Oregon Wine Board Meeting Minutes September 11, 2012

These meeting minutes list individuals in attendance and missing at the September 11, 2012 Oregon Wine Board (OWB) meeting, held via conference call. Dewey Weddington provided a marketing update focused on planning for Oregon Wine Month and the Oregon Wine Industry Symposium. The meeting also included discussion of the 2011-2012 year-end financial review and a presentation of the budget for the following year. The meeting lasted 2 hours 6 minutes, and the Board went into Executive Session after the meeting was adjourned

Formalizations après la lettre : studies in Medieval logic and semantics

This thesis is on the history and philosophy of logic and semantics. Logic can be described as the ‘science of reasoning’, as it deals primarily with correct patterns of reasoning. However, logic as a discipline has undergone dramatic changes in the last two centuries: while for ancient and medieval philosophers it belonged essentially to the realm of language studies, it has currently become a sub-branch of mathematics. This thesis attempts to establish a dialogue between the modern and the medieval traditions in logic, by means of ‘translations’ of the medieval logical theories into the modern framework of symbolic logic, i.e. formalizations. One of its conclusions is that, when properly understood within their own framework, the interest of medieval logical theories for modern investigations go beyond mere historical interest, but that a thorough conceptual analysis of such theories must be undertaken in order to avoid conceptual misprojections. While such translations of medieval into modern logic have been attempted before, the approach presented here is innovative in that attention is paid to the similarities as well as to the dissimilarities between the two traditions, and to what can be learned from the medieval masters for modern investigations in logic and semantics.LEI Universiteit LeidenPhilosoph

Detecting Large Concept Extensions for Conceptual Analysis

When performing a conceptual analysis of a concept, philosophers are interested in all forms of expression of a concept in a text---be it direct or indirect, explicit or implicit. In this paper, we experiment with topic-based methods of automating the detection of concept expressions in order to facilitate philosophical conceptual analysis. We propose six methods based on LDA, and evaluate them on a new corpus of court decision that we had annotated by experts and non-experts. Our results indicate that these methods can yield important improvements over the keyword heuristic, which is often used as a concept detection heuristic in many contexts. While more work remains to be done, this indicates that detecting concepts through topics can serve as a general-purpose method for at least some forms of concept expression that are not captured using naive keyword approaches

Comparative Genomics of 274 Vibrio Cholerae Genomes Reveals Mobile Functions Structuring Three Niche Dimensions

Vibrio cholerae is a globally dispersed pathogen that has evolved with humans for centuries, but also includes non-pathogenic environmental strains. Here, we identify the genomic variability underlying this remarkable persistence across the three major niche dimensions space, time, and habitat. Taking an innovative approach of genome-wide association applicable to microbial genomes (GWAS-M), we classify 274 complete V. cholerae genomes by niche, including 39 newly sequenced for this study with the Ion Torrent DNA-sequencing platform. Niche metadata were collected for each strain and analyzed together with comprehensive annotations of genetic and genomic attributes, including point mutations (single-nucleotide polymorphisms, SNPs), protein families, functions and prophages. Our analysis revealed that genomic variations, in particular mobile functions including phages, prophages, transposable elements, and plasmids underlie the metadata structuring in each of the three niche dimensions. This underscores the role of phages and mobile elements as the most rapidly evolving elements in bacterial genomes, creating local endemicity (space), leading to temporal divergence (time), and allowing the invasion of new habitats. Together, we take a data-driven approach for comparative functional genomics that exploits high-volume genome sequencing and annotation, in conjunction with novel statistical and machine learning analyses to identify connections between genotype and phenotype on a genome-wide scale

Impact of phosphate dosing on the microbial ecology of drinking water distribution systems: fieldwork studies in chlorinated networks

Phosphate is routinely dosed to ensure regulatory compliance for lead in drinking water distribution systems. Little is known about the impact of the phosphate dose on the microbial ecology in these systems and in particular the endemic biofilms. Disturbance of the biofilms and embedded material in distribution can cause regulatory failures for turbidity and metals. To investigate the impact of phosphate on developing biofilms, pipe wall material from four independent pipe sections was mobilised and collected using two twin-flushing operations a year apart in a chlorinated UK network pre- and post-phosphate dosing. Intensive monitoring was undertaken, including turbidity and water physico-chemistry, traditional microbial culture-based indicators, and microbial community structure via sequencing the 16S rRNA gene for bacteria and the ITS2 gene for fungi. Whole metagenome sequencing was used to study shifts in functional characteristics following the addition of phosphate. As an operational consequence, turbidity responses from the phosphate-enriched water were increased, particularly from cast iron pipes. Differences in the taxonomic composition of both bacteria and fungi were also observed, emphasising a community shift towards microorganisms able to use or metabolise phosphate. Phosphate increased the relative abundance of bacteria such as Pseudomonas, Paenibacillus, Massilia, Acinetobacter and the fungi Cadophora, Rhizophagus and Eupenicillium. Whole metagenome sequencing showed with phosphate a favouring of sequences related to Gram-negative bacterium type cell wall function, virions and thylakoids, but a reduction in the number of sequences associated to vitamin binding, methanogenesis and toxin biosynthesis. With current faecal indicator tests only providing risk detection in bulk water samples, this work improves understanding of how network changes effect microbial ecology and highlights the potential for new approaches to inform future monitoring or control strategies to protect drinking water quality