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A review of SWAT applications, performance and future needs for simulation of hydro-climatic extremes

Hydro-climatic extremes, such as droughts and floods, have most likely increased due to climatic change and could lead to severe impacts on socio-economic, structural and environmental sectors. With nearly 4000 publications, the Soil and Water Assessment Tool (SWAT) is clearly one of the most extensively used ecohydrological models worldwide. The model has been widely used for projecting the impacts of future hydro-climatic changes, but application for extreme streamflow conditions is still rarely reported. To date, SWAT application reviews have focused on compilations of SWAT studies for specific or relatively new applications such as eco-hydrological modelling, ecosystem services, sub-daily simulations, and pesticide fate and transport simulations. However, no existing SWAT review studies have focused on simulation of hydro-climatic extremes. Furthermore, this research aims to bridge this gap by compiling and reviewing the findings of studies reporting SWAT hydro-climatic extremes including highlighting the performance and future research needs. A total of 111 articles have been identified since 1999; most of these studies were conducted in the United States and China. These articles can be divided into extreme flow assessments, drought studies, flood studies, drought and flood studies, SWAT coupling with other models, and SWAT improvements. Most of the extreme performance assessment studies reported “satisfactory ”performance, with a particular emphasis on peak flow comparisons. Future research needs regarding this topic include: (1) a unified SWAT extreme performance assessment framework; (2) SWAT improvements that result in improved replication of peak and low flows; (3) reliability assessment of global and satellite products for SWAT extreme simulations; (4) bias correction of CMIP6 and regional climate projections; (5) comparison of SWAT + and SWAT for extreme flow simulations in different types of basins; (6) development of an extreme flow module within an overall SWAT modelling system; and (7) integration of artificial intelligence within SWAT modelling.

54 ENVIRONMENTAL SCIENCES↗

Theory of the Lamb Shift and fine structure in muonic {sup 4}He ions and the muonic {sup 3}He– {sup 4}He Isotope Shift

We provide an up to date summary of the theory contributions to the 2S → 2P Lamb shift and the fine structure of the 2P state in the muonic helium ion (μ{sup 4}He){sup +}. This summary serves as the basis for the extraction of the alpha particle charge radius from the muonic helium Lamb shift measurements at the Paul Scherrer Institute, Switzerland. Individual theory contributions needed for a charge radius extraction are compared and compiled into a consistent summary. The influence of the alpha particle charge distribution on the elastic two-photon exchange is studied to take into account possible model-dependencies of the energy levels on the electric form factor of the nucleus. We also discuss the theory uncertainty which enters the extraction of the {sup 3}He–{sup 4}He isotope shift from the muonic measurements. The theory uncertainty of the extraction is much smaller than a present discrepancy between previous isotope shift measurements. This work completes our series of n=2 theory compilations in light muonic atoms which we have performed already for muonic hydrogen, deuterium, and helium-3 ions.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Coal-based graphene oxide-like materials: A comprehensive review

Coal is the most abundant energy and hydrocarbon resource in the United States which has been primarily used for power generation. With the increasing retirement of coal power plants and transition to a low-carbon emission economy, the future use of coal will likely shift to a feedstock source for production of valuable materials for different applications. In this review, the latest research reported on production of graphene-like materials in a powder form from coal is compiled and discussed. Here, this review includes: 1) brief background information on graphene and related materials (GRM); 2) relevant material, resource, economic, and socioeconomic information regarding suitability of coal as a potential feedstock for production of GRM; 3) a summary of common approaches for coal upgrading for preparation of more suitable precursors for production of GRM; 4) a compilation and analysis of the reported routes and methods for preparation of GRM from coal and coal derivatives; and 5) reported potential applications of coal-based GRM.

36 MATERIALS SCIENCE↗

Lightweight runtime checking of C programs with RTC

The C Programming Language is known for being an efficient language that can be compiled on almost any architecture and operating system. However the absence of dynamic safety checks and a relatively weak type system allows programmer oversights that are hard to spot. In this paper, we present RTC, a runtime monitoring tool that instruments unsafe code and monitors the program execution. RTC is built on top of the ROSE compiler infrastructure. RTC finds memory bugs and arithmetic overflows and underflows, and run-time type violations. Most of the instrumentations are directly added to the source file and only require a minimal runtime system. As a result, the instrumented code remains portable. In tests against known error detection benchmarks, RTC found 98% of all memory related bugs and had zero false positives. Finally, in performance tests conducted with well known algorithms, such as binary search and MD5, we determined that our tool has an average run-time overhead rate of 9.7× and memory overhead rate of 3.5×.

97 MATHEMATICS AND COMPUTING↗

A genome-scale phylogeny of the kingdom Fungi

Phylogenomic studies using genome-scale amounts of data have greatly improved understanding of the tree of life. Despite the diversity, ecological significance, and biomedical and industrial importance of fungi, evolutionary relationships among several major lineages remain poorly resolved, especially those near the base of the fungal phylogeny. To examine poorly resolved relationships and assess progress toward a genome-scale phylogeny of the fungal kingdom, we compiled a phylogenomic data matrix of 290 genes from the genomes of 1,644 species that includes representatives from most major fungal lineages. We also compiled 11 data matrices by subsampling genes or taxa from the full data matrix based on filtering criteria previously shown to improve phylogenomic inference. Analyses of these 12 data matrices using concatenation- and coalescent-based approaches yielded a robust phylogeny of the fungal kingdom, in which ~85% of internal branches were congruent across data matrices and approaches used. We found support for several historically poorly resolved relationships as well as evidence for polytomies likely stemming from episodes of ancient diversification. By examining the relative evolutionary divergence of taxonomic groups of equivalent rank, we found that fungal taxonomy is broadly aligned with both genome sequence divergence and divergence time but also identified lineages where current taxonomic circumscription does not reflect their levels of evolutionary divergence. Finally, our results provide a robust phylogenomic framework to explore the tempo and mode of fungal evolution and offer directions for future fungal phylogenetic and taxonomic studies.

59 BASIC BIOLOGICAL SCIENCES↗

Quantifying cover crop effects on soil health and productivity

The dataset presented here supports the research paper entitled “A calculator to quantify cover crop effects on soil health and productivity”. Soil health (sometimes used synonymously with soil quality) is a concept that describes soil as a living system to sustain plants, animals, and human. Soil physical, chemical, and biological properties, along with their interactions, are required to quantify soil health. The use of cover crops in agricultural rotations may enhance soil health, yet there has been little progress in understanding how external factors such as climate, soil type, and agronomic practices affect soil and cash crop responses. In response, this dataset compiles measurements from 281 studies and provides an analysis of field-measured changes in 38 soil health indicators due to cover crop usage. Environmental and background indicators were also compiled to assess how climatic and management practices affect soil and cash crop responses to cover crops, with specific categories including climate type (tropical, arid, temperate, and continental), soil texture (coarse, medium, and fine), cover crop type (legume, grass, multi-species mixture, and other), and cash crop type (corn, soybean, wheat, vegetable, corn-soybean rotation, corn-soybean-wheat rotation, and other). An unbalanced analysis of variation was used to determine the hierarchy of most to least important factors that affected responsiveness of each soil health indicator. Based on the hierarchy structure, a soil health calculator was then developed to quantify the response of 13 parameters – erosion, runoff, weed suppression, soil aggregate stability, leaching, infiltration, microbial biomass carbon, soil bulk density, soil organic carbon, soil nitrogen, microbial biomass nitrogen, cash crop yield, and saturated hydraulic conductivity – to cover crops. The presented data in the calculator report the mean change in parameter values based on all combinations of climate, soil texture, cover crop type, and cash crop type.

54 ENVIRONMENTAL SCIENCES↗

Implementation of data citations and persistent identifiers at the ORNL DAAC

A requirement of data archives is that data holdings can be easily discovered, accessed, and used. One approach to improving data discovery and access is through data citations coupled with Digital Object Identifiers (DOI). The Oak Ridge National Laboratory Distributed Active Archive Center (ORNL DAAC) since 1998 has issued data citations that have been accepted and used in peer-reviewed journals. Citation elements established by the ORNL DAAC are similar to those used for journal articles (authors, year, product title, and information to locate), and beginning in 2007 included a DOI that is persistent, actionable, specific, and complete. The approach used at the ORNL DAAC also allows for referring to subsets of the data, by including within the citation the temporal and spatial extent, and parameters used. Data citations allow readers to find data and reproduce the results of the research article, and also use those data to test new hypotheses, design new sample collections, or construct or evaluate models. The ORNL DAAC uses a manual method to compile data citations and has developed a database that links research articles and their use of specific ORNL DAAC data products. Automation of the data citation compilation process, as is the case for articles, will enable data citations to become a more common practice. In addition to enhancing discovery and access of the data used in a research article, the citation gives credit to data generators, data centers and their funders, and, through citation indices, determine the scientific impact of a data set.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

Evaluation and comparison of benchmark QSAR models to predict a relevant REACH endpoint: The bioconcentration factor (BCF)

The bioconcentration factor (BCF) is an important bioaccumulation hazard assessment metric in many regulatory contexts. Its assessment is required by the REACH regulation (Registration, Evaluation, Authorization and Restriction of Chemicals) and by CLP (Classification, Labeling and Packaging). We challenged nine well-known and widely used BCF QSAR models against 851 compounds stored in an ad-hoc created database. The goodness of the regression analysis was assessed by considering the determination coefficient (R{sup 2}) and the Root Mean Square Error (RMSE); Cooper's statistics and Matthew's Correlation Coefficient (MCC) were calculated for all the thresholds relevant for regulatory purposes (i.e. 100 L/kg for Chemical Safety Assessment; 500 L/kg for Classification and Labeling; 2000 and 5000 L/kg for Persistent, Bioaccumulative and Toxic (PBT) and very Persistent, very Bioaccumulative (vPvB) assessment) to assess the classification, with particular attention to the models' ability to control the occurrence of false negatives. As a first step, statistical analysis was performed for the predictions of the entire dataset; R{sup 2}>0.70 was obtained using CORAL, T.E.S.T. and EPISuite Arnot–Gobas models. As classifiers, ACD and log P-based equations were the best in terms of sensitivity, ranging from 0.75 to 0.94. External compound predictions were carried out for the models that had their own training sets. CORAL model returned the best performance (R{sup 2}{sub ext}=0.59), followed by the EPISuite Meylan model (R{sup 2}{sub ext}=0.58). The latter gave also the highest sensitivity on external compounds with values from 0.55 to 0.85, depending on the thresholds. Statistics were also compiled for compounds falling into the models Applicability Domain (AD), giving better performances. In this respect, VEGA CAESAR was the best model in terms of regression (R{sup 2}=0.94) and classification (average sensitivity>0.80). This model also showed the best regression (R{sup 2}=0.85) and sensitivity (average>0.70) for new compounds in the AD but not present in the training set. However, no single optimal model exists and, thus, it would be wise a case-by-case assessment. Yet, integrating the wealth of information from multiple models remains the winner approach. - Highlights: • REACH encourages the use of in silico methods in the assessment of chemicals safety. • The performances of nine BCF models were evaluated on a benchmark database of 851 chemicals. • We compared the models on the basis of both regression and classification performance. • Statistics on chemicals out of the training set and/or within the applicability domain were compiled. • The results show that QSAR models are useful as weight-of-evidence in support to other methods.

54 ENVIRONMENTAL SCIENCES↗

Identification of mycotoxins by UHPLC–QTOF MS in airborne fungi and fungi isolated from industrial paper and antique documents from the Archive of Bogotá

Mold deterioration of historical documents in archives and libraries is a frequent and complex phenomenon that may have important economic and cultural consequences. In addition, exposure to toxic fungal metabolites might produce health problems. In this work, samples of broths of fungal species isolated from the documentary material and from indoor environmental samples of the Archive of Bogotá have been analyzed to investigate the presence of mycotoxins. High resolution mass spectrometry made possible to search for a large number of mycotoxins, even without reference standards available at the laboratory. For this purpose, a screening strategy based on ultra-high pressure liquid chromatography coupled to quadrupole-time of flight mass spectrometry (UHPLC–QTOF MS) under MS{sup E} mode was applied. A customized home-made database containing elemental composition for around 600 mycotoxins was compiled. The presence of the (de)protonated molecule measured at its accurate mass was evaluated in the samples. When a peak was detected, collision induced dissociation fragments and characteristic isotopic ions were also evaluated and used for tentative identification, based on structure compatibility and comparison with literature data (if existing). Up to 44 mycotoxins were tentatively identified by UHPLC–QTOF MS. 34 of these tentative compounds were confirmed by subsequent analysis using a targeted LC–MS/MS method, supporting the strong potential of QTOF MS for identification/elucidation purposes. The presence of mycotoxins in these samples might help to reinforce safety measures for researchers and staff who work on reception, restoration and conservation of archival material, not only at the Archive of Bogotá but worldwide. - Highlights: • Mold deterioration of historical documents is a frequent and complex phenomenon. • Samples of broths of fungal species isolated from Archive of Bogotá analyzed. • UHPLC–QTOF MS (MS{sup E}) applied for mycotoxins screening, without reference standards. • Customized home-made database for around 600 mycotoxins compiled. • 44 mycotoxins tentatively identified, 34 of which confirmed by LC–MS/MS.

54 ENVIRONMENTAL SCIENCES↗

Chemical thermodynamic data. 1. The concept of links to the chemical elements and the historical development of key thermodynamic data [plus Supplementary Electronic Annex 2]

Chemical thermodynamic data remain a keystone for geochemical modeling and reactive transport simulation as applied to an increasing number of applications in the earth sciences, as well as applications in other areas including metallurgy, material science, and industrial process design. The last century has seen the development of a large body of thermodynamic data and a number of major compilations. The past several decades have seen the development of thermodynamic databases in digital form designed to support computer calculations. However, problems with thermodynamic data appear to be persistent. One problem pertains to the use of inconsistent primary key reference data. Such data pertain to elemental reference forms and key, stoichiometrically simple chemical species including metal oxides, CO 2 , water, and aqueous species such as Na + and Cl - . A consistent set of primary key data (standard Gibbs energies, standard enthalpies, and standard entropies for key chemical species) for 298.15K and 1 bar pressure is essential. Thermochemical convention is to define the standard Gibbs energy and the standard enthalpy of an individual chemical species in terms of formation from reference forms of the constituent chemical elements. We propose a formal concept of “links” to the elemental reference forms. This concept involves a documented understanding of all reactions and calculations leading to values for a formation property (standard Gibbs energy or enthalpy). A valid link consists of two parts: (a) the path of reactions and corrections and (b) the associated data, which are key data. Such a link differs from a bare “key” or “reference” datum in that it requires additional information. Some or all of its associated data may also be key data. In evaluating a reported thermodynamic datum, one should identify the links to the chemical elements, a process which can be time-consuming and which may lead to a dead end (an incomplete link). The use of two or more inconsistent links to the same elemental reference form in a thermodynamic database will result in an inconsistency in the database. Thus, in constructing a database, it is important to establish a set of reliable links (generally resulting in a set of primary reference data) and then correct all data adopted subsequently for consistency with that set. Recommended values of key data have not been constant through history. We review some of this history through the lens of major compilations and other influential reports, and note a number of problem areas. Finally, we illustrate the concepts developed in this paper by applying them to some key species of geochemical interest, including liquid water; quartz and aqueous silica; and gibbsite, corundum, and the aqueous aluminum ion.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Stable isotope equilibria in the dihydrogen-water-methane-ethane-propane system. Part 2: Experimental determination of hydrogen isotopic equilibrium for ethane-H2 from 30 to 200 °C and propane-H2 from 75 to 200 °C

The stable isotopic compositions of light n-alkanes, including methane, ethane, and propane, are often used to identify the sources and thermal maturity of natural gas samples. Though stable isotopic compositions of these molecules are commonly assumed to be controlled by kinetic isotope effects, recent studies have proposed both carbon and hydrogen isotopic equilibrium may also occur in some samples. Assessing whether samples are in isotopic equilibrium requires knowledge of light alkane equilibrium fractionation factors over geologically relevant temperatures for formation and storage (up to ∼300 °C). In this study, we report experimental results of hydrogen isotopic equilibrium between ethane and H2 from 30 to 200 °C and propane and H2 from 75 to 200 °C. We compare these results with high-level theoretical calculations and provide a preferred polynomial fit to describe equilibrium fractionation factors. Comparison of these fractionation factors with a compilation of ∼500 compiled environmental gas samples supports the proposal that many (∼50%) of these natural gas samples exhibit hydrogen isotopic compositions consistent with having formed in or attained methane-ethane-propane hydrogen isotopic equilibrium over geologically relevant temperatures for formation and storage (50–300 °C).

Turner, Andrew C↗

Geothermal play fairway analysis, part 1: Example from the Snake River Plain, Idaho

The Snake River Plain (SRP) volcanic province overlies the track of the Yellowstone hotspot, a thermal anomaly that extends deep into the mantle. Most of the area is underlain by a basaltic volcanic province that overlies a mid-crustal intrusive complex, which in turn provides the long-term heat flux needed to sustain geothermal systems. Previous studies have identified several known geothermal resource areas within the SRP. For the geothermal study presented herein, our goals were to: (1) adapt the methodology of Play Fairway Analysis (PFA) for geothermal exploration to create a formal basis for its application to geothermal systems, (2) assemble relevant data for the SRP from publicly available and private sources, and (3) build a geothermal PFA model for the SRP and identify the most promising plays, using GIS-based software tools that are standard in the petroleum industry. The study focused on identifying three critical resource parameters for exploitable hydrothermal systems in the SRP: heat source, reservoir and recharge permeability, and cap or seal. Data included in the compilation for heat source were heat flow, distribution and ages of volcanic vents, groundwater temperatures, thermal springs and wells, helium isotope anomalies, and reservoir temperatures estimated using geothermometry. Reservoir and recharge permeability was inferred from the analysis of stress orientations and magnitudes, post-Miocene faults, and subsurface structural lineaments based on magnetics and gravity data. Data for cap or seal included the distribution of impermeable lake sediments and clay-seal associated with hydrothermal alteration below the regional aquifer. These data were used to compile Common Risk Segment maps for heat, permeability, and seal, which were combined to create a Composite Common Risk Segment map for all southern Idaho that reflects the risk associated with geothermal resource exploration and identifies favorable resource tracks. Our regional assessment indicated that undiscovered geothermal resources may be located in several areas of the SRP. Two of these areas, the western SRP and Camas Prairie, were selected for more detailed assessment, during which heat, permeability, and seal were evaluated using newly collected field data and smaller grid parameters to refine the location of potential resources. These higher resolution assessments illustrate the flexibility of our approach over a range of scales.

54 ENVIRONMENTAL SCIENCES↗

Helium interaction with solutes and impurities in neutron-irradiated nanostructured ferritic alloys: A first principles study

Density functional theory calculations are performed to explore the binding between He and alloying solutes, impurities, and transmutation products expected in neutron irradiated nanostructured ferritic alloys (NFAs), here 14YWT is taken as an example. Elements that exhibit significant binding (attraction) with an interstitial He are Y (binding energy = 0.46 eV), Mg (0.32), O (0.33), Ti (0.16), and C (0.15). Those that provide significant binding to a substitutional He are O (1.44), Y (1.24), N (0.73), H (0.56), Mg (0.52), Ti (0.34), Si (0.34), C (0.33), Al (0.32), Ni (0.26), Ta (0.23), and Mn (0.16). The presence of these elements in Fe matrix could reduce the transport of He towards oxide particles, dislocations, and internal boundaries, and could promote He bubble nucleation in the matrix. For convenience, we compile existing binding energy data of He with He n and He n V (He-vacancy) clusters. Dissociation pathway analysis reveals that, in general, the most likely dissociation of a He n V cluster is by a sequential emission of individual He atoms. Furthermore, larger bubbles are more prone to dissociation than smaller ones. In addition, we estimate the binding energy (segregation energy) of He in bulk Y 2 Ti 2 O 7 (YTO) single crystal, YTO/Fe interface, and YTO particle embedded in Fe, with respect to interstitial He in Fe, from existing formation energies of He in these structures. We also compile available data of He binding with Fe self-interstitial atom (SIA), SIA clusters, and edge and screw dislocations. Note that given the absence of DFT data, the binding with SIA clusters and dislocations are gathered from simulations with empirical potentials. Finally, the data presented in this paper is important to inform multiscale simulations of He bubble accumulation.

36 MATERIALS SCIENCE↗

Nuclear Data Sheets for A=69

Experimental data on ground– and excited–state properties for all known nuclei with mass number A=69 have been compiled and evaluated. States populated in radioactive decay, as well as in nuclear reactions, have been considered. For these nuclei, level and decay schemes, as well as tables of nuclear properties, are given in detail. This work supersedes the 2000 evaluation by M.R. Bhat and J.K. Tuli (2000Bh05)

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Working Party on International Nuclear Data Evaluation Cooperation (WPEC)

The OECD Nuclear Energy Agency (NEA) organizes cooperation between the major nuclear data evaluation projects in the world. The NEA Working Party on International Nuclear Data Evaluation Cooperation (WPEC) was established to promote the exchange of information on nuclear data evaluation, measurement, nuclear model calculation, validation, and related topics, and to provide a framework for cooperative activities between the participating projects. The working party assesses nuclear data improvement needs and addresses these needs by initiating joint activities in the framework of dedicated WPEC subgroups. Studies recently completed comprise a number of works related to nuclear data covariance and associated processing issues, as well as more specific studies related to the resonance parameter representation in the unresolved resonance region, the gamma production from fission product capture reactions, the {sup 235}U capture cross section, the EXFOR database, and the improvement of nuclear data for advanced reactor systems. Ongoing activities focus on the evaluation of {sup 239}Pu in the resonance region, scattering angular distribution in the fast energy range, and reporting/usage of experimental data for evaluation in the resolved resonance region. New activities include two subgroups on improved fission product yield evaluation methodologies and on modern nuclear database structures. Future activities under discussion include a pilot project for a Collaborative International Evaluated Library Organization (CIELO) and methods to provide feedback from nuclear and covariance data adjustment for improvement of nuclear data. In addition to the above mentioned short-term task-oriented subgroups, WPEC also hosts a longer-term subgroup charged with reviewing and compiling the most important nuclear data requirements in a high priority request list (HPRL)

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Nuclear Data Sheets for A=243

We present available information pertaining to the nuclear structure of all nuclei with mass numbers A=243. Various decay and reaction data are evaluated and compared. Adopted data, levels, spin, parity and configuration assignments are given. When there are insufficient data, expected values from systematics of nuclear properties or/and theoretical calculations are quoted. Unexpected or discrepant experimental results are also noted. A summary and compilation of the discovery of various isotopes in this mass region is given in 2013Fr02 ( 243 Np, 243 Pu, 243 Am, 243 Cm, 243 Bk, and 243 Cf), 2011Me01 ( 243 Es), and 2013Th02 ( 243 Fm).

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗