Copula-based robust optimal block designs.

Blocking is often used to reduce known variability in designed experiments by collecting together homogeneous experimental units. A common modeling assumption for such experiments is that responses from units within a block are dependent. Accounting for such dependencies in both the design of the experiment and the modeling of the resulting data when the response is not normally distributed can be challenging, particularly in terms of the computation required to find an optimal design. The application of copulas and marginal modeling provides a computationally efficient approach for estimating population-average treatment effects. Motivated by an experiment from materials testing, we develop and demonstrate designs with blocks of size two using copula models. Such designs are also important in applications ranging from microarray experiments to experiments on human eyes or limbs with naturally occurring blocks of size two. We present a methodology for design selection, make comparisons to existing approaches in the literature, and assess the robustness of the designs to modeling assumptions.

Optimal designs for copula models.

Copula modelling has in the past decade become a standard tool in many areas of applied statistics. However, a largely neglected aspect concerns the design of related experiments. Particularly the issue of whether the estimation of copula parameters can be enhanced by optimizing experimental conditions and how robust all the parameter estimates for the model are with respect to the type of copula employed. In this paper an equivalence theorem for (bivariate) copula models is provided that allows formulation of efficient design algorithms and quick checks of whether designs are optimal or at least efficient. Some examples illustrate that in practical situations considerable gains in design efficiency can be achieved. A natural comparison between different copula models with respect to design efficiency is provided as well.

Safety and feasibility of exhaled breath condensate collection in ventilated infants and children.

The aim of this study was to develop a technique for the collection of exhaled breath condensate (EBC) from ventilated children and assess its safety and feasibility. Collection of EBC is used to investigate markers of oxidative stress in the lower airway. No studies have assessed its safety in ventilated children. An in vitro model was developed by connecting a ventilator to an artificial lung; 14 clinical and ventilatory parameters were measured during EBC collection from ventilated children. Levels of 8-isoprostane were measured following collection with and without humidification of the inhaled gas. Amount of water vapour collected was linearly related to time and to minute ventilation in the in vitro model. EBC collections (n = 68) were made from ventilated children. In the nonhumidified group, the mean (range) positive end-expiratory pressure increased by 4.1% (2.8-5.5%) and the peak inspiratory flow decreased by 6.1% (11.0-1.3%) during collection. Detectable levels of 8-isoprostane were only found in 10 out of 18 nonhumidified EBC samples (median (range) 4.7 pg x mL(-1) (0-5.8)). Collection of exhaled breath condensate from ventilated infants and children is feasible and safe. Discontinuation of humidification is likely to be important in standardising the measurement of inflammatory parameters in exhaled breath condensate collected from ventilated children.

Large-scale chromatin decondensation and recondensation regulated by transcription from a natural promoter.

We have examined the relationship between transcription and chromatin structure using a tandem array of the mouse mammary tumor virus (MMTV) promoter driving a ras reporter. The array was visualized as a distinctive fluorescent structure in live cells stably transformed with a green fluorescent protein (GFP)-tagged glucocorticoid receptor (GR), which localizes to the repeated MMTV elements after steroid hormone treatment. Also found at the array by immunofluorescence were two different steroid receptor coactivators (SRC1 and CBP) with acetyltransferase activity, a chromatin remodeler (BRG1), and two transcription factors (NFI and AP-2). Within 3 h after hormone addition, arrays visualized by GFP-GR or DNA fluorescent in situ hybridization (FISH) decondensed to varying degrees, in the most pronounced cases from a approximately 0.5-microm spot to form a fiber 1-10 microm long. Arrays later recondensed by 3-8 h of hormone treatment. The degree of decondensation was proportional to the amount of transcript produced by the array as detected by RNA FISH. Decondensation was blocked by two different drugs that inhibit polymerase II, 5,6-dichloro-1-beta-D-ribofuranosylbenzimidazole (DRB) and alpha-amanitin. These observations demonstrate a role for polymerase in producing and maintaining decondensed chromatin. They also support fiber-packing models of higher order structure and suggest that transcription from a natural promoter may occur at much higher DNA-packing densities than reported previously.

Dynamics of gene targeting and chromatin remodelling by nuclear receptors.

Activation of the murine-mammary-tumour virus (MMTV) promoter by the glucocorticoid receptor (GR) is associated with a chromatin structural transition in the B nucleosome region of the viral long terminal repeat (LTR). We have reconstituted this nucleoprotein transition with chromatin assembled on MMTV LTR DNA with Drosophila embryo extracts, purified GR, and HeLa nuclear extract. Chromatin remodelling in vitro is ATP-dependent and maps to a region identical with that found in vivo. We demonstrate specific, glucocorticoid response element dependent, binding of purified GR to a large, multi-nucleosome MMTV chromatin array and show that GR-dependent chromatin remodelling is a multistep process. In the absence of ATP, GR binds to multiple sites on the chromatin array and inhibits nuclease access to GR recognition sites. On the addition of ATP, GR induces remodelling resulting in a large increase in access of enzymes to their sites within the transition region. These findings are complemented by studies in living cells; using a tandem array of MMTV-Ras reporter elements and a form of GR labelled with the green fluorescent protein, we have observed direct targeting of the receptor to response elements in live mouse cells. Whereas the ligand-activated receptor is associated with the MMTV promoter for observable periods, photobleaching experiments provide direct evidence that the hormone-occupied receptor undergoes rapid exchange between chromatin and the nucleoplasmic compartment. The results both in vitro and in vivo are consistent with a dynamic model ('hit and run') in which GR first binds to chromatin after ligand activation, recruits a remodelling activity and is then lost from the template.

The glucocorticoid receptor: rapid exchange with regulatory sites in living cells.

Steroid receptors bind to site-specific response elements in chromatin and modulate gene expression in a hormone-dependent fashion. With the use of a tandem array of mouse mammary tumor virus reporter elements and a form of glucocorticoid receptor labeled with green fluorescent protein, targeting of the receptor to response elements in live mouse cells was observed. Photobleaching experiments provide direct evidence that the hormone-occupied receptor undergoes rapid exchange between chromatin and the nucleoplasmic compartment. Thus, the interaction of regulatory proteins with target sites in chromatin is a more dynamic process than previously believed.

Optimal and practicable designs for measuring plaque pH-profiles.

The shape of the plaque pH-profile after consumption of a food item determines the food's potential caries risk. This and related facts have caused an increased interest in measurements of plaque pH-profiles during the last decade. A standard design for these measurements is to take equally spaced observations over a certain period of time. The theory of optimal experimental design gives methods for positioning the measurements of a pH-profile in an optimized way. The objective is to minimize the effort given a desired precision of the estimated profile characteristic or to maximize the precision given the number of measurements. We show that a reduction in the number of measurements up to 50 per cent or a respective improvement in precision of the estimates as compared to standardly applied designs is possible. This implies less inconvenience for the subjects and better compliance with the needs of investigation. Our study is intended to demonstrate the applicability of the theory of optimal experimental design which has the potential to improve the efficiency of medical research.

Profilocephalometric analysis: a combination of the cephalophotometric and the architectural-structural craniofacial analyses.

A number of cephalometric analyses are presently being used in the assessment of dentofacial deformities. These cephalometrics are mostly based on hard tissue assessment alone, although a few methods using soft tissue only or partially hard and partially soft tissues exist. Most of the analyses use angular and linear measurements, although some are based mainly on measurements of relationships. When the various cephalometric analyses are compared, considerable inconsistency comes to light; so much so, that cephalometrics sometimes cannot be considered as a primary diagnostic tool. A combination of two relationship analyses, one based on soft tissue assessment and one based on hard tissue assessment, incorporating the craniofacial complex, is presented to provide a higher degree of diagnostic accuracy. This combination analysis is based on only a few critical hard tissue landmarks of the cranial base that are used for the total assessment of the facial hard, dental, and soft tissues. This has eliminated inappropriate landmarks and lines that existed in each of the original analyses. The cephalophotometric and architectural-structural craniofacial analyses have been adjusted accordingly and renamed the profilocephalometric analysis.

[Pharmacokinetic investigations of the transfer of antibiotics into amniotic fluid. Part III: Oxacillin (author's transl)]. / Pharmakokinetische Untersuchungen zum Ubertritt von Antibiotika in das Fruchtwasser am Ende der Schwangerschaft. 3. Teil : Oxacillin

After intravenous administration of 2 g of Oxacillin to 12 gravidae at the end of their pregnancy short-interval tests were made of the Oxacillin levels in the mothers' serum and -- intra-amnionic catheter in position -- in the amniotic fluid. The following pharmaco-kinetic data were determined: fictitious initial Oxacillin level (79 mcg/ml), elimination constant (1,044 h-1), half-value of elimination (39,88 min), fictitious distribution volume (25,31), distribution coefficient (0,3617 ml/g), total clearance (26,431 l/h) and invasion constant (0,0084 h-1). All given data were statistically confirmed. For the para-placental passage of Oxacillin a permeability factor (chi) of 0,0084 was found. This factor indicates how easy Oxacillin passes trough the fetal membrane into the amniotic fluid. Ampicillin diffuses about 43 times and Cephalotin diffuses about 2,4 times better trough fetal membrane -- permeability factor 0,357 or 0,02 --, probably because of its weaker link to serum albumin. Under our conditions the amnionic levels reached 12 mcg/ml on the average. With 8-12 g Oxacillin daily bactericidal levels in the amniotic fluid are reached.