Bayesian reconstruction of Mycobacterium tuberculosis transmission networks in a high incidence area over two decades in Malawi reveals associated risk factors and genomic variants.

Understanding host and pathogen factors that influence tuberculosis (TB) transmission can inform strategies to eliminate the spread of Mycobacterium tuberculosis (Mtb). Determining transmission links between cases of TB is complicated by a long and variable latency period and undiagnosed cases, although methods are improving through the application of probabilistic modelling and whole-genome sequence analysis. Using a large dataset of 1857 whole-genome sequences and comprehensive metadata from Karonga District, Malawi, over 19 years, we reconstructed Mtb transmission networks using a two-step Bayesian approach that identified likely infector and recipient cases, whilst robustly allowing for incomplete case sampling. We investigated demographic and pathogen genomic variation associated with transmission and clustering in our networks. We found that whilst there was a significant decrease in the proportion of infectors over time, we found higher transmissibility and large transmission clusters for lineage 2 (Beijing) strains. By performing evolutionary convergence testing (phyC) and genome-wide association analysis (GWAS) on transmitting versus non-transmitting cases, we identified six loci, PPE54, accD2, PE_PGRS62, rplI, Rv3751 and Rv2077c, that were associated with transmission. This study provides a framework for reconstructing large-scale Mtb transmission networks. We have highlighted potential host and pathogen characteristics that were linked to increased transmission in a high-burden setting and identified genomic variants that, with validation, could inform further studies into transmissibility and TB eradication

Condensation of Excitons in Cu2O at Ultracold Temperatures: Experiment and Theory

We present experiments on the luminescence of excitons confined in a potential trap at milli-Kelvin bath temperatures under cw-excitation. They reveal several distinct features like a kink in the dependence of the total integrated luminescence intensity on excitation laser power and a bimodal distribution of the spatially resolved luminescence. Furthermore, we discuss the present state of the theoretical description of Bose-Einstein condensation of excitons with respect to signatures of a condensate in the luminescence. The comparison of the experimental data with theoretical results with respect to the spatially resolved as well as the integrated luminescence intensity shows the necessity of taking into account a Bose-Einstein condensed excitonic phase in order to understand the behaviour of the trapped excitons.Comment: 41 pages, 23 figure

Characterization of deposits formed on diesel injectors in field test and from thermal oxidative degradation of n-hexadecane in a laboratory reactor

Solid deposits from commercially available high-pressure diesel injectors (HPDI) were analyzed to study the solid deposition from diesel fuel during engine operation. The structural and chemical properties of injector deposits were compared to those formed from the thermal oxidative stressing of a diesel fuel range model compound, n-hexadecane at 160°C and 450 psi for 2.5 h in a flow reactor. Both deposits consist of polyaromatic compounds (PAH) with oxygen moieties. The similarities in structure and composition of the injector deposits and n-hexadecane deposits suggest that laboratory experiments can simulate thermal oxidative degradation of diesel in commercial injectors. The formation of PAH from n-hexadecane showed that aromatization of straight chain alkanes and polycondensation of aromatic rings was possible at temperatures as low as 160°C in the presence of oxygen. A mechanism for an oxygen-assisted aromatization of cylcoalkanes is proposed

Direct observation of active material concentration gradients and crystallinity breakdown in LiFePO4 electrodes during charge/discharge cycling of lithium batteries

The phase changes that occur during discharge of an electrode comprised of LiFePO4, carbon, and PTFE binder have been studied in lithium half cells by using X-ray diffraction measurements in reflection geometry. Differences in the state of charge between the front and the back of LiFePO4 electrodes have been visualized. By modifying the X-ray incident angle the depth of penetration of the X-ray beam into the electrode was altered, allowing for the examination of any concentration gradients that were present within the electrode. At high rates of discharge the electrode side facing the current collector underwent limited lithium insertion while the electrode as a whole underwent greater than 50% of discharge. This behavior is consistent with depletion at high rate of the lithium content of the electrolyte contained in the electrode pores. Increases in the diffraction peak widths indicated a breakdown of crystallinity within the active material during cycling even during the relatively short duration of these experiments, which can also be linked to cycling at high rate

Identifying mixed Mycobacterium tuberculosis infections from whole genome sequence data.

BACKGROUND: Mixed, polyclonal Mycobacterium tuberculosis infection occurs in natural populations. Developing an effective method for detecting such cases is important in measuring the success of treatment and reconstruction of transmission between patients. Using whole genome sequence (WGS) data, we assess two methods for detecting mixed infection: (i) a combination of the number of heterozygous sites and the proportion of heterozygous sites to total SNPs, and (ii) Bayesian model-based clustering of allele frequencies from sequencing reads at heterozygous sites. RESULTS: In silico and in vitro artificially mixed and known pure M. tuberculosis samples were analysed to determine the specificity and sensitivity of each method. We found that both approaches were effective in distinguishing between pure strains and mixed infection where there was relatively high (> 10%) proportion of a minor strain in the mixture. A large dataset of clinical isolates (n = 1963) from the Karonga Prevention Study in Northern Malawi was tested to examine correlations with patient characteristics and outcomes with mixed infection. The frequency of mixed infection in the population was found to be around 10%, with an association with year of diagnosis, but no association with age, sex, HIV status or previous tuberculosis. CONCLUSIONS: Mixed Mycobacterium tuberculosis infection was identified in silico using whole genome sequence data. The methods presented here can be applied to population-wide analyses of tuberculosis to estimate the frequency of mixed infection, and to identify individual cases of mixed infections. These cases are important when considering the evolution and transmission of the disease, and in patient treatment

Vocal imitations and the identification of sound events

International audienceIt is commonly observed that a speaker vocally imitates a sound that she or he intends to communicate to an interlocutor. We report on an experiment that examined the assumption that vocal imitations can e ffectively communicate a referent sound, and that they do so by conveying the features necessary for the identifi cation of the referent sound event. Subjects were required to sort a set of vocal imitations of everyday sounds. The resulting clusters corresponded in most of the cases to the categories of the referent sound events, indicating that the imitations enabled the listeners to recover what was imitated. Furthermore, a binary decision tree analysis showed that a few characteristic acoustic features predicted the clusters. These features also predicted the classi fication of the referent sounds, but did not generalize to the categorization of other sounds. This showed that, for the speaker, vocally imitating a sound consists of conveying the acoustic features important for recognition, within the constraints of human vocal production. As such vocal imitations prove to be a phenomenon potentially useful to study sound identifi cation

Asteroids' physical models from combined dense and sparse photometry and scaling of the YORP effect by the observed obliquity distribution

The larger number of models of asteroid shapes and their rotational states derived by the lightcurve inversion give us better insight into both the nature of individual objects and the whole asteroid population. With a larger statistical sample we can study the physical properties of asteroid populations, such as main-belt asteroids or individual asteroid families, in more detail. Shape models can also be used in combination with other types of observational data (IR, adaptive optics images, stellar occultations), e.g., to determine sizes and thermal properties. We use all available photometric data of asteroids to derive their physical models by the lightcurve inversion method and compare the observed pole latitude distributions of all asteroids with known convex shape models with the simulated pole latitude distributions. We used classical dense photometric lightcurves from several sources and sparse-in-time photometry from the U.S. Naval Observatory in Flagstaff, Catalina Sky Survey, and La Palma surveys (IAU codes 689, 703, 950) in the lightcurve inversion method to determine asteroid convex models and their rotational states. We also extended a simple dynamical model for the spin evolution of asteroids used in our previous paper. We present 119 new asteroid models derived from combined dense and sparse-in-time photometry. We discuss the reliability of asteroid shape models derived only from Catalina Sky Survey data (IAU code 703) and present 20 such models. By using different values for a scaling parameter cYORP (corresponds to the magnitude of the YORP momentum) in the dynamical model for the spin evolution and by comparing synthetics and observed pole-latitude distributions, we were able to constrain the typical values of the cYORP parameter as between 0.05 and 0.6.Comment: Accepted for publication in A&A, January 15, 201

The small binary asteroid (939) Isberga

In understanding the composition and internal structure of asteroids, their density is perhaps the most diagnostic quantity. We aim here to characterize the surface composition, mutual orbit, size, mass, and density of the small main-belt binary asteroid (939) Isberga. For that, we conduct a suite of multi-technique observations, including optical lightcurves over many epochs, near-infrared spectroscopy, and interferometry in the thermal infrared. We develop a simple geometric model of binary systems to analyze the interferometric data in combination with the results of the lightcurve modeling. From spectroscopy, we classify Ibserga as a Sq-type asteroid, consistent with the albedo of 0.14$^{+0.09}_{-0.06}$ (all uncertainties are reported as 3-$\sigma$ range) we determine (average albedo of S-types is 0.197 $\pm$ 0.153, Pravec et al., 2012, Icarus 221, 365-387). Lightcurve analysis reveals that the mutual orbit has a period of 26.6304 $\pm$ 0.0001 h, is close to circular, and has pole coordinates within 7 deg. of (225, +86) in ECJ2000, implying a low obliquity of 1.5 deg. The combined analysis of lightcurves and interferometric data allows us to determine the dimension of the system and we find volume-equivalent diameters of 12.4$^{+2.5}_{-1.2}$ km and 3.6$^{+0.7}_{-0.3}$ km for Isberga and its satellite, circling each other on a 33 km wide orbit. Their density is assumed equal and found to be $2.91^{+1.72}_{-2.01}$ g.cm$^{-3}$, lower than that of the associated ordinary chondrite meteorites, suggesting the presence of some macroporosity, but typical of S-types of the same size range (Carry, 2012, P\&SS 73, 98-118). The present study is the first direct measurement of the size of a small main-belt binary. Although the interferometric observations of Isberga are at the edge of MIDI capabilities, the method described here is applicable to others suites of instruments (e.g, LBT, ALMA).Comment: 12 pages, 6 figures, 4 table