An application of the 2-nitrobenzenesulfenyl method to proteomic profiling of human colorectal carcinoma: A novel approach for biomarker discovery

In the development of novel biomarkers, the proteomic approach is advantageous because using it the cancer-associated proteins can be directly identified. We previously developed a 2-nitrobenzenesulfenyl (NBS) method to improve quantitative proteome analysis. Here, we applied this method to proteomic profiling of colorectal carcinoma (CRC) to identify novel proteins with altered expression in CRC. Each pair of tumor and normal tissue specimens from 12 CRC patients was analyzed, and approximately 5000 NBS-labeled paired peaks were quantified. Peaks with altered signal intensities (>1.5-fold) and occurring frequently in the samples (>70%) were selected, and 128 proteins were identified by MS/MS analyses as differentially expressed proteins in CRC tissues. Many proteins were newly revealed to be CRC related; 30 were reported in earlier studies of CRC. Six proteins that were up-regulated in CRC (ZYX, RAN, RCN1, AHCY, LGALS1, and VIM) were further characterized and validated by Western blot and immunohistochemistry. All six were found to be CRC-localized, either in cancer cells or in stroma cells near the cancer cells. These results indicate that the proteins identified in this study are novel candidates for CRC markers, and that the NBS method is useful in proteome mining to discover novel biomarkers.     

Compact electrostatic levitator for diffraction measurements with a two axis diffractometer and a laboratory x-ray source

A compact electrostatic levitator was developed for the structural analysis of high-temperature liquids by x-ray diffraction methods. The size of the levitator was 200 mm in diameter and 200 mm in height and can be set up on a two axis diffractometer with a laboratory x-ray source, which is very convenient in performing structural measurements of high-temperature liquids. In particular, since the laboratory x-ray source allows a great amount of user time, preliminary or challenging experiments can be performed with trial and error, which prepares and complements synchrotron x-ray experiments. The present small apparatus also provides the advantage of portability and facility of setting. To demonstrate the capability of this electrostatic levitator, the static structure factors of alumina and silicon samples in their liquid phases were successfully measured.     

Evolutionary Learning of a Fuzzy Behavior Based Controller for a Nonholonomic Mobile Robot in a Class of Dynamic Environments

This paper presents an approach for evolving optimum behaviors for a nonholonomic mobile robot in a class of dynamic environments. A new evolutionary algorithm reflecting some powerful features in the natural evolutionary process to have flexibility to deal with changes in the environment is used to evolve optimum behaviors. Furthermore, a fuzzy set based multi-objective fitness evaluation function is adopted in the evolutionary algorithm. The multi-objective evaluation function is designed so that it allows incorporating complex linguistic features that a human observer would desire in the behaviors of the mobile robot movements. To illustrate the effectiveness of the proposed method, simulation results are compared using a conventional evolutionary algorithm.     

Variational Bayes solution of linear neural networks and its generalization performance

It is well known that in unidentifiable models, the Bayes estimation provides much better generalization performance than the maximum likelihood (ML) estimation. However, its accurate approximation by Markov chain Monte Carlo methods requires huge computational costs. As an alternative, a tractable approximation method, called the variational Bayes (VB) approach, has recently been proposed and has been attracting attention. Its advantage over the expectation maximization (EM) algorithm, often used for realizing the ML estimation, has been experimentally shown in many applications; nevertheless, it has not yet been theoretically shown. In this letter, through analysis of the simplest unidentifiable models, we theoretically show some properties of the VB approach. We first prove that in three-layer linear neural networks, the VB approach is asymptotically equivalent to a positive-part James-Stein type shrinkage estimation. Then we theoretically clarify its free energy, generalization error, and training error. Comparing them with those of the ML estimation and the Bayes estimation, we discuss the advantage of the VB approach. We also show that unlike in the Bayes estimation, the free energy and the generalization error are less simply related with each other and that in typical cases, the VB free energy well approximates the Bayes one, while the VB generalization error significantly differs from the Bayes one.     

Resource-Bounded Measure and Learnability

We consider the resource-bounded measure of polynomial-time learnable subclasses of polynomial-size circuits. We show that if EXP ≠ MA, then every PAC-learnable subclass of P/poly has EXP-measure zero. We introduce a nonuniformly computable variant of resource-bounded measure and show that, for every fixed polynomial q , any polynomial-time learnable subclass of circuits of size q has measure zero with respect to P/poly. We relate our results to the question of whether the class of Boolean circuits is polynomial-time learnable. Received July 15, 1998, and in final form September 9, 1999.     

Pattern recognition as conceptual morphogenesis

Pattern recognition is our mental activity in which we formulate, select, modify, and adjust our concepts or our frames of reference so that we can see a ``form' in objects. We can tentatively formulate this viewpoint as the principle of minimum entropy (or entropy-like function). Different algorithms in clustering and pattern recognition are given new interpretations in the light of this unifying principle.     

Adsorption isotherms of pigments from alkali-refined vegetable oils with clay minerals

Adsorption isotherms of pigments from alkali-refined oils (rapeseed, soybean, wheatgerm, safflower, corn, cottonseed and sunflower) were measured to investigate the applicability of the Langmuir and Freundlich equations and to elucidate the adsorption characteristics of pigments on sepiolites and standard activated clay. The Freundlich equation was more applicable to the experimental adsorption isotherms. The equilibrium amount adsorbed, acidity, pore size distribution and inflection of the Freundlich isotherms could be explained by assuming that pigments were adsorbed on the stronger acid sites in smaller pores at low concentration, and then in the larger ones when the concentration increased. The amount adsorbed increased with a rise in adsorption temperatures from 70 to 110°C, and the heat of adsorption was below 10 kcal/mol. The results indicate that pigments were physically adsorbed on the acid sites activated at higher adsorption temperatures.     

On intractability of the classUP

The classUP [V] is the class of sets accepted by polynomial-time nondeterministic Turing machines which have at most one accepting path for every input. The complexity of this class closely relates to that of computing inverses ofone-way functions, where a one-way function is a one-to-one, length-increasing, and polynomial-time computable function whose inverse cannot be computed within polynomial time. It is known [GS], [K] that there exists a one-way function if and only ifP UP. In this paper the intractability of sets inUP is investigated in terms of polynomial-time reducibility to a sparse set. It is shown thatUP has a set that is _m ^P -reducible to no sparse set ifP UP. We interpret this structural property in the relation with approximation algorithms: it is shown that ifP UP, thenUP has a set with no 1-APT approximation and, furthermore,UP has a set that is not _m ^P -reducible to any set with a 1-APT approximation. The implication of this result in the study of one-way functions is also discussed. In order to prove the main theorem, we introduce a variation of tree-pruning methods.This paper was written while the author visited the Department of Mathematics, University of California, Santa Barbara. This research was supported in part by the National Science Foundation under Grant CCR-8611980.