Novel fluorescence detection technique for non-contact temperature sensing in microchip PCR

DNA amplification using Polymerase Chain Reaction (PCR) in a small volume is used in Lab-on-a-chip systems involving DNA manipulation. For few microliters of volume of liquid, it becomes difficult to measure and monitor the thermal profile accurately and reproducibly, which is an essential requirement for successful amplification. Conventional temperature sensors are either not biocompatible or too large and hence positioned away from the liquid leading to calibration errors. In this work we present a fluorescence based detection technique that is completely biocompatible and measures directly the liquid temperature. PCR is demonstrated in a 3 ILL silicon-glass microfabricated device using non-contact induction heating whose temperature is controlled using fluorescence feedback from SYBR green I dye molecules intercalated within sensor DNA. The performance is compared with temperature feedback using a thermocouple sensor. Melting curve followed by gel electrophoresis is used to confirm product specificity after the PCR cycles. (c) 2007 Elsevier B.V. All rights reserved.

Self-Assembly of a Nanoscopic Prism via a New Organometallic Pt3 Acceptor and Its Fluorescent Detection of Nitroaromatics

A nanoscale-sized cage with a trigonal prismatic shape is prepared by coordination-driven self-assembly of a predesigned organometallic Pt-3 acceptor with an organic clip-type ligand. This trigonal prism is fluorescent and undergoes efficient fluorescence quenching by nitroaromatics, which are the chemical signatures of many explosives.

Performance of RT-PCR-ELISA for the detection of peste des petits ruminants virus

A highly sensitive and specific reverse transcription polymerase chain reaction enzyme linked immunosorbent assay (RT-PCR-ELISA) was developed for the objective detection of nucleoprotein (N) gene of peste des petits ruminants (PPR) virus from field outbreaks or experimentally infected sheep. Two primers (IndF and Np4) and one probe (Sp3) available or designed for the amplification/probing of the 'N' gene of PPR virus, were chosen for labeling and use in RT-PCR-ELISA based on highest analytical sensitivity of detection of infective virus or N-gene containing recombinant plasmid, higher nucleotide homology at the primer binding sites of the 'N' gene sequences available and the ability to amplify PPR viral genome from different sources of samples. RT-PCR was performed with unlabeled IndF and Np4 digoxigenin labeled primers followed by a microplate hybridization probe reaction with biotin labeled Sp3 probe. RT-PCR-ELISA was found to be 10-fold more sensitive than the conventional RT-PCR followed by agarose gel based detection of PCR product. Based on the Mean (mean +/- 3S.D.) optical density (OD) values of 47 RT-PCR negative samples, OD values above 0.306 were considered positive in RT-PCR-ELISA. A total of 82 oculo-nasal swabs and tissue samples from suspected PPR cases were analyzed by RT-PCR and RT-PCR-ELISA, which revealed 54.87 and 58.54% positivity, respectively. From an experimentally infected sheep, both RT-PCR and RT-PCR-ELISA could detect the virus from 6 days post-infection up to 9 days in oculo-nasal swabs. On post-mortem, PPR viral genome was detected in spleen, lymph node, lung, heart and liver. The correlation co-efficient between RT-PCR-ELISA OD values and either TCID50 of virus or molecules of DNA was 0.622 and 0.657, respectively. The advantages of RT-PCR-ELISA over the conventional agarose gel based detection of RT-PCR products are discussed. (c) 2006 Elsevier B.V. All rights reserved.

Usefulness of DARPA dataset for intrusion detection system evaluation

The MIT Lincoln Laboratory IDS evaluation methodology is a practical solution in terms of evaluating the performance of Intrusion Detection Systems, which has contributed tremendously to the research progress in that field. The DARPA IDS evaluation dataset has been criticized and considered by many as a very outdated dataset, unable to accommodate the latest trend in attacks. Then naturally the question arises as to whether the detection systems have improved beyond detecting these old level of attacks. If not, is it worth thinking of this dataset as obsolete? The paper presented here tries to provide supporting facts for the use of the DARPA IDS evaluation dataset. The two commonly used signature-based IDSs, Snort and Cisco IDS, and two anomaly detectors, the PHAD and the ALAD, are made use of for this evaluation purpose and the results support the usefulness of DARPA dataset for IDS evaluation.

Detection of alpha(2u)-globulin and its bound putative pheromones in the preputial gland of the Indian commensal rat (Rattus rattus) using mass spectrometry

The role of pheromones and pheromone-binding proteins in the laboratory rat has been extensively investigated. However, we have previously reported that the preputial gland of the Indian commensal rat produces a variety of pheromonal molecules and preputial glands would seem to be the predominant source for pheromonal communication. The presence of pheromone-binding proteins has not yet been identified in the preputial gland of the Indian commensal rat; therefore, the experiments were designed to unravel the alpha(2u)-globulin (alpha 2u) and its bound volatiles in the commensal rat. Total preputial glandular proteins were first fractionated by sodium dodecyl sulfate/polyacrylamide gel electrophoresis (SDS-PAGE) and subsequently analyzed by mass spectrometry. Further, we purified alpha 2u and screened for the presence of bound pheromonal molecules with the aid of gas chromatography/mass spectrometry (GC/MS). A novel alpha 2u was identified with a high score and this protein has not been previously described as present in the preputial gland of Indian commensal rats.This novel alpha 2u was then characterized by tandem mass spectrometry (MS/MS). Peptides with m/z values of 969, 1192, 1303 and 1876 were further fragmented with the aid of MS/MS and generated de novo sequences which provided additional evidence for the presence of alpha 2u in the preputial gland. Finally, we identified the presence of farnesol 1 and 2 bound to alpha 2u. The present investigation confirms the presence of alpha 2u (18.54 kDa) in the preputial gland of the Indian commensal rat and identifies farnesol 1 and 2 as probably involved in chemo-communication by the Indian commensal rat.Copyright (C) 2010 John Wiley & Sons, Ltd.

Selection of intrusion detection system threshold bounds for effective sensor fusion

The motivation behind the fusion of Intrusion Detection Systems was the realization that with the increasing traffic and increasing complexity of attacks, none of the present day stand-alone Intrusion Detection Systems can meet the high demand for a very high detection rate and an extremely low false positive rate. Multi-sensor fusion can be used to meet these requirements by a refinement of the combined response of different Intrusion Detection Systems. In this paper, we show the design technique of sensor fusion to best utilize the useful response from multiple sensors by an appropriate adjustment of the fusion threshold. The threshold is generally chosen according to the past experiences or by an expert system. In this paper, we show that the choice of the threshold bounds according to the Chebyshev inequality principle performs better. This approach also helps to solve the problem of scalability and has the advantage of failsafe capability. This paper theoretically models the fusion of Intrusion Detection Systems for the purpose of proving the improvement in performance, supplemented with the empirical evaluation. The combination of complementary sensors is shown to detect more attacks than the individual components. Since the individual sensors chosen detect sufficiently different attacks, their result can be merged for improved performance. The combination is done in different ways like (i) taking all the alarms from each system and avoiding duplications, (ii) taking alarms from each system by fixing threshold bounds, and (iii) rule-based fusion with a priori knowledge of the individual sensor performance. A number of evaluation metrics are used, and the results indicate that there is an overall enhancement in the performance of the combined detector using sensor fusion incorporating the threshold bounds and significantly better performance using simple rule-based fusion.

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.

A Wavelet based Teager Energy Operator for Spike Detection in Microelectrode Array Recordings

Spike detection in neural recordings is the initial step in the creation of brain machine interfaces. The Teager energy operator (TEO) treats a spike as an increase in the `local' energy and detects this increase. The performance of TEO in detecting action potential spikes suffers due to its sensitivity to the frequency of spikes in the presence of noise which is present in microelectrode array (MEA) recordings. The multiresolution TEO (mTEO) method overcomes this shortcoming of the TEO by tuning the parameter k to an optimal value m so as to match to frequency of the spike. In this paper, we present an algorithm for the mTEO using the multiresolution structure of wavelets along with inbuilt lowpass filtering of the subband signals. The algorithm is efficient and can be implemented for real-time processing of neural signals for spike detection. The performance of the algorithm is tested on a simulated neural signal with 10 spike templates obtained from [14]. The background noise is modeled as a colored Gaussian random process. Using the noise standard deviation and autocorrelation functions obtained from recorded data, background noise was simulated by an autoregressive (AR(5)) filter. The simulations show a spike detection accuracy of 90%and above with less than 5% false positives at an SNR of 2.35 dB as compared to 80% accuracy and 10% false positives reported [6] on simulated neural signals.

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.

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.