Strain-specific differences in Neisseria gonorrhoeae associated with the phase variable gene repertoire

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited - © 2005 Jordan et al; licensee BioMed Central Ltd.Background: There are several differences associated with the behaviour of the four main experimental Neisseria gonorrhoeae strains, FA1090, FA19, MS11, and F62. Although there is data concerning the gene complements of these strains, the reasons for the behavioural differences are currently unknown. Phase variation is a mechanism that occurs commonly within the Neisseria spp. and leads to switching of genes ON and OFF. This mechanism may provide a means for strains to express different combinations of genes, and differences in the strain-specific repertoire of phase variable genes may underlie the strain differences. Results: By genome comparison of the four publicly available neisserial genomes a revised list of 64 genes was created that have the potential to be phase variable in N. gonorrhoeae, excluding the opa and pilC genes. Amplification and sequencing of the repeat-containing regions of these genes allowed determination of the presence of the potentially unstable repeats and the ON/OFF expression state of these genes. 35 of the 64 genes show differences in the composition or length of the repeats, of which 28 are likely to be associated with phase variation. Two genes were expressed differentially between strains causing disseminated infection and uncomplicated gonorrhoea. Further study of one of these in a range of clinical isolates showed this association to be due to sample size and is not maintained in a larger sample. Conclusion: The results provide us with more evidence as to which genes identified through comparative genomics are indeed phase variable. The study indicates that there are large differences between these four N. gonorrhoeae strains in terms of gene expression during in vitro growth. It does not, however, identify any clear patterns by which previously reported behavioural differences can be correlated with the phase variable gene repertoire.This study is funded by a Wellcome Trust Project Grant

Estimating the number needed to treat from continuous outcomes in randomised controlled trials: methodological challenges and worked example using data from the UK Back Pain Exercise and Manipulation (BEAM) trial

Background Reporting numbers needed to treat (NNT) improves interpretability of trial results. It is unusual that continuous outcomes are converted to numbers of individual responders to treatment (i.e., those who reach a particular threshold of change); and deteriorations prevented are only rarely considered. We consider how numbers needed to treat can be derived from continuous outcomes; illustrated with a worked example showing the methods and challenges. Methods We used data from the UK BEAM trial (n = 1, 334) of physical treatments for back pain; originally reported as showing, at best, small to moderate benefits. Participants were randomised to receive 'best care' in general practice, the comparator treatment, or one of three manual and/or exercise treatments: 'best care' plus manipulation, exercise, or manipulation followed by exercise. We used established consensus thresholds for improvement in Roland-Morris disability questionnaire scores at three and twelve months to derive NNTs for improvements and for benefits (improvements gained+deteriorations prevented). Results At three months, NNT estimates ranged from 5.1 (95% CI 3.4 to 10.7) to 9.0 (5.0 to 45.5) for exercise, 5.0 (3.4 to 9.8) to 5.4 (3.8 to 9.9) for manipulation, and 3.3 (2.5 to 4.9) to 4.8 (3.5 to 7.8) for manipulation followed by exercise. Corresponding between-group mean differences in the Roland-Morris disability questionnaire were 1.6 (0.8 to 2.3), 1.4 (0.6 to 2.1), and 1.9 (1.2 to 2.6) points. Conclusion In contrast to small mean differences originally reported, NNTs were small and could be attractive to clinicians, patients, and purchasers. NNTs can aid the interpretation of results of trials using continuous outcomes. Where possible, these should be reported alongside mean differences. Challenges remain in calculating NNTs for some continuous outcomes

Exploration of the Eucalyptus globulus gene pool

The first Europeans to discover Eucalyptus globulus were French explorers in 1792. Its seed was rapidly spread throughout the world in the 19th century and this was the species by which much of the world first knew the genus. However, it was in the industrial forests of the 20th century that this species, once considered the ‘Prince of Eucalypts’, achieved greatest prominence due to its fast growth and superior pulp qualities. Formal breeding first commenced in 1966 in Portugal and in the late 1980’s large base population trials from open-pollinated seed collections from native stands were established in many countries. These trials have provided unprecedented insights into the quantitative genetic control of numerous traits of economic and ecological importance and how this variation is spatially distributed in the native range of the species. However with large, fully pedigreed breeding populations becoming available for quantitative analysis and the rapidly expanding knowledge of DNA sequence variation, we are now at the threshold of a new understanding of this important eucalypt gene pool. Indications of the significance of non-additive genetic effects are becoming available. The E. globulus chloroplast genome has now been sequenced and several genome maps have been published. Studies of the variation in nuclear microsatellites and the lignin biosynthesis gene CCR confirm the complex, spatially structured nature of the native gene pool. Strong spatial structuring of the chloroplast genome has provided a tool for tracking seed migration and the geographic origin of exotic landraces. Highly divergent lineages of chloroplast DNA have been discovered and studies of the hypervariable JLA+ region argue that some components of the E. globulus gene pool have been assimilated from other species following hybridisation

Wellbeing at Work: Four Perspectives on What User Experiences with Artifacts May Contribute

Part 2: User Experiences and Wellbeing at Work (UX@Work)International audienceMost work involves the use of artifacts; thus, user experience (UX) is a factor in how most employees experience their work. This study revisits the tool, media, dialogue-partner, and system perspectives on artifact use to explore how UX may contribute to wellbeing at work. It is found that artifacts foster positive UX when they lend the user expressive power (tool), are transparent (media) or perceptive (dialogue partner).They foster negative UX when they break the user’s task focus or make the user a mere system component. These findings are discussed and refined by elaborating the classic concepts of ready to hand and present at hand

Design and Culture in the Making of Happiness

Design responds to the needs of individuals, being happiness and wellbeing the subject of an increasing number of studies, which gave rise to a new discipline, Positive Psychology. From these new approaches and concerns related to subjective well-being comes Positive Design, whose objective is to promote the well-being of individuals and communities in connection with a culture of innovation. The cultural routes made accessible through wayfinding systems, make it possible to put Heritage in dialogue, emphasize the culture, memory and history of communities, providing citizens with meaningful experiences that will have an impact both in the short and long run, thus becoming agents for the happiness of individuals. This article discusses the concept of Positive Design based on Positive Psychology, analyzes the evolution and importance of Heritage in the Culture of peoples and communities, questioning how the Wayfinding Systems developed for cultural promotion can integrate the practice of Positive Design and how this contributes to the subjective well-being of individuals

Dynamics of direct inter-pack encounters in endangered African wild dogs

Aggressive encounters may have important life history consequences due to the potential for injury and death, disease transmission, dispersal opportunities or exclusion from key areas of the home range. Despite this, little is known of their detailed dynamics, mainly due to the difficulties of directly observing encounters in detail. Here, we describe detailed spatial dynamics of inter-pack encounters in African wild dogs (Lycaon pictus), using data from custom-built high-resolution GPS collars in 11 free-ranging packs. On average, each pack encountered another pack approximately every 7 weeks and met each neighbour twice each year. Surprisingly, intruders were more likely to win encounters (winning 78.6% of encounters by remaining closer to the site in the short term). However, intruders did tend to move farther than residents toward their own range core in the short-term (1 h) post-encounter, and if this were used to indicate losing an encounter, then the majority (73.3%) of encounters were won by residents. Surprisingly, relative pack size had little effect on encounter outcome, and injuries were rare (<15% of encounters). These results highlight the difficulty of remotely scoring encounters involving mobile participants away from static defendable food resources. Although inter-pack range overlap was reduced following an encounter, encounter outcome did not seem to drive this, as both packs shifted their ranges post-encounter. Our results indicate that inter-pack encounters may be lower risk than previously suggested and do not appear to influence long-term movement and ranging

Primary non Hodgkin's lymphoma of the lacrimal sac

<p>Abstract</p> <p>Background</p> <p>Primary Non Hodgkin's Lymphoma (NHL) of the lacrimal sac is rare.</p> <p>Methods</p> <p>The clinical features of a 78 year old female who presented with epiphora and swelling of the left lacrimal sac are described.</p> <p>Results</p> <p>Computerised tomography showed a mass involving the left lacrimal sac. Histopathological examination revealed a diffuse large B cell NHL. Immunohistological examination demonstrated B cell origin. Chemotherapy could not be administered due to co morbid conditions. The patient was treated with radiotherapy to a dose of 45 Gy in 25 fractions. Patient is disease free and on follow up after 36 months.</p> <p>Conclusion</p> <p>Primary radiotherapy is a treatment option with curative potential for localized NHL of the lacrimal sac and may be considered in patients who cannot tolerate appropriate chemotherapy.</p

Approximating the Turaev-Viro Invariant of Mapping Tori is Complete for One Clean Qubit

The Turaev-Viro invariants are scalar topological invariants of three-dimensional manifolds. Here we show that the problem of estimating the Fibonacci version of the Turaev-Viro invariant of a mapping torus is a complete problem for the one clean qubit complexity class (DQC1). This complements a previous result showing that estimating the Turaev-Viro invariant for arbitrary manifolds presented as Heegaard splittings is a complete problem for the standard quantum computation model (BQP). We also discuss a beautiful analogy between these results and previously known results on the computational complexity of approximating the Jones polynomial.Comment: 16 pages, 8 figures, presented at TQC '11. Added reference

Psychological wellbeing, physical impairments and rural aging in a developing country setting

<p>Abstract</p> <p>Background</p> <p>There has been very little research on wellbeing, physical impairments and disability in older people in developing countries.</p> <p>Methods</p> <p>A community survey of 1147 older parents, one per household, aged sixty and over in rural Thailand. We used the Burvill scale of physical impairment, the Thai Psychological Wellbeing Scale and the brief WHO Disability Assessment Schedule. We rated received and perceived social support separately from children and from others and rated support to children. We used weighted analyses to take account of the sampling design.</p> <p>Results</p> <p>Impairments due to arthritis, pain, paralysis, vision, stomach problems or breathing were all associated with lower wellbeing. After adjusting for disability, only impairment due to paralysis was independently associated with lowered wellbeing. The effect of having two or more impairments compared to none was associated with lowered wellbeing after adjusting for demographic factors and social support (adjusted difference -2.37 on the well-being scale with SD = 7.9, p < 0.001) but after adjusting for disability the coefficient fell and was non-significant. The parsimonious model for wellbeing included age, wealth, social support, disability and impairment due to paralysis (the effect of paralysis was -2.97, p = 0.001). In this Thai setting, received support from children and from others and perceived good support from and to children were all independently associated with greater wellbeing whereas actual support to children was associated with lower wellbeing. Low received support from children interacted with paralysis in being especially associated with low wellbeing.</p> <p>Conclusion</p> <p>In this Thai setting, as found in western settings, most of the association between physical impairments and lower wellbeing is explained by disability. Disability is potentially mediating the association between impairment and low wellbeing. Received support may buffer the impact of some impairments on wellbeing in this setting. Giving actual support to children is associated with less wellbeing unless the support being given to children is perceived as good, perhaps reflecting parental obligation to support adult children in need. Improving community disability services for older people and optimizing received social support will be vital in rural areas in developing countries.</p