An intercomparison of CH3O2 measurements by Fluorescence Assay by Gas Expansion and Cavity Ring–Down Spectroscopy within HIRAC (Highly Instrumented Reactor for Atmospheric Chemistry)

Simultaneous measurements of CH3O2 radical concentrations have been performed using two different methods in the Leeds HIRAC (Highly Instrumented Reactor for Atmospheric Chemistry) chamber at 295 K and in 80 mbar of a mixture of 3 : 1 He : O2 and 100 mbar or 1000 mbar of synthetic air. The first detection method consisted of the indirect detection of CH3O2 using the conversion of CH3O2 into CH3O by excess NO with subsequent detection of CH3O by fluorescence assay by gas expansion (FAGE). The FAGE instrument was calibrated for CH3O2 in two ways. In the first method, a known concentration of CH3O2 was generated using the 185 nm photolysis of water vapour in synthetic air at atmospheric pressure followed by the conversion of the generated OH radicals to CH3O2 by reaction with CH4 / O2. This calibration can be used for experiments performed in HIRAC at 1000 mbar in air. In the second method, calibration was achieved by generating a near steady-state of CH3O2 and then switching off the photolysis lamps within HIRAC and monitoring the subsequent decay of CH3O2 which was controlled via its self-reaction, and analysing the decay using second order kinetics. This calibration could be used for experiments performed at all pressures. In the second detection method, CH3O2 has been measured directly using Cavity Ring-Down Spectroscopy (CRDS) using the absorption at 7487.98 cm-1 in the A <– X (ν12) band with the optical path along the ~1.4 m chamber diameter. Analysis of the second-order kinetic decays of CH3O2 by self-reaction monitored by CRDS has been used for the determination of the CH3O2 absorption cross section at 7487.98 cm-1, both at 100 mbar of air and at 80 mbar of a 3 : 1 He : O2 mixture, from which σCH3O2 = (1.49 ± 0.19) × 10–20 cm2 molecule-1 was determined for both pressures. The absorption spectrum of CH3O2 between 7486 and 7491 cm-1 did not change shape when the total pressure was increased to 1000 mbar, from which we determined that σCH3O2 is independent of pressure over the pressure range 100–1000 mbar in air. CH3O2 was generated in HIRAC using either the photolysis of Cl2 with UV black lamps in the presence of CH4 and O2 or the photolysis of acetone at 254 nm in the presence of O2. At 1000 mbar of synthetic air the correlation plot of [CH3O2]FAGE against [CH3O2]CRDS gave a gradient of 1.10 ± 0.02. At 100 mbar of synthetic air the gradient of the FAGE – CRDS correlation plot had a gradient of 1.06 ± 0.01 and at 80 mbar of 3 : 1 He : O2 mixture the correlation plot gradient was 0.91 ± 0.02. These results provide a validation of the FAGE method to determine concentrations of CH3O2

Computed cardiopulmonography and the idealized lung clearance index, iLCI2.5, in early-stage cystic fibrosis.

This study explored the use of computed cardiopulmonography (CCP) to assess lung function in early-stage cystic fibrosis (CF). CCP has two components. The first is a particularly accurate technique for measuring gas exchange. The second is a computational cardiopulmonary model where patient-specific parameters can be estimated from the measurements of gas exchange. Twenty-five participants (14 healthy controls, 11 early-stage CF) were studied with CCP. They were also studied with a standard clinical protocol to measure the lung clearance index (LCI2.5). Ventilation inhomogeneity, as quantified through CCP parameter σlnCl, was significantly greater (P < 0.005) in CF than in controls, and anatomical deadspace relative to predicted functional residual capacity (DS/FRCpred) was significantly more variable (P < 0.002). Participant-specific parameters were used with the CCP model to calculate idealized values for LCI2.5 (iLCI2.5) where extrapulmonary influences on the LCI2.5, such as breathing pattern, had all been standardized. Both LCI2.5 and iLCI2.5 distinguished clearly between CF and control participants. LCI2.5 values were mostly higher than iLCI2.5 values in a manner dependent on the participant's respiratory rate (r = 0.46, P < 0.05). The within-participant reproducibility for iLCI2.5 appeared better than for LCI2.5, but this did not reach statistical significance (F ratio = 2.2, P = 0.056). Both a sensitivity analysis on iLCI2.5 and a regression analysis on LCI2.5 revealed that these depended primarily on an interactive term between CCP parameters of the form σlnCL*(DS/FRC). In conclusion, the LCI2.5 (or iLCI2.5) probably reflects an amalgam of different underlying lung changes in early-stage CF that would require a multiparameter approach, such as potentially CCP, to resolve.NEW & NOTEWORTHY Computed cardiopulmonography is a new technique comprising a highly accurate sensor for measuring respiratory gas exchange coupled with a cardiopulmonary model that is used to identify a set of patient-specific characteristics of the lung. Here, we show that this technique can improve on a standard clinical approach for lung function testing in cystic fibrosis. Most particularly, an approach incorporating multiple model parameters can potentially separate different aspects of pathological change in this disease

A Scalable Permutation Approach Reveals Replication and Preservation Patterns of Network Modules in Large Datasets.

Network modules-topologically distinct groups of edges and nodes-that are preserved across datasets can reveal common features of organisms, tissues, cell types, and molecules. Many statistics to identify such modules have been developed, but testing their significance requires heuristics. Here, we demonstrate that current methods for assessing module preservation are systematically biased and produce skewed p values. We introduce NetRep, a rapid and computationally efficient method that uses a permutation approach to score module preservation without assuming data are normally distributed. NetRep produces unbiased p values and can distinguish between true and false positives during multiple hypothesis testing. We use NetRep to quantify preservation of gene coexpression modules across murine brain, liver, adipose, and muscle tissues. Complex patterns of multi-tissue preservation were revealed, including a liver-derived housekeeping module that displayed adipose- and muscle-specific association with body weight. Finally, we demonstrate the broader applicability of NetRep by quantifying preservation of bacterial networks in gut microbiota between men and women

Elevated serum alpha-1 antitrypsin is a major component of GlycA-associated risk for future morbidity and mortality

Background GlycA is a nuclear magnetic resonance (NMR) spectroscopy biomarker that predicts risk of disease from myriad causes. It is heterogeneous; arising from five circulating glycoproteins with dynamic concentrations: alpha-1 antitrypsin (AAT), alpha-1-acid glycoprotein (AGP), haptoglobin (HP), transferrin (TF), and alpha-1-antichymotrypsin (AACT). The contributions of each glycoprotein to the disease and mortality risks predicted by GlycA remain unknown. Methods We trained imputation models for AAT, AGP, HP, and TF from NMR metabolite measurements in 626 adults from a population cohort with matched NMR and immunoassay data. Levels of AAT, AGP, and HP were estimated in 11,861 adults from two population cohorts with eight years of follow-up, then each biomarker was tested for association with all common endpoints. Whole blood gene expression data was used to identify cellular processes associated with elevated AAT. Results Accurate imputation models were obtained for AAT, AGP, and HP but not for TF. While AGP had the strongest correlation with GlycA, our analysis revealed variation in imputed AAT levels was the most predictive of morbidity and mortality for the widest range of diseases over the eight year follow-up period, including heart failure (meta-analysis hazard ratio = 1.60 per standard deviation increase of AAT, P-value = 1×10−10), influenza and pneumonia (HR = 1.37, P = 6×10−10), and liver diseases (HR = 1.81, P = 1×10−6). Transcriptional analyses revealed association of elevated AAT with diverse inflammatory immune pathways. Conclusions This study clarifies the molecular underpinnings of the GlycA biomarker’s associated disease risk, and indicates a previously unrecognised association between elevated AAT and severe disease onset and mortality.Peer reviewe

Relation of gallbladder function and Helicobacter pylori infection to gastric mucosa inflammation in patients with symptomatic cholecystolithiasis

Background. Inflammatory alterations of the gastric mucosa are commonly caused by Helicobacter pylori (Hp) infection in patients with symptomatic gallstone disease. However, the additional pathogenetic role of an impaired gallbladder function leading to an increased alkaline duodenogastric reflux is controversially discussed. Aim:To investigate the relation of gallbladder function and Hp infection to gastric mucosa inflammation in patients with symptomatic gallstones prior to cholecystectomy. Patients: Seventy-three patients with symptomatic gallstones were studied by endoscopy and Hp testing. Methods: Gastritis classification was performed according to the updated Sydney System and gallbladder function was determined by total lipid concentration of gallbladder bile collected during mainly laparoscopic cholecystectomy. Results: Fifteen patients revealed no, 39 patients mild, and 19 moderate to marked gastritis. No significant differences for bile salts, phospholipids, cholesterol, or total lipids in gallbladder bile were found between these three groups of patients. However, while only 1 out of 54 (< 2%) patients with mild or no gastritis was found histologically positive for Hp, this infection could be detected in 14 (74%) out of 19 patients with moderate to marked gastritis. Conclusion: Moderate to marked gastric mucosa inflammation in gallstone patients is mainly caused by Hp infection, whereas gallbladder function is not related to the degree of gastritis. Thus, an increased alkaline duodenogastric reflux in gallstone patients seems to be of limited pathophysiological relevance. Copyright (c) 2006 S. Karger AG, Basel

An intercomparison of HO₂ measurements by fluorescence assay by gas expansion and cavity ring-down spectroscopy within HIRAC (Highly Instrumented Reactor for Atmospheric Chemistry)

The HO2 radical was monitored simultaneously using two independent techniques in the Leeds HIRAC atmospheric simulation chamber at room temperature and total pressures of 150 mbar and 1000 mbar of synthetic air. In the first method, HO2 was measured indirectly following sampling through a pinhole expansion to 3 mbar when sampling from 1000 mbar and 1 mbar when sampling from 150 mbar, with subsequent addition of NO to convert it to OH which was detected via laser-induced fluorescence spectroscopy using the FAGE (fluorescence assay by gas expansion) technique. The FAGE method is used widely to measure HO2 concentrations in the field, and was calibrated using the 185 nm photolysis of water vapour in synthetic air with a limit of detection at 1000 mbar of 1.6 × 106 molecule cm-3 for an averaging time of 30 s. In the second method, HO2 was measured directly and absolutely without the need for a calibration using Cavity Ring Down Spectroscopy (CRDS) with the optical path across the entire ~ 1.4 m width of the chamber, with excitation of the first O-H overtone at 1506.43 nm using a diode laser, and with a sensitivity determined from an Allan deviation plot of 3.0 × 108 and 1.5 109 molecule cm-3 at 150 mbar and 1000 mbar, respectively, for an averaging period of 30 s. HO2 was generated in HIRAC by the photolysis of Cl2 using black lamps in the presence of methanol in synthetic air and was monitored by FAGE and CRDS for ~ 5–10 minute periods with the lamps on and also during the HO2 decay after the lamps were switched off. At 1000 mbar total pressure the correlation plot of [HO2]FAGE versus [HO2]CRDS gave a gradient of 0.836 0.004 for HO2 concentrations in the range ~ 4–100 × 109 molecule cm-3 while at 150 mbar total pressure the corresponding gradient was 0.903 0.002 for HO2 concentrations in the range ~ 6–750 × 108 molecule cm-3 . For the period after the lamps were switched off, the second-order decay of the HO2 FAGE signal via its self-reaction was used to calculate the FAGE calibration constant for both 150 and 1000 mbar total pressure. This enabled a calibration of the FAGE method at 150 mbar, an independent measurement of the FAGE calibration at 1000 mbar, and an independent determination of the HO2 cross section at 1506.43 nm, HO2, at both pressures. For CRDS, the HO2 concentration obtained using HO2 determined using previous reported spectral data for HO2 and the kinetic decay of HO2 method agreed to within 20 and 12 % at 150 and 1000 mbar, respectively. For the FAGE method a very good agreement (difference within 8 %) has been obtained at 1000 mbar between the water vapour calibration method and the kinetic decay of the HO2 fluorescence signal method. This is the first intercomparison for HO2 between FAGE and CRDS methods, and the good agreement between HO2 concentrations measured using the indirect FAGE method and the direct CRDS method provides a validation for the FAGE method, which is used widely for field measurements of HO2 in the atmosphere

Integrative analysis of the plasma proteome and polygenic risk of cardiometabolic diseases.

Cardiometabolic diseases are frequently polygenic in architecture, comprising a large number of risk alleles with small effects spread across the genome1-3. Polygenic scores (PGS) aggregate these into a metric representing an individual's genetic predisposition to disease. PGS have shown promise for early risk prediction4-7 and there is an open question as to whether PGS can also be used to understand disease biology8. Here, we demonstrate that cardiometabolic disease PGS can be used to elucidate the proteins underlying disease pathogenesis. In 3,087 healthy individuals, we found that PGS for coronary artery disease, type 2 diabetes, chronic kidney disease and ischaemic stroke are associated with the levels of 49 plasma proteins. Associations were polygenic in architecture, largely independent of cis and trans protein quantitative trait loci and present for proteins without quantitative trait loci. Over a follow-up of 7.7 years, 28 of these proteins associated with future myocardial infarction or type 2 diabetes events, 16 of which were mediators between polygenic risk and incident disease. Twelve of these were druggable targets with therapeutic potential. Our results demonstrate the potential for PGS to uncover causal disease biology and targets with therapeutic potential, including those that may be missed by approaches utilizing information at a single locus

A Novel Pathway of TEF Regulation Mediated by MicroRNA-125b Contributes to the Control of Actin Distribution and Cell Shape in Fibroblasts

BACKGROUND: Thyrotroph embryonic factor (TEF), a member of the PAR bZIP family of transcriptional regulators, has been involved in neurotransmitter homeostasis, amino acid metabolism, and regulation of apoptotic proteins. In spite of its relevance, nothing is known about the regulation of TEF. PRINCIPAL FINDINGS: p53-dependent genotoxic agents have been shown to be much more harmful for PAR bZIP-deficient mice as compared to wild type animals. Here we demonstrate that TEF expression is controlled by p53 through upregulation of microRNA-125b, as determined by both regulating the activity of p53 and transfecting cells with microRNA-125b precursors. We also describe a novel role for TEF in controlling actin distribution and cell shape in mouse fibroblasts. Lack of TEF is accompanied by dramatic increase of cell area and decrease of elongation (bipolarity) and dispersion (multipolarity). Staining of actin cytoskeleton also showed that TEF (-/-) cells are characterized by appearance of circumferential actin bundles and disappearance of straight fibers. Interestingly, transfection of TEF (-/-) fibroblasts with TEF induced a wild type-like phenotype. Consistent with our previous findings, transfection of wild type fibroblasts with miR-125b promoted a TEF (-/-)-like phenotype, and a similar but weaker effect was observed following exogenous expression of p53. CONCLUSIONS/SIGNIFICANCE: These findings provide the first evidence of TEF regulation, through a miR-125b-mediated pathway, and describes a novel role of TEF in the maintenance of cell shape in fibroblasts

Polygenic risk scores in cardiovascular risk prediction: A cohort study and modelling analyses

Background: Polygenic risk scores (PRSs) can stratify populations into cardiovascular disease (CVD) risk groups. We aimed to quantify the potential advantage of adding information on PRSs to conventional risk factors in the primary prevention of CVD. Methods and findings: Using data from UK Biobank on 306,654 individuals without a history of CVD and not on lipid-lowering treatments (mean age [SD]: 56.0 [8.0] years; females: 57%; median follow-up: 8.1 years), we calculated measures of risk discrimination and reclassification upon addition of PRSs to risk factors in a conventional risk prediction model (i.e., age, sex, systolic blood pressure, smoking status, history of diabetes, and total and high-density lipoprotein cholesterol). We then modelled the implications of initiating guideline-recommended statin therapy in a primary care setting using incidence rates from 2.1 million individuals from the Clinical Practice Research Datalink. The C-index, a measure of risk discrimination, was 0.710 (95% CI 0.703–0.717) for a CVD prediction model containing conventional risk predictors alone. Addition of information on PRSs increased the C-index by 0.012 (95% CI 0.009–0.015), and resulted in continuous net reclassification improvements of about 10% and 12% in cases and non-cases, respectively. If a PRS were assessed in the entire UK primary care population aged 40–75 years, assuming that statin therapy would be initiated in accordance with the UK National Institute for Health and Care Excellence guidelines (i.e., for persons with a predicted risk of ≥10% and for those with certain other risk factors, such as diabetes, irrespective of their 10-year predicted risk), then it could help prevent 1 additional CVD event for approximately every 5,750 individuals screened. By contrast, targeted assessment only among people at intermediate (i.e., 5% to <10%) 10-year CVD risk could help prevent 1 additional CVD event for approximately every 340 individuals screened. Such a targeted strategy could help prevent 7% more CVD events than conventional risk prediction alone. Potential gains afforded by assessment of PRSs on top of conventional risk factors would be about 1.5-fold greater than those provided by assessment of C-reactive protein, a plasma biomarker included in some risk prediction guidelines. Potential limitations of this study include its restriction to European ancestry participants and a lack of health economic evaluation. Conclusions: Our results suggest that addition of PRSs to conventional risk factors can modestly enhance prediction of first-onset CVD and could translate into population health benefits if used at scale

An interaction map of circulating metabolites, immune gene networks, and their genetic regulation

Background: Immunometabolism plays a central role in many cardiometabolic diseases. However, a robust map of immune-related gene networks in circulating human cells, their interactions with metabolites, and their genetic control is still lacking. Here, we integrate blood transcriptomic, metabolomic, and genomic profiles from two population-based cohorts (total N = 2168), including a subset of individuals with matched multi-omic data at 7-year follow-up. Results: We identify topologically replicable gene networks enriched for diverse immune functions including cytotoxicity, viral response, B cell, platelet, neutrophil, and mast cell/basophil activity. These immune gene modules show complex patterns of association with 158 circulating metabolites, including lipoprotein subclasses, lipids, fatty acids, amino acids, small molecules, and CRP. Genome-wide scans for module expression quantitative trait loci (mQTLs) reveal five modules with mQTLs that have both cis and trans effects. The strongest mQTL is in ARHGEF3 (rs1354034) and affects a module enriched for platelet function, independent of platelet counts. Modules of mast cell/basophil and neutrophil function show temporally stable metabolite associations over 7-year follow-up, providing evidence that these modules and their constituent gene products may play central roles in metabolic inflammation. Furthermore, the strongest mQTL in ARHGEF3 also displays clear temporal stability, supporting widespread trans effects at this locus. Conclusions: This study provides a detailed map of natural variation at the blood immunometabolic interface and its genetic basis, and may facilitate subsequent studies to explain inter-individual variation in cardiometabolic disease.Peer reviewe