Monitoring Daily QA 3 constancy for routine quality assurance on linear accelerators

The purpose of this study was to evaluate the suitability of the Daily QA 3 (Sun Nuclear Corporation, Melbourne, USA) device as a safe quality assurance device for control of machine specific parameters, such as linear accelerator output, beam quality and beam flatness and symmetry. Measurements were performed using three Varian 2300iX linear accelerators. The suitability of Daily QA 3 as a device for quality control of linear accelerator parameters was investigated for both 6 and 10 MV photons and 6, 9, 12, 15 and 18 MeV electrons. Measurements of machine specific using the Daily QA 3 device were compared to corresponding measurements using a simpler constancy meter, Farmer chamber and plane parallel ionisation chamber in a water tank. The Daily QA 3 device showed a linear dose response making it a suitable device for detection of output variations during routine measurements. It was noted that over estimations of variations compared with Farmer chamber readings were seen if the Daily QA 3 wasn’t calibrated for output and sensitivity on a regular eight to ten monthly basis. Temperature-pressure correction factors calculated by Daily QA 3 also contributed towards larger short term variations seen in output measurements. Energy, symmetry and flatness variations detected by Daily QA 3 were consistent with measurements performed in water tank using a parallel plate chamber. It was concluded that the Daily QA 3 device is suitable for routine daily and fortnightly quality assurance of linear accelerator beam parameters however a regular eight-ten monthly dose and detector array calibration will improve error detection capabilities of the device.     

Energy diagrams and mechanism for proton pumping in cytochrome c oxidase

The powerful technique of energy diagrams has been used to analyze the mechanism for proton pumping in cytochrome c oxidase. Energy levels and barriers are derived starting out from recent kinetic experiments for the O to E transition, and are then refined using general criteria and a few additional experimental facts. Both allowed and non-allowed pathways are obtained in this way. A useful requirement is that the forward and backward rate should approach each other for the full membrane gradient. A key finding is that an electron on heme a (or the binuclear center) must have a significant lowering effect on the barrier for proton uptake, in order to prevent backflow from the pump-site to the N-side. While there is no structural gating in the present mechanism, there is thus an electronic gating provided by the electron on heme a. A quantitative analysis of the energy levels in the diagrams, leads to Prop-A of heme a₃ as the most likely position for the pump-site, and the Glu278 region as the place for the transition state for proton uptake. Variations of key redox potentials and pK_a values during the pumping process are derived for comparison to experiments.     

The role of PGR5 in the redox poising of photosynthetic electron transport

The pgr5 mutant of Arabidopsis thaliana has been described as being deficient in cyclic electron flow around photosystem I, however, the precise role of the PGR5 protein remains unknown. To address this issue, photosynthetic electron transport was examined in intact leaves of pgr5 and wild type A. thaliana. Based on measurements of the kinetics of P700 oxidation in far red light and re-reduction following oxidation in the presence of DCMU, we conclude that this mutant is able to perform cyclic electron flow at a rate similar to the wild type. The PGR5 protein is therefore not essential for cyclic flow. However, cyclic flow is affected by the pgr5 mutation under conditions where this process is normally enhanced in wild type leaves, i.e. high light or low CO₂ concentrations resulted in enhancement of cyclic electron flow. This suggests a different capacity to regulate cyclic flow in response to environmental stimuli in the mutant. We also show that the pgr5 mutant is affected in the redox poising of the chloroplast, with the electron transport chain being substantially reduced under most conditions. This may result in defective feedback regulation of photosynthetic electron transport under some conditions, thus providing a rationale for the reduced efficiency of cyclic electron flow.     

Sequential monitoring of randomization tests: stratified randomization

In many clinical trials, it is desirable to establish a sequential monitoring plan, whereby the test statistic is computed at an interim point or points in the trial and a decision is made whether to stop early due to evidence of treatment efficacy. In this article, we will set up a sequential monitoring plan for randomization-based inference under the permuted block design, stratified block design, and stratified urn design. We will also propose a definition of information fraction in these settings and discuss its calculation under these different designs.     

Linear Contrasts in Experimental Design with Non‐Identical Error Distributions

Estimation of linear contrasts in experimental design, and testing their assumed values, is considered when the error distributions from block to block are not necessarily identical. The normal‐theory solutions are shown to have low efficiencies as compared to the solutions presented here.     

Identification of drought tolerant Chickpea genotypes through multi trait stability index

Drought is a major and constantly increasing abiotic stress factor, thus limiting chickpea production. Like other crops, Kabuli Chickpea genotypes are screened for drought stress through Multi-environment trials (METs). Although, METs analysis is generally executed taking into account only one trait, which provides less significant reliability for the recommendation of genotypes as compared to multi trait-based analysis. Multi trait-based analysis could be used to recommend genotypes across diverse environments. Hence, current research was conducted for selection of superior genotypes through multi-trait stability index (MTSI) by using mixed and fixed effect models under six diverse environments. The genotypic stability was computed for all traits individually using the weighted average of absolute scores from the singular value decomposition of the matrix of best linear unbiased predictions for the genotype vs environment interaction (GEI) effects produced by a linear mixed-effect model index. A superiority index, WAASBY was measured to reflect the MPS (Mean performance and stability). The selection differential for the WAASBY index was 11.2%, 18.49% and 23.30% for grain yield (GY), primary branches per plant (PBP) and Stomatal Conductance (STOMA) respectively. Positive selection differential (0.80% ≤ selection differential ≤ 13.00%) were examined for traits averaged desired to be increased and negative (-0.57% ≤ selection differential ≤ -0.23%) for those traits desired to be reduced. The MTSI may be valuable to the plant breeders for the selection of genotypes based on many characters as being strong and simple selection process. Analysis of MTSI for multiple environments revealed that, the genotypes G20, G86, G31, G28, G116, G12, G105, G45, G50, G10, G30, G117, G81, G48, G85, G17, G32, G4, and G37 were the most stable and high yielding out of 120 chickpea genotypes, probably due to high MPS of selected traits under various environments. It is concluded that identified traits can be utilized as genitors in hybridization programs for the development of drought tolerant Kabuli Chickpea breeding material.     

Multiple Linear Regression on Canonical Correlation Variables

When the explanatory variables of a linear model are split into two groups, two notions of collinearity are defined: a collinearity between the variables of each group, of which the mean is called residual collinearity, and a collinearity between the two groups called explained collinearity. Canonical correlation analysis provides information about the collinearity: large canonical correlation coefficients correspond to some small eigenvalues and eigenvectors of the correlation matrix and characterise the explained collinearity. Other small eigenvalues of this matrix correspond to the residual collinearity. A selection of predictors can be performed from the canonical correlation variables, according to their partial correlation coefficient with the explained variable. In the proposed application, the results obtained by the selection of canonical variables are better than those given by classical regression and by principal component regression.     

Interlinking hare and lynx dynamics using a century’s worth of annual data

The classic fur trade records on Canadian lynx (Lynx canadensis) have rarely been analysed in direct conjunction with data on its principal prey, the snowshoe hare (Lepus americanus). Comparable long-term data for hare exist only for a region south of Hudson Bay. We fitted a bivariate log-linear time-series model to this hare and lynx data to disentangle the within- and between-population interactions of these species. To reduce problems with fur returns being non-normal and non-linearly related to abundance, we transformed the fur returns to a normal distribution based on sample quantiles. The estimated effect on next year’s lynx abundance of a 1% increase in current hare abundance was a 0.23% (SE = 0.05) increase in lynx. Conversely, a 1% increase in current lynx abundance corresponded to a 0.46% (SE = 0.12) decrease in next year’s hare abundance. This contrasts with some earlier studies. However, these studies mixed hare data from south of Hudson Bay with lynx totals for all of Canada. Despite this asymmetry of interaction strengths, coefficients of determination were similar for hare versus lynx and lynx versus hare, because hare abundance varies more than lynx. Both species showed clear intraspecific density-dependence of about equal strength. A 1% increase in current abundance increased next year’s abundance by about 0.75%. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Automated measurement of permethylated serum N-glycans by MALDI–linear ion trap mass spectrometry

The use of N-glycan mass spectrometry for clinical diagnostics requires the development of robust high-throughput profiling methods. Still, structural assignment of glycans requires additional information such as MS² fragmentation or exoglycosidase digestions. We present a setting which combines a MALDI ionization source with a linear ion trap analyzer. This instrumentation allows automated measurement of samples thanks to the crystal positioning system, combined with MSⁿ sequencing options. 2,5-Dihydroxybenzoic acid, commonly used for the analysis of glycans, failed to produce the required reproducibility due to its non-homogeneous crystallization properties. In contrast, α-cyano-4-hydroxycinnamic acid provided a homogeneous crystallization pattern and reproducibility of the measurements. Using serum N-glycans as a test sample, we focused on the automation of data collection by optimizing the instrument settings. Glycan structures were confirmed by MS² analysis. Although sample processing still needs optimization, this method provides a reproducible and high-throughput approach for measurement of N-glycans using a MALDI–linear ion trap instrument.