An international, multicentre evaluation and description of Burkholderia pseudomallei infection in cystic fibrosis

BACKGROUND: Several cases of Burkholderia pseudomallei infection in CF have been previously reported. We aimed to identify all cases globally, risk factors for acquisition, clinical consequences, and optimal treatment strategies. METHODS: We performed a literature search to identify all published cases of B. pseudomallei infection in CF. In addition we hand-searched respiratory journals, and contacted experts in infectious diseases and CF around the world. Supervising clinicians for identified cases were contacted and contemporaneous clinical data was requested. RESULTS: 25 culture-confirmed cases were identified. The median age at acquisition was 21 years, mean FEV(1) % predicted was 60 %, and mean BMI was 19.5 kg/m(2). The location of acquisition was northern Australia or south-east Asia for most. 19 patients (76 %) developed chronic infection, which was usually associated with clinical decline. Successful eradication strategies included a minimum of two weeks of intravenous ceftazidime, followed by a consolidation phase with trimethoprim/sulfamethoxazole, and this resulted in a higher chance of success when instituted early. Three cases of lung transplantation have been recorded in the setting of chronic B. pseudomallei infection. CONCLUSION: Chronic carriage of B. pseudomallei in patients with CF appears common after infection, in contrast to the non-CF population. This is often associated with an accelerated clinical decline. Lung transplantation has been performed in select cases of chronic B. pseudomallei infection. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12890-015-0109-9) contains supplementary material, which is available to authorized users

Protocols and Structures for Inference: A RESTful API for Machine Learning

Diversity in machine learning APIs (in both software toolkits and web services), works against realising machine learning’s full potential, making it difficult to draw on individual algorithms from different products or to compose multiple algorithms to solve complex tasks. This paper introduces the Protocols and Structures for Inference (PSI) service architecture and specification, which presents inferential entities—relations, attributes, learners and predictors—as RESTful web resources that are accessible via a common but flexible and extensible interface. Resources describe the data they ingest or emit using a variant of the JSON schema language, and the API has mechanisms to support non-JSON data and future extension of service features

Water diffusion in atmospherically relevant α-pinene secondary organic material

Secondary organic material (SOM) constitutes a large mass fraction of atmospheric aerosol particles. Understanding its impact on climate and air quality relies on accurate models of interactions with water vapour. Recent research shows that SOM can be highly viscous and can even behave mechanically like a solid, leading to suggestions that particles exist out of equilibrium with water vapour in the atmosphere. In order to quantify any kinetic limitation we need to know water diffusion coefficients for SOM, but this quantity has, until now, only been estimated and has not yet been measured. We have directly measured water diffusion coefficients in the water soluble fraction of α-pinene SOM between 240 and 280 K. Here we show that, although this material can behave mechanically like a solid, at 280 K water diffusion is not kinetically limited on timescales of 1 s for atmospheric-sized particles. However, diffusion slows as temperature decreases. We use our measured data to constrain a Vignes-type parameterisation, which we extend to lower temperatures to show that SOM can take hours to equilibrate with water vapour under very cold conditions. Our modelling for 100 nm particles predicts that under mid to upper tropospheric conditions radial inhomogeneities in water content produce a low viscosity surface region and more solid interior, with implications for heterogeneous chemistry and ice nucleation

Football-induced fatigue in hypoxia impairs repeated sprint ability and perceptual-cognitive skills

The present study investigated the effects of football-induced fatigue during hypoxia on RS and perceptual-cognitive skills. Ten male semi-professional football players underwent four sessions; a control session (0-m) to quantify RS in a non-fatigued state; and three further sessions at hypoxia (0-m;1500-m;3000-m) examining RS and perceptual-cognitive skill responses for a given physical workload. Anticipation and decision-making accuracy were obtained at the 30-min mark of each half. The mean number of trials (%) in which the player made the correct response was used for analysis. HR, TC, RPE and % saturation of O2 were measured during the warm-up, football-induced fatigue and RS test. It was found that HR, RPE and % saturation of O2 were different between conditions (P<0.05; ES=0.44-6.13). Further, RS were affected by football-induced fatigue for DC (4.8%; P=0.019; ES=0.68) and AV (5.5%; P=0.006; ES=0.79). In hypoxia, it was observed that football-induced fatigue decreased by 6.5% in DC, 6.3% in AV and 3.1% in PV at 1500-m compared to 0-m (P<0.05). Further significant changes were found at 3000-m compared to 0-m decreasing 12.8% in DC, 12.8% in AV and 6.2% in PV (P<0.0005). More pronounced declines in perceptual-cognitive skills were found as altitude increased (5.0-12.5 %; P<0.05; ES=1.17-2.41) and between both halves (5.3-6.7 %; P<0.05). The data demonstrates that the RS test was highly sensitive to fatigue and hypoxia for a given physical load. Simulated matches in hypoxia revealed larger decreases, when compared to normoxia in RS and perceptual-cognitive skills, highlighting the need for optimal acclimatisation strategies, including physical and technical preparation, prior to playing a

Improved annotation of 3' untranslated regions and complex loci by combination of strand-specific direct RNA sequencing, RNA-seq and ESTs

The reference annotations made for a genome sequence provide the framework for all subsequent analyses of the genome. Correct annotation is particularly important when interpreting the results of RNA-seq experiments where short sequence reads are mapped against the genome and assigned to genes according to the annotation. Inconsistencies in annotations between the reference and the experimental system can lead to incorrect interpretation of the effect on RNA expression of an experimental treatment or mutation in the system under study. Until recently, the genome-wide annotation of 3-prime untranslated regions received less attention than coding regions and the delineation of intron/exon boundaries. In this paper, data produced for samples in Human, Chicken and A. thaliana by the novel single-molecule, strand-specific, Direct RNA Sequencing technology from Helicos Biosciences which locates 3-prime polyadenylation sites to within +/- 2 nt, were combined with archival EST and RNA-Seq data. Nine examples are illustrated where this combination of data allowed: (1) gene and 3-prime UTR re-annotation (including extension of one 3-prime UTR by 5.9 kb); (2) disentangling of gene expression in complex regions; (3) clearer interpretation of small RNA expression and (4) identification of novel genes. While the specific examples displayed here may become obsolete as genome sequences and their annotations are refined, the principles laid out in this paper will be of general use both to those annotating genomes and those seeking to interpret existing publically available annotations in the context of their own experimental dataComment: 44 pages, 9 figure

p16 Mutation Spectrum in the Premalignant Condition Barrett's Esophagus

Background: Mutation, promoter hypermethylation and loss of heterozygosity involving the tumor suppressor gene p16 (CDKN2a/INK4a) have been detected in a wide variety of human cancers, but much less is known concerning the frequency and spectrum of p16 mutations in premalignant conditions. Methods and Findings: We have determined the p16 mutation spectrum for a cohort of 304 patients with Barrett’s esophagus, a premalignant condition that predisposes to the development of esophageal adenocarcinoma. Forty seven mutations were detected by sequencing of p16 exon 2 in 44 BE patients (14.5%) with a mutation spectrum consistent with that caused by oxidative damage and chronic inflammation. The percentage of patients with p16 mutations increased with increasing histologic grade. In addition, samples from 3 out of 19 patients (15.8%) who underwent esophagectomy were found to have mutations. Conclusions: The results of this study suggest the environment of the esophagus in BE patients can both generate an

Von Bezold assimilation effect reverses in stereoscopic conditions

Lightness contrast and lightness assimilation are opposite phenomena: in contrast, grey targets appear darker when bordering bright surfaces (inducers) rather than dark ones; in assimilation, the opposite occurs. The question is: which visual process favours the occurrence of one phenomenon over the other? Researchers provided three answers to this question. The first asserts that both phenomena are caused by peripheral processes; the second attributes their occurrence to central processes; and the third claims that contrast involves central processes, whilst assimilation involves peripheral ones. To test these hypotheses, an experiment on an IT system equipped with goggles for stereo vision was run. Observers were asked to evaluate the lightness of a grey target, and two variables were systematically manipulated: (i) the apparent distance of the inducers; and (ii) brightness of the inducers. The retinal stimulation was kept constant throughout, so that the peripheral processes remained the same. The results show that the lightness of the target depends on both variables. As the retinal stimulation was kept constant, we conclude that central mechanisms are involved in both lightness contrast and lightness assimilation

Fly-Tox: A panel of transgenic flies expressing pest and pollinator cytochrome P450s

This is the final version. Available from the publisher via the DOI in this record.There is an on-going need to develop new insecticides that are not compromised by resistance and that have improved environmental profiles. However, the cost of developing novel compounds has increased significantly over the last two decades. This is in part due to increased regulatory requirements, including the need to screen both pest and pollinator insect species to ensure that pre-existing resistance will not hamper the efficacy of a new insecticide via cross-resistance, or adversely affect non-target insect species. To add to this problem the collection and maintenance of toxicologically relevant pest and pollinator species and strains is costly and often difficult. Here we present Fly-Tox, a panel of publicly available transgenic Drosophila melanogaster lines each containing one or more pest or pollinator P450 genes that have been previously shown to metabolise insecticides. We describe the range of ways these tools can be used, including in predictive screens to avoid pre-existing cross-resistance, to identify potential resistance-breaking inhibitors, in the initial assessment of potential insecticide toxicity to bee pollinators, and identifying harmful pesticide-pesticide interactions.European Research Council (ERC)European Union's Horizon 2020 research and innovation programmeBiotechnology and Biological Sciences Research Council (BBSRC