Quantifying fracture geometry with X-ray tomography: Technique of Iterative Local Thresholding (TILT) for 3D image segmentation

This paper presents a new method—the Technique of Iterative Local Thresholding (TILT)—for processing 3D X-ray computed tomography (xCT) images for visualization and quantification of rock fractures. The TILT method includes the following advancements. First, custom masks are generated by a fracture-dilation procedure, which significantly amplifies the fracture signal on the intensity histogram used for local thresholding. Second, TILT is particularly well suited for fracture characterization in granular rocks because the multi-scale Hessian fracture (MHF) filter has been incorporated to distinguish fractures from pores in the rock matrix. Third, TILT wraps the thresholding and fracture isolation steps in an optimized iterative routine for binary segmentation, minimizing human intervention and enabling automated processing of large 3D datasets. As an illustrative example, we applied TILT to 3D xCT images of reacted and unreacted fractured limestone cores. Other segmentation methods were also applied to provide insights regarding variability in image processing. The results show that TILT significantly enhanced separability of grayscale intensities, outperformed the other methods in automation, and was successful in isolating fractures from the porous rock matrix. Because the other methods are more likely to misclassify fracture edges as void and/or have limited capacity in distinguishing fractures from pores, those methods estimated larger fracture volumes (up to 80 %), surface areas (up to 60 %), and roughness (up to a factor of 2). These differences in fracture geometry would lead to significant disparities in hydraulic permeability predictions, as determined by 2D flow simulations.     

<Emphasis Type="Italic">Deepwater Horizon</Emphasis> Oil Spill Impacts on Salt Marsh Fiddler Crabs (<Emphasis Type="Italic">Uca</Emphasis> spp.)

The Deepwater Horizon oil spill was the largest marine oil spill in US waters to date and one of the largest worldwide. Impacts of this spill on salt marsh vegetation have been well documented, although impacts on marsh macroinvertebrates have received less attention. To examine impacts of the oil spill on an important marsh invertebrate and ecosystem engineer, we conducted a meta-analysis on fiddler crabs (Uca spp.) using published sources and newly available Natural Resources Damage Assessment (NRDA) and Gulf of Mexico Research Initiative (GoMRI) data. Fiddler crabs influence marsh ecosystem structure and function through their burrowing and feeding activities and are key prey for a number of marsh and estuarine predators. We tested the hypothesis that the spill affected fiddler crab burrow density (crab abundance), burrow diameter (crab size), and crab species composition. Averaged across multiple studies, sites, and years, our synthesis revealed a negative effect of oiling on all three metrics. Burrow densities were reduced by 39 % in oiled sites, with impacts and incomplete recovery observed over 2010–2014. Burrow diameters were reduced from 2010 to 2011, but appeared to have recovered by 2012. Fiddler crab species composition was altered through at least 2013 and only returned to reference conditions where marsh vegetation recovered, via restoration planting in one case. Given the spatial and temporal extent of data analyzed, this synthesis provides compelling evidence that the Deepwater Horizon spill suppressed populations of fiddler crabs in oiled marshes, likely affecting other ecosystem attributes, including marsh productivity, marsh soil characteristics, and associated predators.     

Present-day oxidative subsidence of organic soils and mitigation in the Sacramento-San Joaquin Delta,California, USA

Subsidence of organic soils in the Sacramento-San Joaquin Delta threatens sustainability of the California (USA) water supply system and agriculture. Land-surface elevation data were collected to assess present-day subsidence rates and evaluate rice as a land use for subsidence mitigation. To depict Delta-wide present-day rates of subsidence, the previously developed SUBCALC model was refined and calibrated using recent data for CO₂ emissions and land-surface elevation changes measured at extensometers. Land-surface elevation change data were evaluated relative to indirect estimates of subsidence and accretion using carbon and nitrogen flux data for rice cultivation. Extensometer and leveling data demonstrate seasonal variations in land-surface elevations associated with groundwater-level fluctuations and inelastic subsidence rates of 0.5–0.8 cm yr^–1. Calibration of the SUBCALC model indicated accuracy of ±0.10 cm yr^–1 where depth to groundwater, soil organic matter content and temperature are known. Regional estimates of subsidence range from <0.3 to >1.8 cm yr^–1. The primary uncertainty is the distribution of soil organic matter content which results in spatial averaging in the mapping of subsidence rates. Analysis of leveling and extensometer data in rice fields resulted in an estimated accretion rate of 0.02–0.8 cm yr^–1. These values generally agreed with indirect estimates based on carbon fluxes and nitrogen mineralization, thus preliminarily demonstrating that rice will stop or greatly reduce subsidence. Areas below elevations of –2 m are candidate areas for implementation of mitigation measures such as rice because there is active subsidence occurring at rates greater than 0.4 cm yr^–1.     

Identification of Uranyl Minerals Using Oxygen K‐Edge X‐Ray Absorption Spectroscopy

Although most of the world's uranium exists as pitchblende or uraninite, this mineral can be weathered to a great variety of secondary uranium minerals, most containing the uranyl cation. Anthropogenic uranium compounds can also react in the environment, leading to spatial–chemical alterations that could be useful for nuclear forensics analyses. Soft X‐ray absorption spectroscopy (XAS) has the advantages of being non‐destructive, element‐specific and sensitive to electronic and physical structure. The soft X‐ray probe can also be focused to a spot size on the order of tens of nanometres, providing chemical information with high spatial resolution. However, before XAS can be applied at high spatial resolution, it is necessary to find spectroscopic signatures for a variety of uranium compounds in the soft X‐ray spectral region. To that end, we collected the near edge X‐ray absorption fine structure (NEXAFS) spectra of a variety of common uranyl‐bearing minerals, including uranyl carbonates, oxyhydroxides, phosphates and silicates. We find that uranyl compounds can be distinguished by class (carbonate, oxyhydroxide, phosphate or silicate) based on their oxygen K‐edge absorption spectra. This work establishes a database of reference spectra for future spatially resolved analyses. We proceed to show scanning X‐ray transmission microscopy (STXM) data from a schoepite particle in the presence of an unknown contaminant.     

High Precision Sr‐Nd‐Hf‐Pb Isotopic Compositions of USGS Reference Material BCR‐2

The Lamont‐Doherty Earth Observatory radiogenic isotope group has been systematically measuring Sr‐Nd‐Pb‐Hf isotopes of USGS reference material BCR‐2 (Columbia River Basalt 2), as a chemical processing and instrumental quality control monitor for isotopic measurements. BCR‐2 is now a widely used geochemical inter‐laboratory reference material (RM), with its predecessor BCR‐1 no longer available. Recognising that precise and accurate data on RMs is important for ensuring analytical quality and for comparing data between different laboratories, we present a compilation of multiple digestions and analyses made on BCR‐2 during the first author's dissertation research. The best estimates of Sr, Nd and Hf isotope ratios and measurement reproducibilities, after filtering at the 2s level for outliers, were ⁸⁷Sr/⁸⁶Sr = 0.705000 ± 11 (2s, 16 ppm, n = 21, sixteen digestions, one outlier), ¹⁴³Nd/¹⁴⁴Nd = 0.512637 ± 13 (2s, 25 ppm, n = 27, thirteen digestions, one outlier) and ¹⁷⁶Hf/¹⁷⁷Hf = 0.282866 ± 11 (2s, 39 ppm, n = 25, thirteen digestions, no outliers). Mean Nd and Hf values were within error of those reported by Weis et al. (2006, 2007) in their studies of RMs; mean Sr values were just outside the 2s uncertainty range of both laboratories. Moreover, a survey of published Sr‐Nd‐Hf data shows that our results fall within the range of reported values, but with a smaller variability. Our Pb isotope results on acid leached BCR‐2 aliquots (n = 26, twelve digestions, two outliers) were ²⁰⁶Pb/²⁰⁴Pb = 18.8029 ± 10 (2s, 55 ppm), ²⁰⁷Pb/²⁰⁴Pb = 15.6239 ± 8 (2s, 52 ppm), ²⁰⁸Pb/²⁰⁴Pb = 38.8287 ± 25 (2s, 63 ppm). We confirm that unleached BCR‐2 powder is contaminated with Pb, and that sufficient leaching prior to digestion is required to achieve accurate values for the uncontaminated Pb isotopic compositions.     

藏北羌塘南部埃迪卡拉系达布热组的建立及其地质意义

羌塘位于青藏高原腹地,构造上处于冈瓦纳大陆北缘。因其特殊的构造位置,羌塘地体的起源及构造演化对于探讨青藏高原的早期形成演化、冈瓦纳大陆裂解,以及特提斯洋演化等关键科学问题至关重要。最近,在羌塘南部达布热地区发现一套碎屑岩夹玄武岩的岩石组合,碎屑岩具有低成分成熟度的特点,虽然岩石发生了低绿片岩相变质,但仍然保留了原岩类复理石沉积的特点。根据碎屑锆石定年结果,该套地层中碎屑锆石的最年轻年龄为550Ma左右。此外,该套地层中玄武岩夹层的测年结果表明,该套地层形成于埃迪卡拉纪(约550Ma)。结合地层剖面及区域地层对比,建立了埃迪卡拉纪达布热组。达布热组是羌塘地区首次发现的埃迪卡拉纪地层,该组地层的建立为探讨冈瓦纳大陆北缘构造演化提供了重要线索。     

Adjoint analysis of Buckley-Leverett and two-phase flow equations

This paper analyzes the adjoint equations and boundary conditions for porous media flow models, specifically the Buckley-Leverett equation, and the compressible two-phase flow equations in mass conservation form. An adjoint analysis of a general scalar hyperbolic conservation law whose primal solutions include a shock jump is initially presented, and the results are later specialized to the Buckley-Leverett equation. The non-convexity of the Buckley-Leverett flux function results in adjoint characteristics that are parallel to the shock front upstream of the shock and emerge from the shock front downstream of the shock. Thus, in contrast to the behavior of Burgers’ equation where the adjoint is continuous at a shock, the Buckley-Leverett adjoint, in general, contains a discontinuous jump across the shock. Discrete adjoint solutions from space-time discontinuous Galerkin finite element approximations of the Buckley-Leverett equation are shown to be consistent with the derived closed-form analytical solutions. Furthermore, a general result relating the adjoint equations for different (though equivalent) primal equations is used to relate the two-phase flow adjoints to the Buckley-Leverett adjoint. Adjoint solutions from space-time discontinuous Galerkin finite element approximations of the two-phase flow equations are observed to obey this relationship.     

Upstream—Downstream Shifts in Peak Recruitment of the Native Olympia Oyster in San Francisco Bay During Wet and Dry Years

Understanding the conditions that drive variation in recruitment of key estuarine species can be important for effective conservation and management of their populations. The Olympia oyster (Ostrea lurida) is native to the Pacific coast of North America and has been a target of conservation efforts, though relatively little information on larval recruitment exists across much of its range. This study examined the recruitment of Olympia oysters at biweekly to monthly intervals at four sites in northern San Francisco Bay from 2010 to 2015 (except 2013). Mean monthly temperatures warmed at all sites during the study, while winter (January–April) mean monthly salinity decreased significantly during a wet year (2011), but otherwise remained high as a result of a drought. A recurring peak in oyster recruitment was identified in mid-estuary, in conditions corresponding to a salinity range of 25–30 and >16 °C at the time of settlement (April–November). Higher average salinities and temperatures were positively correlated with greater peak recruitment. Interannual variation in the timing of favorable conditions for recruitment at each site appears to explain geographic and temporal variation in recruitment onset. Higher winter/spring salinities and warmer temperatures at the time of recruitment corresponded with earlier recruitment onset within individual sites. Across all sites, higher winter/spring salinities were also correlated with earlier onset and earlier peak recruitment. Lower winter salinities during 2011 also resulted in a downstream shift in the location of peak recruitment.     

Defining the Potential of Nanoscale Re‐Os Isotope Systematics Using Atom Probe Microscopy

Atom probe microscopy (APM) is a relatively new in situ tool for measuring isotope fractions from nanoscale volumes (< 0.01 μm³). We calculate the theoretical detectable difference of an isotope ratio measurement result from APM using counting statistics of a hypothetical data set to be ± 4δ or 0.4% (2s). However, challenges associated with APM measurements (e.g., peak ranging, hydride formation and isobaric interferences), result in larger uncertainties if not properly accounted for. We evaluate these factors for Re‐Os isotope ratio measurements by comparing APM and negative thermal ionisation mass spectrometry (N‐TIMS) measurement results of pure Os, pure Re, and two synthetic Re‐Os‐bearing alloys from Schwander et al. (2015, Meteoritics and Planetary Science, 50, 893) [the original metal alloy (HSE) and alloys produced by heating HSE within silicate liquid (SYN)]. From this, we propose a current best practice for APM Re‐Os isotope ratio measurements. Using this refined approach, mean APM and N‐TIMS ¹⁸⁷Os/¹⁸⁹Os measurement results agree within 0.05% and 2s (pure Os), 0.6–2% and 2s (SYN) and 5–10% (HSE). The good agreement of N‐TIMS and APM ¹⁸⁷Os/¹⁸⁹Os measurements confirms that APM can extract robust isotope ratios. Therefore, this approach permits nanoscale isotope measurements of Os‐bearing alloys using the Re‐Os geochronometer that could not be measured by conventional measurement principles.