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Search Results: 1 - 10 of 425 matches for " Tracey Chillingworth "
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Critical points and symmetries of a free energy function for biaxial nematic liquid crystals
David Chillingworth
Physics , 2014, DOI: 10.1088/0951-7715/28/5/1483
Abstract: We describe a general model for the free energy function for a homogeneous medium of mutually interacting molecules, based on the formalism for a biaxial nematic liquid crystal set out by Katriel {\em et al.} (1986) in an influential paper in {\em Liquid Crystals} {\bf 1} and subsequently called the KKLS formalism. The free energy is expressed as the sum of an entropy term and an interaction (Hamiltonian) term. Using the language of group representation theory we identify the order parameters as averaged components of a linear transformation, and characterise the full symmetry group of the entropy term in the liquid crystal context as a wreath product $SO(3)\wr Z_2$. The symmetry-breaking role of the Hamiltonian, pointed out by Katriel {\em et al.}, is here made explicit in terms of centre manifold reduction at bifurcation from isotropy. We use tools and methods of equivariant singularity theory to reduce the bifurcation study to that of a $D_3\,$-invariant function on ${\bf R}^2$, ubiquitous in liquid crystal theory, and to describe the 'universal' bifurcation geometry in terms of the superposition of a familiar swallowtail controlling uniaxial equilibria and another less familiar surface controlling biaxial equilibria. In principle this provides a template for {\em all} nematic liquid crystal phase transitions close to isotropy, although further work is needed to identify the absolute minima that are the critical points representing stable phases.
Dynamics of an impact oscillator near a degenerate graze
D R J Chillingworth
Physics , 2010,
Abstract: We give a complete analysis of low-velocity dynamics close to grazing for a generic one degree of freedom impact oscillator. This includes nondegenerate (quadratic) grazing and minimally degenerate (cubic) grazing, corresponding respectively to nondegenerate and degenerate {\em chatter}. We also describe the dynamics associated with generic one-parameter bifurcation at a more degenerate (quartic) graze, showing in particular how this gives rise to the often-observed highly convoluted structure in the stable manifolds of chattering orbits. The approach adopted is geometric, using methods from singularity theory.
The Complete Genome Sequence and Comparative Genome Analysis of the High Pathogenicity Yersinia enterocolitica Strain 8081
Nicholas R Thomson ,Sarah Howard,Brendan W Wren,Matthew T. G Holden,Lisa Crossman,Gregory L Challis,Carol Churcher,Karen Mungall,Karen Brooks,Tracey Chillingworth,Theresa Feltwell,Zahra Abdellah,Heidi Hauser,Kay Jagels,Mark Maddison,Sharon Moule,Mandy Sanders,Sally Whitehead,Michael A Quail,Gordon Dougan,Julian Parkhill,Michael B Prentice
PLOS Genetics , 2006, DOI: 10.1371/journal.pgen.0020206
Abstract: The human enteropathogen, Yersinia enterocolitica, is a significant link in the range of Yersinia pathologies extending from mild gastroenteritis to bubonic plague. Comparison at the genomic level is a key step in our understanding of the genetic basis for this pathogenicity spectrum. Here we report the genome of Y. enterocolitica strain 8081 (serotype 0:8; biotype 1B) and extensive microarray data relating to the genetic diversity of the Y. enterocolitica species. Our analysis reveals that the genome of Y. enterocolitica strain 8081 is a patchwork of horizontally acquired genetic loci, including a plasticity zone of 199 kb containing an extraordinarily high density of virulence genes. Microarray analysis has provided insights into species-specific Y. enterocolitica gene functions and the intraspecies differences between the high, low, and nonpathogenic Y. enterocolitica biotypes. Through comparative genome sequence analysis we provide new information on the evolution of the Yersinia. We identify numerous loci that represent ancestral clusters of genes potentially important in enteric survival and pathogenesis, which have been lost or are in the process of being lost, in the other sequenced Yersinia lineages. Our analysis also highlights large metabolic operons in Y. enterocolitica that are absent in the related enteropathogen, Yersinia pseudotuberculosis, indicating major differences in niche and nutrients used within the mammalian gut. These include clusters directing, the production of hydrogenases, tetrathionate respiration, cobalamin synthesis, and propanediol utilisation. Along with ancestral gene clusters, the genome of Y. enterocolitica has revealed species-specific and enteropathogen-specific loci. This has provided important insights into the pathology of this bacterium and, more broadly, into the evolution of the genus. Moreover, wider investigations looking at the patterns of gene loss and gain in the Yersinia have highlighted common themes in the genome evolution of other human enteropathogens.
Meningococcal Genetic Variation Mechanisms Viewed through Comparative Analysis of Serogroup C Strain FAM18
Stephen D Bentley ,George S Vernikos,Lori A. S Snyder,Carol Churcher,Claire Arrowsmith,Tracey Chillingworth,Ann Cronin,Paul H Davis,Nancy E Holroyd,Kay Jagels,Mark Maddison,Sharon Moule,Ester Rabbinowitsch,Sarah Sharp,Louise Unwin,Sally Whitehead,Michael A Quail,Mark Achtman,Bart Barrell,Nigel J Saunders,Julian Parkhill
PLOS Genetics , 2007, DOI: 10.1371/journal.pgen.0030023
Abstract: The bacterium Neisseria meningitidis is commonly found harmlessly colonising the mucosal surfaces of the human nasopharynx. Occasionally strains can invade host tissues causing septicaemia and meningitis, making the bacterium a major cause of morbidity and mortality in both the developed and developing world. The species is known to be diverse in many ways, as a product of its natural transformability and of a range of recombination and mutation-based systems. Previous work on pathogenic Neisseria has identified several mechanisms for the generation of diversity of surface structures, including phase variation based on slippage-like mechanisms and sequence conversion of expressed genes using information from silent loci. Comparison of the genome sequences of two N. meningitidis strains, serogroup B MC58 and serogroup A Z2491, suggested further mechanisms of variation, including C-terminal exchange in specific genes and enhanced localised recombination and variation related to repeat arrays. We have sequenced the genome of N. meningitidis strain FAM18, a representative of the ST-11/ET-37 complex, providing the first genome sequence for the disease-causing serogroup C meningococci; it has 1,976 predicted genes, of which 60 do not have orthologues in the previously sequenced serogroup A or B strains. Through genome comparison with Z2491 and MC58 we have further characterised specific mechanisms of genetic variation in N. meningitidis, describing specialised loci for generation of cell surface protein variants and measuring the association between noncoding repeat arrays and sequence variation in flanking genes. Here we provide a detailed view of novel genetic diversification mechanisms in N. meningitidis. Our analysis provides evidence for the hypothesis that the noncoding repeat arrays in neisserial genomes (neisserial intergenic mosaic elements) provide a crucial mechanism for the generation of surface antigen variants. Such variation will have an impact on the interaction with the host tissues, and understanding these mechanisms is important to aid our understanding of the intimate and complex relationship between the human nasopharynx and the meningococcus.
Molien series and low-degree invariants for a natural action of ${\bf SO}(3)\wr{\bf Z}_2$
David Chillingworth,Reiner Lauterbach,Stefano Turzi
Physics , 2014, DOI: 10.1088/1751-8113/48/1/015203
Abstract: We investigate the invariants of the $25$-dimensional real representation of the group ${\bf SO}(3)\wr{\bf Z}_2$ given by the left and right actions of ${\bf SO}(3)$ on $5\times 5$ matrices together with matrix transposition; the action on column vectors is the irreducible $5$-dimensional representation of ${\bf SO}(3)$. The $25$-dimensional representation arises naturally in the study of nematic liquid crystals, where the second-rank orientational order parameters of a molecule are represented by a symmetric $3\times3$ traceless symmetric matrix, and where a rigid rotation in ${\bf R}^3$ induces a linear transformation of this space of matrices. The entropy contribution to a free energy density function in this context turns out to have ${\bf SO}(3)\wr{\bf Z}_2$ symmetry. Although it is unrealistic to expect to describe the complete algebraic structure of the ring of invariants, we are able to calculate the Molien series giving the number of linearly independent invariants at each homogeneous degree, and to express this as a rational function indicating the degrees of invariant polynomials that constitute a basis of 19 primary invariants. The algebra of invariants up to degree 4 is investigated in detail.
Bifurcation from a normally degenerate manifold
D. R. J. Chillingworth,L. Sbano
Mathematics , 2008, DOI: 10.1112/plms/pdp055
Abstract: Local bifurcation theory typically deals with the response of a degenerate but isolated equilibrium state or periodic orbit of a dynamical system to perturbations controlled by one or more independent parameters, and characteristically uses tools from singularity theory. There are many situations, however, in which the equilibrium state or periodic orbit is not isolated but belongs to a manifold $S$ of such states, typically as a result of continuous symmetries in the problem. In this case the bifurcation analysis requires a combination of local and global methods, and is most tractable in the case of normal nondegeneracy, that is when the degeneracy is only along $S$ itself and the system is nondegenerate in directions normal to $S$. In this paper we consider the consequences of relaxing normal nondegeneracy, which can generically occur within 1-parameter families of such systems. We pay particular attention to the simplest but important case where $\dim S=1$ and where the normal degeneracy occurs with corank 1. Our main focus is on uniform degeneracy along $S$, although we also consider aspects of the branching structure for solutions when the degeneracy varies at different places on $S$. The tools are those of singularity theory adapted to global topology of $S$, which allow us to explain the bifurcation geometry in natural way. In particular, we extend and give a clear geometric setting for earlier analytical results of Hale and Taboas.
The genome of Rhizobium leguminosarum has recognizable core and accessory components
J Peter W Young, Lisa C Crossman, Andrew WB Johnston, Nicholas R Thomson, Zara F Ghazoui, Katherine H Hull, Margaret Wexler, Andrew RJ Curson, Jonathan D Todd, Philip S Poole, Tim H Mauchline, Alison K East, Michael A Quail, Carol Churcher, Claire Arrowsmith, Inna Cherevach, Tracey Chillingworth, Kay Clarke, Ann Cronin, Paul Davis, Audrey Fraser, Zahra Hance, Heidi Hauser, Kay Jagels, Sharon Moule, Karen Mungall, Halina Norbertczak, Ester Rabbinowitsch, Mandy Sanders, Mark Simmonds, Sally Whitehead, Julian Parkhill
Genome Biology , 2006, DOI: 10.1186/gb-2006-7-4-r34
Abstract: The 7.75 Mb genome comprises a circular chromosome and six circular plasmids, with 61% G+C overall. All three rRNA operons and 52 tRNA genes are on the chromosome; essential protein-encoding genes are largely chromosomal, but most functional classes occur on plasmids as well. Of the 7,263 protein-encoding genes, 2,056 had orthologs in each of three related genomes (Agrobacterium tumefaciens, Sinorhizobium meliloti, and Mesorhizobium loti), and these genes were over-represented in the chromosome and had above average G+C. Most supported the rRNA-based phylogeny, confirming A. tumefaciens to be the closest among these relatives, but 347 genes were incompatible with this phylogeny; these were scattered throughout the genome but were over-represented on the plasmids. An unexpectedly large number of genes were shared by all three rhizobia but were missing from A. tumefaciens.Overall, the genome can be considered to have two main components: a 'core', which is higher in G+C, is mostly chromosomal, is shared with related organisms, and has a consistent phylogeny; and an 'accessory' component, which is sporadic in distribution, lower in G+C, and located on the plasmids and chromosomal islands. The accessory genome has a different nucleotide composition from the core despite a long history of coexistence.The symbiosis between legumes and N2-fixing bacteria (rhizobia) is of huge agronomic benefit, allowing many crops to be grown without N fertilizer. It is a sophisticated example of coupled development between bacteria and higher plants, culminating in the organogenesis of root nodules [1]. There have been many genetic analyses of rhizobia, notably of Sinorhizobium meliloti (the symbiont of alfalfa), Bradyrhizobium japonicum (soybean), and Rhizobium leguminosarum, which has biovars that nodulate peas and broad beans (biovar viciae), clovers (biovar trifolii), or kidney beans (biovar phaseoli).The Rhizobiales, an α-proteobacterial order that also includes mammalian pathogens B
Finding the Right Plugin: Mosquitoes Have the Answer
Tracey Chapman
PLOS Biology , 2012, DOI: 10.1371/journal.pbio.1000273
Abstract:
The Soup in My Fly: Evolution, Form and Function of Seminal Fluid Proteins
Tracey Chapman
PLOS Biology , 2012, DOI: 10.1371/journal.pbio.0060179
Abstract:
Physiotherapeutic management strategies for the treatment of cystic fibrosis in adults
Tracey Daniels
Journal of Multidisciplinary Healthcare , 2010, DOI: http://dx.doi.org/10.2147/JMDH.S8878
Abstract: iotherapeutic management strategies for the treatment of cystic fibrosis in adults Review (6706) Total Article Views Authors: Tracey Daniels Published Date November 2010 Volume 2010:3 Pages 201 - 212 DOI: http://dx.doi.org/10.2147/JMDH.S8878 Tracey Daniels York Hospitals NHS Trust Cystic Fibrosis Unit, York Teaching Hospitals Foundation NHS Trust, York, UK Abstract: Physiotherapy has long been considered a cornerstone of condition management for people with cystic fibrosis (CF). The presentation of CF has changed over time with an increased life expectancy and increased expectations of people with CF to have a complete lifestyle. In turn, the scope of strategies used in physiotherapy for CF have also changed dramatically over the years, moving away from routine postural drainage and manual techniques toward an individualized regimen including the choice of many different forms of airway clearance, such as both independent and assisted, exercise, treatments to promote continence and good posture, inhalation therapy, oxygen, and noninvasive ventilation. This article describes the techniques and overall strategies used by physiotherapists in helping people with CF to manage the symptoms and progression of their condition.
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