Association mapping of partitioning loci in barley

Background: Association mapping, initially developed in human disease genetics, is now being applied to plant species. The model species Arabidopsis provided some of the first examples of association mapping in plants, identifying previously cloned flowering time genes, despite high population sub-structure. More recently, association genetics has been applied to barley, where breeding activity has resulted in a high degree of population sub-structure. A major genotypic division within barley is that between winter- and spring-sown varieties, which differ in their requirement for vernalization to promote subsequent flowering. To date, all attempts to validate association genetics in barley by identifying major flowering time loci that control vernalization requirement (VRN-H1 and VRN-H2) have failed. Here, we validate the use of association genetics in barley by identifying VRN-H1 and VRN-H2, despite their prominent role in determining population sub-structure. Results: By taking barley as a typical inbreeding crop, and seasonal growth habit as a major partitioning phenotype, we develop an association mapping approach which successfully identifies VRN-H1 and VRN-H2, the underlying loci largely responsible for this agronomic division. We find a combination of Structured Association followed by Genomic Control to correct for population structure and inflation of the test statistic, resolved significant associations only with VRN-H1 and the VRN-H2 candidate genes, as well as two genes closely linked to VRN-H1 (HvCSFs1 and HvPHYC). Conclusion: We show that, after employing appropriate statistical methods to correct for population sub-structure, the genome-wide partitioning effect of allelic status at VRN-H1 and VRN-H2 does not result in the high levels of spurious association expected to occur in highly structured samples. Furthermore, we demonstrate that both VRN-H1 and the candidate VRN-H2 genes can be identified using association mapping. Discrimination between intragenic VRN-H1 markers was achieved, indicating that candidate causative polymorphisms may be discerned and prioritised within a larger set of positive associations. This proof of concept study demonstrates the feasibility of association mapping in barley, even within highly structured populations. A major advantage of this method is that it does not require large numbers of genome-wide markers, and is therefore suitable for fine mapping and candidate gene evaluation, especially in species for which large numbers of genetic markers are either unavailable or too costly.

Numerical conformal mapping and mesh generation for polygonal and multiply-connected regions

Details are given of a boundary-fitted mesh generation method for use in modelling free surface flow and water quality. A numerical method has been developed for generating conformal meshes for curvilinear polygonal and multiply-connected regions. The method is based on the Cauchy-Riemann conditions for the analytic function and is able to map a curvilinear polygonal region directly onto a regular polygonal region, with horizontal and vertical sides. A set of equations have been derived for determining the lengths of these sides and the least-squares method has been used in solving the equations. Several numerical examples are presented to illustrate the method.

Evaluation of a boundary integral representation for the conformal mapping of the unit disk onto a simply-connected domain

A representation of the conformal mapping g of the interior or exterior of the unit circle onto a simply-connected domain Ω as a boundary integral in terms ofƒ|∂Ω is obtained, whereƒ :=g -l. A product integration scheme for the approximation of the boundary integral is described and analysed. An ill-conditioning problem related to the domain geometry is discussed. Numerical examples confirm the conclusions of this discussion and support the analysis of the quadrature scheme.

Mapping the platelet profile for functional genomic studies and demonstration of the effect size of the GP6 locus

BACKGROUND: Evidence suggests the wide variation in platelet response within the population is genetically controlled. Unraveling the complex relationship between sequence variation and platelet phenotype requires accurate and reproducible measurement of platelet response. OBJECTIVE: To develop a methodology suitable for measuring signaling pathway-specific platelet phenotype, to use this to measure platelet response in a large cohort, and to demonstrate the effect size of sequence variation in a relevant model gene. METHODS: Three established platelet assays were evaluated: mobilization of [Ca(2+)](i), aggregometry and flow cytometry, each in response to adenosine 5'-diphosphate (ADP) or the glycoprotein (GP) VI-specific crosslinked collagen-related peptide (CRP). Flow cytometric measurement of fibrinogen binding and P-selectin expression in response to a single, intermediate dose of each agonist gave the best combination of reproducibility and inter-individual variability and was used to measure the platelet response in 506 healthy volunteers. Pathway specificity was ensured by blocking the main subsidiary signaling pathways. RESULTS: Individuals were identified who were hypo- or hyper-responders for both pathways, or who had differential responses to the two agonists, or between outcomes. 89 individuals, retested three months later using the same methodology, showed high concordance between the two visits in all four assays (r(2) = 0.872, 0.868, 0.766 and 0.549); all subjects retaining their phenotype at recall. The effect of sequence variation at the GP6 locus accounted for approximately 35% of the variation in the CRP-XL response. CONCLUSION: Genotyping-phenotype association studies in a well-characterized, large cohort provides a powerful strategy to measure the effect of sequence variation in genes regulating the platelet response.

Mapping the trickle out benefits of social and environmental enterprises: a pilot study of an East African eco business

• Objectives The objective of this paper is to propose a framework for mapping the sustainable development and poverty alleviation impacts of social and environmental enterprises in Africa. This framework is then piloted with reference to an East African Ecobusiness. • Prior Work This paper is based on data collected as part of a wider research project examining social and environmental enterprises across the 19 countries of Southern and Eastern Africa. In total, the sustainable development and poverty alleviation impacts of 20 in-depth case studies in 4 countries are being examined. • Approach Data was collected using in-depth interviews with multiple stakeholders associated with the case study business. Secondary materials were also analysed and a quantitative survey of customers undertaken. • Results In addition to their impacts on the environment, African eco businesses can also have substantial social, economic and wider poverty alleviation impacts. This paper maps the impacts of a case study East African ecobusiness, as part of developing a social and environmental enterprise impact framework for Africa and the wider developing world. In our case study, positive and negative impacts are identified, while questions are raised in relation to tradeoffs between social and environmental objectives and temporal dimensions of impact. The usefulness of existing frameworks for understanding the social, environmental and development impacts of these kinds of organisations are also considered. • Implications This paper outlines the necessity of building an African-centric impact map to capture the multi-level poverty alleviation and sustainable development impacts of social and environmental enterprise activity in developing world environments. The framework proposed also offers guidance to businesses operating in Africa about the factors that might be considered as part of their wider social and environmental responsibilities. • Value Assessing the impact of social and environmental enterprises, especially as a route to development within low income countries, is receiving increasing attention in academia and beyond. This paper presents a useful contribution to the scarce literature on social and environmental enterprises in Africa.

Evaluation of reach and grasp robot-assisted therapy suggests similar functional recovery patterns on proximal and distal arm segments in sub-acute hemiplegia

This paper provides some additional evidence in support of the hypothesis that robot therapies are clinically beneficial in neurorehabilitation. Although only 4 subjects were included in the study, the design of the intervention and the measures were done so as to minimise bias. The results are presented as single case studies, and can only be interpreted as such due to the study size. The intensity of intervention was 16 hours and the therapy philosophy (based on Carr and Shepherd) was that coordinated movements are preferable to joint based therapies, and that coordinating distal movements (in this case grasps) helps not only to recover function in these areas, but has greater value since the results are immediately transferable to daily skills such as reach and grasp movements.

Taxonomic free sorting: a successful method with older consumers and a novel approach to preference mapping

Taxonomic free sorting (TFS) is a fast, reliable and new technique in sensory science. The method extends the typical free sorting task where stimuli are grouped according to similarities, by asking respondents to combine their groups two at a time to produce a hierarchy. Previously, TFS has been used for the visual assessment of packaging whereas this study extends the range of potential uses of the technique to incorporate full sensory analysis by the target consumer, which, when combined with hedonic liking scores, was used to generate a novel preference map. Furthermore, to fully evaluate the efficacy of using the sorting method, the technique was evaluated with a healthy older adult consumer group. Participants sorted eight products into groups and described their reason at each stage as they combined those groups, producing a consumer-specific vocabulary. This vocabulary was combined with hedonic data from a separate group of older adults, to give the external preference map. Taxonomic sorting is a simple, fast and effective method for use with older adults, and its combination with liking data can yield a preference map constructed entirely from target consumer data.

Operational active fire mapping and burnt area identification applicable to Mexican Nature Protection Areas using MODIS and NOAA-AVHRR direct readout data

Since 1999, the National Commission for the Knowledge and Use of the Biodiversity (CONABIO) in Mexico has been developing and managing the “Operational program for the detection of hot-spots using remote sensing techniques”. This program uses images from the MODerate resolution Imaging Spectroradiometer (MODIS) onboard the Terra and Aqua satellites and from the Advanced Very High Resolution Radiometer of the National Oceanic and Atmospheric Administration (NOAA-AVHRR), which are operationally received through the Direct Readout station (DR) at CONABIO. This allows the near-real time monitoring of fire events in Mexico and Central America. In addition to the detection of active fires, the location of hot spots are classified with respect to vegetation types, accessibility, and risk to Nature Protection Areas (NPA). Besides the fast detection of fires, further analysis is necessary due to the considerable effects of forest fires on biodiversity and human life. This fire impact assessment is crucial to support the needs of resource managers and policy makers for adequate fire recovery and restoration actions. CONABIO attempts to meet these requirements, providing post-fire assessment products as part of the management system in particular for satellite-based burnt area mapping. This paper provides an overview of the main components of the operational system and will present an outlook to future activities and system improvements, especially the development of a burnt area product. A special focus will also be placed on the fire occurrence within NPAs of Mexico

Identifying, mapping, and monitoring the impact of hybrid firms

There is growing recognition that hybrid organizations can play a critical role in tackling intractable global sustainable development challenges. At the same time, acute social, environmental, and economic challenges are opening up “opportunity” spaces for hybrids. Different institutional contexts are also leading to variable hybrid forms linked to the focus of their mission and their profit-oriented status. This article presents a process for identifying, mapping, and building impact indicators based on a study of 20 hybrid organizations in Sub-Saharan Africa.