DichroMatch: a website for similarity searching of circular dichroism spectra

Circular dichroism (CD) spectroscopy is a widely used method for examining the structure, folding and conformational changes of proteins. A new online CD analysis server (DichroMatch) has been developed for identifying proteins with similar spectral characteristics by detecting possible structurally and functionally related proteins and homologues. DichroMatch includes six different methods for determining the spectral nearest neighbours to a query protein spectrum and provides metrics of how similar these spectra are and, if corresponding crystal structures are available for the closest matched proteins, information on their secondary structures and fold classifications. By default, DichroMatch uses all the entries in the Protein Circular Dichroism Data Bank (PCDDB) for its comparison set, providing the broadest range of publicly available protein spectra to match with the unknown protein. Alternatively, users can download or create their own specialized data sets, thereby enabling comparisons between the structures of related proteins such as wild-type versus mutants or homologues or a series of spectra of the same protein under different conditions. The DichroMatch server is freely available at http://dichromatch.cryst.bbk.ac.uk

Mutagenesis of the NaChBac sodium channel discloses a functional role for a conserved S6 asparagine

Asparagine is conserved in the S6 transmembrane segments of all voltage-gated sodium, calcium, and TRP channels identified to date. A broad spectrum of channelopathies including cardiac arrhythmias, epilepsy, muscle diseases, and pain disorders is associated with its mutation. To investigate its effects on sodium channel functional properties, we mutated the simple prokaryotic sodium channel NaChBac. Electrophysiological characterization of the N225D mutant reveals that this conservative substitution shifts the voltage-dependence of inactivation by 25 mV to more hyperpolarized potentials. The mutant also displays greater thermostability, as determined by synchrotron radiation circular dichroism spectroscopy studies of purified channels. Based on our analyses of high-resolution structures of NaChBac homologues, we suggest that the side-chain amine group of asparagine 225 forms one or more hydrogen bonds with different channel elements and that these interactions are important for normal channel function. The N225D mutation eliminates these hydrogen bonds and the structural consequences involve an enhanced channel inactivation

A Signal Processing Perspective on Hyperspectral Unmixing: Insights from Remote Sensing

peer reviewe

Knowledge integration in a multiple classifier system

This paper introduces a knowledge integration framework based on Dempster-Shafer's mathematical theory of evidence for integrating classification results derived from multiple classifiers. This framework enables us to understand in which situations the classifiers give uncertain responses, to interpret classification evidence, and allows the classifiers to compensate for their individual deficiencies. Under this framework, we developed algorithms to model classification evidence and combine classification evidence form difference classifiers, we derived inference rules from evidential intervals for reasoning about classification results. The algorithms have been implemented and tested. Implementation issues, performance analysis and experimental results are presented.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/44300/1/10489_2004_Article_BF00117809.pd

Fourier descriptors and handwritten digit recognition

This paper presents the results of a comparative study of various Fourier descriptor representations and their use in recognition of unconstrained handwritten digits. Certain characteristics of five distinct Fourier descriptor representations of handwritten digits are discussed, and illustrations of ambiguous digit classes introduced by use of these Fourier descriptor representations are presented. It is concluded that Fourier descriptors are practically effective only within the framework of an intelligent system, capable of reasoning about digit hypotheses. We describe a hypothesisgenerating algorithm based on Fourier descriptors which allows a classifier to associate more than one digit class with each input. Such hypothesis-generating schemes can be very effective in systems employing multiple classifiers. We compare the performance of the five Fourier descriptor representations based on experiment results produced by a particular hypothesis-generating classifier for a test set of 14000 handwritten digits. It is found that some Fourier descriptor formulations are more successful than others for handwritten digit recognition.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/46057/1/138_2005_Article_BF01212429.pd

NaChBac: The Long Lost Sodium Channel Ancestor

In excitable cells, the main mediators of sodium conductance across membranes are voltage-gated sodium channels (Na(V)s). Eukaryotic Na(V)s are essential elements in neuronal signaling and muscular contraction and in humans have been causally related to a variety of neurological and cardiovascular channelopathies. They are complex heavily glycosylated intrinsic membrane proteins present in only trace quantities that have proven to be challenging objects of study. However, in recent years, a number of simpler prokaryotic sodium channels have been identified, with NaChBac from Bacillus halodurans being the most well-characterized to date. The availability of a bacterial Na(V) that is amenable to heterologous expression and functional characterization in both bacterial and mammalian systems has provided new opportunities for structure--function studies. This review describes features of NaChBac as an exemplar of this class of bacterial channels, compares prokaryotic and eukaryotic Na(V)s with respect to their structural organization, pharmacological profiling, and functional kinetics, and discusses how voltage-gated ion channels may have evolved to deal with the complex functional demands of higher organisms

Fusion of Multiple Handwritten Word Recognition Techniques

Fusion of multiple handwritten word recognition techniques is described. A novel borda count for fusion based on ranks and confidence values is proposed. Three techniques with two different conventional segmentation algorithms in conjunction with backpropagation and radial basis function neural networks have been used in this research. Development has taken place at the University of Missouri and Griffith University. All experiments were performed on real-world handwritten words taken from the CEDAR benchmark database. The word recognition results are very promising and highest (91 96) among published results for handwritten words