Characterising HIV-associated Mycobacterium tuberculosis blood stream infection

Despite the success of antiretroviral therapy roll-out, one-million people still die with HIV-infection annually. In high-burden settings, tuberculosis remains the most common proximal cause of hospital admission and death in people living with HIV. In post-mortem series, 90% of fatal HIV-associated tuberculosis is ‘disseminated’. This is a form of tuberculosis which has been poorly characterised and, despite the high associated-mortality, never been the subject of interventional trials to define optimal treatment strategies. This thesis contends that the mode of severe HIV-associated tuberculosis is blood stream infection. First it is argued with reference to historical literature that blood stream dissemination is part of the natural history of post-primary tuberculosis infection, and that HIV-associated M. tuberculosis blood stream infection (MTBBSI) can be conceived of as a reversion to, and exaggerated form of this natural history. Using data from a large cohort (n=571) of HIV-infected inpatients with CD4 cell count <350 cells/mm3 and a new TB diagnosis from Khayelitsha Hospital, South Africa (the KDHTB study), the extent and magnitude of MTBBSI is shown to be a major determinant of clinical phenotype and mortality risk. Systematic, quantitative markers of blood stream dissemination, including TB blood culture, urine-lipoarabinomannan (uLAM), and urine GeneXpert MTB/RIF testing (uXpert), can be combined into a ‘disseminated TB score. KDHTB patients have high prevalence of abnormal sodium and fluid balance, metabolic acidosis associated with acute kidney injury, hyperlactataemia, infiltrative liver and splenic pathology, and anaemia. Each of these pathophysiologies in turn correlates to disseminated TB score, and to risk of death, suggesting bacterial burden and MTBBSI are central to the pathophysiology of severe HIV-associated tuberculosis. An individual patient data meta-analysis, with 20 independent data sets comprising over 6000 patients, is used to establish the prevalence of TB blood culture positive disease amongst critically unwell HIV-infected inpatients. This shows that MTBBSI is more common than previous estimates suggest, is a strong independent association with mortality risk, and is also associated with specific increased risk of death if empirical treatment is delayed. The development of tools to identify and measure MTBBSI is described, including Xpert-ultra testing of blood, and the use of a novel dye, DMN-trehalose, to perform direct microscopy on patient blood samples. These techniques are used to provide the first description of the pharmacodynamics of MTBBSI, by serially quantifying blood bacilli load over the first 72-hours of standard TB therapy, in 28 patients with high predicted probability of bacteraemia. In this cohort, risk of mortality is related to several summary measures of MTBBSI dynamics in the first 72-hours of therapy, suggesting this approach can be used to define biomarkers of treatment response. In conclusion, MTBBSI is a highly-specific diagnosis responsible for substantial mortality in hospitalised people living with HIV. Interventions with strengthened bacteriocidal activity, focussed on reducing bacterial burden, are warranted for MTBBSI. Tools developed in this thesis, including potential pharmacodynamic biomarkers, should facilitate such trials

Measuring Invisible Particle Masses Using a Single Short Decay Chain

We consider the mass measurement at hadron colliders for a decay chain of two steps, which ends with a missing particle. Such a topology appears as a subprocess of signal events of many new physics models which contain a dark matter candidate. From the two visible particles coming from the decay chain, only one invariant mass combination can be formed and hence it is na\"ively expected that the masses of the three invisible particles in the decay chain cannot be determined from a single end point of the invariant mass distribution. We show that the event distribution in the $\log(E_{1T}/E_{2T})$ vs. invariant mass-squared plane, where $E_{1T}$, $E_{2T}$ are the transverse energies of the two visible particles, contains the information of all three invisible particle masses and allows them to be extracted individually. The experimental smearing and combinatorial issues pose challenges to the mass measurements. However, in many cases the three invisible particle masses in the decay chain can be determined with reasonable accuracies.Comment: 45 pages, 32 figure

A cross-sectional survey of cardiovascular health and lifestyle habits of hospital staff in the UK: Do we look after ourselves?

Background: A high prevalence of stress-related disorders is well known among healthcare professionals. We set out to assess the prevalence of cardiovascular risk factors and compliance with national dietary and physical activity recommendations in NHS staff in the UK with comparison between clinical and non-clinical staff, and national surveys. Design: A multi-centre cross-sectional study. Methods: A web-based questionnaire was developed to include anonymised data on demographics, job role, cardiovascular risk factors and diseases, dietary habits, physical activity and barriers towards healthy lifestyle. This was distributed to staff in four NHS hospitals via emails. Results: A total of 1158 staff completed the survey (response rate 13%) with equal distribution between the clinical and non-clinical groups. Most staff were aged 26–60 years and 79% were women. Half of the staff were either overweight or obese (51%) with no difference between the groups (P = 0.176), but there was a lower prevalence of cardiovascular risk factors compared to the general population. The survey revealed a low compliance (17%) with the recommended intake of five-a-day portions of fruit and vegetables, and that of moderate or vigorous physical activity (56%), with no difference between the clinical and non-clinical staff (P = 0.6). However, more clinical staff were exceeding the alcohol recommendations (P = 0.02). Lack of fitness facilities and managerial support, coupled with long working hours, were the main reported barriers to a healthy lifestyle. Conclusions: In this survey of UK NHS staff, half were found to be overweight or obese with a lower prevalence of cardiovascular risk factors compared to the general population. There was a low compliance with the five-a-day fruit and vegetables recommendation and physical activity guidelines, with no difference between the clinical and non-clinical staff

Software Product Line Engineering via Software Transplantation

Software Product Lines (SPLs) improve time-to-market, enhance software quality, and reduce maintenance costs. Current SPL reengineering practices are largely manual and require domain knowledge. Thus, adopting and, to a lesser extent, maintaining SPLs are expensive tasks, preventing many companies from enjoying their benefits. To address these challenges, we introduce Foundry, an approach utilizing software transplantation to reduce the manual effort of SPL adoption and maintenance. Foundry enables integrating features across different codebases, even codebases that are unaware that they are contributing features to a software product line. Each product produced by Foundry is pure code, without variability annotation, unlike feature flags, which eases variability management and reduces code bloat. We realise Foundry in prodScalpel, a tool that transplants multiple organs (i.e., a set of interesting features) from donor systems into an emergent product line for codebases written in C. Given tests and lightweight annotations identifying features and implantation points, prodScalpel automates feature extraction and integration. To evaluate its effectiveness, our evaluation compares feature transplantation using prodScalpel to the current state of practice: on our dataset, prodScalpel’s use speeds up feature migration by an average of 4.8 times when compared to current practice

Paradoxical upgrading reaction in extra-pulmonary tuberculosis: association with vitamin D therapy

SETTING: Glasgow, Scotland, UK. BACKGROUND: Paradoxical reactions in tuberculosis (TB) are a notable example of our incomplete understanding of host-pathogen interactions during anti-tuberculosis treatment. OBJECTIVES: To determine risk factors for a TB paradoxical reaction, and specifically to assess for an independent association with vitamin D use. DESIGN: Consecutive human immunodeficiency virus (HIV) negative adult patients treated for extra-pulmonary TB were identified from an Extended Surveillance of Mycobacterial Infections database. In our setting, vitamin D was variably prescribed for newly diagnosed TB patients. A previously published definition of paradoxical TB reaction was retrospectively applied to, and data on all previously described risk factors were extracted from, centralised electronic patient records. The association with vitamin D use was assessed using multivariate logistic regression. RESULTS: Of the 249 patients included, most had TB adenopathy; 222/249 had microbiologically and/or histologically confirmed TB. Vitamin D was prescribed for 57/249 (23%) patients; 37/249 (15%) were classified as having paradoxical reactions. Younger age, acid-fast bacilli-positive invasive samples, multiple disease sites, lower lymphocyte count and vitamin D use were found to be independent risk factors. CONCLUSION: We speculate that vitamin D-mediated signalling of pro-inflammatory innate immune cells, along with high antigenic load, may mediate paradoxical reactions in anti-tuberculosis treatment

Pleosporales

One hundred and five generic types of Pleosporales are described and illustrated. A brief introduction and detailed history with short notes on morphology, molecular phylogeny as well as a general conclusion of each genus are provided. For those genera where the type or a representative specimen is unavailable, a brief note is given. Altogether 174 genera of Pleosporales are treated. Phaeotrichaceae as well as Kriegeriella, Zeuctomorpha and Muroia are excluded from Pleosporales. Based on the multigene phylogenetic analysis, the suborder Massarineae is emended to accommodate five families, viz. Lentitheciaceae, Massarinaceae, Montagnulaceae, Morosphaeriaceae and Trematosphaeriaceae

Flow cytometry method for absolute counting and single-cell phenotyping of mycobacteria

Detection and accurate quantitation of viable Mycobacterium tuberculosis is fundamental to understanding mycobacterial pathogenicity, tuberculosis (TB) disease progression and outcomes; TB transmission; drug action, efficacy and drug resistance. Despite this importance, methods for determining numbers of viable bacilli are limited in accuracy and precision owing to inherent characteristics of mycobacterial cell biology – including the tendency to clump, and “differential” culturability – and technical challenges consequent on handling an infectious pathogen under biosafe conditions. We developed an absolute counting method for mycobacteria in liquid cultures using a bench-top flow cytometer, and the low-cost fluorescent dyes Calcein-AM (CA) and SYBR-gold (SG). During exponential growth CA+ cell counts are highly correlated with CFU counts and can be used as a real-time alternative to simplify the accurate standardisation of inocula for experiments. In contrast to CFU counting, this method can detect and enumerate cell aggregates in samples, which we show are a potential source of variance and bias when using established methods. We show that CFUs comprise a sub-population of intact, metabolically active mycobacterial cells in liquid cultures, with CFU proportion varying by growth conditions. A pharmacodynamic application of the flow cytometry method, exploring kinetics of fluorescent probe defined subpopulations compared to CFU is demonstrated. Flow cytometry derived Mycobacterium bovis bacillus Calmette-Guérin (BCG) time-kill curves differ for rifampicin and kanamycin versus isoniazid and ethambutol, as do the relative dynamics of discrete morphologically-distinct subpopulations of bacilli revealed by this high-throughput single-cell technique

Functional Polymorphism of the Mu-Opioid Receptor Gene (OPRM1) Influences Reinforcement Learning in Humans

Previous reports on the functional effects (i.e., gain or loss of function), and phenotypic outcomes (e.g., changes in addiction vulnerability and stress response) of a commonly occurring functional single nucleotide polymorphism (SNP) of the mu-opioid receptor (OPRM1 A118G) have been inconsistent. Here we examine the effect of this polymorphism on implicit reward learning. We used a probabilistic signal detection task to determine whether this polymorphism impacts response bias to monetary reward in 63 healthy adult subjects: 51 AA homozygotes and 12 G allele carriers. OPRM1 AA homozygotes exhibited typical responding to the rewarded response—that is, their bias to the rewarded stimulus increased over time. However, OPRM1 G allele carriers exhibited a decline in response to the rewarded stimulus compared to the AA homozygotes. These results extend previous reports on the heritability of performance on this task by implicating a specific polymorphism. Through comparison with other studies using this task, we suggest a possible mechanism by which the OPRM1 polymorphism may confer reduced response to natural reward through a dopamine-mediated decrease during positive reinforcement learning

Natural Predictions for the Higgs Boson Mass and Supersymmetric Contributions to Rare Processes

In the context of No-Scale F-SU(5), a model defined by the convergence of the F-lipped SU(5) Grand Unified Theory, two pairs of hypothetical TeV scale vector-like supersymmetric multiplets with origins in F-theory, and the dynamically established boundary conditions of No-Scale Supergravity, we predict that the lightest CP-even Higgs boson mass lies within the range of 119.0 GeV to 123.5 GeV, exclusive of the vector-like particle contribution to the mass. With reports by the CMS, ATLAS, CDF, and D0 Collaborations detailing enticing statistical excesses in the vicinity of 120 GeV in searches for the Standard Model Higgs boson, all signs point to an imminent discovery. While basic supersymmetric constructions such as mSUGRA and the CMSSM have already suffered overwhelming reductions in viable parameterization during the LHC's initial year of operation, about 80% of the original No-Scale F-SU(5) model space remains viable after analysis of the first 1.1 fb^{-1} of integrated luminosity. This model is moreover capable of handily explaining the small excesses recently reported in the CMS multijet supersymmetry search, and also features a highly favorable "golden" subspace which may simultaneously account for the key rare process limits on the muon anomalous magnetic moment (g - 2) and the branching ratio of the flavor-changing neutral current decay b to s\gamma. In addition, the isolated mass parameter responsible for the global particle mass normalization, the gaugino boundary mass M_{1/2}, is dynamically determined at a secondary local minimization of the minimum of the Higgs potential V_{min}, in a manner which is deeply consistent with all precision measurements at the physical electroweak scale.Comment: Physics Letters B Version, 10 pages, 2 figures, 2 table