Comparison of two different EPID-based solutions performing pretreatment quality assurance: 2D portal dosimetry versus 3D forward projection method

PurposeThe aim of this paper is to characterize two different EPID-based solutions for pre-treatment VMAT quality assurance, the 2D portal dosimetry and the 3D projection technique. Their ability to catch the main critical delivery errors was studied.MethodsMeasurements were performed with a linac accelerator equipped with EPID aSi1000, Portal Dose Image Prediction (PDIP), and PerFRACTION softwares. Their performances were studied simulating perturbations of a reference plan through systematic variations in dose values and micromultileaf collimator position. The performance of PDIP, based on 2D forward method, was evaluated calculating gamma passing rate (%GP) between no-error and error-simulated measurements. The impact of errors with PerFRACTION, based on 3D projection technique, was analyzed by calculating the difference between reference and perturbed DVH (%ΔD). Subsequently pre-treatment verification with PerFRACTION was done for 27 patients of different pathologies.ResultsThe sensitivity of PerFRACTION was slightly higher than sensitivity of PDIP, reaching a maximum of 0.9. Specificity was 1 for PerFRACTION and 0.6 for PDIP. The analysis of patients’ DVHs indicated that the mean %ΔD was (1.2 ± 1.9)% for D2%, (0.6 ± 1.7)% for D95% and (−0.0 ± 1.2)% for Dmean of PTV. Regarding OARs, we observed important discrepancies on DVH but that the higher dose variations were in low dose area (<10 Gy).ConclusionsThis study supports the introduction of the new 3D forward projection method for pretreatment QA raising the claim that the visualization of the delivered dose distribution on patient anatomy has major advantages over traditional portal dosimetry QA systems.     

The use of eddy covariance to infer the net carbon dioxide uptake of Brazilian rain forest

• 1 Eddy covariance measurements of CO₂ flux, based on four and six week campaigns in Rondôdnia, Brazil, have been used in conjunction with a model to scale up data to a whole year, and thus estimate the carbon balance of the tropical forest ecosystem, and the changes in carbon balance expected from small interannual variations in climatological conditions.
• 2 One possible source of error in this estimation arises from the difficulty in measuring fluxes under stably stratified meteorological conditions, such as occur frequently at night. Flux may be ‘lost’ because of low velocity advection, caused by nocturnal radiative cooling at sites on raised ground. Such effects may be detected by plotting the net ecosystem flux of CO₂, F_eco is a function of wind speed. If flux is ‘lost’ then F_eco is expected to decline with wind speed. In the present data set, this did not occur, and F_eco was similar to the nocturnal flux estimated independently from chamber measurements.
• 3 The model suggests that in 1992/3, the Gross Primary Productivity (GPP) was 203.3 mol C m^?2 y^?1 and ecosystem respiration was 194.8 mol C m^?2 y^?1, giving an ecosystem carbon balance of 8.5 mol C m^?2 y^?1, equivalent to a sink of 1.0 ton C ha^?1 y^?1. However, the sign and magnitude of this figure is very sensitive to temperature, because of the strong influence of temperature on respiration.
• 4 The model also suggests that the effect of temperature on the net carbon balance is strongly dependent on the partial pressure of CO₂.

     

Estimating the sensitivity of cervical cytology: errors of interpretation and test limitations

The objective of this study was to estimate: (i) the sensitivity of cytologists in recognizing abnormal smears; (ii) the sensitivity of cervical cytology as a method of detecting abnormal smears among those obtained in the presence of cervical intraepithelial neoplasia (CIN). Study subjects were 61 women with a histologically confirmed CIN identified through colpohistological and cytologic screening. For objective (i) new smears were taken from study subjects just before treatment, mixed with routine preparations, interpreted by unaware cytologists and then blindly reviewed by a group of three expert supervisors, who reached a consensus diagnosis. Cytologists classified as positive for squamous intraepithelial lesion (SIL) 30 of the 34 smears judged as positive by supervisors (100% of smears classified as high-grade and 67% of smears classified as low-grade SIL by the supervisors). Our approach, based on creating a set of smears with a high a priori probability of being positive, proved to be an efficient way of estimating errors of interpretation. For objective (ii), smears taken at the moment of diagnosis, just before biopsy, were also reviewed by the same supervisors. These CIN cases were identified among asymptomatic women independently of cytological findings and results are therefore not subject to verification bias. Among the 33 histological CINII/III, four (12%) smears had no atypical cells (three negatives and one unsatisfactory) at review. The same proportion was 26% (four negatives and one unsatisfactory) among the 19 histological CINI. No significant differences in smear content were found between the seven ‘false negatives’ and a sample of ‘true positives’ and ‘true negatives’ for a number of formal adequacy criteria (including presence of endocervical cells). Strong differences were found between positive smears taken just before biopsy and those taken just before treatment (in 11 women the first smear only was positive, while the opposite was never observed), suggesting an effect of punch biopsy in removing lesions.     

A review of software tools for spell‐checking taxon names in vegetation databases

Correct spelling of taxon names in vegetation databases is a fundamental prerequisite for many data processing steps. However, manual detection and correction of spelling mistakes is inefficient, prone to errors and non‐reproducible, especially when scanning large databases. Here, I review six software tools that spell‐check taxon names in vegetation databases: (1) the Global Names Resolver, (2) the Interim Register of Marine and Nonmarine Genera, (3) the Taxonomic Name Resolution Service and R packages (4) Plantminer, (5) Taxonstand and (6) tpl. In particular, I test their capacity to spell‐check names across the taxonomic ranks and organism groups frequently encountered in vegetation data and challenge their ability to screen names from different geographic regions. Performance by software tools differed widely in these tests. Backed up by multiple reference lists, the Global Names Resolver emerged as the most versatile software tool. All software solutions currently suffer from some minor limitations, including an inability to spell‐check names of hybrid taxa. Furthermore, some spelling mistakes, by their nature, cannot be resolved unambiguously. Given these limitations, taxon names should be spell‐checked with software tools in a semi‐automatic rather than an automatic way.     

High rates of phasing errors in highly polymorphic species with low levels of linkage disequilibrium

Short read sequencing of diploid individuals does not permit the direct inference of the sequence on each of the two homologous chromosomes. Although various phasing software packages exist, they were primarily tailored for and tested on human data, which differ from other species in factors that influence phasing, such as SNP density, amounts of linkage disequilibrium (LD) and sample sizes. Despite becoming increasingly popular for other species, the reliability of phasing in non‐human data has not been evaluated to a sufficient extent. We scrutinized the phasing accuracy for Drosophila melanogaster, a species with high polymorphism levels and reduced LD relative to humans. We phased two D. melanogaster populations and compared the results to the known haplotypes. The performance increased with size of the reference panel and was highest when the reference panel and phased individuals were from the same population. Full genomic SNP data and inclusion of sequence read information also improved phasing. Despite humans and Drosophila having similar switch error rates between polymorphic sites, the distances between switch errors were much shorter in Drosophila with only fragments <300–1500 bp being correctly phased with ≥95% confidence. This suggests that the higher SNP density cannot compensate for the higher recombination rate in D. melanogaster. Furthermore, we show that populations that have gone through demographic events such as bottlenecks can be phased with higher accuracy. Our results highlight that statistically phased data are particularly error prone in species with large population sizes or populations lacking suitable reference panels.     

Inference on system parameters in a model for interacting species

A system of p interacting species whose behaviour can be approximated by a Markovian model is considered. Estimates for system parameters are obtained by the method of moments, when the means, variances and covariances can be estimated from observed population sizes over a period of time. Further, approximate standard errors of these estimates are obtained using the -technique.     

Estimators of repeatability

Summary Analysis of variance and principal components methods have been suggested for estimating repeatability. In this study, six estimation procedures are compared: ANOVA, principal components based on the sample covariance matrix and also on the sample correlation matrix, a related multivariate method (structural analysis) based on the sample covariance matrix and also on the sample correlation matrix, and maximum likelihood estimation. A simulation study indicates that when the standard linear model assumptions are met, the estimators are quite similar except when the repeatability is small. Overall, maximum likelihood appears the preferred method. If the assumption of equal variance is relaxed, the methods based on the sample correlation matrix perform better although others are surprisingly robust. The structural analysis method (with sample correlation matrix) appears to be best.Paper number 776 from the Department of Meat and Animal Science, University of Wisconsin-Madison.     

密度制约竞争二种群Volterra方程解的有界性及参数估计

本文给出密度制约且相互竞争二种群Volterra方程解的一种有界性及存在唯一性的证明。基于此,参考单种群Logistic方程反问题的方法”,给出了该Volterra方程参数的一种估计。