A Bayesian analysis of the two-period crossover design for clinical trials

Statisticians have been critical of the use of the two-period crossover designs for clinical trials because the estimate of the treatment difference is biased when the carryover effects of the two treatments are not equal. In the standard approach, if the null hypothesis of equal carryover effects is not rejected, data from both periods are used to estimate and test for treatment differences; if the null hypothesis is rejected, data from the first period alone are used. A Bayesian analysis based on the Bayes factor against unequal carryover effects is given. Although this Bayesian approach avoids the "all-or-nothing" decision inherent in the standard approach, it recognizes that with small trials it is difficult to provide unequivocal evidence that the carryover effects of the two treatments are equal, and thus that the interpretation of the difference between treatment effects is highly dependent on a subjective assessment of the reality or not of equal carryover effects.     

How to evaluate the environmental safety of microbial plant protection products: A proposal

Plant protection products with active micro-organisms are allegedly less hazardous to the environment and wildlife than synthetic chemical pesticides. Nevertheless, they need a proper pre-marketing environmental safety evaluation because of their potential toxicity and pathogenicity. Scientific and technical guidance on such a safety evaluation for regulatory purposes is scarce. Therefore, a risk decision tree is proposed to provide such guidance and to discern the acceptable from the unacceptable environmental risks. The decision tree is based on the risk criteria of the European Union. It takes integrally into account the characterisation, identification and efficacy and also emission, exposure, environmental effects and, finally, the environmental risk assessment. Case by case expert judgement remains necessary in view of limited knowledge of microbial ecology, limited experience with regulatory test protocols and taxonomic difficulties in relation to the indigenousness of active micro-organisms. The decision tree offers regulatory guidance on the environmental safety evaluation of microbial plant protection products.     

Non‐consumptive effects of predation: does perceived risk strengthen the genetic integration of behaviour and morphology in stickleback?

Predators can shape genetic correlations in prey by altering prey perception of risk. We manipulated perceived risk to test whether such non‐consumptive effects tightened behavioural trait correlations in wild‐caught stickleback from high‐ compared to low‐risk environments due to genetic variation in plasticity. We expected tighter genetic correlations within perceived risk treatments than across them, and tighter genetic correlations in high‐risk than in low‐risk treatments. We identified genetic variation in plasticity, with genetic correlations between boldness, sociality, and antipredator morphology, as expected, being tighter within treatments than across them, for both of two populations. By contrast, genetic correlations did not tighten with exposure to risk. Tighter phenotypic correlations in wild stickleback may thus arise because predators induce correlational selection on environmental components of these traits, or because predators tighten residual correlations by causing environmental heterogeneity that is controlled in the laboratory. Our study places phenotypic integration firmly into an ecological context.     

Natural Stressors and Ranavirus Susceptibility in Larval Wood Frogs (Rana sylvatica)

Chronic exposure to stressors has been shown to suppress immune function in vertebrates, making them more susceptible to pathogens. It is less clear, however, whether many natural stressors are immunosuppressive. Moreover, whether stressors make disease more likely or more severe in populations is unclear because animals respond to stressors both behaviorally and physiologically. We tested whether chronic exposure to three natural stressors of wood frog tadpoles—high-densities, predator-cues, and low-food conditions—influence their susceptibility to a lethal ranavirus both individually in laboratory experiments, and collectively in outdoor mesocosms. Prior to virus exposure, we observed elevated corticosterone only in low-food treatments, although other treatments altered rates of growth and development as well as tadpole behavior. None of the treatments, however, increased susceptibility to ranavirus as measured by the proportion of tadpoles that became infected or died, or the time to death compared to controls. In fact, mortality in the mesocosms was actually lower in the high-density treatment even though most individuals became infected, largely because of increased rates of metamorphosis. Overall we find no support for the hypothesis that chronic exposure to common, ecologically relevant challenges necessarily elevates corticosterone levels in a population or leads to more severe ranaviral disease or epidemics. Conditions may, however, conspire to make ranavirus infection more common in metamorphosing amphibians.     

ON THE NEED FOR IMPROVED PROTECTIONS OF INCAPACITATED AND NON‐BENEFITING RESEARCH SUBJECTS

In this article, it is claimed that the protective provisions for adults with impaired decision‐making capacity are misguided, insofar as they do not conclusively state whether research on this group should be permitted only as an exception, and as they arbitrarily allow for some groups to benefit from such research while others will not. Moreover, the presumed or former will of the subject is given insufficient weight, and the minimal risk standard does not make sense in this context. Because of these problems, the present guidelines allow for the possibility of vulnerable people being exploited, something that is hidden behind a guise of solidarity. Instead we need to address the real issues at stake by rewriting the present statutes. It is suggested that new guidelines should be in some continuity with earlier efforts. However, in order to protect these subjects there is additional need for appointed representatives who monitor research and for legal obligations to compensate for any injuries suffered. Without these or similar measures we won't have an adequate system in place for the protection of non‐benefiting persons who are unable to consent to research.     

Sequential hypothesis testing with spatially correlated presence-absence data

A pest management decision to initiate a control treatment depends upon an accurate estimate of mean pest density. Presence-absence sampling plans significantly reduce sampling efforts to make treatment decisions by using the proportion of infested leaves to estimate mean pest density in lieu of counting individual pests. The use of sequential hypothesis testing procedures can significantly reduce the number of samples required to make a treatment decision. Here we construct a mean-proportion relationship for Oligonychus perseae Tuttle, Baker, and Abatiello, a mite pest of avocados, from empirical data, and develop a sequential presence-absence sampling plan using Bartlett's sequential test procedure. Bartlett's test can accommodate pest population models that contain nuisance parameters that are not of primary interest. However, it requires that population measurements be independent, which may not be realistic because of spatial correlation of pest densities across trees within an orchard. We propose to mitigate the effect of spatial correlation in a sequential sampling procedure by using a tree-selection rule (i.e., maximin) that sequentially selects each newly sampled tree to be maximally spaced from all other previously sampled trees. Our proposed presence-absence sampling methodology applies Bartlett's test to a hypothesis test developed using an empirical mean-proportion relationship coupled with a spatial, statistical model of pest populations, with spatial correlation mitigated via the aforementioned tree-selection rule. We demonstrate the effectiveness of our proposed methodology over a range of parameter estimates appropriate for densities of O. perseae that would be observed in avocado orchards in California.     

THE DUAL BENEFITS OF APOSEMATISM: PREDATOR AVOIDANCE AND ENHANCED RESOURCE COLLECTION

Theories of aposematism often focus on the idea that warning displays evolve because they work as effective signals to predators. Here, we argue that aposematism may instead evolve because, by enhancing protection, it enables animals to become more exposed and thereby gain resource‐gathering benefits, for example, through a wider foraging niche. Frequency‐dependent barriers (caused by enhanced conspicuousness relative to other prey and low levels of predator education) are generally assumed to make the evolution of aposematism particularly challenging. Using a deterministic, evolutionary model we show that aposematic display could evolve relatively easily if it enabled prey to move more freely around their environments, or become exposed in some other manner that provides fitness benefits unrelated to predation risk. Furthermore, the model shows that the traits of aposematic conspicuousness and behavior which lead to raised exposure positively affect each other, so that the optimal level of both tends to increase when the traits exist together, compared to when they exist in isolation. We discuss the ecological and evolutionary consequences of aposematism. One conclusion is that aposematism could be a key evolutionary innovation, because by widening habitat use it may promote adaptive radiation as a byproduct of enhanced ecological opportunity.     

Impact of antimicrobial residues on gut communities: are the new regulations effective?

Veterinary medicines are subject to a rigorous evaluation with regard to safety, efficacy and quality before they are licensed. For drugs used in food producing animals, it is necessary to establish what is referred to as the acceptable daily intake (ADI), this is defined as an estimate of the amount of a substance, expressed on a body weight basis, that can be ingested daily over a lifetime without appreciable risk to human health. It is necessary to determine a toxicological, pharmacological and microbiological ADI. This article describes a recently harmonized guideline that outlines the process for determining the need for a microbiological ADI and discusses the test systems that take into account the complexity of the human intestinal flora. The described process is used to address the effects of antimicrobial drug residues on human intestinal flora for regulatory purposes. The guideline does not recommend any one particular system for use in regulatory decision making but provides recommendations for a harmonized approach to establish a microbiological ADI and offers test options rather than specifying a testing regimen. The process and the challenges of this new guideline are discussed.     

Estimating species trees using multiple-allele DNA sequence data

Several techniques, such as concatenation and consensus methods, are available for combining data from multiple loci to produce a single statement of phylogenetic relationships. However, when multiple alleles are sampled from individual species, it becomes more challenging to estimate relationships at the level of species, either because concatenation becomes inappropriate due to conflicts among individual gene trees, or because the species from which multiple alleles have been sampled may not form monophyletic groups in the estimated tree. We propose a Bayesian hierarchical model to reconstruct species trees from multiple-allele, multilocus sequence data, building on a recently proposed method for estimating species trees from single allele multilocus data. A two-step Markov Chain Monte Carlo (MCMC) algorithm is adopted to estimate the posterior distribution of the species tree. The model is applied to estimate the posterior distribution of species trees for two multiple-allele datasets--yeast (Saccharomyces) and birds (Manacus-manakins). The estimates of the species trees using our method are consistent with those inferred from other methods and genetic markers, but in contrast to other species tree methods, it provides credible regions for the species tree. The Bayesian approach described here provides a powerful framework for statistical testing and integration of population genetics and phylogenetics.     

Difference in Web Construction Behavior at Newly Occupied Web Sites Between Two Cyclosa Species

Animals make decisions based on subjective assessments of their environment. To determine their future foraging activities, animals probably assess food availability from past foraging experiences. Thus, foraging also functions as a way for animals to collect information, with the uncertainty of an assessment decreasing as foraging activity increases. This suggests that different needs for a correct assessment may affect the investment made in foraging activities. Orb‐web spiders sometimes relocate their webs and relocation rate differs among species. After web relocation, several spider species have been reported to construct the first webs at newly occupied web sites using less silk than usual, possibly to avoid the risk of an overinvestment at sites where food availability has not been determined. Nevertheless, they may pay a cost, because of inadequate decision‐making, if webs constructed with less silk convey less information and increase the uncertainty of an assessment. We expect that stronger site tenacity necessitates a greater requirement for correct assessment of web site and the degree to which spiders reduce the amount of web silk in the first web after web relocation is smaller in species that use the same site longer. To test this hypothesis, we examined web construction in two orb‐web spiders, Cyclosa octotuberculata and C. argenteoalba. At the same time we found that these two species exhibit different web‐site tenacity, as C. octotuberculata does not relocate its webs as frequently as does C. argenteoalba. After artificially induced web relocation, C. argenteoalba constructed webs that were initially smaller and contained only about 2/3 of the silk in control webs that were constructed at the original site. In contrast, C. octotuberculata did not exhibit such decreases in web size or in the amount of web silk used. This result is consistent with our hypothesis.     

Ecologists should not use statistical significance tests to interpret simulation model results

Simulation models are widely used to represent the dynamics of ecological systems. A common question with such models is how changes to a parameter value or functional form in the model alter the results. Some authors have chosen to answer that question using frequentist statistical hypothesis tests (e.g. ANOVA). This is inappropriate for two reasons. First, p‐values are determined by statistical power (i.e. replication), which can be arbitrarily high in a simulation context, producing minuscule p‐values regardless of the effect size. Second, the null hypothesis of no difference between treatments (e.g. parameter values) is known a priori to be false, invalidating the premise of the test. Use of p‐values is troublesome (rather than simply irrelevant) because small p‐values lend a false sense of importance to observed differences. We argue that modelers should abandon this practice and focus on evaluating the magnitude of differences between simulations. Synthesis Researchers analyzing field or lab data often test ecological hypotheses using frequentist statistics (t‐tests, ANOVA, etc.) that focus on p‐values. Field and lab data usually have limited sample sizes, and p‐values are valuable for quantifying the probability of making incorrect inferences in that situation. However, modern ecologists increasingly rely on simulation models to address complex questions, and those who were trained in frequentist statistics often apply the hypothesis‐testing approach inappropriately to their simulation results. Our paper explains why p‐values are not informative for interpreting simulation models, and suggests better ways to evaluate the ecological significance of model results.     

Use of in vivo genetic toxicity data for risk assessment

Mutagenicity studies have been used to identify specific agents as potential carconogens or other human health hazards; however, they have been used minimally for risk assessment or in determining permissible levels of human exposure. The poor predictive value of in vitro mutagenesis tests for carcinogenic activity and a lack of mechanistic understanding of the roles of mutagens in the induction of specific cancers have made these tests unattractive for the purpose of risk assessment. However, the limited resources available for carcinogen testing and large number of chemicals which need to be evaluated necessitate the incorporation of more efficient methods into the evaluation process. In vivo genetic toxicity testing can be recommended for this purpose because in vivo assays incorporate the metabolic activation pathways that are relevant to humans. We propose the use of a multiple end-point in vivo comprehensive testing protocol (CTP) using rodents. Studies using sub-acute exposure to low levels of test agents by routes consistent with human exposure can be a useful adjunct to methods currently used to provide data for risk assessment. Evaluations can include metabolic and pharmacokinetic endpoints, in addition to genetic toxicity studies, in order to provide a comprehensive examination of the mechanism of toxicity of the agent. A parallelogram approach can be used to estimate effects in non-accessible human tissues by using data from accessible human tissues and analogous tissues in animals. A categorical risk assessment procedure can be used which would consider, in order of priority, genetic damage in man, genetic damage in animals that is highly relevant to disease outcome (mutation, chromosome damage), and data from animals that is of less certain relevance to disease. Action levels of environmental exposure would be determined based on the lowest observed effect levels or the highest observed no effect levels, using sub-acute low level exposure studies in rodents. As an example, the known genotoxic effects of benzene exposure at low levels in man and animals are discussed. The lowest observed genotoxic effects were observed at about 1–10 parts per million for man and 0.04–0.1 parts per million in subacute animal studies. If genetic toxicity is to achieve a prominent role in evaluating carcinogens and characterizing germ-cell mutagens, minimal testing requirements must be established to ascertain the risk associated with environmental mutagen exposure. The use of the in vivo approach described here should provide the information needed to meet this goal. In addition, it should allow truly epigenetic or non-genotoxic carcinogens to be distinguished from the genotoxic carcinogens that are not detected by in vitro methods.     

Interactive effects of acclimation temperature and short‐term stress exposure on resistance traits in the butterfly Bicyclus anynana

The ability to buffer detrimental effects of environmental stress on fitness is of great ecological importance because, in nature, pronounced environmental variation may regularly induce stress. Furthermore, several stressors may interact in a synergistic manner. In the present study, plastic responses in cold, heat and starvation resistance are investigated in the tropical butterfly Bicyclus anynana Butler, 1879, using a full factorial design with two acclimation temperatures (20 and 27 °C) and four short‐term stress treatments (control, cold, heat, starvation). Warm‐acclimated butterflies are more heat‐ but less cold‐tolerant as expected. Short‐term cold and starvation exposure reduce cold and heat resistance, and short‐term heat exposure decreases cold but increases heat resistance. Starvation resistance is not affected by any of the short‐term treatments. Thus, the effects of short‐term stress exposure are either neutral or negative, except for a positive effect of heat exposure on heat resistance, indicating the negative effects of pre‐exposure to stress. Interestingly, significant interactions between acclimation temperature and short‐term stress exposure for heat and cold resistance are found, demonstrating that larger temperature differences incur more damage. Therefore, animals may not generally be able to benefit from pre‐exposure to stress (through ‘hardening’), depending on their previously experienced conditions. The complex interactions between environmental variation, stress and resistance are highlighted, warranting further investigations.     

A tale of two pesticides: how common insecticides affect aquatic communities

1. Recent ecotoxicology studies show that pesticide exposure can alter community composition, structure and function. Generally, community responses to pesticides are driven by trait‐ and density‐mediated indirect effects resulting from sublethal and lethal effects of pesticide exposure on vulnerable taxa. These effects depend upon the concentration of the pesticide and the frequency of exposure. 2. While more research is needed to understand community‐level responses to pesticide exposure, testing the effects of multitudes of registered chemicals on ecologically relevant communities is overwhelming. Recent reviews suggest that contaminants with similar modes of action should produce comparable community‐level responses because they have similar direct effects and, as a result, similar indirect effects; this hypothesis remains largely untested. 3. We subjected pond communities [containing zooplankton, phytoplankton, periphyton and leopard frog tadpoles (Rana pipiens)] to several applications (single applications of medium or high concentrations or weekly applications of a lower concentration) of two acetylcholine esterase inhibiting insecticides, malathion and carbaryl that have comparable toxicity for aquatic organisms. 4. We found that both insecticides cause comparable trophic cascades that affect zooplankton and phytoplankton abundances; however, their effects on amphibians diverged, especially when exposed to higher concentrations of insecticides. Malathion caused a trophic cascade beginning with a decline in cladocerans followed by increases in phytoplankton. At a medium concentration, this cascade also caused a subsequent decrease in periphyton. Carbaryl caused a similar trophic cascade with the highest application, a weak trophic cascade with the medium application and no cascade with smallest application. Malathion directly reduced tadpole survival at all concentrations. Survivors in the two higher treatments were larger at metamorphosis while survivors in the lowest treatments were smaller and developed slowly. In contrast, carbaryl was not directly toxic to tadpoles, but indirectly reduced survival because slow growth and development prevented some tadpoles from metamorphosing before the mesocosms dried at medium and low applications. 5. These results suggest that these common pesticides, which share the same mode of action, have similar effects on zooplankton and algae, but differences in the strength and timing of their effects on tadpoles reduce the generality of responses at higher trophic levels. Overall, general predictive models of contaminant effects could be improved by incorporating the relative timing of direct and indirect effects of exposure.     

Utility and relevance of aquatic oligochaetes in Ecological Risk Assessment

Ecological risk assessment (EcoRA) provides both a process and a framework to evaluate the potential for adverse ecological effects occurring as a result of exposure to contaminants or other stressors. EcoRA begins with problem formulation/hazard identification, progresses to effects and exposure assessment, and culminates with risk characterization (an estimate of the incidence and severity of any adverse effects likely to occur). Key components of EcoRA include determining: stressors/contaminants of concern; sensitive, exposed biota; and, appropriate tests and organisms for evaluating effects. Aquatic oligochaetes are not generally used directly in EcoRA because of three major perceptions. First, EcoRA personnel are generally not familiar with or comfortable using this group of organisms. Second, there is believed to be a paucity of widely accepted toxicity tests with these organisms. Third, their taxonomy is considered difficult and uncertain. In fact, aquatic oligochaetes potentially have great utility and relevance to EcoRAs because of factors including: their importance in the aquatic food chain (e.g. prey to fauna including fish and waterfowl; as a vector for contaminant movement through the food chain from bacteria); many species are widely distributed and well studied; representatives include fresh, estuarine and marine species; as a group, they range from sensitive to insensitive over a wide range of environmental insults; they have a long history of use in pollution monitoring and assessment; and, relevant toxicity and biaccumulation tests exist. Toxicity testing under defined conditions is appropriate for problem formulation while more realistic testing for effects assessment (e.g. microcosms) is logistically easier with this group of organisms than with others due to their relatively small size. The importance of aquatic oligochaetes for EcoRA, in particular of sediments, is particularly compelling.     

Nonparametric comparison of two survival-time distributions in the presence of dependent censoring

When testing the null hypothesis that treatment arm-specific survival-time distributions are equal, the log-rank test is asymptotically valid when the distribution of time to censoring is conditionally independent of randomized treatment group given survival time. We introduce a test of the null hypothesis for use when the distribution of time to censoring depends on treatment group and survival time. This test does not make any assumptions regarding independence of censoring time and survival time. Asymptotic validity of this test only requires a consistent estimate of the conditional probability that the survival event is observed given both treatment group and that the survival event occurred before the time of analysis. However, by not making unverifiable assumptions about the data-generating mechanism, there exists a set of possible values of corresponding sample-mean estimates of these probabilities that are consistent with the observed data. Over this subset of the unit square, the proposed test can be calculated and a rejection region identified. A decision on the null that considers uncertainty because of censoring that may depend on treatment group and survival time can then be directly made. We also present a generalized log-rank test that enables us to provide conditions under which the ordinary log-rank test is asymptotically valid. This generalized test can also be used for testing the null hypothesis when the distribution of censoring depends on treatment group and survival time. However, use of this test requires semiparametric modeling assumptions. A simulation study and an example using a recent AIDS clinical trial are provided.     

Predictive testing: presymptomatic diagnosis in neurogenetic disorders

Presymptomatic testing is available since 15 years for Huntington disease and it is now possible for a number of other neurogenetic disorders, mostly neurodegenerative disorders. The possibility of determining the genetic status of an at-risk person for the disorder which run in his family raises questions because of the absence of preventive and curative treatments in most instances. In addition, being carrier does not tell you when the disease will start and how it will evolve, impairing the possibilities of planning the future. A pluridisciplinary approach to predictive testing with care before, during and after the test taking into account the medical, social and psychological aspects of the disease is good practice. At the present time, only a minority of at-risk individuals request presymptomatic testing and almost 50 % do not pursue until the results. The consequences of the test may be harmful, more frequently after an unfavorable than after a favorable result. Although the motivations and the outcome in terms of request for prenatal testing after a carrier result are different in Huntington's disease and spinocerebellar ataxias, our experience underlines the benefit of pluridisciplinary care and of time for decision taking. For other disorders like familial Alzheimer's disease, or familial Creutzfeldt-Jakob disease, the experience in presymptomatic testing is still limited but the situation seems similar to Huntington's disease because of the presence of dementia. It will be interesting to study the motivations and the outcome of the tests in disorders like autosomal dominant spastic paraplegias which usually do not reduce the life expectancy. Nevertheless, the overall situation might change greatly when efficient treatments will become available in these disorders.     

Exposure to noise pollution across North American passerines supports the noise filter hypothesis

The noise filter hypothesis predicts that species using higher sound frequencies should be more tolerant of noise pollution, because anthropogenic noise is more intense at low frequencies. Recent work analysed continental‐scale data on anthropogenic noise across the USA and found that passerine species inhabiting more noise‐polluted areas do not have higher peak song frequency but have more complex songs. However, this metric of song complexity is of ambiguous interpretation, because it can indicate either diverse syllables or a larger frequency bandwidth. In the latter case, the finding would support the noise filter hypothesis, because larger frequency bandwidths mean that more sound energy spreads to frequencies that are less masked by anthropogenic noise. We reanalysed how passerine song predicts exposure to noise using a more thorough dataset of acoustic song measurements, and showed that it is large frequency bandwidths, rather than diverse syllables, that predict the exposure of species to noise pollution. Given that larger bandwidths often encompass higher maximum frequencies, which are less masked by anthropogenic noise, our result suggests that tolerance to noise pollution might depend mostly on having the high‐frequency parts of song little masked by noise, thus preventing acoustic communication from going entirely unnoticed at long distances.     

Auto-adaptive Alpha Allocation: A Strategy to Mitigate Risk on Study Assumptions

In some clinical development programs, there are potential biomarkers with promising but uncertain predictive effect, while the probability of success in the overall population cannot be readily dismissed. It is risky to focus only on the overall population, or just the biomarker subpopulation. In 2009, Chen and Beckman proposed a Bayesian decision framework to optimize the type I error rate (alpha) allocation in a Phase III clinical study with possible predictive subset effect. The utilization of internal data in this framework is of particular interest because it provides an opportunity to mitigate the potential risk of misspecified study assumptions using an auto-adaptive strategy. In this paper, we examine this auto-adaptive strategy in detail through extensive numerical case studies and provide guidance on the appropriate use of partial current trial (internal) data in this data-driven optimization framework. We show that internal data can be used to inform the alpha allocation to hypothesis testing in the overall population and the subgroup. The resulting adaptive testing strategy is robust with respect to the uncertainty in the predictive subgroup effect and biomarker prevalence.     

Competence and Ability

It is nearly universally thought that the kind of decision‐making competence that gives one a strong prima facie right to make one's own medical decisions essentially involves having an ability (or abilities) of some sort, or having a certain level or degree of ability (or abilities). When put under philosophical scrutiny, however, this kind of theory does not hold up. I will argue that being competent does not essentially involve abilities, and I will propose and defend a theory of decision‐making competence according to which one is competent only if one possesses a certain kind of rationality in making treatment decisions.