Using the negative binomial distribution to model overdispersion in ecological count data

A Poisson process is a commonly used starting point for modeling stochastic variation of ecological count data around a theoretical expectation. However, data typically show more variation than implied by the Poisson distribution. Such overdispersion is often accounted for by using models with different assumptions about how the variance changes with the expectation. The choice of these assumptions can naturally have apparent consequences for statistical inference. We propose a parameterization of the negative binomial distribution, where two overdispersion parameters are introduced to allow for various quadratic mean-variance relationships, including the ones assumed in the most commonly used approaches. Using bird migration as an example, we present hypothetical scenarios on how overdispersion can arise due to sampling, flocking behavior or aggregation, environmental variability, or combinations of these factors. For all considered scenarios, mean-variance relationships can be appropriately described by the negative binomial distribution with two overdispersion parameters. To illustrate, we apply the model to empirical migration data with a high level of overdispersion, gaining clearly different model fits with different assumptions about mean-variance relationships. The proposed framework can be a useful approximation for modeling marginal distributions of independent count data in likelihood-based analyses.     

First evidence for a stereoselective incorporation of nonylphenol diastereomers in soil-derived organo-clay complexes

Environmental processes can affect the stereochemical properties of organic pollutants. In particular, biotic processes like microbial transformations or membrane penetration alter the ratios of enantiomers as well as diastereomers. These effects have been intensively used not only in environmental studies but also in medicine, toxicology, pharmacy, and agricultural sciences. However, in order to identify unambiguously biotic-initiated alteration of organic compounds, the knowledge on the stereoselective effect of all relevant processes is mandatory. Therefore, here we report the first evidence for a stereospecific formation of non-extractable residues of a xeniobiotic in a highly relevant soil subfraction, the organo-clay complexes. In this study, soils were spiked with labeled and unlabeled nonylphenol isomer, and incubation experiments were performed to study its long-term incorporation behavior into soil-derived organo-clay complexes under abiotic and biotic conditions. Besides the extractable particle-associated proportion especially the humic fractions comprising the bound residues have been analyzed by GC/MS. Our results from biotic experiments revealed alterations of the diastereomeric composition of the contaminant in the different soil humic subfractions. A depletion of the first eluting diastereomer as expressed by diastereomeric ratios around 0.6 has been observed for the extractable fraction, whereas the non-extractable proportion was enriched in the first diastereomer (diasteremoric ratio around 1.0). On the contrary, the diastereomeric ratios remained unaffected during the abiotic experiments (diasteremoric ratio around 0.8). These systematic observations give clear evidence that the process of microbial-assisted incorporation of nonylphenol into soil organo-clay complexes is a stereoselective process. To our knowledge, this is the first report on a stereoselective incorporation process of organic substances forming non-extractable residues. Consequently, the formation of non-extractable residues has to be considered in environmental studies dealing with stereoselective analysis of organic pollutants in soils to study their microbial transformation.     

Metabolic fate of the 14C-labeled herbicide clodinafop-propargyl in a sediment–water system

The metabolic fate of ¹⁴C-phenyl-labeled herbicide clodinafop-propargyl (¹⁴C-CfP) was studied for 28 days in lab assays using a sediment–water system derived from a German location. Mineralization was 5.21% of applied ¹⁴C after 28 days exhibiting a distinct lag phase until day 14 of incubation. Portions of radioactivity remaining in water phases decreased at moderate rate to 18.48% after 28 days; 62.46% were still detected in water after 14 days. Soxhlet extraction of the sediment using acetonitrile released 35.56% of applied ¹⁴C with day 28, while 33.99% remained as non-extractable residues. A remarkable increase of bound ¹⁴C was observed between 14 and 28 days correlating with the distinct increase of mineralization. No correlation was found throughout incubation with microbial activity of the sediment as determined by dimethyl sulfoxide reduction. Dissolved oxygen and pH value of water phases remained almost constant for 28 days. Analyses of Soxhlet extracts of the sediment and ethyl acetate extracts of water phases by radio-TLC and radio-HPLC revealed that CfP was rapidly cleaved to free acid clodinafop (Cf), which was further (bio-) transformed. DT₅₀ values (based on radio-HPLC) were below 1 day (CfP) and slightly above 28 days (Cf). Further metabolites were not detected. Fractionation of humic and non-humic components of the sediment demonstrated that CfP's non-extractable residues were predominantly associated with fulvic acids up to 14 days of incubation (3.36%), whereas after 28 days, the majority of radioactivity was found in the humin/mineral fraction (13.30% of applied ¹⁴C). Due to high-performance size-exclusion chromatography of the fulvic acids fraction derived from assays incubated for 28 days, this portion of ¹⁴C was firmly, possibly covalently bound to fulvic acids and did not consist of CfP or Cf. Using an isolation strategy comprising preincubation of sediment with CfP and mineralization of ¹⁴C-CfP as criterion, a microorganism was isolated from the sediment examined. It grew on ¹⁴C-CfP as sole carbon source with evolution of ¹⁴CO₂. The bacterium was characterized by growth on commonly used carbon sources and 16S rDNA sequence analysis. Its sequence exhibited high similarity with that of Nocardioides aromaticivorans strain H-1 (98.85%; DSM 15131, JCM 11674).     

Desorption of arsenic from clay and humic acid-coated clay by dissolved phosphate and silicate

Arsenic (As) contaminated aquifers contain iron minerals and clays that strongly bind As at their surfaces. It was suggested that As mobilization is driven by natural organic matter (including fulvic acids (FA) and humic acids (HA)) present in the aquifers either via providing reducing equivalents for reductive dissolution of Fe(III) (hydr)oxides or via competitive desorption of As from the mineral surfaces. In the present study we quantified sorption of As(III) and As(V) to Ca(2+)-homoionized illite (IL) and to kaolinite (Kao) as well as to HA-coated clays, i.e., illite-HA (IL-HA) and kaolinite-HA (Kao-HA) at neutral pH. Clay-HA complexes sorbed 28-50% more As than clay-only systems upon addition of 100μM As(III)/As(V) to 0.5g of clay or HA-clay with Ca(2+) probably playing an important role for HA binding to the clay surface and As binding to the HA. When comparing sorption of As(V) and As(III) to clay and HA-clay complexes, As(V) sorption was generally higher by 15-32% than sorption of As(III) to the same complexes. IL and IL-HA sorbed 11-28% and 6-11% more As compared to Kao and Kao-HA, respectively. In a second step, we then followed desorption of As from Kao, Kao-HA, IL and IL-HA by 100 and 500μM phosphate or silicate both at high (0.41-0.77μmol As/g clay), and low (0.04 to 0.05μmol As/g clay) As loadings. Phosphate desorbed As to a larger extent than silicate regardless of the amount of As loaded to clay minerals, both in the presence and absence of HA, and both for illite and kaolinite. At high loadings of As, the desorption of both redox species of As from clay-HA complexes by phosphate/silicate ranged from 32 to 72% compared to 2-54% in clay only systems meaning that As was desorbed to a larger extent from HA-coated clays compared to clay only systems. When comparing As(III) desorption by phosphate/silicate to As(V) desorption in high As-loading systems, there was no clear trend for which As species is desorbed to a higher extent in the four clay systems meaning that both As species behave similarly regarding desorption from clay surfaces by phosphate/silicate. Similarly, no significant differences were found in high As-loading systems in the amount of As desorbed by phosphate/silicate when comparing Kao vs. IL and Kao-HA vs IL-HA systems meaning that both clay types behave similarly regarding desorption of As by phosphate/silicate. At low As loadings, up to 80% of As was desorbed by phosphate and silicate with no noticeable differences being observed between different As species, different types of clay, clay vs clay-HA or the type of desorbant (phosphate and silicate). The results of this study showed that HA sorption to Ca(2+)-homoionized clay minerals can increase As binding to the clay although the As sorbed to the clay-HA is also released to a greater extent by competing ions such as phosphate and silicate. Desorption of As depended on the initial loadings of As onto the clay/clay-HA. Based on our results, the effect of humic substances on sorption of As and on desorption of As by phosphate and silicate has to be considered in order to fully understand and evaluate the environmental behavior of As in natural environments.     

Distribution, fate and formation of non-extractable residues of a nonylphenol isomer in soil with special emphasis on soil derived organo-clay complexes

Anthropogenic contaminants like nonylphenols (NP) are added to soil, for instance if sewage-sludge is used as fertilizer in agriculture. A commercial mixture of NP consists of more than 20 isomers. For our study, we used one of the predominate isomers of NP mixtures, 4-(3,5-dimethylhept-3-yl)phenol, as a representative compound. The aim was to investigate the fate and distribution of the isomer within soil and soil derived organo-clay complexes. Therefore, (14)C- and (13)C-labeled NP was added to soil samples and incubated up to 180 days. Mineralization was measured and soil samples were fractionated into sand, silt and clay; the clay fraction was further separated in humic acids, fulvic acids and humin. The organo-clay complexes pre-incubated for 90 or 180 days were re-incubated with fresh soil for 180 days, to study the potential of re-mobilization of incorporated residues. The predominate incorporation sites of the nonylphenol isomer in soil were the organo-clay complexes. After 180 days of incubation, 22 % of the applied (14)C was mineralized. The bioavailable, water extractable portion was low (9 % of applied (14)C) and remained constant during the entire incubation period, which could be explained by an incorporation/release equilibrium. Separation of organo-clay complexes, after extraction with solvents to release weakly incorporated, bioaccessible portions, showed that non-extractable residues (NER) were preferentially located in the humic acid fraction, which was regarded as an effect of the chemical composition of this fraction. Generally, 27 % of applied (14)C was incorporated into organo-clay complexes as NER, whereas 9 % of applied (14)C was bioaccessible after 180 days of incubation. The re-mobilization experiments showed on the one hand, a decrease of the bioavailability of the nonylphenol residues due to stronger incorporation, when the pre-incubation period was increased from 90 to 180 days. On the other hand, a shift of these residues from the clay fraction to other soil fractions was observed, implying a dynamic behavior of incorporated residues, which may result in bioaccessibility of the NER of nonylphenol.     

Multicenter clinical experience with non-invasive cell-free DNA screening for monosomy X and related X-chromosome variants

Objective

We aimed to investigate how the presence of fetal anomalies and different X chromosome variants influences Cell-free DNA (cfDNA) screening results for monosomy X.

Methods

From a multicenter retrospective survey on 673 pregnancies with prenatally suspected or confirmed Turner syndrome, we analyzed the subgroup for which prenatal cfDNA screening and karyotype results were available. A cfDNA screening result was defined as true positive (TP) when confirmatory testing showed 45,X or an X-chromosome variant.

Results

We had cfDNA results, karyotype, and phenotype data for 55 pregnancies. cfDNA results were high risk for monosomy X in 48/55, of which 23 were TP and 25 were false positive (FP). 32/48 high-risk cfDNA cases did not show fetal anomalies. Of these, 7 were TP. All were X-chromosome variants. All 16 fetuses with high-risk cfDNA result and ultrasound anomalies were TP. Of fetuses with abnormalities, those with 45,X more often had fetal hydrops/cystic hygroma, whereas those with “variant” karyotypes had different anomalies.

Conclusion

Both, 45,X or X-chromosome variants can be detected after a high-risk cfDNA result for monosomy X. When there are fetal anomalies, the result is more likely a TP. In the absence of fetal anomalies, it is most often an FP or X-chromosome variant.     

Presentation of ventriculomegaly at 11–14 weeks of gestation: An analysis of longitudinal data

Objectives

The aim of this study was to examine the value of the sonographic measurements of the choroid plexus and the lateral ventricles at 11–14 gestational weeks in fetuses that had the diagnosis of second-trimester ventriculomegaly (VM) as a clinical reference.

Methods

The standard axial plane used for biparietal diameter measurement from 2D stored images in the first trimester was used to calculate the ratio between the choroid plexus and lateral ventricle diameter (PDVDR), the choroid plexus and lateral ventricle length (PLVLR) and the choroid plexus and lateral ventricle area (PAVAR) in 100 normal and 15 fetuses diagnosed with second-trimester VM.

Results

In fetuses with VM, the measurements of PDVDR, PLVLR and PAVAR were all significantly smaller compared to normal fetuses (p = < 0.001, <0.001, <0.01). Four out of seven cases with mild VM had measurements below the 5th percentile (57%). 75% of cases with moderate or severe VM had at least one measurement below the 5th percentile.

Conclusions

Since the axial plane of the fetal head is obtained in all first-trimester routine screenings, the measurements of PDVDR, PLVLR and PAVAR could easily be integrated into routine examinations for an early detection of VM.     

A relict trematosauroid (Amphibia: Temnospondyli) from the Middle Jurassic of the Junggar Basin (NW China)

A temnospondyl ilium from the uppermost Toutunhe Formation (Middle Jurassic, Callovian) of the southern Junggar Basin is described. Among the known temnospondyls it is very unusual in morphology because of its very long and slender shaft. It compares closely only to the ilium of one of the latest known trematosaurids from the Ladinian of southern Germany. The Toutunhe Formation has also yielded vertebrae and skull fragments of temnospondyls which belong to the brachyopid Gobiops from the Upper Jurassic of Mongolia. Brachyopoid ilia do not, however, display a morphology similar to that of the new specimen. It is therefore concluded that this specimen represents a second taxon of temnospondyl from the Toutunhe Formation, which probably represents the latest surviving trematosauroid. The Trematosauroidea, which was hitherto exclusively known from the Lower to early Upper Triassic, therefore joins the Brachyopoidea – and possibly the Capitosauroidea – as another group of temnospondyls which survived the end-Triassic mass extinction.     

Hermaphroditism in brown shrimp: lessons from field data and modelling

This study was undertaken to further clarify whether the brown shrimp, Crangon crangon (Linnaeus 1758), is a gonochorist, a facultative or an obligate hermaphrodite. Juvenile shrimps were sampled from intertidal habitats along the German Wadden Sea coast with a push net and from a power plant water inlet to quantify the share of primary females. Length-based sex ratios were determined for about 27,000 individuals using external characteristics. Observed sex ratios were mainly female-biased, and also large males occurred regularly in the catch. This indicates that sex at hatch is not male as would be characteristic for an obligate protandric hermaphrodite and that not all male shrimps change sex. A cohort-based computer simulation, including sex-specific growth rates, mortality and seasonally varying recruitment, generated sex ratios comparable to the field. The observed decline in the proportion of males with increasing size can be explained solely by faster growth of females without involving hermaphroditism. Based on temperature-dependent growth and moult rates as well as length-specific numbers of eggs per female, the potential egg production of primary and secondary females was modelled, yielding contributions of secondary females of <1%. Sex change in C. crangon has previously been observed and may be interpreted as an evolutionary relict of this species having evolved in a habitat characterized by lower population densities, lower predation levels and increased longevity compared to today’s living conditions in North Sea coastal waters.     

Determinants of reproductive potential and population size in open populations of Patella vulgata

The importance of external and internal population processes in determining variation in reproductive output and variation in population size were quantified with model simulations for open populations of the sequentially hermaphroditic limpet Patella vulgata using field data from the Isle of Man and South West Ireland. Cross-correlation analyses of model outputs and elasticity analyses show that population dynamics are dominated by the effects of large females, and that recruitment adds little to reproductive output. However, populations experiencing low but highly variable recruitment appear male limited and recruitment pulses carrying young males into the population are correlated to reproductive output with a 2–5-year lag. We conclude that pulses in recruitment can be a major structuring force in these limpet populations, but site-specific post-recruitment processes will determine the relative importance of recruitment to population dynamics and the lag between recruitment and reproductive output.