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PubMed2001

Estimation of the number of "true" null hypotheses in multivariate analysis of neuroimaging data.

The repeated testing of a null univariate hypothesis in each of many sites (either regions of interest or voxels) is a common approach to the statistical analysis of brain functional images. Procedures, such as the Bonferroni, are available to maintain the Type I error of the set of tests at a specified level. An initial assumption of these methods is a "global null hypothesis," i.e., the statistics computed on each site are assumed to be generated by null distributions. This framework may be too conservative when a significant proportion of the sites is affected by the experimental manipulation. This report presents the development of a rigorous statistical procedure for use with a previously reported graphical method, the P plot, for estimation of the number of "true" null hypotheses in the set. This estimate can then be used to sharpen existing multiple comparison procedures. Performance of the P plot method in the multiple comparison problem is investigated in simulation studies and in the analysis of autoradiographic data.

Anesthesia, General↗
PubMed1977

On an empirical calculus of reinforcement magnitude.

Current available measures of sexual orientation are briefly reviewed. A novel sexual orientation measure is proposed, based on experiments in operant psychology. Previous relevant studies are reviewed, and it is suggested that a deficiency is their reliance on a single response as the dependent variable. The matching law is introduced, and it is argued that this provides a potentially powerful framework within which the relative reinforcement magnitudes of sexual stimuli may be computed, using as the dependent variable the relative rates of two responses. The proposed assessment method provides a means of answering the question "What is the reinforcement magnitude of various classes of erotic stimuli for a given individual?"

Conditioning, Operant↗
PubMed2006

The neurocognitive bases of human multimodal food perception: consciousness.

This review explores how we become aware of the (integrated) flavor of food. In recent years, progress has been made understanding the neural correlates of consciousness. Experimental and computational data have been largely based on the visual system. Contemporary neurobiological frameworks of consciousness are reviewed, concluding that neural reverberation among forward- and back-projecting neural ensembles across brain areas is a common theme. In an attempt to extrapolate these concepts to the oral-sensory and olfactory systems involved with multimodal flavor perception, the integration of the sensory information of which into a flavor gestalt has been reviewed elsewhere (Verhagen, J.V., Engelen, L., 2006. The neurocognitive bases of human multimodal food perception: Sensory integration. Neurosci. Biobehav. Rev. 30(5): 613_650), I reconceptualize the flavor-sensory system by integrating it into a larger neural system termed the Homeostatic Interoceptive System (HIS). This system consists of an oral (taste, oral touch, etc.) and non-oral part (non oral-thermosensation, pain, etc.) which are anatomically and functionally highly similar. Consistent with this new concept and with a large volume of experimental data, I propose that awareness of intraoral food is related to the concomitant reverberant self-sustained activation of a coalition of neuronal subsets in agranular insula and orbitofrontal cortex (affect, hedonics) and agranular insula and perirhinal cortex (food identity), as well as the amygdala (affect and identity) in humans. I further discuss the functional anatomy in relation essential nodes. These formulations are by necessity to some extent speculative.

Brain↗
PubMed2005

Attention and visual perception.

Somewhere between the retina and our conscious visual experience, the majority of the information impinging on the eye is lost. We are typically aware of only either the most salient parts of a visual scene or the parts that we are actively paying attention to. Recent research on visual neurons in monkeys is beginning to show how the brain both selects and discards incoming visual information. For example, what happens to the responses of visual neurons when attention is directed to one element, such as an oriented colored bar, embedded among an array of other oriented bars? Some of this research shows that attention to the oriented bar restricts the receptive field of visual neurons down to this single element. However, other research shows that attention to this single element affects the responses of neurons with receptive fields throughout the visual field. In this review, these two seemingly contradictory results are shown to actually be mutually consistent. A simple computational model is described that explains these results, and also provides a framework for predicting a variety of additional neurophysiological, neuroimaging and behavioral studies of attention.

Animals↗
PubMed2004

Noise, delays, robustness, canalization and all that.

A biological system such as a developing embryo can withstand many perturbations. What is the basis of this robustness both against noise and mutation? Recent advances in modeling may throw new light on this old problem. First, recent theoretical and experimental work clearly demonstrates the importance of noise and time delays for the proper functioning of genetic networks: noise and delays are simply part of the normal operating constraints. By contrast, sweeping statements have been made recently about a so-called 'robustness' of biological processes, based on work that neglects noise and delays completely. I submit that studying the stability of complex biological systems with such omissions is an unnecessary, inadequate and potentially disastrous simplification. I review the existing alternatives and propose using them to construct a modeling framework that overcomes all serious limitations.

Computational Biology↗
PubMed2000

Consistency of posterior distributions for neural networks.

In this paper we show that the posterior distribution for feedforward neural networks is asymptotically consistent. This paper extends earlier results on universal approximation properties of neural networks to the Bayesian setting. The proof of consistency embeds the problem in a density estimation problem, then uses bounds on the bracketing entropy to show that the posterior is consistent over Hellinger neighborhoods. It then relates this result back to the regression setting. We show consistency in both the setting of the number of hidden nodes growing with the sample size, and in the case where the number of hidden nodes is treated as a parameter. Thus we provide a theoretical justification for using neural networks for nonparametric regression in a Bayesian framework.

Bayes Theorem↗
PubMed2002

Banburismus and the brain: decoding the relationship between sensory stimuli, decisions, and reward.

This article relates a theoretical framework developed by British codebreakers in World War II to the neural computations thought to be responsible for forming categorical decisions about sensory stimuli. In both, a weight of evidence is computed and accumulated to support or oppose the alternative interpretations. A decision is reached when the evidence reaches a threshold value. In the codebreaking scheme, the threshold determined the speed and accuracy of the decision process. Here we propose that in the brain, the threshold may be controlled by neural circuits that calculate the rate of reward.

Animals↗
PubMed2002

Diffusion tensor brain imaging and tractography.

Diffusion-tensor MR imaging is a promising tool to evaluate white-matter integrity by quantitative and graphic maps including neural fiber tractogram. Current challenges afoot are to obtain higher quality diffusion-weighted MR images (high SNR, isotropic voxel, and high spatial resolution), to create a robust mathematical framework to process the data, to construct a user-friendly computer-based algorithm, to reveal determinants of diffusion process, and to establish analytical methodology.

Adrenoleukodystrophy↗
PubMed2005

Personalized nutrition communication through ICT application: how to overcome the gap between potential effectiveness and reality.

The potential effectiveness of personalized nutrition communication through the Internet is promising in terms of addressing personal relevance, flexibility, interactive options and amount of people that can be reached. However, little research on the contribution to behaviour change has been done. The MyFood program at Wageningen University aims at providing insight into strategies to implement personalized nutrition communication through interactive tools. In this article we present the framework for research on social acceptance of personalized nutrition communication through interactive computer technology as part of the MyFood program.

Communication↗
PubMed2004

Simulation of the plastic behavior of amorphous glassy bis-phenol-A-polycarbonate.

A protocol for studying the plastic deformation of amorphous glassy polymers is presented. The protocol is based on a viable computational procedure which combines constant-stress molecular dynamics simulations and fixed-cell energy minimizations, followed by kinetic, configurational, and energy analyses. It is shown that the computational results can be accounted for within a "potential energy landscape" theoretical framework, in which the plastic transition is interpreted as a crossing between and a collapse onto each other of "ideal (thermodynamic) structures." The procedure is applied to bis-phenol-A-polycarbonate (BPA-PC), but is equally valid for a wide variety of polymeric species. Allowing for the limited size of the simulation cell, the high strain rate, and the fact that the simulation are conducted at low temperature, the values of the density, Young's modulus, yield strain, yield stress, activation energy, and activation volume are in fair agreement with the experimental data on BPA-PC. The analysis of the results shows that the plastic relaxation for this polymer has both a collective and cooperative character (as in classical percolation theories), involves a significant fraction of the simulation cell, and can be viewed as a "nanoscopic shear band."

Journal Article↗
PubMed2006

Using grid techniques for drug target identification.

The completion of the sequencing of the human genome has opened an unprecedented opportunity in the discovery of novel drug targets for disease therapy. However, one of the major challenges facing the drug discovery community is the expanding of data and the need of large-scale computational power in a collaborative environment. Grid techniques can present an architectural framework that aims to provide access to heterogeneous resources in a secure, reliable and scalable manner across various administrative boundaries for drug discovery, which has been a promising strategy for solving large-scale problems in modern pharmaceutical R&D. In this review, we discuss the current applications of Grid technology in drug target protein identification process; and an overview of drug target discovery system architecture, focusing in particular on the data manager service system architecture is also proposed.

Animals↗
PubMed2002

Multiple genome rearrangement: a general approach via the evolutionary genome graph.

MOTIVATION: In spite of a well-known fact that genome rearrangements are supposed to be viewed in the light of the evolutionary relationships within and between the species involved, no formal underlying framework based on the evolutionary considerations for treating the questions arising in the area has been proposed. If such an underlying framework is provided, all the basic questions in the area can be posed in a biologically more appropriate and useful form: e.g., the similarity between two genomes can then be computed via the nearest ancestor, rather than 'directly', ignoring the evolutionary connections. RESULTS: We outline an evolution-based general framework for answering questions related to the multiple genome rearrangement. In the proposed model, the evolutionary genome graph (EG-graph) encapsulates an evolutionary history of a genome family. For a set of all EG-graphs, we introduce a family of similarity measures, each defined via a fixed set of genome transformations. Given a set of genomes and restricting ourselves to the transpositions, an algorithm for constructing an EG-graph is presented. We also present the experimental results in the form of an EG-graph for a set of concrete genomes (for several species). This EG-graph turns out to be very close to the corresponding known phylogenetic tree.

Algorithms↗
PubMed2001

Statistical prediction of single-stranded regions in RNA secondary structure and application to predicting effective antisense target sites and beyond.

Single-stranded regions in RNA secondary structure are important for RNA-RNA and RNA-protein interactions. We present a probability profile approach for the prediction of these regions based on a statistical algorithm for sampling RNA secondary structures. For the prediction of phylogenetically-determined single-stranded regions in secondary structures of representative RNA sequences, the probability profile offers substantial improvement over the minimum free energy structure. In designing antisense oligonucleotides, a practical problem is how to select a secondary structure for the target mRNA from the optimal structure(s) and many suboptimal structures with similar free energies. By summarizing the information from a statistical sample of probable secondary structures in a single plot, the probability profile not only presents a solution to this dilemma, but also reveals 'well-determined' single-stranded regions through the assignment of probabilities as measures of confidence in predictions. In antisense application to the rabbit beta-globin mRNA, a significant correlation between hybridization potential predicted by the probability profile and the degree of inhibition of in vitro translation suggests that the probability profile approach is valuable for the identification of effective antisense target sites. Coupling computational design with DNA-RNA array technique provides a rational, efficient framework for antisense oligonucleotide screening. This framework has the potential for high-throughput applications to functional genomics and drug target validation.

Algorithms↗
PubMed2002

Do effective interactions depend on the choice of coordinates?

A common approach to complex systems such as colloidal suspensions or polymer solutions describes the mesoscopic behavior using effective interactions. These potentials act between the macromolecular entities and can be derived by integrating out the microscopic degrees of freedom. The remaining macroparticle coordinates need to be chosen a priori. Two obvious choices are (i) the centers of mass and (ii) distinct microscopic entities, such as special "tagged" monomers. Here we compare both in the framework of the Asakura-Oosawa colloid-ideal polymer mixture. Using computer simulations, we find that although the effective pair interaction between colloid and polymer differ markedly, correlation functions are in fair agreement.

Journal Article↗
PubMed2005

Band-gap engineering in two-dimensional semiconductor-dielectric photonic crystals.

This paper reports the multiple band gaps in the two-dimensional semiconductor-dielectric photonic crystals of several compositions: semiconductor cylinders in the dielectric background. We consider both square lattice and hexagonal lattice arrangements and compute extensive band structures using a plane-wave method within the framework of an efficient standard eigenvalue problem for both E and H polarizations. The whole range of filling fraction has been explored to claim the existence of the lowest (the so-called acoustic) band gap and multiple higher-energy band gaps within the first 30 to 40 bands for various compositions. Such semiconductor-dielectric photonic crystals which are shown to possess huge lowest band gaps below a threshold frequency (the plasma frequency omega(p) ) have an advantage over the dielectric photonic crystals in the emerging technology based on the photonic crystals.

Journal Article↗
PubMed2005

Application of the finite-size Lyapunov exponent to particle tracking velocimetry in fluid mechanics experiments.

A finite-size (or scale) Lyapunov exponent (FSLE), lambdaa(x), is presented in a statistical mechanical framework and employed to characterize mixing in a variety of laboratory and computational fluid mechanics experiments. The FSLE is the exponential rate at which two particles separate from a distance x to ax. Laboratory particle tracking experiments are used to study penetrative convection and flow in porous media while computational experiments are used to study Lévy processes and deterministic diffusion. The apparent scaling relation lambaa(x) approximately Cax(-beta(a)) of the FSLE holds over intermediate initial separations where the laboratory experiment data is most accurate and asymptotically for the computational experiments. The dependence of the exponent beta on a decreases with increasing a. In the matched index porous system, Ca is also a function of mean fluid velocity. The exponent beta is alpha when the Lévy process is alpha-stable and in this case beta is independent of a.

Journal Article↗
PubMed2005

Optimal erasure protection for scalably compressed video streams with limited retransmission.

This paper shows how the priority encoding transmission (PET) framework may be leveraged to exploit both unequal error protection and limited retransmission for RD-optimized delivery of streaming media. Previous work on scalable media protection with PET has largely ignored the possibility of retransmission. Conversely, the PET framework has not been harnessed by the substantial body of previous work on RD optimized hybrid forward error correction/automatic repeat request schemes. We limit our attention to sources which can be modeled as independently compressed frames (e.g., video frames), where each element in the scalable representation of each frame can be transmitted in one or both of two transmission slots. An optimization algorithm determines the level of protection which should be assigned to each element in each slot, subject to transmission bandwidth constraints. To balance the protection assigned to elements which are being transmitted for the first time with those which are being retransmitted, the proposed algorithm formulates a collection of hypotheses concerning its own behavior in future transmission slots. We show how the PET framework allows for a decoupled optimization algorithm with only modest complexity. Experimental results obtained with Motion JPEG2000 compressed video demonstrate that substantial performance benefits can be obtained using the proposed framework.

Algorithms↗
PubMed2004

Autoassociator networks: insights into infant cognition.

This paper presents autoassociator neural networks. A first section reviews the architecture of these models, common learning rules, and presents sample simulations to illustrate their abilities. In a second section, the ability of these models to account for learning phenomena such as habituation is reviewed. The contribution of these networks to discussions about infant cognition is highlighted. A new, modular approach is presented in a third section. In the discussion, a role for these learning models in a broader developmental framework is proposed.

Artificial Intelligence↗