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

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

Analgesic efficacy of orally administered\ud buprenorphine in rats: methodologic\ud considerations

Buprenorphine has been widely recommended for treatment of pain in rodents. We have previously documented that the recommended postoperative oral dose of buprenorphine in male Long-Evans rats, 0.5 mg/kg, is not as effective as the recommended parenteral dose of buprenorphine (0.05 mg/kg, s.c.) as an analgesic (21). In the series of experiments reported here, we compared: the analgesic effect of buprenorphine when prepared in two ways in the laboratory with that of a commercially available injectable solution of buprenorphine; the analgesic effect of buprenorphine in Long-Evans rats with that in Sprague-Dawley rats; and Long-Evans and Sprague-Dawley rats for development of pica, a commonly reported side effect of buprenorphine. We followed the pica experiment with assessment of the effectiveness of buprenorphine in establishing a conditioned flavor aversion. The results indicated that method of preparation did not result in any significant differences in the efficacy of injected buprenorphine. Strain of rat was not associated with a significant difference in the efficacy of buprenorphine. However, a significant strain difference was found in development of pica. Buprenorphine treatment was effective in inducing a conditioned flavor aversion. We concluded that the recommended oral dose of buprenorphine (0.5 mg/kg) is ineffective as an analgesic, and that this was not the result of method of preparation of the buprenorphine or strain of rat used. Furthermore, we\ud concluded that buprenorphine treatment may induce gastrointestinal distress in both strains tested. The results reaffirm our previous conclusion that oral administration of buprenorphine at 0.5 mg/kg, despite the general recommendation, is not a reasonable treatment for postsurgical pain in rats