Detection,amplification and sequence homology of sodC in clinical isolates of Salmonella sp

Background & objectives: Periplasmic copper and zinc superoxide dismutase (Cu,Zn-SOD or SodC) is an important component of the antioxidant shield which protects bacteria from the phagocytic oxidative burst. Cu,Zn-SODs protect Gram-negative bacteria against oxygen damage which have also been shown to contribute to the pathogenicity of these bacterial species. We report the presence of SodC in drug resistant Salmonella sp. isolated from patients suffering from enteric fever. Further sodC was amplified, cloned into Escherichia coli and the nucleotide sequence and amino acid sequence homology were compared with the standard strain Salmonella Typhimurium 14028. Methods: Salmonella enterica serovar Typhi (S. Typhi) and Salmonellaenterica serovar Paratyphi (S. Paratyphi) were isolated and identified from blood samples of the patients. The isolates were screened for the presence of Cu, Zn-SOD by PAGE using KCN as inhibitor of Cu,Zn-SOD. The gene (sodC) was amplified by PCR, cloned and sequenced. The nucleotide and amino acid sequences of sodC were compared using CLUSTAL X.Results: SodC was detected in 35 per cent of the Salmonella isolates. Amplification of the genomic DNA of S. Typhi and S. Paratyphi with sodC specific primers resulted in 519 and 515 bp amplicons respectively. Single mutational difference at position 489 was observed between thesodC of S. Typhi and S. Paratyphi while they differed at 6 positions with the sodC of S. Typhimurium 14028. The SodC amino acid sequences of the two isolates were homologous but 3 amino acid difference was observed with that of standard strain S. Typhimurium 14028.Interpretation & conclusions: The presence of SodC in pathogenic bacteria could be a novel candidate as phylogenetic marker.

Detection of multiple source locations using a glowworm metaphor with applications to collective robotics

This paper presents a glowworm swarm based algorithm that finds solutions to optimization of multiple optima continuous functions. The algorithm is a variant of a well known ant-colony optimization (ACO) technique, but with several significant modifications. Similar to how each moving region in the ACO technique is associated with a pheromone value, the agents in our algorithm carry a luminescence quantity along with them. Agents are thought of as glowworms that emit a light whose intensity is proportional to the associated luminescence and have a circular sensor range. The glowworms depend on a local-decision domain to compute their movements. Simulations demonstrate the efficacy of the proposed glowworm based algorithm in capturing multiple optima of a multimodal function. The above optimization scenario solves problems where a collection of autonomous robots is used to form a mobile sensor network. In particular, we address the problem of detecting multiple sources of a general nutrient profile that is distributed spatially on a two dimensional workspace using multiple robots.

Detection of a periodic structure hidden in random background: the role of signal amplitude in the matched filter detection method

The matched filter method for detecting a periodic structure on a surface hidden behind randomness is known to detect up to (r(0)/Lambda) gt;= 0.11, where r(0) is the coherence length of light on scattering from the rough part and 3 is the wavelength of the periodic part of the surface-the above limit being much lower than what is allowed by conventional detection methods. The primary goal of this technique is the detection and characterization of the periodic structure hidden behind randomness without the use of any complicated experimental or computational procedures. This paper examines this detection procedure for various values of the amplitude a of the periodic part beginning from a = 0 to small finite values of a. We thus address the importance of the following quantities: `(a)lambda) `, which scales the amplitude of the periodic part with the wavelength of light, and (r(0))Lambda),in determining the detectability of the intensity peaks.

Performance analysis of a suprathreshold, stochastic resonance based nonlinear detector

In this paper we introduce a nonlinear detector based on the phenomenon of suprathreshold stochastic resonance (SSR). We first present a model (an array of 1-bit quantizers) that demonstrates the SSR phenomenon. We then use this as a pre-processor to the conventional matched filter. We employ the Neyman-Pearson(NP) detection strategy and compare the performances of the matched filter, the SSR-based detector and the optimal detector. Although the proposed detector is non-optimal, for non-Gaussian noises with heavy tails (leptokurtic) it shows better performance than the matched filter. In situations where the noise is known to be leptokurtic without the availability of the exact knowledge of its distribution, the proposed detector turns out to be a better choice than the matched filter.

On resampling detection and its application to detect image tampering

Usually digital image forgeries are created by copy-pasting a portion of an image onto some other image. While doing so, it is often necessary to resize the pasted portion of the image to suit the sampling grid of the host image. The resampling operation changes certain characteristics of the pasted portion, which when detected serves as a clue of tampering. In this paper, we present deterministic techniques to detect resampling, and localize the portion of the image that has been tampered with. Two of the techniques are in pixel domain and two others in frequency domain. We study the efficacy of our techniques against JPEG compression and subsequent resampling of the entire tampered image.

Transient signal detection using wigner-ville distribution and wavelet denoising

The problem of detecting an unknown transient signal in noise is considered. The SNR of the observed data is first enhanced using wavelet domain filter The output of the wavelet domain filter is then transformed using a Wigner-Ville transform,which separates the spectrum of the observed signal into narrow frequency bands. Each subband signal at the output of the Wigner-ville block is subjected kto wavelet based level dependent denoising (WBLDD)to supress colored noise A weighted sum of the absolute value of outputs of WBLDD is passed through an energy detector, whose output is used as test statistic to take the final decision. By assigning weights proportional to the energy of the corresponding subband signals, the proposed detector approximates a frequency domain matched filter Simulation results are presented to show that the performance of the proposed detector is better than that of the wavelet packet transform based detector.

Pressure sensor based tsunami detection system: A laboratory study

In this paper, we present the study and implementation of a low-cost system to detect the occurrences of tsunamis at significantly smaller laboratory scale. The implementation is easily scalable for real-time deployment. Information reported in this paper includes the experimentally recorded response from the pressure sensor giving an indication as well as an alarm at remote place for the detection of water turbulence similar to the case of tsunami. It has been found that the system developed works very well in the laboratory scale.

Multiple imaging with an aberration optimized hololens array

The imaging performance of hololenses formed with four different geometries were studied through an analysis of their third-order aberration coefficients. It is found that the geometry proposed by Brandt (1969) gives the least residual aberration with minimum variation of this aberration with the reconstruction angle. When the ideal position of one of the construction beams is changed in order to generate a hololens array, the residual aberration is found to increase sharply, which in turn affects the image resolution among the multiplied images in the output. A hololens array was generated using Brandt's geometry with the help of a one-dimensional sinusoidal grating. The results of multiple imaging with the hololens array are presented. The image resolution is reasonably high and can be further improved by reducing the f-number of the hololenses.

Parallel circuit partitioning on a reduced array architecture

The physical design of a VLSI circuit involves circuit partitioning as a subtask. Typically, it is necessary to partition a large electrical circuit into several smaller circuits such that the total cross-wiring is minimized. This problem is a variant of the more general graph partitioning problem, and it is known that there does not exist a polynomial time algorithm to obtain an optimal partition. The heuristic procedure proposed by Kernighan and Lin1,2 requires O(n2 log2n) time to obtain a near-optimal two-way partition of a circuit with n modules. In the VLSI context, due to the large problem size involved, this computational requirement is unacceptably high. This paper is concerned with the hardware acceleration of the Kernighan-Lin procedure on an SIMD architecture. The proposed parallel partitioning algorithm requires O(n) processors, and has a time complexity of O(n log2n). In the proposed scheme, the reduced array architecture is employed with due considerations towards cost effectiveness and VLSI realizability of the architecture.The authors are not aware of any earlier attempts to parallelize a circuit partitioning algorithm in general or the Kernighan-Lin algorithm in particular. The use of the reduced array architecture is novel and opens up the possibilities of using this computing structure for several other applications in electronic design automation.

Acoustic emission technique for leak detection in an end shield of a pressurised heavy water reactor

This paper discusses a successful application of the Acoustic Emission Technique (AET) for the detection and location of leak paths present on an inaccessible side of an end shield of a Pressurised Heavy Water Reactor (PHWR). The methodology was based on the fact that air- and water-leak AE signals have different characteristic features. Baseline data was generated from a sound end shield of a PHWR for characterising the background noise. A mock-up end shield system with saw-cut leak paths was used to verify the validity of the methodology. It was found that air-leak signals under pressurisation (as low as 3 psi) could be detected by frequency domain analysis. Signals due to air leaks from various locations of defective end shield were acquired and analysed. It was possible to detect and locate leak paths. The presence of detected leak paths was further confirmed by an alternative test.

Detection of Tsunami Wave Generation and Propagation Using Fiber Bragg Grating Sensors

This paper describes the design and development of a Fiber Bragg Grating (FBG) sensor system for monitoring tsunami waves generated in the deep ocean. An experimental setup was designed and fabricated to simulate the generation and propagation of a tsunami wave. The characteristics and efficiency of the developed FBG sensor was evaluated with a standard commercial Digiquartz sensor. For real time monitoring of tsunami waves, FBG sensors bonded to a cantilever is used and the wavelength shifts (Delta lambda(B)) in the reflected spectra resulting from the strain/pressure imparted on the FBGs have been recorded using a high-speed Micron Optics FBG interrogation system. The parameters sensed are the signal burst during tsunami generation and pressure variations at different places as the tsunami wave propagates away from the source of generation. The results obtained were compared with the standard commercial sensor used in tsunami detection. The observations suggest that the FBG sensor was highly sensitive and free from many of the constraints associated with the commercial tsunameter.

Detection of moisture stress by indicator plots — A simulation

The possibility of advanced indication of moisture stress in a crop by small prepared plots with compacted or partially sand-substituted soils is examined by an analytical simulation. A series of soils and three crops are considered for the simulation. The moisture characteristics of the soils are calculated with an available model. Using average potential evapotranspiration values and a simple actual evapotranspiration model, the onset of moisture stress in the natural and indicator plots is calculated for different degrees of sand substitution and compaction. Cases where sand substitution fails are determined. The effect of intervening rainfall and limited root depth on the beginning of moisture stress is investigated.

sRNAscanner: A Computational Tool for Intergenic Small RNA Detection in Bacterial Genomes

Background:Bacterial non-coding small RNAs (sRNAs) have attracted considerable attention due to their ubiquitous nature and contribution to numerous cellular processes including survival, adaptation and pathogenesis. Existing computational approaches for identifying bacterial sRNAs demonstrate varying levels of success and there remains considerable room for improvement. Methodology/Principal Findings: Here we have proposed a transcriptional signal-based computational method to identify intergenic sRNA transcriptional units (TUs) in completely sequenced bacterial genomes. Our sRNAscanner tool uses position weight matrices derived from experimentally defined E. coli K-12 MG1655 sRNA promoter and rho-independent terminator signals to identify intergenic sRNA TUs through sliding window based genome scans. Analysis of genomes representative of twelve species suggested that sRNAscanner demonstrated equivalent sensitivity to sRNAPredict2, the best performing bioinformatics tool available presently. However, each algorithm yielded substantial numbers of known and uncharacterized hits that were unique to one or the other tool only. sRNAscanner identified 118 novel putative intergenic sRNA genes in Salmonella enterica Typhimurium LT2, none of which were flagged by sRNAPredict2. Candidate sRNA locations were compared with available deep sequencing libraries derived from Hfq-co-immunoprecipitated RNA purified from a second Typhimurium strain (Sittka et al. (2008) PLoS Genetics 4: e1000163). Sixteen potential novel sRNAs computationally predicted and detected in deep sequencing libraries were selected for experimental validation by Northern analysis using total RNA isolated from bacteria grown under eleven different growth conditions. RNA bands of expected sizes were detected in Northern blots for six of the examined candidates. Furthermore, the 5'-ends of these six Northern-supported sRNA candidates were successfully mapped using 5'-RACE analysis. Conclusions/Significance: We have developed, computationally examined and experimentally validated the sRNAscanner algorithm. Data derived from this study has successfully identified six novel S. Typhimurium sRNA genes. In addition, the computational specificity analysis we have undertaken suggests that similar to 40% of sRNAscanner hits with high cumulative sum of scores represent genuine, undiscovered sRNA genes. Collectively, these data strongly support the utility of sRNAscanner and offer a glimpse of its potential to reveal large numbers of sRNA genes that have to date defied identification. sRNAscanner is available from: http://bicmku.in:8081/sRNAscanner or http://cluster.physics.iisc.ernet.in/sRNAscanner/.