Implication of correlations among some common stability statistics — a Monte Carlo simulations

Stability analysis of multilocation trials is often based on a mixed two-way model. Two stability measures in frequent use are the environmental variance (S _i ² )and the ecovalence (W _i). Under the two-way model the rank orders of the expected values of these two statistics are identical for a given set of genotypes. By contrast, empirical rank correlations among these measures are consistently low. This suggests that the two-way mixed model may not be appropriate for describing real data. To check this hypothesis, a Monte Carlo simulation was conducted. It revealed that the low empirical rank correlation amongS _i ² and W _i is most likely due to sampling errors. It is concluded that the observed low rank correlation does not invalidate the two-way model. The paper also discusses tests for homogeneity of S _i ² as well as implications of the two-way model for the classification of stability statistics.     

Testing multivariate patterns of within-island differentiation in Podarcis dugesii from Madeira

Podarcis dugesii is a polymorphic species found on the ecologically-heterogeneous Atlantic island of Madeira. Patterns of geographic variation in size-free body dimensions (body shape), scalation, and size were portrayed on maps with isophene contours. There was no dominant pattern of among-site variation as seen in several other island lizards, although some linear combinations of morphological variables showed evidence of clines towards the east coast. Multivariate statistical techniques were developed to evaluate whether morphological variation contained an ecology-related spatial pattern, after removal of the effects of statistical non-independence of studied populations. Specifically, a partial correlation matrix comparison method provided evidence to support a proposed elevation model of among-site divergence in scalation and body size, with both an alternative rainfall model and spatial non-independence held constant. Similar divergence in scalation has been observed in other lizard species on other island archipelagos as well on some continental areas. The rainfall model was rejected for both body shape and scalation. The degree of within-population polymorphism in body shape and scalation showed no clear geographic trends in general, although the elevation and rainfall models could not be rejected for female scalation.     

Causes of covariation of phenotypic traits among populations

Morphological and life-history traits often vary among populations of a species. Traits generally do not vary independently, but show patterns of covariation that can arise from genetic and environmental influences on phenotype. Covariance of traits may arise at an among-population level when genetically influenced traits diverge among populations in a correlated manner. Genetic correlations caused by pleiotropy and/or gene linkage can cause traits to evolve together, but among-population covariance can also arise among traits that are not genetically correlated. For example, “selective covariance” can arise when natural selection directly causes correlated change in a suite of traits. Similarly, mutation, migration, and drift may also sometimes cause correlated genetic changes among populations. Because covariation of traits among populations can arise by several different processes, the evolution of suites of traits must be interpreted with great caution. We discuss the sources of among-population covariance and illustrate one approach to identifying the sources' using data on floral traits of Dalechampia scandens (Euphorbiaceae).     

S-Sample Smooth Goodness of Fit Testing: Rederivation and Monte Carlo Assessment

S-sample smooth goodness of fit tests may be constructed using components from one sample goodness of fit testing. Each sample could be assessed for consistency with a target distribution using these components, although that is not our objective here. Contrasts in the components may be used to assess consistency of the samples with each other. If all the samples are consistent, we could then conveniently perform a one-sample goodness of fit test for the target distribution. If the samples are not consistent, an LSD-type analysis can be performed on the one-sample components to identify where the differences between occur. This approach gives a detailed and informative scrutiny of the data.     

Fluorescence spectroscopy of H‐ras transfected murine fibroblasts: A comparison with Monte Carlo simulations

Autofluorescence properties of tissues have been widely used to diagnose various types of malignancies. In this study, we measured the autofluorescence properties of H‐ras transfected murine fibroblasts and the counterpart control cells. The pair of cells is genetically identical except for the transfected H‐ras gene. We applied Monte Carlo simulations to evaluate the relative contributions of Rayleigh and Mie scattering effects towards fluorescence in an in vitro model system of normal and H‐ras transfected fibroblasts. The experimental results showed that fluorescence emission intensity was higher for normal cells than the malignant counterpart cells by about 30%. In normal cells, linearity in emission intensity was observed for cell densities of up to 1.0 × 10⁶ cells/ml whereas for transformed cells it was up to 1.4 × 10⁶ cells/ml. Nuclear volume changes give good account for the differences in the intrinsic fluorescence between normal and malignant cells. The Monte Carlo (MC) code, newly developed for this study, explains both predominant experimental features: the large fluorescence intensity differences between the transfected and the corresponding control cells as well as the phenomena of the red shift in the excitation spectra as a function of cell density. The contribution of Rayleigh scattering was found to be predominant compared to Mie scattering. © 2009 Wiley Periodicals, Inc. Biopolymers 93: 132–140, 2010. This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com     

Effect of the presence of amniotic fluid for optical transabdominal fetal monitoring using Monte Carlo simulations

About a third of babies are delivered by Cesarean section. There has been an increase in maternal deaths during labor due to complications with subsequent births after a C-section. Therefore, there is a clinical motivation to reduce the C-section rate. Current techniques are, however, inefficient at determining fetal distress leading to a high false positive rate for complications and ultimately a C-section. For the current study, Monte Carlo simulations were used to calculate the amount of signal received on a model of a pregnant mother, as well as, the percent of the signal that comes from the fetal layer. Models with and without a 1 mm amniotic fluid were compared and showed differing trends.     

A comparison of phenotypic variation and covariation patterns and the role of phylogeny, ecology, and ontogeny during cranial evolution of new world monkeys

Similarity of genetic and phenotypic variation patterns among populations is important for making quantitative inferences about past evolutionary forces acting to differentiate populations and for evaluating the evolution of relationships among traits in response to new functional and developmental relationships. Here, phenotypic co variance and correlation structure is compared among Platyrrhine Neotropical primates. Comparisons range from among species within a genus to the superfamily level. Matrix correlation followed by Mantel's test and vector correlation among responses to random natural selection vectors (random skewers) were used to compare correlation and variance/covariance matrices of 39 skull traits. Sampling errors involved in matrix estimates were taken into account in comparisons using matrix repeatability to set upper limits for each pairwise comparison. Results indicate that covariance structure is not strictly constant but that the amount of variance pattern divergence observed among taxa is generally low and not associated with taxonomic distance. Specific instances of divergence are identified. There is no correlation between the amount of divergence in covariance patterns among the 16 genera and their phylogenetic distance derived from a conjoint analysis of four already published nuclear gene datasets. In contrast, there is a significant correlation between phylogenetic distance and morphological distance (Mahalanobis distance among genus centroids). This result indicates that while the phenotypic means were evolving during the last 30 millions years of New World monkey evolution, phenotypic covariance structures of Neotropical primate skulls have remained relatively consistent. Neotropical primates can be divided into four major groups based on their feeding habits (fruit-leaves, seed-fruits, insect-fruits, and gum-insect-fruits). Differences in phenotypic covariance structure are correlated with differences in feeding habits, indicating that to some extent changes in interrelationships among skull traits are associated with changes in feeding habits. Finally, common patterns and levels of morphological integration are found among Platyrrhine primates, suggesting that functional/developmental integration could be one major factor keeping covariance structure relatively stable during evolutionary diversification of South American monkeys.     

The quantitative genetics of fluctuating asymmetry: a comparison of two models

The genetic basis of fluctuating asymmetry (FA), a measure of random deviations from perfect bilateral symmetry, has been the subject of much recent work. In this paper we compare two perspectives on the quantitative genetic analysis of FA and directional asymmetry (DA). We call these two approaches the character-state model and the environmental responsiveness model. In the former approach, the right and left sides are viewed as separate traits whose genetic coupling is manifested by the genetic correlation. This model leads to the relationship, h2(DA) = h2[(1-rA)/(1-rp)), where h2 is the heritability of each component trait (assumed to be the same), rA and rp are the genetic and phenotypic correlations between traits, respectively. Simulation shows that, under this model, the heritability of FA is considerably less than that of DA, except when heritabilities are very close to zero. The environmental responsiveness model permits genetic variance in FA even when the genetic correlation between traits is + 1. Simulation shows that under this model the heritability of FA can be uncoupled from that of DA. The additive and nonadditive components of the component (right and left) traits, their DA and FA values are estimated using a diallel cross of seven inbred lines of the sand cricket, Gryllus firmus. Four leg measurements were made and both the individual DA and FA values and the compound measures DASUM and CFA estimated. The heritabilities of the compound measures are slightly larger than the individual estimates. Dominance variance is observed in the individual traits but predicted to be an even smaller component of the phenotypic variance than the additive genetic variance. The estimated values confirm this, although a previous study has demonstrated that dominance variance is present. Because the heritabilities of FA are generally larger than those of DA, which never exceed 0.02, the environmental responsiveness model is more consistent with the data than the character-state model. A review of other data suggests that both sources of variation might be found in some species.     

Testing amniote models of prey transport kinematics: a quantitative analysis of mouth opening patterns in lizards

Two models have been proposed to describe the prey transport kinematics of terrestrial vertebrates (Bramble and Wake, 1985; Reilly and Lauder, 1990). The critical difference between the models is the presence or absence of a slow open-II phase (SO-II) in the gape profile during mouth opening. Each of these models has been applied to lizards, however to date, lizard feeding kinematics have not been adequately quantified to assess the utility of these models for this clade. Neither model has been sufficiently tested due to the lack of a methodology to assess the specific differences between the models. We describe a method that uses explicit mathematical criteria to define the kinematic phases in tetrapod feeding. This "slope analysis& is used to precisely quantify and compare the transport kinematics of seven lizard species. Lizard transport kinematics were highly variable both within and across taxa. However, several common gape cycle patterns were identified. The predominant patterns were slow-fast opening (37.3%), fast opening only (22.9%) and slow opening only (21.2%). The most common pattern explicitly fits the prediction of the Reilly and Lauder model while the other two are similar to patterns observed in salamanders. Thus, lizards possess both the slow opening-fast opening pattern predicted for amniotes and the more primitive, simple opening pattern characteristic of more basal tetrapods. Plateau phases were found in only 12.8% of the profiles and only a fourth of these (3.4% of the total) explicitly fit the Bramble and Wake model (slow opening, plateau, fast opening) and two species never exhibited plateaus in their gape cycles. Thus, it is clear that the Bramble and Wake model is not supported as a generalized model for lizards or generalized tetrapods.     

Sex-biased genetic component distribution among populations: additive genetic and maternal contributions to phenotypic differences among populations of Chinook salmon

An approach frequently used to demonstrate a genetic basis for population-level phenotypic differences is to employ common garden rearing designs, where observed differences are assumed to be attributable to primarily additive genetic effects. Here, in two common garden experiments, we employed factorial breeding designs between wild and domestic, and among wild populations of Chinook salmon (Oncorhynchus tshawytscha). We measured the contribution of additive (V(A)) and maternal (V(M)) effects to the observed population differences for 17 life history and fitness-related traits. Our results show that, in general, maternal effects contribute more to phenotypic differences among populations than additive genetic effects. These results suggest that maternal effects are important in population phenotypic differentiation and also signify that the inclusion of the maternal source of variation is critical when employing models to test population differences in salmon, such as in local adaptation studies.     

Genetic correlations between basal and maximum metabolic rates in a wild rodent: consequences for evolution of endothermy

According to the aerobic capacity model, endothermy in birds and mammals evolved as a correlated response to selection for an ability of sustained locomotor activity, rather than in a response to direct selection for thermoregulatory capabilities. A key assumption of the model is that aerobic capacity is functionally linked to basal metabolic rate (BMR). The assumption has been tested in several studies at the level of phenotypic variation among individuals or species, but none has provided a clear answer whether the traits are genetically correlated. Here we present results of a genetic analysis based on measurements of the basal and the maximum swim- and cold-induced oxygen consumption in about 1000 bank voles from six generations of a laboratory colony, reared from animals captured in the field. Narrow sense heritability (h2) was about 0.5 for body mass, about 0.4 for mass-independent basal and maximum metabolic rates, and about 0.3 for factorial aerobic scopes. Dominance genetic and common environmental (= maternal) effects were not significant. Additive genetic correlation between BMR and the swim-induced aerobic capacity was high and positive, whereas correlation resulting from specific-environmental effects was negative. However, BMR was not genetically correlated with the cold-induced aerobic capacity. The results are consistent with the aerobic capacity model of the evolution of endothermy in birds and mammals.     

Data cloning: easy maximum likelihood estimation for complex ecological models using Bayesian Markov chain Monte Carlo methods

We introduce a new statistical computing method, called data cloning, to calculate maximum likelihood estimates and their standard errors for complex ecological models. Although the method uses the Bayesian framework and exploits the computational simplicity of the Markov chain Monte Carlo (MCMC) algorithms, it provides valid frequentist inferences such as the maximum likelihood estimates and their standard errors. The inferences are completely invariant to the choice of the prior distributions and therefore avoid the inherent subjectivity of the Bayesian approach. The data cloning method is easily implemented using standard MCMC software. Data cloning is particularly useful for analysing ecological situations in which hierarchical statistical models, such as state-space models and mixed effects models, are appropriate. We illustrate the method by fitting two nonlinear population dynamics models to data in the presence of process and observation noise.     

Development of a deformable phantom for experimental verification of 4D Monte Carlo simulations in a deforming anatomy

PurposeTo verify the accuracy of 4D Monte Carlo (MC) simulations, using the 4DdefDOSXYZnrc user code, in a deforming anatomy. We developed a tissue-equivalent and reproducible deformable lung phantom and evaluated 4D simulations of delivered dose to the phantom by comparing calculations against measurements.MethodsA novel deformable phantom consisting of flexible foam, emulating lung tissue, inside a Lucite external body was constructed. A removable plug, containing an elastic tumor that can hold film and other dosimeters, was inserted in the phantom. Point dose and position measurements were performed inside and outside the tumor using RADPOS 4D dosimetry system. The phantom was irradiated on an Elekta Infinity linac in both stationary and moving states. The dose delivery was simulated using delivery log files and the phantom motion recorded with RADPOS.ResultsReproducibility of the phantom motion was determined to be within 1 mm. The phantom motion presented realistic features like hysteresis. MC calculations and measurements agreed within 2% at the center of tumor. Outside the tumor agreements were better than 5% which were within the positional/dose reading uncertainties at the measurement points. More than 94% of dose points from MC simulations agreed within 2%/2 mm compared to film measurements.ConclusionThe deformable lung phantom presented realistic and reproducible motion characteristics and its use for verification of 4D dose calculations was demonstrated. Our 4DMC method is capable of accurate calculations of the realistic dose delivered to a moving and deforming anatomy during static and dynamic beam delivery techniques.     

Evaluation of a commercial VMC++ Monte Carlo based treatment planning system for electron beams using EGSnrc/BEAMnrc simulations and measurements

In the present work, Monte Carlo (MC) models of electron beams (energies 4, 12 and 18 MeV) from an Elekta SL25 medical linear accelerator were simulated using EGSnrc/BEAMnrc user code. The calculated dose distributions were benchmarked by comparison with measurements made in a water phantom for a wide range of open field sizes and insert combinations, at a single source-to-surface distance (SSD) of 100 cm. These BEAMnrc models were used to evaluate the accuracy of a commercial MC dose calculation engine for electron beam treatment planning (Oncentra MasterPlan Treament Planning System (OMTPS) version 1.4, Nucletron) for two energies, 4 and 12 MeV. Output factors were furthermore measured in the water phantom and compared to BEAMnrc and OMTPS. The overall agreement between predicted and measured output factors was comparable for both BEAMnrc and OMTPS, except for a few asymmetric and/or small insert cutouts, where larger deviations between measurements and the values predicted from BEAMnrc as well as OMTPS computations were recorded. However, in the heterogeneous phantom, differences between BEAMnrc and measurements ranged from 0.5 to 2.0% between two ribs and 0.6–1.0% below the ribs, whereas the range difference between OMTPS and measurements was the same (0.5–4.0%) in both areas. With respect to output factors, the overall agreement between BEAMnrc and measurements was usually within 1.0% whereas differences up to nearly 3.0% were observed for OMTPS. This paper focuses on a comparison for clinical cases, including the effects of electron beam attenuations in a heterogeneous phantom. It, therefore, complements previously reported data (only based on measurements) in one other paper on commissioning of the VMC++ dose calculation engine.These results demonstrate that the VMC++ algorithm is more robust in predicting dose distribution than Pencil beam based algorithms for the electron beams investigated.     

Time domain measures of inter-channel EEG correlations: a comparison of linear, nonparametric and nonlinear measures

Correlations between ten-channel EEGs obtained from thirteen healthy adult participants were investigated. Signals were obtained in two behavioral states: eyes open no task and eyes closed no task. Four time domain measures were compared: Pearson product moment correlation, Spearman rank order correlation, Kendall rank order correlation and mutual information. The psychophysiological utility of each measure was assessed by determining its ability to discriminate between conditions. The sensitivity to epoch length was assessed by repeating calculations with 1, 2, 3, …, 8 s epochs. The robustness to noise was assessed by performing calculations with noise corrupted versions of the original signals (SNRs of 0, 5 and 10 dB). Three results were obtained in these calculations. First, mutual information effectively discriminated between states with less data. Pearson, Spearman and Kendall failed to discriminate between states with a 1 s epoch, while a statistically significant separation was obtained with mutual information. Second, at all epoch durations tested, the measure of between-state discrimination was greater for mutual information. Third, discrimination based on mutual information was more robust to noise. The limitations of this study are discussed. Further comparisons should be made with frequency domain measures, with measures constructed with embedded data and with the maximal information coefficient.     

GEANT4 Monte Carlo simulations for virtual clinical trials in breast X-ray imaging: Proof of concept

Virtual clinical trials (VCT) are in-silico reproductions of medical examinations, which adopt digital models of patients and simulated devices. They are intended to produce clinically equivalent outcome data avoiding long execution times, ethical issues related to radiation induced risks and huge costs related to real clinical trials with a patient population. In this work, we present a platform for VCT in 2D and 3D X-ray breast imaging. The VCT platform uses Monte Carlo simulations based on the Geant4 toolkit and patient breast models derived from a cohort of high resolution dedicated breast CT (BCT) volume data sets. Projection images of the breast and three-dimensional glandular dose maps are generated for a given breast model, by simulating both 2D full-field digital mammography (DM) and 3D BCT examinations. Uncompressed voxelized breast models were derived from segmented patient images. Compressed versions of the digital breast phantoms for DM were generated using a previously published digital compression algorithm. The Monte Carlo simulation framework has the capability of generating and tracking ~10⁵ photons/s using a server equipped with 16-cores and 3.0 GHz clock speed. The VCT platform will provide a framework for scanner design optimization, comparison between different scanner designs and between different modalities or protocols on computational breast models, without the need for scanning actual patients as in conventional clinical trials.     

The coevolution of male and female genitalia in a mammal: A quantitative genetic insight

Male genitalia are among the most phenotypically diverse morphological traits, and sexual selection is widely accepted as being responsible for their evolutionary divergence. Studies of house mice suggest that the shape of the baculum (penis bone) affects male reproductive fitness and experimentally imposed postmating sexual selection has been shown to drive divergence in baculum shape across generations. Much less is known of the morphology of female genitalia and its coevolution with male genitalia. In light of this, we used a paternal half-sibling design to explore patterns of additive genetic variation and covariation underlying baculum shape and female vaginal tract size in house mice (Mus musculus domesticus). We applied a landmark-based morphometrics approach to measure baculum size and shape in males and the length of the vaginal tract and width of the cervix in females. Our results reveal significant additive genetic variation in house mouse baculum morphology and cervix width, as well as evidence for genetic covariation between male and female genital measures. Our data thereby provide novel insight into the potential for the coevolutionary divergence of male and female genital traits in a mammal.     

Testing the potential seed availability in dung samples: comparison of two seedling emergence methods

To optimize the estimation of species composition and viable seed content of herbivore faeces and to make different approaches comparable, two seedling emergence methods are evaluated. The Ter Heerdt method (TH) employs concentrated samples, potentially increasing and accelerating seedling emergence, as shown for soil samples (95% of all seedlings emerged within 6 weeks). Samples are kept under controlled conditions (glasshouse or climate room). Secondly, a common garden method (CG) using unconcentrated samples so that seasonal changes could fulfill the germination requirements of a broad species spectrum (experiment duration approximately 15 months) was applied. The methods were tested by the use of sheep faeces samples, collected during a six-day grazing period in a threatened dry grassland (Allio-Stipetum capillatae).Both methods proved largely similar in species composition (QS=0.81) and viable seed content (QS=0.69). More species (e.g. monocotyls) and a higher seedling emergence of hard-seeded species (Fabaceae and Cistaceae) were found in the CG method. Besides a higher emergence of some small-seeded winter annuals, few other species emerged exclusively by use of the TH method. Nevertheless, all species detected by only one method were found in low individual numbers (4).Depending on research interest and availability of space and time, the most appropriate method can be chosen. If the main focus is on the species composition, unconcentrated faeces samples can be studied by CG. In case the overall viable seed content is more important and/or a shorter time period is available, TH serves as a suitable alternative.