Closure procedures for monotone bi-factorial dose-response designs

Summary.   Two goals of multiple-dose factorial trials are (i) demonstrating improved effectiveness of a fixed combination over each of its components as well as (ii) identifying a safe and effective dose range. The authors address both goals though with focus on the second by closure procedures that guarantee strong control of the familywise error rate. Two different families of null hypotheses are investigated for bi-factorial dose–response designs that are monotone with respect to the matrix partial order. One is suitable to find the minimum effective dose(s) and the other one is large enough to identify the highest effective dose step(s). Likelihood ratio tests and appropriate multiple contrast tests are applied to an unbalanced clinical trial example taken from Hung (2000, Statistics in Medicine 19, 2079–2087). Full computer code written in the R language is available from the Internet.     

Temperature dependence of the inhibitory effects of orthovanadate on shortening velocity in fast skeletal muscle.

We have investigated the effects of the orthophosphate (P(i)) analog orthovanadate (Vi) on maximum shortening velocity (Vmax) in activated, chemically skinned, vertebrate skeletal muscle fibers. Using new "temperature-jump" protocols, reproducible data can be obtained from activated fibers at high temperatures, and we have examined the effect of increased [Vi] on Vmax for temperatures in the range 5-30 degrees C. We find that for temperatures < or = 20 degrees C, increasing [Vi] inhibits Vmax; for temperatures > or = 25 degrees C, increasing [Vi] does not inhibit Vmax. Attached cross-bridges bound to Vi are thought to be an analog of the weakly bound actin-myosin.ADP-P(i) state. The data suggest that the weakly bound Vi state can inhibit velocity at low temperature, but not at high temperature, with the transition occurring over a narrow temperature range of < 5 degrees C. This suggests a highly cooperative interaction. The data also define a Q10 for Vmax of 2.1 for chemically skinned rabbit psoas fibers over the temperature range of 5-30 degrees C.     

A method for determining weights for excess relative risk and excess absolute risk when applied in the calculation of lifetime risk of cancer from radiation exposure

Radiation-related risks of cancer can be transported from one population to another population at risk, for the purpose of calculating lifetime risks from radiation exposure. Transfer via excess relative risks (ERR) or excess absolute risks (EAR) or a mixture of both (i.e., from the life span study (LSS) of Japanese atomic bomb survivors) has been done in the past based on qualitative weighting. Consequently, the values of the weights applied and the method of application of the weights (i.e., as additive or geometric weighted means) have varied both between reports produced at different times by the same regulatory body and also between reports produced at similar times by different regulatory bodies. Since the gender and age patterns are often markedly different between EAR and ERR models, it is useful to have an evidence-based method for determining the relative goodness of fit of such models to the data. This paper identifies a method, using Akaike model weights, which could aid expert judgment and be applied to help to achieve consistency of approach and quantitative evidence-based results in future health risk assessments. The results of applying this method to recent LSS cancer incidence models are that the relative EAR weighting by cancer solid cancer site, on a scale of 0–1, is zero for breast and colon, 0.02 for all solid, 0.03 for lung, 0.08 for liver, 0.15 for thyroid, 0.18 for bladder and 0.93 for stomach. The EAR weighting for female breast cancer increases from 0 to 0.3, if a generally observed change in the trend between female age-specific breast cancer incidence rates and attained age, associated with menopause, is accounted for in the EAR model. Application of this method to preferred models from a study of multi-model inference from many models fitted to the LSS leukemia mortality data, results in an EAR weighting of 0. From these results it can be seen that lifetime risk transfer is most highly weighted by EAR only for stomach cancer. However, the generalization and interpretation of radiation effect estimates based on the LSS cancer data, when projected to other populations, are particularly uncertain if considerable differences exist between site-specific baseline rates in the LSS and the other populations of interest. Definitive conclusions, regarding the appropriate method for transporting cancer risks, are limited by a lack of knowledge in several areas including unknown factors and uncertainties in biological mechanisms and genetic and environmental risk factors for carcinogenesis; uncertainties in radiation dosimetry; and insufficient statistical power and/or incomplete follow-up in data from radio-epidemiological studies.     

Potential errors in fiber length measurements resulting from lever arm rotation during mechanical testing of muscle cells

In single muscle cell preparations fibers are often suspended between connectors, extending perpendicularly from a force transducer, and the lever arm of a torque motor. The fiber does not move along a horizontal plane when shortened or lengthened by lever arm rotation. An error from the true length (TL) is introduced if the expected length (EL) is calibrated along this horizontal optical plane. Lever arm length (LAL), initial fiber length (FL(i)), connector length (CL), and the magnitude of EL all contribute to this error. A mathematical model was used to determine the TL during shortening (0.96-0.80 FL(i)) and lengthening (1.10-1.50 FL(i)) at a constant LAL of 13.6mm. CL had the greatest impact on error. For FL(i) = 2mm at the longest CL modeled (15 mm), an expected shortening of 0.20 FL(i) produced a true shortening of ～ 0.17 FL(i), and an expected stretch to 1.50 FL(i) resulted in a true stretch to almost 1.60 FL(i). Under these conditions, the true sarcomere length would be 4% and 6% longer than expected during shortening and lengthening, respectively. Because of their non-linear nature, length errors at long CL's may result in an over-estimation of unloaded shortening velocity during slack tests and a left-ward shift in the passive tension-fiber length relationship at long fiber lengths. Measurement errors decreased dramatically with shorter CL's, becoming negligible (<1%) at CL = 3mm. We recommend that investigators keep CL as short as possible. Alternatively, we provide a method for adjusting the magnitude of the EL to yield a desired TL.     

Thyroid cancer following scalp irradiation: a reanalysis accounting for uncertainty in dosimetry

In the 1940s and 1950s, over 20,000 children in Israel were treated for tinea capitis (scalp ringworm) by irradiation to induce epilation. Follow-up studies showed that the radiation exposure was associated with the development of malignant thyroid neoplasms. Despite this clear evidence of an effect, the magnitude of the dose-response relationship is much less clear because of probable errors in individual estimates of dose to the thyroid gland. Such errors have the potential to bias dose-response estimation, a potential that was not widely appreciated at the time of the original analyses. We revisit this issue, describing in detail how errors in dosimetry might occur, and we develop a new dose-response model that takes the uncertainties of the dosimetry into account. Our model for the uncertainty in dosimetry is a complex and new variant of the classical multiplicative Berkson error model, having components of classical multiplicative measurement error as well as missing data. Analysis of the tinea capitis data suggests that measurement error in the dosimetry has only a negligible effect on dose-response estimation and inference as well as on the modifying effect of age at exposure.     

Leukaemia and thyroid cancer in emergency workers of the Chernobyl accident:

This work focuses on the direct epidemiological assessment of the risks of radiation-induced leukaemia and thyroid cancer in emergency workers (EW) after the Chernobyl accident. The Russian National Medical Dosimetric Registry (RNMDR) contains data for 168 000 EW as of January 1, 1996. The analysis relates to 48 leukaemias and 47 thyroid cancers, diagnosed and verified. Radiation risks are estimated by comparing the EW data with national data for a male population of the same age distribution. For leukaemia, an excess relative risk per Gy (ERR/Gy) of 4.30 (95% CI: 0.83, 7.75) is obtained, while the excess absolute risk per 10⁴ person-years (PY) Gy (EAR/10⁴ PY Gy) is found to be 1.31 (95% CI: 0.23, 2.39); for thyroid cancer an ERR/Gy of 5.31 (95% CI: 0.04, 10.58) is obtained, and an EAR/10⁴ PY Gy of 1.15 (95% CI: 0.08, 2.22).     

Importance of the conserved Walker B glutamate residues, 556 and 1201, for the completion of the catalytic cycle of ATP hydrolysis by human P-glycoprotein (ABCB1)

The human MDR1 (ABCB1) gene product, P-glycoprotein (Pgp), functions as an ATP-dependent efflux pump for a variety of chemotherapeutic drugs. In this study, we assessed the role of conserved glutamate residues in the Walker B domain of the two ATP sites (E556 and E1201, respectively) during the catalytic cycle of human Pgp. The mutant Pgps (E556Q, E556A, E1201Q, E1201A, E556/1201Q, and E556/1201A) were characterized using a vaccinia virus based expression system. Although steady-state ATP hydrolysis and drug transport activities were abrogated in both E556Q and E1201Q mutant Pgps, [alpha-(32)P]-8-azidoADP was trapped in the presence of vanadate (Vi), and the release of trapped [alpha-(32)P]-8-azidoADP occurred to a similar extent as in wild-type Pgp. This indicates that these mutations do not affect either the first hydrolysis event or the ADP release step. Similar results were also obtained when Glu residues were replaced with Ala (E556A and E1201A). Following the first hydrolysis event and release of [alpha-(32)P]-8-azidoADP, both E556Q and E1201Q mutant Pgps failed to undergo another cycle of Vi-induced [alpha-(32)P]-8-azidoADP trapping. Interestingly, the double mutants E556/1201Q and E556/1201A trapped [alpha-(32)P]-8-azidoADP even in the absence of Vi, and the occluded nucleotide was not released after incubation at 37 degrees C for an extended period. In addition, the properties of transition state conformation of the double mutants generated in the absence of Vi were found to be similar to that of the wild-type protein trapped in the presence of Vi (Pgp x [alpha-(32)P]-8-azidoADP xVi). Thus, in contrast to the single mutants, the double mutants appear to be defective in the ADP release step. In aggregate, these data suggest that E556 and E1201 residues in the Walker B domains may not be critical as catalytic carboxylates for the cleavage of the bond between the gamma-P and the beta-P of ATP during hydrolysis but are essential for the second ATP hydrolysis step and completion of the catalytic cycle.     

Thyroid cancer risk in areas of Ukraine and Belarus affected by the Chernobyl accident

The purpose of the present study was to analyze the thyroid cancer incidence risk after the Chernobyl accident and its degree of dependence on time and age. Data were analyzed for 1034 settlements in Ukraine and Belarus, in which more than 10 measurements of the (131)I content in human thyroids had been performed in May/June 1986. Thyroid doses due to the Chernobyl accident were assessed for the birth years 1968-1985 and related to thyroid cancers that were surgically removed during the period 1990-2001. The central estimate for the linear coefficient of the EAR dose response was 2.66 (95% CI: 2.19; 3.13) cases per 10(4) PY-Gy; for the quadratic coefficient, it was -0.145 (95% CI: -0.171; -0.119) cases per 10(4) PY-Gy(2). The EAR was found to be higher for females than for males by a factor of 1.4. It decreased with age at exposure and increased with age attained. The central estimate for the linear coefficient of the ERR dose response was 18.9 (95% CI: 11.1; 26.7) Gy(-1); for the quadratic coefficient, it was -1.03 (95% CI: -1.46; -0.60) Gy(-2). The ERR was found to be smaller for females than for males by a factor of 3.8 and decreased strongly with age at exposure. Both EAR and ERR were higher in the Belarusian settlements than in the Ukrainian settlements. In contrast to ERR, EAR increases with time after exposure. At the end of the observation period, excess risk estimates were found to be close to those observed in a major pooled analysis of seven studies of childhood thyroid cancer after external exposures.     

The Role of Human Error Analysis in Occupational and Environmental Risk Assessment: A Serbian Experience

Human error analysis is certainly a challenge today for all involved in safety and environmental risk assessment. The risk assessment process should not ignore the role of humans in accidental events and the consequences that may derive from human error. This article presents a case study of the Success Likelihood Index Method (SLIM) applied to the Electric Power Company of Serbia (EPCS), with the aim to disclose the importance of human error analysis in risk assessment. A database on work-related injuries, accidents, and critical interventions that occurred over a 10-year period in the EPCS provided the basis for this study. The research comprised analysis of 1074 workplaces, with a total of 3997 employees. A detailed analysis identified 10 typical human errors, performance shaping factors (PSFs), and estimated human error probability (HEP). Based on the obtained research results one can conclude that PSF control remains crucial for human error reduction, and thus prevention of occupational injuries and fatalities (the number of injuries decreased from 58 in 2012 to 44 in 2013, no fatalities recorded). Furthermore, the case study performed at the EPCS confirmed that the SLIM is highly applicable for quantification of human errors, comprehensive, and easy to perform.     

Pollen flow in the wildservice tree, Sorbus torminalis (L.) Crantz. I. Evaluating the paternity analysis procedure in continuous populations

The joint development of polymorphic molecular markers and paternity analysis methods provides new approaches to investigate ongoing patterns of pollen flow in natural plant populations. However, paternity studies are hindered by false paternity assignment and the nondetection of true fathers. To gauge the risk of these two types of errors, we performed a simulation study to investigate the impact on paternity analysis of: (i) the assumed values for the size of the breeding male population (NBMP), and (ii) the rate of scoring error in genotype assessment. Our simulations were based on microsatellite data obtained from a natural population of the entomophilous wild service tree, Sorbus torminalis (L.) Crantz. We show that an accurate estimate of NBMP is required to minimize both types of errors, and we assess the reliability of a technique used to estimate NBMP based on parent-offspring genetic data. We then show that scoring errors in genotype assessment only slightly affect the assessment of paternity relationships, and conclude that it is generally better to neglect the scoring error rate in paternity analyses within a nonisolated population.     

Estimation of genotyping error rate from repeat genotyping,unintentional recaptures and known parent–offspring comparisons in 16 microsatellite loci for brown rockfish (Sebastes auriculatus)

Genotyping errors are present in almost all genetic data and can affect biological conclusions of a study, particularly for studies based on individual identification and parentage. Many statistical approaches can incorporate genotyping errors, but usually need accurate estimates of error rates. Here, we used a new microsatellite data set developed for brown rockfish (Sebastes auriculatus) to estimate genotyping error using three approaches: (i) repeat genotyping 5% of samples, (ii) comparing unintentionally recaptured individuals and (iii) Mendelian inheritance error checking for known parent–offspring pairs. In each data set, we quantified genotyping error rate per allele due to allele drop‐out and false alleles. Genotyping error rate per locus revealed an average overall genotyping error rate by direct count of 0.3%, 1.5% and 1.7% (0.002, 0.007 and 0.008 per allele error rate) from replicate genotypes, known parent–offspring pairs and unintentionally recaptured individuals, respectively. By direct‐count error estimates, the recapture and known parent–offspring data sets revealed an error rate four times greater than estimated using repeat genotypes. There was no evidence of correlation between error rates and locus variability for all three data sets, and errors appeared to occur randomly over loci in the repeat genotypes, but not in recaptures and parent–offspring comparisons. Furthermore, there was no correlation in locus‐specific error rates between any two of the three data sets. Our data suggest that repeat genotyping may underestimate true error rates and may not estimate locus‐specific error rates accurately. We therefore suggest using methods for error estimation that correspond to the overall aim of the study (e.g. known parent–offspring comparisons in parentage studies).     

A reanalysis of thyroid neoplasms in the Israeli tinea capitis study accounting for dose uncertainties

In the 1940s and 1950s, children in Israel were treated for tinea capitis by irradiation to the scalp to induce epilation. Follow-up studies of these patients and of other radiation- exposed populations show an increased risk of malignant and benign thyroid tumors. Those analyses, however, assume that thyroid dose for individuals is estimated precisely without error. Failure to account for uncertainties in dosimetry may affect standard errors and bias dose-response estimates. For the Israeli tinea capitis study, we discuss sources of uncertainties and adjust dosimetry for uncertainties in the prediction of true dose from X-ray treatment parameters. We also account for missing ages at exposure for patients with multiple X-ray treatments, since only ages at first treatment are known, and for missing data on treatment center, which investigators use to define exposure. Our reanalysis of the dose response for thyroid cancer and benign thyroid tumors indicates that uncertainties in dosimetry have minimal effects on dose-response estimation and for inference on the modifying effects of age at first exposure, time since exposure, and other factors. Since the components of the dose uncertainties we describe are likely to be present in other epidemiological studies of patients treated with radiation, our analysis may provide a model for considering the potential role of these uncertainties.     

Variability, repeatability and phenotypic relationships of several characteristics of production and semen quality in rabbit

A total of 2140 ejaculates from 156 adult males pertaining to four groups of bucks were analysed and the following traits were recorded: pH, ejaculate volume (V), mass motility (Mm), individual motility (Mi), concentration (Cn), total number of spermatozoa per ejaculate (TSE), percentage of sperm viability (Vi), percentage of sperm with acrosome integrity (NAR), percentage of sperm normalcy (Nr), percentage of sperm morphological abnormalities of head (H), neck-midpiece (Nm) and tail (T) and presence of proximal and distal cytoplasmic droplet (Dp, Dd). Principal component (PC) analysis and phenotypic correlations were performed in order to examine the relationships between qualitative and quantitative traits of rabbit semen. The repeatability of the traits measured was also estimated. Phenotypic correlations between sperm traits were estimated as the residual correlation from an analysis of variance, including the effects of: genetic type of the male, order of the ejaculate, day of collection and the permanent non-additive random effect of the male to which the observation corresponds. The repeatability of these traits was analysed separately, in a set of univariate analyses, using VCE software. The previously defined mixed model was used for this analysis. The principal component analysis was performed using the Princomp procedure of the SAS v.8 package. The first four PC explained 62% of total variation: 23%, 18%, 12% and 8%, respectively. Percentage of sperm viability, NAR, Nr, T and Nm were the predominant variables in the first PC. Mass motility, Mi, pH, Cn and TSE were located in the second. Percentage of sperm with the presence of proximal and distal cytoplasmic droplet, NAR, Vi and Nr were the predominant traits in the third and V defined the fourth. Repeatability of semen quality traits was moderate for most of the traits. The highest values (about 0.45) corresponded to V, Cn, Nr and Dp and the lowest (about 0.10) to H and Nm. Repeatability of the first ejaculate was greater than that of the second for pH, Mm, Mi, H, Dp and Dd.     

Risk of second primary thyroid cancer after radiotherapy for a childhood cancer in a large cohort study: an update from the childhood cancer survivor study

Previous studies have indicated that thyroid cancer risk after a first childhood malignancy is curvilinear with radiation dose, increasing at low to moderate doses and decreasing at high doses. Understanding factors that modify the radiation dose response over the entire therapeutic dose range is challenging and requires large numbers of subjects. We quantified the long-term risk of thyroid cancer associated with radiation treatment among 12,547 5-year survivors of a childhood cancer (leukemia, Hodgkin lymphoma and non-Hodgkin lymphoma, central nervous system cancer, soft tissue sarcoma, kidney cancer, bone cancer, neuroblastoma) diagnosed between 1970 and 1986 in the Childhood Cancer Survivor Study using the most current cohort follow-up to 2005. There were 119 subsequent pathologically confirmed thyroid cancer cases, and individual radiation doses to the thyroid gland were estimated for the entire cohort. This cohort study builds on the previous case-control study in this population (69 thyroid cancer cases with follow-up to 2000) by allowing the evaluation of both relative and absolute risks. Poisson regression analyses were used to calculate standardized incidence ratios (SIR), excess relative risks (ERR) and excess absolute risks (EAR) of thyroid cancer associated with radiation dose. Other factors such as sex, type of first cancer, attained age, age at exposure to radiation, time since exposure to radiation, and chemotherapy (yes/no) were assessed for their effect on the linear and exponential quadratic terms describing the dose-response relationship. Similar to the previous analysis, thyroid cancer risk increased linearly with radiation dose up to approximately 20 Gy, where the relative risk peaked at 14.6-fold (95% CI, 6.8-31.5). At thyroid radiation doses >20 Gy, a downturn in the dose-response relationship was observed. The ERR model that best fit the data was linear-exponential quadratic. We found that age at exposure modified the ERR linear dose term (higher radiation risk with younger age) (P < 0.001) and that sex (higher radiation risk among females) (P = 0.008) and time since exposure (higher radiation risk with longer time) (P < 0.001) modified the EAR linear dose term. None of these factors modified the exponential quadratic (high dose) term. Sex, age at exposure and time since exposure were found to be significant modifiers of the radiation-related risk of thyroid cancer and as such are important factors to account for in clinical follow-up and thyroid cancer risk estimation among childhood cancer survivors.     

The effects of force inhibition by sodium vanadate on cross-bridge binding, force redevelopment, and Ca2+ activation in cardiac muscle

Strongly bound, force-generating myosin cross-bridges play an important role as allosteric activators of cardiac thin filaments. Sodium vanadate (Vi) is a phosphate analog that inhibits force by preventing cross-bridge transition into force-producing states. This study characterizes the mechanical state of cross-bridges with bound Vi as a tool to examine the contribution of cross-bridges to cardiac contractile activation. The K(i) of force inhibition by Vi was approximately 40 microM. Sinusoidal stiffness was inhibited with Vi, although to a lesser extent than force. We used chord stiffness measurements to monitor Vi-induced changes in cross-bridge attachment/detachment kinetics at saturating [Ca(2+)]. Vi decreased chord stiffness at the fastest rates of stretch, whereas at slow rates chord stiffness actually increased. This suggests a shift in cross-bridge population toward low force states with very slow attachment/detachment kinetics. Low angle x-ray diffraction measurements indicate that with Vi cross-bridge mass shifted away from thin filaments, implying decreased cross-bridge/thin filament interaction. The combined x-ray and mechanical data suggest at least two cross-bridge populations with Vi; one characteristic of normal cycling cross-bridges, and a population of weak-binding cross-bridges with bound Vi and slow attachment/detachment kinetics. The Ca(2+) sensitivity of force (pCa(50)) and force redevelopment kinetics (k(TR)) were measured to study the effects of Vi on contractile activation. When maximal force was inhibited by 40% with Vi pCa(50) decreased, but greater force inhibition at higher [Vi] did not further alter pCa(50). In contrast, the Ca(2+) sensitivity of k(TR) was unaffected by Vi. Interestingly, when force was inhibited by Vi k(TR) increased at submaximal levels of Ca(2+)-activated force. Additionally, k(TR) is faster at saturating Ca(2+) at [Vi] that inhibit force by > approximately 70%. The effects of Vi on k(TR) imply that k(TR) is determined not only by the intrinsic properties of the cross-bridge cycle, but also by cross-bridge contribution to thin filament activation.     

Laplace approximation in measurement error models

Likelihood analysis for regression models with measurement errors in explanatory variables typically involves integrals that do not have a closed-form solution. In this case, numerical methods such as Gaussian quadrature are generally employed. However, when the dimension of the integral is large, these methods become computationally demanding or even unfeasible. This paper proposes the use of the Laplace approximation to deal with measurement error problems when the likelihood function involves high-dimensional integrals. The cases considered are generalized linear models with multiple covariates measured with error and generalized linear mixed models with measurement error in the covariates. The asymptotic order of the approximation and the asymptotic properties of the Laplace-based estimator for these models are derived. The method is illustrated using simulations and real-data analysis.     

Common Slope Tests for Bivariate Errors‐in‐Variables Models

Likelihood ratio tests are derived for bivariate normal structural relationships in the presence of group structure. These tests may also be applied to less restrictive models where only errors are assumed to be normally distributed. Tests for a common slope amongst those from several datasets are derived for three different cases – when the assumed ratio of error variances is the same across datasets and either known or unknown, and when the standardised major axis model is used. Estimation of the slope in the case where the ratio of error variances is unknown could be considered as a maximum likelihood grouping method. The derivations are accompanied by some small sample simulations, and the tests are applied to data arising from work on seed allometry.