Category Archives: Earth Science

Impacts of 25 years of groundwater extraction on subsidence in the Mekong delta, Vietnam

Many major river deltas in the world are subsiding and consequently become increasingly vulnerable to flooding and storm surges, salinization and permanent inundation. For the Mekong Delta, annual subsidence rates up to several centimetres have been reported. Excessive groundwater extraction is suggested as the main driver. As groundwater levels drop, subsidence is induced through aquifer compaction. Over the past 25 years, groundwater exploitation has increased dramatically, transforming the delta from an almost undisturbed hydrogeological state to a situation with increasing aquifer depletion. Yet the exact contribution of groundwater exploitation to subsidence in the Mekong delta has remained unknown. In this study we deployed a delta-wide modelling approach, comprising a 3D hydrogeological model with an integrated subsidence module. This provides a quantitative spatially-explicit assessment of groundwater extraction-induced subsidence for the entire Mekong delta since the start of widespread overexploitation of the groundwater reserves. We find that subsidence related to groundwater extraction has gradually increased in the past decades with highest sinking rates at present. During the past 25 years, the delta sank on average ~18 cm as a consequence of groundwater withdrawal. Current average subsidence rates due to groundwater extraction in our best estimate model amount to 1.1 cm yr−1, with areas subsiding over 2.5 cm yr−1, outpacing global sea level rise almost by an order of magnitude. Given the increasing trends in groundwater demand in the delta, the current rates are likely to increase in the near future.

NSF-funded ACM Turing Awardees: A Look at 50 Years of Computing’s Greatest Visionaries

This year marks 50 years of the ACM A.M. Turing Award, the highest distinction in computer science, often regarded as the “Nobel Prize of Computing.” Since 1966, the Association for Computing Machinery (ACM) has recognized on an annual basis individuals who have contributed lasting and major technical accomplishments to computing.

The name of the award recognizes Alan M. Turing, who is often credited as a key founder of the field of artificial intelligence. More than half of the 65

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This is an NSF News item.

IFBRP Open House and Stakeholder Group Comment Analysis

In March 2017, Perkins + Will and the City of Duluth presented two high-level concept plans to the Irving-Fairmount Brownfields Plan stakeholders in a several different settings: an organized stakeholder meeting (open house), a small group meeting with businesses, a small group meeting with parents at Edison Raleigh School, and the City’s St. Louis River Technical Advisory Committee (EDA TAC). The analysis attached represents an organization of the comments in a framework to identify the main themes and concerns across the different settings.

Statement of John Morris, Associate Administrator of NTIA’s Office of Policy Analysis and Development, on the U.S. Copyright Office study of Section 1201 of the Digital Millennium Copyright Act

FOR IMMEDIATE RELEASE: 
June 22, 2017
News Media Contact: 
NTIA, Office of Public Affairs
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Statement of John Morris, Associate Administrator for NTIA’s Office of Policy Analysis and Development, on the U.S. Copyright Office study of Section 1201 of the Digital Millennium Copyright Act:

Uptake of Nickel by Synthetic Mackinawite

The uptake of aqueous Ni(II) by synthetic mackinawite (FeS) was examined in anaerobic batch experiments at near-neutral pH (5.2 to 8.4). Initial molar ratios of Ni(II) to FeS ranged from 0.008 to 0.83 and maximum Ni concentrations in mackinawite, expressed as the cation mol fraction, were as high as XNi = 0.56 (Fe1-xNixS; 0  x  1). Greater than 99% Ni removal from solution occurred when Ni loading remained below 0.13 ± 0.03 (1σ) mol Ni per mol FeS due to sorption of Ni at the mackinawite surface. Characterization of experimental solids using X-ray diffraction and Raman spectroscopy showed patterns characteristic of nanocrystalline mackinawite; no evidence of nickel monosulfide (α-NiS or millerite), polydymite (Ni3S4), or godlevskite [(Ni,Fe)9S8] formation was indicated regardless of the amount of Ni loading. Slight expansion of the c-axis correlated with increasing Ni content in synthetic mackinawite, from c = 5.07 ± 0.01 Å at XNi = 0.02 to c = 5.10 ± 0.01 Å at XNi = 0.38. Ni K-edge extended X-ray absorption fine structure (EXAFS) spectra of synthetic Ni-bearing mackinawite are similar in phase and amplitude to the Fe K-edge EXAFS spectrum of Ni-free mackinawite, indicating that the molecular environment of Ni2+ in Ni-bearing mackinawite is similar to that of Fe2+ in Ni-free mackinawite. EXAFS data fitting of Ni-bearing mackinawite with XNi = 0.42 indicated a coordination number of 4.04 ± 0.30 and an average Ni-S bond distance of 2.28 Å, in good agreement with the Fe-S bond distance of 2.26 Å in mackinawite, tetrahedral Fe coordination, and slight lattice expansion along the c-axis. At lower Ni loadings (XNi = 0.05 – 0.11), EXAFS analysis showed a decrease in Ni-S coordination towards CN = 3, which reflects the influence of sorbed Ni. Continued Ni uptake, past the maximum amount of sorption, was accompanied by proportional molar release of Fe to solution. Interstitial occupancy of Ni within the mackinawite interlayer may be transitional to structural substitution of Fe. The Ni-mackinawite solid-solution is described by a one-site binary mixing model: ln⁡〖K_d 〗=ln〖 K〗_e-W/RT (1-2X_Ni )where Kd is the distribution coefficient, Ke is the ratio of equilibrium constants for Ni-mackinawite and mackinawite (14.4 ± 1.3), W is an ion interaction parameter, and XNi is the mole fraction of end-member NiS in the solid solution. The experimentally determined value of W is 17.74 ± 1.15 kJ/mol and indicates significant non-ideality of the solid solution. Transformation processes were evaluated by aging Ni-mackinawite with polysulfides and solutions saturated with air. Reaction of Ni-mackinawite with polysulfides led to the formation of pyrite (FeS2) and Ni retention in the solid phase. When Ni-mackinawite was aged in the presence of dissolved oxygen, transformation to goethite (FeOOH) and violarite (FeNi2S4) was observed.

Global Atmosphere Watch Workshop on Measurement-Model Fusion for Global Total Atmospheric Deposition (MMF-GTAD)

The World Meteorological Organization’s (WMO) Global Atmosphere Watch (GAW) Programme coordinates high-quality observations of atmospheric composition from global to local scales with the aim to drive high-quality and high-impact science while co-producing a new generation of products and services. In line with this vision, GAW’s Scientific Advisory Group for Total Atmospheric Deposition (SAG-TAD) has a mandate to produce global maps of wet, dry and total atmospheric deposition for important atmospheric chemicals to enable research into biogeochemical cycles and assessments of ecosystem and human health effects.

The most suitable scientific approach for this activity is the emerging technique of measurement-model fusion for total atmospheric deposition. This technique requires global-scale measurements of atmospheric trace gases, particles, precipitation composition and precipitation depth, as well as predictions of the same from global/regional chemical transport models. The fusion of measurement and model results requires data assimilation and mapping techniques.

The objective of the GAW Workshop on Measurement-Model Fusion for Global Total Atmospheric Deposition (MMF-GTAD), an initiative of the SAG-TAD, was to review the state-of-the-science and explore the feasibility and methodology of producing, on a routine retrospective basis, global maps of atmospheric gas and aerosol concentrations as well as wet, dry and total deposition via measurement-model fusion techniques; as well as to develop a path forward for a GAW MMF-GTAD project.

The three-day workshop was attended by 41 participants from 12 countries with expertise in atmospheric measurements and modelling, data assimilation, and ecosystem and human health effects.

Bacteriophages as indicators of faecal pollution and enteric virus removal

Bacteriophages are an attractive alternative to fecal indicator bacteria (FIB), particularly as surrogates of enteric virus fate and transport due to their closer morphological and biological properties compared to FIB. Based on a meta-analysis of published data, we summarize concentrations of coliphages (F+ and somatic), Bacteroides spp. and enterococci bacteriophages (phages) in human waste, non-human waste, fresh and marine waters as well as removal through wastewater treatment processes. We also provide comparisons with FIB and enteric viruses whenever possible. Lastly, we examine fate and transport characteristics in the environment and provide an overview of the methods available for detection and enumeration of bacteriophages. In summary, concentrations of FIB bacteriophages in various sources were consistently lower than FIB, but more reflective of infectious enteric virus levels. Our investigation supports use of bacteriophages as viral surrogates especially for wastewater treatment processes, while additional research is needed to clarify their utility as indicators of viral fate and transport in the ambient water.

EPA Method 1615. Measurement of Enterovirus and Norovirus Occurrence in Water by Culture and RT-qPCR. II. Total Culturable Virus Assay

A standardized method is required when national studies on virus occurrence in environmental and drinking waters utilize multiple analytical laboratories. The U.S Environmental Protection Agency’s (USEPA) Method 1615 was developed with the goal of providing such a standard for measuring Enterovirus and Norovirus in these waters. Virus is concentrated from water using an electropositive filter, eluted from the filter surface with beef extract, and then concentrated further using organic flocculation. Herein we present the protocol from Method 1615 for filter elution, secondary concentration, and measurement of total culturable viruses. A portion of the concentrated eluate from each sample is inoculated onto ten replicate flasks of Buffalo Green Monkey kidney cells. The number of flasks demonstrating cytopathic effects is used to quantify the most probable number (MPN) of infectious units per liter. The method uses a number of quality controls to increase data quality and to reduce interlaboratory and intralaboratory variation. Laboratories must meet defined performance standards. Method 1615 was evaluated by examining virus recovery from reagent-grade and ground waters seeded with Sabin poliovirus type 3. Mean poliovirus recoveries with the total culturable assay were 111% in reagent grade water and 58% in groundwaters.

Mineralizing urban net-zero water treatment: Phase II field results and design recommendations

Net-zero water (NZW) systems, or water management systems achieving high recycling rates and low residuals generation so as to avoid water import and export, can also conserve energy used to heat and convey water, while economically restoring local eco-hydrology. However, design and operating experience are extremely limited. The objective of this paper is to present the results of the second phase of operation of an advanced oxidation-based NZW pilot system designed, constructed, and operated for a period of two years, serving an occupied four-person apartment. System water was monitored, either continuously or thrice daily, for routine water quality parameters, minerals, and MicroTox® in-vitro toxicity, and intermittently for somatic and male-specific coliphage, adenovirus, Cryptosporidium, Giardia, emerging organic constituents (non-quantitative), and the Florida drinking water standards. All 115 drinking water standards with the exception of bromate were met in this phase. Neither virus nor protozoa were detected in the treated water, with the exception of measurement of adenovirus genome copies attributed to accumulation of inactive genetic material in hydraulic dead zones. Chemical oxygen demand was mineralized to 90% in treatment. Total dissolved solids were maintained at ∼500 mg/L at steady state, partially through aerated aluminum electrocoagulation. Bromate accumulation is projected to be controlled by aluminum electrocoagulation with separate disposal of backwash water. Further development of such systems and their automated/remote process control systems is recommended.

Advancing Consumer Product Composition and Chemical Use Information to Facilitate Risk-Based Decision Making

This presentation describes EPA efforts to collect, model, and measure publically available consumer product data for use in exposure assessment. The development of the ORD Chemicals and Products database will be described, as will machine-learning based models for predicting chemical function. Finally, the talk describes new mass spectrometry-based methods for measuring chemicals in formulation and articles.

Integrating Aggregate Exposure Pathway (AEP) and Adverse Outcome Pathway (AOP) Frameworks to Estimate Exposure-relevant Responses

High throughput toxicity testing (HTT) holds the promise of providing data for tens of thousands of chemicals that currently have no data due to the cost and time required for animal testing. Interpretation of these results require information linking the perturbations seen in vitro with adverse outcomes in vivo and requires knowledge of how estimated exposure to the chemicals compare to the in vitro concentrations that show an effect. This abstract discusses how Adverse Outcome Pathways (AOPs) can be used to link HTT with adverse outcomes of regulatory significance and how Aggregate Exposure Pathways (AEPs) can connect concentrations of environment stressors at a source with an expected target site concentration designed to provide exposure estimates that are comparable to concentrations identified in HTT.

Towards the Next Generation Air Quality Modeling System: Current Progress on Implementing Chemistry into MPAS-A

The community multiscale air quality (CMAQ) model of the U.S. Environmental Protection Agency is one of the most widely used air quality model worldwide; it is employed for both research and regulatory applications at major universities and government agencies for improving understanding of the formation and transport of air pollutants. It is noted, however, that air quality issues and climate change assessments need to be addressed globally recognizing the linkages and interactions between meteorology and atmospheric chemistry across a wide range of scales. Therefore, an effort is currently underway to develop the next generation air quality modeling system (NGAQM) that will be based on a global integrated meteorology and chemistry system. The model for prediction across scales-atmosphere (MPAS-A), a global fully compressible non-hydrostatic model with seamlessly refined centroidal Voronoi grids, has been chosen as the meteorological driver of this modeling system. The initial step of adapting MPAS-A for the NGAQM was to implement and test the physics parameterizations and options that are preferred for retrospective air quality simulations (see the work presented by R. Gilliam, R. Bullock, and J. Herwehe at this workshop). The next step, presented herein, would be to link the chemistry from CMAQ to MPAS-A to build a prototype for the NGAQM. Furthermore, the techniques to harmonize transport processes between CMAQ and MPAS-A, methodologies to connect the chemistry module with MPAS-A, and computational issues such as parallelism and I/O structure are being addressed.

NSF offers opportunity for media to deploy to Greenland

Greenland ice sheet

The National Science Foundation (NSF) is accepting proposals from media professionals to visit Greenland and report on scientific research in the Arctic supported by NSF’s Office of Polar Programs.

Competitive proposals must include the following:

• A documented ability to reach the widest possible U.S. audience across a variety of platforms (broadcast, print, web and social media).

• A solid field plan that indicates how the outlet will clearly and

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This is an NSF News item.

THE CONCEPT OF REFERENCE CONDITION, REVISITED

Ecological assessments of aquatic ecosystems depend on the ability to compare current conditions against some expectation of how they could be in the absence of significant human disturbance. The concept of a ‘‘reference condition’’ is often used to describe the standard or benchmark against which current condition is compared. If assessments are to be conducted consistently, then a common understanding of the definitions and complications of reference condition is necessary. A 2006 paper (Stoddard et al., 2006, Ecological Applications 16:1267-1276) made an early attempt at codifying the reference condition concept; in this presentation we will revisit the points raised in that paper (and others) and examine how our thinking has changed in a little over 10 years.Among the issues to be discussed: (1) the “moving target” created when reference site data are used to set thresholds in large scale assessments; (2) natural vs. human disturbance and their effects on reference site distributions; (3) circularity and the use of biological data to assist in reference site identification; (4) using site-scale (in-stream or in-lake) measurements vs. landscape-level human activity to identify reference conditions.

Predictive Toxicology and Computer Simulation of Male Reproductive Development (Duke U KURe and PMRC research day)

The reproductive tract is a complex, integrated organ system with diverse embryology and unique sensitivity to prenatal environmental exposures that disrupt morphoregulatory processes and endocrine signaling. U.S. EPA’s in vitro high-throughput screening (HTS) database (ToxCastDB) was used to profile the bioactivity of 54 chemicals with male developmental consequences across ~800 molecular and cellular features. The in vitro bioactivity on molecular targets could be condensed into 156 gene annotations in a bipartite network. These results highlighted the role of estrogen and androgen signaling pathways in male reproductive tract development, and importantly, broadened the list of molecular targets to include GPCRs, cytochrome-P450s, vascular remodeling proteins, and retinoic acid signaling. A multicellular agent-based model was used to simulate the complex interactions between morphoregulatory, endocrine, and environmental influences during genital tubercle (GT) development. Spatially dynamic signals (e.g., SHH, FGF10, and androgen) were implemented in the model to address differential adhesion, cell motility, proliferation, and apoptosis. Under control of androgen signaling, urethral tube closure was an emergent feature of the model that was linked to gender-specific rates of ventral mesenchymal proliferation and urethral plate endodermal apoptosis. A systemic parameter sweep was used to examine the sensitivity of crosstalk between genetic deficiency and environmental disruption pathways. The in silico impact of subtle variations in SHH and FGF10 activity (simulating individual variability) with respect to dose-dependent androgen receptor insufficiency was modeled in a simulated population. Hypospadias could occur at 70% SHH and 70% FGF10 sufficiency with merely a 5% reduction in AR sufficiency. In conclusion, multiscale systems modeling provides a means to simulate population-level responses to reveal critical thresholds in teratogenesis for complex interactions between genetic (e.g., FGF10 polymorphism), environmental (e.g., androgen receptor disruption), and lifestyle (e.g., cholesterol deficiency for SHH) factors.

Differential genomic effects of six different TiO2 nanomaterials on human liver HepG2 cells

Engineered nanoparticles are reported to cause liver toxicity in vivo. To better assess the mechanism of the in vivo liver toxicity, we used the human hepatocarcinoma cells (HepG2) as a model system. Human HepG2 cells were exposed to 6 TiO2 nanomaterials (with dry primary particle sizes ranging from 22 to 214 nm, either 0.3, 3 or 30 g/ml) for three days. In culture media with 10% fetal bovine serum the hydrodynamic sizes ranged from 328 to 534 nm. With respect to physical-chemical characteristics, hydrodynamic agglomerated particle size rather than dry particle size or surface area correlated best with our biological and genomic outcomes. Even though all six NPs are composed of TiO2, they elicited fairly different canonical pathway responses. Some of these canonical pathways changed by nano-TiO2 in vitro treatments have been already reported in literature, such as NRF2-mediated stress response, fatty acid metabolism, cell cycle and apoptosis, immune response, cholesterol biosynthesis and glycolysis. But this genomic study also revealed some novel effects such as protein synthesis, protein ubiquitination, hepatic fibrosis and cancer related signaling pathways. More importantly, this genomic analysis of HepG2 cells treated with 6 nano-TiO2 linked some of the in vitro canonical pathways to in vivo adverse outcomes, e.g., NRF2 mediated response pathways to oxidative stress, acute phase response to inflammation, cholesterol biosynthesis to steroid hormones alteration, fatty acid metabolism changes to lipid homeostasis alteration, G2/M cell checkpoint regulation to apoptosis and hepatic fibrosis/stellate cell activation to liver fibrosis. This study revealed some possible mechanisms through which nanoparticles caused liver toxicity in vivo.

Adverse Outcome Pathways – Organizing Toxicological Information to Improve Decision Making

The number of chemicals for which environmental regulatory decisions are required far exceeds the current capacity for toxicity testing. High throughput screening (HTS) commonly used for drug discovery has the potential to increase this capacity. The adverse outcome pathway (AOP) concept has emerged as a natural framework for connecting high throughput toxicity testing (HTT) results to potential impacts on humans and wildlife populations. An AOP consists of two main components that describe the biological mechanisms driving toxicity. Key events represent biological processes essential for causing the adverse outcome that are also measurable experimentally. Key event relationships capture the biological processes connecting the key events. Evidence documented for each KER based on measurements of the KEs can provide the confidence needed for extrapolating HTT from early key events to overt toxicity represented by later key events based on the AOP. The IPCS mode of action (MOA) framework incorporates information required for making a chemical-specific toxicity determination. Given the close relationship between the AOP and MOA frameworks, it is possible to assemble an MOA by incorporating HTT results, chemical properties including absorption, distribution, metabolism, and excretion (ADME), and an AOP describing the biological basis of toxicity thereby streamlining the process. While current applications focus on the assessment of risk for environmental chemicals, these approaches fit naturally into the safety assessment of pharmaceuticals and well as target discovery and HTS applied to novel drug discovery.

An Integrative data mining approach to identifying Adverse Outcome Pathway (AOP) Signatures

The Adverse Outcome Pathway (AOP) framework is a tool for making biological connections and summarizing key information across different levels of biological organization to connect biological perturbations at the molecular level to adverse outcomes for an individual or population. Computational approaches to explore and determine these connections can accelerate the assembly of AOPs. By leveraging the wealth of publicly available data covering chemical effects on biological systems, computationally-predicted AOPs (cpAOPs) were assembled via data mining of high-throughput screening (HTS) in vitro data, in vivo data and other disease phenotype information. Frequent Itemset Mining (FIM) was used to find associations between the gene targets of ToxCast HTS assays and disease data from Comparative Toxicogenomics Database (CTD) by using the chemicals as the common aggregators between datasets. The method was also used to map gene expression data to disease data from CTD. A cpAOP network was defined by considering genes and diseases as nodes and FIM associations as edges. This network contained 18,283 gene to disease associations for the ToxCast data and 110,253 for CTD gene expression. Two case studies show the value of the cpAOP network by extracting subnetworks focused either on fatty liver disease or the Aryl Hydrocarbon Receptor (AHR). The subnetwork surrounding fatty liver disease included many genes known to play a role in this disease. When querying the cpAOP network with the AHR gene, an interesting subnetwork including glaucoma was identified. While substantial literature exists to support the potential for AHR ligands to elicit glaucoma, it was not explicitly captured in the public annotation information in CTD. The subnetwork from this analysis suggests a cpAOP that includes changes in CYP1B1 expression. These case studies highlight the value in integrating multiple data sources when defining cpAOPs for HTS data.