Qualitative and quantitative comparison of allergen component-specific to birch and grass analyzed by ImmunoCAP assay and Euroline immunoblot test.

Summary: Background.In the diagnostic work up of allergy, determining allergen component-specific immunoglobulin E (IgE) is important for diagnosis, prognosis and choice of treatment. The purpose of this study was to evaluate the performance of the immunoblotting assay (Euroline) in detection of IgE antibodies against timothy grass and birch pollen allergen components compared to fluorescent enzyme assay (ImmunoCAP, Phadia 250). Methods. A total of 128 serum samples from patients allergic to timothy grass and birch pollen were analysed. The levels of IgE antibodies to timothy grass and birch pollen were measured using Euroline DPA-Dx pollen 1 and ImmunoCAP assay. The two methods were then compared on binary (positive vs negative), semi-quantitative (IgE classes) and quantitative (concentration) levels. The two methods were also compared to results from skin prick testing. Results. The Euroline method showed a positive percentage agreement of 93% and negative percentage agreement of 94% with an overall accuracy of 94% when compared to ImmunoCAP. Kappa analysis showed moderate strength of agreement between the methods in determining IgE classes for 7/11 components tested. All components showed a positive correlation when analysed using Spearman's rank correlation. Conclusions. Overall, we found that there is good correlation between the Euroline and ImmunoCAP methods in measuring IgE sensitization.

The relation between age and airway epithelial barrier function.

BACKGROUND: The prevalence of age-associated diseases, such as chronic obstructive pulmonary disease (COPD), is increasing as the average life expectancy increases around the world. We previously identified a gene signature for ageing in the human lung which included genes involved in apical and tight junction assembly, suggesting a role for airway epithelial barrier dysfunction with ageing. AIM: To investigate the association between genes involved in epithelial barrier function and age both in silico and in vitro in the airway epithelium. METHODS: We curated a gene signature of 274 genes for epithelial barrier function and tested the association with age in two independent cohorts of bronchial brushings from healthy individuals with no respiratory disease, using linear regression analysis (FDR < 0.05). Protein-protein interactions were identified using STRING©. The barrier function of primary bronchial epithelial cells at air-liquid interface and CRISPR-Cas9-induced knock-down of target genes in human bronchial 16HBE14o-cells was assessed using Trans epithelial resistance (TER) measurement and Electric cell-surface impedance sensing (ECIS) respectively. RESULTS: In bronchial brushings, we found 55 genes involved in barrier function to be significantly associated with age (FDR < 0.05). EPCAM was most significantly associated with increasing age and TRPV4 with decreasing age. Protein interaction analysis identified CDH1, that was negatively associated with higher age, as potential key regulator of age-related epithelial barrier function changes. In vitro, barrier function was lower in bronchial epithelial cells from subjects > 45 years of age and significantly reduced in CDH1-deficient 16HBE14o-cells. CONCLUSION: The significant association between genes involved in epithelial barrier function and age, supported by functional studies in vitro, suggest a role for epithelial barrier dysfunction in age-related airway disease.

The Microbiome in Bronchial Biopsies from Smokers and Ex-Smokers with Stable COPD - A Metatranscriptomic Approach.

Current knowledge about the respiratory microbiome is mainly based on 16S ribosomal RNA gene sequencing. Newer sequencing approaches, such as metatranscriptomics, offer the technical ability to measure the viable microbiome response to environmental conditions such as smoking as well as to explore its functional role by investigating host-microbiome interactions. However, knowledge about its feasibility in respiratory microbiome research, especially in lung biopsies, is still very limited. RNA sequencing was performed in bronchial biopsies from clinically stable smokers (n = 5) and ex-smokers (n = 6) with COPD not using (inhaled) steroids. The Trinity assembler was used to assemble non-human reads in order to allow unbiased taxonomical and microbial transcriptional analyses. Subsequently, host-microbiome interactions were analyzed based on associations with host transcriptomic data. Ultra-low levels of microbial mass (0.009%) were identified in the RNA-seq data. Overall, no differences were identified in microbiome diversity or transcriptional profiles of microbial communities or individual microbes between COPD smokers and ex-smokers in the initial test dataset as well as a larger replication dataset. We identified an upregulated host gene set, related to the simultaneous presence of Bradyrhizobium, Roseomonas, Brevibacterium.spp., which were related to PERK-mediated unfolded protein response (UPR) and expression of the microRNA-155-5p. Our results show that metatranscriptomic profiling in bronchial biopsy samples from stable COPD patients yields ultra-low levels of microbial mass. Further, this study illustrates the potential of using transcriptional profiling of the host and microbiome to gain more insight into their interaction in the airways.

Do overweight/obesity and low levels of leisure-time vigorous physical activity moderate the effect of occupational physical activity on self-rated health of construction workers?

PURPOSE: To investigate the combined effects of occupational physical activity (OPA) and either overweight/obesity or low levels of leisure-time vigorous physical activity (LTVPA) on self-rated health. METHODS: A longitudinal study was performed among 29,987 construction workers with complete data on 2 Workers' Health Surveillance Programs during 2010-2018. Self-reported OPA involved strenuous work postures and manual material handling. Low level of LTVPA was defined as self-reported vigorous activity for less than three times per week lasting at least 20 min per session. Overweight and obesity were based on Body Mass Index (BMI) (25.0 ≤ BMI < 30.0 kg/m2 and BMI ≥ 30.0 kg/m2, respectively) using measured body height and weight. Self-rated health was measured using a single item question. Logistic regression analysis was used to investigate the associations between the separate risk factors at baseline and self-rated health at follow-up. The combined effects of demanding OPA and either overweight/obesity or low level of LTVPA on self-rated health were analyzed using the relative excess risk due to interaction (RERI). RESULTS: Mean follow-up duration was 31.7 (SD = 14.9) months. Construction workers with strenuous work postures (OR 1.35 95% CI 1.25-1.46), manual material handling (OR 1.29 95% CI 1.19-1.40), obesity (OR 1.31 95% CI 1.17-1.47) and low LTVPA (OR 1.13 95% CI 1.01-1.25) were more likely to report poor self-rated health at follow-up. No statistically significant interaction effects were found for OPA and obesity or low LTVPA. CONCLUSIONS: OPA, obesity and low level of LTVPA were separate risk factors for poor self-rated health, but did not appear to have a synergistic effect.

Pre-treatment allergen-specific IgE analysis and outcomes of allergen immunotherapy.

Summary: Background. Patients show varied results to allergen immunotherapy (AIT. The reason for this variability is unclear. Objective. To describe the relationship between AIT efficacy and demographic characteristics, as well as pre-treatment plasma levels of specific IgE-antibodies to grass and birch pollen. Methods. A retrospective study was performed based on medical records of 128 patients who received AIT. The patients completed a questionnaire and pre-AIT plasma levels of allergen-specific IgE to grass and birch pollen were measured using EUROLINE DPA-Dx pollen 1 method. Results. Seventy percent of patients classified their allergic symptoms as less severe after AIT. Twenty-seven percent had received AIT targeting only grass pollen, 19% targeting only birch pollen, and 55% targeting both grass and birch. A total of 35 different IgE profiles were found across our study population. On comparison of the demographic characteristics and concentration of allergen-specific IgE-antibodies, no statistically significant differences could be found.Conclusions. The majority of patients rated their allergic symptoms as less severe after AIT. No clear relationship could be demonstrated between pre-treatment allergen-specific IgE concentration, or demographic characteristics, and effect of AIT. There may be other factors underlying the different responses to AIT.

Responsivity and Reproducibility of Sputum Inflammatory Biomarkers During COPD Exacerbation and Stable Phases - A Pilot Study.

INTRODUCTION: There is a great interest to identify airway biomarkers to evaluate the potential and efficacy of anti-inflammatory therapeutic interventions. In this pilot study, we compared cytokine mRNA and protein levels of IL-6, IL-8, CCL2, CCL4, and TNF-α, as well as LTB-4 expression regarding their reproducibility and responsivity in induced sputum in COPD patients. METHODS: We recruited a cohort of 17 patients with a moderate COPD exacerbation, necessitating antibiotics and/or oral corticosteroids. Patients were followed for two consecutive stable phase visits. Cytokine mRNA and protein levels were measured in induced sputum samples. RESULTS: IL-6 and CCL4 protein levels decreased from exacerbation to stable phase, whereas their mRNA expression showed the same trend (not statistically significant). Coefficients of variation were overall lower (ie, more favorable for responsiveness) at protein levels compared to mRNA levels. No significant differences were observed in the reproducibility between cytokine mRNA expression and protein measurements. IL-6, IL-8, CCL2, and TNF-α gene expression levels yielded moderate to high intraclass correlation coefficients and/or Spearman correlation coefficients between both stable phase samples in contrast to their protein levels. CONCLUSION: Our findings suggest that several protein levels yield better responsivity with lower noise-to-signal ratios compared to their respective mRNA levels. In contrast, cytokine mRNA expression was more reproducible as it varied less in a stable state than proteins. Future studies are needed with a larger sample size to further evaluate the differences of responsivity and reproducibility between cytokine mRNA and protein measurements, not only during exacerbations.

Ultra-low-dose CT combined with noise reduction techniques for quantification of emphysema in COPD patients: An intra-individual comparison study with standard-dose CT.

PURPOSE: Phantom studies in CT emphysema quantification show that iterative reconstruction and deep learning-based noise reduction (DLNR) allow lower radiation dose. We compared emphysema quantification on ultra-low-dose CT (ULDCT) with and without noise reduction, to standard-dose CT (SDCT) in chronic obstructive pulmonary disease (COPD). METHOD: Forty-nine COPD patients underwent ULDCT (third generation dual-source CT; 70ref-mAs, Sn-filter 100kVp; median CTDIvol 0.38 mGy) and SDCT (64-multidetector CT; 40mAs, 120kVp; CTDIvol 3.04 mGy). Scans were reconstructed with filtered backprojection (FBP) and soft kernel. For ULDCT, we also applied advanced modelled iterative reconstruction (ADMIRE), levels 1/3/5, and DLNR, levels 1/3/5/9. Emphysema was quantified as Low Attenuation Value percentage (LAV%, ≤-950HU). ULDCT measures were compared to SDCT as reference standard. RESULTS: For ULDCT, the median radiation dose was 84 % lower than for SDCT. Median extent of emphysema was 18.6 % for ULD-FBP and 15.4 % for SDCT (inter-quartile range: 11.8-28.4 % and 9.2 %-28.7 %, p = 0.002). Compared to SDCT, the range in limits of agreement of emphysema quantification as measure of variability was 14.4 for ULD-FBP, 11.0-13.1 for ULD-ADMIRE levels and 10.1-13.9 for ULD-DLNR levels. Optimal settings were ADMIRE 3 and DLNR 3, reducing variability of emphysema quantification by 24 % and 27 %, at slight underestimation of emphysema extent (-1.5 % and -2.9 %, respectively). CONCLUSIONS: Ultra-low-dose CT in COPD patients allows dose reduction by 84 %. State-of-the-art noise reduction methods in ULDCT resulted in slight underestimation of emphysema compared to SDCT. Noise reduction methods (especially ADMIRE 3 and DLNR 3) reduced variability of emphysema quantification in ULDCT by up to 27 % compared to FBP.

Prevalence of DNA of regular occupants in vehicles.

People will deposit, redistribute and remove biological traces when they interact with their environment. Understanding the dynamics of trace DNA is crucial to assess both the optimal sampling strategy to recover traces and the relevance of DNA evidence in the context of a case. This paper addresses the prevalence of DNA of drivers, passengers, and unknown individuals in vehicles. Five vehicles with a regular driver only, and five vehicles with a regular driver and regular passenger have each been sampled at twenty locations. Based on the findings, we propose a sampling strategy for investigative purposes as well as for evaluative purposes when evaluating the findings given scenarios that propose the person-of-interest as either the driver or passenger in a vehicle.

Calculating LRs for presence of body fluids from mRNA assay data in mixtures.

Messenger RNA (mRNA) profiling can identify body fluids present in a stain, yielding information on what activities could have taken place at a crime scene. To account for uncertainty in such identifications, recent work has focused on devising statistical models to allow for probabilistic statements on the presence of body fluids. A major hurdle for practical adoption is that evidentiary stains are likely to contain more than one body fluid and current models are ill-suited to analyse such mixtures. Here, we construct a likelihood ratio (LR) system that can handle mixtures, considering the hypotheses H1: the sample contains at least one of the body fluids of interest (and possibly other body fluids); H2: the sample contains none of the body fluids of interest (but possibly other body fluids). Thus, the LR-system outputs an LR-value for any combination of mRNA profile and set of body fluids of interest that are given as input. The calculation is based on an augmented dataset obtained by in silico mixing of real single body fluid mRNA profiles. These digital mixtures are used to construct a probabilistic classification method (a 'multi-label classifier'). The probabilities produced are subsequently used to calculate an LR, via calibration. We test a range of different classification methods from the field of machine learning, ways to preprocess the data and multi-label strategies for their performance on in silico mixed test data. Furthermore, we study their robustness to different assumptions on background levels of the body fluids. We find logistic regression works as well as more flexible classifiers, but shows higher robustness and better explainability. We test the system's performance on lab-generated mixture samples, and discuss practical usage in case work.

Early hydroxychloroquine but not chloroquine use reduces ICU admission in COVID-19 patients.

BACKGROUND: The global push for the use of hydroxychloroquine (HCQ) and chloroquine (CQ) against COVID-19 has resulted in an ongoing discussion about the effectivity and toxicity of these drugs. Recent studies report no effect of (H)CQ on 28-day mortality. We investigated the effect of HCQ and CQ in hospitalized patients on the non-ICU COVID-ward. METHODS: A nationwide, observational cohort study was performed in The Netherlands. Hospitals were given the opportunity to decide independently on the use of three different COVID-19 treatment strategies: HCQ, CQ, or no treatment. We compared the outcomes between these groups. The primary outcomes were 1) death on the COVID-19 ward, and 2) transfer to the intensive care unit (ICU). RESULTS: The analysis included 1064 patients from 14 hospitals: 566 patients received treatment with either HCQ (n = 189) or CQ (n = 377), and 498 patients received no treatment. In a multivariate propensity-matched weighted competing regression analysis, there was no significant effect of (H)CQ on mortality on the COVID ward. However, HCQ was associated with a significantly decreased risk of transfer to the ICU (hazard ratio (HR) = 0.47, 95% CI = 0.27-0.82, p = 0.008) when compared with controls. This effect was not found in the CQ group (HR = 0.80, 95% CI = 0.55-1.15, p = 0.207), and remained significant after competing risk analysis. CONCLUSION: The results of this observational study demonstrate a lack of effect of (H)CQ on non-ICU mortality. However, we show that the use of HCQ - but not CQ - is associated with a 53% reduction in risk of transfer of COVID-19 patients from the regular ward to the ICU. Recent prospective studies have reported on 28-day, all-cause mortality only; therefore, additional prospective data on the early effects of HCQ in preventing transfer to the ICU are still needed.

Determinants of SARS-CoV-2 receptor gene expression in upper and lower airways.

The recent outbreak of the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), which causes coronavirus disease 2019 (COVID-19), has led to a worldwide pandemic. One week after initial symptoms develop, a subset of patients progresses to severe disease, with high mortality and limited treatment options. To design novel interventions aimed at preventing spread of the virus and reducing progression to severe disease, detailed knowledge of the cell types and regulating factors driving cellular entry is urgently needed. Here we assess the expression patterns in genes required for COVID-19 entry into cells and replication, and their regulation by genetic, epigenetic and environmental factors, throughout the respiratory tract using samples collected from the upper (nasal) and lower airways (bronchi). Matched samples from the upper and lower airways show a clear increased expression of these genes in the nose compared to the bronchi and parenchyma. Cellular deconvolution indicates a clear association of these genes with the proportion of secretory epithelial cells. Smoking status was found to increase the majority of COVID-19 related genes including ACE2 and TMPRSS2 but only in the lower airways, which was associated with a significant increase in the predicted proportion of goblet cells in bronchial samples of current smokers. Both acute and second hand smoke were found to increase ACE2 expression in the bronchus. Inhaled corticosteroids decrease ACE2 expression in the lower airways. No significant effect of genetics on ACE2 expression was observed, but a strong association of DNA- methylation with ACE2 and TMPRSS2- mRNA expression was identified in the bronchus.

Ten-year fracture risk predicted by proximal femur Hounsfield units.

Colon cancer screening occurs at younger ages than osteoporosis screening. Bone density measurements using virtual colonoscopy performed for colon cancer screening can provide an early warning sign of patients at potential risk for osteoporosis-related fractures. Earlier identification may improve treatment and potentially fracture prevention. INTRODUCTION: Opportunistic osteoporosis screening with computed tomography colonography (CTC) offers an opportunity to capitalize on earlier colorectal cancer screening to identify patients at risk of future fractures. The purpose of this study is to evaluate 10-year fracture and specifically hip fracture risk based on Hounsfield units (HU) obtained from CTC. METHODS: We identified all CTC scans between 2004 and 2007 of patients 40 years and older with 10 years minimum follow-up. Hounsfield units were measured within the proximal femur and fractures identified via worldwide military records. Patients were stratified into two cohorts based on the presence or lack of a fracture in the wrist, spine, hip, or proximal humerus. Hounsfield unit measurements were compared between groups using Student's t test and the HU threshold was calculated that best approximated an 80% sensitivity to optimally screen patients for fracture risk. The odds ratio, negative predictive value, 10-year incidence of fracture, and survival curves were calculated. RESULTS: We identified 3711 patients with 183 fractures over 10 years. The HU threshold that corresponded with an 80% sensitivity to identify fractures was 112 HU. The negative predictive value (NPV) for overall fractures and hip fractures was over 97%. The 10-year fracture incidence was higher in patients below 112 HU compared to those above for both overall fractures (6.3% vs 1.7%) and hip fractures (2.7% vs 0.07%). The 112 HU threshold corresponds with an odds ratio for overall fracture and hip fractures of 2.5 (95% confidence interval (CI), 1.7-3.6) and 24.5 (95% CI, 3.3-175.5), respectively. CONCLUSION: In the 10 years following CTC, patients who experienced a fracture had lower hip HU. Decreasing HU on CTC may be an early warning sign of fracture potential.

Body fluid identification and assignment to donors using a targeted mRNA massively parallel sequencing approach - results of a second EUROFORGEN / EDNAP collaborative exercise.

In a previous EUROFORGEN/EDNAP collaborative exercise, we tested two assays for targeted mRNA massively parallel sequencing for the identification of body fluids/tissues, optimized for the Illumina MiSeq/FGx and the Ion Torrent PGM/S5 platforms, respectively. The task of the second EUROFORGEN/EDNAP collaborative exercise was to analyze dried body fluid stains with two different multiplexes, the former Illumina 33plex mRNA panel for body fluid/tissue identification and a 35plex cSNP panel for assignment of body fluids/tissues to donors that was introduced in a proof-of-concept study recently. The coding region SNPs (cSNPs) are located within the body fluid specific mRNA transcripts and represent a direct link between the body fluid and the donor. We predicted the origin of the stains using a partial least squares discriminant analysis (PLS-DA) model, where most of the single source samples were correctly predicted. The mixed body fluid stains showed poorer results, however, at least one component was predicted correctly in most stains. The cSNP data demonstrated that coding region SNPs can give valuable information on linking body fluids/tissues with donors in mixed body fluid stains. However, due to the unfavorable performance of some cSNPs, the interpretation remains challenging. As a consequence, additional markers are needed to increase the discrimination power in each body fluid/tissue category.

Marked TGF-ß-regulated miRNA expression changes in both COPD and control lung fibroblasts.

COPD is associated with disturbed tissue repair, possibly due to TGF-ß-regulated miRNA changes in fibroblasts. Our aim was to identify TGF-ß-regulated miRNAs and their differential regulation and expression in COPD compared to control fibroblasts. Small RNA sequencing was performed on TGF-ß-stimulated and unstimulated lung fibroblasts from 15 COPD patients and 15 controls. Linear regression was used to identify TGF-ß-regulated and COPD-associated miRNAs. Interaction analysis was performed to compare miRNAs that responded differently to TGF-ß in COPD and control. Re-analysis of previously generated Ago2-IP data and Enrichr were used to identify presence and function of potential target genes in the miRNA-targetome of lung fibroblasts. In total, 46 TGF-ß-regulated miRNAs were identified in COPD and 86 in control fibroblasts (FDR < 0.05). MiR-27a-5p was the most significantly upregulated miRNA. MiR-148b-3p, miR-589-5p and miR-376b-3p responded differently to TGF-ß in COPD compared to control (FDR < 0.25). MiR-660-5p was significantly upregulated in COPD compared to control (FDR < 0.05). Several predicted targets of miR-27a-5p, miR-148b-3p and miR-660-5p were present in the miRNA-targetome, and were mainly involved in the regulation of gene transcription. In conclusion, altered TGF-ß-induced miRNA regulation and differential expression of miR-660-5p in COPD fibroblasts, may represent one of the mechanisms underlying aberrant tissue repair and remodelling in COPD.

Determining how diluted bloodstains were derived: Inferring distinctive characteristics and formulating a guideline.

In forensic settings, diluted bloodstains are regularly encountered for example when bloodstains are mixed with tap-/rainwater, after deliberate cleaning attempts, or when blood is dropped on a wet surface such as a towel. Such diluted bloodstain scenarios can be subdivided into sequences of events in which a blood drop was either (1) readily diluted (a mixture of blood and water is deposited); (2) deposited on a surface that was readily moistened (first water, then blood) or (3) deposited and subsequently moistened (first blood, then water). Current bloodstain pattern analysis (BPA) lacks data and tools to distinguish these three ways of derivation of a diluted bloodstain that vary in the sequence of deposition of blood and water on textile. In this study, 880 bloodstains were examined for characteristics that can be used to determine the derivation of diluted bloodstains. A guideline to assist BPA-analysts in interpreting diluted bloodstains was extracted. The added value of this guideline was confirmed by conducting two surveys: one survey with and one without the guideline. A third survey confirmed that the characteristics also function on a broader range of textile types that have different weave and knit styles. This guideline can aid BPA-experts to determine, in an objective way, how diluted bloodstains derived which can aid in determining which activities took place at a crime scene.

Age-related gene and miRNA expression changes in airways of healthy individuals.

Knowledge on age-related miRNA changes in healthy individuals and their interaction with mRNAs is lacking. We studied age-related mRNA and miRNA expression changes and their interactions in normal airways. RNA and small RNA sequencing was performed on bronchial biopsies of 86 healthy individuals (age: 18-73) to determine age-related expression changes. Per age-related miRNA we determined the enrichment of age-related predicted targets and their correlation. We identified 285 age-related genes and 27 age-related miRNAs. Pathway enrichment showed that genes higher expressed with age were involved in synapse-related processes. Genes lower expressed with age were involved in cell cycle regulation, the immune system and DNA damage/repair. MiR-146a-5p, miR-146b-5p and miR-142-5p were lower expressed with increasing age and we found a significant enrichment for predicted targets of these miRNAs among genes that were higher expressed with age. The expression levels of the enriched predicted targets RIMS2 and IGSF1 were negatively correlated with both miR-146a-5p and miR-146b-5p. RIMS2 was present in the enriched process, i.e. positive regulation of synaptic transmission. In conclusion, genes decreased with ageing are involved in several of the ageing hallmarks. Genes higher expressed with ageing were involved in synapse-related processes, of which RIMS2 is potentially regulated by two age-related miRNAs.

[Subcontracting a steam sterilization activity: Impact on surgical instruments]. / Externalisation de l'activité de stérilisation : impact sur l'état des instruments chirurgicaux.

Subcontracting our institution's sterilization activity induced the implementation of an automated cleaning facility. Following this development, some of the resterilizable stainless steel needle holders started to show abnormal corrosion. Our study goal was to investigate the causes of this corrosion in order to optimize the sterilization circuit. A full sterilization process mapping and Ishikawa diagram enabled us to identify potential causes of corrosion. The needle holders' intrinsic characteristics, like steel quality and manufacturing, were analyzed as well as extrinsic factors such as the influence of preprocessing soaking conditions, steel passivation, water quality and the impact of corrosion inhibitors. Each potential factor of corrosion was tested in real conditions on needle holders' kits. The needle holders steel grade complies with medical standards and the tests showed that passivation and pre-processing conditions were not involved in the occurrence of corrosion, contrary to soaking length and use of softened rinsing water, containing more chloride than reverse osmosis water, and, thus conducive to rust formation. Moreover, corrosion inhibitors were deemed ineffective or incompatible. Due to this analysis, the incidence of corrosion was reduced by switching softened water to osmosis water and by introducing dynamic drying in the automated cleaning process. In addition, this work stresses the importance of minimizing waiting times and auditing the sterilization circuit before any subcontracting. Management Guidelines related to sterilization's outsourcing would probably have helped to limit this episode.