A case study of an individual participant data meta-analysis of diagnostic accuracy showed that prediction regions represented heterogeneity well

The diagnostic accuracy of a screening tool is often characterized by its sensitivity and specificity. An analysis of these measures must consider their intrinsic correlation. In the context of an individual participant data meta-analysis, heterogeneity is one of the main components of the analysis. When using a random-effects meta-analytic model, prediction regions provide deeper insight into the effect of heterogeneity on the variability of estimated accuracy measures across the entire studied population, not just the average. This study aimed to investigate heterogeneity via prediction regions in an individual participant data meta-analysis of the sensitivity and specificity of the Patient Health Questionnaire-9 for screening to detect major depression. From the total number of studies in the pool, four dates were selected containing roughly 25%, 50%, 75% and 100% of the total number of participants. A bivariate random-effects model was fitted to studies up to and including each of these dates to jointly estimate sensitivity and specificity. Two-dimensional prediction regions were plotted in ROC-space. Subgroup analyses were carried out on sex and age, regardless of the date of the study. The dataset comprised 17,436 participants from 58 primary studies of which 2322 (13.3%) presented cases of major depression. Point estimates of sensitivity and specificity did not differ importantly as more studies were added to the model. However, correlation of the measures increased. As expected, standard errors of the logit pooled TPR and FPR consistently decreased as more studies were used, while standard deviations of the random-effects did not decrease monotonically. Subgroup analysis by sex did not reveal important contributions for observed heterogeneity; however, the shape of the prediction regions differed. Subgroup analysis by age did not reveal meaningful contributions to the heterogeneity and the prediction regions were similar in shape. Prediction intervals and regions reveal previously unseen trends in a dataset. In the context of a meta-analysis of diagnostic test accuracy, prediction regions can display the range of accuracy measures in different populations and settings

Oxidation of gaseous hydrocarbons by alkene-utilizing bacteria

Gaseous alkenes are widespread in the environment due to the emission of these hydrocarbons by industry and due to their production from natural sources as for instance ethene by plants, fungi and bacteria. Micro-organisms have developed the potential to oxidize these hydrocarbons. Alkenes can either be co-oxidized by alkane-utilizing bacteria and/or used as carbon and energy source by specific alkene-utilizing bacteria. Alkane-utilizing micro-organisms have extensively been investigated and described. Potential applications of alkane-utilizing micro-organisms e.g. the epoxidation of alkenes have been recorded. in numerous patents. The scope of the research presented was to gain, in a concerted action between microbiologists and process engineers, more fundamental knowledge on the behaviour of alkene-utilizing bacteria in either a gas/solid bioreactor or in a multiphase bioreactor. This thesis mainly deals with microbiological aspects.Chapters 2, 3 and 4 subsequently deal with the isolation and characterization of propene- and 1-butene-utilizing Xanthobacter spp., with Nocardia spp. utilizing both 1,3-butadiene and isoprene as sole source of carbon and energy and with a Nocardia sp. capable of growth on trans -2-butene. The initial oxidation of propene, 2-butene, 1,3-butadiene and isoprene by these bacteria is mediated by a mono- oxygenase. The mono-oxygenase present in propene-grown Xanthobacter spp. is different from hydrocarbon mono-oxygenases described until now in view of substrate specificity towards hydrocarbons and in view of activities measured in the presence of potential inhibitors of the mono-oxygenase. Both Xanthobacter spp. and alkadiene-utilizing Nocardia spp. possess a mono-oxygenase which catalyses an epoxidation reaction. On the other hand, the trans -2-butene-grown Nocardia sp. which is also able to grow on gaseous n-alkanes, carries out a hydroxylation reaction instead of an epoxidation reaction. A degradation route of trans -2-butene via crotonic acid was proposed on basis of inhibitor experiments, simultaneous adaptation studies and enzyme activities.Possible applications of alkene-grown bacteria are the production of (chiral) epoxyalkanes and the removal of alkenes from gas phases and therefore an optimal production of the bacteria is essential. Microbial growth on either ethene or propene in chemostat cultures is dealt with in chapter 5. By using a simple growth model and experimentally derived growth parameters with a Xanthobacter sp. and a Mycobacterium sp. the dilution rate resulting in the optimal biomass production could be calculated. Measured and mathematically derived production rates agreed well.The potential to produce epoxyalkanes from alkenes was investigated using washed cell suspensions of alkene-grown Xanthobacter spp. The results are given in chapter 6. Chapter 7 represents a extended survey of gaseous hydrocarbon utilization and oxidation by alkene-grown bacteria. Some selected alkene-utilizing micro-organisms were investigated in more detail to provide a better understanding of the ability to grow on hydrocarbons and the oxidation of gaseous and volatile hydrocarbons. From such observations it was obvious that a 1-hexene-utilizing Pseudomonas and a trans -2-butene-utilizing Nocardia TB1 resemble alkane-utilizing bacteria. Other alkene-utilizing micro-organisms consist of a specific group, which are not able to hydroxylate alkanes. Alkene-grown bacteria were capable to excrete epoxides and using an appropriate combination of bacterium and alkene almost every epoxide could be produced. Finally, it was shown that most epoxides formed were either oxidized to CO 2 and H 2 O, or hydrolysed by alkene-grown bacteria.Chapter 8, 9 and 10 deal with some aspects of the behaviour of alkene-utilizing bacteria in gas/solid bioreactors. 1,2-Epoxyethane formation by propene-grown Mycobacterium Py1 cells was studied in such a reactor because no accumulation of the toxic epoxide occurs in the vicinity of the bacteria. Prolonged 1,2-epoxyethane formation was dependent on co-factor regeneration. In a subsequent experiment, it was demonstrated that the presence of a metabolizable co-substrate enhanced the epoxide production.Ethene is a plant hormone and has already detrimental effects on stored fruits and vegetables at concentrations of 1 vpm in the gas phase. Therefore, ethene has to be removed from the vicinity of stored agricultural products. alkene-grown bacteria capable of oxidizing ethene may be an alternative of known chemical/physical ethene-removal systems from storage facilities. Ethene-grown Mycobacterium E3 oxidizes ethene to the desired low concentrations even when immobilized on carriers like lava, perlite or in alginate. Chapter 9 describes the characteristics of ethene-grown Mycobacterium E3 immobilized on various supports. However, the operational stability of Mycobacterium E3 immobilized on the supports tested was insufficient. In a subsequent investigation the operational stability of Mycobacterium E3 on compost was tested, and surprisingly, a good operational stability was found while possibly even cellgrowth or induction of mono-oxygenase enzyme was obtained also at very low ethene concentrations. From the efficiency of conversion of ethene and the rate of ethene production by fruits and vegetables, it was calculated that bioscrubbers can be of relatively small dimensions in relation to storage facilities

Read-across of ready biodegradability based on the substrate specificity of N-alkyl polypropylene polyamine-degrading microorganisms

The biodegradation of N-alkyl polypropylene polyamines (NAPPs) was studied using pure and mixed cultures to enable read-across of ready biodegradability test results. Two Pseudomonas spp. were isolated from activated sludge with N-oleyl alkyl propylene diamine and N-coco alkyl dipropylene triamine, respectively. Both strains utilized all NAPPs tested as the sole source of carbon, nitrogen and energy for growth. Mineralization of NAPPs was independent of the alkyl chain length and the size of the polyamine moiety. NAPPs degraded in closed bottle tests (CBTs) using both river water and activated sludge. However, ready biodegradability of NAPPs with alkyl chain lengths of 16–18 carbon atoms and polyamine moieties with three and four nitrogen atoms could not be demonstrated. Biodegradation in the CBT was hampered by their limited bioavailability, making assessment of the true ready biodegradability of these highly adsorptive surfactants impossible. All NAPPs are therefore classified as readily biodegradable through read-across. Read-across is justified by the broad substrate specificity of NAPP-degrading microorganisms, their omnipresence and the mineralization of NAPPs

Anaerobic degradation of long-chain alkylamines by a denitrifying Pseudomonas stutzeri

The anaerobic degradation of tetradecylamine and other long-chain alkylamines by a newly isolated denitrifying bacterium was studied. Strain ZN6 was isolated from a mixture of soil and active sludge and was identified as representing Pseudomonas stutzeri, based on partial 16S rRNA gene sequence analysis. Strain ZN6 was a mesophilic, motile, Gram-negative rod-shaped bacterium and was able to grow on a variety of compounds including even-numbered primary fatty amines with alkyl chains ranging from C4 to C18 coupled to nitrate reduction. Alkylamines were used as sole carbon, energy and nitrogen source and were completely mineralized. Nitrate was dissimilated by ZN6 to nitrite. When strain ZN6 was grown under nitrate limitation, nitrite was slowly dissimilated further. When cocultivated with the complete denitrifier Castellaniella defragens ZN3, anaerobic degradation under denitrifying of alkylamines by strain ZN6 was slightly faster. Strain ZN3 is a complete denitrifier, unable to convert tetradecylamine, and was copurified from the same enrichment culture as strain ZN6. The proposed pathway for the degradation of alkylamines in strain ZN6 starts with C¿N cleavages to alkanals and further oxidation to the corresponding fatty acid

Accurate assessment of the biodegradation of cationic surfactants in activated sludge reactors (OECD TG 303A)

The continuous-fed activated sludge test (OECD TG 303A) was used to predict the removal of cationic surfactants from wastewater in activated sludge plants. However, a method to differentiate between adsorption and biodegradation is not provided in these guidelines. Assessment of removal by biodegradation was possible with analysis of the surfactant present in mixed liquid suspended solids in combination with a simple equation. This equation was derived from the mass balance of the activated sludge unit in steady state. The removal by biodegradation of decylamine, tetradecylamine, octadecylamine, dioctadecylmethylamine and dioctadecyldimethylammonium chloride that have different capacities to adsorb was >99.9%, >99.9%, 98.2%, 94.2%, and 69.0%, respectively. The total removal of all five cationic surfactants from the influent was =98.8%. The removal of octadecylamine spiked at different influent concentrations indicated first order kinetic