Design and analysis of group sequential clinical trials with multiple primary endpoints

In many phase III clinical trials, it is desirable to separately assess the treatment effect on two or more primary endpoints. Consider the MERIT-HF study, where two endpoints of primary interest were time to death and the earliest of time to first hospitalization or death (The International Steering Committee on Behalf of the MERIT-HF Study Group, 1997, American Journal of Cardiology 80[9B], 54J-58J). It is possible that treatment has no effect on death but a beneficial effect on first hospitalization time, or it has a detrimental effect on death but no effect on hospitalization. A good clinical trial design should permit early stopping as soon as the treatment effect on both endpoints becomes clear. Previous work in this area has not resolved how to stop the study early when one or more endpoints have no treatment effect or how to assess and control the many possible error rates for concluding wrong hypotheses. In this article, we develop a general methodology for group sequential clinical trials with multiple primary endpoints. This method uses a global alpha-spending function to control the overall type I error and a multiple decision rule to control error rates for concluding wrong alternative hypotheses. The method is demonstrated with two simulated examples based on the MERIT-HF study.     

The Effect of Extended Anaerobic Treatments on the Chromosomes of Vicia faba

The effects of extended anaerobic treatments on Vicia faba lateral root-tip chromosomes were determined. It was observed that aberrations resulted from these treatments, and that the frequency varied from root to root as well as from experiment to experiment. It was suggested that the inconsistency observed might be due to variation in the abilities of different roots to produce energy via fermentation routes. If this were true, an inhibition of fermentation would result in a more consistent aberration frequency. A fermentation inhibitor, NaF, was used in combination with extended anaerobic treatments. The observed frequency of aberrations after the combined treatments was generally higher and considerably less variable. Although other hypotheses might account for the NaF effect, the hypothesis most compatible with the evidence is that the effect is due to energy deprivation. The experimental results are discussed in terms of the aforementioned effect and in terms of three alternative hypotheses for the production of chromosomal aberrations as a consequence of a lack of energy. It is concluded that damage might result from a build-up of normal cellular compounds to abnormally high concentrations which would act directly or indirectly on the chromosomes, from the breakdown of DNA as an energy source, or simply as a result of the fact that the chromosome needs energy to remain intact.     

The effect of extended anaerobic treatments on the chromosomes of Vicia faba

The effects of extended anaerobic treatments on Vicia faba lateral root-tip chromosomes were determined. It was observed that aberrations resulted from these treatments, and that the frequency varied from root to root as well as from experiment to experiment. It was suggested that the inconsistency observed might be due to variation in the abilities of different roots to produce energy via fermentation routes. If this were true, an inhibition of fermentation would result in a more consistent aberration frequency. A fermentation inhibitor, NaF, was used in combination with extended anaerobic treatments. The observed frequency of aberrations after the combined treatments was generally higher and considerably less variable. Although other hypotheses might account for the NaF effect, the hypothesis most compatible with the evidence is that the effect is due to energy deprivation. The experimental results are discussed in terms of the aforementioned effect and in terms of three alternative hypotheses for the production of chromosomal aberrations as a consequence of a lack of energy. It is concluded that damage might result from a build-up of normal cellular compounds to abnormally high concentrations which would act directly or indirectly on the chromosomes, from the breakdown of DNA as an energy source, or simply as a result of the fact that the chromosome needs energy to remain intact.     

Can resource use be the link between productivity and species richness in mammals?

Species richness has been shown to be affected by primary productivity at various spatial scales. However, the mechanisms behind this effect are still poorly understood. Under the assumption that primary productivity is directly related to energy availability for an animal assemblage, the hypotheses are that (i) primary productivity will affect the number of ways different food resources can be combined into species specific niches and (ii) it will also determine the number of specialist species that can be supported. These hypotheses were tested on the herbivorous mammalian fauna of Australia. Productivity only had a weak effect on the number of food resource combinations in this case. Specialization was most common at low and high productivity. In addition there were significant differences in where different types of specialization was the most common. This study seeks an energetic mechanism to explain an energetic relationship and though no clear effect was found for resource use it identified a possible link between productivity and species richness.     

How scientists perceive the evolutionary origin of human traits: Results of a survey study

Various hypotheses have been proposed for why the traits distinguishing humans from other primates originally evolved, and any given trait may have been explained both as an adaptation to different environments and as a result of demands from social organization or sexual selection. To find out how popular the different explanations are among scientists, we carried out an online survey among authors of recent scientific papers in journals covering relevant fields of science (paleoanthropology, paleontology, ecology, evolution, human biology). Some of the hypotheses were clearly more popular among the 1,266 respondents than others, but none was universally accepted or rejected. Even the most popular of the hypotheses were assessed “very likely” by <50% of the respondents, but many traits had 1–3 hypotheses that were found at least moderately likely by >70% of the respondents. An ordination of the hypotheses identified two strong gradients. Along one gradient, the hypotheses were sorted by their popularity, measured by the average credibility score given by the respondents. The second gradient separated all hypotheses postulating adaptation to swimming or diving into their own group. The average credibility scores given for different subgroups of the hypotheses were not related to respondent's age or number of publications authored. However, (paleo)anthropologists were more critical of all hypotheses, and much more critical of the water‐related ones, than were respondents representing other fields of expertise. Although most respondents did not find the water‐related hypotheses likely, only a small minority found them unscientific. The most popular hypotheses were based on inherent drivers; that is, they assumed the evolution of a trait to have been triggered by the prior emergence of another human‐specific behavioral or morphological trait, but opinions differed as to which of the traits came first.     

The importance of being familiar: individual recognition and social behavior in sea trout (Salmo trutta)

This study addressed two hypotheses: (1) that individual recognitionis used to reduce the cost of contesting resources in sea troutand (2) that the hatchery environment selects against individualrecognition. Predictions from these hypotheses were tested inlaboratory experiments where behavior and growth were studiedin juvenile sea trout. In tact groups of familiar fish werecompared with groups that contained both familiar and unfamiliarindividuals. In general, the results were in agreement withthe first hypothesis. Familiar fish in intact groups had morestable dominance ranks, higher food intake, and better utilizationof food. Familiarity also reduced the distance to the nearestneighbor. Furthermore, initiators of conflicts were more likelyto win against familiar fish than against strangers. These resultssupport game-theory-based hypotheses explaining the dear-enemyphenomenon as an effect of familiarity A picture emerges inwhich familiarity stabilizes the hierarchical structure of agroup and governs behavioral modifications that will promotefeeding and growth, in turn leading to higher fitness. The secondhypothesis, which predicted a reduced effect of individual recognitionin sea-ranched trout, was not strongly supported because familiarityaffected sea-ranched and wild trout similarly in most respects.However, familiarity was not beneficial for growth in sea-ranchedtrout, whereas it increased growth rate in wild fish. In addition,sea-ranched trout tended to maintain larger distances to theirnearest neighbors than did wild trout.     

Regulation of energy liberation during steady sarcomere shortening

Energy liberation rate (E) during steady muscle shortening is a monotonic increasing or biphasic function of the shortening velocity (V). The study examines three plausible hypotheses for explaining the biphasic E-V relationship (EVR): 1) the cross-bridge (XB) turnover rate from non-force-generating (weak) to force-generating (strong) conformation decreases as V increases; 2) XB kinetics is determined by the number of strong XBs (XB-XB cooperativity); and 3) the affinity of troponin for calcium is modulated by the number of strong XBs (XB-Ca cooperativity). The relative role of the various energy-regulating mechanisms is not well defined. The hypotheses were tested by coupling calcium kinetics with XB cycling. All three hypotheses yield identical steady-state characteristics: 1) hyperbolic force-velocity relationship; 2) quasi-linear stiffness-force relationship; and 3) biphasic EVR, where E declines at high V due to decrease in the number of cycling XBs or in the weak-to-strong transition rate. The hypotheses differ in the ability to describe the existence of both monotonic and biphasic EVRs and in the effect of intracellular free calcium concentration ([Ca2+]i) on the EVR peak. Monotonic and biphasic EVRs with a shift in EVR peak to higher velocity at higher [Ca2+]i are obtained only by XB-Ca cooperativity. XB-XB cooperativity provides only biphasic EVRs. A direct effect of V on XB kinetics predicts that EVR peak is obtained at the same velocity independently of [Ca2+]i. The study predicts that measuring the dependence of the EVR on [Ca2+]i allows us to test the hypotheses and to identify the dominant energy-regulating mechanism. The established XB-XB and XB-Ca mechanisms provide alternative explanations to the various reported EVRs.     

Condition-dependent genetic benefits of extrapair fertilization in female blue tits Cyanistes caeruleus

In many socially monogamous birds, both partners perform extrapair copulations (EPC). As this behaviour potentially inflicts direct costs on females, they are currently hypothesized to search for genetic benefits for descendants, either as 'good' or 'complementary' genes. Although these hypotheses have found some support, several studies failed to find any beneficial consequence of EPC, and whether this behaviour is adaptive to females is subject to discussion. Here, we test these two hypotheses in a natural population of blue tits by accounting for the effect of most parameters known to potentially affect extrapair fertilization. Results suggest that female body mass affected the type of extrapair genetic benefits obtained. Heavy females obtained extrapair fertilizations when their social male was of low quality (as reflected by sexual display) and produced larger extrapair than within-pair chicks. Lean females obtained extrapair fertilizations when their social mate was genetically similar, thereby producing more heterozygous extrapair chicks. Our results suggest that mating patterns may be condition-dependent.     

Positive effects of helpers on reproductive success in the brown treecreeper and the general importance of future benefits

1. Numerous studies of cooperatively breeding species have tested for effects of helpers on reproductive success to evaluate hypotheses for the evolution of cooperation, but relatively few have used experimental or statistical approaches that control for the confounding effects of breeder and territory quality. 2. In the brown treecreeper Climacteris picumnus, most helpers are male offspring of the breeding pair that have delayed dispersal. We analysed 5 years of data (97 territory-years) using hierarchical linear modelling to test for effects of helpers on reproductive success while controlling for confounding factors. 3. The number of helpers was related positively to reproductive success even after controlling for differences between territories and breeders. A threshold effect was observed, with success increasing most with the presence of a second helper (i.e. at group size of four). 4. Feeding at the nest was one mechanism responsible for this effect, as larger groups had higher total feeding rates at all nesting stages. Higher total feeding rates, as well as higher feeding rates by helpers, were correlated in turn with greater reproductive success. 5. An analysis of the effects of helper feeding rate on reproductive success in groups with just one helper produced only weak support for a positive effect of helpers. Controlled comparisons of this kind utilize only a small fraction of the total data available and thus have limited statistical power compared to hierarchical or mixed-modelling. 6. A number of hypotheses to explain the evolution and maintenance of helping behaviour are consistent with our results for brown treecreepers including kin selection and hypotheses based on future direct benefits. 7. A previous synthesis of studies of helper effects that controlled for confounding factors suggested a pattern in which male helpers rarely have positive effects on reproductive success. However, revising that synthesis to include recent hierarchical or mixed-modelling studies suggests that helpers of both sexes usually have positive effects, and that the relative importance of future direct benefits may have been underestimated.     

Ordination of simulated complex forest succession: A new test of ordination methods

A model of a 1/12th ha forest stand, FORET, generated 10 000 years of simulated species succession. Approximately the first third of these results were analyzed by principal component analysis as if they were collected field data to give the trajectory of the community particle in a collapsed species space. The ordination axis orientation was performed on a dispersion matrix and correlation matrix between species. In both cases, however, the eigen vectors were applied to the data matrix which had not been transformed to unit species variance. This facilitated comparison of species dispersion and correlation structure; it emerged they were very different. Correlation structure gave large weights to understory species while dispersion emphasized the dominant overstory species. This implies a decomposition of simulated stand behavior into overstory and understory, even though such decomposition was not formally built into the model. This decomposition would seem to pertain to real vegetation. Principal component analysis was able to express insightful differences between data structure with and without the unit variance transformation implicit in the correlation matrix. This flexibility of the ordination method proved valuable in uncovering unsuspected ordering principles in the model. Complex simulated data allow the ordination technique to demonstrate its capacity to generate new hypotheses, which hypotheses can then be simply validated by a return to the structure of the model but with the hindsight of the analysis. The generation of new hypotheses is not possible if the simulation is of a simple coenocline; on the other hand, ordination of test field data does not allow the simple validation of new hypotheses, for in the field there is not a defined algorithm to which the researcher can return.     

Believers and Beaters: A Case Study of Supernatural Beliefs and Child Rearing in the Bahama Islands

The research described in this article tests the hypothesis that caretakers who fear the supernatural will inflict more pain on the children in their charge than will those caretakers who do not fear the supernatural. The hypothesis is drawn from a larger body of theory which states that child training practices influence adult personality, including beliefs in the supernatural—these beliefs in turn influence the training of children. In order to test the hypothesis it was necessary to find a group of people whose adults differ from each other in theirbeliefs in the supernatural and whose children receive differential training. The village of Congo Town, located on Andros Island in the Bahamas, provides such a group of people. In the course of ethnographic fieldwork carried out in 1968 in this village, twenty caretakers were interviewed about the training given to their forty-eight children and grandchildren, as well as about their beliefs in the supernatural. Differences both in beliefs in the supernatural and in child training practices exist. Three specific hypotheses are derived from the major hypothesis described above. Each of these hypotheses is found to be supported by data gathered in Congo Town. Since each of the derived hypotheses receives support, it is concluded that the major hypothesis is confirmed.     

Seed-mass effects in four Mediterranean Quercus species (Fagaceae) growing in contrasting light environments

Three hypotheses have been proposed to explain the functional relationship between seed mass and seedling performance: the reserve effect (larger seeds retain a larger proportion of reserves after germinating), the metabolic effect (seedlings from larger seeds have slower relative growth rates), and the seedling-size effect (larger seeds produce larger seedlings). We tested these hypotheses by growing four Mediterranean Quercus species under different light conditions (3, 27, and 100% of available radiation). We found evidence for two of the three hypotheses, but none of the four species complied with all three hypotheses at the same time. The reserve effect was not found in any species, the metabolic effect was found in three species (Q. ilex, Q. pyrenaica, and Q. suber), and the seedling-size effect in all species. Light availability significantly affected the relationships between seed size and seedling traits. For Q. ilex and Q. canariensis, a seedling-size effect was found under all three light conditions, but only under the lowest light (3%) for Q. suber and Q. pyrenaica. In all species, the correlation between seed mass and seedling mass increased with a decrease in light, suggesting that seedlings growing in low light depend more upon their seed reserves. A causal model integrates the three hypotheses, suggesting that larger seeds generally produced larger seedlings.     

Red herring or low illumination? The peninsula effect revisited

Aim The peninsula effect is the prediction that the number of species declines from a peninsula's base to its tip. We evaluated evidence for and against the peninsula effect, and conducted a field study designed to test alternative hypotheses for that effect. Location The Florida peninsula, USA. Methods First, we critically reviewed the accumulated literature on peninsula effects; second, we sampled microcrustaceans in palustrine wetlands on the ridges of peninsular Florida. Site selection in our field study accounted for historical effects and partially controlled for habitat effects. Statistical analyses further accounted for habitat effects, leaving peninsular geometry as the remaining causative mechanism for residual variation in species richness regression analyses. Results Our literature review found mixed evidence (49% of cases) for a peninsula effect. However, most study designs did not control for alternative hypotheses, most comparisons of alternative hypotheses were qualitative, and most studies focused on vertebrate animals. Our field study found that freshwater microcrustaceans inhabiting isolated wetlands on Florida’s peninsular ridges do not exhibit a peninsula effect. Essentially, no variation in microcrustacean species richness could be attributed to peninsular geometry, but 82.5% of variation in species richness was attributed to habitat and sampling effort. Main conclusions Although our research results support the ‘red herring’ label for the peninsula effect, our literature review leads us to argue that more illumination (in the form of study design and quantitative analysis) is needed if mechanisms causing the peninsula effect hypothesis are to be resolved. Future studies of peninsula effects need to control for alternative causative hypotheses (geometry, habitat or history) in study design, and compare quantitatively the effects of hypothesized mechanisms on peninsular diversity patterns. Additionally, studies of taxa other than vertebrate animals need to be conducted for generality. Our study may serve as an example of such an approach.     

Silica deposition in relation to ageing of leaf tissues in Sasa veitchii (Carriere) Rehder (Poaceae: Bambusoideae)

BACKGROUND AND AIMS: Silica deposition is one of the important characteristics of plants in the family Poaceae. There have been many investigations into the distribution, deposition and physiological functions of silica in this family. Two hypotheses on silica deposition have been proposed based on these studies. First, that silica deposition occurs passively as a result of water uptake by plants, and second, that silica deposition is controlled positively by plants. To test these two apparently contradictory hypotheses, silica deposition in relation to the ageing of leaf tissues in Sasa veitchii was investigated. METHODS: Tissues were examined using a light microscope and a scanning electron microscope equipped with an energy dispersive X-ray microanalyser. KEY RESULTS: The deposition process differed depending on cell type. In mesophyll tissue, fusoid cells deposited large amounts of silica depending on leaf age after maturation, while chlorenchyma cells deposited little. In epidermal tissue, comprised of eight cell types, only silica cells deposited large amounts of silica during the leaf's developmental process and none after maturation. Bulliform cells, micro-hairs and prickle hairs deposited silica densely and continuously after leaf maturation. Cork cells, guard cells, long cells and subsidiary cells deposited silica at low levels. CONCLUSIONS: The significance of these observations is discussed in relation to the two hypotheses proposed for silica deposition in Poaceae. The results of the present study clearly indicate that both hypotheses are compatible with each other dependent on cell types.     

THE EFFECT OF ORDERED CHARACTERS ON PHYLOGENETIC RECONSTRUCTION

Abstract Morphological structures are likely to undergo more than a single change during the course of evolution. As a result, multistate characters are common in systematic studies and must be dealt with. Particularly interesting is the question of whether or not multistate characters should be treated as ordered (additive) or unordered (non-additive). In accepting a particular hypothesis of order, numerous others are necessarily rejected. We review some of the criteria often used to order character states and the underlying assumptions inherent in these criteria.
The effects that ordered multistate characters can have on phylogenetic reconstruction are examined using 27 data sets. It has been suggested that hypotheses of character state order are more informative then hypotheses of unorder and may restrict the number of equally parsimonious trees as well as increase tree resolution. Our results indicate that ordered characters can produce more, equal or less equally parsimonious trees and can increase, decrease or have no effect on tree resolution. The effect on tree resolution can be a simple gain in resolution or a dramatic change in sister-taxa relationships. In cases where several outgroups are included in the data matrix, hypotheses of order can change character polarities by altering outgroup topology. Ordered characters result in a different topology from unordered characters only when the hierarchy of the cladogram disagrees with the investigator's a priori hypothesis of order. If the best criterion for assessing character evolution is congruence with other characters, the practice of ordering multistate characters is inappropriate.