Using a Bayesian network to clarify areas requiring research in a host–pathogen system

Bayesian network analyses can be used to interactively change the strength of effect of variables in a model to explore complex relationships in new ways. In doing so, they allow one to identify influential nodes that are not well studied empirically so that future research can be prioritized. We identified relationships in host and pathogen biology to examine disease‐driven declines of amphibians associated with amphibian chytrid fungus (Batrachochytrium dendrobatidis). We constructed a Bayesian network consisting of behavioral, genetic, physiological, and environmental variables that influence disease and used them to predict host population trends. We varied the impacts of specific variables in the model to reveal factors with the most influence on host population trend. The behavior of the nodes (the way in which the variables probabilistically responded to changes in states of the parents, which are the nodes or variables that directly influenced them in the graphical model) was consistent with published results. The frog population had a 49% probability of decline when all states were set at their original values, and this probability increased when body temperatures were cold, the immune system was not suppressing infection, and the ambient environment was conducive to growth of B. dendrobatidis. These findings suggest the construction of our model reflected the complex relationships characteristic of host–pathogen interactions. Changes to climatic variables alone did not strongly influence the probability of population decline, which suggests that climate interacts with other factors such as the capacity of the frog immune system to suppress disease. Changes to the adaptive immune system and disease reservoirs had a large effect on the population trend, but there was little empirical information available for model construction. Our model inputs can be used as a base to examine other systems, and our results show that such analyses are useful tools for reviewing existing literature, identifying links poorly supported by evidence, and understanding complexities in emerging infectious‐disease systems.     

Using variance components to estimate power in a hierarchically nested sampling design

We used variance components to assess allocation of sampling effort in a hierarchically nested sampling design for ongoing monitoring of early life history stages of the federally endangered Devils Hole pupfish (DHP) (Cyprinodon diabolis). Sampling design for larval DHP included surveys (5 days each spring 2007–2009), events, and plots. Each survey was comprised of three counting events, where DHP larvae on nine plots were counted plot by plot. Statistical analysis of larval abundance included three components: (1) evaluation of power from various sample size combinations, (2) comparison of power in fixed and random plot designs, and (3) assessment of yearly differences in the power of the survey. Results indicated that increasing the sample size at the lowest level of sampling represented the most realistic option to increase the survey’s power, fixed plot designs had greater power than random plot designs, and the power of the larval survey varied by year. This study provides an example of how monitoring efforts may benefit from coupling variance components estimation with power analysis to assess sampling design.     

Immobilization of mercury by pyrite (FeS2)

Elemental mercury (Hg⁰) is a metal with a number of atypical properties, which has resulted in its use in myriad anthropogenic processes. However, these same properties have also led to severe local subsurface contamination at many places where it has been used. As such, we studied the influence of various parameters on Hg(II) sorption onto pyrite (pH, time, Hg(II) concentration), a potential subsurface reactive barrier. Batch sorption studies revealed that total Hg(II) removal increases with both pH and time. X-ray absorption spectroscopy analysis showed that a transformation in the coordination environment at low pH occurred during aging over 2 weeks, to form an ordered monolayer of monodentate Hg-Cl complexes on pyrite. In column studies packed with pure quartz sand, the transport of Hg(II) was significantly retarded by the presence of a thin pyrite-sand reactive barrier, although dissolved oxygen inhibited Hg(II) sorption onto pyrite in the column.     

Use of man-made impoundment in mitigating acid mine drainage in the North Branch Potomac River

The US Department of the Army, Baltimore District Corps of Engineers, oversees a long-term monitoring study to assess and evaluate effects of the Jennings-Randolph reservoir on biota in the North Branch Potomac River. The reservoir was intended, in part, to mitigate effects of acid mine drainage originating in upstream and headwater areas. The present study assessed recovery of benthos and fish in this system, six years after completion of the reservoir. Higher pH and lower iron and sulfate concentrations were observed upstream of the reservoir compared to preimpoundment conditions, suggesting better overall water quality in the upper North Branch. Water quality improved slightly directly downstream of the reservoir. However, the reservoir itself was poorly colonized by macrophytes and benthic organisms, and plankton composition suggested either metal toxicity and/or nutrient limitation. One large tributary to the North Branch and the reservoir (Stony River) was shown to have high (and possibly toxic) levels of manganese, iron, zinc, and aluminum due to subsurface coal mine drainage. Macroinvertebrate diversity and number of taxa were higher in sites downstream of the reservoir in the present study. Compared with previous years, the present study suggested relatively rapid recovery in the lower North Branch due to colonization from two major unimpacted tributaries in this system: Savage River and South Branch Potomac. Abundance of certain mayfly species across sites provided the most clear evidence of longitudinal gradients in water quality parameters and geomorphology. Fish data were consistent with macroinvertebrate results, but site-to-site variation in species composition was greater. Data collected between 1982 and 1987 suggested that certain fish species have unsuccessfully attempted to colonize sites directly downstream of the reservoir despite the more neutral pH water there. Our results show that recovery of biota in the North Branch Potomac was attributed to decreased acid inputs from mining operations and dilution from the Savage River, which contributed better water quality. Continued improvement of North Branch Potomac biota may not be expected unless additional mitigation attempts, either within the reservoir or upstream, are undertaken.     

Assessment of the photochemistry of OH and NO3 on Jeju Island during the Asian-dust-storm period in the spring of 2001

In this study, we examined the influence of the long-range transport of dust particles and air pollutants on the photochemistry of OH and NO3 on Jeju Island, Korea (33.17 degrees N, 126.10 degrees E) during the Asian-dust-storm (ADS) period of April 2001. Three ADS events were observed during the periods of April 10-12, 13-14, and 25-26. Average concentration levels of daytime OH and nighttime NO3 on Jeju Island during the ADS period were estimated to be about 1x10(6) and 2x10(8) moleculescm(-3) ( approximately 9 pptv), respectively. OH levels during the ADS period were lower than those during the non-Asian-dust-storm (NADS) period by a factor of 1.5. This was likely to result from higher CO levels and the significant loading of dust particles, reducing the photolysis frequencies of ozone. Decreases in NO3 levels during the ADS period was likely to be determined mainly by the enhancement of the N2O5 heterogeneous reaction on dust aerosol surfaces. Averaged over 24 h, the reaction between HO2 and NO was the most important source of OH during the study period, followed by ozone photolysis, which contributed more than 95% of the total source. The reactions with CO, NO2, and non-methane hydrocarbons (NMHCs) during the study period were major sinks for OH. The reaction of N2O5 on aerosol surfaces was a more important sink for nighttime NO3 during the ADS due to the significant loading of dust particles. The reaction of NO3 with NMHCs and the gas-phase reaction of N2O5 with water vapor were both significant loss mechanisms during the study period, especially during the NADS. However, dry deposition of these oxidized nitrogen species and a heterogeneous reaction of NO3 were of no importance.     

The Role of Cloud Processing in the Relationship Between Wet Deposited Sulphur and Sulphur Dioxide Emissions

It is well established that wet deposition of sulphate in the UKhas fallen by a much smaller fraction than have emissions of sulphur dioxide. Dry deposition of sulphur has decreased in proportion to the decline in emissions. A number of suggestionshave been made which offer possible explanations for this non-linearity between emissions and wet deposition. In this paper amodel of the processing of sulphur dioxide by aqueous phase cloudchemistry in a cloudy boundary layer is presented. This work doesnot simulate all the details of the mechanisms by which sulphate is incorporated into precipitation. It does, however, explorethe non-linearity of this oxidation process. It is shown that theoxidation of sulphur dioxide, in these conditions, over the UK isdominated by oxidation by ozone. The rate of sulphate productionis then controlled by the availability of the one basic trace gasin the atmosphere ammonia. Using realistic concentrations of thereacting species this is found to simulate well the observed non-linearity. The model predicts that sulphate and sulphur dioxideconcentrations will be uncorrelated in the cloudy boundary layerbut that ammonium and sulphate will be well correlated. Fieldobservations at a cloudy site in Northern England are consistentwith these predictions.