Elimination of the reaction rate 'scale effect': application of the Lagrangian reactive particle-tracking method to simulate mixing-limited, field-scale biodegradation at the Schoolcraft (MI, USA) site

This is the peer reviewed version of the following article: [Ding, D., Benson, D. A., Fernàndez‐Garcia, D., Henri, C. V., Hyndman, D. W., Phanikumar, M. S., & Bolster, D. (2017). Elimination of the reaction rate “scale effect”: Application of the Lagrangian reactive particle‐tracking method to simulate mixing‐limited, field‐scale biodegradation at the Schoolcraft (MI, USA) site. Water Resources Research, 53, 10,411–10,432. https://doi.org/10.1002/2017WR021103], which has been published in final form at https://doi.org/10.1002/2017WR021103. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving.Measured (or empirically fitted) reaction rates at groundwater remediation sites are typically much lower than those found in the same material at the batch or laboratory scale. The reduced rates are commonly attributed to poorer mixing at the larger scales. A variety of methods have been proposed to account for this scaling effect in reactive transport. In this study, we use the Lagrangian particle-tracking and reaction (PTR) method to simulate a field bioremediation experiment at the Schoolcraft, MI site. A denitrifying bacterium, Pseudomonas Stutzeri strain KC (KC), was injected to the aquifer, along with sufficient substrate, to degrade the contaminant, carbon tetrachloride (CT), under anaerobic conditions. The PTR method simulates chemical reactions through probabilistic rules of particle collisions, interactions, and transformations to address the scale effect (lower apparent reaction rates for each level of upscaling, from batch to column to field scale). In contrast to a prior Eulerian reaction model, the PTR method is able to match the field-scale experiment using the rate coefficients obtained from batch experiments.Peer ReviewedPostprint (author's final draft

Introduction to Special Section: The Quest for Sustainability of Heavily Stressed Aquifers at Regional to Global Scales

This is the peer reviewed version of the following article: Butler, J. J., Gomez-Hernandez, J. J., Perrone, D., & Hyndman, D. (2021). Introduction to special section: The quest for sustainability of heavily stressed aquifers at regional to global scales. Water Resources Research, 57, e2021WR030446, which has been published in final form at https://doi.org/10.1029/2021WR030446. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving.The authors acknowledge financial support from the United States National Science Foundation (NSF), via grant EAR 1542320, to organize the Chapman meeting. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the NSF.Butler Jr., JJ.; Gómez-Hernández, JJ.; Perrone, D.; Hyndman, DW. (2021). Introduction to Special Section: The Quest for Sustainability of Heavily Stressed Aquifers at Regional to Global Scales. Water Resources Research. 57(8):1-4. https://doi.org/10.1029/2021WR030446S1457

Geostatistical analysis of centimeter-scale hydraulic conductivity variations at the MADE site

This is the published version. Copyright American Geophysical Union[1] Spatial variations in hydraulic conductivity (K) provide critical controls on solute transport in the subsurface. Recently, new direct-push tools were developed for high-resolution characterization of K variations in unconsolidated settings. These tools were applied to obtain 58 profiles (vertical resolution of 1.5 cm) from the heavily studied macrodispersion experiment (MADE) site. We compare the data from these 58 profiles with those from the 67 flowmeter profiles that have served as the primary basis for characterizing the heterogeneous aquifer at the site. Overall, the patterns of variation displayed by the two data sets are quite similar, in terms of both large-scale structure and autocorrelation characteristics. The direct-push K values are, on average, roughly a factor of 5 lower than the flowmeter values. This discrepancy appears to be attributable, at least in part, to opposite biases between the two methods, with the current versions of the direct-push tools underestimating K in the highly permeable upper portions of the aquifer and the flowmeter overestimating K in the less permeable lower portions. The vertically averaged K values from a series of direct-push profiles in the vicinity of two pumping tests at the site are consistent with the K estimates from those tests, providing evidence that the direct-push estimates are of a reasonable magnitude. The results of this field demonstration show that direct-push profiling has the potential to characterize highly heterogeneous aquifers with a speed and resolution that has not previously been possible

EON-ROSE and the Canadian Cordillera Array – Building Bridges to Span Earth System Science in Canada

EON-ROSE (Earth-System Observing Network - Réseau d’Observation du Système terrestrE) is a new initiative for a pan-Canadian research collaboration to holistically examine Earth systems from the ionosphere into the core. The Canadian Cordillera Array (CC Array) is the pilot phase, and will extend across the Cordillera from the Beaufort Sea to the U.S. border. The vision for EON-ROSE is to install a network of telemetered observatories to monitor solid Earth, environmental and atmospheric processes. EON-ROSE is an inclusive, combined effort of Canadian universities, federal, provincial and territorial government agencies, industry, and international collaborators. Brainstorming sessions and several workshops have been held since May 2016. The first station will be installed at Kluane Lake Research Station in southwestern Yukon during the summer of 2018. The purpose of this report is to provide a framework for continued discussion and development.RÉSUMÉEON-ROSE (Earth-System Observing Network - Réseau d’Observation du Système terrestrE) est une nouvelle initiative de collaboration de recherche pancanadienne visant à étudier de manière holistique les systèmes terrestres, depuis l’ionosphère jusqu’au noyau. Le Réseau canadien de la cordillère (CC Array) en est la phase pilote, laquelle couvrira toute la Cordillère, de la mer de Beaufort jusqu’à la frontière étasunienne. L’objectif d’EON-ROSE est d’installer un réseau d’observatoires télémétriques pour suivre en continu les processusterrestres, environnementaux et atmosphériques. EON-ROSE est un effort combiné et inclusif des universités canadiennes, des organismes gouvernementaux fédéraux, provinciaux et territoriaux, de l’industrie et de collaborateurs internationaux. Des séances de remue-méninges et plusieurs ateliers ont été tenus depuis mai 2016. La première station sera installée à la station de recherche du lac Kluane, dans le sud-ouest du Yukon, au cours de l’été 2018. Le but du présent rapport est de fournir un cadre de discussion et de développement continu

Impacts of the 2004 tsunami on groundwater resources in Sri Lanka, Water Resour

[1] The 26 December 2004 tsunami caused widespread destruction and contamination of coastal aquifers across southern Asia. Seawater filled domestic open dug wells and also entered the aquifers via direct infiltration during the first flooding waves and later as ponded seawater infiltrated through the permeable sands that are typical of coastal aquifers. In Sri Lanka alone, it is estimated that over 40,000 drinking water wells were either destroyed or contaminated. From February through September 2005, a team of United States, Sri Lankan, and Danish water resource scientists and engineers surveyed the coastal groundwater resources of Sri Lanka to develop an understanding of the impacts of the tsunami and to provide recommendations for the future of coastal water resources in south Asia. In the tsunami-affected areas, seawater was found to have infiltrated and mixed with fresh groundwater lenses as indicated by the elevated groundwater salinity levels. Seawater infiltrated through the shallow vadose zone as well as entered aquifers directly through flooded open wells. Our preliminary transport analysis demonstrates that the intruded seawater has vertically mixed in the aquifers because of both forced and free convection. Widespread pumping of wells to remove seawater was effective in some areas, but overpumping has led to upconing of the saltwater interface and rising salinity. We estimate that groundwater recharge from several monsoon seasons will reduce salinity of many sandy Sri Lankan coastal aquifers. However, the continued sustainability of these small and fragile aquifers for potable water will be difficult because of the rapid growth of human activities that results in more intensive groundwater pumping and increased pollution. Long-term sustainability of coastal aquifers is also impacted by the decrease in sand replenishment of the beaches due to sand mining and erosion

Dengue disease outbreak definitions are implicitly variable.

Infectious diseases rarely exhibit simple dynamics. Outbreaks (defined as excess cases beyond response capabilities) have the potential to cause a disproportionately high burden due to overwhelming health care systems. The recommendations of international policy guidelines and research agendas are based on a perceived standardised definition of an outbreak characterised by a prolonged, high-caseload, extra-seasonal surge. In this analysis we apply multiple candidate outbreak definitions to reported dengue case data from Brazil to test this assumption. The methods identify highly heterogeneous outbreak characteristics in terms of frequency, duration and case burden. All definitions identify outbreaks with characteristics that vary over time and space. Further, definitions differ in their timeliness of outbreak onset, and thus may be more or less suitable for early intervention. This raises concerns about the application of current outbreak guidelines for early warning/identification systems. It is clear that quantitatively defining the characteristics of an outbreak is an essential prerequisite for effective reactive response. More work is needed so that definitions of disease outbreaks can take into account the baseline capacities of treatment, surveillance and control. This is essential if outbreak guidelines are to be effective and generalisable across a range of epidemiologically different settings

Financial time series prediction using spiking neural networks

In this paper a novel application of a particular type of spiking neural network, a Polychronous Spiking Network, was used for financial time series prediction. It is argued that the inherent temporal capabilities of this type of network are suited to non-stationary data such as this. The performance of the spiking neural network was benchmarked against three systems: two "traditional", rate-encoded, neural networks; a Multi-Layer Perceptron neural network and a Dynamic Ridge Polynomial neural network, and a standard Linear Predictor Coefficients model. For this comparison three non-stationary and noisy time series were used: IBM stock data; US/Euro exchange rate data, and the price of Brent crude oil. The experiments demonstrated favourable prediction results for the Spiking Neural Network in terms of Annualised Return and prediction error for 5-Step ahead predictions. These results were also supported by other relevant metrics such as Maximum Drawdown and Signal-To-Noise ratio. This work demonstrated the applicability of the Polychronous Spiking Network to financial data forecasting and this in turn indicates the potential of using such networks over traditional systems in difficult to manage non-stationary environments. © 2014 Reid et al

Forest Plant and Bird Communities in the Lau Group, Fiji

We examined species composition of forest and bird communities in relation to environmental and human disturbance gradients on Lakeba (55.9 km²), Nayau (18.4 km²), and Aiwa Levu (1.2 km²), islands in the Lau Group of Fiji, West Polynesia. The unique avifauna of West Polynesia (Fiji, Tonga, Samoa) has been subjected to prehistoric human-caused extinctions but little was previously known about this topic in the Lau Group. We expected that the degree of human disturbance would be a strong determinant of tree species composition and habitat quality for surviving landbirds, while island area would be unrelated to bird diversity.All trees > 5 cm diameter were measured and identified in 23 forest plots of 500 m² each. We recognized four forest species assemblages differentiated by composition and structure: coastal forest, dominated by widely distributed species, and three forest types with differences related more to disturbance history (stages of secondary succession following clearing or selective logging) than to environmental gradients (elevation, slope, rockiness). Our point counts (73 locations in 1 or 2 seasons) recorded 18 of the 24 species of landbirds that exist on the three islands. The relative abundance and species richness of birds were greatest in the forested habitats least disturbed by people. These differences were due mostly to increased numbers of columbid frugivores and passerine insectivores in forests on Lakeba and Aiwa Levu. Considering only forested habitats, the relative abundance and species richness of birds were greater on the small but completely forested (and uninhabited) island of Aiwa Levu than on the much larger island of Lakeba.Forest disturbance history is more important than island area in structuring both tree and landbird communities on remote Pacific islands. Even very small islands may be suitable for conservation reserves if they are protected from human disturbance

EPHA2 Is Associated with Age-Related Cortical Cataract in Mice and Humans

Age-related cataract is a major cause of blindness worldwide, and cortical cataract is the second most prevalent type of age-related cataract. Although a significant fraction of age-related cataract is heritable, the genetic basis remains to be elucidated. We report that homozygous deletion of Epha2 in two independent strains of mice developed progressive cortical cataract. Retroillumination revealed development of cortical vacuoles at one month of age; visible cataract appeared around three months, which progressed to mature cataract by six months. EPHA2 protein expression in the lens is spatially and temporally regulated. It is low in anterior epithelial cells, upregulated as the cells enter differentiation at the equator, strongly expressed in the cortical fiber cells, but absent in the nuclei. Deletion of Epha2 caused a significant increase in the expression of HSP25 (murine homologue of human HSP27) before the onset of cataract. The overexpressed HSP25 was in an underphosphorylated form, indicating excessive cellular stress and protein misfolding. The orthologous human EPHA2 gene on chromosome 1p36 was tested in three independent worldwide Caucasian populations for allelic association with cortical cataract. Common variants in EPHA2 were found that showed significant association with cortical cataract, and rs6678616 was the most significant in meta-analyses. In addition, we sequenced exons of EPHA2 in linked families and identified a new missense mutation, Arg721Gln, in the protein kinase domain that significantly alters EPHA2 functions in cellular and biochemical assays. Thus, converging evidence from humans and mice suggests that EPHA2 is important in maintaining lens clarity with age