The Airway Microbiota in Cystic Fibrosis: A Complex Fungal and Bacterial Community—Implications for Therapeutic Management

International audienceBackground Given the polymicrobial nature of pulmonary infections in patients with cystic fibrosis (CF), it is essential to enhance our knowledge on the composition of the microbial community to improve patient management. In this study, we developed a pyrosequencing approach to extensively explore the diversity and dynamics of fungal and prokaryotic populations in CF lower airways. Methodology and Principal Findings Fungi and bacteria diversity in eight sputum samples collected from four adult CF patients was investigated using conventional microbiological culturing and high-throughput pyrosequencing approach targeting the ITS2 locus and the 16S rDNA gene. The unveiled microbial community structure was compared to the clinical profile of the CF patients. Pyrosequencing confirmed recently reported bacterial diversity and observed complex fungal communities, in which more than 60% of the species or genera were not detected by cultures. Strikingly, the diversity and species richness of fungal and bacterial communities was significantly lower in patients with decreased lung function and poor clinical status. Values of Chao1 richness estimator were statistically correlated with values of the Shwachman-Kulczycki score, body mass index, forced vital capacity, and forced expiratory volume in 1 s (p = 0.046, 0.047, 0.004, and 0.001, respectively for fungal Chao1 indices, and p = 0.010, 0.047, 0.002, and 0.0003, respectively for bacterial Chao1 values). Phylogenetic analysis showed high molecular diversities at the sub-species level for the main fungal and bacterial taxa identified in the present study. Anaerobes were isolated with Pseudomonas aeruginosa, which was more likely to be observed in association with Candida albicans than with Aspergillus fumigatus

On the refactoring of activity labels in business process models

Large corporations increasingly utilize business process models for documenting and redesigning their operations. The extent of such modeling initiatives with several hundred models and dozens of often hardly trained modelers calls for automated quality assurance. While formal properties of control flow can easily be checked by existing tools, there is a notable gap for checking the quality of the textual content of models, in particular, its activity labels. In this paper, we address the problem of activity label quality in business process models. We designed a technique for the recognition of labeling styles, and the automatic refactoring of labels with quality issues. More specifically, we developed a parsing algorithm that is able to deal with the shortness of activity labels, which integrates natural language tools like WordNet and the Stanford Parser. Using three business process model collections from practice with differing labeling style distributions, we demonstrate the applicability of our technique. In comparison to a straightforward application of standard natural language tools, our technique provides much more stable results. As an outcome, the technique shifts the boundary of process model quality issues that can be checked automatically from syntactic to semantic aspects