Species status of Neisseria gonorrhoeae: Evolutionary and epidemiological inferences from multilocus sequence typing

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 - Copyright @ 2007 Bennett et al; licensee BioMed Central Ltd.Background: Various typing methods have been developed for Neisseria gonorrhoeae, but none provide the combination of discrimination, reproducibility, portability, and genetic inference that allows the analysis of all aspects of the epidemiology of this pathogen from a single data set. Multilocus sequence typing (MLST) has been used successfully to characterize the related organisms Neisseria meningitidis and Neisseria lactamica. Here, the same seven locus Neisseria scheme was used to characterize a diverse collection of N. gonorrhoeae isolates to investigate whether this method would allow differentiation among isolates, and to distinguish these three species. Results: A total of 149 gonococcal isolates were typed and submitted to the Neisseria MLST database. Although relatively few (27) polymorphisms were detected among the seven MLST loci, a total of 66 unique allele combinations (sequence types, STs), were observed, a number comparable to that seen among isolate collections of the more diverse meningococcus. Patterns of genetic variation were consistent with high levels of recombination generating this diversity. There was no evidence for geographical structuring among the isolates examined, with isolates collected in Liverpool, UK, showing levels of diversity similar to a global collection of isolates. There was, however, evidence that populations of N. meningitidis, N. gonorrhoeae and N. lactamica were distinct, with little support for frequent genetic recombination among these species, with the sequences from the gdh locus alone grouping the species into distinct clusters. Conclusion: The seven loci Neisseria MLST scheme was readily adapted to N. gonorrhoeae isolates, providing a highly discriminatory typing method. In addition, these data permitted phylogenetic and population genetic inferences to be made, including direct comparisons with N. meningitidis and N. lactamica. Examination of these data demonstrated that alleles were rarely shared among the three species. Analysis of variation at a single locus, gdh, provided a rapid means of identifying misclassified isolates and determining whether mixed cultures were present.This study is funded by the Wellcome Trust and European Unio

Position and motion estimation for visual robot control with planar targets

This paper addresses two problems in visually-controlled robots. The first consists of positioning the end-effector of a robot manipulator on a plane of interest by using a monocular vision system. The problem amounts to estimating the transformation between the coordinates of an image point and its three-dimensional location supposing that only the camera intrinsic parameters are known. The second problem consists of positioning the robot end-effector with respect to an object of interest free to move on a plane, and amounts to estimating the camera displacement in a stereo vision system in the presence of motion constraints. For these problems, some solutions are proposed through dedicated optimizations based on decoupling the effects of rotation and translation and based on an a-priori imposition of the degrees of freedom of the system. These solutions are illustrated via simulations and experiments. ©2009 ACA.published_or_final_versionThe 7th Asian Control Conference (ASCC 2009), Hong Kong, China, 27-29 August 2009. In Proceedings of the Asian Control Conference, 2009, p. 372-37

HIV sero-positive status among clients aged ≥ 50 years that presented for care in a tertiary health facility in northeastern Nigeria.

The introduction of highly active antiretroviral therapy (HAART) has transformed HIV infection from hopeless to manageable health condition comparable to non-infectious diseases such as asthma and diabetes mellitus. This modest achievement has reduced morbidity and mortality and increased longevity and quality of life among HIV infected persons. Although reports from developing countries such as Nigeria, shows that youth within the reproductive are most affected by the scourge of HIV/AIDS. Older patients with features that may be indicative of HIV infection are often overlooked in favour of other differential diagnosis. Objective: To document HIV positive sero-status among client aged 50 years and above that necessitated HIV test as part of their clinical evaluation after voluntary counseling and testing at a tertiary health facility. Method: Record of 1674 adults participants that presented for care between January 2009- December 2013, were retrieved for this study. Results: The HIV-seropositive status among the participants was 370 (22.1%). It showed a female preponderance of 136 (26.0%) than 234 (20.0%) in males. The peak annual prevalence was observed in the year 2010, steady decline was observed thereafter. Overall, older participants between 60-70 years had higher HIV-seropositivity status. This study shows one out four males and five females with index of suspicion either based on clinical presentation or risky sexual behavior are positive for HIV infection. Conclusion: This report underscores the need to explore other risk factors that may be peculiar to older segment of the society and introduce HIV intervention strategies for the older populations. Delivery of HIV intervention measures and services to this segment of the population is expedient. Measures and interventions should take into consideration the peculiarities, specific vulnerabilities and HIV-related challenges faced by this group of clients

Differential transcriptomic and metabolic profiles of M. africanum- and M. tuberculosis-infected patients after, but not before, drug treatment.

The epidemiology of Mycobacterium tuberculosis (Mtb) and M. africanum (Maf) suggests differences in their virulence, but the host immune profile to better understand the pathogenesis of tuberculosis (TB) have not been studied. We compared the transcriptomic and metabolic profiles between Mtb- and Maf-infected TB cases to identify host biomarkers associated with lineages-specific pathogenesis and response to anti-TB chemotherapy. Venous blood samples from Mtb- and Maf-infected patients obtained before and after anti-TB treatment were analyzed for cell composition, gene expression and metabolic profiles. Prior to treatment, similar transcriptomic profiles were seen in Maf- and Mtb-infected patients. In contrast, post treatment, over 1600 genes related to immune responses and metabolic diseases were differentially expressed between the groups. Notably, the upstream regulator hepatocyte nuclear factor 4-alpha (HNF4α), which regulated 15% of these genes, was markedly enriched. Serum metabolic profiles were similar in both group pre-treatment, but the decline in pro-inflammatory metabolites post treatment were most pronounced in Mtb-infected patients. Together, the differences in both peripheral blood transcriptomic and serum metabolic profiles between Maf- and Mtb-infected patients observed over the treatment period, might be indicative of intrinsic host factors related to susceptibility to TB and/or differential efficacy of the standard anti-TB treatment on the two lineages

Quantum Simulation of Spin Chains Coupled to Bosonic Modes with Superconducting Circuits

We propose the implementation of a digital quantum simulation of spin chains coupled to bosonic field modes in superconducting circuits. Gates with high fidelities allows one to simulate a variety of Ising magnetic pairing interactions with transverse field, Tavis-Cummings interaction between spins and a bosonic mode, and a spin model with three-body terms. We analyze the feasibility of the implementation in realistic circuit quantum electrodynamics setups, where the interactions are either realized via capacitive couplings or mediated by microwave resonators.Comment: Chapter in R. S. Anderssen et al. (eds.), Mathematics for Industry 11 (Springer Japan, 2015

Immunogenic Mycobacterium africanum Strains Associated with Ongoing Transmission in The Gambia

In West Africa, Mycobacterium tuberculosis strains co-circulate with M. africanum, and both pathogens cause pulmonary tuberculosis in humans. Given recent findings that M. tuberculosis T-cell epitopes are hyperconserved, we hypothesized that more immunogenic strains have increased capacity to spread within the human host population. We investigated the relationship between the composition of the mycobacterial population in The Gambia, as measured by spoligotype analysis, and the immunogenicity of these strains as measured by purified protein derivative-induced interferon-γ release in ELISPOT assays of peripheral blood mononuclear cells. We found a positive correlation between strains with superior spreading capacity and their relative immunogenicity. Although our observation is true for M. tuberculosis and M. africanum strains, the association was especially pronounced in 1 M. africanum sublineage, characterized by spoligotype shared international type 181, which is responsible for 20% of all tuberculosis cases in the region and therefore poses a major public health threat in The Gambia

Developing and applying heterogeneous phylogenetic models with XRate

Modeling sequence evolution on phylogenetic trees is a useful technique in computational biology. Especially powerful are models which take account of the heterogeneous nature of sequence evolution according to the "grammar" of the encoded gene features. However, beyond a modest level of model complexity, manual coding of models becomes prohibitively labor-intensive. We demonstrate, via a set of case studies, the new built-in model-prototyping capabilities of XRate (macros and Scheme extensions). These features allow rapid implementation of phylogenetic models which would have previously been far more labor-intensive. XRate's new capabilities for lineage-specific models, ancestral sequence reconstruction, and improved annotation output are also discussed. XRate's flexible model-specification capabilities and computational efficiency make it well-suited to developing and prototyping phylogenetic grammar models. XRate is available as part of the DART software package: http://biowiki.org/DART .Comment: 34 pages, 3 figures, glossary of XRate model terminolog

Determinants of adults' intention to vaccinate against pandemic swine flu

This article has been made available through the Brunel Open Access Publishing Fund.This article has been made available through the Brunel Open Access Publishing Fund.Background: Vaccination is one of the cornerstones of controlling an influenza pandemic. To optimise vaccination rates in the general population, ways of identifying determinants that influence decisions to have or not to have a vaccination need to be understood. Therefore, this study aimed to predict intention to have a swine influenza vaccination in an adult population in the UK. An extension of the Theory of Planned Behaviour provided the theoretical framework for the study. Methods: Three hundred and sixty two adults from the UK, who were not in vaccination priority groups, completed either an online (n = 306) or pen and paper (n = 56) questionnaire. Data were collected from 30th October 2009, just after swine flu vaccination became available in the UK, and concluded on 31st December 2009. The main outcome of interest was future swine flu vaccination intentions. Results: The extended Theory of Planned Behaviour predicted 60% of adults’ intention to have a swine flu vaccination with attitude, subjective norm, perceived control, anticipating feelings of regret (the impact of missing a vaccination opportunity), intention to have a seasonal vaccine this year, one perceived barrier: “I cannot be bothered to get a swine flu vaccination” and two perceived benefits: “vaccination decreases my chance of getting swine flu or its complications” and “if I get vaccinated for swine flu, I will decrease the frequency of having to consult my doctor,” being significant predictors of intention. Black British were less likely to intend to have a vaccination compared to Asian or White respondents. Conclusions: Theoretical frameworks which identify determinants that influence decisions to have a pandemic influenza vaccination are useful. The implications of this research are discussed with a view to maximising any future pandemic influenza vaccination uptake using theoretically-driven applications.This article is available through the Brunel Open Access Publishing Fund