Towards a Conceptualization of Sociomaterial Entanglement

In knowledge representation, socio-technical systems can be modeled as multiagent systems in which the local knowledge of each individual agent can be seen as a context. In this paper we propose formal ontologies as a means to describe the assumptions driving the construction of contexts as local theories and to enable interoperability among them. In particular, we present two alternative conceptualizations of the notion of sociomateriality (and entanglement), which is central in the recent debates on socio-technical systems in the social sciences, namely critical and agential realism. We thus start by providing a model of entanglement according to the critical realist view, representing it as a property of objects that are essentially dependent on different modules of an already given ontology. We refine then our treatment by proposing a taxonomy of sociomaterial entanglements that distinguishes between ontological and epistemological entanglement. In the final section, we discuss the second perspective, which is more challenging form the point of view of knowledge representation, and we show that the very distinction of information into modules can be at least in principle built out of the assumption of an entangled reality

High occurrence of Flavescence dorée phytoplasma early in the season on grapevines infected with grapevine yellows

Research NoteA survey for the presence of phytoplasmas associated with grapevine yellows in about 500 Italian vineyards was conducted from 1999 to 2004. Grapevines with the earliest symptoms were mostly infected with Flavescence dorée type C phytoplasma (FD-C). As the season advanced, a steady relative decrease in the occurrence of FD-C coincided with a clear relative increase in Bois noir phytoplasma. The relative occurrence of Flavescence dorée type D phytoplasma remained stable.

Flavescence doree in France and Italy - Occurrence of closely related phytoplasma isolates and their near relationships to Palatinate grapevine yellows and an alder yellows phytoplasma

Grapevine yellows (GY) are diseases of Vitis vinifera caused by phytoplasmas. On the basis of DNA analysis, it is possible to distinguish different groups and subgroups among grapevine phytoplasmas. Flavescence doree (FD), the most serious problem in European vineyards, is caused by a phytoplasma which belongs to the elm yellows group (EY or 16SrV), Differences between 7 phytoplasma isolates in this group, found until now in French, Italian and German grapevines, and 4 phytoplasmas in the same group, isolated mainly from elm and alder in Europe and America, were investigated. These 11 EY-group isolates plus 3 non-EY phytoplasmas, were compared by PCR-RFLP analyses of two different DNA fragments using 8 restriction enzymes. Two French and two Italian grapevine isolates, classified as FD, appeared to be closely related and were also closer to an Italian alder phytoplasma. One French and one Italian FD isolate always showed the same restriction pattern. On the opposite, the three German grapevine isolates related to alder phytoplasmas in Germany appeared to be closer to the two elm phytoplasmas from America and Europe.

Geometrically Precise Building Blocks: the Self-Assembly of beta-Peptides

Peptides comprised entirely of b-amino acids, or b-peptides, have attracted substantial interest over the past 25 years due to their unique structural and chemical characteristics. b-Peptides form well-defined secondary structures that exhibit different geometries compared with their a-peptide counterparts, giving rise to their foldamer classification. b-Peptide foldamers can be functionalized easily and are metabolically stable and, together with the predictable side-chain topography, have led to the design of a growing number of bioactive b-peptides with a range of biological targets. The strategic engineering of chemical and topographic properties has also led to the design of b-peptide mimics of higher-order oligomers. More recently, the ability of these peptides to self-assemble into complex structures of controlled geometries has been exploited in materials applications. The focus of thismini-review is on how the unique structural features of b-peptide assemblies have been exploited in the design of self-assembled proteomimetic bundles and nanomaterials

Towards an Ontological Modelling of Preference Relations

Preference relations are intensively studied in Economics, but they are also approached in AI, Knowledge Representation, and Conceptual Modelling, as they provide a key concept in a variety of domains of application. In this paper, we propose an ontological foundation of preference relations to formalise their essential aspects across domains. Firstly, we shall discuss what is the ontological status of the relata of a preference relation. Secondly, we investigate the place of preference relations within a rich taxonomy of relations (e.g. we ask whether they are internal or external, essential or contingent, descriptive or nondescriptive relations). Finally, we provide an ontological modelling of preference relation as a module of a foundational (or upper) ontology (viz. OntoUML). The aim of this paper is to provide a sharable foundational theory of preference relation that foster interoperability across the heterogeneous domains of application of preference relations

Reification and Truthmaking Patterns

Reification is a standard technique in conceptual modeling, which consists of including in the domain of discourse entities that may otherwise be hidden or implicit. However, deciding what should be rei- fied is not always easy. Recent work on formal ontology offers us a simple answer: put in the domain of discourse those entities that are responsible for the (alleged) truth of our propositions. These are called truthmakers. Re-visiting previous work, we propose in this paper a systematic analysis of truthmaking patterns for properties and relations based on the ontolog- ical nature of their truthmakers. Truthmaking patterns will be presented as generalization of reification patterns, accounting for the fact that, in some cases, we do not reify a property or a relationship directly, but we rather reify its truthmakers

Grapevine yellows: Comparison of different procedures for DNA extraction and amplification with PCR for routine diagnosis of phytoplasmas in grapevine

In order to devise a procedure to be used as reference for detection of grapevine phytoplasmas and monitoring of Flavescence dorée, 12 combinations comprising three methods of plant DNA extraction and 4 procedures for amplification in polymerase chain reaction of phytoplasma DNA were examined in parallel using the same plant tissues infected with phytoplasmas. In a first series tissues of periwinkles (Catharanthus roseus) infected with phytoplasma isolates of the Elm yellows group (16SrV) and maintained in the greenhouse, were used. In a second series tissues of grapevines (Vitis vinifera) naturally infected with Flavescence dorée or Palatinate grapevine yellows phytoplasma were used. The DNA preparations obtained with each of the three extraction procedures were used undiluted or serially diluted, as target DNA in the 4 nested-polymerase chain reactions. The results showed differences in the efficiency among different methods of extraction as well as in the sensitivity among the DNA amplification procedures, which improved when DNA extracted from field grapevines was diluted. After additional comparative validation on numerous field-collected samples of GY-affected grapevines, the quickest extraction procedure was selected for use in routine diagnosis, with nested-PCR amplification either of ribosomal DNA or of the FD9 DNA fragment specific for Flavescence dorée and other 16SrV group phytoplasmas

Visualizing Natural Image Statistics

Natural image statistics is an important area of research in cognitive sciences and computer vision. Visualization of statistical results can help identify clusters and anomalies as well as analyze deviation, distribution and correlation. Furthermore, they can provide visual abstractions and symbolism for categorized data. In this paper, we begin our study of visualization of image statistics by considering visual representations of power spectra, which are commonly used to visualize different categories of images. We show that they convey a limited amount of statistical information about image categories and their support for analytical tasks is ineffective. We then introduce several new visual representations, which convey different or more information about image statistics. We apply ANOVA to the image statistics to help select statistically more meaningful measurements in our design process. A task-based user evaluation was carried out to compare the new visual representations with the conventional power spectra plots. Based on the results of the evaluation, we made further improvement of visualizations by introducing composite visual representations of image statistics

Serverification of Molecular Modeling Applications: the Rosetta Online Server that Includes Everyone (ROSIE)

The Rosetta molecular modeling software package provides experimentally tested and rapidly evolving tools for the 3D structure prediction and high-resolution design of proteins, nucleic acids, and a growing number of non-natural polymers. Despite its free availability to academic users and improving documentation, use of Rosetta has largely remained confined to developers and their immediate collaborators due to the code's difficulty of use, the requirement for large computational resources, and the unavailability of servers for most of the Rosetta applications. Here, we present a unified web framework for Rosetta applications called ROSIE (Rosetta Online Server that Includes Everyone). ROSIE provides (a) a common user interface for Rosetta protocols, (b) a stable application programming interface for developers to add additional protocols, (c) a flexible back-end to allow leveraging of computer cluster resources shared by RosettaCommons member institutions, and (d) centralized administration by the RosettaCommons to ensure continuous maintenance. This paper describes the ROSIE server infrastructure, a step-by-step 'serverification' protocol for use by Rosetta developers, and the deployment of the first nine ROSIE applications by six separate developer teams: Docking, RNA de novo, ERRASER, Antibody, Sequence Tolerance, Supercharge, Beta peptide design, NCBB design, and VIP redesign. As illustrated by the number and diversity of these applications, ROSIE offers a general and speedy paradigm for serverification of Rosetta applications that incurs negligible cost to developers and lowers barriers to Rosetta use for the broader biological community. ROSIE is available at http://rosie.rosettacommons.org