Abstract-An adaptive spatial fuzzy c-means clustering algorithm is presented in this paper for the segmentation of three-dimensional (3-D) magnetic resonance (MR) images. The input images may be corrupted by noise and intensity nonuniformity (INU) artifact. The proposed algorithm takes into account the spatial continuity constraints by using a dissimilarity index that allows spatial interactions between image voxels. The local spatial continuity constraint reduces the noise effect and the classification ambiguity. The INU artifact is formulated as a multiplicative bias field affecting the true MR imaging signal. By modeling the log bias field as a stack of smoothing -spline surfaces, with continuity enforced across slices, the computation of the 3-D bias field reduces to that of finding the -spline coefficients, which can be obtained using a computationally efficient two-stage algorithm. The efficacy of the proposed algorithm is demonstrated by extensive segmentation experiments using both simulated and real MR images and by comparison with other published algorithms.Index Terms-Adaptive spatial fuzzy clustering, intensity nonuniformity correction, MR image segmentation, spatial continuity constraint, spline approximation.

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Abstract-Detecting blood vessels in retinal images with the presence of bright and dark lesions is a challenging unsolved problem. In this paper, a novel multiconcavity modeling approach is proposed to handle both healthy and unhealthy retinas simultaneously. The differentiable concavity measure is proposed to handle bright lesions in a perceptive space. The line-shape concavity measure is proposed to remove dark lesions which have an intensity structure different from the line-shaped vessels in a retina. The locally normalized concavity measure is designed to deal with unevenly distributed noise due to the spherical intensity variation in a retinal image. These concavity measures are combined together according to their statistical distributions to detect vessels in general retinal images. Very encouraging experimental results demonstrate that the proposed method consistently yields the best performance over existing state-of-the-art methods on the abnormal retinas and its accuracy outperforms the human observer, which has not been achieved by any of the state-of-the-art benchmark methods. Most importantly, unlike existing methods, the proposed method shows very attractive performances not only on healthy retinas but also on a mixture of healthy and pathological retinas.

Microarray gene expression data generally suffers from missing value problem due to a variety of experimental reasons. Since the missing data points can adversely affect downstream analysis, many algorithms have been proposed to impute missing values. In this survey, we provide a comprehensive review of existing missing value imputation algorithms, focusing on their underlying algorithmic techniques and how they utilize local or global information from within the data, or their use of domain knowledge during imputation. In addition, we describe how the imputation results can be validated and the different ways to assess the performance of different imputation algorithms, as well as a discussion on some possible future research directions. It is hoped that this review will give the readers a good understanding of the current development in this field and inspire them to come up with the next generation of imputation algorithms.

It is well known that at low-bit-rate block discrete cosine transform compressed image exhibits visually annoying blocking and ringing artifacts. In this paper, we propose a noniterative, wavelet-based deblocking algorithm to reduce both types of artifacts. The algorithm exploits the fact that block discontinuities are constrained by the dc quantization interval of the quantization table, as well as the behavior of wavelet modulus maxima evolution across wavelet scales to derive appropriate threshold maps at different wavelet scales. Since ringing artifacts occur near strong edges, which can be located either along block boundaries or within blocks, suppression of block discontinuities does not always reduce ringing artifacts. By exploiting the behavior of ringing artifacts in the wavelet domain, we propose a simple yet effective method for the suppression of such artifacts. The proposed algorithm can suppress both block discontinuities and ringing artifacts effectively while preserving true edges and textural information. Simulation results and extensive comparative study with both iterative and noniterative methods reported in the literature have shown the effectiveness of our algorithm.Index Terms-Block discrete cosine transform (BDCT), blocking artifacts, overcomplete wavelet, wavelet deblocking.

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Mutant prevention concentration (MPC) has been proposed as a new measure of antibiotic potency by which the ability to restrict selection of resistant mutants is evaluated. To determine whether MPC provides potency information unavailable from the more customary measurement of the MIC, 18 fluoroquinolones were examined for their ability to block the growth of Mycobacterium smegmatis and to select resistant mutants from wild-type populations. Both MPC and MIC were affected by changes in the moiety at the fluoroquinolone C-8 position and in alkyl groups attached to the C-7 piperazinyl ring. When eight resistant mutants, altered in the gyrase A protein, were tested with fluoroquinolones having either a methoxy or a hydrogen at the C-8 position, the MIC for the most resistant mutant correlated better with the MPC than did the MIC for wild-type cells. For C-8-fluorine derivatives, which were generally less active than the C-8-methoxy compounds but which were more active than C-8-hydrogen derivatives, the MICs for both the mutant and the wild type correlated well with the MPCs. Thus, measurement of the MICs for wild-type cells can reflect the ability of a quinolone to restrict the selection of resistance, but often it does not. With the present series of compounds, the most potent contained a C-8-methoxy and a small group attached to the C-7 ring.To develop more effective antituberculosis agents, we have been studying the fluoroquinolones. These compounds, which act by trapping gyrase on DNA, are generally used only as second-line therapeutics because resistance mutations in Mycobacterium tuberculosis often render them ineffective. For example, in the early 1990s a strain of M. tuberculosis resistant to isoniazid, rifampin, streptomycin, and ethambutol spread among immunocompromised persons in New York City (1). Patients were treated with the fluoroquinolone ciprofloxacin, and within a few months some were found harboring strains of M. tuberculosis that were resistant to fluoroquinolones as well as to the four other agents (11). When we examined these strains, we noticed that some fluoroquinolones (e.g., sparfloxacin) were more effective than others (e.g., ciprofloxacin) at blocking the growth of resistant mutants after the data were normalized to the results obtained with wild-type cells (5,12). This observation led to the idea that some quinolones might be better than others at trapping resistant gyrase in mycobacteria. Subsequent work showed that compounds with a methoxy group attached to the C-8 position (C-8-OMe) were particularly effective against resistant mutants (5, 13).While examining the effects of C-8-OMe groups we observed a complex relationship between the recovery of resistant mutants and the fluoroquinolone concentration (6). Increases in fluoroquinolone concentration cause the fraction of cells that form colonies on quinolone-containing agar to drop sharply to a plateau and then drop sharply a second time. We proposed that the plateau is due to the presence of first-step, resistant mutants in the popu...

Analysis of complex protein samples by two-dimensional electrophoresis (2-DE) is often more difficult in the presence of a few predominant proteins. In plasma, proteins such as albumin mask proteins of lower abundance, as well as significantly limiting the amount of protein that can be loaded onto the immobilized pH gradient strip. In this paper the Gradiflow, a preparative electrophoresis system, has been used to deplete human plasma of the highly abundant protein albumin under native and denatured conditions. A three step protocol incorporating a charge separation to collect proteins with an isoelectric point greater than albumin and two size separations to isolate proteins larger and smaller than albumin, was used. When the albumin depleted fractions were analysed on pH 3-10 2-DE gels, proteins that were masked by albumin were revealed and proteins not seen in the unfractionated plasma sample were visualised. Matrix-assisted laser desorption/ionisation-time of flight mass spectrometry analysis confirmed the identification of the protein that lies beneath albumin to be C4B-binding protein alpha chain. The liquid fractions from the Gradiflow separations were also analysed by liquid chromatography-tandem mass spectrometry to confirm the proteins were separated according to their size and charge mobility in an electric field.