Efficient and cost-effective experimental determination of kinetic constants and data: the success of a Bayesian systematic approach to drug transport, receptor binding, continuous culture and cell transport kinetics

Details about the parameters of kinetic systems are crucial for progress in both medical and industrial research, including drug development, clinical diagnosis and biotechnology applications. Such details must be collected by a series of kinetic experiments and investigations. The correct design of the experiment is essential to collecting data suitable for analysis, modelling and deriving the correct information. We have developed a systematic and iterative Bayesian method and sets of rules for the design of enzyme kinetic experiments. Our method selects the optimum design to collect data suitable for accurate modelling and analysis and minimises the error in the parameters estimated. The rules select features of the design such as the substrate range and the number of measurements. We show here that this method can be directly applied to the study of other important kinetic systems, including drug transport, receptor binding, microbial culture and cell transport kinetics. It is possible to reduce the errors in the estimated parameters and, most importantly, increase the efficiency and cost-effectiveness by reducing the necessary amount of experiments and data points measured. (C) 2003 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Comparative evaluation of a new effective population size estimator based on approximate Bayesian computation

We describe and evaluate a new estimator of the effective population size (N-e), a critical parameter in evolutionary and conservation biology. This new "SummStat" N-e. estimator is based upon the use of summary statistics in an approximate Bayesian computation framework to infer N-e. Simulations of a Wright-Fisher population with known N-e show that the SummStat estimator is useful across a realistic range of individuals and loci sampled, generations between samples, and N-e values. We also address the paucity of information about the relative performance of N-e estimators by comparing the SUMMStat estimator to two recently developed likelihood-based estimators and a traditional moment-based estimator. The SummStat estimator is the least biased of the four estimators compared. In 32 of 36 parameter combinations investigated rising initial allele frequencies drawn from a Dirichlet distribution, it has the lowest bias. The relative mean square error (RMSE) of the SummStat estimator was generally intermediate to the others. All of the estimators had RMSE > 1 when small samples (n = 20, five loci) were collected a generation apart. In contrast, when samples were separated by three or more generations and Ne less than or equal to 50, the SummStat and likelihood-based estimators all had greatly reduced RMSE. Under the conditions simulated, SummStat confidence intervals were more conservative than the likelihood-based estimators and more likely to include true N-e. The greatest strength of the SummStat estimator is its flexible structure. This flexibility allows it to incorporate any, potentially informative summary statistic from Population genetic data.

Health benefits of probiotics: are mixtures more effective than single strains?

PURPOSE: Most studies on probiotics utilise single strains, sometimes incorporated into yoghurts. There are fewer studies on efficacy of mixtures of probiotic strains. This review examines the evidence that (a) probiotic mixtures are beneficial for a range of health-related outcomes and (b) mixtures are more or less effective than their component strains administered separately. RESULTS: Mixtures of probiotics had beneficial effects on the end points including irritable bowel syndrome and gut function, diarrhoea, atopic disease, immune function and respiratory tract infections, gut microbiota modulation, inflammatory bowel disease and treatment of Helicobacter pylori infection. However, only 16 studies compared the effect of a mixture with that of its component strains separately, although in 12 cases (75%), the mixture was more effective. CONCLUSION: Probiotic mixtures appear to be effective against a wide range of end points. Based on a limited number of studies, multi-strain probiotics appear to show greater efficacy than single strains, including strains that are components of the mixtures themselves. However, whether this is due to synergistic interactions between strains or a consequence of the higher probiotic dose used in some studies is at present unclear.

Health benefits of probiotics: are mixtures more effective than single strains?

Probiotic mixtures appear to be effective against a wide range of end points. Based on a limited number of studies, multi-strain probiotics appear to show greater efficacy than single strains, including strains that are components of the mixtures themselves. However, whether this is due to synergistic interactions between strains or a consequence of the higher probiotic dose used in some studies is at present unclear.

Effective elements of cognitive behaviour therapy for psychosis: results of a novel type of subgroup analysis based on principal stratification

Background. Meta-analyses show that cognitive behaviour therapy for psychosis (CBT-P) improves distressing positive symptoms. However, it is a complex intervention involving a range of techniques. No previous study has assessed the delivery of the different elements of treatment and their effect on outcome. Our aim was to assess the differential effect of type of treatment delivered on the effectiveness of CBT-P, using novel statistical methodology. Method. The Psychological Prevention of Relapse in Psychosis (PRP) trial was a multi-centre randomized controlled trial (RCT) that compared CBT-P with treatment as usual (TAU). Therapy was manualized, and detailed evaluations of therapy delivery and client engagement were made. Follow-up assessments were made at 12 and 24 months. In a planned analysis, we applied principal stratification (involving structural equation modelling with finite mixtures) to estimate intention-to-treat (ITT) effects for subgroups of participants, defined by qualitative and quantitative differences in receipt of therapy, while maintaining the constraints of randomization. Results. Consistent delivery of full therapy, including specific cognitive and behavioural techniques, was associated with clinically and statistically significant increases in months in remission, and decreases in psychotic and affective symptoms. Delivery of partial therapy involving engagement and assessment was not effective. Conclusions. Our analyses suggest that CBT-P is of significant benefit on multiple outcomes to patients able to engage in the full range of therapy procedures. The novel statistical methods illustrated in this report have general application to the evaluation of heterogeneity in the effects of treatment.

Simple and effective technical procedures for the packing and application of nanospray PicoFrit HPLC columns for proteomic analyses

A simple procedure was developed for packing PicoFrit HPLC columns with chromatographic stationary phase using a reservoir fabricated from standard laboratory HPLC fittings. Packed columns were mounted onto a stainless steel ultra-low volume precolumn filter assembly containing a 0.5-mu m pore size steel frit. This format provided a conduit for the application of the nanospray voltage and protected the column from obstruction by sample material. The system was characterised and operational performance assessed by analysis of a range of peptide standards (n = 9).

An effective approach for selection of terrain modelling method

This letter presents an effective approach for selection of appropriate terrain modeling methods in forming a digital elevation model (DEM). This approach achieves a balance between modeling accuracy and modeling speed. A terrain complexity index is defined to represent a terrain's complexity. A support vector machine (SVM) classifies terrain surfaces into either complex or moderate based on this index associated with the terrain elevation range. The classification result recommends a terrain modeling method for a given data set in accordance with its required modeling accuracy. Sample terrain data from the lunar surface are used in constructing an experimental data set. The results have shown that the terrain complexity index properly reflects the terrain complexity, and the SVM classifier derived from both the terrain complexity index and the terrain elevation range is more effective and generic than that designed from either the terrain complexity index or the terrain elevation range only. The statistical results have shown that the average classification accuracy of SVMs is about 84.3% ± 0.9% for terrain types (complex or moderate). For various ratios of complex and moderate terrain types in a selected data set, the DEM modeling speed increases up to 19.5% with given DEM accuracy.

Landscape connectivity: a key to effective habitat restoration in lowland agricultural landscapes

Landscape scale habitat restoration has the potential to reconnect habitats in fragmented landscapes. This study investigates landscape connectivity as a key to effective habitat restoration in lowland agricultural landscapes and applies these findings to transferable management recommendations. The study area is the Stonehenge World Heritage Site, UK, where landscape scale chalk grassland restoration has been implemented. Here, the ecological benefits of landscape restoration and the species, habitat and landscape characteristics that facilitate or impede the enhancement of biodiversity and landscape connectivity were investigated. Lepidoptera were used as indictors of restoration success and results showed restoration grasslands approaching the ecological conditions of the target chalk grassland habitat and increasing in biodiversity values within a decade. Restoration success is apparent for four species with a broad range of grass larval host plants (e.g. Melanargia galathea, Maniola jurtina) or with intermediate mobility (Polyommatus icarus). However, two species with specialist larval host plants and low mobility (Lysandra bellargus), are restricted to chalk grassland fragments. Studies of restoration grassland of different ages show that recent grassland restoration (1 or 2 years old) may reduce the functional isolation of chalk grassland fragments. A management experiment showed that mowing increases boundary following behaviour in two species of grassland Lepidoptera; Maniola jurtina and Zygaena filipendulae. Analysis of the landscape scale implications of the grassland restoration illustrates an increase in grassland habitat network size and in landscape connectivity, which is likely to benefit the majority of grassland associated Lepidoptera. Landscape and habitat variables can be managed to increase the success of restoration projects including the spatial targeting of receptor sites, vegetation structure and selection of seed source and management recommendations are provided that are transferrable to other species-rich grassland landscape scale restoration projects. Overall results show restoration success for some habitats and species within a decade. However, additional management is required to assist the re-colonisation of specialist species. Despite this, habitat restoration at the landscape scale can be an effective, long term approach to enhance butterfly biodiversity and landscape connectivity.

Hydrophilic sulfonated bis-1,2,4-triazine ligands are highly effective reagents for separating actinides(iii) from lanthanides(iii) via selective formation of aqueous actinide complexes

We report the first examples of hydrophilic 6,6′-bis(1,2,4-triazin-3-yl)-2,2′-bipyridine (BTBP) and 2,9-bis(1,2,4-triazin-3-yl)-1,10-phenanthroline (BTPhen) ligands, and their applications as actinide(III) selective aqueous complexing agents. The combination of a hydrophobic diamide ligand in the organic phase and a hydrophilic tetrasulfonated bis-triazine ligand in the aqueous phase is able to separate Am(III) from Eu(III) by selective Am(III) complex formation across a range of nitric acid concentrations with very high selectivities, and without the use of buffers. In contrast, disulfonated bis-triazine ligands are unable to separate Am(III) from Eu(III) in this system. The greater ability of the tetrasulfonated ligands to retain Am(III) selectively in the aqueous phase than the corresponding disulfonated ligands appears to be due to the higher aqueous solubilities of the complexes of the tetrasulfonated ligands with Am(III). The selectivities for Am(III) complexation observed with hydrophilic tetrasulfonated bis-triazine ligands are in many cases far higher than those found with the polyaminocarboxylate ligands previously used as actinide-selective complexing agents, and are comparable to those found with the parent hydrophobic bis-triazine ligands. Thus we demonstrate a feasible alternative method to separate actinides from lanthanides than the widely studied approach of selective actinide extraction with hydrophobic bis-1,2,4-triazine ligands such as CyMe4-BTBP and CyMe4-BTPhen.