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At least 343 records · Page 19

The metagenomic data life-cycle: standards and best practices

Metagenomics data analyses from independent studies can only be compared if the analysis workflows are described in a harmonised way. In this overview, we have mapped the landscape of data standards available for the description of essential steps in metagenomics: (1) material sampling, (2) material sequencing (3) data analysis and (4) data archiving & publishing. Taking examples from marine research, we summarise essential variables used to describe material sampling processes and sequencing procedures in a metagenomics experiment. These aspects of metagenomics dataset generation have been to some extent addressed by the scientific community but greater awareness and adoption is still needed. We emphasise the lack of standards relating to reporting how metagenomics datasets are analysed and how the metagenomics data analysis outputs should be archived and published. We propose best practice as a foundation for a community standard to enable reproducibility and better sharing of metagenomics datasets, leading ultimately to greater metagenomics data reuse and repurposing.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

Single-Use Destructive Assay for Uranium Hexafluoride Sampling

Sampling uranium hexafluoride (UF6) for the determination of enrichments by destructive analysis (DA) is a critical component in the International Atomic Energy Agency’s layered safeguards approach for uranium processing facilities. Typically, gram-quantity UF6 samples are collected during inspections and stored under tag-and-seal until transportation to an off-site analytical laboratory. The shipping times can be long, and evolving restrictions on radioactive/corrosive materials shipments may increasingly limit the IAEA’s ability to transport UF6 samples easily. Pacific Northwest National Laboratory has developed a low-cost UF6 sampling technology called Single-Use Destructive Assay (SUDA) that addresses these challenges, as well as provides DA sample geometries that can be tailored for different analytical methods, including potential on-site analyses. The SUDA samplers, along with a unique holder, are designed for direct attachment to existing taps at uranium processing facilities, allowing gaseous UF6 to come into direct contact with a zeolite film. The SUDA technology features the ability to capture uranium in a more easily shipped and handled form as the solid, more stable, and relatively less hazardous hydrated uranyl fluoride (UO2F2•nH2O), which is formed through the controlled hydrolysis of UF6. We have recently simulated uranium collection under enrichment plant sampling conditions to further improve our understanding of SUDA sampling. Presented here is our recent work on measuring the relationship between sampling conditions and uranium collection, which includes control of the uranium-mass-to-zeolite ratio and assessing variable UF6 gas and sampling parameters that can affect collection using the SUDA sampler.

Pope, Timothy R.↗

Effects of Sintering Temperature on Structural, Morphological and Magnetic Properties of Strontium Ferrite Nanoparticles

In the present investigation, structural, morphological and magnetic properties of SrFe{sub 2}O{sub 4} ferrite nanoparticles prepared by a sol–gel method were studied. The techniques used in this investigation were thermogravimetric analysis/differential thermal analysis (TGA/DTA), X-ray diffraction (XRD), energy-dispersive X-ray spectroscopy (EDX), field emission scanning electron microscopy (FESEM), Fourier transform infrared spectrometry (FT-IR), vibrating sample magnetometry (VSM) and Curie temperature analysis. The average crystallite sizes of the SrFe{sub 2}O{sub 4} were calculated using the Scherrer formula and found in the range of 11–22 nm, and this can be attributed to the grain growth of the particles. The lattice parameter of SrFe{sub 2}O{sub 4} nanoparticles decreased from 6.64 to 6.51 nm as the sintering temperature was raised from 600 to 900 °C. FT-IR analysis confirmed that bands in the range 430–590 cm{sup − 1} are due to the stretching vibration of oxygen atom and metal ions (M–O) that is Fe–O confirming the formation of spinel ferrite. Surface morphology of the samples has been studied using FESEM. The elemental composition along with their relative ratios was given by EDX and was found to be in agreement with their initial calculated values. The saturation magnetization, magnetic coercivity and remanence increase with an increasing sintering temperature from 600 to 900 °C. The present study reports the Curie temperature with an amount of 551 °C of the synthesized strontium nanoferrites using the Faraday technique.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

Giant Exfoliation Induced Magnetic Coercivity in Fe 3 GaTe 2

Permanent magnets with strong anisotropy and high coercivity underpin modern information and energy technologies, yet rare-earth-free alternatives remain limited. Here, we show that thickness engineering via mechanical exfoliation induces hard magnetic behavior in the van der Waals ferromagnet Fe 3 GaTe 2 . Bulk crystals exhibit Curie temperatures above 350 K but negligible room-temperature coercivity. When thinned below ∼100 nm, the coercive field is dramatically enhanced, reaching nearly 1 T at room temperature for in-plane fields—comparable to conventional hard magnets. Micromagnetic analysis reveals a crossover in magnetization reversal from domain-mediated processes in bulk samples to quasi-coherent rotation in thin flakes, driven by increased effective anisotropy and suppressed domain formation. This thickness-dependent transition enables tuning of magnetic hardness without chemical modification. Combined with high saturation magnetization and robust room-temperature performance, Fe 3 GaTe 2 emerges as a promising rare-earth-free material for spintronic applications. Its layered structure further allows integration into van der Waals heterostructures, where large in-plane coercivity can stabilize magnetic states against perturbations and interlayer coupling, offering potential for high-density nonvolatile memory and domain-wall-based devices.

36 MATERIALS SCIENCE↗

Developing new alkaline ceramics as possible CO 2 chemisorbents at high temperatures: The lithium and sodium yttriates (LiYO 2 and NaYO 2 ) cases

In this work, lithium and sodium yttriates (LiYO 2 and NaYO 2 ) were synthesized, characterized and tested as possible carbon dioxide (CO 2 ) captors. All the experimental syntheses and analyses were supported by the theoretical thermodynamic calculations, showing that both ceramics would be able to chemisorb CO 2 in a wide temperature range. Therefore, both ceramics were prepared by solid-state reaction and structurally characterized. In fact, the structural characterization evidenced that sodium atoms are located in a octahedral close-packed structure, while lithium ions are not so packed. The lithium ions are, indeed, in a highly distorted tetrahedron, tending to square-planar coordination. Then, based on the theoretical and structural analysis, LiYO 2 and NaYO 2 samples were investigated for the CO 2 capture process through dynamic and isothermal thermogravimetric experiments. All these experiments showed that LiYO 2 has better CO 2 capture properties than NaYO 2 , which was further correlated with the crystal structures of each ceramic. Furthermore, both ceramics presented similar CO 2 capture efficiencies regardless of the CO 2 concentration. Finally, LiYO 2 sample was tested for cyclic CO 2 chemisorption-desorption processes. The obtained results showed that the CO 2 capture efficiency is maintained high at least through 10 cycles. Therefore, these alkaline yttriates seem to present interesting alternatives as high and moderate temperature CO 2 captors, applicable for post-combustion industrial capture processes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Synthesis and characterization in AuCu–Si nanostructures

Au/Cu bilayers with different Au:Cu concentrations (25:75, 50:50 and 75:25 at.%) were deposited on Si(100) substrates by thermal evaporation. The thicknesses of all Au/Cu bilayers were 150 nm. The alloys were prepared by thermal diffusion into a vacuum oven with argon atmosphere at 690 K during 1 h. X-ray diffraction analysis revealed different phases of AuCu and CuSi alloys in the samples after annealing process. CuSi alloys were mainly obtained for 25:75 at.% samples, meanwhile the AuCuII phase dominates for samples prepared with 50:50 at.%. Additionally, the Au:Cu alloys with 75:25 at.%, produce Au{sub 2}Cu{sub 3} and Au{sub 3}Cu phases. The formed alloys were characterized by scanning electron microscopy (SEM), atomic force microscopy (AFM), transmission electron microscopy (TEM) and energy dispersive spectroscopy (EDS) to study the morphology and the elemental concentration of the formed alloys. - Highlights: • AuCu/Si alloy thin films were prepared by thermal diffusion. • Alloys prepared with 50 at.% of Au produce the AuCuII phase. • Alloys prepared with 75 at.% of Au produce Au{sub 3}Cu and Au{sub 2}Cu{sub 3} phases. • All alloys present diffusion of Si and Cu through the CuSi alloy formation.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

Preparation and characterization of magnetic CsH{sub 2}PW{sub 12}O{sub 40}/Fe–SiO{sub 2} nanocatalysts for biodiesel production

Graphical abstract: In this study, a series of magnetic CsH{sub 2}PW{sub 12}O{sub 40}/Fe–SiO{sub 2} nanocatalysts were prepared and tested for biodiesel production. The best operational conditions were CH3OH/oil = 12/1 at 60 °C with mechanical stirring, the biodiesel yield reaches to 81% in 4 h. Also notably, recovery of the catalyst can be achieved easily with the help of an external magnet with no need for expensive ultracentrifugation. - Highlights: • Effects of preparation conditions for biodiesel production were studied. • The CsH{sub 2}PW{sub 12}O{sub 40}/Fe–SiO{sub 2} catalyst is efficient catalyst for biodiesel production. • The reaction conditions were found methanol/oil = 12/1, T = 60 °C. - Abstract: The magnetic CsH{sub 2}PW{sub 12}O{sub 40}/Fe–SiO{sub 2} nanocatalysts were prepared via combination of sol–gel and impregnation methods. The effects of different H{sub 3}PW{sub 12}O{sub 40}/(Fe–SiO{sub 2}) weight percentage, loading of Cs as a promotor and calcination conditions on the catalytic performance has been studied. It was found that the catalyst with H{sub 3}PW{sub 12}O{sub 40}/Fe–SiO{sub 2} = 4 wt.% and Cs = 2 wt.% is an optimal catalyst for biodiesel production. The activity of optimal catalyst was studied in different operational conditions. The best operational conditions were CH{sub 3}OH/oil = 12/1 at 60 °C with mechanical stirring rate of 500 rpm and the biodiesel yield reaches to 81% in 4 h. Characterization of catalysts was carried out by using scanning electron microscopy (SEM), X-ray diffraction (XRD), Fourier transform-infrared spectroscopy (FT-IR), vibrating sample magnetometry (VSM), N{sub 2} adsorption–desorption measurements methods, Thermal gravimetric analysis (TGA) and differential scanning calorimetry (DSC)

36 MATERIALS SCIENCE↗

Influences of defects evolvement on the properties of sputtering deposited ZnO:Al films upon hydrogen annealing

Understanding how the defects interact with each other and affect the properties of ZnO:Al films is very important for improving their performance as a transparent conductive oxide (TCO). In the present work, we studied the effects of hydrogen annealing on the structural, optical and electrical properties of ZnO:Al films prepared by magnetron sputtering. High resolution transmission electron microscopy observations reveal that annealing at ∼300 {sup o}C induces the formation of partial dislocations (PD) and stacking faults (SF), which disrupt the lattice periodicity leading to decreased grain size. Annealing at temperatures above ∼500 {sup o}C can remove the PD and SF, but large number of zinc vacancies will be generated. Our results show that when films are annealed at ∼500 {sup o}C, the oxygen-related defects (interstitials O{sub i}, etc.) in the as-grown films can be remarkably removed or converted, which lead to increments in the carrier concentration, mobility, and the transmittance in the visible range. At annealing temperatures above 550 {sup o}C, the hydrogen etching effect becomes predominant, and Al donors are deactivated by zinc vacancies. We also find an abnormal endothermic process by thermal analysis and an abnormal increase in the resistivity during heating the sample under hydrogen atmosphere, based on which the interaction of O{sub i} with the defects (mainly Al donors and PD) is discussed. It is also demonstrated that by annealing the as-grown AZO films at ∼500 {sup o}C under hydrogen atmosphere, high performance TCO films with a low resistivity of 4.48 × 10{sup −4} Ωcm and high transmittance of above 90% in the visible light are obtained.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Alpha Air Sample Counting Efficiency Versus Dust Loading: Evaluation of a Large Data Set

Dust loading on air sample filters is known to cause a loss of efficiency for direct counting of alpha activity on the filters, but the amount of dust loading and the correction factor needed to account for attenuated alpha particles is difficult to assess. In this paper, correction factors are developed by statistical analysis of a large database of air sample results for a uranium and plutonium processing facility at the Savannah River Site. As is typically the case, dust-loading data is not directly available, but sample volume is found to be a reasonable proxy measure; the amount of dust loading is inferred by a combination of the derived correction factors and a Monte Carlo model. The technique compares the distribution of activity ratios [beta/(beta + alpha)] by volume and applies a range of correction factors on the raw alpha count rate. The best-fit results with this method are compared with MCNP modeling of activity uniformly deposited in the dust and analytical laboratory results of digested filters. Finally, a linear fit is proposed to evenly-deposited alpha activity collected on filters with dust loading over a range of about 2 mg cm -2 to 1,000 mg cm -2 .

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Accelerating the identification of novel secondary metabolites in bioenergy plant root exudates using MicroED

Small molecule metabolites drive inter- and intraspecies communication and dependencies in diverse biological systems, yet a large proportion of these important chemical compounds remain uncharacterized in plants and microbes. Approximately 90% of the metabolites in root exudate profiles are unknown compounds, despite the importance of root exudate composition in plant-microbe interactions. We need advanced analytical capabilities that will support rapid discovery and structural elucidation of metabolites from biological samples that may be limited in quantity and high in complexity. To fill this gap, this project aimed to develop an integrated workflow involving metabolite extraction, separation, and crystallization from plant root exudates followed by characterization using nuclear magnetic resonance (NMR) spectroscopy, mass spectrometry, and microcrystal electron diffraction (MicroED). Using crude root exudates from sorghum, this project successfully developed higher throughput exudate fractionation strategies to obtain pure compounds for crystallization and identified crystals in multiple fractions that diffracted. Additional efforts to increase the throughput of high-quality crystal generation for MicroED, such as crystallization screening and crystallization chaperone exploration, will be needed to further advance root exudate metabolite identification. The overall optimized sample preparation process can then be integrated with the existing data collection and data analysis pipelines for MicroED at PNNL to facilitate more rapid natural product discovery.

59 BASIC BIOLOGICAL SCIENCES↗

Invertible Temper Modeling using Normalizing Flows and the Effects of Structure Preserving Loss

Advanced manufacturing research and development is typically small-scale, owing to costly experiments associated with these novel processes. Deep learning techniques could help accelerate this development cycle but frequently struggle in small-data regimes like the advanced manufacturing space. While prior work has applied deep learning to modeling visually plausible advanced manufacturing microstructures, little work has been done on data-driven modeling of how microstructures are affected by heat treatment, or assessing the degree to which synthetic microstructures are able to support existing workflows. We propose to address this gap by using invertible neural networks (normalizing flows) to model the effects of heat treatment, e.g., tempering. The model is developed using scanning electron microscope imagery from samples produced using shear-assisted processing and extrusion (ShAPE) manufacturing. This approach not only produces visually and topologically plausible samples, but also captures information related to a sample’s material properties or experimental process parameters. We also demonstrate that topological data analysis, used in prior work to characterize microstructures, can also be used to stabilize model training, preserve structure, and improve downstream results. We assess directions for future work and identify our approach as an important step towards end-to-end deep learning system for accelerating advanced manufacturing research and development.

Howland, Sylvia↗

Round Robin Analysis of Uranium Isotopics on Cotton Swipes Measured Using Microextraction-Based Sampling Versus Conventional Bulk Analysis

A comparison of microextraction sampling methods to directly analyze uranium isotopics on cotton swipes was performed concurrently with traditional bulk-processing methods. For the microextraction sampling approach, two different detection platforms were evaluated, a quadrupole-based inductively coupled plasma mass spectrometer (ICP-MS) and the liquid sampling-atmospheric pressure glow discharge (LS-APGD) coupled to an Orbitrap mass spectrometer. Results presented from this innovative sampling approach (i.e., microextraction) are compared with a more traditional approach employed for analysis of cotton-based environmental swipes, namely bulk ashing/digestion, separation, and subsequent analysis by high-precision multi-collector ICP-MS. Overall, the microextraction approach proved to be a reliable and accurate means to determine isotopic ratios of uranium collected on cotton swipes. The ICP-MS-based detection had relative standard deviations of <0.65% for the major isotopic determinations, whereas the LS-APGD-Orbitrap method had relative standard deviations of <3%. The percent relative difference for the 235 U/ 238 U ratios, in comparison to the expected values, was <1% for ICP-MS and <4% for the microplasma-Orbitrap method. Additionally, the microextraction ICP-MS accurately (<2%) and precisely (<5%) determined the minor isotopic compositions (i.e., 234 U/ 238 U and 236 U/ 238 U).

ICP-MS↗

A mobile system for a comprehensive online-characterization of nanoparticle aggregates based on wide-angle light scattering and laser-induced incandescence

A mobile demonstrator for the comprehensive online-characterization of gas-borne nanoparticle aggregates is presented. Two optical measurement techniques are combined, both utilizing a pulsed Nd:YAG laser as light source. Aggregate size and fractal dimension are measured by Wide-Angle Light Scattering (WALS). An ellipsoidal mirror images elastically scattered light from scattering angles between 10° and 165° onto a CCD-camera chip resulting in an almost complete scattering diagram with high angular resolution. Primary particle size and volume fraction are measured by time-resolved Laser-Induced Incandescence (TiRe-LII). Here, particles are heated up to about 3000 K by the short laser pulse, the enhanced thermal radiation signal is detected with gated photomultiplier tubes. Analysis of the signal decay time and maximum LII-signal allows for the determination of primary particle diameter and volume fraction. The performance of the system is demonstrated by combined measurements on soot nanoparticle aggregates from a soot aerosol generator. Particle and aggregate sizes are varied by using different equivalence ratios of the combustion in the generator. Soot volume fraction can be adjusted by different levels of dilution with air. Online-measurements were carried out demonstrating the favorable performance of the system and the potential for industrial applications such as process control and product development. The particle properties obtained are confirmed through transmission electron microscopy analysis on representative samples.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

In Situ Catalytic Fast Pyrolysis using Red Mud Catalyst: Impact of catalytic fast pyrolysis temperature and biomass feedstocks

Catalytic fast pyrolysis (CFP) has been considered as a very promising approach for converting lignocellulosic biomass into higher-quality bio-oils followed by hydrotreating to produce fuelrange products. A reactive, robust, and low-cost catalyst is required to drive the CFP process. Red mud, a side-product produced during the refining of bauxite to alumina, appears to be an effective catalyst for in situ CFP of biomass. In this paper, we report the impact of CFP reaction temperature on the conversion of a pinyon juniper feedstock to bio-oils using red mud as the catalyst and then to fuel-range hydrocarbons by hydrotreating of the produced bio-oil. The yield and quality of the CFP bio-oil produced and the yield and quality of hydrotreated final products were determined. When the CFP process temperature was lowered from 450 to 400ºC, the bio-oil yield increased with minimal differences in the oxygen content, hydrogen-to-carbon ratio, water content, etc. In addition, CFP bio-oils at both temperatures were processed in a single-stage continuous hydrotreater without reactor plugging during the testing period (i.e., ~100 hours on stream). The yield of CFP bio-oil produced at 400ºC was lower than the yield at 450ºC. However, the overall yield, from biomass to hydrocarbon fuel, was still higher for CFP processing at 400ºC than for processing at 450ºC. This indicates the potential for enhancing overall carbon efficiency, including CFP processing and hydrotreating, by employing red mud catalysts for biomass pyrolysis and tuning the CFP parameters. Detailed analysis of bio-oil and hydrotreated products showed a lower content of lignin-derived species in both samples. Furthermore, CFP processing of three different biomass feedstocks corroborated red mud catalyst development for producing improved quality bio-oil and, when combined with hydrotreating, for the production of fuel range hydrocarbons.

Santosa, Daniel M.↗

Sampling and Analysis Plan for LSL2 Underground Storage Tank Evaluation of PFAS in Soil: Protection of Groundwater

This SAP gathers all pertinent information relevant to the sampling and analysis of soil at the removal site for a former 10,000-gallon UST and reference sites in the vicinity of the excavation site. Data Quality Objectives establishes the process and steps for the acquisition of data. Data Flow Diagram establishes the decisions and next steps. Quality Assurance Project Plan establishes the quality requirements for data collection, including planning, implementation, and assessment of sampling, field measurements, and laboratory analysis. The work is being completed for DOE-SC Pacific Northwest Site Office.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Effect of Nd Substitution on Properties of Multiferroic Bismuth Ferrite Synthesized by Sol-Gel Auto-combustion Method

In this work, pure and Nd-doped bismuth ferrite nanocrystals with the general formula of Bi{sub 1−x}Nd{sub x}FeO{sub 3} (x = 0, 0.05, 0.1, 0.15, 0.2) were synthesized via the sol-gel auto-combustion method at two different calcination temperatures (550 and 650{sup ∘}C). Phase analysis and investigating structural, thermal, and magnetic properties and measuring the size of nanoparticles have been done by using X-ray diffraction (XRD), transmission electron microscopy (TEM), thermogravimetric and differential thermal analysis (TG/DTA), and vibrating sample magnetometry (VSM). For undoped BiFeO{sub 3} (BFO), increasing calcination temperature will increase the average size of nanocrystals. On the other hand, the average size of nanoparticles is decreased by increasing the concentration of neodymium in the structure of BFO. By entering neodymium to the structure of bismuth ferrite at the calcination temperature of 550{sup ∘}C, the ferromagnetic properties decline. However, at 650{sup ∘}C, ferromagnetic properties are improved which is due to a fall in the number of Fe{sup 2+} ions. In this case, by decreasing the Fe{sup 2+} ions, remanent and saturation magnetization increase.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

High Resolution Neutron Radiography and Tomography of Hydrided Zircaloy-4 Cladding Materials

Neutron radiography for hydrogen analysis was performed with several Zircaloy-4 cladding samples with controlled hydrogen concentrations up to 1100 ppm. Hydrogen charging was performed in a process tube that was heated to facilitate hydrogen absorption by the metal. A correlation between the hydrogen concentration in the hydrided tubes and the neutron intensity was established, by which hydrogen content can be determined precisely in a small area (55 m x 55 m). Radiography analysis was also performed to evaluate the heating rate and its correlation with the hydrogen distribution through hydrided materials. In addition to radiography analysis, tomography experiments were performed on Zircaloy-4 tube samples to study the local hydrogen distribution. Through tomography analysis a 3D reconstruction of the tube was evaluated in which an uneven hydrogen distribution in the circumferential direction can be observed.

hydride↗

pnnl/memgaze

MemGaze is a memory analysis toolset that combines high-resolution trace analysis and low overhead measurement, both with respect to time and space. It provides high-resolution by collecting world-level memory access traces, where the highest resolution supported is back-to-back sequences. It achieves low-overhead in space and time by leveraging sampling and various methods of hardware support for collecting traces. Its post-mortem trace processing provides multiresolution analysis for locations vs. operations; accesses vs. spatio-temporal reuse, and reuse (distance, rate, volume) vs. access patterns.

Central, PNNL Developer↗