Nucleic acid amplification testing for Neisseria gonorrhoeae: An ongoing challenge

Nucleic acid amplification tests (NAATs) for the detection of Neisseria gonorrhoeae became available in the early 1990s. Although offering several advantages over traditional detection methods, N. gonorrhoeae NAATs do have some limitations. These include cost, risk of carryover contamination, inhibition, and inability to provide antibiotic resistance data. In addition, there are sequence-related limitations that are unique to N. gonorrhoeae NAATs. In particular, false-positive results are a major consideration. These primarily stem from the frequent horizontal genetic exchange occurring within the Neisseria genus, leading to commensal Neisseria species acquiring N. gonorrhoeae genes. Furthermore, some N. gonorrhoeae subtypes may lack specific sequences targeted by a particular NAAT. Therefore, NAAT false-negative results because of sequence variation may occur in some gonococcal populations. Overall, the N. gonorrhoeae species continues to present a considerable challenge for molecular diagnostics. The need to evaluate N. gonorrhoeae NAATs before their use in any new patient population and to educate physicians on the limitations of these tests is emphasized in this review.

Chromogenic in situ hybridisation testing for HER2 gene amplification in breast cancer produces highly reproducible results concordant with fluorescence in situ hybridisation and immunohistochemistry

Aims: The objective of this study was to evaluate the accuracy, ease of use and reproducibility of chromogenic in situ hybridisation (CISH) for HER2 testing by studying its inter-laboratory concordance in five Australian pathology laboratories. Methods: The HER2 status of 49 breast cancers was determined by CISH twice in two different laboratories. Each sample had previously been tested by immunohistochemistry (IHC; 2+ and 3+ cases selected) and fluorescence in situ hybridisation ( FISH). Participating laboratories were blinded to these test results. Oestrogen receptor ( ER) status was also evaluated for each cancer. Results: High correlation was observed between FISH and CISH results. No cases showing high gene amplification by FISH were scored as non-amplified by CISH ( kappa coefficient=1). High correlation was observed between IHC and CISH, all IHC 3+ samples showing amplification by CISH. Inter-laboratory CISH concordance was also good ( kappa coefficient=0.67). Fifty-six per cent of HER2-amplified samples tested ER positive, while 42% of ER-positive cases showed HER2 gene amplification, confirming that HER2 testing should not be confined to ER-negative breast cancers. Conclusions: These findings demonstrate that CISH is a robust test to assess HER2 status in breast cancer and therefore is an important addition to the HER2 testing algorithm.

Raman amplification and performance altering effects

This thesis presents an experimental investigation into several applications of the Raman scattering effect in communication optical fibres as well as how some of these applications can be modified to enhance the resulting performance. The majority of the work contained within is based on laboratory results using many commercially available components. The results can be divided into and presented in three main parts: Firstly, a novel application of a known effect is used to broaden Raman pump light in order to achieve a more continuous distribution of gain with respect to wavelength. Multiple experimental results are presented, all based around the prior spreading of the pump spectrum before being used in the desired transmission fibre. Gathered results show that a notable improvement can be obtained from applying such a technique along with the scope for further optimisation work. Secondly, an investigation into the interaction between the well known effect of Four Wave Mixing (FWM) and Raman scattering is provided. The work provides an introduction to the effect as well commenting on previous literature regarding the effect and its mitigation. In response to existing research experimental results are provided detailing some limitations of proposed schemes along with concepts of how further alleviation from the deleterious effects maybe obtained. Lastly, the distributed nature of the Raman gain process is explored. A novel technique on how a near constant distribution of gain can be employed is implemented practically. The application of distributed gain is then applied to the generation of optical pulses with special mathematical properties within a laboratory setting and finally the effect of pump noise upon distributed gain techniques is acknowledged.

Phase dependent forward three wave amplification in photorefractive BSO

The results of three wave mixing experiments in photorefractive Bi12SiO20 are presented. The results confirm theoretical predictions that amplification by three wave mixing is strongly dependent on the phase relationship between the three beams at the input to the medium.

Amplification of temporally modulated signal beams via two-wave mixing in Bi12SiO20

A theoretical analysis of two-wave mixing in a BSO crystal is developed in the undepleted-pump approximation for a modulated signal beam. It is shown that, for a modulation of high enough frequency, significant ac amplification is possible at three distinct values of pump-beam detuning. A signal beam that is amplitude modulated by a square wave is analyzed by means of the theory, and experimental results are presented in confirmation of the analysis. Finally, it is shown that in the presence of absorption the optimum detunings for dc and ac amplification are different.

A practical phase sensitive amplification scheme for two channel phase regeneration

A "black-box" phase sensitive amplifier is presented achieving simultaneous suppression of deterministic phase distortion on two independent 42.66 Gbit/s DPSK modulated signal wavelengths.

Impact of Raman amplification on a 2 Tb/s coherent WDM system

The impact of hybrid erbium-doped fiber amplifier (EDFA)/Raman amplification on a spectrally efficient coherent-wavelength-division-multiplexed (CoWDM) optical communication system is experimentally studied and modeled. Simulations suggested that 23-dB Raman gain over an unrepeatered span of 124 km single-mode fiber would allow a decrease of the mean input power of ~6 dB for a fixed bit-error rate (BER). Experimentally we demonstrated 1.2-dB Q-factor improvement for a 2-Tb/s seven-band CoWDM with backward Raman amplification. The system delivered an optical signal-to-noise ratio of 35 dB at the output of the receiver preamplifier providing a worst-case BER of 2 × 10 -6 over 49 subcarriers at 42.8 Gbaud, leaving a system margin (in terms of Q -factor) of ~4 dB from the forward-error correction threshold.

All-optical OFDM and distributed Raman amplification : challenges to enable high capacities and extend reach

We review recent advances in all-optical OFDM technologies and discuss the performance of a field trial of a 2 Tbit/s Coherent WDM over 124 km with distributed Raman amplification. The results indicate that careful optimisation of the Raman pumps is essential. We also consider how all-optical OFDM systems perform favourably against energy consumption when compared with alternative coherent detection schemes. We argue that, in an energy constrained high-capacity transmission system, direct detected all-optical OFDM with `ideal' Raman amplification is an attractive candidate for metro area datacentre interconnects with ~100 km fibre spans, with an overall energy requirement at least three times lower than coherent detection techniques.

"Magic" dispersion maps with distributed Raman amplification

We analyze pulse propagation in an optical fiber with a periodic dispersion map and distributed amplification. Using an asymptotic theory and a momentum method, we identify a family of dispersion management schemes that are advantageous for massive multichannel soliton transmission. For the case of two-step dispersion maps with distributed Raman amplification to compensate for the fiber loss, we find special schemes that have optimal (chirp-free) launch point locations that are independent of the fiber dispersion. Despite the variation of dispersion with wavelength due to the fiber dispersion slope, the transmission in several different channels can be optimized simultaneously using the same optimal launch point. The theoretical predictions are verified by direct numerical simulations. The obtained results are applied to a practical multichannel transmission system.

Optimal dispersion maps for multichannel soliton transmission with distributed Raman amplification

Using an asymptotic theory and a momentum method, we identify a family of dispersion management schemes with distributed Raman amplification, which are advantageous for massive multichannel soliton transmission. For the case of two-step dispersion maps, special schemes are found that have optimal (chirp-free) launch point locations that are independent of the fibre dispersion. Despite the variation of dispersion with wavelength due to the fibre dispersion slope, the transmission in several different channels can be optimized simultaneously using the same optimal launch point. The theoretical results are verified by direct numerical simulations.

1-Tb/s DWDM amplification in a fiber optical parametric amplifier

We report less than 1-dB cross-talk penalty for 26 DWDM channels modulated at 43.7 Gb/s RZ-DPSK when amplified by a fiber optical parametric amplifier showing compatibility with high-capacity (> 1 Tb/s) communication systems. © 2010 Optical Society of America.