Comparison of models and lattice-gas simulations for Liesegang patterns

For more than a century Liesegang patterns – self-organized, quasi-periodic structures occurring in diffusion-limited chemical reactions with two components – have been attracting scientists. The pattern formation can be described by four basic empirical laws. In addition to many experiments, several models have been devised to understand the formation of the bands and rings. Here we review the most important models and complement them with detailed three-dimensional lattice-gas simulations. We show how the mean-field predictions can be reconciled with experimental data by a redefinition of the distances suggested by our lattice-gas simulations.     

How to quantify deterministic and random influences on the statistics of the foreign exchange market

It is shown that price changes of the U.S. dollar-German mark exchange rates upon different delay times can be regarded as a stochastic Marcovian process. Furthermore, we show how Kramers-Moyal coefficients can be estimated from the empirical data. Finally, we present an explicit Fokker-Planck equation which models very precisely the empirical probability distributions, in particular, their non-Gaussian heavy tails.     

基于因子分析方法的相位同步脑电源的时-空动力学分析

头皮脑电时间序列的相关性是大脑皮层源的相位同步性的一种体现,因此对相位同步源进行定位,同时找到源对应的时间序列在脑成像研究领域具有重要意义.基于Rössler 模型提出仿真相位同步偶极子源的时间序列的方法,利用时间序列进行同心四层球头模型正演,获得仿真头皮脑电数据.提出了基于最大似然因子分析的相位同步脑电源的时-空动力学分析方法,对仿真和真实头皮脑电数据进行了验证,并与主成分分析法进行对比.仿真实验结果表明:最大似然因子分析法估计的时间序列与仿真源的时间序列具有更高的相关系数,同时估计源与仿真源 关键词： 脑电图 相位同步 因子分析 主成分分析     

Investigating the neural basis for fMRI-based functional connectivity in a blocked design: application to interregional correlations and psycho-physiological interactions

This paper investigates how well different kinds of fMRI functional connectivity analysis reflect the underlying interregional neural interactions. This is hard to evaluate using real experimental data where such relationships are unknown. Rather, we use a biologically realistic neural model to simulate both neuronal activities and multiregional fMRI data from a blocked design. Because we know how every element in the model is related to every other element, we can compare functional connectivity measurements across different spatial and temporal scales. We focus on (1) psycho-physiological interaction (PPI) analysis, which is a simple brain connectivity method that characterizes the activity in one brain region by the interaction between another region's activity and a psychological factor, and (2) interregional correlation analysis. We investigated the neurobiological underpinnings of PPI using simulated neural activities and fMRI signals generated by a large-scale neural model that performs a visual delayed match-to-sample task. Simulated fMRI data are generated by convolving integrated synaptic activities (ISAs) with a hemodynamic response function. The simulation was done under three task conditions: high-attention, low-attention and a control task ('passive viewing'). We investigated how biological and scanning parameters affect PPI and compared these with functional connectivity measures obtained using correlation analysis. We performed correlational and PPI analyses with three types of time-series data: ISA, fMRI and deconvolved fMRI (which yields estimated neural signals) obtained using a deconvolution algorithm. The simulated ISA can be considered as the 'gold standard' because it represents the underlying neural activity. Our main findings show (1) that evaluating the change in an interregional functional connection using the difference in regression coefficients (as is essentially done in the PPI method) produces results that better reflect the underlying changes in neural interrelationships than does evaluating the functional connectivity difference as a change in correlation coefficient; (2) that using fMRI and deconvolved fMRI data led to similar conclusions in the PPI-based functional connectivity results, and these generally agreed with the nature of the underlying neural interactions; and (3) the functional connectivity correlation measures often led to different conclusions regarding significance for different scanning and hemodynamic parameters, but the significances of the PPI regression parameters were relatively robust. These results highlight the way in which neural modeling can be used to help validate the inferences one can make about functional connectivity based on fMRI data.     

An independent component analysis-based approach on ballistocardiogram artifact removing

Interest about simultaneous electroencephalography (EEG) and functional magnetic resonance imaging (fMRI) data acquisition has rapidly increased during the last years because of the possibility that the combined method offers to join temporal and spatial resolution, providing in this way a powerful tool to investigate spontaneous and evoked brain activities. However, several intrinsic features of MRI scanning become sources of artifacts on EEG data. Noise sources of a highly predictable nature such as those related to the pulse MRI sequence and those determined by magnetic gradient switching during scanning do not represent a major problem and can be easily removed. On the contrary, the ballistocardiogram (BCG) artifact, a large signal visible on all EEG traces and related to cardiac activity inside the magnetic field, is determined by sources that are not fully stereotyped and causing important limitations in the use of artifact-removing strategies. Recently, it has been proposed to use independent component analysis (ICA) to remove BCG artifact from EEG signals. ICA is a statistical algorithm that allows blind separation of statistically independent sources when the only available information is represented by their linear combination. An important drawback with most ICA algorithms is that they exhibit a stochastic behavior: each run yields slightly different results such that the reliability of the estimated sources is difficult to assess. In this preliminary report, we present a method based on running the FastICA algorithm many times with slightly different initial conditions. Clustering structure in the signal space of the obtained components provides us with a new way to assess the reliability of the estimated sources.     

基于自适应模板法的脑电信号转移熵分析

脑电信号是一种产生机理相当复杂且非常微弱的随机信号, 综合反映了大脑组织的脑电活动及大脑的功能状态. 由于脑电信号的微弱性, 传统的基本模板方法在脑电信号分析上得到了良好的应用. 为进一步提升分析脑电信号的性能, 提出了一种新的基于自适应模板的转移熵方法并分析了青少年脑电与成年人脑电信号. 结果表明: 对于青少年脑电还是成年人脑电, 与基本模板法相比, 基于自适应模板法的转移熵可以更显著地表示脑电信号的耦合作用, 并且具有更好的区分度, 这将能更好地捕捉到信号中的动态信息、系统动力学复杂性的改变. 同时, 该方法将更有利于医学临床诊断的辅助检测, 对脑电信号是否处于病理状态的诊断提供了新的更好的判断依据.     

Physical implications of multi-neighbor activations in the master equation

In this letter we show how multi-neighbor activations can arise from applications of the master equation to physical models, and how such randomized activations can be solved by homotopy mapping.     

Thermal imaging of a vein of the forearm: Analysis and thermal modelling

We analyse the infrared images obtained on a human forearm. In a first part, we present a basic thermal model explaining the temperature at the surface of the skin in the presence of sources such as veins. In a second part, we propose to analyse the infrared images obtained after thermal solicitation. We show how the use of low amplitude, health-safe, periodical heating or a transient thermal solicitation allows to improve notably the contrast of the images and to extract the radius, depth and the blood flow velocity in a vein.     

Modulation of electroencephalograph activity by manual acupuncture stimulation in healthy subjects:An autoregressive spectral analysis

To investigate whether and how manual acupuncture(MA) modulates brain activities,we design an experiment where acupuncture at acupoint ST36 of the right leg is used to obtain electroencephalograph(EEG) signals in healthy subjects.We adopt the autoregressive(AR) Burg method to estimate the power spectrum of EEG signals and analyze the relative powers in delta(0 Hz-4 Hz),theta(4 Hz-8 Hz),alpha(8 Hz-13 Hz),and beta(13 Hz-30 Hz) bands.Our results show that MA at ST36 can significantly increase the EEG slow wave relative power(delta band) and reduce the fast wave relative powers(alpha and beta bands),while there are no statistical differences in theta band relative power between different acupuncture states.In order to quantify the ratio of slow to fast wave EEG activity,we compute the power ratio index.It is found that the MA can significantly increase the power ratio index,especially in frontal and central lobes.All the results highlight the modulation of brain activities with MA and may provide potential help for the clinical use of acupuncture.The proposed quantitative method of acupuncture signals may be further used to make MA more standardized.     

Modulation of electroencephalograph activities by manual acupuncture stimulation in healthy subjects: An autoregressive spectral analysis

To investigate whether and how manual acupuncture (MA) modulates brain activities, we design an experiment that acupuncture at acupoint ST36 of right leg to obtain electroencephalograph (EEG) signals in healthy subjects. We adopt autoregressive (AR) Burg method to estimate the power spectrum of EEG signals and analyze the relative powers in delta (0 Hz-4 Hz), theta (4 Hz-8 Hz), alpha (8 Hz-13 Hz), and beta (13 Hz-30 Hz) bands. Our results show that MA at ST36 can significantly increase the EEG slow wave relative power (delta band) and reduce the fast wave relative powers (alpha and beta bands), while there are no statistical differences in theta band relative power between different acupuncture states. In order to quantify the ratio of slow to fast wave EEG activity, we compute the power ratio index. It is found that the MA can significantly increase the power ratio index, especially in frontal and central lobes. All the results highlight the modulation of brain activities with MA and may provide potential helps in clinical treatment of acupuncture. The proposed quantitative method of acupuncture signals may be further used to make MA more standardized.     

A resolution measure for three-dimensional microscopy

A three-dimensional (3D) resolution measure for the conventional optical microscope is introduced which overcomes the drawbacks of the classical 3D (axial) resolution limit. Formulated within the context of a parameter estimation problem and based on the Cramer-Rao lower bound, this 3D resolution measure indicates the accuracy with which a given distance between two objects in 3D space can be determined from the acquired image. It predicts that, given enough photons from the objects of interest, arbitrarily small distances of separation can be estimated with prespecified accuracy. Using simulated images of point source pairs, we show that the maximum likelihood estimator is capable of attaining the accuracy predicted by the resolution measure. We also demonstrate how different factors, such as extraneous noise sources and the spatial orientation of the imaged object pair, can affect the accuracy with which a given distance of separation can be determined.     

Statistical mechanics of networks: Estimation and uncertainty

Exponential random graph models (ERGMs) are powerful tools for formulating theoretical models of network generation or learning the properties of empirical networks. They can be used to construct models that exactly reproduce network properties of interest. However, tuning these models correctly requires computationally intractable maximization of the probability of a network of interest—maximum likelihood estimation (MLE). We discuss methods of approximate MLE and show that, though promising, simulation based methods pose difficulties in application because it is not known how much simulation is required. An alternative to simulation methods, maximum pseudolikelihood estimation (MPLE), is deterministic and has known asymptotic properties, but standard methods of assessing uncertainty with MPLE perform poorly. We introduce a resampling method that greatly outperforms the standard approach to characterizing uncertainty with MPLE. We also introduce ERGMs for dynamic networks—temporal ERGM (TERGM). In an application to modeling cosponsorship networks in the United States Senate, we show how recently proposed methods for dynamic network modeling can be integrated into the TERGM framework, and how our resampling method can be used to characterize uncertainty about network dynamics.     

Cosmic inflation and model comparison

We analyze the implications for inflation of the recently released Planck Cosmic Microwave Background data and explain why the single-field slow-roll scenarios with minimal kinetic terms are favored. Within this class of models, we show how Bayesian model comparison can be used to further exclude about one third of the inflationary scenarios. We also study the end of inflation and show that Planck can already constrain the reheating phase. Finally, we conclude by discussing how future missions will be able to improve our knowledge of the inflationary mechanism.     

A comparison of Gamma and Gaussian dynamic convolution models of the fMRI BOLD response

Blood oxygenation level-dependent (BOLD) contrast-based functional magnetic resonance imaging (fMRI) has been widely utilized to detect brain neural activities and great efforts are now stressed on the hemodynamic processes of different brain regions activated by a stimulus. The focus of this paper is the comparison of Gamma and Gaussian dynamic convolution models of the fMRI BOLD response. The convolutions are between the perfusion function of the neural response to a stimulus and a Gaussian or Gamma function. The parameters of the two models are estimated by a nonlinear least-squares optimal algorithm for the fMRI data of eight subjects collected in a visual stimulus experiment. The results show that the Gaussian model is better than the Gamma model in fitting the data. The model parameters are different in the left and right occipital regions, which indicate that the dynamic processes seem different in various cerebral functional regions.     

Robustness and Flexibility of Neural Function through Dynamical Criticality

In theoretical biology, robustness refers to the ability of a biological system to function properly even under perturbation of basic parameters (e.g., temperature or pH), which in mathematical models is reflected in not needing to fine-tune basic parameter constants; flexibility refers to the ability of a system to switch functions or behaviors easily and effortlessly. While there are extensive explorations of the concept of robustness and what it requires mathematically, understanding flexibility has proven more elusive, as well as also elucidating the apparent opposition between what is required mathematically for models to implement either. In this paper we address a number of arguments in theoretical neuroscience showing that both robustness and flexibility can be attained by systems that poise themselves at the onset of a large number of dynamical bifurcations, or dynamical criticality, and how such poising can have a profound influence on integration of information processing and function. Finally, we examine critical map lattices, which are coupled map lattices where the coupling is dynamically critical in the sense of having purely imaginary eigenvalues. We show that these map lattices provide an explicit connection between dynamical criticality in the sense we have used and “edge of chaos” criticality.     

Estimation of the effective and functional human cortical connectivity with structural equation modeling and directed transfer function applied to high-resolution EEG

Different brain imaging devices are presently available to provide images of the human functional cortical activity, based on hemodynamic, metabolic or electromagnetic measurements. However, static images of brain regions activated during particular tasks do not convey the information of how these regions are interconnected. The concept of brain connectivity plays a central role in the neuroscience, and different definitions of connectivity, functional and effective, have been adopted in literature. While the functional connectivity is defined as the temporal coherence among the activities of different brain areas, the effective connectivity is defined as the simplest brain circuit that would produce the same temporal relationship as observed experimentally among cortical sites. The structural equation modeling (SEM) is the most used method to estimate effective connectivity in neuroscience, and its typical application is on data related to brain hemodynamic behavior tested by functional magnetic resonance imaging (fMRI), whereas the directed transfer function (DTF) method is a frequency-domain approach based on both a multivariate autoregressive (MVAR) modeling of time series and on the concept of Granger causality.

This study presents advanced methods for the estimation of cortical connectivity by applying SEM and DTF on the cortical signals estimated from high-resolution electroencephalography (EEG) recordings, since these signals exhibit a higher spatial resolution than conventional cerebral electromagnetic measures. To estimate correctly the cortical signals, we used a subject's multicompartment head model (scalp, skull, dura mater, cortex) constructed from individual MRI, a distributed source model and a regularized linear inverse source estimates of cortical current density. Before the application of SEM and DTF methodology to the cortical waveforms estimated from high-resolution EEG data, we performed a simulation study, in which different main factors (signal-to-noise ratio, SNR, and simulated cortical activity duration, LENGTH) were systematically manipulated in the generation of test signals, and the errors in the estimated connectivity were evaluated by the analysis of variance (ANOVA). The statistical analysis returned that during simulations, both SEM and DTF estimators were able to correctly estimate the imposed connectivity patterns under reasonable operative conditions, that is, when data exhibit an SNR of at least 3 and a LENGTH of at least 75 s of nonconsecutive EEG recordings at 64 Hz of sampling rate.

Hence, effective and functional connectivity patterns of cortical activity can be effectively estimated under general conditions met in any practical EEG recordings, by combining high-resolution EEG techniques and linear inverse estimation with SEM or DTF methods. We conclude that the estimation of cortical connectivity can be performed not only with hemodynamic measurements, but also with EEG signals treated with advanced computational techniques.     

Solutions of singular integral equations from gas dynamics and plasma physics

In this paper we give the explicit form of the solutions of the singular integral equations associated with some models of gas dynamics and plasma physics which are extensively investigated in the existing literature. In particular, we deal with equations on infinite and semi-infinite contours, where the data are assumed to be meromorphic functions. In this context we rederive some published results and present some new results which show how our method can be successfully used to obtain the explicit form of the solutions in much more general cases than those found in the literature.     

The role of sensitivity and uncertainty analysis in combustion modelling

Models play an important role in improving our understanding of combustion processes and more and more are able to assist in the design of advanced energy conversion devices. Due to constant improvements in computing power and techniques such as automatic kinetic mechanism generation, we have the ability to represent combustion processes with increasing levels of detail. This is particularly true for kinetic processes where complex mechanisms are being developed which describe the oxidation of both conventional and alternative fuels. These mechanisms may comprise of up to hundreds of species and thousands of reactions with thermo-kinetic data derived from a wide variety of sources including direct measurements, global combustion experiments, and theoretical calculations. However, significant uncertainties in the data used to parametrise combustion models still exist. These input uncertainties propagate through models of combustion devices leading to uncertainties in the prediction of key combustion properties. In order to improve confidence in these models to the extent where they can successfully be used in design, input uncertainties need to be reduced as far as possible. This requires focussing efforts on those parameters which drive predictive uncertainty, which may be identified through sensitivity analysis. The paper will describe the methodologies available for the sensitivity and uncertainty analysis of combustion models with examples focussed on chemical kinetics. It will then discuss how such techniques can be incorporated into strategies for model improvement and will try to provide some future perspectives on how we can proceed in this direction as a research community.     

Low depth quantum circuits for Ising models

A scheme for measuring complex temperature partition functions of Ising models is introduced. Two applications of this scheme are presented. First, through appropriate Wick rotations, those amplitudes can be analytically continued to yield estimates for partition functions of Ising models. Bounds on the estimated error are provided through a central-limit theorem whose validity extends beyond the present context; it holds for example for estimations of the Jones polynomial. The kind of state preparations and measurements involved in this application can be made independent of the system size or the parameters of the system being simulated. Second, the scheme allows to accurately estimate non-trivial invariants of links. Another result concerns the computational power of estimations of partition functions for real temperature classical ferromagnetic Ising models. We provide conditions under which estimating such partition functions allows to reconstruct scattering amplitudes of quantum circuits, making the problem BQP-hard. We also show fidelity overlaps for ground states of quantum Hamiltonians, which serve as a witness to quantum phase transitions, can be estimated from classical Ising model partition functions. Finally, we discuss how accurate corner magnetisation measurements on thermal states of two-dimensional Ising models lead to fully polynomial random approximation schemes (FPRAS) for the partition function.