Remotely sensed above-ground storage tank dataset for object detection and infrastructure assessment.

Remotely sensed imagery has increased dramatically in quantity and public availability. However, automated, large-scale analysis of such imagery is hindered by a lack of the annotations necessary to train and test machine learning algorithms. In this study, we address this shortcoming with respect to above-ground storage tanks (ASTs) that are used in a wide variety of industries. We annotated available high-resolution, remotely sensed imagery to develop an original, publicly available multi-class dataset of ASTs. This dataset includes geospatial coordinates, border vertices, diameters, and orthorectified imagery for over 130,000 ASTs from five labeled classes (external floating roof tanks, closed roof tanks, spherical pressure tanks, sedimentation tanks, and water towers) across the contiguous United States. This dataset can be used directly or to train machine learning algorithms for large-scale risk and hazard assessment, production and capacity estimation, and infrastructure evaluation.

Total Social Costs and Benefits of Long-Distance Hydropower Transmission.

Increasing amounts of hydropower are being exported from Canada to the northern United States. Recently proposed projects would increase transmission capacity to U.S. population centers without increasing generation. This avoids generation-side impacts from hydroelectric development and introduces power to the U.S. energy mix that is dispatchable, unlike wind and solar, with greenhouse gas emissions generally lower than those of fossil fuels. There is, however, a lack of analysis comparing high upfront capital costs to social benefits and controversy over valuation of social costs of hydropower from existing generation given the negligible marginal cost of production. This analysis evaluates direct and indirect costs in comparison to alternatives for a 1250 MW transmission line from Canada to New York City currently under development to replace the recent loss of ∼15 TWh year-1 of nuclear generation. For the case study considered, we find that long-distance transmission avoids $13.2 billion ($12.1-14.4 billion) in total social costs by 2050. This includes $4.2 billion ($3.4-5.1 billion) from premature mortality in disproportionately Hispanic and African American or Black counties (roughly 306 avoided deaths). In an extensive sensitivity analysis, results are robust to all modeling choices other than the cost assigned to hydropower: the nominal dollar value of hydropower imports (payments from buyer to seller) commonly used in cost-benefit analysis leads to substantial underestimates of net benefits from transmission projects. The opportunity cost of these imports (e.g., environmental benefits foregone in alternative export markets) is a better metric for cost but is difficult to estimate.

Emerald ash borer intensifies harvest regimes on private land.

Invasive forest insects have significant direct impacts on forest ecosystems and they are also generating new risks, uncertainties, and opportunities for forest landowners. The growing prevalence and inexorable spread of invasive insects across the United States, combined with the fact that the majority of the nation's forests are controlled by thousands of autonomous private landowners, raises an important question: To what extent will private landowners alter their harvest practices in response to insect invasions? Using a quasi-experimental design, we conducted a causal analysis to investigate the influence of the highly impactful emerald ash borer (EAB) on (1) annual probability of harvest; (2) intensity of harvest; and (3) diameter of harvested trees, for both ash and non-ash species on private land throughout the Midwest and mid-Atlantic regions of the United States. We found that EAB detection had a negative impact on annual harvest probability and a positive impact on harvest intensity, resulting in a net increase in harvested biomass. Furthermore, our estimates suggest that EAB detection will influence private landowners to harvest greater quantities of ash, relative to non-ash species. We also found that harvested trees in EAB-infested areas had smaller diameters, on average, compared with those unaffected by EAB. These results can help policymakers, forest managers, and extension programs to anticipate and better advise landowners and managers about their options and the associated outcomes for forests.

Social science research to inform solar geoengineering.

What are the benefits and drawbacks, and for whom?.

Communicating Arsenic's Risks.

Arsenic is a naturally occurring toxic metalloid that has many human health implications. Its strong prevalence in the bedrock and thus much of the well water in New England puts many private well owners at risk. It is also found in food products, particularly those that contain rice. Despite the documented health risks, arsenic is not high on the list of concerns for residents of the region. This study will describe two types of environmental communication efforts that have been undertaken by the Dartmouth Toxic Metals Superfund Research Program (DTMSRP)-the development and evaluation of a comprehensive website, Arsenic and You, and a mental models research approach to better understand the disconnect between expert and community perceptions of arsenic risk. We find that there are knowledge gaps between the two, particularly regarding the origin of arsenic in drinking water and food, the necessity of testing well water, and the process for treating water that is above recommended limits. Moreover, the mental models approach provides a structured framework for better understanding these gaps. A website can address some of these disconnects, and it is important to have a "one-stop shop" for vetted information on the risks and steps to reduce exposure.

Effects of temperature, salinity, and sediment organic carbon on methylmercury bioaccumulation in an estuarine amphipod.

Mercury (Hg) is a global contaminant that poses a human health risk in its organic form, methylmercury (MeHg), through consumption of fish and fishery products. Bioaccumulation of Hg in the aquatic environment is controlled by a number of factors expected to be altered by climate change. We examined the individual and combined effects of temperature, sediment organic carbon, and salinity on the bioaccumulation of MeHg in an estuarine amphipod, Leptocheirus plumulosus, when exposed to sediment from two locations in the Gulf of Maine (Kittery and Bass Harbor) that contained different levels of MeHg and organic carbon. Higher temperatures and lower organic carbon levels individually increased uptake of MeHg by L. plumulosus as measured by the biota-sediment accumulation factor (BSAF), while the effect of salinity on BSAF differed by sediment source. Multi-factor statistical modeling using all data revealed a significant interaction between temperature and organic carbon for both sediments, in which increased temperature had a negative effect on BSAF at the lowest carbon levels and a positive effect at higher levels. Our results suggest that increased temperature and carbon loading, of a magnitude expected as a result from climate change, could be associated with a net decrease in amphipod BSAF of 50 to 71%, depending on sediment characteristics. While these are only first-order projections, our results indicate that the future fate of MeHg in marine food webs is likely to depend on a number of factors beyond Hg loading.

Trade-offs between three forest ecosystem services across the state of New Hampshire, USA: timber, carbon, and albedo.

Forests are more frequently being managed to store and sequester carbon for the purposes of climate change mitigation. Generally, this practice involves long-term conservation of intact mature forests and/or reductions in the frequency and intensity of timber harvests. However, incorporating the influence of forest surface albedo often suggests that long rotation lengths may not always be optimal in mitigating climate change in forests characterized by frequent snowfall. To address this, we investigated trade-offs between three ecosystem services: carbon storage, albedo-related radiative forcing, and timber provisioning. We calculated optimal rotation length at 498 diverse Forest Inventory and Analysis forest sites in the state of New Hampshire, USA. We found that the mean optimal rotation lengths across all sites was 94 yr (standard deviation of sample means = 44 yr), with a large cluster of short optimal rotation lengths that were calculated at high elevations in the White Mountain National Forest. Using a regression tree approach, we found that timber growth, annual storage of carbon, and the difference between annual albedo in mature forest vs. a post-harvest landscape were the most important variables that influenced optimal rotation. Additionally, we found that the choice of a baseline albedo value for each site significantly altered the optimal rotation lengths across all sites, lowering the mean rotation to 59 yr with a high albedo baseline, and increasing the mean rotation to 112 yr given a low albedo baseline. Given these results, we suggest that utilizing temperate forests in New Hampshire for climate mitigation purposes through carbon storage and the cessation of harvest is appropriate at a site-dependent level that varies significantly across the state.

Integration of ecological-biological thresholds in conservation decision making.

In the Anthropocene, coupled human and natural systems dominate and only a few natural systems remain relatively unaffected by human influence. On the one hand, conservation criteria based on areas of minimal human impact are not relevant to much of the biosphere. On the other hand, conservation criteria based on economic factors are problematic with respect to their ability to arrive at operational indicators of well-being that can be applied in practice over multiple generations. Coupled human and natural systems are subject to economic development which, under current management structures, tends to affect natural systems and cross planetary boundaries. Hence, designing and applying conservation criteria applicable in real-world systems where human and natural systems need to interact and sustainably coexist is essential. By recognizing the criticality of satisfying basic needs as well as the great uncertainty over the needs and preferences of future generations, we sought to incorporate conservation criteria based on minimal human impact into economic evaluation. These criteria require the conservation of environmental conditions such that the opportunity for intergenerational welfare optimization is maintained. Toward this end, we propose the integration of ecological-biological thresholds into decision making and use as an example the planetary-boundaries approach. Both conservation scientists and economists must be involved in defining operational ecological-biological thresholds that can be incorporated into economic thinking and reflect the objectives of conservation, sustainability, and intergenerational welfare optimization.

A Community-Driven Intervention in Tuftonboro, New Hampshire, Succeeds in Altering Water Testing Behavior.

Maximum contaminant levels created by the U.S. Environmental Protection Agency under the Safe Drinking Water Act do not apply to private wells. Rather, the onus is on individual households to undertake regular water testing. Several barriers exist to testing and treating water from private wells, including a lack of awareness about both well water as a potential source of contaminants and government-recommended water testing schedules; a health literacy level that may not be sufficient to interpret complex environmental health messages; the inconvenience of water testing; the financial costs of testing and treatment; and a myriad of available treatment options. The existence of these barriers is problematic because well water can be a source of hazardous contaminants. This article describes an initiative--undertaken by the Tuftonboro (New Hampshire) Conservation Commission, with support from state agencies and a research program at Dartmouth College--to increase water testing rates in a rural region with a relatively high number of wells. The project prompted more water tests at the state laboratory in one day than in the prior six years. This suggests that community-driven, collaborative efforts to overcome practical barriers could be successful at raising testing rates and ultimately improving public health.

Genetic polymorphisms modify bladder cancer recurrence and survival in a USA population-based prognostic study.

OBJECTIVE: To identify genetic variants that modify bladder cancer prognosis focusing on genes involved in major biological carcinogenesis processes (apoptosis, proliferation, DNA repair, hormone regulation, immune surveillance, and cellular metabolism), as nearly half of patients with bladder cancer experience recurrences reliable predictors of this recurrent phenotype are needed to guide surveillance and treatment. PATIENTS AND METHODS: We analysed variant genotypes hypothesised to modify these processes in 563 patients with urothelial-cell carcinoma enrolled in a population-based study of incident bladder cancer conducted in New Hampshire, USA. After diagnosis, patients were followed over time to ascertain recurrence and survival status, making this one of the first population-based studies with detailed prognosis data. Cox proportional hazards regression was used to assess the relationship between single nucleotide polymorphisms (SNPs) and prognosis endpoints. RESULTS: Patients with aldehyde dehydrogenase 2 (ALDH2) variants had a shorter time to first recurrence (adjusted non-invasive hazard ratio [HR] 1.90, 95% confidence interval [CI] 1.29-2.78). There was longer survival among patients with non-invasive tumours associated with DNA repair X-ray repair cross-complementing protein 4 (XRCC4) heterozygous genotype compared with wild-type (adjusted HR 0.53, 95% CI 0.38-0.74). Time to recurrence was shorter for patients who had a variant allele in vascular cellular adhesion molecule 1 (VCAM1) and were treated with immunotherapy (P interaction < 0.001). CONCLUSIONS: Our analysis suggests candidate prognostic SNPs that could guide personalised bladder cancer surveillance and treatment.

Benthic and pelagic pathways of methylmercury bioaccumulation in estuarine food webs of the northeast United States.

Methylmercury (MeHg) is a contaminant of global concern that bioaccumulates and bioamagnifies in marine food webs. Lower trophic level fauna are important conduits of MeHg from sediment and water to estuarine and coastal fish harvested for human consumption. However, the sources and pathways of MeHg to these coastal fisheries are poorly known particularly the potential for transfer of MeHg from the sediment to biotic compartments. Across a broad gradient of human land impacts, we analyzed MeHg concentrations in food webs at ten estuarine sites in the Northeast US (from the Hackensack Meadowlands, NJ to the Gulf of Maine). MeHg concentrations in water column particulate material, but not in sediments, were predictive of MeHg concentrations in fish (killifish and Atlantic silversides). Moreover, MeHg concentrations were higher in pelagic fauna than in benthic-feeding fauna suggesting that MeHg delivery to the water column from methylation sites from within or outside of the estuary may be an important driver of MeHg bioaccumulation in estuarine pelagic food webs. In contrast, bulk sediment MeHg concentrations were only predictive of concentrations of MeHg in the infaunal worms. Our results across a broad gradient of sites demonstrate that the pathways of MeHg to lower trophic level estuarine organisms are distinctly different between benthic deposit feeders and forage fish. Thus, even in systems with contaminated sediments, transfer of MeHg into estuarine food webs maybe driven more by the efficiency of processes that determine MeHg input and bioavailability in the water column.

Nuclear repulsion enables division autonomy in a single cytoplasm.

BACKGROUND: Current models of cell-cycle control, based on classic studies of fused cells, predict that nuclei in a shared cytoplasm respond to the same CDK activities to undergo synchronous cycling. However, synchrony is rarely observed in naturally occurring syncytia, such as the multinucleate fungus Ashbya gossypii. In this system, nuclei divide asynchronously, raising the question of how nuclear timing differences are maintained despite sharing a common milieu. RESULTS: We observe that neighboring nuclei are highly variable in division-cycle duration and that neighbors repel one another to space apart and demarcate their own cytoplasmic territories. The size of these territories increases as a nucleus approaches mitosis and can influence cycling rates. This nonrandom nuclear spacing is regulated by microtubules and is required for nuclear asynchrony, as nuclei that transiently come in very close proximity will partially synchronize. Sister nuclei born of the same mitosis are generally not persistent neighbors over their lifetimes yet remarkably retain similar division cycle times. This indicates that nuclei carry a memory of their birth state that influences their division timing and supports that nuclei subdivide a common cytosol into functionally distinct yet mobile compartments. CONCLUSIONS: These findings support that nuclei use cytoplasmic microtubules to establish "cells within cells." Individual compartments appear to push against one another to compete for cytoplasmic territory and insulate the division cycle. This provides a mechanism by which syncytial nuclei can spatially organize cell-cycle signaling and suggests size control can act in a system without physical boundaries.

Protein aggregation behavior regulates cyclin transcript localization and cell-cycle control.

Little is known about the active positioning of transcripts outside of embryogenesis or highly polarized cells. We show here that a specific G1 cyclin transcript is highly clustered in the cytoplasm of large multinucleate cells. This heterogeneous cyclin transcript localization results from aggregation of an RNA-binding protein, and deletion of a polyglutamine stretch in this protein results in random transcript localization. These multinucleate cells are remarkable in that nuclei cycle asynchronously despite sharing a common cytoplasm. Notably, randomization of cyclin transcript localization significantly diminishes nucleus-to-nucleus differences in the number of mRNAs and synchronizes cell-cycle timing. Thus, nonrandom cyclin transcript localization is important for cell-cycle timing control and arises due to polyQ-dependent behavior of an RNA-binding protein. There is a widespread association between polyQ expansions and RNA-binding motifs, suggesting that this is a broadly exploited mechanism to produce spatially variable transcripts and heterogeneous cell behaviors. PAPERCLIP:

Using Bayesian networks to discover relations between genes, environment, and disease.

We review the applicability of Bayesian networks (BNs) for discovering relations between genes, environment, and disease. By translating probabilistic dependencies among variables into graphical models and vice versa, BNs provide a comprehensible and modular framework for representing complex systems. We first describe the Bayesian network approach and its applicability to understanding the genetic and environmental basis of disease. We then describe a variety of algorithms for learning the structure of a network from observational data. Because of their relevance to real-world applications, the topics of missing data and causal interpretation are emphasized. The BN approach is then exemplified through application to data from a population-based study of bladder cancer in New Hampshire, USA. For didactical purposes, we intentionally keep this example simple. When applied to complete data records, we find only minor differences in the performance and results of different algorithms. Subsequent incorporation of partial records through application of the EM algorithm gives us greater power to detect relations. Allowing for network structures that depart from a strict causal interpretation also enhances our ability to discover complex associations including gene-gene (epistasis) and gene-environment interactions. While BNs are already powerful tools for the genetic dissection of disease and generation of prognostic models, there remain some conceptual and computational challenges. These include the proper handling of continuous variables and unmeasured factors, the explicit incorporation of prior knowledge, and the evaluation and communication of the robustness of substantive conclusions to alternative assumptions and data manifestations.

Interannual variability in the timing of New England shellfish toxicity and relationships to environmental forcing.

Routine monitoring along the coast of the Gulf of Maine (GoM) reveals shellfish toxicity nearly every summer, but at varying times, locations, and magnitudes. The responsible toxin is known to be produced by the dinoflagellate Alexandrium fundyense, yet there is little apparent association between Alexandrium abundance and shellfish toxicity. One possibility is that toxic cells are persistent in offshore areas and variability in shellfish toxicity is caused not by changes in overall abundance, but rather by variability in transport processes. Measurements of offshore Alexandrium biomass are scarce, so we bypass cell abundance as an explanatory variable and focus instead on the relations between shellfish toxicity and concurrent metrics of GoM meteorology, hydrology, and oceanography. While this yields over two decades (1985-2005) of data representing a variety of interannual conditions, the toxicity data are gappy in spatial and temporal coverage. We address this through a combination of parametric curve fitting and hierarchical cluster analysis to reveal eight archetypical modes of seasonal toxicity timing. Groups of locations are then formed that have similar interannual patterns in these archetypes. Finally, the interannual patterns within each group are related to available environmental metrics using classification trees. Results indicate that a weak cross-shore sea surface temperature (SST) gradient in the summer is the strongest correlate of shellfish toxicity, likely by signifying a hydrological connection between offshore Alexandrium populations and near-shore shellfish beds. High cumulative downwelling wind strength early in the season is revealed as a precursor consistent with this mechanism. Although previous studies suggest that alongshore transport is important in moving Alexandrium from the eastern to western GoM, alongshore SST gradient is not an important correlate of toxicity in our study. We conclude by discussing the implications of our results for designing efficient and effective shellfish monitoring programs along the GoM coast.

Weighted multiple testing procedures for genomic studies.

With the rapid development of biological technology, measurement of thousands of genes or SNPs can be carried out simultaneously. Improved procedures for multiple hypothesis testing when the number of tests is very large are critical for interpreting genomic data. In this paper, we review recent developments on three distinct but closely related methods involving p-value weighting to improve statistical power while also controlling for the false discovery rate or the family wise error rate.

Bayesian networks in environmental and resource management.

This overview article for the special series, "Bayesian Networks in Environmental and Resource Management," reviews 7 case study articles with the aim to compare Bayesian network (BN) applications to different environmental and resource management problems from around the world. The article discusses advances in the last decade in the use of BNs as applied to environmental and resource management. We highlight progress in computational methods, best-practices for model design and model communication. We review several research challenges to the use of BNs in environmental and resource management that we think may find a solution in the near future with further research attention.

A Bayesian network model for integrative river rehabilitation planning and management.

As rehabilitation of previously channelized rivers becomes more common worldwide, flexible integrative modeling tools are needed to help predict the morphological, hydraulic, economic, and ecological consequences of the rehabilitation activities. Such predictions can provide the basis for planning and long-term management efforts that attempt to balance the diverse interests of river system stakeholders. We have previously reported on a variety of modeling methods and decision support concepts that can assist with various aspects of the river rehabilitation process. Here, we bring all of these tools together into a probability network model that links management actions, through morphological and hydraulic changes, to the ultimate ecological and economic consequences. Although our model uses a causal graph representation common to Bayesian networks, we do not limit ourselves to discrete-valued nodes or conditional Gaussian distributions as required by most Bayesian network implementations. This precludes us from carrying out easy probabilistic inference but gives us the advantages of functional and distributional flexibility and enhanced predictive accuracy, which we believe to be more important in most environmental management applications. We exemplify model application to a large, recently completed rehabilitation project in Switzerland.

A conserved G1 regulatory circuit promotes asynchronous behavior of nuclei sharing a common cytoplasm.

Synthesis and accumulation of conserved cell cycle regulators such as cyclins are thought to promote G1/S and G2/M transitions in most eukaryotes. When cells at different stages of the cell cycle are fused to form heterokaryons, the shared complement of regulators in the cytoplasm induces the nuclei to become synchronized. However, multinucleate fungi often display asynchronous nuclear division cycles, even though the nuclei inhabit a shared cytoplasm. Similarly, checkpoints can induce nuclear asynchrony in multinucleate cells by arresting only the nucleus that receives damage. The cell biological basis for nuclear autonomy in a common cytoplasm is not known. Here we show that in the filamentous fungus Ashbya gossypii, sister nuclei born from one mitosis immediately lose synchrony in the subsequent G1 interval. A conserved G1 transcriptional regulatory circuit involving the Rb-analogue Whi5p promotes the asynchronous behavior yet Whi5 protein is uniformly distributed among nuclei throughout the cell cycle. The homologous Whi5p circuit in S. cerevisiae employs positive feedback to promote robust and coherent entry into the cell cycle. We propose that positive feedback in this same circuit generates timing variability in a multinucleate cell. These unexpected findings indicate that a regulatory program whose products (mRNA transcripts) are translated in a common cytoplasm can nevertheless promote variability in the individual behavior of sister nuclei.

Improving water quality assessments through a hierarchical Bayesian analysis of variability.

Water quality measurement error and variability, while well-documented in laboratory-scale studies, is rarely acknowledged or explicitly resolved in most model-based water body assessments, including those conducted in compliance with the United States Environmental Protection Agency (USEPA) Total Maximum Daily Load (TMDL) program. Consequently, proposed pollutant loading reductions in TMDLs and similar water quality management programs may be biased, resulting in either slower-than-expected rates of water quality restoration and designated use reinstatement or, in some cases, overly conservative management decisions. To address this problem, we present a hierarchical Bayesian approach for relating actual in situ or model-predicted pollutant concentrations to multiple sampling and analysis procedures, each with distinct sources of variability. We apply this method to recently approved TMDLs to investigate whether appropriate accounting for measurement error and variability will lead to different management decisions. We find that required pollutant loading reductions may in fact vary depending not only on how measurement variability is addressed but also on which water quality analysis procedure is used to assess standard compliance. As a general strategy, our Bayesian approach to quantifying variability may represent an alternative to the common practice of addressing all forms of uncertainty through an arbitrary margin of safety (MOS).