Application of power functions to chromatographic data for the enhancement of signal to noise ratios and separation resolution

Chromatographic detection responses are recorded digitally. A peak is represented ideally by a Guassian distribution. Raising a Guassian distribution to the power ‘n’ increases the height of the peak to that power, but decreases the standard deviation by √n. Hence there is an increasing disparity in detection responses as the signal moves from low level noise, with a corresponding decrease in peak width. This increases the S/N ratio and increases peak to peak resolution. The ramifications of these factors are that poor resolution in complex chromatographic data can be improved, and low signal responses embedded at near noise levels can be enhanced. The application of this data treatment process is potentially very useful in 2D-HPLC where sample dilution occurs between dimension, reducing signal response, and in the application of post-reaction detection methods, where band broadening is increased by virtue of reaction coils. In this work power functions applied to chromatographic data are discussed in the context of (a) complex separation problems, (b) 2D-HPLC separations, and (c) post-column reaction detectors.

Imprinted CDKN1C is a tumor suppressor in rhabdoid tumor and activated by restoration of SMARCB1 and histone deacetylase inhibitors

SMARCB1 is deleted in rhabdoid tumor, an aggressive paediatric malignancy affecting the kidney and CNS. We hypothesized that the oncogenic pathway in rhabdoid tumors involved epigenetic silencing of key cell cycle regulators as a consequence of altered chromatin-remodelling, attributable to loss of SMARCB1, and that this hypothesis if proven could provide a biological rationale for testing epigenetic therapies in this disease. We used an inducible expression system to show that the imprinted cell cycle inhibitor CDKN1C is a downstream target for SMARCB1 and is transcriptionally activated by increased histone H3 and H4 acetylation at the promoter. We also show that CDKN1C expression induces cell cycle arrest, CDKN1C knockdown with siRNA is associated with increased proliferation, and is able to compete against the anti-proliferative effect of restored SMARCB1 expression. The histone deacetylase inhibitor (HDACi), Romidepsin, specifically restored CDKN1C expression in rhabdoid tumor cells through promoter histone H3 and H4 acetylation, recapitulating the effect of SMARCB1 on CDKNIC allelic expression, and induced cell cycle arrest in G401 and STM91-01 rhabdoid tumor cell lines. CDKN1C expression was also shown to be generally absent in clinical specimens of rhabdoid tumor, however CDKN1A and CDKN1B expression persisted. Our observations suggest that maintenance of CDKN1C expression plays a critical role in preventing rhabdoid tumor growth. Significantly, we report for the first time, parallels between the molecular pathways of SMARCB1 restoration and Romidepsin treatment, and demonstrate a biological basis for the further exploration of histone deacetylase inhibitors as relevant therapeutic reagents in the treatment of rhabdoid tumor.

Understanding the sources of uncertainty to reduce the risks of undesirable outcomes in large-scale freshwater ecosystem restoration projects: an example from the Murray–Darling Basin, Australia

There are a growing number of large-scale freshwater ecological restoration projects worldwide. Assessments of the benefits and costs of restoration often exclude an analysis of uncertainty in the modelled outcomes. To address this shortcoming we explicitly model the uncertainties associated with measures of ecosystem health in the estuary of the Murray– Darling Basin, Australia and how those measures may change with the implementation of a Basin-wide Plan to recover water to improve ecosystem health. Specifically, we compare two metrics – one simple and one more complex – to manage end-of-system flow requirements for one ecosystem asset in the Basin, the internationally important Coorong saline wetlands. Our risk assessment confirms that the ecological conditions in the Coorong are likely to improve with implementation of the Basin Plan; however, there are risks of a Type III error (where the correct answer is found for the wrong question) associated with using the simple metric for adaptive management. 

Compositional effects on the restoration behaviour in Mg-Zn-Re alloys

Additions of rare earth elements to magnesium alloys are qualitatively reported in the literature to retard recrystallisation. However, their effect in the presence of other (non-rare earth) alloy additions has not been systematically shown nor has the effect been quantified. The microstructural restoration following the hot deformation of Mg-xZn-yRE (x = 2.5 and 5 wt.%, y = 0 and 1 wt.%, and RE = Gd and Y) alloys has been studied using double hit compression testing and microscopy. It was found that, in the absence of rare earth additions, increases in zinc level had a negligible influence on the kinetics of restoration and the microstructure developed both during extrusion and throughout double hit testing. Adding rare earth elements to Mg-Zn alloys was found to retard restoration of the microstructure and maintain finer recrystallised grains. However, in the Mg-Zn-RE alloys, increasing the zinc concentration from 2.5 wt.% to 5 wt.% accelerated the restoration process, most likely due to a depletion of rare earth elements from solid solution and modification of the particles present in the matrix.

Improved 2D‐HPLC of red wine by incorporating pre‐process signal‐smoothing algorithms

Twomultidimensional HPLC separations of an Australian red wine are presented, >70% of the available separation space was used. A porous graphitic carbon (PGC) stationary phase was used as the first dimension in both separations with both RP core–shell and hydrophilic interaction chromatography fully porous columns used separately in the second dimension. To overcome peak analysis problems caused by signal noise and low detection limits, the data were pre-processed with penalised least-squares smoothing. The PGC × RP combination separated 85 peaks with a spreading angle of 71 and the PGC × hydrophilic interaction chromatography separated 207 peaks with a spreading angle of 80. Both 2D-HPLC steps were completed in 76 min using a comprehensive stop-and-go approach. A smoothing step was added to peak-picking processes and was able to greatly reduce the number of false peaks present due to noise in the chromatograms. The required thresholds were not able to ignore the noise because of the small magnitude of the peaks; 1874 peaks were located in the non-smoothed PGC × RP separation that reduced to 227 peaks after smoothing was included.