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At least 37 records · Page 2

VirION2: a short- and long-read sequencing and informatics workflow to study the genomic diversity of viruses in nature

Microbes play fundamental roles in shaping natural ecosystem properties and functions, but do so under constraints imposed by their viral predators. However, studying viruses in nature can be challenging due to low biomass and the lack of universal gene markers. Though metagenomic short-read sequencing has greatly improved our virus ecology toolkit—and revealed many critical ecosystem roles for viruses—microdiverse populations and fine-scale genomic traits are missed. Some of these microdiverse populations are abundant and the missed regions may be of interest for identifying selection pressures that underpin evolutionary constraints associated with hosts and environments. Though long-read sequencing promises complete virus genomes on single reads, it currently suffers from high DNA requirements and sequencing errors that limit accurate gene prediction. Here we introduce VirION2, an integrated short- and long-read metagenomic wet-lab and informatics pipeline that updates our previous method (VirION) to further enhance the utility of long-read viral metagenomics. Using a viral mock community, we first optimized laboratory protocols (polymerase choice, DNA shearing size, PCR cycling) to enable 76% longer reads (now median length of 6,965 bp) from 100-fold less input DNA (now 1 nanogram). Using a virome from a natural seawater sample, we compared viromes generated with VirION2 against other library preparation options (unamplified, original VirION, and short-read), and optimized downstream informatics for improved long-read error correction and assembly. VirION2 assemblies combined with short-read based data (‘enhanced’ viromes), provided significant improvements over VirION libraries in the recovery of longer and more complete viral genomes, and our optimized error-correction strategy using long- and short-read data achieved 99.97% accuracy. In the seawater virome, VirION2 assemblies captured 5,161 viral populations (including all of the virus populations observed in the other assemblies), 30% of which were uniquely assembled through inclusion of long-reads, and 22% of the top 10% most abundant virus populations derived from assembly of long-reads. Viral populations unique to VirION2 assemblies had significantly higher microdiversity means, which may explain why short-read virome approaches failed to capture them. These findings suggest the VirION2 sample prep and workflow can help researchers better investigate the virosphere, even from challenging low-biomass samples. Our new protocols are available to the research community on protocols.io as a ‘living document’ to facilitate dissemination of updates to keep pace with the rapid evolution of long-read sequencing technology.

Long-reads↗

Bending and shear improvements in 3D-printed core sandwich composites through modification of resin uptake in the skin/core interphase region

Fused deposition modeling (FDM) printed polymers are rarely used as a structural material due to anisotropic and low mechanical properties compared with conventional composites. In recent years, greater need has been expressed for recycling of materials, such as recyclable FDM, at the end of service life to reduce environmental pollution and manufacture cost. However, how the amount of resin uptake in the skin and skin/core interphase affects the bending and shear performance of the sandwich composites when replacing the low strength and ductile core (conventional core) with a high strength and brittle core (FDM printed PLA (polylactic acid) core) still remains unclear. A new manufacturing routine is needed to improve the incorporation of FDM printed polymers in composite structures. In this work, FDM printed PLA was used as core material and sandwiched between two unidirectional glass fiber reinforced polymer (GFRP) skins to form a sandwich composite by compression-molding (CM) process, which provides a good manufacturing strategy for skin/core interphase modification. The significance of the CM process is proved by investigating the effect of resin uptake on bending and in-plane/out-of-plane shear performances. Current first order shear deformation (FSDT) theory lacks a direct connection between the in-plane shear stress and out-of-shear stress in the core region of sandwich composites. With the help of DIC, a connection between the in-plane shear and the out-of-plane shear strain was built and in-plane shear properties can acquire through out-of-plane shear properties, hence reducing the redundancy of sample preparation or the need for simulation. A significant improvement was found compared with the optimized resin uptake (Optimized resin uptake range: 20.43%–22.86 wt%) 3D-printed PLA core sandwich composite and lowest performance sandwich composite (Improvement: in-plane shear strength (~34%)/modulus (~29%), out-of-plane shear strength (~25%)/modulus (~31%), specific peak bending load (~19%)). Finally, compared with balsa core sandwich composites, the 3D-printed cores are suitable for use in composite sandwich structures in many applications with a satisfactory strength-to-weight ratio.

3D-printed core sandwich composite↗

Modular automated bottom-up proteomic sample preparation for high-throughput applications

Manual proteomic sample preparation methods limit sample throughput and often lead to poor data quality when thousands of samples must be analyzed. Automated liquid handler systems are increasingly used to overcome these issues for many of the sample preparation steps. Here, we detail a step-by-step protocol to prepare samples for bottom-up proteomic analysis for Gram-negative bacterial and fungal cells. The full modular protocol consists of three optimized protocols to: (A) lyse Gram-negative bacteria and fungal cells; (B) quantify the amount of protein extracted; and (C) normalize the amount of protein and set up tryptic digestion. These protocols have been developed to facilitate rapid, low variance sample preparation of hundreds of samples, be easily implemented on widely-available Beckman-Coulter Biomek automated liquid handlers, and allow flexibility for future protocol development. By using this workflow 50 micrograms of protein from 96 samples can be prepared for tryptic digestion in under an hour. We validate these protocols by analyzing 47 Pseudomonas putida and Rhodosporidium toruloides samples and show that this modular workflow provides robust, reproducible proteomic samples for high-throughput applications. The expected results from these protocols are 94 peptide samples from Gram-negative bacterial and fungal cells prepared for bottom-up quantitative proteomic analysis without the need for desalting column cleanup and with protein relative quantity variance (CV%) below 15%.

59 BASIC BIOLOGICAL SCIENCES↗

Benchmarking Optimizers for Qumode State Preparation with Variational Quantum Algorithms

Quantum state preparation involves preparing a target state from an initial system, a process integral to applications such as quantum machine learning and solving systems of linear equations. Recently, there has been a growing interest in qumodes due to advancements in the field and their potential applications. However there is a notable gap in the literature specifically addressing this area. This paper aims to bridge this gap by providing performance benchmarks of various optimizers used in state preparation with Variational Quantum Algorithms. We conducted extensive testing across multiple scenarios, including different target states, both ideal and sampling simulations, and varying numbers of basis gate layers. Our evaluations offer insights into the complexity of learning each type of target state and demonstrate that some optimizers perform better than others in this context. Notably, the Powell optimizer was found to be exceptionally robust against sampling errors, making it a preferred choice in scenarios prone to such inaccuracies. Additionally, the Simultaneous Perturbation Stochastic Approximation optimizer was distinguished for its efficiency and ability to handle increased parameter dimensionality effectively.

Kan, Shuwen [Fordham University]↗

One-Pot Synthesis of Melamine Formaldehyde Resin-Derived N-Doped Porous Carbon for CO 2 Capture Application

The design and synthesis of porous carbons for CO 2 adsorption have attracted tremendous interest owing to the ever-soaring concerns regarding climate change and global warming. Herein, for the first time, nitrogen-rich porous carbon was prepared with chemical activation (KOH) of commercial melamine formaldehyde resin (MF) in a single step. It has been shown that the porosity parameters of the as-prepared carbons were successfully tuned by controlling the activating temperature and adjusting the amount of KOH. Thus, as-prepared N-rich porous carbon shows a large surface area of 1658 m 2 /g and a high N content of 16.07 wt%. Benefiting from the unique physical and textural features, the optimal sample depicted a CO 2 uptake of up to 4.95 and 3.30 mmol/g at 0 and 25 °C under 1 bar of pressure. More importantly, as-prepared adsorbents show great CO 2 selectivity over N 2 and outstanding recyclability, which was prominently important for CO 2 capture from the flue gases in practical application. An in-depth analysis illustrated that the synergetic effect of textural properties and surface nitrogen decoration mainly determined the CO 2 capture performance. However, the textural properties of carbons play a more important role than surface functionalities in deciding CO 2 uptake. In view of cost-effective synthesis, outstanding textural activity, and the high adsorption capacity together with good selectivity, this advanced approach becomes valid and convenient in fabricating a unique highly efficient N-rich carbon adsorbent for CO 2 uptake and separation from flue gases.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Destructive Analysis of TRISO Particles: Crush/Burn/Leach Followed by Davies-Gray Titration and IDMS

The accurate accounting of nuclear materials is a cornerstone of international nuclear safeguards. One emerging challenge in this domain is the fabrication of TRIstructural ISOtropic (TRISO) particle fuels. Although these innovative fuel forms are critical for advanced reactor applications, their robust refractory ceramics and coating compositions present significant obstacles to destructive analysis (DA) methods. Ensuring full and quantitative recovery from these particles is essential for accurate mass accountancy. The current study was initiated to address these challenges, first by validating a previously established destructive method developed by Oak Ridge National Laboratory (ORNL) for the quantitative recovery of uranium from TRISO particles and then following that process with uranium content determination through isotope dilution mass spectrometry (IDMS) and Davies-Gray titration. This study expands on the scope of a digestive method that was developed under the Advanced Gas Reactor Fuel Development and Qualification program and is currently implemented in both the Coated Particle Fuel Development Laboratory and Irradiated Fuels Examination Laboratory at ORNL. The success of the previous Advanced Gas Reactor work relied on developing a DA method to evaluate the fabrication process and reactor experiments. The methodology described in this report was designed to rigorously investigate the efficacy of the crush/burn/leach sample preparation of TRISO particles; it aims to quantify uranium recovery while also assessing the effects of TRISO constituents (e.g., silicon and zirconium) on analytical precision and accuracy. By comparing the results from the titration method and IDMS, we sought to determine whether existing analytical procedures accepted by the International Atomic Energy Agency (IAEA) could be effectively translated to TRISO fuel forms. The team employed an approach that involved processing replicate TRISO samples, optimizing the milling (i.e., crushing) step and performing serial leaches. The elemental composition of the analytical samples was examined to prepare for interference studies in the second year of this project. The integration of gamma spectrometry to verify residual uranium activity further strengthened the validation. Statistical methods were applied to the collected data to evaluate the uncertainties arising from sampling, sample preparation and uranium quantification. These uncertainties were then compared to the IAEA’s international target values (ITVs). Additional data collected in upcoming project work will strengthen the uncertainty estimates. Ultimately, it is hoped that this project will contribute materially to the body of work related to characterization of TRISO based fuels for the purpose of material accountancy and its applications to international safeguards.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Preparing for successful protein crystallization experiments

Crystal-based structural methods, including X-ray crystallography, are frequently utilized for the determination of high-resolution structures of biomolecules. All crystal-based diffraction methods first require the preparation of biomolecular crystals, and careful sample preparation for crystallization experiments can increase the frequency of success. In this article, strategies to optimize factors that can impact crystallization are presented, from which buffers and reducing agents are most favorable to which crystallization techniques could be used.

36 MATERIALS SCIENCE↗

Improvements in iridium target chemistry

Abstract We developed and optimized the dissolution and separation chemistry of iridium (Ir) from irradiated Ir pellets and prepared Ir counting samples for analysis by a silicon drift detector. Previous Ir chemistry techniques used on the irradiated Ir pellets are tedious, lengthy, and require extra safety precautions and planning due to the use of perchloric acid in the dissolution step. The dissolution and separations method described in this paper are safer, eliminating the use of perchloric acid, more efficient, and can successfully replace the previous procedure.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗

An optimized approach and inflation media for obtaining complimentary mass spectrometry-based omics data from human lung tissue

Human disease states are biomolecularly multifaceted and can span across phenotypic states, therefore it is important to understand diseases on all levels, across cell types, and within and across microanatomical tissue compartments. To obtain an accurate and representative view of the molecular landscape within human lungs, this fragile tissue must be inflated and embedded to maintain spatial fidelity of the location of molecules and minimize molecular degradation for molecular imaging experiments. Here, we evaluated agarose inflation and carboxymethyl cellulose embedding media and determined effective tissue preparation protocols for performing bulk and spatial mass spectrometry-based omics measurements. Mass spectrometry imaging methods were optimized to boost the number of annotatable molecules in agarose inflated lung samples. This optimized protocol permitted the observation of unique lipid distributions within several airway regions in the lung tissue block. Laser capture microdissection of these airway regions followed by high-resolution proteomic analysis allowed us to begin linking the lipidome with the proteome in a spatially resolved manner, where we observed proteins with high abundance specifically localized to the airway regions. We also compared our mass spectrometry results to lung tissue samples preserved using two other inflation/embedding media, but we identified several pitfalls with the sample preparation steps using this preservation method. Overall, we demonstrated the versatility of the inflation method, and we can start to reveal how the metabolome, lipidome, and proteome are connected spatially in human lungs and across disease states through a variety of different experiments.

59 BASIC BIOLOGICAL SCIENCES↗

High-Throughput Characterization and Optimization of Polyamide Hydrolase Activity Using Open Port Sampling Interface Mass Spectrometry

Enzymatic biodegradation of polymers, such as polyamides (PA), has the potential to cost-effectively reduce plastic waste, but enhancements in degradation efficiency are needed. Engineering enzymes through directed evolution is one pathway toward identification of critical domains needed for improving activity. However, screening such enzymatic libraries (100s-to-1000s of samples) is time-consuming. Here we demonstrate the use of robotic autosampler (PAL) and immediate drop on demand technology (I.DOT) liquid handling systems coupled with open-port sampling interface-mass spectrometry (OPSI-MS) to screen for PA6 and PA66 hydrolysis by 6-aminohexanoate-oligomer endo-hydrolase (nylon hydrolase, NylC) in a high-throughput (8–20 s/sample) manner. The OPSI-MS technique required minimal sample preparation and was amenable to 96-well plate formats for automated processing. Enzymatic hydrolysis of PA characteristically produced soluble linear oligomer products that could be identified by OPSI-MS. Incubation temperatures and times were optimized for PA6 (65 °C, 24 h) and PA66 (75 °C, 24 h) over 108 experiments. In addition, the I.DOT/OPSI-MS quantified production of PA6 linear dimer (8.3 ± 1.6 μg/mL) and PA66 linear monomer (13.5 ± 1.5 μg/mL) by NylC with a lower limit of detection of 0.029 and 0.032 μg/mL, respectively. For PA6 and PA66, linear oligomer production corresponded to 0.096 ± 0.018% and 0.204 ± 0.028% conversion of dry pellet mass, respectively. The developed methodology is expected to be utilized to assess enzymatic hydrolysis of engineered enzyme libraries, comprising hundreds to thousands of individual samples.

47 OTHER INSTRUMENTATION↗

Real-Time Screening for Uranium Enrichment by Paper Spray Ionization Mass Spectrometry for Field Applications

A rapid isotope ratio screening technique for uranium enrichment is demonstrated by utilizing paper spray ionization (PSI) high-resolution mass spectrometry (HRMS). Measurements were conducted using an ambient ionization mass spectrometer coupled to a custom-made JEOL PSI attachment apparatus, with de minimus sample preparation requirements. The current method detection limit for individual isotopes (e.g., 235 U and 238 U) is approximately 50 pg, with subsequent optimization expected to further improve U isotopic sensitivity. The PSI analytical method described herein can support rapid analysis (both in-field and in-lab screening) of isotopes-of-interest, as demonstrated by empirical differentiation of depleted uranium (DU) and low enriched uranium (LEU) analytical aliquots. Furthermore, this analytical workflow holds promise for applications in nuclear forensics, international nuclear safeguards, and nonproliferation missions.

Anions↗

Site-specific plan-view (S)TEM sample preparation from thin films using a dual-beam FIB-SEM

To fully evaluate the atomic structure, and associated properties of materials using transmission electron microscopy, examination of samples from three non-collinear orientations is needed. This is particularly challenging for thin films and nanoscale devices built on substrates due to limitations with plan-view sample preparation. In this work, a new method for preparation of high-quality, site-specific, plan-view TEM samples from thin-films grown on substrates, is presented and discussed. Here, it is based on using a dual-beam focused ion beam scanning electron microscope (FIB-SEM) system. To demonstrate the method, the samples were prepared from thin films of perovskite oxide BaSnO 3 grown on a SrTiO 3 substrate and metal oxide IrO 2 on a TiO 2 substrate, ranging from 20–80 nm in thicknesses using molecular beam epitaxy. While the method is optimized for the thin films, it can be extended to other site-specific plan-view samples and devices build on wafers. Aberration-corrected STEM was used to evaluate the quality of the samples and their applicability for atomic-resolution imaging and analysis.

BaSnO3↗

In Situ XAFS, XRD, and DFT Characterization of the Sulfur Adsorption Sites on Cu and Ce Exchanged Y Zeolites

Adsorptive desulfurization with Cu and Ce ion-exchanged Y zeolite (CuCeY) has proven to be an effective method for the removal of sulfur compounds from hydrocarbon fuels. In this study, Cu and Ce exchanged Y materials including CuY, CeY, and CuCeY were prepared and examined to investigate the mechanism behind the superior sulfur adsorption and selectivity of CuCeY. In situ conditions were used to study the materials as prepared for optimal desulfurization. X-ray diffraction (XRD) confirmed the absence of large well-ordered crystalline phases from metallic or oxide Cu and Ce after the reduction of the samples. The oxidation states and local environments of Cu and Ce were determined using X-ray adsorption fine structure (XAFS) analysis and correlated to theoretical findings obtained from density functional theory (DFT) calculations. XAFS data indicate the successful reduction of Cu species to Cu + and Cu o , and Ce to Ce 3+ . Analysis of XAFS spectra located Cu and Ce within the Y zeolite framework with Cu cations in the six-member ring sites and as small metallic Cu clusters. Ce cations were found to occupy both six-member ring and hexagonal prism sites. Furthermore, these results reveal the structure of CuCeY as prepared for desulfurization and provide insight into its superior sulfur adsorption performance.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Optimization performance, fidelity, and cost: SIAM VQE

This dataset contains files storing results from classically-simulated quantum subroutines within a dynamical mean-field theory workflow, and jupyter notebooks processing the data in these files to generate plots. The files store: (1) Results from variational quantum eigensolver (VQE) simulations searching for optimal parameters allowing parametrized quantum circuits to prepare approximations to ground states of different Anderson impurity models (AIMs) (2) Results from simulations of a quantum Lanczos algorithm (QLA) estimating the Lanczos coefficients defining the continued-fraction representation of an (AIM) Green’s function Description: Any file named vqe_gs_results* stores approximations to the ground state and energy of a given AIM estimated using three different methods: (1) Numerical diagonalization (2) Ideal VQE simulation (3) VQE simulation with sampling noise For each VQE simulations metadata about the optimization (optimization results plus number of quantum circuits that would have been executed on real hardware) is also stored. Any file named qla_dos_results* estimations for the Lanczos coefficients defining the Green’s function of an AIM. The stored estimations are achieved using different methods: (1) Numerical Lanczos algorithm from initial states obtained from numerical diagonalization (2) Simulated quantum Lanczos algorithm from initial states prepared from parametrized quantum circuits yielded by corresponding ideal and noisy VQE subroutines. The dataset is used and described in M. Karabin et al., "Quantum solver for single-impurity Anderson models with particle-hole symmetry", Phys. Rev. Research 8, 033066 (2026). DOI: https://doi.org/10.1103/7ys3-tl4l

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Sample Preparation Method for Low-Level Total 129 I Measurements by ICP-MS

Trace-level measurements of iodine’s isotopic ( 129 I and 127 I) and chemical species distributions are needed for an accurate understanding of radioiodine migration in the Hanford subsurface. Pacific Northwest National Laboratory (PNNL) previously developed a novel analytical method for iodine characterization that uses ion chromatography (IC) coupled to inductively coupled mass spectrometry (ICP-MS). While the method can measure speciated forms of 129 I at levels below the drinking water standard, an interference from molybdenum (Mo) prevents the assay from quantifying the $\underline{total}$ 129 I concentration in many Hanford sample matrices. In this work, solvent extraction was evaluated as a sample preparation method for eliminating the Mo interference. A series of 10 experiments was conducted in which solutions containing known amounts of iodate or iodide were treated by solvent extraction, and the extracted solutions were analyzed for total iodine concentrations by ICP MS. Several extraction parameters such as reagent concentrations and chemical reaction times were systematically adjusted in attempts to optimize the extraction process. While solvent extraction was shown to be effective at removing Mo, there was a consistent inability to recover more than approximately 75% of the total iodine in most experiments. This would reduce the ability to detect 129 I at levels near the drinking water standard. Additionally, the extraction efficiencies in several experiments were highly variable, suggesting that solvent extraction could add significant uncertainty to radioiodine measurements. We recommend evaluating ion exchange as an alternative sample preparation approach in fiscal year (FY) 2024.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Machine learning in nuclear materials research

Nuclear materials are often demanded to function for extended time in extreme environments, including high radiation fluxes with associated transmutations, high temperature and temperature gradients, mechanical stresses, and corrosive coolants. They also have a wide range of microstructural and chemical makeups, resulting in multifaceted and often out-of-equilibrium interactions. Machine learning (ML) is increasingly being used to tackle these complex time-dependent interactions and aid researchers in developing models and making predictions, sometimes with better accuracy than traditional modeling that focuses on one or two parameters at a time. Conventional practices of acquiring new experimental data in nuclear materials research are often slow and expensive, limiting the opportunity for data-centric ML, but new methods are changing that paradigm. Here we review high-throughput computational and experimental data approaches, especially robotic experimentation and active learning that is based on Gaussian process and Bayesian optimization. We show ML examples in structural materials (e.g., reactor pressure vessel (RPV) alloys and radiation detecting scintillating materials) and highlight new techniques of high-throughput sample preparation and characterizations, and automated radiation/environmental exposures and real-time online diagnostics. Herein, this review suggests that ML models of material constitutive relations in plasticity, damage, and even electronic and optical responses to radiation are likely to become powerful tools as they develop. Finally, we speculate on how the recent trends of using natural language processing (NLP) to aid the collection and analysis of literature data, interpretable artificial intelligence (AI), and the use of streamlined scripting, database, workflow management, and cloud computing platforms that will soon make the utilization of ML techniques as commonplace as the spreadsheet curve-fitting practices of today.

36 MATERIALS SCIENCE↗

The use of synchrotron X-ray fluorescent imaging to study distribution and content of elements in chemically fixed single cells: a case study using mouse pancreatic beta-cells

Synchrotron X-ray fluorescence microscopy (SXRF) presents a valuable opportunity to study the metallome of single cells because it simultaneously provides high-resolution subcellular distribution and quantitative cellular content of multiple elements. Different sample preparation techniques have been used to preserve cells for observations with SXRF, with a goal to maintain fidelity of the cellular metallome. In this case study, mouse pancreatic beta-cells have been preserved with optimized chemical fixation. We show that cell-to-cell variability is normal in the metallome of beta-cells due to heterogeneity and should be considered when interpreting SXRF data. Additionally, we determined the impact of several immunofluorescence (IF) protocols on metal distribution and quantification in chemically fixed beta-cells and found that the metallome of beta-cells was not well preserved for quantitative analysis. However, zinc and iron qualitative analysis could be performed after IF with certain limitations. To help minimize metal loss using samples that require IF, we describe a novel IF protocol that can be used with chemically fixed cells after the completion of SXRF.

59 BASIC BIOLOGICAL SCIENCES↗

Synthesis of NiRu-Layered Double Hydroxide for Enhanced Oxygen Evolution Reaction

Nickel−ruthenium layered double hydroxide (NiRu-LDH) was synthesized by coprecipitation using formamide as both solvent and intercalant. The synthesis was performed at various temperatures to study the impact of temperature on electrochemical performance. Temperature plays a vital role in optimizing LDH synthesis to enhance oxygen evolution reaction (OER) efficiency. The optimal temperature yielded a well-defined morphology with balanced crystallinity, leading to more active sites and improved charge transfer. Electrochemical tests indicated that the NiRu-LDH sample prepared at 50 °C (NiRu-LDH-50) required only 280 mV overpotential versus the reversible hydrogen electrode to achieve 10 mA/cm 2 and exhibited a low Tafel slope of 52 mV/dec, demonstrating excellent catalytic kinetics. This study presents the synthesis of NiRu-LDH via coprecipitation and emphasizes how reaction temperature influences LDH structural properties and OER performance.

Catalysts↗