes, neutrophils, and viral load were obtained from the corneas of infected mice. C57BL/6 (B6) mice were used at Oakland University, Department of Biological Sciences, and the outcome measurements were divided into training and testing data sets. The HSV-1 nonlinear dynamic model is proposed based on the observed data patterns and biological system information. The simulation results of the proposed model showed that they consistently fit the experimental data set. In addition, the sensitivity test and model validation diagnostics are considered to determine the most significant key parameters that affect the dynamics of the HSV-1 system.     

Bioelectrical parameters of the whole human body obtained through bioelectrical impedance analysis

Knowledge of electrical properties of body tissues across the frequency spectrum is useful for tissue characterization. The bioelectric impedance analysis method, operating from 1 to 250 kHz (multi-frequency), was used in 23 normal male human subjects between the ages of 21 and 52 years, for estimation of their bioelectrical parameters. Amplitude of the output current was set to 800 microA(RMS). The experimental data showed that bioelectric parameters were highly dependent on frequency and the presence of a threshold frequency around 4 kHz. In order to explain the unusual features observed in our experimental data, the human body was simulated through the Cole-Fricke-Cole model (RC circuit) and the Extended Cole-Fricke-Cole model (RLC circuit). The simulated data showed that the Extended Cole-Fricke-Cole model had a higher accuracy than the traditional Cole-Fricke-Cole model. These results suggest that the unusual features could be due to the possible existence of inductive effects in biological cells and body tissues and that the inductive parameter and the threshold frequency could be used for characterizing the healthy tissues as well as the traditional bioelectric parameters.     

Profiting from pilot studies: Analysing mortality using Bayesian models with informative priors

Pilot studies are often used to help design ecological studies. Ideally the pilot data are incorporated into the full-scale study data, but if the pilot study's results indicate a need for major changes to experimental design, then pooling pilot and full-scale study data is difficult. The default position is to disregard the preliminary data. But ignoring pilot study data after a more comprehensive study has been completed forgoes statistical power or costs more by sampling additional data equivalent to the pilot study's sample size. With Bayesian methods, pilot study data can be used as an informative prior for a model built from the full-scale study dataset. We demonstrate a Bayesian method for recovering information from otherwise unusable pilot study data with a case study on eucalypt seedling mortality. A pilot study of eucalypt tree seedling mortality was conducted in southeastern Australia in 2005. A larger study with a modified design was conducted the following year. The two datasets differed substantially, so they could not easily be combined. Posterior estimates from pilot dataset model parameters were used to inform a model for the second larger dataset. Model checking indicated that incorporating prior information maintained the predictive capacity of the model with respect to the training data. Importantly, adding prior information improved model accuracy in predicting a validation dataset. Adding prior information increased the precision and the effective sample size for estimating the average mortality rate. We recommend that practitioners move away from the default position of discarding pilot study data when they are incompatible with the form of their full-scale studies. More generally, we recommend that ecologists should use informative priors more frequently to reap the benefits of the additional data.     

The impact of using related individuals for haplotype reconstruction in population studies

Recent studies have highlighted the dangers of using haplotypes reconstructed directly from population data for a fine-scale mapping analysis. Family data may help resolve ambiguity, yet can be costly to obtain. This study is concerned with the following question: How much family data (if any) should be used to facilitate haplotype reconstruction in a population study? We conduct a simulation study to evaluate how changes in family information can affect the accuracy of haplotype frequency estimates and phase reconstruction. To reconstruct haplotypes, we introduce an EM-based algorithm that can efficiently accommodate unrelated individuals, parent-child trios, and arbitrarily large half-sib pedigrees. Simulations are conducted for a diverse set of haplotype frequency distributions, all of which have been previously published in empirical studies. A wide variety of important results regarding the effectiveness of using pedigree data in a population study are presented in a coherent, unified framework. Insight into the different properties of the haplotype frequency distribution that can influence experimental design is provided. We show that a preliminary estimate of the haplotype frequency distribution can be valuable in large population studies with fixed resources.     

Ageing effects on path integration and landmark navigation

Navigation abilities show marked decline in both normal ageing and dementia. Path integration may be particularly affected, as it is supported by the hippocampus and entorhinal cortex, both of which show severe degeneration with ageing. Age differences in path integration based on kinaesthetic and vestibular cues have been clearly demonstrated, but very little research has focused on visual path integration, based only on optic flow. Path integration is complemented by landmark navigation, which may also show age differences, but has not been well studied either. Here we present a study using several simple virtual navigation tasks to explore age differences in path integration both with and without landmark information. We report that, within a virtual environment that provided only optic flow information, older participants exhibited deficits in path integration in terms of distance reproduction, rotation reproduction, and triangle completion. We also report age differences in triangle completion within an environment that provided landmark information. In all tasks, we observed a more restricted range of responses in the older participants, which we discuss in terms of a leaky integrator model, as older participants showed greater leak than younger participants. Our findings begin to explain the mechanisms underlying age differences in path integration, and thus contribute to an understanding of the substantial decline in navigation abilities observed in ageing.     

Efficient parameter estimation for spatio-temporal models of pattern formation: case study of Drosophila melanogaster

MOTIVATION: Diffusable and non-diffusable gene products play a major role in body plan formation. A quantitative understanding of the spatio-temporal patterns formed in body plan formation, by using simulation models is an important addition to experimental observation. The inverse modelling approach consists of describing the body plan formation by a rule-based model, and fitting the model parameters to real observed data. In body plan formation, the data are usually obtained from fluorescent immunohistochemistry or in situ hybridizations. Inferring model parameters by comparing such data to those from simulation is a major computational bottleneck. An important aspect in this process is the choice of method used for parameter estimation. When no information on parameters is available, parameter estimation is mostly done by means of heuristic algorithms. RESULTS: We show that parameter estimation for pattern formation models can be efficiently performed using an evolution strategy (ES). As a case study we use a quantitative spatio-temporal model of the regulatory network for early development in Drosophila melanogaster. In order to estimate the parameters, the simulated results are compared to a time series of gene products involved in the network obtained with immunohistochemistry. We demonstrate that a (mu,lambda)-ES can be used to find good quality solutions in the parameter estimation. We also show that an ES with multiple populations is 5-140 times as fast as parallel simulated annealing for this case study, and that combining ES with a local search results in an efficient parameter estimation method.