Novel views on endotyping asthma, its remission, and COPD

The chapters presented in this thesis provide an overview of what is known about asthma remission, further characterize of complete asthma remission, elaborate on the asthma- obesity complexity, apply cutting edge techniques to endotype asthma and COPD as well as novel devices to analyze airway remodeling and small airways dysfunction. Various conclusions have been made: I. In order to elucidate the pathophysiological state of asthma remission, future studies should focus on complete asthma remission, since this phenomenon is likely to yield superior prognostic and scientific impact. This is of interest, since elucidation of the pathophysiology of asthma remission could potentially lead to new treatment options for asthma. II. To clearly predict asthma remission later in life, we need to integrate biomarkers with clinical features at asthma-onset. III. Measuring particles of exhaled air correlates with large, and indirectly, small airways parameters, in asthmatics, clinical-, complete asthma remission subjects, and healthy controls. IV. Transcriptomic bronchial cell typing (e.g. single-cell RNA-sequencing) characterizes the landscape of lung-resident structural and inflammatory cells and their interactions, enabling us to identify differences in proportions and transcriptional output of cells between asthmatics and healthy. V. Optical coherence tomography enables us to quantify extracellular matrix components in the airway wall, such as collagen. This now allows for future studies ‘in vivo’ to explore the clinical characteristics and the underlying pathobiology related to airway remodeling in asthma and asthma remission. VI. The asthma-obesity syndrome is a common combination of diseases with its own distinct pathophysiological processes. VII. There will presumably be no room for serum periostin in COPD clinical decision- making. VIII.Transcriptomic profiling can be implemented as a biomarker for COPD patient prognosis. Unavoidably, aforementioned conclusions lead to new questions and recommendations for future studies. These recommendations include: I. To expand our knowledge on asthma remission by implementing single-cell RNA-sequencing on blood samples, bronchial- and nasal brushes, and bronchial biopsies of subjects with clinical and complete asthma remission, while comparing to asthmatics and healthy controls. II. To test single-nucleus RNA-sequencing in the ARMSTRONG study. This method enables sequencing of frozen biopsy samples of former datasets, consequently extending the number of subjects. III. To analyze exhaled, aberrant proteins linked to asthma, instead of merely counting exhaled particles. IV. To compare metabolomic breathprints of various asthma severities. V. To introduce novel methods in small airways disease-phenotypes in asthma, which enable visualization of airtrapping and gas exchange, such as functional MRI. VI. To study the effects of leptin and adiponectin in the asthma-obesity syndrome. Specifying the eligibility for bariatric surgery in patients with severe asthma and morbid obesity, in order to treat this phenotype more safely. VII. To analyze the presence of airway remodeling – defined by optical coherence tomography and histological parameters - in complete and clinical asthma remission, compared to asthmatics and healthy controls. VIII.To correlate optical coherence tomography-defined airway wall remodeling parameters with both fixed airway obstruction and single-cell RNA sequencing inflammatory cell types or proportions

Genetic Variation in Spatio-Temporal Confined USA300 Community-Associated MRSA Isolates: A Shift from Clonal Dispersion to Genetic Evolution?

NTRODUCTION: Community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) are increasingly isolated, with USA300-0114 being the predominant clone in the USA. Comparative whole genome sequencing of USA300 isolates collected in 2002, 2003 and 2005 showed a limited number of single nucleotide polymorphisms and regions of difference. This suggests that USA300 has undergone rapid clonal expansion without great genomic diversification. However, whole genome comparison of CA-MRSA has been limited to isolates belonging to USA300. The aim of this study was to compare the genetic repertoire of different CA-MRSA clones with that of HA-MRSA from the USA and Europe through comparative genomic hybridization (CGH) to identify genetic clues that may explain the successful and rapid emergence of CA-MRSA. MATERIALS AND METHODS: Hierarchical clustering based on CGH of 48 MRSA isolates from the community and nosocomial infections from Europe and the USA revealed dispersed clustering of the 19 CA-MRSA isolates. This means that these 19 CA-MRSA isolates do not share a unique genetic make-up. Only the PVL genes were commonly present in all CA-MRSA isolates. However, 10 genes were variably present among 14 USA300 isolates. Most of these genes were present on mobile elements. CONCLUSION: The genetic variation present among the 14 USA300 isolates is remarkable considering the fact that the isolates were recovered within one month and originated from a confined geographic area, suggesting continuous evolution of this clone

3D modelling of heating of thermionic cathodes by high-pressure arc plasmas

Numerical investigation of steady-state interaction of a high-pressure argon plasma with a cylindrical tungsten cathode is reported. A whole ‘zoo’ of very diverse modes of current transfer is revealed. Detailed results are given for the first five (three-dimensional) 3D spot modes, four of them branching off from the diffuse mode and one from the first axially symmetric spot mode. Divergences in the general pattern of solutions, which have been present in preceding works, are resolved. Hypotheses on stability of steady-state solutions, available in the literature, are analysed. It is found that these hypotheses provide an explanation of the fact that the transition between diffuse and spot modes is difficult to reproduce in the experiment but they do not explain the indication that it is the low-voltage branch of the first 3D spot mode that seems to occur in the experiment. Thus, the question of stability of steady-state solutions remains open: an accurate stability analysis, as well as additional experimental information is required.info:eu-repo/semantics/publishedVersio

New methods to analyse microarray data that partially lack a reference signal

BACKGROUND: Microarray-based Comparative Genomic Hybridisation (CGH) has been used to assess genetic variability between bacterial strains. Crucial for interpretation of microarray data is the availability of a reference to compare signal intensities to reliably determine presence or divergence each DNA fragment. However, the production of a good reference becomes unfeasible when microarrays are based on pan-genomes.When only a single strain is used as a reference for a multistrain array, the accessory gene pool will be partially represented by reference DNA, although these genes represent the genomic repertoire that can explain differences in virulence, pathogenicity or transmissibility between strains. The lack of a reference makes interpretation of the data for these genes difficult and, if the test signal is low, they are often deleted from the analysis. We aimed to develop novel methods to determine the presence or divergence of genes in a Staphylococcus aureus multistrain PCR product microarray-based CGH approach for which reference DNA was not available for some probes. RESULTS: In this study we have developed 6 new methods to predict divergence and presence of all genes spotted on a multistrain Staphylococcus aureus DNA microarray, published previously, including those gene spots that lack reference signals. When considering specificity and PPV (i.e. the false-positive rate) as the most important criteria for evaluating these methods, the method that defined gene presence based on a signal at least twice as high as the background and higher than the reference signal (method 4) had the best test characteristics. For this method specificity was 100% and 82% for MRSA252 (compared to the GACK method) and all spots (compared to sequence data), respectively, and PPV were 100% and 76% for MRSA252 (compared to the GACK method) and all spots (compared to sequence data), respectively. CONCLUSION: A definition of gene presence based on signal at least twice as high as the background and higher than the reference signal (method 4) had the best test characteristics, allowing the analysis of 6-17% more of the genes not present in the reference strain. This method is recommended to analyse microarray data that partially lack a reference signal

Survival in COPD patients treated with bronchoscopic lung volume reduction

Background and objective: Severe COPD patients can significantly benefit from bronchoscopic lung volume reduction (BLVR) treatments with coils or endobronchial valves. However, the potential impact of BLVR on survival is less understood. Therefore, our aim was to investigate the survival rate in patients who are evaluated for BLVR treatment and whether there is a difference in survival rate between patients who undergo BLVR treatment and patients who do not. Methods: We included patients with COPD who visited our hospital for a consultation evaluating their eligibility for BLVR treatment and who performed pulmonary function tests during this visit. Furthermore, vital status was verified. Results: In total 1471 patients were included (63% female, mean age 61 years). A total of 531 patients (35%) died during follow-up and the median survival time of the total population was 2694 days (95% confidence interval(CI) 2462–2926) which is approximately 7.4 years. The median survival time of patients who were treated with BLVR was significantly longer compared to patients who were not treated with BLVR (3133 days versus 2503 days, p < 0.001), and BLVR was found to be an independent predictor of survival when adjusting for other survival-influencing factors such as age, gender or severity of disease. Conclusions: Our results suggest that bronchoscopically reducing lung volume in patients with severe hyperinflation may lead to a survival benefit for a population with a severely reduced life expectancy

Long-acting dual bronchodilator therapy (indacaterol/glycopyrronium) versus nebulized short-acting dual bronchodilator (salbutamol/ipratropium) in chronic obstructive pulmonary disease:A double-blind, randomized, placebo-controlled trial

Introduction: Most guidelines recommend long-acting bronchodilators over short-acting bronchodilators for patients with chronic obstructive pulmonary disease (COPD). The available evidence for the guidelines was based on dry powder or pressurized metered dose inhalers, but not nebulizations. Nevertheless, there is considerable, poorly evidenced based, use of short acting nebulized bronchodilators. Methods: This was an investigator initiated, randomized, active controlled, cross-over, double-blind and double-dummy single centre study in patients with stable COPD. The active comparators were indacaterol/glycopyrronium 110/50 μg as Ultibro® via Breezhaler® (IND/GLY) and salbutamol/ipratropium 2,5/0,5 mg via air driven nebulization (SAL/IPR), both given as a single dose on separate days. The primary end point was the area under the FEV1 curve from baseline till 6 h. Secondary end points included change in Borg dyspnoea score, adverse events and change in hyperinflation measured by the inspiratory capacity. Results: A total of 33 COPD patients completed the trial and were evaluable, most of them were ex-smokers. The difference between the tested regimens for the primary endpoint, FEV1 AUC 0–6 h, 2965 ± 1544 mL (mean ± SD) for IND/GLY versus 3513 ± 1762 mL for SAL/IPR, was not significant (P = 0.08). The peak in FEV1 was higher and was reached faster with SAL/IPR compared to IND/GLY. No other significant differences were detected for the secondary endpoints including the Borg score, or adverse events. Conclusion: Among patients with stable COPD, dry powder long-acting single inhalation of a LABA and a LAMA (IND/GLY) was not superior compared to nebulized short-acting salbutamol plus ipratropium (SAL/IPR) in its bronchodilating effects over 6 h.The effects of the nebulization kicked in faster and peaked higher. The observed differences may be caused by the difference in dosing between the two regimens. The improvement in Borg dyspnoea score did not favour the nebulization. Long-term outcomes were not assessed in this study

Supershear bursts in the propagation of a tensile crack in linear elastic material

Since the early years of the linear elastic theory of fracture [linear elastic fracture mechanics (LEFM)], scientists have sought to understand and predict how fast cracks grow in a material or slip fronts propagate along faults. While shear cracks can travel faster than the shear wave speed, the Rayleigh wave speed is the limiting speed theoretically predicted for tensile failure. This work uncovers the existence of supershear episodes in the tensile (mode I) rupture of linearly elastic materials beyond the maximum allowable (sub-Rayleigh) speed predicted by the classical theory of dynamic fracture. While the admissible rupture speeds predicted by LEFM are verified for smooth crack fronts, we present numerically how a supershear burst can emerge from a discontinuity in crack front curvature. Using a spectral formulation of the three-dimensional elastodynamic equations coupled with a cohesive model of fracture, we study how these short-lived bursts create shock waves persisting far from the discontinuity site. This study provides insight on crack front instabilities present in the rapid tensile failure of brittle materials due to large distortions of the rupture front