The NCBO OBOF to OWL Mapping

Two of the most significant formats for biomedical ontologies are the Open Biomedical Ontologies Format (OBOF) and the Web Ontology Language (OWL). To make it possible to translate ontologies between these two representation formats, the National Center for Biomedical Ontology (NCBO) has developed a mapping between the OBOF and OWL formats as well as inter-conversion software. The goal was to allow the sharing of tools, ontologies, and associated data between the OBOF and Semantic Web communities.

OBOF does not have a formal grammar, so the NCBO had to capture its intended semantics to map it to OWL.

This official NCBO mapping was used to make all OBO Foundry ontologies available in OWL. 

Availability: This mapping functionality can be embedded into OBO-Edit and Protégé-OWL ontology editors. This software is available at: http://bioontology.org/wiki/index.php/OboInOwl:Main_Pag

Co-crystallisation of cytosine with 1,10-phenanthroline: computational screening and experimental realisation

Attempts to co-crystallise the nucleobases adenine, thymine, guanine, and cytosine with 1,10-phenanthroline by ball milling and solvent evaporation methods are described. A 1:1 co-crystal of cytosine and 1,10-phenanthroline can be obtained by grinding or by solvent evaporation. The structure contains two crystallographically independent cytosine and two independent 1,10-phenanthroline molecules (Z′ = 2). The cytosine molecules form two similar but crystallographically independent hydrogen-bonded chains, while the 1,10-phenanthroline molecules are arranged in π-stacks. Between the chains of cytosine and the π-stacks exist N-H⋯N and C-H⋯N interactions. Crystal structure prediction (CSP) calculations were applied to all four systems to assess their potential for co-crystallisation as well as the likely structures and intermolecular interactions that could result from co-crystallisation. Calculations on the cytosine system demonstrate that co-crystallisation results in a lower energy than the crystalline forms of the two starting materials, in line with the co-crystal formation observed. For the systems which did not form a co-crystal, CSP was used to explore potential packing arrangements, but found none which were lower in energy than that of the pure crystalline forms. In these cases there is significant disruption to the nucleobase hydrogen bonding between the pure compound and the hypothetical co-crystal. For pure adenine and guanine, the hydrogen-bonded ribbons form sheets which must be broken, whereas for thymine, the lack of hydrogen bond donors does not allow the hydrogen bonding present for pure thymine to be maintained while forming thymine-1,10-phenanthroline hydrogen bonds

Co-crystallisation of cytosine with 1,10-phenanthroline: computational screening and experimental realisation

Attempts to co-crystallise the nucleobases adenine, thymine, guanine, and cytosine with 1,10-phenanthroline by ball milling and solvent evaporation methods are described. A 1 : 1 co-crystal of cytosine and 1,10-phenanthroline can be obtained by grinding or by solvent evaporation. The structure contains two crystallographically independent cytosine and two independent 1,10-phenanthroline molecules (Z? = 2). The cytosine molecules form two similar but crystallographically independent hydrogen-bonded chains, while the 1,10-phenanthroline molecules are arranged in ?-stacks. Between the chains of cytosine and the ?-stacks exist N–H?N and C–H?N interactions. Crystal structure prediction (CSP) calculations were applied to all four systems to assess their potential for co-crystallisation as well as the likely structures and intermolecular interactions that could result from co-crystallisation. Calculations on the cytosine system demonstrate that co-crystallisation results in a lower energy than the crystalline forms of the two starting materials, in line with the co-crystal formation observed. For the systems which did not form a co-crystal, CSP was used to explore potential packing arrangements, but found none which were lower in energy than that of the pure crystalline forms. In these cases there is significant disruption to the nucleobase hydrogen bonding between the pure compound and the hypothetical co-crystal. For pure adenine and guanine, the hydrogen-bonded ribbons form sheets which must be broken, whereas for thymine, the lack of hydrogen bond donors does not allow the hydrogen bonding present for pure thymine to be maintained while forming thymine-1,10-phenanthroline hydrogen bonds

Portable Curing Frame

A portable curing frame is provided particularly adapted for use with an automated tobacco harvester. The curing frame includes a substantially rectangular frame member including a series of slotted tracks, in the form of slotted tubes, specially designed for receiving a notched portion of the plant stalks. The slotted track is substantially continuous and thereby allows infinitely variable spacing between the plants and optimization of ventilation for air curing. Legs are also provided on the portable curing frame. The legs are displaceable between a retracted position allowing storage of the frames and loading of the frames with tobacco plants and an extended position for supporting the frames and inverted plants above the ground in the field. A locking mechanism is provided to positively retain the legs in both the retracted and extended positions. A triggering mechanism is also provided to release the locking mechanism and allow the legs to be displaced by gravity from the retracted position to the extended position. The tobacco-laden curing frame may be covered by plastic or other material and left in the field to cure. Once curing is completed the cured plants may be mechanically removed from the frames for optimum speed in handling the plants and bringing the tobacco to market

Simulation of carbon fibre composites in an industrial microwave

The ability of microwave radiation to penetrate and interact directly with materials has led to its extensive use in food and drug industries, and more recently in composites manufacturing. Microwave heating of composites allows rapid heat transfer throughout the material thickness with reduced thermal gradients and processing times as well as energy efficiency. Design of microwave systems to process composite parts with various geometries and sizes demands improved understanding of electromagnetic energy distribution and factors influencing it. Finite-element (FE) models can be efficient design tools in such cases, as physical experimentation can be impractical. In this study, a fully-coupled FE model of a carbon fibre composite in an industrial microwave environment is developed using COMSOL Multiphysics®. The effects of the heating process parameters including the number of active magnetrons, specimen thickness and the variation in the frequency of radiation on the electromagnetic field distribution are studied. The FE model showed that a substantial difference in the electromagnetic field distribution exists for the frequencies above 1 GHz compared to the lower frequencies in the microwave regime, resulting in non-uniform heating

Functional Characterization of a Novel Family of Acetylcholine-Gated Chloride Channels in Schistosoma mansoni

Acetylcholine is the canonical excitatory neurotransmitter of the mammalian neuromuscular system. However, in the trematode parasite Schistosoma mansoni, cholinergic stimulation leads to muscle relaxation and a flaccid paralysis, suggesting an inhibitory mode of action. Information about the pharmacological mechanism of this inhibition is lacking. Here, we used a combination of techniques to assess the role of cholinergic receptors in schistosome motor function. The neuromuscular effects of acetylcholine are typically mediated by gated cation channels of the nicotinic receptor (nAChR) family. Bioinformatics analyses identified numerous nAChR subunits in the S. mansoni genome but, interestingly, nearly half of these subunits carried a motif normally associated with chloride-selectivity. These putative schistosome acetylcholine-gated chloride channels (SmACCs) are evolutionarily divergent from those of nematodes and form a unique clade within the larger family of nAChRs. Pharmacological and RNA interference (RNAi) behavioral screens were used to assess the role of the SmACCs in larval motor function. Treatment with antagonists produced the same effect as RNAi suppression of SmACCs; both led to a hypermotile phenotype consistent with abrogation of an inhibitory neuromuscular mediator. Antibodies were then generated against two of the SmACCs for use in immunolocalization studies. SmACC-1 and SmACC-2 localize to regions of the peripheral nervous system that innervate the body wall muscles, yet neither appears to be expressed directly on the musculature. One gene, SmACC-1, was expressed in HEK-293 cells and characterized using an iodide flux assay. The results indicate that SmACC-1 formed a functional homomeric chloride channel and was activated selectively by a panel of cholinergic agonists. The results described in this study identify a novel clade of nicotinic chloride channels that act as inhibitory modulators of schistosome neuromuscular function. Additionally, the iodide flux assay used to characterize SmACC-1 represents a new high-throughput tool for drug screening against these unique parasite ion channels

The association of distraction and caution displayed by pedestrians at a lighted crosswalk

ABSTRACT: The rates of deaths and injuries among pedestrians have fallen in recent years, but still remain public health problems as about 5000 pedestrians die each year. Because pedestrians have been shown to be responsible or partially responsible for many of the crashes in which they are involved, we sought to assess the relationship of distracted walking and performing routine cautionary behaviors of pedestrians crossing a busy street in a southwestern city at an intersection, adjacent a university. The behavior of 866 individuals was recorded by trained observers as pedestrians walked across a 105-foot wide street served by a stop light and zebra painted crosswalk. We defined distracted pedestrians as those wearing headphones, talking on a cell phone, eating, drinking, smoking or talking as they crossed the street. Caution was measured by looking left and right, and entering the crosswalk only when the white proceed light was illuminated. We found that only 13.5% of walkers looked left and right and entered the crosswalk while the white light was flashing. Approximately 20% of walkers were distracted as they crossed the street. Regression analysis indicated that distraction was negatively, but weakly associated with displaying cautious pedestrian behaviors. Because traffic lights were routinely ignored and lack of caution was predicted by distraction, we suggest that inexpensive education efforts target pedestrians near college campuses

Genomic surveillance detects Salmonella enterica serovar Paratyphi A harbouring blaCTX-M-15 from a traveller returning from Bangladesh

Whole genome sequencing (WGS) has been used routinely by Public Health England (PHE) for identification, surveillance and monitoring of resistance determinants in referred Salmonella isolates since 2015. We report the first identified case of extended-spectrum-β-lactamase (ESBL) Salmonella enterica serovar Paratyphi A (S. Paratyphi A) isolated from a traveller returning to England from Bangladesh in November 2017. The isolate (440915) was resistant to ciprofloxacin and harboured both the mobile element ISEcp9 -blaCTX-M-15-hp-tnpA and blaTEM-191, associated with ESBL production. Phenotypic resistance was subsequently confirmed by Antimicrobial Susceptibility Testing (AST). S. Paratyphi A 440915 harboured an IncI1 plasmid previously reported to encode ESBL elements in Enterobacteriaceae and recently described in a S. Typhi isolate from Bangladesh. Results from this study indicate the importance of monitoring imported drug resistance for typhoidal salmonellae as ceftriaxone is the first line antibiotic treatment for complicated enteric fever in England. We conclude that WGS provides a rapid, accurate method for surveillance of drug resistance genes in Salmonella, leading to the first reported case of ESBL producing S. Paratyphi A and continues to inform the national treatment guidelines for management of enteric fever