Comparative Phylogenomics of Pathogenic and Nonpathogenic Species.

The Ascomycete Onygenales order embraces a diverse group of mammalian pathogens, including the yeast-forming dimorphic fungal pathogens Histoplasma capsulatum, Paracoccidioides spp. and Blastomyces dermatitidis, the dermatophytes Microsporum spp. and Trichopyton spp., the spherule-forming dimorphic fungal pathogens in the genus Coccidioides, and many nonpathogens. Although genomes for all of the aforementioned pathogenic species are available, only one nonpathogen had been sequenced. Here, we enhance comparative phylogenomics in Onygenales by adding genomes for Amauroascus mutatus, Amauroascus niger, Byssoonygena ceratinophila, and Chrysosporium queenslandicum--four nonpathogenic Onygenales species, all of which are more closely related to Coccidioides spp. than any other known Onygenales species. Phylogenomic detection of gene family expansion and contraction can provide clues to fungal function but is sensitive to taxon sampling. By adding additional nonpathogens, we show that LysM domain-containing proteins, previously thought to be expanding in some Onygenales, are contracting in the Coccidioides-Uncinocarpus clade, as are the self-nonself recognition Het loci. The denser genome sampling presented here highlights nearly 800 genes unique to Coccidiodes, which have significantly fewer known protein domains and show increased expression in the endosporulating spherule, the parasitic phase unique to Coccidioides spp. These genomes provide insight to gene family expansion/contraction and patterns of individual gene gain/loss in this diverse order--both major drivers of evolutionary change. Our results suggest that gene family expansion/contraction can lead to adaptive radiations that create taxonomic orders, while individual gene gain/loss likely plays a more significant role in branch-specific phenotypic changes that lead to adaptation for species or genera

Multi-Objective Pathfinding in Dynamic Environments

Traditional pathfinding techniques are known for calculating the shortest path from a given start point to a designated target point on a directed graph. These techniques, however, are inapplicable to pathfinding problems where the shortest path may prove to be hazardous for traversal, or where multiple costs of differing unit-types lie along the same path. Moreover, the shortest path may not be optimal if it requires forfeiting a valuable resource. While strategic methods have been proposed in the past to completely avoid paths determined to be dangerous, these methods lack the functionality to provide agents the ability to decide which resources are more valuable for conservation, and which resources possess the greatest risk at being lost. For environments where risk varies dynamically across edges, we propose a solution that can determine a path of least expected weight based on multiple properties of edges. With this Multi-Objective Pathfinding technique, agents can make decisions influenced by highest priority objectives and their preferences to trading off some resources for others. The solution is based on traditional pathfinding techniques, extending their usability to cover strategic and dynamic scenarios where additional properties contained within the search map could render them useless. Nevertheless, our solution is compatible with problems where the goal is to simply find the least weighted path, otherwise known as the objectively resource-conservative path among a set of vertices in a graph

Global dynamics of a vibro-impacting linear oscillator

International audienceThe steady state, vibro-impacting responses of one dimensional, harmonically excited, linear oscillators are studied by using a modern dynamical systems approach allied with numerical simulation. The steady state motions are attracting sets in the system phase space and capture initial conditions in their domains of attraction. Unlike the free, harmonically excited oscillator, the phase space of a vibro-impacting system may be inhabited by many attracting sets. For example, there are sub-harmonic, multi-impact, periodic orbits and chaotic, steady state responses. In order to build a qualitative understanding of vibro-impact response, an attempt is made to build generic topological models of their phase spaces for physically significant parameter ranges. Use is made of the Poincaré section or stroboscopic mapping technique, essentially following an initial impact forwards or backwards in time to subsequent or previous impacts using a computer. The qualitative understanding gained from the analysis and simulations is discussed in an engineering context

Cohomology theory of the kenematical groups

A number of applications of S. Eilenberg and S. Maclane's cohomology theory of groups to the kinematical groups of physics are presented. Within this field, we apply the theory of group exten sions by Abelian and non-Abelian kernels to the study of the algebraic structures of the Galilei, Static and Carroll groups, and introduce to physics the mathematical concepts of group enlargements and prolongations. The global algebraic structures of the kinematical groups are analysed in depth using these tools and a generalisation of kinematical groups is attempted. The use of the methods of homological algebra in classical mechanics is discussed from the new view point of Lagrangian mechanics introduced by Lévy-Leblond. In this direction two advances are made. Homological algebra is introduced to the study of Hamilton's principle and then a reformulation of Levy-Leblond's free Lagrangian mechanics is obtained. Whilst the above author concentrates on a certain second cohomology group, we see that it is a first cohomology group which is more relevant to this approach. The group theoretic discussion of non-inertial motions is initiated using the theory of the loop prolongations of a group Q by a group K, where a loop is a 'non-associative group'. Our preliminary results enable us to give a cohomological description of constant Newtonian acceleration

Effect of excess iron on oxidative dehydrogenation of 1-butene over a series of zinc ferrite catalysts

The influence of excess Fe3+ in ZnFe2O4 for the catalytic oxidative dehydrogenation of 1-butene to 1, 3-butadiene was investigated to try to clarify inconsistencies in the existing literature. A series of nanoscale zinc ferrite powders were produced with increasing Fe: Zn ratios. The materials were characterized by a range of techniques, which showed the presence of α-Fe2O3 as a distinct phase with an increasing excess of Fe3+ and SEM highlighted the increased presence of surface structures on the ferrites at higher Fe: Zn ratios. Reaction testing showed α-Fe2O3to be virtually inactive for the oxidative dehydrogenation of 1-butene. Results for the ferrite catalysts showed a significant decrease in both conversion and yield with an increasing excess of Fe3+. Therefore an excess of Fe3+ has a negative effect on catalytic activity and selectivity of zinc ferrite for the oxidative dehydrogenation of 1-butene, but acts as a promoter for competing hydrogenation and combustion side reactions

Topology of Vibro-Impact Systems in the Neighborhood of Grazing

The grazing bifurcation is considered for the Newtonian model of vibro-impact systems. A brief review on the conditions, sufficient for existence of a grazing family of periodic solutions, is given. The properties of these periodic solutions are discussed. A plenty of results on the topological structure of attractors of vibro-impact systems is known. However, since the considered system is strongly nonlinear, these attractors may be invisible or, at least, very sensitive to changes of parameters of the system. On the other hand, they are observed in experiments and numerical simulations. We offer (Theorem 2) an approach which allows to explain this contradiction and give a new robust mathematical model of the non-hyperbolic dynamics in the neighborhood of grazing.Comment: Submitted to Physica

Sir Matthew Tierney and the foundation of the 1804 Sussex Vaccine Institution

Irish physician Sir Matthew John Tierney (1776–1845) was a vaccine pioneer who learnt the procedure directly from Edward Jenner in Gloucestershire. In 1802 Tierney completed an MD at Glasgow on vaccination and moved to Brighton, where he was appointed physician to the Prince of Wales (the future King George IV). This paper considers Tierney’s role in the foundation of the 1804 Sussex Vaccine Institution. Tierney was the first president of the Institution’s Medical Council. His leadership lay in his knowledge of vaccination (including transporting cowpox material) and his close relationship with the Prince of Wales. The Institution’s official name was the Royal Sussex Jennerian Society for the Extermination of the Small-pox and offered vaccination at 16 stations across the county and one in Kent. Vaccination was undertaken by local surgeons at their houses at set hours. In its first year, the Institution vaccinated 946 individuals, of whom 509 for free. Despite this, concerns were raised over uptake by poorer members of society. The Institution’s Brighton station was probably absorbed into the new 1809 dispensary. Tierney’s promotion of vaccination and instructions for new practitioners represent the embryonic beginnings of evidence-based medicine and modern medical education in Brighton