Down-regulation of endothelial TLR4 signalling after apo A-I gene transfer contributes to improved survival in an experimental model of lipopolysaccharide-induced inflammation

The protective effects of high-density lipoprotein (HDL) under lipopolysaccharide (LPS) conditions have been well documented. Here, we investigated whether an effect of HDL on Toll-like receptor 4 (TLR4) expression and signalling may contribute to its endothelial-protective effects and to improved survival in a mouse model of LPS-induced inflammation and lethality. HDL cholesterol increased 1.7-fold (p < 0.005) and lung endothelial TLR4 expression decreased 8.4-fold (p < 0.005) 2 weeks after apolipoprotein (apo) A-I gene transfer. Following LPS administration in apo A-I gene transfer mice, lung TLR4 and lung MyD88 mRNA expression, reflecting TLR4 signalling, were 3.0-fold (p < 0.05) and 2.1-fold (p < 0.05) lower, respectively, than in LPS control mice. Concomitantly, LPS-induced lung neutrophil infiltration, lung oedema and mortality were significantly attenuated following apo A–I transfer. In vitro, supplementation of HDL or apo A–I to human microvascular endothelial cells-1 24 h before LPS administration reduced TLR4 expression, as assessed by fluorescent-activated cell sorting, and decreased the LPS-induced MyD88 mRNA expression and NF-κB activity, independently of LPS binding. In conclusion, HDL reduces TLR4 expression and signalling in endothelial cells, which may contribute significantly to the protective effects of HDL in LPS-induced inflammation and lethality

The trans-ancestral genomic architecture of glycemic traits

Glycemic traits are used to diagnose and monitor type 2 diabetes and cardiometabolic health. To date, most genetic studies of glycemic traits have focused on individuals of European ancestry. Here we aggregated genome-wide association studies comprising up to 281,416 individuals without diabetes (30% non-European ancestry) for whom fasting glucose, 2-h glucose after an oral glucose challenge, glycated hemoglobin and fasting insulin data were available. Trans-ancestry and single-ancestry meta-analyses identified 242 loci (99 novel; P < 5 x 10(-8)), 80% of which had no significant evidence of between-ancestry heterogeneity. Analyses restricted to individuals of European ancestry with equivalent sample size would have led to 24 fewer new loci. Compared with single-ancestry analyses, equivalent-sized trans-ancestry fine-mapping reduced the number of estimated variants in 99% credible sets by a median of 37.5%. Genomic-feature, gene-expression and gene-set analyses revealed distinct biological signatures for each trait, highlighting different underlying biological pathways. Our results increase our understanding of diabetes pathophysiology by using trans-ancestry studies for improved power and resolution. A trans-ancestry meta-analysis of GWAS of glycemic traits in up to 281,416 individuals identifies 99 novel loci, of which one quarter was found due to the multi-ancestry approach, which also improves fine-mapping of credible variant sets.Peer reviewe

Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals &lt;1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data

Genome-wide Trans-ethnic Meta-analysis Identifies Seven Genetic Loci Influencing Erythrocyte Traits and a Role for RBPMS in Erythropoiesis

Genome-wide association studies (GWASs) have identified loci for erythrocyte traits in primarily European ancestry populations. We conducted GWAS meta-analyses of six erythrocyte traits in 71,638 individuals from European, East Asian, and African ancestries using a Bayesian approach to account for heterogeneity in allelic effects and variation in the structure of linkage disequilibrium between ethnicities. We identified seven loci for erythrocyte traits including a locus (RBPMS/GTF2E2) associated with mean corpuscular hemoglobin and mean corpuscular volume. Statistical fine-mapping at this locus pointed to RBPMS at this locus and excluded nearby GTF2E2. Using zebrafish morpholino to evaluate loss of function, we observed a strong in vivo erythropoietic effect for RBPMS but not for GTF2E2, supporting the statistical fine-mapping at this locus and demonstrating that RBPMS is a regulator of erythropoiesis. Our findings show the utility of trans-ethnic GWASs for discovery and characterization of genetic loci influencing hematologic traits

Turnaround time prediction for clinical chemistry samples using machine learning

Objectives: Turnaround time (TAT) is an essential performance indicator of a medical diagnostic laboratory. Accurate TAT prediction is crucial for taking timely action in case of prolonged TAT and is important for efficient organization of healthcare. The objective was to develop a model to accurately predict TAT, focusing on the automated pre-analytical and analytical phase. Methods: A total of 90,543 clinical chemistry samples from Erasmus MC were included and 39 features were analyzed, including priority level and workload in the different stages upon sample arrival. PyCaret was used to evaluate and compare multiple regression models, including the Extra Trees (ET) Regressor, Ridge Regression and K Neighbors Regressor, to determine the best model for TAT prediction. The relative residual and SHAP (SHapley Additive exPlanations) values were plotted for model evaluation. Results: The regression-tree-based method ET Regressor performed best with an R2 of 0.63, a mean absolute error of 2.42 min and a mean absolute percentage error of 7.35%, where the average TAT was 30.09 min. Of the test set samples, 77% had a relative residual error of at most 10%. SHAP value analysis indicated that TAT was mainly influenced by the workload in pre-analysis upon sample arrival and the number of modules visited. Conclusions: Accurate TAT predictions were attained with the ET Regressor and features with the biggest impact on TAT were identified, enabling the laboratory to take timely action in case of prolonged TAT and helping healthcare providers to improve planning of scarce resources to increase healthcare efficiency

Design of fork-join networks of First-In-First-Out and infinite-server queues applied to clinical chemistry laboratories

This paper considers optimal design of queueing networks in which each node consists of a single-server FIFO queue and an infinite-server queue, which is referred to as incubation queue. Upon service completion at a FIFO queue, a job splits (forks) into two parts: the first part is routed to the next node on its route, and the second part is placed in the incubation queue. Routing of the jobs of multiple types is governed by a central decision maker that decides on the routes for each job type and aims to minimize the mean turnaround time of the jobs, i.e., the time spent in the system until service completion at the FIFO queue in the last node, and at all incubation queues on the job's route, which may be viewed as a join operation. We provide explicit results for the turnaround time when all service and inter-arrival time distributions are exponential and invoke the Queueing Network Analyzer when these distributions are general. We then develop a Simulated Annealing approach to find the optimal routing configuration. We apply our approach to determine the optimal routing configuration in a chemistry analyzer line

A critical review of laboratory performance indicators

Healthcare budgets worldwide are under constant pressure to reduce costs while improving efficiency and quality. This phenomenon is also visible in clinical laboratories. Efficiency gains can be achieved by reducing the error rate and by improving the laboratory’s layout and logistics. Performance indicators (PIs) play a crucial role in this process as they allow for performance assessment. This review aids in the process for selecting laboratory PIs—which is not trivial—by providing an overview of frequently used PIs in the literature that can also be used in clinical laboratories. We conducted a systematic review of the laboratory medicine literature on PIs. As the testing process in clinical laboratories can be viewed as a production process, we also reviewed the production processes literature on PIs. The reviewed literature relates to the design, optimization or performance assessment of such processes. The most frequently cited PIs relate to pre-analytical errors, timeliness, resource utilization, cost, and the amount of congestion. Their citation frequency in the literature is used as a proxy for their importance. PIs are discussed in terms of their definition, measurability and impact. The use of suitable PIs is crucial in production processes, including clinical laboratories. By also reviewing the production processes literature, additional relevant PIs for clinical laboratories were found. The PIs in the laboratory medicine literature mostly relate to laboratory errors, while the PIs in the production processes literature relate to the amount of congestion in the process

A critical review of laboratory performance indicators

Healthcare budgets worldwide are under constant pressure to reduce costs while improving efficiency and quality. This phenomenon is also visible in clinical laboratories. Efficiency gains can be achieved by reducing the error rate and by improving the laboratory’s layout and logistics. Performance indicators (PIs) play a crucial role in this process as they allow for performance assessment. This review aids in the process for selecting laboratory PIs—which is not trivial—by providing an overview of frequently used PIs in the literature that can also be used in clinical laboratories. We conducted a systematic review of the laboratory medicine literature on PIs. As the testing process in clinical laboratories can be viewed as a production process, we also reviewed the production processes literature on PIs. The reviewed literature relates to the design, optimization or performance assessment of such processes. The most frequently cited PIs relate to pre-analytical errors, timeliness, resource utilization, cost, and the amount of congestion. Their citation frequency in the literature is used as a proxy for their importance. PIs are discussed in terms of their definition, measurability and impact. The use of suitable PIs is crucial in production processes, including clinical laboratories. By also reviewing the production processes literature, additional relevant PIs for clinical laboratories were found. The PIs in the laboratory medicine literature mostly relate to laboratory errors, while the PIs in the production processes literature relate to the amount of congestion in the process

Precision Measurement of the Helium Flux in Primary Cosmic Rays of Rigidities 1.9 GV to 3 TV with the Alpha Magnetic Spectrometer on the International Space Station

Knowledge of the precise rigidity dependence of the helium flux is important in understanding the origin, acceleration, and propagation of cosmic rays. A precise measurement of the helium flux in primary cosmic rays with rigidity (momentum/charge) from 1.9 GV to 3 TV based on 50 million events is presented and compared to the proton flux. The detailed variation with rigidity of the helium flux spectral index is presented for the first time. The spectral index progressively hardens at rigidities larger than 100 GV. The rigidity dependence of the helium flux spectral index is similar to that of the proton spectral index though the magnitudes are different. Remarkably, the spectral index of the proton to helium flux ratio increases with rigidity up to 45 GV and then becomes constant; the flux ratio above 45 GV is well described by a single power law

Epigenome-Wide Association Study Reveals CpG Sites Associated with Thyroid Function and Regulatory Effects on KLF9

Background: Thyroid hormones play a key role in differentiation and metabolism and are known regulators of gene expression through both genomic and epigenetic processes including DNA methylation. The aim of this study was to examine associations between thyroid hormones and DNA methylation. Methods: We carried out a fixed-effect meta-analysis of epigenome-wide association study (EWAS) of blood DNA methylation sites from 8 cohorts from the ThyroidOmics Consortium, incorporating up to 7073 participants of both European and African ancestry, implementing a discovery and replication stage. Statistical analyses were conducted using normalized beta CpG values as dependent and log-transformed thyrotropin (TSH), free thyroxine, and free triiodothyronine levels, respectively, as independent variable in a linear model. The replicated findings were correlated with gene expression levels in whole blood and tested for causal influence of TSH and free thyroxine by two-sample Mendelian randomization (MR). Results: Epigenome-wide significant associations (p-value <1.1E-7) of three CpGs for free thyroxine, five for free triiodothyronine, and two for TSH concentrations were discovered and replicated (combined p-values = 1.5E-9 to 4.3E-28). The associations included CpG sites annotated to KLF9 (cg00049440) and DOT1L (cg04173586) that overlap with all three traits, consistent with hypothalamic-pituitary-thyroid axis physiology. Significant associations were also found for CpGs in FKBP5 for free thyroxine, and at CSNK1D/LINCO1970 and LRRC8D for free triiodothyronine. MR analyses supported a causal effect of thyroid status on DNA methylation of KLF9. DNA methylation of cg00049440 in KLF9 was inversely correlated with KLF9 gene expression in blood. The CpG at CSNK1D/LINC01970 overlapped with thyroid hormone receptor alpha binding peaks in liver cells. The total additive heritability of the methylation levels of the six significant CpG sites was between 25% and 57%. Significant methylation QTLs were identified for CpGs at KLF9, FKBP5, LRRC8D, and CSNK1D/LINC01970. Conclusions: We report novel associations between TSH, thyroid hormones, and blood-based DNA methylation. This study advances our understanding of thyroid hormone action particularly related to KLF9 and serves as a proof-of-concept that integrations of EWAS with other -omics data can provide a valuable tool for unraveling thyroid hormone signaling in humans by complementing and feeding classical in vitro and animal studies