Application of highly portable MinION nanopore sequencing technology for the monitoring of nosocomial tuberculosis infection

Referral hospitals in sub-Saharan Africa concentrate large numbers of tuberculosis (TB) and multidrug-resistant TB (MDR-TB) patients, failed by community TB services. We have previously shown, from enhanced screening and through autopsy studies, a significant burden of missed TB infections at the University Teaching Hospital, Lusaka, Zambia, with many patients dying or being discharged without treatment. With minimal TB isolation facilities and minimal political will to invest in broader screening and isolation, the risk of nosocomial transmission is likely to be extremely high. Studies from other hospitals in low burden settings and in South Africa have shown that next generation sequencing (NGS) is a very powerful tool for rapidly sequencing whole TB genomes and comparing them to confirm or rule out nosocomial transmission. The established platforms for NGS analysis, such as Illumina, are very expensive, immobile, and require regular maintenance, making them a costly inclusion on a research proposal or programmatic intervention grant in Africa. MinION nanopore sequencing has changed the NGS landscape with cheap portable sequencers, rapid simple library preparation (15min), and automated real-time analysis tools. The application of highly portable MinION nanopore sequencing technology for the monitoring of nosocomial TB infection will be discussed. Preliminary data from our pediatric pneumonia study will demonstrate the detection of TB in induced sputum from children admitted to the University Teaching Hospital

From solar to stellar corona: the role of wind, rotation and magnetism

Observations of surface magnetic fields are now within reach for many stellar types thanks to the development of Zeeman-Doppler Imaging. These observations are extremely useful for constraining rotational evolution models of stars, as well as for characterizing the generation of magnetic field. We recently demonstrated that the impact of coronal magnetic field topology on the rotational braking of a star can be parametrized with a scalar parameter: the open magnetic flux. However, without running costly numerical simulations of the stellar wind, reconstructing the coronal structure of the large scale magnetic field is not trivial. An alternative -broadly used in solar physics- is to extrapolate the surface magnetic field assuming a potential field in the corona, to describe the opening of the field lines by the magnetized wind. This technique relies on the definition of a so-called source surface radius, which is often fixed to the canonical value of 2.5Rsun. However this value likely varies from star to star. To resolve this issue, we use our extended set of 2.5D wind simulations published in 2015, to provide a criteria for the opening of field lines as well as a simple tool to assess the source surface radius and the open magnetic flux. This allows us to derive the magnetic torque applied to the star by the wind from any spectropolarimetric observation. We conclude by discussing some estimations of spin-down time scales made using our technique, and compare them to observational requirements.Comment: Accepted for publication in the Astrophysical Journa

Program Synthesis for Program Analysis

In this article, we propose a unified framework for designing static analysers based on program synthesis. For this purpose, we identify a fragment of second-order logic with restricted quantification that is expressive enough to model numerous static analysis problems (e.g., safety proving, bug finding, termination and non-termination proving, refactoring). As our focus is on programs that use bit-vectors, we build a decision procedure for this fragment over finite domains in the form of a program synthesiser. We provide instantiations of our framework for solving a diverse range of program verification tasks such as termination, non-termination, safety and bug finding, superoptimisation, and refactoring. Our experimental results show that our program synthesiser compares positively with specialised tools in each area as well as with general-purpose synthesisers

Diabetes and male sex are key risk factor correlates of the extent of coronary artery calcification: A Euro-CCAD study.

Background and aimsAlthough much has been written about the conventional cardiovascular risk factor correlates of the extent of coronary artery calcification (CAC), few studies have been carried out on symptomatic patients. This paper assesses the potential ability of risk factors to associate with an increasing CAC score.MethodsFrom the European Calcific Coronary Artery Disease (Euro-CCAD) cohort, we retrospectively investigated 6309 symptomatic patients, 62% male, from Denmark, France, Germany, Italy, Spain and the USA. All had conventional cardiovascular risk factor assessment and CT scanning for CAC scoring.ResultsAmong all patients, male sex (OR = 4.85, p<0.001) and diabetes (OR = 2.36, p<0.001) were the most important risk factors of CAC extent, with age, hypertension, dyslipidemia and smoking also showing a relationship. Among patients with CAC, age, diabetes, hypertension and dyslipidemia were associated with an increasing CAC score in males and females, with diabetes being the strongest dichotomous risk factor (p<0.001 for both). These results were echoed in quantile regression, where diabetes was consistently the most important correlate with CAC extent in every quantile in both males and females. To a lesser extent, hypertension and dyslipidemia were also associated in the high CAC quantiles and the low CAC quantiles respectively.ConclusionIn addition to age and male sex in the total population, diabetes is the most important correlate of CAC extent in both sexes

Program Synthesis for Program Analysis

In this paper, we propose a unified framework for designing static analysers based on program synthesis. For this purpose, we identify a fragment of second-order logic with restricted quantification that is expressive enough to model numerous static analysis problems (e.g., safety proving, bug finding, termination and non-termination proving, refactoring). As our focus is on programs that use bit-vectors, we build a decision procedure for this fragment over finite domains in the form of a program synthesiser. We provide instantiations of our framework for solving a diverse range of program verification tasks such as termination, non-termination, safety and bug finding, superoptimisation and refactoring. Our experimental results show that our program synthesiser compares positively with specialised tools in each area as well as with general-purpose synthesisers

Late Holocene droughts in the Fertile Crescent recorded in a speleothem from northern Iraq

Droughts have had large impacts on past and present societies. High-resolution paleoclimate data are essential to place recent droughts in a meaningful historical context and to predict regional future changes with greater accuracy. Such records, however, are very scarce in the Middle East in general, and the Fertile Crescent in particular. Here we present a 2400 year long speleothem-based multiproxy record from Gejkar Cave in northern Iraq. Oxygen and carbon isotopes and magnesium are faithful recorders of effective moisture. The new Gejkar record not only shows that droughts in 1998–2000 and 2007–2010, which have been argued to be a contributing factor to Syrian civil war, were extreme compared to the current mean climate, but they were also superimposed on a long-term aridification trend that already started around or before 950 C.E. (Common Era). This long-term trend is not captured by tree ring records and climate models, emphasizing the importance of using various paleoclimate proxy data to evaluate and improve climate models and to correctly inform policy makers about future hydroclimatic changes in this drought-prone region