Crystallization of nanoparticles induced by precipitation of trace polymeric additives
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99 GENERAL AND MISCELLANEOUS↗
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A novel method for measuring ultra-trace levels of U and Th in Au, Pt, Ir, and W matrices using ICP-QQQ-MS employing an O 2 reaction gas
A mass shift method using ICP-MS/MS with O 2 reaction gas is used for ultra-trace determinations of U and Th in samples containing W, Ir, Pt, and Au derived polyatomic interferants without the need for extensive chemical sample preprocessing.
Harouaka, Khadouja↗
Evaluation and mitigation of trace 210Pb contamination on copper surfaces
Clean materials are required to construct and operate many low-background physics experiments. High-purity copper has found broad use because of its physical properties and availability. In this paper, we describe methods to assay and mitigate Pb-210 contamination on copper surfaces, such as from exposure to environmental radon or coming from bulk impurities. We evaluated the efficacy of wet etching on commercial samples and observed that Po-210 contamination from the copper bulk does not readily pass into solution. During the etch, the polonium appears to trap at the copper-etchant boundary, such that it is effectively concentrated at the copper surface. We observed a different behavior for Pb-210; high-sensitivity measurements of the alpha emissivity versus time indicate the lowest level of Pb-210 contamination ever reported for a commercial copper surface: 0 +/- 12 nBq/cm2 (1-sigma). Additionally, we have demonstrated the effectiveness of mitigating trace Pb-210 and Po-210 surface backgrounds using custom, high-purity electroplating techniques. These approaches were evaluated utilizing assays performed with an XIA UltraLo-1800 alpha spectrometer.
radon, copper, copper cleaning, dark matter, Pb-21↗
Tracing Service for Tracing-Driven Glidein Optimizations
Glideins, also known as pilots, play a pivotal role in the GlideinWMS framework: they provide tailored execution environments for user jobs to run on diverse, complex resources in a distributed setting. The framework includes several heuristics that determine the behavior of a Glidein such as how long to wait for new jobs, the wait time before a Glidein terminates etc., However, being aware of resources utilized and time exhausted during a Glidein failure and resubmission, for example, can be invaluable for its optimization. Our idea is to add a tracing service to the Glidein that will provide a closer observation of the end-to-end progress of a Glidein’s milestones and facilitates a better understanding of the overall framework as well as its reliability. The tracing service will not only gather more information about the Glidein itself to make way for optimizations but also allow user jobs to do the same.
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
Trace explosive residue detection of HMX and RDX in post-detonation dust from an open-air environment
Explosives are often used in industry, geology, mining, and other applications, but it is not always clear what remains after a detonation or the fate and transport of any residual material. The goal of this study was to determine to what extent intact molecules of high explosive (HE) compounds are detectable and quantifiable from post-detonation dust and particulates in a field experiment with varied topography. We focused on HMX (1,3,5,7-Tetranitro-1,3,5,7-tetrazocane), which is less studied in field detonation literature, as the primary explosive material and RDX (1,3,5-Trinitroperhydro-1,3,5-triazine) as the secondary material. The experiment was conducted at Site 300, Lawrence Livermore National Laboratory’s Experimental Test Site, in California, USA. Two 20.4 kg and one 40.8 kg above ground explosions (primarily comprised of LX-14, an HMX-based polymer-bonded high explosive) were detonated on an open-air firing area on separate days. The complex terrain of the firing area (e.g., buildings, berm, low-height obstacles) was advantageous to study HE deposition in relation to plume dynamics. Three types of samples were collected up to 100 m away from each shot: surface swipes of aluminum plates, surface swipes of fixed objects, and filters from air samples. We used atmospheric flow tube-mass spectrometry (AFT-MS) to quantify picogram levels of molecular residue of HE material in the post-detonation dust. An aliquot of sample extract in methanol (e.g., 1 µL of 0.5 mL) was placed onto a resistive material and then thermally desorbed into the AFT-MS. We successfully detected and quantified both HMX and RDX in many of the samples. Based on mass (pg) detected and solution dilution, we back-calculated the mass collected on the swipe or filter (ng per sample). The aerial distribution of molecular residue was consistent with the path of the plume, which was strongly determined by wind speed and direction at the time of each shot. The quantity of material detected appeared to correlate more with distance from the shot and the wind conditions than with shot size. This study demonstrates that the picogram detection levels of AFT-MS are well-suited for quantification of analytes (e.g., HMX and RDX) in environmental samples.
atmospheric flow tube-mass spectrometry (AFT-MS), ↗
Effects of hydrogen isotope type on oxidation rates for trace releases
Not Available
Shurtz, Randy C. (ORCID:0000000227420334)↗
A blockchain empowered and privacy preserving digital contact tracing platform
Not Available
Bandara, Eranga↗
New diagnostic sea surface current fields to trace floating algae in the Yellow Sea
Not provided.
Environmental Sciences & Ecology↗
Refined views of ancient ocean chemistry: Tracking trace element incorporation in pyrite framboids using atom probe tomography
The trace element chemistry of pyrite can be used to determine the origin, timing, and conditions of formation of ore deposits; as a vectoring tool for mineral exploration; and to determine the evolution of the Earth’s oceanic and atmospheric chemistry. However, little is known about whether trace elements are held with the pyrite structure or within nano-inclusions of other phases. This distinction is important for two primary reasons. First, trace element incorporation into the pyrite structure can affect the partitioning of other trace elements. Second, if trace elements are held within nano-inclusions, the partition coefficient of the mineral phases that make up the nano-inclusion, rather than pyrite, are the critical consideration in related interpretations. Previous studies addressing this topic have used laser ablation inductively coupled plasma mass spectrometry; however, the resulting data do not provide sufficient spatial resolution to delineate trace element distributions unless the inclusions are large. Further, they use these flat element profiles in time resolved laser ablation output graphs to argue that pyrite trace element content provides a direct relationship between trace element content of seawater and pyrite trace element content. To improve resolution, we have used atom probe tomography to characterize trace element distributions in pyrite framboids from the Cariaco Basin and Demerara Rise in three-dimensions at sub-nanometer resolution. Manganese was found to be concentrated in the pyrite nanocrystal part of the original framboid structure. In contrast, Ni was mostly found along the grain boundary, though it still appeared to be contained within the pyrite structure. Copper was concentrated in later pyrite overgrowths, and As varied in its location. These observations suggest that some important trace elements are incorporated into pyrite during early diagenesis, even in euxinic settings dominated by water-column pyrite formation. Statistical analysis was used to determine whether trace elements were incorporated in the lattice or within nanoscale inclusions (referred to here are nano-inclusions). We found that As, Ni, Cu, and Mn were commonly held within the pyrite structure, but As, Ni, and Cu can also be held as nano-inclusions or within grain interfaces. Incorporation of As is known to enhance the incorporation of other trace elements and in this case appears to correlated to elevated Ni and Cu concentrations in the Cariaco Basin samples. Furthermore, understanding these relationships strongly impacts our ability to utilize pyrite trace metal concentrations to analyze and quantify early ocean chemistry and its evolution through time.
54 ENVIRONMENTAL SCIENCES↗
Machine Learning Assisted HPC Workload Trace Generation for Leadership Scale Storage Systems
Monitoring and analyzing a wide range of I/O activities in an HPC cluster is important in maintaining mission-critical performance in a large-scale, multi-user, parallel storage system. Center-wide I/O traces can provide high-level information and fine-grained activities per application or per user running in the system. Studying such large-scale traces can provide helpful insights into the system. It can be used to develop predictive methods for making predictive decisions, adjusting scheduling policies, or providing decisions for the design of next-generation systems. However, sharing real-world I/O traces to expedite such research efforts leaves a few concerns; i) the cost of sharing the large traces is expensive due to this large size, and ii) privacy concern is an issue.We address such issues by building an end-to-end machine learn- ing (ML) workflow that can generate I/O traces for large-scale HPC applications. We leverage ML based feature selection and gener- ative models for I/O trace generation. The generative models are trained on I/O traces collected by the darshan I/O characterization tool over a period of one year. We present a two-step generation process consisting of two deep-learning models, called the feature generator and the trace generator. The combination of two-step generative models provides robustness by reducing the bias of the model and accounting for the stochastic nature of the I/O traces across different runs of an application. We evaluate the performance of the generative models and show that the two-step model can generate time-series I/O traces with less than 20% root mean square error.
Paul, Arnab↗
BigNeuron: a resource to benchmark and predict performance of algorithms for automated tracing of neurons in light microscopy datasets
BigNeuron is an open community bench-testing platform with the goal of setting open standards for accurate and fast automatic neuron tracing. We gathered a diverse set of image volumes across several species that is representative of the data obtained in many neuroscience laboratories interested in neuron tracing. Here, we report generated gold standard manual annotations for a subset of the available imaging datasets and quantified tracing quality for 35 automatic tracing algorithms. The goal of generating such a hand-curated diverse dataset is to advance the development of tracing algorithms and enable generalizable benchmarking. Together with image quality features, we pooled the data in an interactive web application that enables users and developers to perform principal component analysis, t-distributed stochastic neighbor embedding, correlation and clustering, visualization of imaging and tracing data, and benchmarking of automatic tracing algorithms in user-defined data subsets. The image quality metrics explain most of the variance in the data, followed by neuromorphological features related to neuron size. Furthermore, we observed that diverse algorithms can provide complementary information to obtain accurate results and developed a method to iteratively combine methods and generate consensus reconstructions. The consensus trees obtained provide estimates of the neuron structure ground truth that typically outperform single algorithms in noisy datasets. However, specific algorithms may outperform the consensus tree strategy in specific imaging conditions. Finally, to aid users in predicting the most accurate automatic tracing results without manual annotations for comparison, we used support vector machine regression to predict reconstruction quality given an image volume and a set of automatic tracings.
97 MATHEMATICS AND COMPUTING↗
Traveler: Navigating Task Parallel Traces for Performance Analysis
Understanding the behavior of software in execution is a key step in identifying and fixing performance issues. This is especially important in high performance computing contexts where even minor performance tweaks can translate into large savings in terms of computational resource use. To aid performance analysis, developers may collect an execution trace —a chronological log of program activity during execution. As traces represent the full history, developers can discover a wide array of possibly previously unknown performance issues, making them an important artifact for exploratory performance analysis. However, interactive trace visualization is difficult due to issues of data size and complexity of meaning. Traces represent nanosecond-level events across many parallel processes, meaning the collected data is often large and difficult to explore. The rise of asynchronous task parallel programming paradigms complicates the relation between events and their probable cause. Here, to address these challenges, we conduct a continuing design study in collaboration with high performance computing researchers. We develop diverse and hierarchical ways to navigate and represent execution trace data in support of their trace analysis tasks. Through an iterative design process, we developed Traveler , an integrated visualization platform for task parallel traces. Traveler provides multiple linked interfaces to help navigate trace data from multiple contexts. We evaluate the utility of Traveler through feedback from users and a case study, finding that integrating multiple modes of navigation in our design supported performance analysis tasks and led to the discovery of previously unknown behavior in a distributed array library.
97 MATHEMATICS AND COMPUTING↗
Gas-mediated trace element incorporation into rhyolite-hosted topaz: A synchrotron microbeam XAS study
Magmatic gas exsolving during late-stage cooling of shallow magmas has been considered an important facilitator of low-pressure alteration and metal transport. However, the chemical properties of such gas, particularly its metal transport mechanisms and capacity, remain elusive. Trace elements in minerals produced by gas-mediated surface reaction or precipitation from gas capture details of gas composition and reaction pathways. However, interpretation of mineral trace element contents is dependent on understanding crystallographic controls on gas/mineral partitioning. Here, this work investigates the structural accommodation of As, Mn, Ga, Ge, Fe, and Ti in vapor-deposited topaz of vesicular topaz rhyolite from the Thomas Range, Utah, through single-crystal synchrotron microbeam X-ray techniques on picogram quantities of those trace elements. X-ray absorption near edge structure (XANES) data indicates that these elements are incorporated into topaz as As 5+ , Fe 3+ , Mn 3+ , Ti 4+ , Ga 3+ , and Ge 4+ . Extended X-ray absorption fine structure (EXAFS) analysis for these trace elements, compared to EXAFS of structural Al and Si, reveals that As 5+ and Ge 4+ are incorporated directly into the tetrahedral site of the topaz structure, with the octahedral site accommodating Mn 3+ , Fe 3+ , Ga 3+ , and Ti 4+ . For As 5+ and Fe 3+ , the structural impact of substitution extends to at least second neighbors (other elements were only resolvable to first neighbors). Further interpretation of the EXAFS results suggests that the substitution of Ti 4+ results in increased distortion of the octahedral site, while the other trace elements induce more uniform expansion correlating in magnitude to their ionic radius. Comparison of quantified X-ray fluorescence (XRF) data for two topaz crystals from this rhyolite reveals variable trace element concentrations for As 5+ , Fe 3+ , Ga 3+ , and Ti 4+ , reflective of a source gas undersaturated in these trace elements changing in concentration over the period of topaz deposition. The identical Ge 4+ content of the two topaz crystals suggests that Ge 4+ in the gas was buffered by the growth of another Ge 4+ -bearing phase, such as quartz. The very low Mn 3+ content in the topaz crystals does not reflect the abundance of Mn 3+ in the gas (saturation of Mn is evidenced by coexisting bixbyite). Instead, it suggests a strong Jahn-Teller inhibitory effect to the substitution of Mn 3+ for Al 3+ in the distorted octahedral site of topaz. It is proposed that exsolution of an HF-enriched gas from cooling rhyolitic magma led to local scouring of Al, Si, and trace metals from the magma. Once topaz crystals nucleated, self-catalyzed reactions that recycle HF led to continued growth of topaz.
36 MATERIALS SCIENCE↗
Identifying impacts of contact tracing on HIV epidemiological inference from phylogenetic data
Abstract Robust sampling methods are foundational to inferences using phylogenies. Yet the impact of using contact tracing, a type of non-uniform sampling used in public health applications such as infectious disease outbreak investigations, has not been investigated in the molecular epidemiology field. To understand how contact tracing influences a recovered phylogeny, we developed a new simulation tool called SEEPS (Sequence Evolution and Epidemiological Process Simulator) that allows for the simulation of contact tracing and the resulting transmission tree, pathogen phylogeny, and corresponding virus genetic sequences. Importantly, SEEPS takes within-host evolution into account when generating pathogen phylogenies and sequences from transmission histories. Using SEEPS, we demonstrate that contact tracing can significantly impact the structure of the resulting tree, as described by popular tree statistics. Contact tracing generates phylogenies that are less balanced than the underlying transmission process, less representative of the larger epidemiological process, and affects the internal/external branch length ratios that characterize specific epidemiological scenarios. We also examined real data from a 2007–2008 Swedish HIV-1 outbreak and the broader 1998–2010 European HIV-1 epidemic to highlight the differences in contact tracing and expected phylogenies. Aided by SEEPS, we show that the data collection of the Swedish outbreak was strongly influenced by contact tracing even after downsampling, while the broader European Union epidemic showed little evidence of universal contact tracing, agreeing with the known epidemiological information about sampling and spread. Overall, our results highlight the importance of including possible non-uniform sampling schemes when examining phylogenetic trees. For that, SEEPS serves as a useful tool to evaluate such impacts, thereby facilitating better phylogenetic inferences of the characteristics of a disease outbreak. SEEPS is available at https://github.com/MolEvolEpid/SEEPS.
Virology↗
TRACE Input Modernization
This work presents a Tom’s Obvious Minimal Language (TOML)-based representation of input for the US Nuclear Regulatory Commission’s TRAC/RELAP Advanced Computational Engine (TRACE) thermal hydraulics code. Implemented using the Workbench Analysis Sequence Processor (WASP), the approach maps traditional TRACE input structures to a hierarchical format composed of named parameters, typed values, and native data collections. The resulting representation preserves TRACE’s existing modeling capabilities while providing a modern, structured interface for model development and management. WASP further extends TOML through a file import directive that supports modular model composition and reusable input organization. In addition, WASP provides extended array data entry convenience with various data repeat and interpolation capabilities. Examples of the new TOML syntax are provided for major TRACE input categories, including hydraulic components, heat structures, control systems, and trip logic. The TOML representation establishes a foundation for improved validation, tooling, automation, and model maintainability while remaining compatible with existing TRACE workflows. To facilitate migration to the TOML-based input format, the TRACE executable now supports conversion of native TRACE input into an intermediate JSON representation. A Python utility subsequently transforms the JSON data into an equivalent TOML model. Lastly, the TRACE executable now supports execution using TOML-formatted input.
Lefebvre, Robert A. [Oak Ridge National Laboratory↗
Consistent Controls on Trace Metal Micronutrient Speciation in Wetland Soils and Stream Sediments
Trace metal are essential for microbially-mediated biogeochemical processes occurring in anoxic wetland soils and stream bed sediments, but low availability of these elements may inhibit anaerobic element cycling and transformations. Solid-phase speciation is likely a critical control on trace metal availability but has seen limited study in anoxic systems having concentrations similar to geological background levels, where metal limitations may be most prevalent. We have investigated trace metal concentrations and solid-phase speciation in three freshwater subsurface aquatic systems: marsh wetland soils, riparian wetland soils, and the sediments of a streambed. These systems displayed low solid-phase trace metal concentrations, generally at or below geological background levels, which generally followed the trend Zn > Cu ≈ Ni > Co and showed no correlation with major element compositions. All soils and sediments were dominated by quartz but varied in clay mineralogy as well as the organic matter, total sulfur, and total iron contents. X-ray absorption near-edge structure (XANES) spectroscopy shows that sulfur speciation in both wetlands is dominated by organic sulfur. Elemental sulfur and iron sulfides together made up <25% of the sulfur in the wetland soils, but the distribution between inorganic and organic forms was reversed in the stream sediments. Ferrous and ferric iron in clay minerals were common species identified by both XANES and extended X-ray absorption fine structure (EXAFS) spectroscopies at all sites. Iron(III) oxides were substantial components in all but the marsh wetland soils. Quantitative analysis of copper, nickel, and zinc XANES spectra revealed similar metal speciation across all sites. Copper speciation was dominated by sulfides, adsorbed species, and minor amounts of copper bound to organic matter; no metallic copper was detected. Nickel speciation also varied little and was dominated by nickel in clay mineral octahedral sheets and nickel sulfide, with adsorbed species also present. Zinc speciation was slightly more varied, with the marsh wetland soils and stream bed sediments containing adsorbed species, zinc associated with clay mineral structures, and zinc bound to reduced sulfur groups on organic matter, whereas the riparian wetland soils lacked clay-associated zinc but contained zinc sulfide. Trace metals bound to reduced sulfur occurred at every site, with a greater sulfur-bound fraction for copper. The fractional abundance of sulfur-bound species showed no relationship with soil or sediment total sulfur content, which varied by two orders of magnitude. More broadly, the observations in this study suggest that trace metal speciation in freshwater wetland soils and stream sediments is consistently dominated by a small set of recurring components which are distinct for each metal. Furthermore, this may represent a general geochemical phenomenon in anoxic soils and sediments containing trace metals at background concentrations (as low as 3 µg g -1 ) that was not predicted from systems that are contaminated with or naturally-enriched in copper, nickel, or zinc.
54 ENVIRONMENTAL SCIENCES↗
Mobilization of trace metals from caprock and formation rocks at the Illinois Basin – Decatur Project demonstration site under geological carbon dioxide sequestration conditions
One concern for geologic CO 2 sequestration is the potential leakage of CO 2 or CO 2 -saturated brine containing trace metals into overlying aquifers, which poses the risk of adversely affecting underground sources of drinking water. In this work, rock and brine samples collected in the Illinois Basin – Decatur Project (IBDP), a large-scale geological CO 2 sequestration demonstration project in Decatur, Illinois, USA, as well as synthetic brine samples were used to understand the mobilization of trace metals as a result of CO 2 –rock–brine interactions under IBDP-specific conditions (50 °C and 20.6 MPa). Rock sample characterization indicated that, at the IBDP site, trace metal concentrations were greatest in cap rock samples from the Eau Claire Formation, compared with those from formations above and below this Formation. The natural brine samples collected from the Mt. Simon Sandstone reservoir were highly reducing and saline, with trace metal concentrations up to 680 times greater than the U.S. Environmental Protection Agency-prescribed drinking water standards. Batch leaching experiments indicated that both trace metal mobilization from rock and immobilization from the brine occurred when high-pressure CO 2 was introduced into the rock-brine system. The amounts of metals mobilized from the rock generally accounted for <5% of the total metals in the rock, but for some metals, including Ni, Pb, and Tl, up to 63% of the metals in the rock were mobilized to the brine. Leaching of trace metals into synthetic brines was different from that into the natural brine. The results of this study provided current information on the trace element sources and will help in risk simulations and experimental design to further evaluate potential impact of leakage on groundwater quality, which is important for future GCS projects to consider for monitoring and containment assurance purposes.
58 GEOSCIENCES↗
PredCom: A Predictive Approach to Collecting Approximated Communication Traces
Communication traces collected from MPI applications are an important source of information for performance optimization as they can help analysts determine communication patterns and identify inefficiencies. However, their collection, especially at scale, is time consuming, since it usually requires running the complete target application on a large number of nodes. In this work, we present PredCom, a tool-chain to generate a predictive communication proxy based on information gathered from a few small scale runs, which allows us to extract approximate communication traces with an accuracy high enough for most analysis goals. For this, we combine LLVM passes on the original source code (to capture static program structure) with parameter prediction (to capture dynamic and scaling behavior). This approach drastically reduces the time needed for collecting the communication traces, even for traces on large numbers of MPI processes. Here, we demonstrate that PredCom generates communication traces of various applications up to 1612x faster with an accuracy loss of 0.11 on average compared to the original large-scale traces, and we show that the generated traces can be used to optimize process placement.
97 MATHEMATICS AND COMPUTING↗