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At least 631 records · Page 35

Rare Events via Cross-Entropy Population Monte Carlo

Rare events are events that happen with very low frequency. Estimating rare event probabilities using Monte Carlo techniques is computationally expensive, often to the point of intractability, and special methods are required. Importance sampling (IS) is a well known technique that uses a proposal distribution in place of a target distribution to lower the variance of the estimator. Key to the success of IS methods is the choice of a proposal distribution, or the parameters governing the distribution. Adaptive importance sampling improves the parameters of a family or population of proposal distributions iteratively through trials. We present a novel cross-entropy population Monte Carlo algorithm, which adapts the parameters of proposals through the cross-entropy method. The proposed method stands apart from previous work in that we are not optimizing a mixture distribution. Instead, we leverage deterministic mixture weights and optimize the distributions individually through a reinterpretation of the typical derivation of the cross-entropy method. Demonstrations on rare event examples show that the algorithm can outperform existing resampling based population Monte Carlo methods, especially for higher-dimensional problems. Finally, we also demonstrate efficacy on a conjunction analysis problem.

97 MATHEMATICS AND COMPUTING↗

Estimating rates and patterns of diversification with incomplete sampling: a case study in the rosids

Premise Recent advances in generating large‐scale phylogenies enable broad‐scale estimation of species diversification. These now common approaches typically are characterized by (1) incomplete species coverage without explicit sampling methodologies and/or (2) sparse backbone representation, and usually rely on presumed phylogenetic placements to account for species without molecular data. We used empirical examples to examine the effects of incomplete sampling on diversification estimation and provide constructive suggestions to ecologists and evolutionary biologists based on those results. Methods We used a supermatrix for rosids and one well‐sampled subclade (Cucurbitaceae) as empirical case studies. We compared results using these large phylogenies with those based on a previously inferred, smaller supermatrix and on a synthetic tree resource with complete taxonomic coverage. Finally, we simulated random and representative taxon sampling and explored the impact of sampling on three commonly used methods, both parametric (RPANDA and BAMM) and semiparametric (DR). Results We found that the impact of sampling on diversification estimates was idiosyncratic and often strong. Compared to full empirical sampling, representative and random sampling schemes either depressed or inflated speciation rates, depending on methods and sampling schemes. No method was entirely robust to poor sampling, but BAMM was least sensitive to moderate levels of missing taxa. Conclusions We suggest caution against uncritical modeling of missing taxa using taxonomic data for poorly sampled trees and in the use of summary backbone trees and other data sets with high representative bias, and we stress the importance of explicit sampling methodologies in macroevolutionary studies.

59 BASIC BIOLOGICAL SCIENCES↗

Characterization of Radiation Induced Defects Across Scales

The Whole Powder Pattern Modelling (WPPM) approach of diffraction line profile analysis (LPA) was applied for the first time on PuO 2 in order to understand the evolution of the microstructural properties as a function of process conditions. Crystallite size distributions and defect concentrations were determined by WPPM on three different PuO 2 samples - including one with a bimodal distribution and compared to the result of more common LPA analyses used in PuO 2 literature studies (e.g. Scherrer equation, double Voigt method). The conclusion was that a lognormal distribution of spherical crystallites with dislocations most closely represent the microstructure of PuO 2 produced by heating Pu 2 (C 2 O 4 ) 3 (H 2 O) 6 •3H 2 O between 650°C and 850°C. The volume-weighted mean column length (Lvol) parameter obtained from the double Voigt method for the monomodal samples were the same as the Lvol obtained from the WPPM within uncertainty. The two LPA methods did not agree on the Lvol parameters of the bimodal distribution sample with only the WPPM getting values that were consistent with the individual components. The WPPM can potentially provide more insight into future studies of the influences on the microstructure properties of PuO 2 .

36 MATERIALS SCIENCE↗

Comparing serial X-ray crystallography and microcrystal electron diffraction (MicroED) as methods for routine structure determination from small macromolecular crystals

Innovative new crystallographic methods are facilitating structural studies from ever smaller crystals of biological macromolecules. In particular, serial X-ray crystallography and microcrystal electron diffraction (MicroED) have emerged as useful methods for obtaining structural information from crystals on the nanometre to micrometre scale. Despite the utility of these methods, their implementation can often be difficult, as they present many challenges that are not encountered in traditional macromolecular crystallography experiments. Here, XFEL serial crystallography experiments and MicroED experiments using batch-grown microcrystals of the enzyme cyclophilin A are described. The results provide a roadmap for researchers hoping to design macromolecular microcrystallography experiments, and they highlight the strengths and weaknesses of the two methods. Specifically, we focus on how the different physical conditions imposed by the sample-preparation and delivery methods required for each type of experiment affect the crystal structure of the enzyme.

36 MATERIALS SCIENCE↗

Detuned synchronized waveform averaging for reducing distortions due to sample interleaving

This invention introduces a method for optimally detuning the ratio of analog-to-digital (ADC) sample rate and trigger rate during waveform averaging to minimize the deleterious effects from sample interleaving. A prescription is described for determining the optimal detuning factor for the ADC or trigger rate in any scenario, depending on the number of ADC cores used and the limited tuning resolution of the clock rates for a specific implementation.

42 ENGINEERING↗

Nanoscale biochemical sample preparation and analysis

Provided herein are methods and systems for biochemical analysis, including compositions and methods for processing and analysis of small cell populations and biological samples (e.g., a robotically controlled chip-based nanodroplet platform). In particular aspects, the methods described herein can reduce total processing volumes from conventional volumes to nanoliter volumes within a single reactor vessel (e.g., within a single droplet reactor) while minimizing losses, such as due to sample evaporation.

Kelly, Ryan T.↗

Enhanced Sampling of Crystal Nucleation with Graph Representation Learnt Variables

In this study, we present a graph neural network-based learning approach using an autoencoder setup to derive low-dimensional variables from features observed in experimental crystal structures. These variables are then biased in enhanced sampling to observe state-to-state transitions and reliable thermodynamic weights. Our approach uses simple convolution and pooling methods. To verify the effectiveness of our protocol, we examined the nucleation of various allotropes and polymorphs of iron and glycine from their molten states. Our graph latent variables when biased in well-tempered metadynamics consistently show transitions between states and achieve accurate free energy calculations in agreement with experiments, both of which are indicators of dependable sampling. This underscores the strength and promise of our graph neural net variables for improved sampling. Furthermore, the protocol shown here should be applicable for other systems and with other sampling methods.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A fast and sensitive size-exclusion chromatography method for plasma extracellular vesicle proteomic analysis

Extracellular vesicles (EVs) carry diverse biomolecules derived from their parental cells, making their components excellent biomarker candidates. However, purifying EVs is a major hurdle in biomarker discovery since current methods require large amounts of samples, are time-consuming and typically have poor reproducibility. Here we describe a simple, fast, and sensitive EV fractionation method using size exclusion chromatography (SEC) on a fast protein liquid chromatography (FPLC) system. Our method uses a Superose 6 Increase 5/150, which has a bed volume of 2.9 mL. The FPLC system and small column size enable reproducible separation of only 50 µL of human plasma in 15 min. To demonstrate the utility of our method, we used longitudinal samples from a group of individuals who underwent intense exercise. A total of 838 proteins were identified, of which, 261 were previously characterized as EV proteins, including classical markers, such as cluster of differentiation (CD)9 and CD81. Quantitative analysis showed low technical variability with correlation coefficients greater than 0.9 between replicates. The analysis captured differences in relevant EV proteins involved in response to physical activity. Our method enables fast and sensitive fractionation of plasma EVs with low variability, which will facilitate biomarker studies in large clinical cohorts.

59 BASIC BIOLOGICAL SCIENCES↗

Spatiotemporal sampling of near-petahertz vortex fields

Measuring the field of visible light with high spatial resolution has been challenging, as many established methods only detect a focus-averaged signal. Here, we introduce a near-field method for optical field sampling that overcomes that limitation by employing the localization of the enhanced near-field of a nanometric needle tip. A probe field perturbs the photoemission from the tip, which is induced by a pump pulse, generating a field-dependent current modulation that can easily be captured with our electronic detection scheme. The approach provides reliable characterization of near-petahertz fields. We show that not only the spiral wavefront of visible femtosecond light pulses carrying orbital angular momentum (OAM) can be resolved but also the field evolution with time in the focal plane. Additionally, our method is polarization sensitive, which makes it applicable to vectorial field reconstruction.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

GIS-Based Modeling of Contaminated Soil Volumes at Multiple Sites in the Formerly Utilized Sites Remedial Action Program - 20149

The remediation of hazardous, toxic, and radioactive waste (HTRW) sites produces cost-related risks associated with the estimation of contaminated soil or debris volumes. Historical risk-management techniques include cost contingencies to cover volume uncertainties that affect project budgeting and decision-making. The Buffalo District teamed with project partners to lessen volume uncertainty and reduce project risks at multiple HTRW sites managed under the Formerly Utilized Sites Remedial Action Program (FUSRAP). Historical remedial investigations under FUSRAP commonly identified the presence of radiological material in site media, the associated human health risk, and then areas of remediation. To manage remedial execution and reduce risk, pre-design or remediation-phase sampling essentially 'chased' contamination, which was not conducive to efficient predictive budgeting derived from Feasibility Study (FS) cost analyses. The Buffalo District first optimized their approach to better understand volume uncertainty by utilizing the Argonne National Laboratory's Bayesian Approaches for Adaptive Spatial Sampling (BAASS) software [1]. BAASS processed soft data (e.g., gamma walk-over data) and spatial sampling data to estimate the lateral extent of contaminated soil irrespective of depth (i.e., gross contamination extent) and define areas of contaminant uncertainty. The software performed a binary transformation of contaminant concentrations at all sampling points based upon remedial action goals or a sum of ratios approach (i.e., clean, impacted, or range of impacts in soil). The model produced two-dimensional (horizontal) contaminant probability contours and statistical uncertainty in the sampling coverage and resulting contaminant extents. This method was translated vertically by partitioning the sampling data into depth brackets that produced a stacked representation of contaminant extents and uncertainty in the subsurface (i.e., similar to construction lifts). The results commonly led to a better understanding of project uncertainty and the need for sampling strategies that produce high-confidence soil volumes, which control costs. The BAASS-based delineations were eventually replaced by Empirical Bayesian Kriging (EBK) methods available in ArcGIS Spatial or 3D Analysts [2]. The EBK method calculates contaminant probability zones derived from user-controlled semivariograms of the spatial datasets. The resulting probability zones (e.g., 50% or 80% of contaminant probability) represent the two-dimensional surface delineation of the overall horizontal remedial area, similarly to BAASS. However, unlike BAASS, the vertical sampling data within these probability zones became vertical control points to contour a subterranean surface that connects subsurface points to the land-surface delineations of contamination. The resulting representation of horizontal and vertical impacts within an enclosed envelop (volume) of soil included uncertainty distributions that are used to plan uncertainty-reduction sampling. These data-driven and math-based models of three-dimensional sampling results produced well-bounded remedial volumes for project planning and better uncertainty predictions during project budgeting. The EBK method was applied to several FUSRAP sites managed by the Buffalo District and compared to less rigorously modeled sites previously remediated by the District. The comparison of modeled to actual remediated volumes provide a basis for validating the volume-estimation method. This comparison is important to ensure modeled volumes match physical boundaries of site remediation. FUSRAP sites with denser investigative sampling and lesser volume uncertainty proved useful in remedial planning and contracting. The Buffalo District noted that historical sites with sparser sampling arrays had greater disparity between estimated volumes and final remedial volumes. The benefit achieved over the cost of detailed soil sampling appears positive for FUSRAP projects, especially where impacts vary widely and appear unbounded by investigation-phase sampling. The subsequent Empirical Bayesian Kriging of contamination coupled with vertical contouring for soil estimations reduces uncertainty in soil volumes or indicates where sampling is required to reduce uncertainty, which together optimize remedial planning and budgeting. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Intramolecular 13 C isotope distributions of butane from natural gases

A single-step method allowing the measurement of 13 C intramolecular distribution of butane isomers (n- and i-butane) from natural gas samples was developed. The method builds up on the one that has been developed for propane, using on-line pyrolysis followed by isotope analysis of the pyrolytic fragments. The isotopic filiation between n-butane and its pyrolytic fragments was elucidated using samples spiked with 13 C on terminal positions. The isotopic filiation for i-butane could not be shown experimentally due to the lack of commercially available enriched i-butane. We thus used a recent model named Reaction Mechanism Generator (RMG) to assess the origin of the fragments arising from i-butane pyrolysis. Butanes from natural gas samples from the Carnarvon Basin (Australia) and the Arkoma Basin (USA) were analyzed. The results are consistent with a model for thermogenic natural gas generation and suggest that combined intramolecular isotope composition of propane and n-butane can be related to the gas maturity. In addition, the method allows the detection and shed light on the mechanism of n-butane and i-butane biodegradation in natural gas reservoirs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

WHONDRS Surface Water and Sediment Non-Purgeable Organic Carbon and FTICR-MS across Glacial Features in Svalbard 2021 (v3)

This dataset supports a broader study examining land-atmosphere gas exchange associated with permafrost and glaciers in Svalbard. The dataset provides geochemistry and organic matter characterization data generated from surface water and sediment. Samples were collected from 8 spatially diverse sites across central Svalbard and also from a more comprehensive temporal and spatial study within one glacial catchment area throughout one summer melt season. Related data were collected and will be published separately in collaboration with Yde and Kleber.This data package was originally published in September 2022. It was updated in March 2023 (v2; new and modified files), and July 2025 (v3; modified files). See the change history section in the readme for details.For details on how to navigate data packages generated by this project, see https://data.ess-dive.lbl.gov/portals/PNNLRiverCorridorSFA/About. This dataset is comprised of one main data folder containing (1) file-level metadata; (2) data dictionary; (3) field metadata; (4) dissolved organic carbon (DOC; measure as non-purgeable organic carbon; NPOC); (5) surface water sampling protocol; (6) sediment extraction protocol; (7) readme; (8) methods codes; (9) international generic sample number (IGSN) mapping file; and (10) folder of high resolution characterization of organic matter via 7 and 12 Tesla (7T and 12T) Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) generated through the Environmental Molecular Sciences Laboratory (EMSL; https://www.pnnl.gov/environmental-molecular-sciences-laboratory). The FTICR folder contains two subfolders containing the 7T and 12T .xml data files and another subfolder containing instructions for using Formularity (https://omics.pnl.gov/software/formularity) and an R script to process the data based on the user's specific needs. All files are .csv, .pdf, .R, .ref, or .xml.

54 ENVIRONMENTAL SCIENCES↗

Galaxy and Mass Assembly: A Comparison between Galaxy–Galaxy Lens Searches in KiDS/GAMA

Strong gravitational lenses are a rare and instructive type of astronomical object. Identification has long relied on serendipity, but different strategies—such as mixed spectroscopy of multiple galaxies along the line of sight, machine-learning algorithms, and citizen science—have been employed to identify these objects as new imaging surveys become available. We report on the comparison between spectroscopic, machine-learning, and citizen-science identification of galaxy–galaxy lens candidates from independently constructed lens catalogs in the common survey area of the equatorial fields of the Galaxy and Mass Assembly survey. In these, we have the opportunity to compare high completeness spectroscopic identifications against high-fidelity imaging from the Kilo Degree Survey used for both machine-learning and citizen-science lens searches. We find that the three methods—spectroscopy, machine learning, and citizen science—identify 47, 47, and 13 candidates, respectively, in the 180 square degrees surveyed. These identifications barely overlap, with only two identified by both citizen science and machine learning. We have traced this discrepancy to inherent differences in the selection functions of each of the three methods, either within their parent samples (i.e., citizen science focuses on low redshift) or inherent to the method (i.e., machine learning is limited by its training sample and prefers well-separated features, while spectroscopy requires sufficient flux from lensed features to lie within the fiber). These differences manifest as separate samples in estimated Einstein radius, lens stellar mass, and lens redshift. The combined sample implies a lens candidate sky density of ∼0.59 deg{sup −2} and can inform the construction of a training set spanning a wider mass–redshift space. A combined approach and refinement of automated searches would result in a more complete sample of galaxy–galaxy lens candidates for future surveys.

79 ASTRONOMY AND ASTROPHYSICS↗

Human Liver Epithelial Cells (HuH7) Response to HCoV-229E Infection Epigenomics (ATAC-Seq) (ACS-DP4)

The purpose of this experiment was to evaluate how wild-type Human coronavirus strain 229E (HCoV-299E) infection alters chromatin accessibility in infected cells. Sample data was obtained from mock-infected cells, UV-inactivated virus treated cells, and replication competent HCoV-229E infected immortalized human liver cells (HuH7) at 24 hours post infection. Samples were processed using ATAC-seq methods for reported bar coded libraries. Sample data was acquired using an Illumina Hi-Seq 2500 sequencer system and further processed for ATAC-Seq expression analysis.

59 BASIC BIOLOGICAL SCIENCES↗