Polarized light imaging of white matter architecture

Polarized light imaging (PLI) is a method to image fiber orientation in gross histological brain sections based on the birefringent properties of the myelin sheaths. The method uses the transmission of polarized light to quantitatively estimate the fiber orientation and inclination angles at every point of the imaged section. Multiple sections can be assembled into a 3D volume, from which the 3D extent of fiber tracts can be extracted. This article describes the physical principles of PLI and describes two major applications of the method: the imaging of white matter orientation of the rat brain and the generation of fiber orientation maps of the human brain in white and gray matter. The strengths and weaknesses of the method are set out.     

Some Statistical-Estimation Methods for Stochastic Finite-State Transducers

Formal translations constitute a suitable framework for dealing with many problems in pattern recognition and computational linguistics. The application of formal transducers to these areas requires a stochastic extension for dealing with noisy, distorted patterns with high variability. In this paper, some estimation criteria are proposed and developed for the parameter estimation of regular syntax-directed translation schemata. These criteria are: maximum likelihood estimation, minimum conditional entropy estimation and conditional maximum likelihood estimation. The last two criteria were proposed in order to deal with situations when training data is sparse. These criteria take into account the possibility of ambiguity in the translations: i.e., there can be different output strings for a single input string. In this case, the final goal of the stochastic framework is to find the highest probability translation of a given input string. These criteria were tested on a translation task which has a high degree of ambiguity.     

Ernest Lepore and Zenon Pylyshyn,What is Cognitive Science?

Minds and Machines -     

Context learning in the rodent hippocampus

We present a Bayesian statistical theory of context learning in the rodent hippocampus. While context is often defined in an experimental setting in relation to specific background cues or task demands, we advance a single, more general notion of context that suffices for a variety of learning phenomena. Specifically, a context is defined as a statistically stationary distribution of experiences, and context learning is defined as the problem of how to form contexts out of groups of experiences that cluster together in time. The challenge of context learning is solving the model selection problem: How many contexts make up the rodent's world? Solving this problem requires balancing two opposing goals: minimize the variability of the distribution of experiences within a context and minimize the likelihood of transitioning between contexts. The theory provides an understanding of why hippocampal place cell remapping sometimes develops gradually over many days of experience and why even consistent landmark differences may need to be relearned after other environmental changes. The theory provides an explanation for progressive performance improvements in serial reversal learning, based on a clear dissociation between the incremental process of context learning and the relatively abrupt context selection process. The impact of partial reinforcement on reversal learning is also addressed. Finally, the theory explains why alternating sequence learning does not consistently result in unique context-dependent sequence representations in hippocampus.     

The relation between color discrimination and color constancy: when is optimal adaptation task dependent?

Color vision supports two distinct visual functions: discrimination and constancy. Discrimination requires that the visual response to distinct objects within a scene be different. Constancy requires that the visual response to any object be the same across scenes. Across changes in scene, adaptation can improve discrimination by optimizing the use of the available response range. Similarly, adaptation can improve constancy by stabilizing the visual response to any fixed object across changes in illumination. Can common mechanisms of adaptation achieve these two goals simultaneously? We develop a theoretical framework for answering this question and present several example calculations. In the examples studied, the answer is largely yes when the change of scene consists of a change in illumination and considerably less so when the change of scene consists of a change in the statistical ensemble of surface reflectances in the environment.     

Generalization in the XCSF classifier system: analysis, improvement, and extension

We analyze generalization in XCSF and introduce three improvements. We begin by showing that the types of generalizations evolved by XCSF can be influenced by the input range. To explain these results we present a theoretical analysis of the convergence of classifier weights in XCSF which highlights a broader issue. In XCSF, because of the mathematical properties of the Widrow-Hoff update, the convergence of classifier weights in a given subspace can be slow when the spread of the eigenvalues of the autocorrelation matrix associated with each classifier is large. As a major consequence, the system's accuracy pressure may act before classifier weights are adequately updated, so that XCSF may evolve piecewise constant approximations, instead of the intended, and more efficient, piecewise linear ones. We propose three different ways to update classifier weights in XCSF so as to increase the generalization capabilities of XCSF: one based on a condition-based normalization of the inputs, one based on linear least squares, and one based on the recursive version of linear least squares. Through a series of experiments we show that while all three approaches significantly improve XCSF, least squares approaches appear to be best performing and most robust. Finally we show how XCSF can be extended to include polynomial approximations.     

A quantum chemical study of the mechanism of action of Vitamin K epoxide reductase (VKOR) II. Transition states

A reaction path including transition states is generated for the Silverman mechanism [R.B. Silverman, Chemical model studies for the mechanism of Vitamin K epoxide reductase, J. Am. Chem. Soc. 103 (1981) 5939-5941] of action for Vitamin K epoxide reductase (VKOR) using quantum mechanical methods (B3LYP/6-311G**). VKOR, an essential enzyme in mammalian systems, acts to convert Vitamin K epoxide, formed by Vitamin K carboxylase, to its (initial) quinone form for cellular reuse. This study elaborates on a prior work that focused on the thermodynamics of VKOR [D.W. Deerfield II, C.H. Davis, T. Wymore, D.W. Stafford, L.G. Pedersen, Int. J. Quant. Chem. 106 (2006) 2944-2952]. The geometries of proposed model intermediates and transition states in the mechanism are energy optimized. We find that once a key disulfide bond is broken, the reaction proceeds largely downhill. An important step in the conversion of the epoxide back to the quinone form involves initial protonation of the epoxide oxygen. We find that the source of this proton is likely a free mercapto group rather than a water molecule. The results are consistent with the current view that the widely used drug Warfarin likely acts by blocking binding of Vitamin K at the VKOR active site and thereby effectively blocking the initiating step. These results will be useful for designing more complete QM/MM studies of the enzymatic pathway once three-dimensional structural data is determined and available for VKOR.     

A simple Hebbian/anti-Hebbian network learns the sparse, independent components of natural images

Slightly modified versions of an early Hebbian/anti-Hebbian neural network are shown to be capable of extracting the sparse, independent linear components of a prefiltered natural image set. An explanation for this capability in terms of a coupling between two hypothetical networks is presented. The simple networks presented here provide alternative, biologically plausible mechanisms for sparse, factorial coding in early primate vision.     

Bronchoalveolar lavage. Quantitation of intraalveolar fluid?

A precise calculation of the amount of intraalveolar fluid is the basis of a quantitative analysis of intraalveolar compounds. Different approaches have been made to cover this important problem. Here, we report a comparative study with five markers: 99mTc-DTPA, 51Cr-EDTA, inulin, urea, and methylene blue in animal experiments as well as in human experiments. The marker substances were added to the lavage fluid, and the "dilution" of the markers, i.e., the alveolar fluid, was calculated. The results showed that in animals with healthy lungs the tracer methods are able to calculate amounts of intraalveolar fluid that are comparable to morphologic findings. In animals as well as in humans, methylene blue and inulin were shown to be useless in determining alveolar fluid volume compared with the tracer methods. In humans, the calculations with the urea method and with Tc-DTPA were in the same magnitude, but there was no individual correlation. We conclude that, at present, the methods to quantitate alveolar fluid volume lack precision and add nothing to a deeper understanding of alveolar biology.