Design considerations for two-stage enrichment clinical trials

When there is a predictive biomarker, enrichment can focus the clinical trial on a benefiting subpopulation. We describe a two-stage enrichment design, in which the first stage is designed to efficiently estimate a threshold and the second stage is a “phase III-like” trial on the enriched population. The goal of this paper is to explore design issues: sample size in Stages 1 and 2, and re-estimation of the Stage 2 sample size following Stage 1. By treating these as separate trials, we can gain insight into how the predictive nature of the biomarker specifically impacts the sample size. We also show that failure to adequately estimate the threshold can have disastrous consequences in the second stage. While any bivariate model could be used, we assume a continuous outcome and continuous biomarker, described by a bivariate normal model. The correlation coefficient between the outcome and biomarker is the key to understanding the behavior of the design, both for predictive and prognostic biomarkers. Through a series of simulations we illustrate the impact of model misspecification, consequences of poor threshold estimation, and requisite sample sizes that depend on the predictive nature of the biomarker. Such insight should be helpful in understanding and designing enrichment trials.     

Inhibition by trifluoperazine of ATP synthesis and hydrolysis by particulate and soluble mitochondrial F1: Competition with H2PO 4 −

The effect of trifluoperazine (TFP) on the ATPase activity of soluble and paniculate F₁ATPase and on ATP synthesis driven by succinate oxidation in submitochondrial particles from bovine heart was studied at pH 7.4 and 8.8. At the two pH. TFP inhibited ATP hydrolysis. Inorganic phosphate protected against the inhibiting action of TFP. The results on the effect of various concentrations of phosphate in the reversal of the action of TFP on hydrolysis at pH 7.4 and 8.8 showed that H₂PO ₄ ^– is the species that competes with TFP. The effect of TFP on oxidative phosphorylation was studied at concentrations that do not produce uncoupling or affect the aerobic oxidation of succinate (<15M). TFP inhibited oxidative phosphorylation to a higher extent at pH 8.8 than at pH 7.4; this was through a diminution in theV _max, and an increase in theK _m for phosphate. Data on phosphate uptake during oxidative phosphorylation at several pH showed that H₂PO ₄ ^– is the true substrate for oxidative phosphorylation. Thus, in both synthesis and hydrolysis of ATP, TFP and H₂PO ₄ ^– interact with a common site. However, there is a difference in the sensitivity to TFP of ATP synthesis and hydrolysis; this is more noticeable at pH 8.8, i.e. ATPase activity of soluble F₁ remains at about 40% of the activity of the control in a concentration range of TFP of 40–100M, whereas in oxidative phosphorylation 14M TFP produces a 60% inhibition of phosphate uptake.     

Rhizodeposition under ambient and elevated CO2 levels

As global CO₂ levels rise, can soils store more carbon and so buffer atmospheric CO₂ levels? Answering this question requires a knowledge of the rates of C inputs to soil and of CO₂ outputs via decomposition. Below-ground inputs from roots are a major component of the C flow into soils but are still poorly understood. In this article, new techniques for measuring rhizodeposition are reviewed and discussed and the need for cross-comparisons between methods is identified. One component of rhizodeposition, root exudation, is examined in more detail and evidence is presented which suggests that current estimates of exudate flow into soils are incorrect. A mechanistic mathematical model is used to explore how exudate flows might change under elevated CO₂.     

Multilocus DNA fingerprints in the plant Cynoglossum officinale L. and their use in the estimation of selfing

We have developed a nonradioactive oligonucleotide multilocus DNA fingerprinting method for Cynoglossum officinale . Of the 19 probes tested, six probes yielded banding patterns for all restriction enzymes used. All but one of the informative probes are repeats with a four-base motif. Approximately 60% of the loci appeared to be polymorphic. The sensitivity of the nonradioactive method was equal to that of the radioactive method. In addition, a new simple calculation method is presented to estimate selfing rates and approximate 95% confidence limits from the DNA fingerprint profiles avoiding 'between-gel' comparisons. The selfing rates differed significantly (as determined from 95% confidence intervals) between naturally pollinated individuals of C. officinale within the experimental population. The estimates ranged from 0 to 70% selfing.     

Short-term variations in catches of the pea moth,Cydia nigricana, in interacting pheromone traps

Short-term variations in the relative catch in each of two or three interacting pheromone traps for the pea moth,Cydia nigricana (F.), were investigated for traps aligned along the wind. The proportional catch in each trap varied widely, although the mean values accorded with previous estimates. Over consecutive short intervals during a single trapping period the proportion caught in the centre trap of a three-trap line was constant. The proportion caught in the upwind trap of two-and three-trap lines showed trends in time. These trends differed between trapping periods, but two lines of traps operated simultaneously gave similar results to each other. It is suggested that these results, which are predicted by a model based on various components of moth orientation behaviour, are caused by changes in systematic behavioural processes, not random effects. Possible mechanisms are discussed.

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Variations à court terme des captures deCydia nigricana dans des pièges à phéromones en interaction

Résumé Des données antérieures concernant les interactions entre des pièges à phéromone alignés le long du vent ont été utilisées pour déduire les caractéristiques du comportement d'orientation deC. nigricana. Ces données ont été introduites dans un modèle de simulation quantitative qui prédisait que quand les captures totales sur une ligne ont été regroupées sur une période globale de piégage, la proportion capturée dans chaque piège devrait aussi avoir des valeurs moyennes semblables, mais varie plus largement que précédemment indiqué. Les simulations concernant des intervalles consécutifs beaucoup plus courts pendant la même période de piégage ont suggéré une forme spécifique de cette variation.Cette note signale des variations à court terme dans la proportion capturée au piège qui confirment ces prédictions. Nous montrons que sur des intervalles consécutifs brefs pendant une simple période de piégage, la proportion capturée dans le piège central d'une ligne de 3 pièges est contstante, bien que sa valeur change suivant les périodes de piégage. La proportion capturée dans le piège face au vent de 2 ou 3 lignes de pièges suit cette tendance dans le temps, ce qui est généralement bien représenté avec des courbes simples. Ces tendances changent suivant les périodes de piégage, mais des lignes de pièges fonctionnant simultanément fournissaient des résultats similaires. On suggère que ces résultats sont dus à des changements dans des processus comportementaux systématiques et non à des effects aléatoires. Les mécanismes possibles sont discutés.

     

Carbon metabolism and gas exchange in leaves of Zea mays L.

The aim of this work was to investigate the mechanism of formation of triose phosphates and 3-phosphoglycerate during photosynthetic induction in leaves of Zea mays. Simultaneous measurements of gas exchange, chlorophyll a fluorescence and metabolite contents of maize leaves were made. Leaves illuminated in the absence of CO₂ showed a build-up of triose phosphates during the first 2 min of illumination which was comparable to the build-up observed in the presence of CO₂. Isolated mesophyll protoplasts, which lack the Calvin cycle, also showed a build-up of triose phosphates upon illumination. Leaves contained amounts of phosphoglycerate mutase and enolase adequate to account for the formation of triose phosphates and 3-phosphoglycerate from intermediates of the C₄ cycle and their precursors.     

Sensitivity of Escherichia coli acrA mutants to psoralen plus near-ultraviolet radiation

The sensitivity to psoralen plus near-ultraviolet radiation (PUVA) was compared in a pair of E. coli strains differing at the acrA locus. Survival was determined for both bacteria and phage lambda. AcrA mutant cells were 40 times more sensitive than wild type to the lethal effect of PUVA. Free lambda phage exposed to PUVA survived as well when plated on acrA mutants as on wild type. In contrast, prophage lambda CI857 ind carried in lysogenic acrA strains was hypersensitive to PUVA. The enhanced sensitivity of bacterial and lambda DNA, when inside acrA cells, was paralleled by an increased photobinding of radiolabelled psoralens in the mutant. Binding was increased specifically to DNA rather than to nucleic acids in general. The difference in psoralen-binding ability determined by the acrA gene persisted after permeabilizing treatment of the cells. The results suggest that the acrA mutation causes an alteration specifically in the environment of the cellular DNA so as to allow increased intercalation and photobinding of psoralens.     

Sapatoxins,aliphatic ester tigliane diterpenes from Sapium indicum

From the unripe fruits of Sapium indicum, three aliphatic esters of the tigliane nucleus were isolated. These compounds were derivatives of 4-deoxyphorbol. Sapatoxin A was identified as 12-O-[n-deca-2,4,6-trienoyl]-4-deoxyphorbol-13-acetate, B as 12-O-[n-deca-2,4,6-trienoyl]-4-deoxy-5-hydroxyphorbol-13-acetate and C as 12-O-[n-deca-2,4,6-trienoyl]-4,20-dideoxy-5-hydroxyphorbol-13-acetate, by spectroscopic analysis and hydrolysis reactions.