Analysis of sex sequences by means of generalized linear mixed models

Adaptive strategies of sex allocation functioning to increase fitness, including strategic allocation of sex in relation to birth order and sex composition of the progeny, have frequently been explored, but the development of a statistical framework for these analyses has lagged behind. In this paper, we contribute to filling this gap by devising a method for analyzing sex sequences based on a proper parameterization of generalized linear mixed models (GLMMs). The method is highly flexible and can be easily extended to investigate sequences of traits or events or other longitudinal data. As a worked example, we focus on the analysis of sex sequences of offspring produced by females in a single reproductive event and develop a method that allows analyzing simultaneously sequences of different length (e.g., clutches of different size) and sequences with missing data, as may frequently happen in “real-world” data sets. Different patterns of allocation among traits or events along the sequence were investigated, and a real data base of sex sequences of eclectus parrots (Eclectus roratus) fledglings produced by different females was analyzed. A tutorial for running the analyses with the R or the SAS software is provided in the Electronic Supplementary Material.     

The proton binding properties of biosorbents

Environmental Chemistry Letters - A broad variety of materials of biological origin have been successfully used in recent decades for the removal of pollutants from waters. These biosorbents...     

Bridging gaps in demographic analysis with phylogenetic imputation

Phylogenetically informed imputation methods have rarely been applied to estimate missing values in demographic data but may be a powerful tool for reconstructing vital rates of survival, maturation, and fecundity for species of conservation concern. Imputed vital rates could be used to parameterize demographic models to explore how populations respond when vital rates are perturbed. We used standardized vital rate estimates for 50 bird species to assess the use of phylogenetic imputation to fill gaps in demographic data. We calculated imputation accuracy for vital rates of focal species excluded from the data set either singly or in combination and with and without phylogeny, body mass, and life-history trait data. We used imputed vital rates to calculate demographic metrics, including generation time, to validate the use of imputation in demographic analyses. Covariance among vital rates and other trait data provided a strong basis to guide imputation of missing vital rates in birds, even in the absence of phylogenetic information. Mean NRMSE for null and phylogenetic models differed by <0.01 except when no vital rates were available or for vital rates with high phylogenetic signal (Pagel's λ > 0.8). In these cases, including body mass and life-history trait data compensated for lack of phylogenetic information: mean normalized root mean square error (NRMSE) for null and phylogenetic models differed by <0.01 for adult survival and <0.04 for maturation rate. Estimates of demographic metrics were sensitive to the accuracy of imputed vital rates. For example, mean error in generation time doubled in response to inaccurate estimates of maturation time. Accurate demographic data and metrics, such as generation time, are needed to inform conservation planning processes, for example through International Union for Conservation of Nature Red List assessments and population viability analysis. Imputed vital rates could be useful in this context but, as for any estimated model parameters, awareness of the sensitivities of demographic model outputs to the imputed vital rates is essential.     

The influence of seasonal vertical temperature gradients on no‐purge sampling of wells

Seasonal changes in ambient temperature create vertical temperature gradients in shallow groundwater (less than 15 m). These temperature gradients can affect in‐well flow dynamics that impact samples collected using no‐purge sampling methods. In late winter, the shallower water is colder, resulting in thermally mixed conditions and uniform contaminant concentrations. In late summer, the shallower water is warmer, resulting in thermally stratified conditions and contaminant distributions in the monitoring well more consistent with the distribution in the surrounding aquifer. The importance of seasonal temperature gradients on in‐well mixing was evaluated in two shallow monitoring wells in Houston, Texas. In each of the two wells, four vertically spaced passive diffusion samples collected in late winter showed a less than 1.3x difference in trichloroethene (TCE) concentration between depths, while the same sampling conducted in late summer showed greater than a 100x difference in TCE concentration between depths. A simple analytical model originally developed to predict vertical soil temperature profiles can also be used to predict the occurrence of thermally stratified and thermally mixed conditions in monitoring wells as a function of time and well depth. The results of this analysis and modeling suggest that shallow monitoring wells in most of the United States and Canada can have significantly different vertical concentration profiles within the well over the course of a year due to seasonal vertical temperature gradients. This can induce additional intra‐annual temporal variability on passive no‐purge sampling results from these shallow wells, potentially making it more difficult to discern true trends in the data. © 2012 Wiley Periodicals, Inc.     

Climate change-induced salinity variation impacts on a stenoecious mangrove species in the Indian Sundarbans

The alterations in the salinity profile are an indirect, but potentially sensitive, indicator for detecting changes in precipitation, evaporation, river run-off, glacier retreat, and ice melt. These changes have a high impact on the growth of coastal plant species, such as mangroves. Here, we present estimates of the variability of salinity and the biomass of a stenoecious mangrove species (Heritiera fomes, commonly referred to as Sundari) in the aquatic subsystem of the lower Gangetic delta based on a dataset from 2004 to 2015. We highlight the impact of salinity alteration on the change in aboveground biomass of this endangered species that, due to different salinity profile in the western and central sectors of the lower Gangetic plain, shows an increase only in the former sector, where the salinity is dropping and low growth in the latter, where the salinity is increasing.     

Mutagenic properties of PM2.5 urban pollution in the Northern Italy: The nitro-compounds contribution

PM2.5 is the breathable fraction of the particulate matter and some adverse health effects, such as respiratory functionality, cardiological diseases and cancer, can be in some measure attributable to this risk factor exposure. Some of the most carcinogen compounds transported by PM2.5 are nitro-compounds. In this study, a strengthened in vitro bioassay — able to predict the mutagenic/carcinogenic activity of the environmental mixtures — was conducted on PM2.5 organic extracts to define the nitro-compounds burden. PM2.5 air pollution was daily monitored, during 2006, in three cities located in the Northern part of Italy (Torino, Pavia and Verona) and the mutagenic properties of the PM2.5 organic extracts were assessed with the Ames test. The bacterial used in this study were three Salmonella typhimurium strains: TA98, nitroreductase-less mutant TA98NR and YG1021 carrying a nitroreductase-producing plasmid. The annual PM2.5 mean level measured in Torino was 46.5 (± 31.6) μg/m³, in Pavia 34.8 (± 25.1) μg/m³, and in Verona 37.3 (± 27.8) μg/m³, while the mutagenicity expressed as TA98 net reverants/m³ was 28.0 (± 22.1), 28.3 (± 24.9), and 34.2 (± 30.9) respectively. Monthly pool bioassays, conducted with the three different strains, showed a greater mutagenic response of the YG1021 in each city. The relationship among the mutagenic answers for YG1021:TA98:TA98NR was about 6:3:1 (p < 0.001). Over nitroreductase activity enhanced the response of 2.2, 2.0 and 1.7 times for Torino, Pavia, and Verona (ANOVA Torino p < 0.05) respectively. Without nitroreductase activity the genotoxicity was limited. These biological findings are able to describe a relevant role played by the nitro compounds in the mutagenic properties of the urban PM2.5 in the Padana plain; moreover the bacterial nitroreductase plays a predominant role in DNA interaction primarily for Torino PM2.5 extracts.     

Multi-Destination and Multi-Purpose Trip Effects in the Analysis of the Demand for Trips to a Remote Recreational Site

One of the basic assumptions of the travel cost method for recreational demand analysis is that the travel cost is always incurred for a single purpose recreational trip. Several studies have skirted around the issue with simplifying assumptions and dropping observations considered as nonconventional holiday-makers or as nontraditional visitors from the sample. The effect of such simplifications on the benefit estimates remains conjectural. Given the remoteness of notable recreational parks, multi-destination or multi-purpose trips are not uncommon. This article examines the consequences of allocating travel costs to a recreational site when some trips were taken for purposes other than recreation and/or included visits to other recreational sites. Using a multi-purpose weighting approach on data from Gros Morne National Park, Canada, we conclude that a proper correction for multi-destination or multi-purpose trip is more of what is needed to avoid potential biases in the estimated effects of the price (travel-cost) variable and of the income variable in the trip generation equation.     

Use of the Contingent Valuation Method in the assessment of a landfill mining project

A comprehensive approach for the evaluation of the economic feasibility of landfill mining (LFM) should take into account not only the direct costs and revenues for the private investor, but also the social benefits or costs (generally called externalities), in such a way that projects generating major social benefits (and no significant private revenues) are not overlooked.With a view to contributing to the development of a common framework for the evaluation of LFM projects, this paper presents the results of a case study where the issue of the assessment of social benefits from a LFM project is addressed. In particular, the Contingent Valuation Method is applied for the monetary assessment of the community-perceived benefits from the remediation of an old uncontrolled waste deposit by means of LFM and the conversion of the area into a park.Based on the results of a survey carried out on a random sample of people living near the old landfill, the economic values of the individual willingness to pay (WTP) for LFM and the subsequent creation of a public park were calculated and the correlations with the relevant variables (distance from the landfill site, age, income, sex, education level) assessed. The results were then suitably extended and the monetary value of the welfare increase of the whole population resident in the area and potentially affected both by LFM and the creation of the park was calculated.     

Risk analysis for road and rail transport of hazardous materials: a GIS approach

An approach to transportation risk analysis for road and rail transport of dangerous goods is proposed, which is based on the use of geographic information systems (GIS) to manage territorial information, coupled with a product data bank in a risk evaluation tool. Such an approach enables to accurately take into account the local data affecting risk analysis, such as population, accident rate, and weather conditions along all the route, by means of a system which can be easily updated. The resulting risk evaluation tool assists in the step of route identification and allows to rapidly perform an accurate transportation risk analysis, for a single transportation event as well as for multiple substances, trips and itineraries.     

Abnormal amniotic fluid levels of CA 125 in second-trimester Down syndrome pregnancies

The aim of this study was to evaluate the concentration of CA 125 in second trimester amniotic fluid from Down syndrome pregnancies. CA 125 was measured in stored amniotic fluid samples from pregnancies of 14–19 weeks' gestation with and without Down syndrome fetuses. CA 125 levels were expressed in multiples of the median (MOM) for normal pregnancies of the same gestational age. Twenty-one pregnancies with Down syndrome fetuses and 63 unaffected controls matched for maternal age, gestational age, and duration of storage were studied. The median MOM values of the affected pregnancies were significantly higher than those of the controls (1·41 MOM versus 0·99 MOM). These findings show that there is an increased concentration of CA 125 in second-trimester amniotic fluid from Down syndrome pregnancies.