Elm Farm Research Centre Bulletin 79 July 2005

Regular newletter from Elm Farm Research Centre (EFRC)covering research, technical and policy articles, views and comment

ORGANIC AGRICULTURE AND FOOD SECURITY

Modelling the impacts of organic production up-scaled to regional and global levels gives an initial quan-tification of the potential extent of changes that large-scale conversion might induce. Optimistic estimates of change with respect to organic yield potential lead to modest impacts on global commodity prices, production, and trade. Conversion in high-input regions in Europe and North America to certified organic decreases production and increases commodity prices. Hunger in this scenario slightly worsens. Transition of low-input areas in Sub-Saharan Africa to non-certified organic leads to in-creased production and decreased prices. Food secu-rity improves slightly in this scenario. The switch for low-input regions helps decrease trade dependency in some commodities. Achievement of productivity levels in these scenarios is dependent on many factors that introduce a significant amount of uncertainty in the results. The extent of these impacts can be improved if concerted effort in research and development for yield and productivity enhancement is supported

The Agricultural Growth and Malting Production of Barley Grains in Northeast Tennessee and Southwest Virginia

The purpose of this study is to explore the history and production processes of beer and examines the components that contribute to its brewing. The narrative will provide a timeline of the processes that are required to create the product of beer beginning with the agricultural products and following the brewing processes that result in beer as the finished product. I will also examine the business of agriculture and grain processing and will provide some historical perspectives of grain, beer, and malting. I will also consider whether the growing, processing, and malting of grains in the East Tennessee and Southwest Virginia Region is feasible as demonstrated through this research and reported findings

Lack of analgesic efficacy in female rats of\ud the commonly recommended oral dose of\ud buprenorphine

Previous work in our laboratory showed that the recommended oral dose of buprenorphine (0.5 mg/kg) was not as effective\ud as the standard therapeutic subcutaneous dose for postoperative analgesia in male Long-Evans (hooded) and Sprague-Dawley (albino) rats. The aim of the current study was to extend this analysis to female rats. We measured the pain threshold in adult female rats in diestrus or proestrus before and 30 and 60 min after oral buprenorphine (0.5 mg/kg,), the standard subcutaneous dose of buprenorphine (0.05 mg/kg), or vehicle only (1 ml/kg each orally and subcutaneously). Female rats showed an increased pain threshold (analgesia) after subcutaneous buprenorphine but no change in pain threshold after either oral buprenorphine or vehicle only. Estrous cycle stage (proestrus versus diestrus) did not affect the analgesic effects of buprenorphine, but rats in proestrus showed significantly lower pain thresholds (less tolerance to pain) than did those in diestrus. These results show that the oral dose of buprenorphine recommended for postoperative analgesic care does not induce significant analgesia in female rats and therefore is not as effective as the standard subcutaneous dose

An automated graphics tool for comparative genomics: the Coulson plot generator.

BACKGROUND: Comparative analysis is an essential component to biology. When applied to genomics for example, analysis may require comparisons between the predicted presence and absence of genes in a group of genomes under consideration. Frequently, genes can be grouped into small categories based on functional criteria, for example membership of a multimeric complex, participation in a metabolic or signaling pathway or shared sequence features and/or paralogy. These patterns of retention and loss are highly informative for the prediction of function, and hence possible biological context, and can provide great insights into the evolutionary history of cellular functions. However, representation of such information in a standard spreadsheet is a poor visual means from which to extract patterns within a dataset. RESULTS: We devised the Coulson Plot, a new graphical representation that exploits a matrix of pie charts to display comparative genomics data. Each pie is used to describe a complex or process from a separate taxon, and is divided into sectors corresponding to the number of proteins (subunits) in a complex/process. The predicted presence or absence of proteins in each complex are delineated by occupancy of a given sector; this format is visually highly accessible and makes pattern recognition rapid and reliable. A key to the identity of each subunit, plus hierarchical naming of taxa and coloring are included. A java-based application, the Coulson plot generator (CPG) automates graphic production, with a tab or comma-delineated text file as input and generating an editable portable document format or svg file. CONCLUSIONS: CPG software may be used to rapidly convert spreadsheet data to a graphical matrix pie chart format. The representation essentially retains all of the information from the spreadsheet but presents a graphically rich format making comparisons and identification of patterns significantly clearer. While the Coulson plot format is highly useful in comparative genomics, its original purpose, the software can be used to visualize any dataset where entity occupancy is compared between different classes. AVAILABILITY: CPG software is available at sourceforge http://sourceforge.net/projects/coulson and http://dl.dropbox.com/u/6701906/Web/Sites/Labsite/CPG.html.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are

ASP-based Discovery of Semi-Markovian Causal Models under Weaker Assumptions

In recent years the possibility of relaxing the so-called Faithfulness assumption in automated causal discovery has been investigated. The investigation showed (1) that the Faithfulness assumption can be weakened in various ways that in an important sense preserve its power, and (2) that weakening of Faithfulness may help to speed up methods based on Answer Set Programming. However, this line of work has so far only considered the discovery of causal models without latent variables. In this paper, we study weakenings of Faithfulness for constraint-based discovery of semi-Markovian causal models, which accommodate the possibility of latent variables, and show that both (1) and (2) remain the case in this more realistic setting