Calculating the exclusion probability and paternity index for X-chromosomal loci in the presence of substructure

There has been recent interest in the use of X-chromosomal loci for forensic and relatedness testing casework, with many authors developing new X-linked short tandem repeat (STR) loci suitable for forensic use. Here we present formulae for two key quantities in paternity testing, the average probability of exclusion and the paternity index, which are suitable for Xchromosomal loci in the presence of population substructure.

Revisiting youden’s index as a useful measure of the misclassification error in meta-analysis of diagnostic studies

The paper considers meta-analysis of diagnostic studies that use a continuous score for classification of study participants into healthy or diseased groups. Classification is often done on the basis of a threshold or cut-off value, which might vary between studies. Consequently, conventional meta-analysis methodology focusing solely on separate analysis of sensitivity and specificity might be confounded by a potentially unknown variation of the cut-off value. To cope with this phenomena it is suggested to use, instead, an overall estimate of the misclassification error previously suggested and used as Youden’s index and; furthermore, it is argued that this index is less prone to between-study variation of cut-off values. A simple Mantel–Haenszel estimator as a summary measure of the overall misclassification error is suggested, which adjusts for a potential study effect. The measure of the misclassification error based on Youden’s index is advantageous in that it easily allows an extension to a likelihood approach, which is then able to cope with unobserved heterogeneity via a nonparametric mixture model. All methods are illustrated at hand of an example on a diagnostic meta-analysis on duplex doppler ultrasound, with angiography as the standard for stroke prevention.

Measuring productivity growth when technological change is biased - a new index and an application to UK agriculture

Productivity growth is conventionally measured by indices representing discreet approximations of the Divisia TFP index under the assumption that technological change is Hicks-neutral. When this assumption is violated, these indices are no longer meaningful because they conflate the effects of factor accumulation and technological change. We propose a way of adjusting the conventional TFP index that solves this problem. The method adopts a latent variable approach to the measurement of technical change biases that provides a simple means of correcting product and factor shares in the standard Tornqvist-Theil TFP index. An application to UK agriculture over the period 1953-2000 demonstrates that technical progress is strongly biased. The implications of that bias for productivity measurement are shown to be very large, with the conventional TFP index severely underestimating productivity growth. The result is explained primarily by the fact that technological change has favoured the rapidly accumulating factors against labour, the factor leaving the sector. (C) 2004 Elsevier B.V. All rights reserved.

Estimating the benefits of farm animal welfare legislation using the contingent valuation method

This paper presents the method and findings of a contingent valuation (CV) study that aimed to elicit United Kingdom citizens' willingness to pay to support legislation to phase out the use of battery cages for egg production in the European Union (EU). The method takes account of various biases associated with the CV technique, including 'warm glow', 'part-whole' and sample response biases. Estimated mean willingness to pay to support the legislation is used to estimate the annual benefit of the legislation to UK citizens. This is compared with the estimated annual costs of the legislation over a 12-year period, which allows for readjustment by the UK egg industry. The analysis shows that the estimated benefits of the legislation outweigh the costs. The study demonstrates that CV is a potentially useful technique for assessing the likely benefits associated with proposed legislation. However, estimates of CV studies must be treated with caution. It is important that they are derived from carefully designed surveys and that the willingness to pay estimation method allows for various biases. (C) 2003 Elsevier Science B.V. All rights reserved.

Assessment of the impact of government animal welfare policy on farm animal welfare in the UK

The paper presents the method and findings of a Delphi expert survey to assess the impact of UK government farm animal welfare policy, form assurance schemes and major food retailer specifications on the welfare of animals on forms. Two case-study livestock production systems are considered, dairy and cage egg production. The method identifies how well the various standards perform in terms of their effects on a number of key farm animal welfare variables, and provides estimates of the impact of the three types of standard on the welfare of animals on forms, taking account of producer compliance. The study highlights that there remains considerable scope for government policy, together with form assurance schemes, to improve the welfare of form animals by introducing standards that address key factors affecting animal welfare and by increasing compliance of livestock producers. There is a need for more comprehensive, regular and random surveys of on-farm welfare to monitor compliance with welfare standards (legislation and welfare codes) and the welfare of farm animals over time, and a need to collect farm data on the costs of compliance with standards.

A cross-taxonomic index for quantifying the health of farmland biodiversity

P>1. The development of sustainable, multi-functional agricultural systems involves reconciling the needs of agricultural production with the objectives for environmental protection, including biodiversity conservation. However, the definition of sustainability remains ambiguous and it has proven difficult to identify suitable indicators for monitoring progress towards, and the successful achievement of, sustainability. 2. In this study, we show that a trait-based approach can be used to assess the detrimental impacts of agricultural change to a broad range of taxonomic groupings and derive a standardised index of farmland biodiversity health, built around an objective of achieving stable or increasing populations in all species associated with agricultural landscapes. 3. To demonstrate its application, we assess the health of UK farmland biodiversity relative to this goal. Our results suggest that the populations of two-thirds of 333 plant and animal species assessed are unsustainable under current UK agricultural practices. 4. We then explore the potential benefits of an agri-environment scheme, Entry Level Stewardship (ELS), to farmland biodiversity in the UK under differing levels of risk mitigation delivery. We show that ELS has the potential to make a significant contribution to progress towards sustainability targets but that this potential is severely restricted by current patterns of scheme deployment. 5.Synthesis and applications: We have developed a cross-taxonomic sustainability index which can be used to assess both the current health of farmland biodiversity and the impacts of future agricultural changes relative to quantitative biodiversity targets. Although biodiversity conservation is just one of a number of factors that must be considered when defining sustainability, we believe our cross-taxonomic index has the potential to be a valuable tool for guiding the development of sustainable agricultural systems.

Animal health and welfare in organic livestock production in Europe: Current state and future challenges

Existing data on animal health and welfare in organic livestock production systems in the European Community countries are reviewed in the light of the demands and challenges of the recently implemented EU regulation on organic livestock production. The main conclusions and recommendations of a three-year networking project on organic livestock production are summarised and the future challenges to organic livestock production in terms of welfare and health management are discussed. The authors conclude that, whilst the available data are limited and the implementation of the EC regulation is relatively recent, there is little evidence to suggest that organic livestock management causes major threats to animal health and welfare in comparison with conventional systems. There are, however, some well-identified areas, like parasite control and balanced ration formulation, where efforts are needed to find solutions that meet with organic standard requirements and guarantee high levels of health and welfare. It is suggested that, whilst organic standards offer an implicit framework for animal health and welfare management, there is a need to solve apparent conflicts between the organic farming objectives in regard to environment, public health, farmer income and animal health and welfare. The key challenges for the future of organic livestock production in Europe are related to the feasibility of implementing improved husbandry inputs and the development of evidence-based decision support systems for health and feeding management.

Consumer welfare effects of introducing and labeling genetically modified food

Non-hypothetical valuations obtained from experimental auctions in three United States and two European locations were used to calculate welfare effects of introducing and labeling of genetically modified food. Under certain assumptions, we find that introduction of genetically modified food has been welfare enhancing, on average, for United States consumers but not so for Europeans and while mandatory labeling has been beneficial for European consumers, such a policy would be detrimental in the United States. (c) 2005 Elsevier B.V. All rights reserved.