Comparison of patient-specific intensity modulated radiation therapy quality assurance for the prostate across multiple institutions

AimTo evaluate the success of a patient-specific intensity modulated radiation therapy (IMRT) quality assurance (QA) practice for prostate cancer patients across multiple institutions using a questionnaire survey.BackgroundThe IMRT QA practice involves different methods of dose distribution verification and analysis at different institutions.Materials and MethodsTwo full-arc volumetric modulated arc therapy (VMAT) plan and 7 fixed-gantry IMRT plan with DMLC were used for patient specific QA across 22 institutions. The same computed tomography image and structure set were used for all plans. Each institution recalculated the dose distribution with fixed monitor units and without any modification. Single-point dose measurement with a cylindrical ionization chamber and dose distribution verification with a multi-detector or radiochromic film were performed, according to the QA process at each institution.ResultsTwenty-two institutions performed the patient-specific IMRT QA verifications. With a single-point dose measurement at the isocenter, the average difference between the calculated and measured doses was 0.5 ± 1.9%. For the comparison of dose distributions, 18 institutions used a two or three-dimensional array detector, while the others used Gafchromic film. In the γ test with dose difference/distance-to-agreement criteria of 3%?3 mm and 2%?2 mm with a 30% dose threshold, the median gamma pass rates were 99.3% (range: 41.7%–100.0%) and 96.4% (range: 29.4%–100.0%), respectively.ConclusionThis survey was an informative trial to understand the verification status of patient-specific IMRT QA measurements for prostate cancer. In most institutions, the point dose measurement and dose distribution differences met the desired criteria.     

Estimating equations with nonignorably missing response data

Troxel, Lipsitz, and Brennan (1997, Biometrics 53, 857-869) considered parameter estimation from survey data with nonignorable nonresponse and proposed weighted estimating equations to remove the biases in the complete-case analysis that ignores missing observations. This paper suggests two alternative modifications for unbiased estimation of regression parameters when a binary outcome is potentially observed at successive time points. The weighting approach of Robins, Rotnitzky, and Zhao (1995, Journal of the American Statistical Association 90, 106-121) is also modified to obtain unbiased estimating functions. The suggested estimating functions are unbiased only when the missingness probability is correctly specified, and misspecification of the missingness model will result in biases in the estimates. Simulation studies are carried out to assess the performance of different methods when the covariate is binary or normal. For the simulation models used, the relative efficiency of the two new methods to the weighting methods is about 3.0 for the slope parameter and about 2.0 for the intercept parameter when the covariate is continuous and the missingness probability is correctly specified. All methods produce substantial biases in the estimates when the missingness model is misspecified or underspecified. Analysis of data from a medical survey illustrates the use and possible differences of these estimating functions.     

Repeatability of dispersal behaviour in a common dwarf spider: evidence for different mechanisms behind short‐ and long‐distance dispersal

Abstract 1. The response of dispersal towards evolution largely depends on its heritability for which upper limits are determined by the trait’s repeatability. 2. In the Linyphiid spider E. atra, we were able to separate long‐ and short‐distance dispersal behaviours (respectively ballooning and rappelling) under laboratory conditions. By performing repeated behavioural trials for females, we show that average dispersal trait values decrease with increasing testing days. By comparing mated and unmated individuals during two periods (before and after mating for the mated group, and the same two periods for the unmated group), we show that mating has no effect on the mean displayed dispersal behaviour or its within‐individual variation. Repeatabilities were high and consistent for ballooning motivation, but not for rappelling. 3. Ballooning motivation can be regarded as highly individual‐specific behaviour, while general pre‐dispersal and rappelling behaviours showed more individual variation. Such difference in repeatability between long‐ and short‐distance dispersal suggests that short‐ and long‐distance dispersal events are triggered by different ecological and evolutionary mechanisms.     

Evaluation of several methods for estimating phylogenetic trees when substitution rates differ over nucleotide sites

Several maximum likelihood and distance matrix methods for estimating phylogenetic trees from homologous DNA sequences were compared when substitution rates at sites were assumed to follow a gamma distribution. Computer simulations were performed to estimate the probabilities that various tree estimation methods recover the true tree topology. The case of four species was considered, and a few combinations of parameters were examined. Attention was applied to discriminating among different sources of error in tree reconstruction, i.e., the inconsistency of the tree estimation method, the sampling error in the estimated tree due to limited sequence length, and the sampling error in the estimated probability due to the number of simulations being limited. Compared to the least squares method based on pairwise distance estimates, the joint likelihood analysis is found to be more robust when rate variation over sites is present but ignored and an assumption is thus violated. With limited data, the likelihood method has a much higher probability of recovering the true tree and is therefore more efficient than the least squares method. The concept of statistical consistency of a tree estimation method and its implications were explored, and it is suggested that, while the efficiency (or sampling error) of a tree estimation method is a very important property, statistical consistency of the method over a wide range of, if not all, parameter values is prerequisite.     

Mapping of Genes for Cooking and Eating Qualities in Thai Jasmine Rice (KDML105)

Thai jasmine rice, KDML 105, is known as the best quality rice.It is known not only for its aroma but also for its good cookingand eating qualities. Amylose content (AC), gel consistency(GC) and gelatinization temperature (GT) are important traitsdetermining rice quality. A population of recombinant inbredlines (RIL) derived from KDML105 x CT9993 cross was used tostudy the genetic control of AC, GC and GT traits. A total of191 markers were used in the linkage map construction. The 1605.3cM linkage map covering nearly the whole rice genome was usedfor QTL (define QTL) analysis. Four QTLs for AC were detectedon chromosomes 3, 4, 6 and 7. These QTLs accounted for 80% ofphenotypic variation explained (PVE) in AC. The presence ofone major gene as well as several modifiers was responsiblefor the expression of the trait. Two QTLs on chromosome 6 andone on chromosome 7 were detected for GC, which accounts for57% of PVE. A single gene of major effect along with modifiergenes controls GC from this cross. The QTLs in the vicinityof waxy locus were major contributors in the expression of ACand GC. The finding that the position of QTLs for AC and GCwere near each other may reflect tight linkage or pleiotropy.Three QTLs were detected, one on chromosome 2 and two on chromosome6, which accounted for 67% of PVE in GT. Just like AC and GC,one major gene and modifier genes governed the variation inGT resulting from the KDML105 x CT9993 cross. Breeding for cookingand eating qualities will largely rely on the preferences ofthe end users.     

A new semiparametric estimation method for accelerated hazard model

The accelerated hazard model has been proposed for more than a decade. However, its application is still very limited, partly due to the complexity of the existing semiparametric estimation method. We propose a new semiparametric estimation method based on a kernel-smoothed approximation to the limit of a profile likelihood function of the model. The method leads to smooth estimating equations and is easy to use. The estimates from the method are proved to be consistent and asymptotically normal. Our numerical study shows that the new method is more efficient than the existing method. The proposed method is employed to reanalyze the data from a brain tumor treatment study.     

Molecular and karyological aspects of Batoidea (Chondrichthyes, Elasmobranchi) phylogeny

Although considerable progress has been made in elucidating the relationships within the Chondrichthyes, there is no agreement as it concerns the systematics of Batoidea, the most derived superorder among cartilaginous fishes, and many different interpretations exist. Our investigation provides the first assessment of relationships among the described batoid species using sequences from both mtDNA and nuclear genes as well as karyological morphology. Our work consists primarily in reconstructing the phylogenetic relationships of Batoidea by examining the mtDNA (16S) and nuclear gene (18S) sequences from 11 batoid species. The three analytical methods (NJ, MP and Bayesian analysis) grouped Rajiformes, Myliobatiformes and Rhinobatiformes. In these trees the two torpedoes diverge from the other batoid fishes. We also compare the molecular data with the available karyological evidence, which consist of the diploid number and the karyotype morphology of eight species belonging to the four orders examined. The results show that the karyological structure in the different species is generally consistent with the various phylogenetical trees, and that Torpediniformes confirm their unique genome organization.