Khalid Sayood

Statistical evaluation of image quality measures

In this work we comprehensively categorize image qual- ity measures, extend measures defined for gray scale images to their multispectral case, and propose novel image quality measures. They are categorized into pixel difference-based, correlation-based, edge-based, spectral-based, context-based and human visual sys- tem (HVS)-based measures. Furthermore we compare these mea- sures statistically for still image compression applications. The sta- tistical behavior of the measures and their sensitivity to coding artifacts are investigated via analysis of variance techniques. Their similarities or differences are illustrated by plotting their Kohonen maps. Measures that give consistent scores across an image class and that are sensitive to coding artifacts are pointed out. It was found that measures based on the phase spectrum, the multireso- lution distance or the HVS filtered mean square error are computa- tionally simple and are more responsive to coding artifacts. We also demonstrate the utility of combining selected quality metrics in build- ing a steganalysis tool.

A new sequence distance measure for phylogenetic tree construction

MOTIVATION Most existing approaches for phylogenetic inference use multiple alignment of sequences and assume some sort of an evolutionary model. The multiple alignment strategy does not work for all types of data, e.g. whole genome phylogeny, and the evolutionary models may not always be correct. We propose a new sequence distance measure based on the relative information between the sequences using Lempel-Ziv complexity. The distance matrix thus obtained can be used to construct phylogenetic trees. RESULTS The proposed approach does not require sequence alignment and is totally automatic. The algorithm has successfully constructed consistent phylogenies for real and simulated data sets. AVAILABILITY Available on request from the authors.

Use of residual redundancy in the design of joint source/channel coders

A technique for providing error protection without the additional overhead required for channel coding is presented. The authors start from the premise that, during source coder design, for the sake of simplicity or due to imperfect knowledge, assumptions have to be made about the source which are often incorrect. This results in residual redundancy at the output of the source coder. The residual redundancy can then be used to provide error protection in much the same way as the insertion of redundancy in convolutional coding provides error protection. The authors develop an approach for utilizing this redundancy. To show the validity of this approach, the authors apply it to image coding using differential pulse code modulation (DPCM), and obtain substantial performance gains, both in terms of objective and subjective measures. >

Inactivation of Phospholipase D Diminishes Acinetobacter baumannii Pathogenesis

ABSTRACT Acinetobacter baumannii is an emerging bacterial pathogen of considerable health care concern. Nonetheless, relatively little is known about the organisms virulence factors or their regulatory networks. Septicemia and ventilator-associated pneumonia are two of the more severe forms of A. baumannii disease. To identify virulence factors that may contribute to these disease processes, genetically diverse A. baumannii clinical isolates were evaluated for the ability to proliferate in human serum. A transposon mutant library was created in a strain background that propagated well in serum and screened for members with decreased serum growth. The results revealed that disruption of A. baumannii phospholipase D (PLD) caused a reduction in the organisms ability to thrive in serum, a deficiency in epithelial cell invasion, and diminished pathogenesis in a murine model of pneumonia. Collectively, these results suggest that PLD is an A. baumannii virulence factor.

Joint source/channel coding for variable length codes

When using entropy coding over a noisy channel, it is customary to protect the highly vulnerable bitstream with an error correcting code. In this paper, we propose a technique which utilizes the residual redundancy at the output of the source coder to provide error protection for entropy coded systems.

Lossless compression of video sequences

We investigate lossless compression schemes for video sequences. A simple adaptive prediction scheme is presented that exploits temporal correlations or spectral correlations in addition to spatial correlations. It is seen that even with motion compensation, schemes that utilize only temporal correlations do not perform significantly better than schemes that utilize only spectral correlations. Hence, we look at hybrid schemes that make use of both spectral and temporal correlations. The hybrid schemes give significant improvement in performance over other techniques. Besides prediction schemes, we also look at some simple error modeling techniques that take into account prediction errors made in spectrally and/or temporally adjacent pixels in order to efficiently encode the prediction residual. Implementation results on standard test sequences indicate that significant improvements can be obtained by the proposed techniques.

A constrained joint source/channel coder design

The design of joint source/channel coders in situations where there is residual redundancy at the output of the source coder is examined. It has previously been shown that this residual redundancy can be used to provide error protection without a channel coder. In this paper, this approach is extended to conventional source coder/convolutional coder combinations. A family of nonbinary encoders is developed which more efficiently use the residual redundancy in the source coder output. It is shown through simulation results that the proposed systems outperform conventional source-channel coder pairs with gains of greater than 9 dB in the reconstruction SNR at high probability of error. >

Joint source/channel coding using arithmetic codes

Reserving space fur a symbol that is not in the source alphabet has been shown to provide excellent error detection. In this paper, we show how to exploit this capability using two sequential decoder structures to provide powerful error correction capability. This joint source/channel coder design provides significant packet loss recovery with minimal rate overhead, and compares favorably with conventional schemes.

Lossless compression of multispectral image data

While spatial correlations are adequately exploited by standard lossless image compression techniques, little success has been attained in exploiting spectral correlations when dealing with multispectral image data. The authors present some new lossless image compression techniques that capture spectral correlations as well as spatial correlation in a simple and elegant manner. The schemes are based on the notion of a prediction tree, which defines a noncausal prediction model for an image. The authors present a backward adaptive technique and a forward adaptive technique. They then give a computationally efficient way of approximating the backward adaptive technique. The approximation gives good results and is extremely easy to compute. Simulation results show that for high spectral resolution images, significant savings can be made by using spectral correlations in addition to spatial correlations. Furthermore, the increase in complexity incurred in order to make these gains is minimal. >

Identification of two small regulatory RNAs linked to virulence in Brucella abortus 2308

Hfq is an RNA‐binding protein that functions in post‐transcriptional gene regulation by mediating interactions between mRNAs and small regulatory RNAs (sRNAs). Two proteins encoded by BAB1_1794 and BAB2_0612 are highly over‐produced in a Brucella abortus hfq mutant compared with the parental strain, and recently, expression of orthologues of these proteins in Agrobacterium tumefaciens was shown to be regulated by two sRNAs, called AbcR1 and AbcR2. Orthologous sRNAs (likewise designated AbcR1 and AbcR2) have been identified in B. abortus 2308. In Brucella, abcR1 and abcR2 single mutants are not defective in their ability to survive in cultured murine macrophages, but an abcR1 abcR2 double mutant exhibits significant attenuation in macrophages. Additionally, the abcR1 abcR2 double mutant displays significant attenuation in a mouse model of chronic Brucella infection. Quantitative proteomics and microarray analyses revealed that the AbcR sRNAs predominantly regulate genes predicted to be involved in amino acid and polyamine transport and metabolism, and Northern blot analyses indicate that the AbcR sRNAs accelerate the degradation of the target mRNAs. In an Escherichia coli two‐plasmid reporter system, overexpression of either AbcR1 or AbcR2 was sufficient for regulation of target mRNAs, indicating that the AbcR sRNAs from B. abortus 2308 perform redundant regulatory functions.