Combining state and transition models with dynamic Bayesian networks

Bashari et al. (2009) propose combining state and transition models (STMs) with Bayesian networks for decision support tools where the focus is on modelling the system dynamics. There is already an extension of Bayesian networks - so-called dynamic Bayesian networks (DBNs) - for explicitly modelling systems that change over time, that has also been applied in ecological modelling. In this paper we propose a combination of STMs and DBNs that overcome some of the limitations of Bashari et al.’s approach including providing an explicit representation of the next state, while retaining its advantages, such an the explicit representation of transitions. We then show that the new model can be applied iteratively to predict into the future consistently with different time frames. We use Bashari et al.’s rangeland management problem as an illustrative case study. We present a comparative complexity analysis of the different approaches, based on the structure inherent in the problem being modelled. This analysis showed that any models that explicitly represent all the transitions only remain tractable when there are natural constraints in the domain. Thus we recommend modellers should analyse these aspects of their problem before deciding whether to use the framework.     

Relationships between simulated water stress and mortality and growth rates in underplanted Toona ciliata Roem. in subtropical Argentinean plantations

Toona ciliata Roem. (Australian red cedar) requires a nurse-tree overstory to prevent damage from drought and irradiation in some regions of north-eastern Argentina. T. ciliata was planted in the understory of Pinus taeda L. (625 stems/ha), Pinus elliottii Engelm. × Pinus caribaea Morelet (625 stems/ha), and Grevillea robusta A. Cunn. (833 stems/ha) nurse trees, which were thinned to 0, 25, 50, 75 and 100% of the initial densities. We measured initial T. ciliata mortality and growth as well as Leaf Area Index (LAI) based on light transmission. T. ciliata soil water availability and its effect on early growth and mortality were examined by modelling drought stress using the two-dimensional forest hydrology model ForWaDy. Simulated patterns in T. ciliata water stress for the different overstory treatments were consistent with observed patterns of mortality. Early mortality was lowest with a G. robusta overstory, with corresponding lowest drought stress values and high modelled soil water contents in the top soil layer in intermediate and high overstory densities. Mortality was highest with a P. elliottii × P. caribaea overstory in treatments with the highest modelled drought stress values in the most open treatments. The model supported our field observations by indicating that water stress was an important limitation to T. ciliata survival and growth on our study sites. The linkage between T. ciliata establishment success, early growth and soil water availability as indicated by ForWaDy, leads us to conclude that the model is a suitable stand management tool for guiding establishment of T. ciliata plantations.     

The impact of commodity price risk management on the profits of a company

It is well recognized that for the producing companies hedging the commodity price using financial products like forwards or futures has become an important part of the company's production process. But apart from the direct impacts of hedging on the production and hedging costs the use of financial products affects the financing of the company: hedging the volatile commodity prices leads to a reduction of the risk premium the company has to pay for its debt capital, since hedging contributes to more confidence of the investors in the redemption of the debt. In this paper we therefore analyze this dependency of hedging and financing and derive optimal hedging extents for companies in different market situations based on a long-term model. By hedging the commodity price, companies can realize a surplus in profits. Thereby, the optimal hedging extent for a monopolist is often up to 100%, whereas for companies in a polypolistic market the optimum is always less than 100%. These results are illustrated by examples for a producing company.     

Performance of single-gene noninvasive prenatal testing for autosomal recessive conditions in a general population setting

Objective

Carrier screening with reflex to single-gene noninvasive prenatal testing (sgNIPT) is an alternative approach for identifying pregnancies at risk for inherited autosomal recessive conditions without the need for a sample from the reproductive partner. This study is the largest clinical validation of this approach in a general population setting.

Methods

The clinical performance of carrier screening with reflex to sgNIPT for cystic fibrosis, spinal muscular atrophy, alpha thalassemias, and beta hemoglobinopathies was assessed by collecting pregnancy outcome data on patients who underwent this testing and comparing the neonatal outcome to the assay-predicted fetal risk.

Results

Of 42,067 pregnant individuals who underwent screening, 7538 carriers (17.9%) had reflex sgNIPT, and neonatal or fetal outcomes were obtained for 528 cases, including 25 affected pregnancies. Outcomes demonstrated high concordance with sgNIPT, for example, all pregnancies with 9 in 10 personalized fetal risk results were affected (positive predictive value (PPV) of 100% for the sub-group) and the sgNIPT assay showed a sensitivity of 96.0% (95% CI: 79.65%–99.90%), specificity of 95.2% (95% CI: 92.98%–96.92%), average PPV of 50.0% (95% CI: 35.23%–64.77%), and negative predictive value (NPV) of 99.8% (95% CI: 98.84%–99.99%). The end-to-end performance of carrier screening with reflex to sgNIPT was calculated to have a sensitivity of 92.4% and specificity of 99.9%, which are unaffected by partner carrier screening or misattributed paternity unlike a traditional carrier screening workflow, which has a 35% sensitivity and a maximum of 25% PPV (1 in 4) in a real-life setting.

Conclusion

This study builds upon earlier findings to confirm that carrier testing with reflex to sgNIPT is highly accurate for general population screening. Given this high accuracy and an NPV of 99.8%, this workflow should be considered as an option for most of the general pregnant population. When the biological partner sample is unavailable, this workflow should be recommended as the first-line approach.     

Greener extraction of polycyclic aromatic hydrocarbons from soil and sediment using eucalyptus oil

Environmental Chemistry Letters - Polycyclic aromatic hydrocarbons are toxic pollutants which persist in the environment. Extraction of polycyclic aromatic hydrocarbons requires large volumes of...     

Effects of La2O3 nanoparticles and bulk-La2O3 on the development of Pfaffia glomerata (Spreng.) Pedersen and respective nutrient element concentration

Environmental Science and Pollution Research - Nanoparticles (NPs) have been progressively applied in the last decades, which may impact the environment. Synthesis of pigments, growing, and...     

Health impact assessment of air pollution in an area of the largest coal mine in Brazil

Environmental Science and Pollution Research - Coal exploration and burning activities are among the activities with the greatest potential to cause atmospheric pollution due to the combustion...     

Kinetics of microbial landfill methane oxidation in biofilters

A methane oxidizing biofilter system fitted to the passive venting system of a harbor sludge landfill in Germany was characterized with respect to the the methanotrophic population, methane oxidizing capacity, and reaction kinetics. Methanotrophic cell counts stabilized on a high level with 1.3 x 10(8) to 7.1 x 10(9) cells g dw(-1) about one year after first biofilter operation, and a maximum of 1.2 x 10(11) cells g dw(-1). Potential methane oxidizing activity varied between 5.3 and 10.7 microg h(-1) g dw(-1). Cell numbers correlated well with methane oxidation activities. Extrapolation of potential activities gave methane removal rates between 35 and 109 g CH4 h(-1) m(-3), calculated for 30 degrees C. Optimum temperature was 38 degrees C for freshly sampled biofilter material and 22 degrees C for a methanotrophic enrichment culture grown at 10 degrees C incubation temperature. Substrate kinetics revealed the presence of a low-affinity methane oxidizing community with a high Vmax of 1.78 micromol CH4 h(-1) g ww(-1) and a high K(M) of 15.1 microM. K(MO2) for methane oxidation was 58 microM. No substantial methane oxidizing activity was detected below 1.7-2.6 vol.-% O2 in the gaseous phase. Methane deprivation led to a decrease in methane oxidation activity within 5-9 weeks but could still be detected after 25 weeks of substrate deprivation and was fully restored within 3 weeks of continuous methane supply. Very high salt loads are leached from the novel biofilter material, expanded clay, yielding electric conductivity values of up to 15 mS cm(-1) in the leachate. Values > 6 mS cm(-1) were shown to depress methane consumption. Water retention characteristics of the material proved to be favourable for methane oxidizing systems with a gas permeable volume of 78% of bulk volume at field capacity water content. Correspondingly, no influence of water content on methane oxidation activity could be detected at water contents between 2.5 and 20 vol.-%.     

Reproductive Success Increases with Local Density of Conspecif ics in a Desert Mustard (Lesquerella fendleri)

We investigated the effects of plant density on reproduction for an insect-pollinated desert mustard (Lesquerella fendleri [Brassicaceae]). Individual reproductive success, as measured by seeds per fruit, proportion of flowers setting fruit, and total seed production, increased with the density of conspecifics within 1 m. However, including the density of conspecifics at greater distances (1–3 m) did not significantly increase the amount of variation in reproductive success explained by the regression model. This implies that processes occurring on a scale of 1 m or less have important effects on reproduction. Total seed production also was greater for high-density plants than for otherwise similar plants with a low-density of conspecifics. We argue that increased pollinator visitation is the most likely cause of this facilitation and that investigations of the effects of rarity on reproductive success should directly consider density along with more commonly used attributes such as population size and fragmentation.     

Immune challenges and visual signalling in tree frogs

In animals, mate-choice is often based on sexual signals that carry information and help the receiver make the best choice to improve the receiver’s fitness. Orange visual sexual signals have been hypothesised to carry immune information because they are often due to carotenoid pigments which are also involved in immunity response. Although many studies have focused on the direct relationships between coloration and immunocompetence, few studies have simultaneously studied immunocompetent response and coloration variation after an immune challenge. We tested this hypothesis on starved and ad libitum-fed males of the European tree frog Hyla arborea. Our results show that male coloration is not a reliable indicator of its immune response capacity in this species. However, after an immune challenge induced by a PHA (Phaseolus vulgaris phytohaemagglutinin) injection, starved males presented a significant coloration loss and this alteration was related to the immune response intensity. Taken together, these results suggest that the brighter (lighter) coloration may be used as a cue by female to exclude males with a recent immune challenge, due to diseases or parasites for example.