Encoding brain network response to free viewing of videos

A challenging goal for cognitive neuroscience researchers is to determine how mental representations are mapped onto the patterns of neural activity. To address this problem, functional magnetic resonance imaging (fMRI) researchers have developed a large number of encoding and decoding methods. However, previous studies typically used rather limited stimuli representation, like semantic labels and Wavelet Gabor filters, and largely focused on voxel-based brain patterns. Here, we present a new fMRI encoding model to predict the human brain’s responses to free viewing of video clips which aims to deal with this limitation. In this model, we represent the stimuli using a variety of representative visual features in the computer vision community, which can describe the global color distribution, local shape and spatial information and motion information contained in videos, and apply the functional connectivity to model the brain’s activity pattern evoked by these video clips. Our experimental results demonstrate that brain network responses during free viewing of videos can be robustly and accurately predicted across subjects by using visual features. Our study suggests the feasibility of exploring cognitive neuroscience studies by computational image/video analysis and provides a novel concept of using the brain encoding as a test-bed for evaluating visual feature extraction.     

Spectral clustering independent component analysis for tissue classification from brain MRI

A spectral angle based feature extraction method, Spectral Clustering Independent Component Analysis (SC-ICA), is proposed in this work to improve the brain tissue classification from Magnetic Resonance Images (MRI). SC-ICA provides equal priority to global and local features; thereby it tries to resolve the inefficiency of conventional approaches in abnormal tissue extraction. First, input multispectral MRI is divided into different clusters by a spectral distance based clustering. Then, Independent Component Analysis (ICA) is applied on the clustered data, in conjunction with Support Vector Machines (SVM) for brain tissue analysis. Normal and abnormal datasets, consisting of real and synthetic T1-weighted, T2-weighted and proton density/fluid-attenuated inversion recovery images, were used to evaluate the performance of the new method. Comparative analysis with ICA based SVM and other conventional classifiers established the stability and efficiency of SC-ICA based classification, especially in reproduction of small abnormalities. Clinical abnormal case analysis demonstrated it through the highest Tanimoto Index/accuracy values, 0.75/98.8%, observed against ICA based SVM results, 0.17/96.1%, for reproduced lesions. Experimental results recommend the proposed method as a promising approach in clinical and pathological studies of brain diseases.     

Comparison between principal component analysis and independent component analysis in electroencephalograms modelling

Principal Component Analysis (PCA) is a classical technique in statistical data analysis, feature extraction and data reduction, aiming at explaining observed signals as a linear combination of orthogonal principal components. Independent Component Analysis (ICA) is a technique of array processing and data analysis, aiming at recovering unobserved signals or 'sources' from observed mixtures, exploiting only the assumption of mutual independence between the signals. The separation of the sources by ICA has great potential in applications such as the separation of sound signals (like voices mixed in simultaneous multiple records, for example), in telecommunication or in the treatment of medical signals. However, ICA is not yet often used by statisticians. In this paper, we shall present ICA in a statistical framework and compare this method with PCA for electroencephalograms (EEG) analysis.We shall see that ICA provides a more useful data representation than PCA, for instance, for the representation of a particular characteristic of the EEG named event-related potential (ERP).     

Gender and weight shape brain dynamics during food viewing

Hemodynamic imaging results have associated both gender and body weight to variation in brain responses to food-related information. However, the spatio-temporal brain dynamics of gender-related and weight-wise modulations in food discrimination still remain to be elucidated. We analyzed visual evoked potentials (VEPs) while normal-weighted men (n = 12) and women (n = 12) categorized photographs of energy-dense foods and non-food kitchen utensils. VEP analyses showed that food categorization is influenced by gender as early as 170 ms after image onset. Moreover, the female VEP pattern to food categorization co-varied with participants' body weight. Estimations of the neural generator activity over the time interval of VEP modulations (i.e. by means of a distributed linear inverse solution [LAURA]) revealed alterations in prefrontal and temporo-parietal source activity as a function of image category and participants' gender. However, only neural source activity for female responses during food viewing was negatively correlated with body-mass index (BMI) over the respective time interval. Women showed decreased neural source activity particularly in ventral prefrontal brain regions when viewing food, but not non-food objects, while no such associations were apparent in male responses to food and non-food viewing. Our study thus indicates that gender influences are already apparent during initial stages of food-related object categorization, with small variations in body weight modulating electrophysiological responses especially in women and in brain areas implicated in food reward valuation and intake control. These findings extend recent reports on prefrontal reward and control circuit responsiveness to food cues and the potential role of this reactivity pattern in the susceptibility to weight gain.     

Resting‐state networks of the neonate brain identified using independent component analysis

Resting‐state functional magnetic resonance imaging (rs‐fMRI) has been successfully used to probe the intrinsic functional organization of the brain and to study brain development. Here, we implemented a combination of individual and group independent component analysis (ICA) of FSL on a 6‐min resting‐state data set acquired from 21 naturally sleeping term‐born (age 26 ± 6.7 d), healthy neonates to investigate the emerging functional resting‐state networks (RSNs). In line with the previous literature, we found evidence of sensorimotor, auditory/language, visual, cerebellar, thalmic, parietal, prefrontal, anterior cingulate as well as dorsal and ventral aspects of the default‐mode‐network. Additionally, we identified RSNs in frontal, parietal, and temporal regions that have not been previously described in this age group and correspond to the canonical RSNs established in adults. Importantly, we found that careful ICA‐based denoising of fMRI data increased the number of networks identified with group‐ICA, whereas the degree of spatial smoothing did not change the number of identified networks. Our results show that the infant brain has an established set of RSNs soon after birth.     

Goal-related activity in V4 during free viewing visual search. Evidence for a ventral stream visual salience map

Natural exploration of complex visual scenes depends on saccadic eye movements toward important locations. Saccade targeting is thought to be mediated by a retinotopic map that represents the locations of salient features. In this report, we demonstrate that extrastriate ventral area V4 contains a retinotopic salience map that guides exploratory eye movements during a naturalistic free viewing visual search task. In more than half of recorded cells, visually driven activity is enhanced prior to saccades that move the fovea toward the location previously occupied by a neuron's spatial receptive field. This correlation suggests that bottom-up processing in V4 influences the oculomotor planning process. Half of the neurons also exhibit top-down modulation of visual responses that depends on search target identity but not visual stimulation. Convergence of bottom-up and top-down processing streams in area V4 results in an adaptive, dynamic map of salience that guides oculomotor planning during natural vision.     

Application of independent component analysis to microarrays

We apply linear and nonlinear independent component analysis (ICA) to project microarray data into statistically independent components that correspond to putative biological processes, and to cluster genes according to over- or under-expression in each component. We test the statistical significance of enrichment of gene annotations within clusters. ICA outperforms other leading methods, such as principal component analysis, k-means clustering and the Plaid model, in constructing functionally coherent clusters on microarray datasets from Saccharomyces cerevisiae, Caenorhabditis elegans and human.     

Principal component analysis of evoked neuronal firing pattern in the human brain

Evoked firing activity (EFA) in neurons of the human thalamic reticular nucleus (Rt) was recorded by microelectrodes using extracellular recording techniques in the course of stereotaxic surgery for dyskinesia. Activity was induced by functionally significant verbal and sensory stimuli together with performance of goal-directed behavioral actions (BA). Use of the principal component method and construction of peristimulus covariance matrices are suggested in view of the presumably convergent nature of EFA in Rt neurons, taking the form of superposing independent components of response and variability in these in the course of BA testing and performance for the purpose of analyzing EFA and interneuronal correlations. The multivariate pattern of Rt EFA time courses during the action of functionally significant stimuli was revealed; this reflects different stages in performance of BA. The dynamics of components of response are revealed and occurrence of rapidly developing interneuronal correlations in functionally significant stages of goal-directed BA are described. Findings point to the efficacy of the suggested approach applied to analysis of EFA neurons.Institute of Chemical Physics, Academy of Sciences of the USSR, Moscow. Translated from Neirofiziologiya, Vol. 22, No. 6, pp. 811–818, November–December, 1990.     

Biochemical analysis of neutral endopeptidase activity reveals independent catabolism of atrial and brain natriuretic peptide

Recent reports presented contradictory results regarding the catabolism of mature atrial (ANP) and brain (BNP) natriuretic peptides in circulation. Especially the role of neutral endopeptidase (NEP) in BNP degradation was conversely discussed. Our present in vitro-studies characterize the NEP-dependent metabolism of ANP and BNP in different tissues via HPLC-analysis using NEP-deficient mice and specific NEP inhibitors. Our results show a strong tissue-dependent degradation pattern of both peptides, which are not only due to the different NEP activities in these tissues. Whereas NEP rapidly degraded ANP, it had no influence in BNP-metabolism. Additional experiments with purified NEP confirmed this result. Moreover, we describe a degradation of ANP and BNP in NEP-deficient- and NEP-inhibited membranes. Consequently, we postulate the existence of at least one further natriuretic peptide (NP) degrading enzyme, which has not been characterized yet. Thus, the commonly accepted model of the natriuretic peptide system with NEP as the central degrading peptidase has to be partly revised. Moreover, the NEP-independent BNP degradation provides an effective means for achieving a beneficial BNP increase in cardiovascular pathology by inhibiting the assumed novel NP-degrading peptidase(s).     

The protein component of human brain thromboplastin

The protein component of human brain tissue thromboplastin (factor III) has been purified by deoxycholate (DOC) extraction, ultracentrifugation, gel filtration and finally repeated preparative polyacrylamide gel electrophoresis (PGE) in the presence of sodium dodecylsulphate (SDS). The final preparations gave one band in analytical PGE. Reduced and alkylated protein appeared as a band of molecular weight about 53 000 in SDS-PGE.The protein had a low solubility in aqueous solutions in the absence of detergents. When recombined with an optimal amount of the phospholipid fraction of tissue thromboplastin (fraction B) the procoagulant thromboplastin activity was regained. Neither alone nor after recombination with phospholipid did the protein catalyze the hydrolysis of aminoacyl-β-naphthylamides or casein.     

Principal component analysis of the cytokine and chemokine response to human traumatic brain injury

There is a growing realisation that neuro-inflammation plays a fundamental role in the pathology of Traumatic Brain Injury (TBI). This has led to the search for biomarkers that reflect these underlying inflammatory processes using techniques such as cerebral microdialysis. The interpretation of such biomarker data has been limited by the statistical methods used. When analysing data of this sort the multiple putative interactions between mediators need to be considered as well as the timing of production and high degree of statistical co-variance in levels of these mediators. Here we present a cytokine and chemokine dataset from human brain following human traumatic brain injury and use principal component analysis and partial least squares discriminant analysis to demonstrate the pattern of production following TBI, distinct phases of the humoral inflammatory response and the differing patterns of response in brain and in peripheral blood. This technique has the added advantage of making no assumptions about the Relative Recovery (RR) of microdialysis derived parameters. Taken together these techniques can be used in complex microdialysis datasets to summarise the data succinctly and generate hypotheses for future study.     

基于时间聚类分析和独立成分分析的癫痫fMRI盲分析方法

提出了一种基于时间聚类分析和独立成分分析的癫痫fMRI数据盲分析方法,并将两种方法有效联合,提取发作间期的癫痫fMRI激活时空信息.该方法首先由时间聚类分析得到与激活相关的时间峰度特征曲线,以此特征作为时间参考信息;再由空间独立成分分析分解fMRI信号得到空间独立成分;最后将每个独立成分所对应的时间曲线与参考曲线做相关分析提取相应脑激活图.提出的方法无需任何关于癫痫fMRI的先验假设信息,有效解决了独立成分的排序问题,实现了对数据的盲分析.仿真试验结果阐明了这一方法的有效性及可靠性,对癫痫数据的试验结果显示空间定位准确性优于统计参数图方法.     

Topography, independent component analysis and dipole source analysis of movement related potentials

The objective of this study was to test, in single subjects, the hypothesis that the signs of voluntary movement-related neural activity would first appear in the prefrontal region, then move to both the medial frontal and posterior parietal regions, progress to the medial primary motor area, lateralize to the contralateral primary motor area and finally involve the cerebellum (where feedback-initiated error signals are computed). Six subjects performed voluntary finger movements while DC coupled EEG was recorded from 64 scalp electrodes. Event-related potentials (ERPs) averaged on the movements were analysed both before and after independent component analysis (ICA) combined with dipole source analysis (DSA) of the independent components. Both a simple topographic analysis of undecomposed ERPs and the ICA/DSA analysis suggested that the original hypothesis was inadequate. The major departure from its predictions was that, while activity over many brain regions did appear at the expected times, it also appeared at unexpected times. Overall, the results suggest that the neuroscientific ‘standard model’, in which neural activity occurs sequentially in a series of discrete local areas each specialized for a particular function, may reflect the true situation less well than models in which large areas of brain shift simultaneously into and out of common activity states. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.

Distribution and activity of pyridoxal kinase in human brain during ontogenesis]

The activity of pyridoxal kinase was sharply increased in whole brain tissue of human, embryos and fetuses within 6-11 weeks of development. In brain stem the maximal values of the enzyme activity was observed at early stages of prenatal development of fetuses. The activity of pyridoxal kinase was increased in cerebral cortex and in the limbic system up to complete maturation of fetuses. It correlated with the fetus age within 14-40 weeks of development as calculated per 1 g of tissue wight or 1 mg of protein. The enzyme is distributed evenly in brain of newborns, babies and adult people. Its activity in grey cortex substance is higher, than in white one. There are 2-10-fold individual fluctuations of pyridoxal kinase activity in brain of people without CNS pathology. In newborns, having prolonged hypoxy at prenatal period, the enzyme activity was on the average by 70-80% lower at different brain parts than in newborns which had no primary asphyxia. A low pyridoxal kinase activity (not more than 1-5% as compared with its normal level) was observed in different brain parts of a child affected by focal gliosis and epilepsy.     

Evoked activity of the human brain during perception of illusory stimuli

Evoked activity of the human brain was studied in 19 right-handed men during the perception of illusory images in Go/NoGo tasks. It was found that the recognition of illusory images was associated with changes in the amplitudes of both early (P1 and P2) and late (P3a and P3b) components of the evoked potentials and with an increase in the latencies of the late components recorded from the occipital, central, and frontal cortical areas, which could be explained by the necessity to store a template in the memory, compare a perceived image with the template, and prepare and execute (or inhibit) a motor response. At the same time, the operation of the brain was more differentiated during the NoGo task compared to the Go task.     

Disentanglement of local field potential sources by independent component analysis

The spontaneous activity of working neurons yields synaptic currents that mix up in the volume conductor. This activity is picked up by intracerebral recording electrodes as local field potentials (LFPs), but their separation into original informative sources is an unresolved problem. Assuming that synaptic currents have stationary placing we implemented independent component model for blind source separation of LFPs in the hippocampal CA1 region. After suppressing contaminating sources from adjacent regions we obtained three main local LFP generators. The specificity of the information contained in isolated generators is much higher than in raw potentials as revealed by stronger phase-spike correlation with local putative interneurons. The spatial distribution of the population synaptic input corresponding to each isolated generator was disclosed by current-source density analysis of spatial weights. The found generators match with axonal terminal fields from subtypes of local interneurons and associational fibers from nearby subfields. The found distributions of synaptic currents were employed in a computational model to reconstruct spontaneous LFPs. The phase-spike correlations of simulated units and LFPs show laminar dependency that reflects the nature and magnitude of the synaptic currents in the targeted pyramidal cells. We propose that each isolated generator captures the synaptic activity driven by a different neuron subpopulation. This offers experimentally justified model of local circuits creating extracellular potential, which involves distinct neuron subtypes.     

Linear modes of gene expression determined by independent component analysis

MOTIVATION: The expression of genes is controlled by specific combinations of cellular variables. We applied Independent Component Analysis (ICA) to gene expression data, deriving a linear model based on hidden variables, which we term 'expression modes'. The expression of each gene is a linear function of the expression modes, where, according to the ICA model, the linear influences of different modes show a minimal statistical dependence, and their distributions deviate sharply from the normal distribution. RESULTS: Studying cell cycle-related gene expression in yeast, we found that the dominant expression modes could be related to distinct biological functions, such as phases of the cell cycle or the mating response. Analysis of human lymphocytes revealed modes that were related to characteristic differences between cell types. With both data sets, the linear influences of the dominant modes showed distributions with large tails, indicating the existence of specifically up- and downregulated target genes. The expression modes and their influences can be used to visualize the samples and genes in low-dimensional spaces. A projection to expression modes helps to highlight particular biological functions, to reduce noise, and to compress the data in a biologically sensible way.     

Multi-resolution independent component analysis for high-performance tumor classification and biomarker discovery

Background

Although high-throughput microarray based molecular diagnostic technologies show a great promise in cancer diagnosis, it is still far from a clinical application due to its low and instable sensitivities and specificities in cancer molecular pattern recognition. In fact, high-dimensional and heterogeneous tumor profiles challenge current machine learning methodologies for its small number of samples and large or even huge number of variables (genes). This naturally calls for the use of an effective feature selection in microarray data classification.

Methods

We propose a novel feature selection method: multi-resolution independent component analysis (MICA) for large-scale gene expression data. This method overcomes the weak points of the widely used transform-based feature selection methods such as principal component analysis (PCA), independent component analysis (ICA), and nonnegative matrix factorization (NMF) by avoiding their global feature-selection mechanism. In addition to demonstrating the effectiveness of the multi-resolution independent component analysis in meaningful biomarker discovery, we present a multi-resolution independent component analysis based support vector machines (MICA-SVM) and linear discriminant analysis (MICA-LDA) to attain high-performance classifications in low-dimensional spaces.

Results

We have demonstrated the superiority and stability of our algorithms by performing comprehensive experimental comparisons with nine state-of-the-art algorithms on six high-dimensional heterogeneous profiles under cross validations. Our classification algorithms, especially, MICA-SVM, not only accomplish clinical or near-clinical level sensitivities and specificities, but also show strong performance stability over its peers in classification. Software that implements the major algorithm and data sets on which this paper focuses are freely available at https://sites.google.com/site/heyaumapbc2011/.

Conclusions

This work suggests a new direction to accelerate microarray technologies into a clinical routine through building a high-performance classifier to attain clinical-level sensitivities and specificities by treating an input profile as a ‘profile-biomarker’. The multi-resolution data analysis based redundant global feature suppressing and effective local feature extraction also have a positive impact on large scale ‘omics’ data mining.