Double differential cross sections for electron ejection from helium by fast protons.

Measurements of the angular and energy distributions of electrons ejected from helium atoms by protons with energies between 20 and 100 keV are presented in tabular and graphical form. The electron energy range is between 5 and 100 eV and the angular range is between 0 and 100 degrees. The distributions have been converted to double differential cross sections by normalisation against other published data. An analysis of the accuracy of the results is presented

Population genetics of trypanosoma brucei rhodesiense: clonality and diversity within and between foci

African trypanosomes are unusual among pathogenic protozoa in that they can undergo their complete morphological life cycle in the tsetse fly vector with mating as a non-obligatory part of this development. Trypanosoma brucei rhodesiense, which infects humans and livestock in East and Southern Africa, has classically been described as a host-range variant of the non-human infective Trypanosoma brucei that occurs as stable clonal lineages. We have examined T. b. rhodesiense populations from East (Uganda) and Southern (Malawi) Africa using a panel of microsatellite markers, incorporating both spatial and temporal analyses. Our data demonstrate that Ugandan T. b. rhodesiense existed as clonal populations, with a small number of highly related genotypes and substantial linkage disequilibrium between pairs of loci. However, these populations were not stable as the dominant genotypes changed and the genetic diversity also reduced over time. Thus these populations do not conform to one of the criteria for strict clonality, namely stability of predominant genotypes over time, and our results show that, in a period in the mid 1990s, the previously predominant genotypes were not detected but were replaced by a novel clonal population with limited genetic relationship to the original population present between 1970 and 1990. In contrast, the Malawi T. b. rhodesiense population demonstrated significantly greater diversity and evidence for frequent genetic exchange. Therefore, the population genetics of T. b. rhodesiense is more complex than previously described. This has important implications for the spread of the single copy T. b. rhodesiense gene that allows human infectivity, and therefore the epidemiology of the human disease, as well as suggesting that these parasites represent an important organism to study the influence of optional recombination upon population genetic dynamics

Discovery of mating in the major African livestock pathogen Trypanosoma congolense

The protozoan parasite, Trypanosoma congolense, is one of the most economically important pathogens of livestock in Africa and, through its impact on cattle health and productivity, has a significant effect on human health and well being. Despite the importance of this parasite our knowledge of some of the fundamental biological processes is limited. For example, it is unknown whether mating takes place. In this paper we have taken a population genetics based approach to address this question. The availability of genome sequence of the parasite allowed us to identify polymorphic microsatellite markers, which were used to genotype T. congolense isolates from livestock in a discrete geographical area of The Gambia. The data showed a high level of diversity with a large number of distinct genotypes, but a deficit in heterozygotes. Further analysis identified cryptic genetic subdivision into four sub-populations. In one of these, parasite genotypic diversity could only be explained by the occurrence of frequent mating in T. congolense. These data are completely inconsistent with previous suggestions that the parasite expands asexually in the absence of mating. The discovery of mating in this species of trypanosome has significant consequences for the spread of critical traits, such as drug resistance, as well as for fundamental aspects of the biology and epidemiology of this neglected but economically important pathogen

VLT/FORS2 comparative transmission spectroscopy II: confirmation of a cloud-deck and Rayleigh scattering in WASP-31b, but no potassium?

This is the author accepted manuscript. The final version is available from OUP via the DOI in this record.We present transmission spectroscopy of the hot-Jupiter WASP-31b using FORS2 on the VLT during two primary transits. The observations cover a wavelength range of ≈400–840 nm. The light curves are corrupted by significant systematics, but these were to first order invariant with wavelength and could be removed using a commonmode correction derived from the white light curves. We reach a precision in the transit depth of ≈140 ppm in 15 nm bins, although the precision varies significantly over the wavelength range. Our FORS2 observations confirm the cloud-deck previously inferred using HST/STIS. We also re-analyse the HST/STIS data using a Gaussian process model, finding excellent agreement with earlier measurements. We reproduce the Rayleigh scattering signature at short wavelengths (. 5300 ˚A) and the cloud-deck at longer wavelengths. However, our FORS2 observations appear to rule out the large potassium feature previously detected using STIS, yet it is recovered from the HST/STIS data, although with reduced amplitude and significance (≈ 2.5σ). The discrepancy between our results and the earlier STIS detection of potassium (≈ 4.3σ) is either a result of telluric contamination of the ground-based observations, or an underestimate of the uncertainties for narrow-band features in HST/STIS when using linear basis models to account for the systematics. Our results further demonstrate the use of ground-based multi-object spectrographs for the study of exoplanet atmospheres, and highlight the need for caution in our interpretation of narrow-band features in low-resolution spectra of hot-Jupiters.This work is based on observations collected at the European Organisation for Astronomical Research in the Southern Hemisphere under ESO programme 096.C-0765. N. P. G. gratefully acknowledges support from the Royal Society in the form of a University Research Fellowship. N. N, D. K. S, and T. M. E. acknowledge funding from the European Research Council under the European Unions Seventh Framework Programme (FP7/2007-2013) / ERC grant agreement no. 336792. J. K. B. is supported by a Royal Astronomical Society Research Fellowship. P.A.W. acknowledges the support of the French Agence Nationale de la Recherche (ANR), under program ANR-12-BS05-0012 ‘Exo-Atmos’. We are grateful to the developers of the NumPy, SciPy, Matplotlib, iPython and Astropy packages, which were used extensively in this work (Jones et al. 01 ; Hunter 2007; P´erez & Granger 2007; Astropy Collaboration et al. 2013)

VLT/FORS2 comparative transmission spectroscopy II: Confirmation of a cloud deck and Rayleigh scattering in WASP-31b, but no potassium?

We present transmission spectroscopy of the hot-Jupiter WASP-31b using the FOcal Reducer and low dispersion Spectrograph 2 (FORS2) on the Very Large Telescope during two primary transits. The observations cover a wavelength range of ≈400–840 nm. The light curves are corrupted by significant systematics, but these were to first-order invariant with wavelength and could be removed using a common-mode correction derived from the white light curves. We reach a precision in the transit depth of ≈140 ppm in 15 nm bins, although the precision varies significantly over the wavelength range. Our FORS2 observations confirm the cloud deck previously inferred using Hubble Space Telescope (HST)/Space Telescope Imaging Spectrograph (STIS). We also re-analyse the HST/STIS data using a Gaussian process model, finding excellent agreement with earlier measurements. We reproduce the Rayleigh scattering signature at short wavelengths (5300 Å) and the cloud deck at longer wavelengths. However, our FORS2 observations appear to rule out the large potassium feature previously detected using STIS, yet it is recovered from the HST/STIS data, although with reduced amplitude and significance (≈2.5σ ). The discrepancy between our results and the earlier STIS detection of potassium (≈4.3σ ) is either a result of telluric contamination of the ground-based observations, or an underestimate of the uncertainties for narrow-band features in HST/STIS when using linear basis models to account for the systematics. Our results further demonstrate the use of ground-based multi-object spectrographs for the study of exoplanet atmospheres, and highlight the need for caution in our interpretation of narrow-band features in low-resolution spectra of hot Jupiters

A combined transmission spectrum of the Earth-sized exoplanets TRAPPIST-1 b and c

Three Earth-sized exoplanets were recently discovered close to the habitable zone of the nearby ultracool dwarf star TRAPPIST-1. The nature of these planets has yet to be determined, since their masses remain unmeasured and no observational constraint is available for the planetary population surrounding ultracool dwarfs, of which the TRAPPIST-1 planets are the first transiting example. Theoretical predictions span the entire atmospheric range from depleted to extended hydrogen-dominated atmospheres. Here, we report a space-based measurement of the combined transmission spectrum of the two inner planets made possible by a favorable alignment resulting in their simultaneous transits on 04 May 2016. The lack of features in the combined spectrum rules out cloud-free hydrogen-dominated atmospheres for each planet at 10-$\sigma$ levels; TRAPPIST-1 b and c are hence unlikely to harbor an extended gas envelope as they lie in a region of parameter space where high-altitude cloud/haze formation is not expected to be significant for hydrogen-dominated atmospheres. Many denser atmospheres remain consistent with the featureless transmission spectrum---from a cloud-free water vapour atmosphere to a Venus-like atmosphere.Comment: Early release to inform further the upcoming review of HST's Cycle 24 proposal

Ground-Based Transmission Spectroscopy with FORS2: A featureless optical transmission spectrum and detection of H2O for the ultra-hot Jupiter WASP-103b

We report ground-based transmission spectroscopy of the highly irradiated and ultra-short period hot-Jupiter WASP-103b covering the wavelength range ≈ 400 – 600 nm using the FORS2 instrument on the Very Large Telescope. The light curves show significant time-correlated noise which is mainly invariant in wavelength and which we model using a Gaussian process. The precision of our transmission spectrum is improved by applying a common-mode correction derived from the white light curve, reaching typical uncertainties in transit depth of ≈ 2 × 10−4 in wavelength bins of 15 nm. After correction for flux contamination from a blended companion star, our observations reveal a featureless spectrum across the full range of the FORS2 observations and we are unable to confirm the Na absorption previously inferred using Gemini/GMOS or the strong Rayleigh scattering observed using broad-band light curves. We performed a Bayesian atmospheric retrieval on the full optical-infrared transmission spectrum using the additional data from Gemini/GMOS, HST/WFC3 and Spitzer observations and recover evidence for H2O absorption at the 4.0 σ level. However, our observations are not able to completely rule out the presence of Na, which is found at 2.0 σ in our retrievals. This may in part be explained by patchy/inhomogeneous clouds or hazes damping any absorption features in our FORS2 spectrum, but an inherently small scale height also makes this feature challenging to probe from the ground. Our results nonetheless demonstrate the continuing potential of ground-based observations for investigating exoplanet atmospheres and emphasise the need for the application of consistent and robust statistical techniques to low-resolution spectra in the presence of instrumental systematics

A functional genomic model for predicting prognosis in idiopathic pulmonary fibrosis

Background: The course of disease for patients with idiopathic pulmonary fibrosis (IPF) is highly heterogeneous. Prognostic models rely on demographic and clinical characteristics and are not reproducible. Integrating data from genomic analyses may identify novel prognostic models and provide mechanistic insights into IPF. Methods: Total RNA of peripheral blood mononuclear cells was subjected to microarray profiling in a training (45 IPF individuals) and two independent validation cohorts (21 IPF/10 controls, and 75 IPF individuals, respectively). To identify a gene set predictive of IPF prognosis, we incorporated genomic, clinical, and outcome data from the training cohort. Predictor genes were selected if all the following criteria were met: 1) Present in a gene co-expression module from Weighted Gene Co-expression Network Analysis (WGCNA) that correlated with pulmonary function (p 1.5 and false discovery rate (FDR) < 2 %; and 3) Predictive of mortality (p < 0.05) in univariate Cox regression analysis. "Survival risk group prediction" was adopted to construct a functional genomic model that used the IPF prognostic predictor gene set to derive a prognostic index (PI) for each patient into either high or low risk for survival outcomes. Prediction accuracy was assessed with a repeated 10-fold cross-validation algorithm and independently assessed in two validation cohorts through multivariate Cox regression survival analysis. Results: A set of 118 IPF prognostic predictor genes was used to derive the functional genomic model and PI. In the training cohort, high-risk IPF patients predicted by PI had significantly shorter survival compared to those labeled as low-risk patients (log rank p < 0.001). The prediction accuracy was further validated in two independent cohorts (log rank p < 0.001 and 0.002). Functional pathway analysis revealed that the canonical pathways enriched with the IPF prognostic predictor gene set were involved in T-cell biology, including iCOS, T-cell receptor, and CD28 signaling. Conclusions: Using supervised and unsupervised analyses, we identified a set of IPF prognostic predictor genes and derived a functional genomic model that predicted high and low-risk IPF patients with high accuracy. This genomic model may complement current prognostic tools to deliver more personalized care for IPF patients

Trichotillometry: the reliability and practicality of hair pluckability as a method of nutritional assessment

<p>Abstract</p> <p>Background</p> <p>A nutritional assessment method that is quick and easy to conduct would be extremely useful in a complex emergency, where currently there is no agreed practical and acceptable method. Hair pluckability has been suggested to be a useful method of assessing protein nutritional status. The aim was to investigate the reliability of the trichotillometer and to explore the effects of patient characteristics on hair epilation force.</p> <p>Methods</p> <p>Three observers plucked hair from twelve participants to investigate the within- and between-observer reliability. To investigate the effect of patient characteristics on hair pluckability, 12 black African and 12 white volunteers were recruited. Participants completed a short questionnaire to provide basic information on their characteristics and hair.</p> <p>Results</p> <p>Mean hair pluckability measurements for the 12 participants obtained by the three observers (39.5 g, 41.2 g and 32.7 g) were significantly different (p < 0.001). Significant variation between patients was also found (p < 0.001). None of the patient characteristics significantly affected hair pluckability, with the exception of age, although this relationship was not consistent.</p> <p>Conclusion</p> <p>Due to significant variation in measurements, hair pluckability does not appear to be a reliable method for assessing adult nutritional status. Hair pluckability could be a useful method of nutritional assessment in complex humanitarian emergencies but only if the reliability was improved.</p

Evaluating priority setting success in healthcare: a pilot study

<p>Abstract</p> <p>Background</p> <p>In healthcare today, decisions are made in the face of serious resource constraints. Healthcare managers are struggling to provide high quality care, manage resources effectively, and meet changing patient needs. Healthcare managers who are constantly making difficult resource decisions desire a way to improve their priority setting processes. Despite the wealth of existing priority setting literature (for example, program budgeting and marginal analysis, accountability for reasonableness, the 'describe-evaluate-improve' strategy) there are still no tools to evaluate how healthcare resources are prioritised. This paper describes the development and piloting of a process to evaluate priority setting in health institutions. The evaluation process was designed to examine the procedural and substantive dimensions of priority setting using a multi-methods approach, including a staff survey, decision-maker interviews, and document analysis.</p> <p>Methods</p> <p>The evaluation process was piloted in a mid-size community hospital in Ontario, Canada while its leaders worked through their annual budgeting process. Both qualitative and quantitative methods were used to analyze the data.</p> <p>Results</p> <p>The evaluation process was both applicable to the context and it captured the budgeting process. In general, the pilot test provided support for our evaluation process and our definition of success, (i.e., our conceptual framework).</p> <p>Conclusions</p> <p>The purpose of the evaluation process is to provide a simple, practical way for an organization to better understand what it means to achieve success in its priority setting activities and identify areas for improvement. In order for the process to be used by healthcare managers today, modification and contextualization of the process are anticipated. As the evaluation process is applied in more health care organizations or applied repeatedly in an organization, it may become more streamlined.</p