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At least 109 records · Page 6

Fisher Forecasting for the DESC with $\texttt{Augur}$

The Vera C. Rubin Observatory Legacy Survey of Space and Time (LSST) has begun its ten-year survey of the entire visible southern hemisphere. To ensure robust cosmological measurements, computationally inexpensive investigations of modeling choices must be made to gauge the performance of proposed cosmological analyses. In this paper, we introduce the $\texttt{Augur}$ tool of the Dark Energy Science Collaboration (DESC), which provides Fisher forecasts for cosmological inference for the LSST using software frameworks designed for DESC science. We test the pipeline by comparing it to forecasts produced by external code and direct sampling of the posterior via nested sampling methods, finding good agreement between all methods. We additionally investigate a range of modeling and hyperparameter choices for a 3$\times$2pt investigation in harmonic space, providing users with diagnostics to obtain reliable forecasts. $\texttt{Augur}$ will be continually updated to be compatible with the other tools in the DESC software ecosystem as additional probes and functionality become available.

Rogozenski, Paul [Carnegie Mellon U.; Arizona U.] ↗

Integrative Multi-PTM Proteomics Reveals Dynamic Global, Redox, Phosphorylation, and Acetylation Regulation in Cytokine-treated Pancreatic Beta Cells

Studying regulation of protein function at a systems level necessitates an understanding of the interplay among diverse post-translational modifications (PTMs). A variety of proteomics sample processing workflows are currently used to study specific PTMs but rarely characterize multiple types of PTMs from the same sample inputs. Method incompatibilities and laborious sample preparation steps complicate large-scale physiological investigations and can lead to variations in results. The single-pot, solid-phase-enhanced sample preparation (SP3) method for sample cleanup is compatible with different lysis buffers and amenable to automation, making it attractive for high-throughput multi-PTM profiling. Herein, we describe an integrative SP3 workflow for multiplexed quantification of protein abundance, cysteine thiol oxidation, phosphorylation, and acetylation. The broad applicability of this approach is demonstrated using cell and tissue samples, and its utility for studying interacting regulatory networks is highlighted in a time-course experiment of cytokine-treated ß-cells. We observed a swift response in global regulation of protein abundances consistent with rapid activation of JAK-STAT and NF-?B signaling pathways. Regulators of these pathways as well as proteins involved in their target processes displayed multi-PTM dynamics indicative of a complex cellular response stages: acute, adaptation, and chronic (prolonged stress). PARP14, a negative regulator of JAK-STAT, had multiple co-localized PTMs that may be involved in intraprotein regulatory crosstalk. Our workflow provides a high-throughput platform that can profile multi-PTMomes from the same sample set, which is valuable in unraveling the functional roles of PTMs and their co-regulation.

proteomics, PTM, automation, SP3, cysteine thiol o↗

Advanced Method Optimization for Sampling and Analysis Instrumentation

This work presents a generalized approach for analytical method optimization that branches the gap between techniques historically employed and accurate modern optimization techniques suitable for various applications. The novelty of the described strategy is the utilization of multivariate, multiobjective optimization with Karush-Kuhn-Tucker conditions to bound the optimization space to solutions within the physical limitations of instrumentation. Briefly, the basic steps outlined in this paper are to (1) determine the objective(s) that should be maximized or minimized based on the goals of the analytical application, (2) conduct a screening experiment, (3) perform ANOVA to determine the parameters which have a statistically significant effect on the objective, (4) conduct an experiment (e.g., Box-Behnken design) to collect data for fitting the objective equation, and (5) determine the physical constraints of the parameters and solve the Lagrangian to determine the optimal method parameters. A broad approach to optimization target selection allows for robust method tuning to develop improved data sets amenable for chemometrics and machine learning algorithm development. Gas chromatography-mass spectrometry was selected as a use case due to its broad use across scientific fields and time-consuming method development involving numerous parameters. In conclusion, this strategy can reduce the cost of research, improve data quality, and enable the rapid development of new analytical technique.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

An Improved Sampling and Baiting Method for Phytophthora tropicalis and P. heveae Detection in Macadamia integrifolia

Macadamia nuts are, economically, the second most important crop in the state of Hawai’i. A recent decline in yield and acreage has been attributed to insect damage and diseases such as Macadamia Quick Decline (MQD) caused by Phytophthora tropicalis and P. heveae. To develop an improved methodology for the diagnosis and treatment of MQD, investigations were undertaken to better understand the pathosystem of the disease. These investigations included sampling from multiple locations from sectioned trees utilizing two methods of tissue collection and isolations using two baiting techniques. The collection of tissue from the cambium and phloem of trees after scraping away the bark and in locations of recent or current sap exudation using a narrow diameter steel awl proved to be an efficient means for the molecular detection of the MQD pathogens from infected trees exhibiting MQD symptoms. In addition, a more efficient and cost-effective baiting method using apple puree was developed.

Plant Sciences↗

Nonparametric Multiparticle Set Methods for Interpreting Environmental Samples

Collection and analysis of environmental samples is commonly used by a range of stakeholders in nuclear safeguards and security contexts. While the ubiquity of samples and their transport in the environment allow regular collection, developing and demonstrating methods for analyzing these samples is difficult. In this work, an environmental sample consists of a set of one or more individual particles. Recent advances in reactor simulation have allowed us to generate data that are more representative of real-world environmental samples, enabling statistically defensible method development and testing. The most notable of these advances is a drastic increase in the number of material depletion regions, which allows our simulations to capture the variation in isotopic composition seen at length scales consistent with environmental samples. Traditional approaches for handling multiparticle samples treat each particle in the sample individually, estimating the quantity of interest (e.g., core-average burnup) resulting from measurement and analysis of signatures (e.g., nuclide assays) from each individual particle. Individual estimates are then averaged to generate a single estimate of the quantity of interest over the entire sample. In this presentation, we introduce two novel approaches for interpreting environmental samples that comprise of multiple particles: (1) the Quantile-Quantile Comparator, which uses a multivariate generalization of quantile-quantile plots for comparing unknown statistical distributions, and (2) the Set Transformer, an attention-based neural network module designed to model interactions among elements (particles) in the input set (sample). Statistically representative sampling cannot be guaranteed as samples are passively collected and are beholden to what particles are available in the environment. These new analysis methods for set-input problems are expected to be more robust than traditional approaches to issues of sampling bias where particles are not uniformly distributed throughout regions of interest, as well as generally outperform traditional approaches by jointly considering all elements in the set. We will present results comparing the performance of traditional single particle approaches and the novel Quantile-Quantile Comparator and Set Transformer for interpretation of simulated environmental samples.

Phathanapirom, Birdy↗

Sampling Microbial Dynamics in the Salish Sea Estuary: Evaluating Methods to Capture Cyanobacteria and Cyanophage

Introduction: Picocyanobacteria from the genera Prochlorococcus and Synechococcus thrive across the globe in aquatic environments, have relatively small genomes, and have growth dynamics regulated by both viral interactions and abiotic conditions, making them excellent model organisms for exploring host-pathogencoevolution. Methods: We developed and refined methods to sample and sequence cyanobacteria, cyanophages, and measured features of their abiotic environment. Results: The protocol described herein can successfully discriminate large-cell eukaryotic organisms, but size fractionation of picocyanobacteria appears to be affected by the presence of free DNA, multicellular structures, and abundant tycheposons. Our preferred final protocol from this exploratory effort included a combination of in-line and single vacuum flask filtrations, which reduced filtration processing time by over threefold in some cases compared to other tested methods, such as a fully in-line sequence or in-site filtrations. We successfully extracted an average of approximately 400–1200 ng for all filter fractions, with some variations between kits. Discussion: The protocol described herein can successfully discriminate large-cell eukaryotic organisms, but size fractionation of picocyanobacteria appears to be affected by the presence of free DNA, multicellular structures, and abundant tycheposons.

Salish Sea↗

A Tip-based Workflow for Sensitive IMAC-based Low Nanogram Level Phosphoproteomics

Analyzing the phosphoproteome at nanoscale poses a significant challenge, mainly due to the substantial sample loss from non-specific surface adsorption during the enrichment of low stoichiometric phosphopeptides. Here, we describe a tandem tip-based phosphoproteomics sample preparation method capable of sequential sample cleanup and enrichment without the need for additional sample transfer, thereby minimizing sample loss. Integration of this method to our recently developed SOP (Surfactant-assisted One-Pot sample preparation) and iBASIL (improved Boosting to Amplify Signal with Isobaric Labeling) approaches creates a streamlined workflow, enabling sensitive, high-throughput nanoscale phosphoproteomics measurements.

Phosphoproteome, Immobilized metal ion affinity ch↗

CORRLA-RS

The CORRLA-RS package provides a suite of statistical methods for sampling multidimensional distributions and to conduct sensitivity and correlation analysis of large scale data in the Rust programming language. The software provides a unique solution to multidimensional constrained sampling problems utilizing a combination of parallelized Markov Chain Monte Carlo methods and traditional rejection sampling. The sensitivity and correlation analysis methods are backed by a high performance randomized singular value decomposition implementation which enables datasets larger than the random access memory (RAM) size to be analyzed. Additionally, CORRLA-RS implements the active subspace identification method using a KD-Tree and the randomized singular value decomposition acting in concert.

Gurecky, William [Oak Ridge National Laboratory (O↗

Towards utility-scale electronic structure with sample-based quantum bootstrap embedding

One of the main applications for which quantum computers are hoped to find utility is in simulating ground state energies and other observables of molecular chemical systems. The recently proposed sample-based diagonalization method is a readily implementable method for this task on current-day hardware using short circuit depths and has been demonstrated on as many as 85 qubits in recent studies. In this work, we combine the recently proposed quantum bootstrap embedding (QBE) method with sampled-based diagonalization (QBE-SQD) and present the first benchmarking study of the QBE method on real quantum hardware, ibm_pittsburgh, a Heron r3 processor with 156 qubits. Our test system is a hydrogen ring with 8 hydrogen atoms in the cc-pVDZ basis. We show that for this system, QBE-SQD using an active space of (8e, 19o) per fragment with a 43 qubit footprint produces a ground state energy accuracy which exceeds that of an SQD calculation with an (8e, 30o) active space with a 67 qubit footprint when using a comparable number of Slater determinants. This demonstrates that the use of quantum bootstrap embedding techniques is a promising path towards extending the capabilities of state-of-the-art quantum eigensolvers on near-term devices.

Bierman, Joel [North Carolina State University, Ra↗

MCCCS-MN

The MCCCS‒MN (Monte Carlo for Complex Chemical Systems‒Minnesota) software is developed by the Siepmann research group at the University of Minnesota. MCCCS‒MN allows for the simulation of multi-component molecular systems in the canonical, isobaric-isothermal (including constant stress for solids), grand-canonical, semi-grand, and Gibbs (NVT, NPT, and more than two simulation boxes) ensembles. It uses the configurational-bias Monte Carlo method to efficiently sample phase space for linear, branched and cyclic chain molecules, the adiabatic nuclear and electronic sampling Monte Carlo method to treat many-body polarization effects, and the aggregation-volume-bias Monte Carlo algorithm to efficiently sample the spatial distribution of associating molecules. MCCCS-MN employs a molecular representation of the system where force fields contain bonded and non-bonded terms. Funding for the development of MCCCS-MN through grants from the National Science Foundation (simulation of fluid phase equilibria and chromatography) and the Department of Energy (simulation of adsorption equilibria) is gratefully acknowledged.

Siepmann, J.Ilja [University of Minnesota - Twin C↗

Direct observation of twisted stacking domains in the van der Waals magnet CrI 3

Van der Waals (vdW) stacking is a powerful technique to achieve desired properties in condensed matter systems through layer-by-layer crystal engineering. A remarkable example is the control over the twist angle between artificially-stacked vdW crystals, enabling the realization of unconventional phenomena in moiré structures ranging from superconductivity to strongly correlated magnetism. Here, we report the appearance of unusual 120° twisted faults in vdW magnet CrI 3 crystals. In exfoliated samples, we observe vertical twisted domains with a thickness below 10 nm. The size and distribution of twisted domains strongly depend on the sample preparation methods, with as-synthesized unexfoliated samples showing tenfold thicker domains than exfoliated samples. Cooling induces changes in the relative populations among different twisting domains, rather than the previously assumed structural phase transition to the rhombohedral stacking. The stacking disorder induced by sample fabrication processes may explain the unresolved thickness-dependent magnetic coupling observed in CrI 3 .

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Sparge Sampling of Molten Salts for Online Monitoring via Laser-Induced Breakdown Spectroscopy

A method was developed to sample molten salts by sparging to generate and transport aerosols to an isolated instrument for compositional analysis by laser-induced breakdown spectroscopy (LIBS). Real-time monitoring of molten salt composition is critical to developing molten salt nuclear reactors, which offer enhanced safety and efficiency. In this article, the sparge sampling method is described and compared with sampling using a Collison nebulizer. The size distribution and transport of aerosols produced from molten eutectic NaNO 3 –KNO 3 salt were compared for multiple gas flow rates (75–1200 mL min –1 ) and transport distances (0.68–2.61 m). Both methods produced aerosols ranging from 0.5 to 5.0 μm determined using a cascade impactor. Aerosols were effectively transported without pre- or trace-heating of gas lines, but transport efficiency was reduced by the formation of agglomerates. Sparge sampling was found to use less sample and less gas than a Collison nebulizer while producing a more concentrated aerosol stream (up to 5 μg L –1 ). The effects of laser energy and delay time on the signal quality of LIBS measurements of these aerosols were also studied. High energy and short delay times were found to enhance signal and repeatability, whereas signal-to-background and signal-to-noise ratios were highest at low energy and longer delay times. The capabilities of this system for online monitoring of molten salts were demonstrated with calibrations for Sr and Li with relative standard deviations of 2.6% and 1.5% and limits of detection of 380 and 180 μg g –1 , respectively.

Aerosols↗

Selection of Sampling and Surrogate Modeling Methods for State-Point Evaluations of an AGN-201M Reactor

Nuclear reactor digital twins (DTs) have been proposed for use as a safeguards technology to efficiently monitor new and novel reactors as they come online. A safeguards DT needs to be capable of detecting misuse and diversion as they occur, requiring physics models to be accurate and efficient. Mathematical surrogate models are capable of achieving the necessary efficiency and can largely maintain the accuracy of higher-order models given a quality training sample. The Multiphysics Object-Oriented Simulation Environment (MOOSE) code framework is specifically equipped to generate training samples and create surrogate models using full-order reactor physics models. Utilizing an operational AGN-201M reactor’s specifications, two surrogate types were trained on samples of variable size, and using Cartesian products, Latin hypercube sampling, and quadrature sampling, each was compared and evaluated on accuracy when compared to a full-order Monte Carlo model. Both surrogate types were able to capture reactivity changes within 0.05 $ of the Monte Carlo model while reducing the computation costs by eight orders of magnitude.

MOOSE↗

A simple and practical wax-encapsulation method for air-sensitive XAS samples

To facilitate X-ray absorption spectroscopy (XAS) measurements of air-sensitive samples, we present a simple method in which materials are encased in common paraffin wax to protect them from air and moisture. We demonstrate the efficacy of this approach using a highly reducing, air- and moisture-sensitive uranium(III) complex, the tris(amide) U[N(SiMe 3 ) 2 ] 3 (1). When finely dispersed in a boron nitride matrix and subsequently encased in inert paraffin wax, samples of 1 remain stable with no visible or spectroscopic degradation after several days under ambient conditions. The viability of this method for XAS measurements was further evaluated across a series of uranium compounds, ranging from uranyl species to highly air- and moisture-sensitive molecular complexes, at the uranium L 3 -edge. Edge energy determinations were highly reproducible (±0.1 eV between replicates) and, where available, showed excellent agreement with literature values. In conclusion, this low-cost, effective, and versatile method offers a viable solution for XAS studies of air-sensitive compounds and materials.

36 MATERIALS SCIENCE↗

Monte Carlo Simulations of Crystal Defects in Open Ensembles

Zero- and two-dimensional crystal defects form in open statistical ensembles, such as the grand canonical, that are usually inaccessible with conventional simulation techniques. This longstanding challenge is overcome with a new Hamiltonian Monte Carlo method that samples energy-biased gradual transformations. In conclusion, the method enables free energy calculations for nonideal point defects and the direct prediction of finite-temperature interface structures.

Grain boundaries↗

Robust surfactant-assisted one-pot sample preparation for label-free single-cell and nanoscale proteomics

With advanced mass spectrometry (MS)-based proteomics, genome-scale proteome coverage can be achieved from bulk cells. However, such bulk measurement obscures cell to cell heterogeneity, precluding proteome profiling of single cells and small numbers of cells of interest. To address this issue, in recent 5 years there are a surge of small sample preparation methods developed for robust effective collection and processing of single cells and small numbers of cells for in-depth MS-based proteome profiling. Based on their broad accessibility, they can be categorized into two types: specific device- and standard PCR tube- or multi-well plate-based methods. Herein we describe the detailed protocol of our recently developed, easily adoptable, Surfactant-assisted One-Pot (SOP) sample preparation coupled with MS method termed SOP-MS for label-free single-cell and nanoscale proteomics. SOP-MS capitalizes on the combination of a MS-compatible surfactant, DDM (n-Dodecyl-ß-D-maltoside), and standard low-bind PCR tube or multi-well plate for ‘all-in-one’ one-pot sample preparation without sample transfer. With its robust and convenient features, SOP-MS can be readily implemented in any MS laboratory for single-cell and nanoscale proteomics. With further improvements in MS detection sensitivity and sample throughput, we believe that SOP-MS could open an avenue for single-cell proteomics with broad applicability in the biological and biomedical research.

Single-cell proteomics, nanoscale proteomics, SOP-↗

Development of a high-throughput method for processing sponge-stick samples to detect viable Bacillus anthracis spores

Since the national validation of the sponge-stick based method for detection of Bacillus anthracis spores in environmental samples, there have not been focused efforts to address the low throughput nature of the method, which processes only one sample at one time. Sample processing remains a serious bottleneck for rapidly analyzing large numbers of samples expected from a biological warfare attack. Therefore, we developed a high-throughput method to simultaneously process multiple sponge-stick samples to be better prepared for rapid response and recovery after wide area anthrax incidents. In this method, sponges are placed in 50 mL tubes containing 25 mL extraction buffer and shaken to release spores, after which the suspension is recovered for analysis. Here, we determined that an additional extraction step, conducted in the same tubes with 10 mL buffer, further increased spore recovery from sponge-stick by approximately 10 %. We determined that orbital shaking and multi-tube vortexing were both more effective than reciprocating shaking for recovering spores. We conducted simultaneous processing of up to 12 sponge-stick samples and demonstrated comparable spore recovery efficiencies to the traditional low-throughput stomacher-based method (approximately 60 % recovery at 10 2 -spore level and 75 % recovery at 10 4 -spore level for both methods in three replicate experiments, P > 0.05 for two-tailed t-tests for each experiment and spore level). We also demonstrated that our high-throughput method could be integrated with Rapid Viability-Polymerase Chain Reaction (RV-PCR) analysis and could detect levels as low as 40 spores per sponge even when challenged by a PCR particulate contaminant.

Anthrax↗

Engineering Methanogenic Microbiomes to Redirect Flux to Biomass

In this study, we present a method for acquiring and characterizing novel microbial consortia that regulates methanogens and methanotrophs through selective cultivation and metagenomic analysis of indigenous microorganisms in the environment. In addition, we present the work performed as part of this project to model the pathways that act as limiting factors in microbial methane metabolism based on a carbon cycle model. In this report, we describe the methods for selective cultivation of methane-metabolism-related microorganisms from environmental samples, the method for monitoring their methane consumption performance, and the method and results for verifying their functions using quantitative PCR and metagenomics techniques. The microbial consortia containing methanotrophs were obtained through selective cultivation and molecular biological verification, and their methane consumption performance was evaluated. In addition, the potential of the existence of bacteriophages interacting with methane metabolism-related microorganisms was identified through metagenomic sequencing.

09 BIOMASS FUELS↗