Facets, Tiers and Gems: Ontology Patterns for Hypernormalisation

There are many methodologies and techniques for easing the task of ontology building. Here we describe the intersection of two of these: ontology normalisation and fully programmatic ontology development. The first of these describes a standardized organisation for an ontology, with singly inherited self-standing entities, and a number of small taxonomies of refining entities. The former are described and defined in terms of the latter and used to manage the polyhierarchy of the self-standing entities. Fully programmatic development is a technique where an ontology is developed using a domain-specific language within a programming language, meaning that as well defining ontological entities, it is possible to add arbitrary patterns or new syntax within the same environment. We describe how new patterns can be used to enable a new style of ontology development that we call hypernormalisation

Measuring Expert Performance at Manually Classifying Domain Entities under Upper Ontology Classes

Classifying entities in domain ontologies under upper ontology classes is a recommended task in ontology engineering to facilitate semantic interoperability and modelling consistency. Integrating upper ontologies this way is difficult and, despite emerging automated methods, remains a largely manual task. Little is known about how well experts perform at upper ontology integration. To develop methodological and tool support, we first need to understand how well experts do this task. We designed a study to measure the performance of human experts at manually classifying classes in a general knowledge domain ontology with entities in the Basic Formal Ontology (BFO), an upper ontology used widely in the biomedical domain. We conclude that manually classifying domain entities under upper ontology classes is indeed very difficult to do correctly. Given the importance of the task and the high degree of inconsistent classifications we encountered, we further conclude that it is necessary to improve the methodological framework surrounding the manual integration of domain and upper ontologies

Intraspecific Variation in Taxonomic Characteristics of the Mayfly \u3ci\u3ePotamanthus Myops\u3c/i\u3e (Walsh)

Data collected from an ecological study of the mayfly Potamanthus rnyops (Walsh) in Michigan showed intraspecific variability in taxonomic characteristics that have been employed by previous investigators for species separation. Nymphal dorsal maculation patterns varied considerably within a single population. Also, the ratio of mandibular tusk length to head length increased with successive nymphal instars. Certain adult taxonomic characteristics, particularly relative male imago eye size and distance of separation, were either too poorly defined or too variable to be conclusive in species identification

Target Optimisation Studies for Surface Muon Production

The current paper discusses possible designs for a stand alone muon target for MuSR studies of condensed matter science. Considering the ISIS 7 mm graphite target as a reference, Geant4 simulations have been performed in order to optimize the target parameters with respect to muon and pion yield. Previous studies suggested that the muon production can be optimized by using a thin graphite slab target with an incident proton energy significantly lower than initially considered. Surface muon production obtained by firing an 800 MeV proton beam energy onto the target is simulated and potential improvements to the target material, geometry and angle orientation with respect to the incoming proton beam as well as an estimated performance of the muon target are presented in this paper. Implications for the ISIS muon facility are also discussed. A comparison of the pion production cross section between experimental data and three theoretical models for the latest four Geant4 versions is also included in this paper

Three Steps to Heaven: Semantic Publishing in a Real World Workflow

Semantic publishing offers the promise of computable papers, enriched visualisation and a realisation of the linked data ideal. In reality, however, the publication process contrives to prevent richer semantics while culminating in a `lumpen' PDF. In this paper, we discuss a web-first approach to publication, and describe a three-tiered approach which integrates with the existing authoring tooling. Critically, although it adds limited semantics, it does provide value to all the participants in the process: the author, the reader and the machine.Comment: Published as part of SePublica 201

Specific Rab GTPase-activating proteins define the Shiga toxin and epidermal growth factor uptake pathways

Rab family guanosine triphosphatases (GTPases) together with their regulators define specific pathways of membrane traffic within eukaryotic cells. In this study, we have investigated which Rab GTPase-activating proteins (GAPs) can interfere with the trafficking of Shiga toxin from the cell surface to the Golgi apparatus and studied transport of the epidermal growth factor (EGF) from the cell surface to endosomes. This screen identifies 6 (EVI5, RN-tre/USP6NL, TBC1D10A–C, and TBC1D17) of 39 predicted human Rab GAPs as specific regulators of Shiga toxin but not EGF uptake. We show that Rab43 is the target of RN-tre and is required for Shiga toxin uptake. In contrast, RabGAP-5, a Rab5 GAP, was unique among the GAPs tested and reduced the uptake of EGF but not Shiga toxin. These results suggest that Shiga toxin trafficking to the Golgi is a multistep process controlled by several Rab GAPs and their target Rabs and that this process is discrete from ligand-induced EGF receptor trafficking

Retrograde transport pathways utilised by viruses and protein toxins

A model has been presented for retrograde transport of certain toxins and viruses from the cell surface to the ER that suggests an obligatory interaction with a glycolipid receptor at the cell surface. Here we review studies on the ER trafficking cholera toxin, Shiga and Shiga-like toxins, Pseudomonas exotoxin A and ricin, and compare the retrograde routes followed by these protein toxins to those of the ER trafficking SV40 and polyoma viruses. We conclude that there is in fact no obligatory requirement for a glycolipid receptor, nor even with a protein receptor in a lipid-rich environment. Emerging data suggests instead that there is no common pathway utilised for retrograde transport by all of these pathogens, the choice of route being determined by the particular receptor utilised

Ricin trafficking in cells

The heterodimeric plant toxin ricin binds exposed galactosyls at the cell surface of target mammalian cells, and, following endocytosis, is transported in vesicular carriers to the endoplasmic reticulum (ER). Subsequently, the cell-binding B chain (RTB) and the catalytic A chain (RTA) are separated reductively, RTA embeds in the ER membrane and then retrotranslocates (or dislocates) across this membrane. The protein conducting channels used by RTA are usually regarded as part of the ER-associated protein degradation system (ERAD) that removes misfolded proteins from the ER for destruction by the cytosolic proteasomes. However, unlike ERAD substrates, cytosolic RTA avoids destruction and folds into a catalytic conformation that inactivates its target ribosomes. Protein synthesis ceases, and subsequently the cells die apoptotically. This raises questions about how this protein avoids the pathways that are normally sanctioned for ER-dislocating substrates. In this review we focus on the molecular events that occur with non-tagged ricin and its isolated subunits at the ER–cytosol interface. This focus reveals that intra-membrane interactions of RTA may control its fate, an area that warrants further investigation

454 pyrosequencing assessment of biodegradative bacteria from thermal hydrolysis processes

Anaerobic treatment process is a cost-effective method for treating organic wastes, since the biogas formed can be used for heat/electricity production and the digester residues can be recycled for other applications. An innovative use of the digestate could be as biodegradative and methanogenic inoculum for the stimulation of methane production in gas-producing or depleted wells. The microbial communities involved in the biodegradation of petrochemical waste are similar to the indigenous microorganisms typically found in unconventional basins. These communities also follow the same cascade of reactions: from the initial breakdown of complex molecules to the production of intermediate compounds used by methanogens. This study carried out a culture-independent assessment of the bacterial community composition of a digestate from the Bran Sands Advanced Digestion Facility (Middleborough, UK) and compared the results with the microbial populations found in unconventional gas basins. The 454 pyrosequencing analyses revealed a bacterial community dominated by Thermotogae, Bacteroidia, Clostridia and Synergistia, which are typically found in unconventional gas systems. The classification of nucleotide sequence reads and assembled contigs revealed a genetic profile characteristic for an anaerobic microbial consortium running fermentative metabolic pathways. The assignment of numerous sequences was related to hydrocarbon decomposition and digestion of cellulosic material, which indicates that the bacterial community is engaged in hydrolysis of plant-derived material. The bacterial community composition suggest that the effluent of the digester can be used as a biodegradative inoculum for the stimulation of methane generation in unconventional wells, where events of microbial methanogenesis have been previously observed