An objective replacement method for censored geochemical data

Geochemical data are commonly censored, that is, concentrations for some samples are reported as less than or greater than some value. Censored data hampers statistical analysis because certain computational techniques used in statistical analysis require a complete set of uncensored data. We show that the simple substitution method for creating an uncensored dataset, e.g., replacement by3/4 times the detection limit, has serious flaws, and we present an objective method to determine the replacement value. Our basic premise is that the replacement value should equal the mean of the actual values represented by the qualified data. We adapt the maximum likelihood approach (Cohen, 1961) to estimate this mean. This method reproduces the mean and skewness as well or better than a simple substitution method using3/4 of the lower detection limit or3/4 of the upper detection limit. For a small proportion of less than substitutions, a simple-substitution replacement factor of 0.55 is preferable to3/4; for a small proportion of greater than substitutions, a simple-substitution replacement factor of 1.7 is preferable to4/3, provided the resulting replacement value does not exceed 100%. For more than 10% replacement, a mean empirical factor may be used. However, empirically determined simple-substitution replacement factors usually vary among different data sets and are less reliable with more replacements. Therefore, a maximum likelihood method is superior in general. Theoretical and empirical analyses show that true replacement factors for less thans decrease in magnitude with more replacements and larger standard deviation; those for greater thans increase in magnitude with more replacements and larger standard deviation. In contrast to any simple substitution method, the maximum likelihood method reproduces these variations. Using the maximum likelihood method for replacing less thans in our sample data set, correlation coefficients were reasonably accurately estimated in 90% of the cases for as much as 40% replacement and in 60% of the cases for 80% replacement. These results suggest that censored data can be utilized more than is commonly realized.     

Extremely alkaline (pH > 12) ground water hosts diverse microbial community

Chemically unusual ground water can provide an environment for novel communities of bacteria to develop. Here, we describe a diverse microbial community that inhabits extremely alkaline (pH > 12) ground water from the Lake Calumet area of Chicago, Illinois, where historic dumping of steel slag has filled in a wetland. Using microbial 16S ribosomal ribonucleic acid gene sequencing and microcosm experiments, we confirmed the presence and growth of a variety of alkaliphilic beta-Proteobacteria, Bacillus, and Clostridium species at pH up to 13.2. Many of the bacterial sequences most closely matched those of other alkaliphiles found in more moderately alkaline water around the world. Oxidation of dihydrogen produced by reaction of water with steel slag is likely a primary energy source to the community. The widespread occurrence of iron-oxidizing bacteria suggests that reduced iron serves as an additional energy source. These results extend upward the known range of pH tolerance for a microbial community by as much as 2 pH units. The community may provide a source of novel microbes and enzymes that can be exploited under alkaline conditions.     

Siphonostomatoid copepods infecting Squalus acutipinnis Regan, 1908 off South Africa

Squalus acutipinnis (previously included in S. megalops) individuals caught off the east, south and west coasts of South Africa were examined for siphonostomatoid copepod infection. Collected siphonostomatoids were fixed and preserved in 70% ethanol and studied under microscopes using both transmitted and incidental light. The copepods were identified and the host-parasite associations estimated by calculating their prevalence, mean intensity and mean abundance. The siphonostomatoids represented four families and six species, and included new host records for Nemesis sp., Lernaeopoda sp. and Eudactylina acanthii, and a new geographical record for E. acanthii. Squalus acutipinnis individuals were infected by relatively low loads of siphonostomatoids. The most commonly found species was Achtheinus pinguis, the only species found off all three coasts. There was no difference in the prevalence of A. pinguis in sharks sampled off the three coasts but the highest mean intensity was found on the East Coast followed by the West Coast. The overall prevalence of A. pinguis was 33.6%, and was an order of magnitude higher than that of the other siphonostomatoids recorded. At such low levels of infection it will thus be necessary to examine a large number of hosts to determine the biodiversity of siphonostomatoids and geographical differences in prevalence in South African waters.     

Limitations of single-basket trading: lessons from the Montreal Protocol for climate policy

Numerous policy options exist to reduce future greenhouse gas emissions. A single-basket approach, which controls aggregate emissions, was adopted by the Kyoto Protocol. Such an approach allows emissions reductions of one gas to be traded with those of other gases in the “basket”, with the trade “price” determined by some weighting metric like the Global Warming Potential. To reduce stratospheric ozone depletion, the Montreal Protocol also dealt with controlling many compounds, but did so employing an alternative, multi-basket scheme. Trading was allowed within each basket, but not among baskets. While the Montreal Protocol has been highly successful using this approach, we show that if a single-basket approach had been adopted the short-term success could have been at risk due to the non-unique relationship between controls and environmental impacts when using a single basket. Using climate policy as an example, and without considering technological and economic constraints, we further show that the magnitude of the ambiguities in impacts associated with a single-basket approach depends on the rapidity of the emission phaseout. Fast phaseouts lead to less ambiguity than do slow ones. These results suggest that for each set of greenhouse gas control policies considered, the benefit of additional flexibility associated with a single-basket approach should be weighed against the associated increased uncertainties in the impacts to ascertain whether a single- or a multi-basket approach has the greater chance of successfully mitigating climate change.     

Effect of advective mass transfer on field scale fluid and solute movement: Field and modeling studies at a waste disposal site in fractured rock at Oak Ridge National Laboratory, Tennessee, USA

Advective mass transfer is a pore scale mass-transfer process that affects fluid and solute movement between pore domains such as fracture and matrix in a structured porous medium. Mechanistically similar to advection in the advection-dispersion of solutes in non-structured porous medium, it redistributes solutes by moving solute and solvent simultaneously between pore domains. While there is much research on diffusive mass transfer that is often referred to as matrix diffusion, there is a lack of information and study for advective mass transfer in the literature. The objective of this research is to study the effects of advective mass transfer on fluid and solute movement between pore domains. First, field hydraulic measurements at a waste disposal site in fractured rock at Oak Ridge National Laboratory (ORNL), Tennessee, USA, are used to calibrate a fracture-matrix, two-pore-domain groundwater flow model. Latin-hypercube sensitivity analysis suggests that the uncertainty of the calibrated model parameters is small and the calibrated flow model is nearly the optimal. Fracture spacing thus obtained is used to calculate diffusive mass transfer coefficients. The individual effects of advective and diffusive mass transfer on solute movement are then quantitatively evaluated. The calculations indicate that pore structure conceptual models may significantly affect the role of advective mass transfer in field and pore-scale mass transfer. In the particular ORNL field site and with a fracture-matrix pore structure model, contribution of advective mass transfer to solute mass movement is about three to eight orders of magnitude smaller than that of diffusive mass transfer.

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Resumen La transferencia de masa advectiva es un proceso de transferencia de masa en escala intersticial que afecta el movimiento de fluido y soluto entre ámbitos porosos tal como fractura y matriz en un medio estructurado poroso. Este proceso, mecánicamente similar a la advección en la dispersión-advección de solutos de medios porosos no estructurados, redistribuye los solutos mediante el movimiento simultáneo de soluto y solvente entre ámbitos porosos. Mientras que existe bastante investigación en transferencia difusiva de masa que frecuentemente se conoce como difusión en matriz, existe falta de información y estudio de transferencia advectiva de masa en la literatura. El objetivo de esta investigación es estudiar los efectos de la transferencia advectiva de masa en el movimiento de fluido y soluto entre ámbitos porosos. Primero se utilizaron mediciones hidráulicas de campo en un sitio de depósito de residuos en roca fracturada en el Laboratorio Nacional Oak Ridge (ORNL), Tennessee, USA, para calibrar un modelo de flujo de agua subterránea de ámbito de dos poros fractura-matriz. Análisis de sensitividad hipercúbico-latino sugieren que la incertidumbre de los parámetros del modelo calibrado es pequeña y que el modelo de flujo calibrado es aproximadamente el óptimo. El espaciamiento de fracturas así obtenido se utiliza para calcular los coeficientes de transferencia de masa difusiva. Luego se evalúa cuantitativamente los efectos individuales de transferencia de masa advectiva y difusiva en el movimiento de soluto. Los cálculos indican que los modelos conceptuales de estructura porosa pueden afectar significativamente el papel de transferencia de masa advectiva en escalas de campo e intersticial de transferencia de masa. En el sitio de campo específico ORNL y con un modelo de estructura porosa de matriz-fractura, la contribución de transferencia de masa advectiva al movimiento de masa soluto es aproximadamente tres a ocho órdenes de magnitud más pequeño que la contribución por transferencia de masa difusiva.

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Résumé Résumé Le transfert advectif de masse est un processus de transfert de masse à léchelle du pore qui affecte les mouvements du fluide et du soluté entre les différents domaines de pores, tel les fractures et la matrice dans un milieu poreux structuré. Mécaniquement similaire à ladvection dans le concept advection-dispersion de solutés dans les milieux non structurés, ce transfert redistribue les solutés simultanément avec le fluide entre les différents domaines poreux. Alors que de nombreuses recherches portent sur les transferts de masse par diffusion, se référant généralement à une diffusion par la matrice, il y a un grand manquement dinformations et détudes sur les transferts de masse par advection dans la littérature. Lobjectif de cette recherche est détudier leffet du transfert advectif de masse de fluide et de soluté entre les différents domaines poreux. Premièrement, les mesures hydrauliques de terrain sur la décharge en milieu fracturé du laboratoire national dOak Ridge ORNL, Tennessee, USA, sont utilisées pour calibrer un modèle hydrogéologique à double porosité fracture-matrice. Lanalyse de sensibilité latin-hypercube suggère que lincertitude sur les paramètres du modèle est faible et que le calibrage est pratiquement optimal. Lespace de fracture résultant permet de calculer les coefficients de transfert de masse par diffusion. Les effets individuels de ladvection et de la diffusion sur les mouvements de solutés sont dés lors évalués. Les calculs indiquent que le modèle conceptuel de la structure des pores peuvent significativement affectés le rôle du transfert advectif de masse à léchelle du pore et du terrain. Dans le cas du site de lORNL et avec un modèle structuré fracture-matrice, la contribution de ladvection au transfert de masse est de lordre de trois-huitième du transfert de masse par diffusion.