Generalized site occupancy models allowing for false positive and false negative errors

Site occupancy models have been developed that allow for imperfect species detection or "false negative" observations. Such models have become widely adopted in surveys of many taxa. The most fundamental assumption underlying these models is that "false positive" errors are not possible. That is, one cannot detect a species where it does not occur. However, such errors are possible in many sampling situations for a number of reasons, and even low false positive error rates can induce extreme bias in estimates of site occupancy when they are not accounted for. In this paper, we develop a model for site occupancy that allows for both false negative and false positive error rates. This model can be represented as a two-component finite mixture model and can be easily fitted using freely available software. We provide an analysis of avian survey data using the proposed model and present results of a brief simulation study evaluating the performance of the maximum-likelihood estimator and the naive estimator in the presence of false positive errors.     

Estimating species richness and accumulation by modeling species occurrence and detectability

A statistical model is developed for estimating species richness and accumulation by formulating these community-level attributes as functions of model-based estimators of species occurrence while accounting for imperfect detection of individual species. The model requires a sampling protocol wherein repeated observations are made at a collection of sample locations selected to be representative of the community. This temporal replication provides the data needed to resolve the ambiguity between species absence and nondetection when species are unobserved at sample locations. Estimates of species richness and accumulation are computed for two communities, an avian community and a butterfly community. Our model-based estimates suggest that detection failures in many bird species were attributed to low rates of occurrence, as opposed to simply low rates of detection. We estimate that the avian community contains a substantial number of uncommon species and that species richness greatly exceeds the number of species actually observed in the sample. In fact, predictions of species accumulation suggest that even doubling the number of sample locations would not have revealed all of the species in the community. In contrast, our analysis of the butterfly community suggests that many species are relatively common and that the estimated richness of species in the community is nearly equal to the number of species actually detected in the sample. Our predictions of species accumulation suggest that the number of sample locations actually used in the butterfly survey could have been cut in half and the asymptotic richness of species still would have been attained. Our approach of developing occurrence-based summaries of communities while allowing for imperfect detection of species is broadly applicable and should prove useful in the design and analysis of surveys of biodiversity.     

Extrinsic and intrinsic controls of zooplankton diversity in lakes

Pelagic crustacean zooplankton were collected from 336 Norwegian lakes covering a wide range of latitude, altitude, lake area, mean depth, production (as chlorophyll a), and fish community structure. Mean zooplankton species richness during the ice-free season was generally low at high latitudes and altitudes. Further, lower species richness was recorded in western lakes, possibly reflecting constraints on migration and dispersal. However, despite obvious spatial limitations, geographic boundaries were only weak predictors of mean zooplankton richness. Similarly, lake surface area did not contribute positively to mean richness such as seen in other ecosystem surveys. Rather, intrinsic factors such as primary production and fish community (planktivore) structure were identified by regression analysis as the major predictors of zooplankton diversity, while a positive correlation was observed between species richness and total zooplankton biomass. However, in spite of a large number of variables included in this study, the predictive power of multiple regression models was modest (<50% variance explained), pointing to a major role for within-lake properties, as yet unidentified intrinsic forces, stochasticity, or dispersal as constraints on zooplankton diversity in these lakes.     

Adding infection to injury: synergistic effects of predation and parasitism on amphibian malformations

We explored the importance of interactions between parasite infection and predation in driving an emerging phenomenon of conservation importance: amphibian limb malformations. We suggest that injury resulting from intraspecific predation in combination with trematode infection contributes to the frequency and severity of malformations in salamanders. By integrating field surveys and experiments, we evaluated the individual and combined effects of conspecific attack and parasite (Ribeiroia ondatrae) infection on limb development of long-toed salamanders (Ambystoma macrodactylum). In the absence of Ribeiroia, abnormalities involved missing digits, feet, or limbs and were similar to those produced by cannibalistic attack in experimental trials. At field sites that supported Ribeiroia, malformations were dominated by extra limbs and digits. Correspondingly, laboratory exposure of larval salamanders to Ribeiroia cercariae over a 30-day period induced high frequencies of malformations, including extra digits, extra limbs, cutaneous fusion, and micromelia. However, salamander limbs exposed to both injury and infection exhibited 3-5 times more abnormalities than those exposed to either factor alone. Infection also caused significant delays in limb regeneration and time-to-metamorphosis. Taken together, these results help to explain malformation patterns observed in natural salamander populations while emphasizing the importance of interactions between parasitism and predation in driving disease.     

Effects of arbuscular mycorrhizal inoculation on uranium and arsenic accumulation by Chinese brake fern (Pteris vittata L.) from a uranium mining-impacted soil

A glasshouse experiment was conducted to investigate U and As accumulation by Chinese brake fern, Pteris vittata L., in association with different arbuscular mycorrhizal fungi (AMF) from a U and As contaminated soil. The soil used contains 111 mg U kg(-1) and 106 mg As kg(-1). P. vittata L. was inoculated with each of three AMF, Glomus mosseae, Glomus caledonium and Glomus intraradices. Two harvests were made during plant growth (two and three months after transplanting). Mycorrhizal colonization depressed plant growth particularly at the early stages. TF (transfer factor) values for As from soil to fronds were higher than 1.0, while those for roots were much lower. Despite the growth depressions, AM colonization had no effect on tissue As concentrations. Conversely, TF values for U were much higher for roots than for fronds, indicating that only very small fraction of U was translocated to fronds (less than 2%), regardless of mycorrhizal colonization. Mycorrhizal colonization significantly increased root U concentrations at both harvests. Root colonization with G. mosseae or G. intraradices led to an increase in TF values for U from 7 (non-inoculation control) to 14 at the first harvest. The highest U concentration of 1574 mg kg(-1) was recorded in roots colonized by G. mosseae at the second harvest. The results suggested that P. vittata in combination with appropriate AMF would play very important roles in bioremediation of contaminated environments characterized by a multi-pollution.     

Photocatalytic oxidation of soot by P25 TiO2 films

The photomineralisation of soot by P25 titania films is studied using FT-IR and the process shown to involve the oxidation of carbon to CO2 exclusively. The efficiency of this process is low, however, with a formal quantum efficiency of 1.1 x 10(-4) molecules of carbon oxidized per incident photon of UVA light. The cause of this low efficiency is attributed largely to the less than intimate contact between the fibrous soot layer and the surface of the photocatalyst.     

Titration Curves: A Useful Instrument for Assessing the Buffer Systems of Acidic Mining Waters (10 pp)

Background, Aims and Scope The acidification of mine waters is generally caused by metal sulfide oxidation, related to mining activities. These waters are characterized by low pH and high acidity due to strong buffering systems. The standard acidity parameter, the Base Neutralization Capacity (BNC) is determined by endpoint titration, and reflects a cumulative parameter of both hydrogen ions and all buffering systems, but does not give information on the individual buffer systems. We demonstrate that a detailed interpretation of titration curves can provide information about the strength of the buffering systems. The buffering systems are of importance for environmental studies and treatment of acidic mining waters. Methods Titrations were carried out by means of an automatic titrator using acidic mining waters from Germany and Canada. The curves were interpreted, compared with each other, to endpoint titration results and to elemental concentrations contained therein. Results and Discussion The titration curves were highly reproducible, and contained information about the strength of the buffer systems present. Interpretations are given, and the classification and comparison of acidic mining waters, by the nature and strength of their buffering systems derived from titration curves are discussed. The BNC-values calculated from the curves were more precise than the ones determined by the standard endpoint titration method. Due to the complex buffer mechanisms in acidic mining waters, the calculation of major metal concentrations from the shape of the titration curve resulted in estimates, which should not be confused with precise elemental analysis results. Conclusion Titration curves provide an inexpensive, valuable and versatile tool, by which to obtain sophisticated information of the acidity in acidic water. The information about the strength of the present buffer systems can help to understand and document the complex nature of acidic mining water buffer systems. Finally, the interpretation of titration curves could help to improve treatment measurements and the ecological understanding of these acidic waters.     

Recent developments in the application of risk analysis to waste technologies

The European waste sector is undergoing a period of unprecedented change driven by business consolidation, new legislation and heightened public and government scrutiny. One feature is the transition of the sector towards a process industry with increased pre-treatment of wastes prior to the disposal of residues and the co-location of technologies at single sites, often also for resource recovery and residuals management. Waste technologies such as in-vessel composting, the thermal treatment of clinical waste, the stabilisation of hazardous wastes, biomass gasification, sludge combustion and the use of wastes as fuel, present operators and regulators with new challenges as to their safe and environmentally responsible operation. A second feature of recent change is an increased regulatory emphasis on public and ecosystem health and the need for assessments of risk to and from waste installations. Public confidence in waste management, secured in part through enforcement of the planning and permitting regimes and sound operational performance, is central to establishing the infrastructure of new waste technologies. Well-informed risk management plays a critical role. We discuss recent developments in risk analysis within the sector and the future needs of risk analysis that are required to respond to the new waste and resource management agenda.     

Comparing the usability and reliability of a generic and a domain-specific medical error taxonomy

Medical error taxonomies are used to report and analyse patient safety incidents. Medical error taxonomies can be generic or domain-specific. In comparing generic and domain-specific medical error taxonomies, the literature compares the information both type of taxonomies classify. There is little evidence the taxonomies have been compared in terms of usability and reliability. Twenty nurses and 21 pharmacists participated in a study comparing the usability and reliability of a generic medical error taxonomy and a medication error taxonomy. The medical error taxonomies utilized were the Patient Safety Event Taxonomy and the NCC MERP Taxonomy of Medication Error. The study found no significant difference in the usability ratings of both taxonomies. The taxonomies required different amount of time to classify patient safety incidents and had significantly different reliability levels. The reliability of the NCC MERP Taxonomy of Medication Error was significantly different when used by nurses and pharmacists. The taxonomy was also preferred by the majority of participants. Some recommendations are made about the design of future medical error taxonomies.     

Detecting deterrence from patrol data

The threat posed to protected areas by the illegal killing of wildlife is countered principally by ranger patrols that aim to detect and deter potential offenders. Deterring poaching is a fundamental conservation objective, but its achievement is difficult to identify, especially when the prime source of information comes in the form of the patrols’ own records, which inevitably contain biases. The most common metric of deterrence is a plot of illegal activities detected per unit of patrol effort (CPUE) against patrol effort (CPUE-E). We devised a simple, mechanistic model of law breaking and law enforcement in which we simulated deterrence alongside exogenous changes in the frequency of offences under different temporal patterns of enforcement effort. The CPUE-E plots were not reliable indicators of deterrence. However, plots of change in CPUE over change in effort (ΔCPUE-ΔE) reliably identified deterrence, regardless of the temporal distribution of effort or any exogenous change in illegal activity levels as long as the time lag between patrol effort and subsequent behavioral change among offenders was approximately known. The ΔCPUE-ΔE plots offered a robust, simple metric for monitoring patrol effectiveness; were no more conceptually complicated than the basic CPUE-E plots; and required no specialist knowledge or software to produce. Our findings demonstrate the need to account for temporal autocorrelation in patrol data and to consider appropriate (and poaching-activity-specific) intervals for aggregation. They also reveal important gaps in understanding of deterrence in this context, especially the mechanisms by which it occurs. In practical applications, we recommend the use of ΔCPUE-ΔE plots in preference to other basic metrics and advise that deterrence should be suspected only if there is a clear negative slope. Distinct types of illegal activity should not be grouped together for analysis, especially if the signs of their occurrence have different persistence times in the environment.