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At least 991 records · Page 55

Assessing the Impact of Measurement Precision on Metabolite Identification Probability in Multidimensional Mass Spectrometry-Based, Reference-Free Metabolomics

Identification of compounds with minimal ambiguity remains a central challenge in mass spectrometry-based metabolomics. Conventional compound identification relies on comparing analytical signatures (e.g., mass-to-charge ratio, collision cross section, tandem mass spectra) against reference data obtained from measurements of authentic chemical standards. The breadth of annotatable compounds using this approach is necessarily limited by availability of authentic standards, analytical throughput, and resolving power of the separations that underly the measurements. The maturation of computational methods, both theory-driven and artificial intelligence/machine learning-based, for prediction of various molecular properties relevant to multidimensional mass spectrometry measurements has opened the door to a new “reference-free” paradigm of compound annotation. Through augmenting existing reference data for molecular properties with computational predictions, the universe of identifiable chemical species can be expanded significantly beyond its current limits. An unexplored aspect of this novel approach is understanding how to gauge confidence in resulting annotations, especially as the compound search space is expanded. Intuitively, the confidence of a compound annotation is related to the inherent discriminatory power of the molecular properties used for identification, as well as the precision with which the properties are measured or predicted. In this work, we characterize this relationship between measurement precision and identification probability in a systematic and quantitative fashion for a defined region of chemical space that includes organic small molecule metabolites. Importantly, this work establishes a framework for conducting metabolite identification probability analysis that enables others to quantify this relationship for their own compounds and properties of interest.

Metabolite Identification↗

Test of lepton universality in beauty-quark decays

The standard model of particle physics currently provides our best description of fundamental particles and their interactions. The theory predicts that the different charged leptons, the electron, muon and tau, have identical electroweak interaction strengths. Previous measurements have shown that a wide range of particle decays are consistent with this principle of lepton universality. This article presents evidence for the breaking of lepton universality in beauty-quark decays, with a significance of 3.1 standard deviations, based on proton–proton collision data collected with the LHCb detector at CERN’s Large Hadron Collider. The measurements are of processes in which a beauty meson transforms into a strange meson with the emission of either an electron and a positron, or a muon and an antimuon. If confirmed by future measurements, this violation of lepton universality would imply physics beyond the standard model, such as a new fundamental interaction between quarks and leptons.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Simple Scattering: Lipid nanoparticle structural data repository

Lipid nanoparticles (LNPs) are being intensively researched and developed to leverage their ability to safely and effectively deliver therapeutics. To achieve optimal therapeutic delivery, a comprehensive understanding of the relationship between formulation, structure, and efficacy is critical. However, the vast chemical space involved in the production of LNPs and the resulting structural complexity make the structure to function relationship challenging to assess and predict. New components and formulation procedures, which provide new opportunities for the use of LNPs, would be best identified and optimized using high-throughput characterization methods. Recently, a high-throughput workflow, consisting of automated mixing, small-angle X-ray scattering (SAXS), and cellular assays, demonstrated a link between formulation, internal structure, and efficacy for a library of LNPs. As SAXS data can be rapidly collected, the stage is set for the collection of thousands of SAXS profiles from a myriad of LNP formulations. In addition, correlated LNP small-angle neutron scattering (SANS) datasets, where components are systematically deuterated for additional contrast inside, provide complementary structural information. The centralization of SAXS and SANS datasets from LNPs, with appropriate, standardized metadata describing formulation parameters, into a data repository will provide valuable guidance for the formulation of LNPs with desired properties. To this end, we introduce Simple Scattering, an easy-to-use, open data repository for storing and sharing groups of correlated scattering profiles obtained from LNP screening experiments. Here, we discuss the current state of the repository, including limitations and upcoming changes, and our vision towards future usage in developing our collective knowledge base of LNPs.

59 BASIC BIOLOGICAL SCIENCES↗

Understanding performance variability in standard and pipelined parallel Krylov solvers

In this work, we collect data from runs of Krylov subspace methods and pipelined Krylov algorithms in an effort to understand and model the impact of machine noise and other sources of variability on performance. We find large variability of Krylov iterations between compute nodes for standard methods that is reduced in pipelined algorithms, directly supporting conjecture, as well as large variation between statistical distributions of runtimes across iterations. Based on these results, we improve upon a previously introduced nondeterministic performance model by allowing iterations to fluctuate over time. We present our data from runs of various Krylov algorithms across multiple platforms as well as our updated non-stationary model that provides good agreement with observations. We also suggest how it can be used as a predictive tool.

97 MATHEMATICS AND COMPUTING↗

Long-run Marginal Emission Rates for Electricity - Workbooks for 2021 Cambium Data

These workbooks contain modeled estimates of long-run marginal emission rates (LRMER) for the contiguous United States. The LRMER is an estimate of the rate of emissions that would be either induced or avoided by a long-term (i.e., more than several years) change in electrical demand. It incorporates both the projected changes to the electric grid, as well as the potential for an incremental change in electrical demand to influence the structural evolution of the grid (i.e., the building and retiring of capital assets, such as generators and transmission lines). It is therefore distinct from the more-commonly-known short-run marginal, which treats grid assets as fixed. The Levelized LRMER worksheet within each workbook is set up to produce a levelized long-run marginal emission rate based on user-provided inputs. These levelized LRMER values are intended for analysts to use when estimating the emissions induced (or avoided) by a long-term change in end-use electricity demand. There are two workbooks that supply the data at two different geographic resolutions: states and GEA regions (20 regions that are similar to, but not exactly the same as, the US EPA's eGRID regions). For more data underlying these emissions factors, see the Cambium 2021 project at https://cambium.nrel.gov/. For more details on the inputs into the scenarios available in the workbooks, see the Standard Scenarios 2021 Report (https://www.nrel.gov/docs/fy22osti/80641.pdf). This data was produced as part of the Cambium project. For more details about the methodology, see the Cambium Documentation: Version 2021 (https://www.nrel.gov/docs/fy22osti/81611.pdf). This data is planned to be updated annually. Information on the latest versions can be found at https://www.nrel.gov/analysis/cambium.html.

24 POWER TRANSMISSION AND DISTRIBUTION↗

PSInet: a new global water potential network

Abstract Given the pressing challenges posed by climate change, it is crucial to develop a deeper understanding of the impacts of escalating drought and heat stress on terrestrial ecosystems and the vital services they offer. Soil and plant water potential play a pivotal role in governing the dynamics of water within ecosystems and exert direct control over plant function and mortality risk during periods of ecological stress. However, existing observations of water potential suffer from significant limitations, including their sporadic and discontinuous nature, inconsistent representation of relevant spatio-temporal scales and numerous methodological challenges. These limitations hinder the comprehensive and synthetic research needed to enhance our conceptual understanding and predictive models of plant function and survival under limited moisture availability. In this article, we present PSInet (PSI—for the Greek letter Ψ used to denote water potential), a novel collaborative network of researchers and data, designed to bridge the current critical information gap in water potential data. The primary objectives of PSInet are as follows. (i) Establishing the first openly accessible global database for time series of plant and soil water potential measurements, while providing important linkages with other relevant observation networks. (ii) Fostering an inclusive and diverse collaborative environment for all scientists studying water potential in various stages of their careers. (iii) Standardizing methodologies, processing and interpretation of water potential data through the engagement of a global community of scientists, facilitated by the dissemination of standardized protocols, best practices and early career training opportunities. (iv) Facilitating the use of the PSInet database for synthesizing knowledge and addressing prominent gaps in our understanding of plants’ physiological responses to various environmental stressors. The PSInet initiative is integral to meeting the fundamental research challenge of discerning which plant species will thrive and which will be vulnerable in a world undergoing rapid warming and increasing aridification.

Forestry↗

Fiber optic computing using distributed feedback

Abstract The widespread adoption of machine learning and other matrix intensive computing algorithms has renewed interest in analog optical computing, which has the potential to perform large-scale matrix multiplications with superior energy scaling and lower latency than digital electronics. However, most optical techniques rely on spatial multiplexing, requiring a large number of modulators and detectors, and are typically restricted to performing a single kernel convolution operation per layer. Here, we introduce a fiber-optic computing architecture based on temporal multiplexing and distributed feedback that performs multiple convolutions on the input data in a single layer. Using Rayleigh backscattering in standard single mode fiber, we show that this technique can efficiently apply a series of random nonlinear projections to the input data, facilitating a variety of computing tasks. The approach enables efficient energy scaling with orders of magnitude lower power consumption than GPUs, while maintaining low latency and high data-throughput.

97 MATHEMATICS AND COMPUTING↗

Cosmology intertwined: A review of the particle physics, astrophysics, and cosmology associated with the cosmological tensions and anomalies

The standard Λ Cold Dark Matter (ΛCDM) cosmological model provides a good description of a wide range of astrophysical and cosmological data. However, there are a few big open questions that make the standard model look like an approximation to a more realistic scenario yet to be found. In this paper, we list a few important goals that need to be addressed in the next decade, taking into account the current discordances between the different cosmological probes, such as the disagreement in the value of the Hubble constant H 0 , the σ 8 – S 8 tension, and other less statistically significant anomalies. While these discordances can still be in part the result of systematic errors, their persistence after several years of accurate analysis strongly hints at cracks in the standard cosmological scenario and the necessity for new physics or generalisations beyond the standard model. In this paper, we focus on the 5.0 σ tension between the Planck CMB estimate of the Hubble constant H 0 and the SH0ES collaboration measurements. After showing the H 0 evaluations made from different teams using different methods and geometric calibrations, we list a few interesting new physics models that could alleviate this tension and discuss how the next decade's experiments will be crucial. Moreover, we focus on the tension of the Planck CMB data with weak lensing measurements and redshift surveys, about the value of the matter energy density Ω m , and the amplitude or rate of the growth of structure ( σ 8 , f σ 8 ). We list a few interesting models proposed for alleviating this tension, and we discuss the importance of trying to fit a full array of data with a single model and not just one parameter at a time. Additionally, we present a wide range of other less discussed anomalies at a statistical significance level lower than the H 0 – S 8 tensions which may also constitute hints towards new physics, and we discuss possible generic theoretical approaches that can collectively explain the non-standard nature of these signals. Finally, we give an overview of upgraded experiments and next-generation space missions and facilities on Earth that will be of crucial importance to address all these open questions.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Data-driven distillation and precision prognosis in traumatic brain injury with interpretable machine learning

Traumatic brain injury (TBI) affects how the brain functions in the short and long term. Resulting patient outcomes across physical, cognitive, and psychological domains are complex and often difficult to predict. Major challenges to developing personalized treatment for TBI include distilling large quantities of complex data and increasing the precision with which patient outcome prediction (prognoses) can be rendered. We developed and applied interpretable machine learning methods to TBI patient data. We show that complex data describing TBI patients' intake characteristics and outcome phenotypes can be distilled to smaller sets of clinically interpretable latent factors. We demonstrate that 19 clusters of TBI outcomes can be predicted from intake data, a ~ 6× improvement in precision over clinical standards. Finally, we show that 36% of the outcome variance across patients can be predicted. These results demonstrate the importance of interpretable machine learning applied to deeply characterized patients for data-driven distillation and precision prognosis.

60 APPLIED LIFE SCIENCES↗

Projected Operational Energy Life Cycle Data Development: 2025 Update

This report documents the data sources and methods used to develop the energy life cycle data for use by the National Institute of Standards and Technology (NIST) Engineering Laboratory (EL) to be used for the development of measurement science and incorporation into decision-support tools for evaluating building and facility capital investments. The data are posted separately under DOI 10.18141/2575194.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Data Integration Aggregated Model For Nuclear Deployment

The data of a nuclear utility or plant are stored in various isolated forms in different systems. These data have different structures and tools and are, therefore, used independently. The integration of data sources is often needed and is performed manually and on an as-needed basis. The integration of the data would enable creating a data warehouse for a single nuclear power plant (NPP) or multiple plants. A data model contains objects that make up a given domain along with their attributes and relationships and could be used as a standard for exchange between applications for simple integration and data aggregation. After a survey of existing models, it was determined that a new model was required to meet the scope of this problem. DIAMOND has been developed in the form of an ontology to meet these needs. An ontology is simply a data model that also acts as a taxonomy for the domain, organizing the objects in a hierarchy with the most general objects at the top.

Browning, JerenM↗

Reconstructing quintessence

We present an Effective Field Theory based reconstruction of quintessence models of dark energy directly from cosmological data. We show that current cosmological data possess enough constraining power to test several quintessence model properties for redshifts z ϵ [0, 1.5] with no assumptions about the behavior of the scalar field potential. We use measurements of the cosmic microwave background, supernovae distances, and the clustering and lensing of galaxies to constrain the evolution of the dark energy equation of state, Swampland Conjectures, the shape of the scalar field reconstructed potential, and the structure of its phase space. The standard cosmological model still remains favored by data and, within quintessence models, deviations from its expansion history are bounded to be below the 10% level at 95% confidence at any redshift below z = 1.5.

79 ASTRONOMY AND ASTROPHYSICS↗

Human Liver Epithelium Response to HCoV-229E Infection Epigenomics (ACS-DP4)

The purpose of this experiment was to evaluate how wild-type Human coronavirus strain 229E (HCoV-229E) infection alters chromatin accessibility in infected cells only. Sample data was obtained for mock and infected (standard and UV-inactivated) immortalized human liver cells (HuH-7) and collected 24 hrs. post infection. Samples were processed using assay for transposase-accessible chromatin using high-throughput sequencing (ATAC-Seq) and generated bar coded library samples were evaluated for RNA sequencing (RNA-Seq) expression analysis. Processed ATAC-Seq datasets are openly accessible from the download button and contain secondary processed RNA-Seq results files and supporting metadata materials. Data download includes a sample naming key, infection titer metadata, normalized counts, and relevant computational source code information supporting data transparency and reuse.

59 BASIC BIOLOGICAL SCIENCES↗

Determining the range of validity of quasar X-ray and UV flux measurements for constraining cosmological model parameters

ABSTRACT We use six different cosmological models to study the recently released compilation of X-ray and UV flux measurements of 2038 quasars (QSOs) which span the redshift range 0.009 ≤ z ≤ 7.5413. We find, for the full QSO data set, that the parameters of the X-ray and UV luminosities LX−LUV relation used to standardize these QSOs depend on the cosmological model used to determine these parameters, i.e. it appears that the full QSO data set includes QSOs that are not standardized and so cannot be used for the purpose of constraining cosmological parameters. Subsets of the QSO data, restricted to redshifts z ≲ 1.5–1.7 obey the LX−LUV relation in a cosmological-model-independent manner, and so can be used to constrain cosmological parameters. The cosmological constraints from these lower z, smaller QSO data subsets are mostly consistent with, but significantly weaker than, those that follow from baryon acoustic oscillation and Hubble parameter measurements.

79 ASTRONOMY AND ASTROPHYSICS↗

Speed of Sound Measurements of R-1130(E) and an Azeotropic Blend of R-1336mzz(Z)/1130(E)

Sound speed data measured using a dual-path pulse-echo instrument are reported for pure trans-1,2-dichloroethene (R-1130(E)) and an azeotropic blend of cis-1,1,1,4,4,4-hexafluorobutene (R-1336mzz(Z)) and R-1130(E) with a composition of 74.8 mass % R-1336mzz(Z) with the balance being R-1130(E). The azeotropic blend of R-1336mzz(Z)/1130(E) is classified as R-514A in ANSI/ASHRAE standard 34. Liquid phase speed of sound data are reported from just above the saturation pressure of pure R-1130(E) or the bubble point pressure of R-514A to a maximum pressure of 26.7 MPa. The relative combined expanded uncertainty in the speed of sound varies from 0.032 % to 0.148 % with the greatest deviations occurring at the lowest sound speeds. At present, no reference Helmholtz-energy-explicit equation of state (EOS) is available for R-1130(E). Therefore, the reported data for pure R-1130(E) are compared to an extended corresponding states (ECS) model. Deviations between the pure R-1130(E) sound speed data and the ECS model were found to be consistently negative ranging between − 4.1 % and − 3.5 %. The R-514A data are compared to a multifluid model inclusive of the established reference Helmholtz-energy-explicit EOS for R-1336mzz(Z) and ECS model for R-1130(E) with estimated binary interaction parameters. Deviations between the experimental speed of sound data and the multifluid model were also found to be consistently negative. However, deviations from the multifluid model were found to be as great as − 17.1 %. The large deviations from the ECS model and multifluid model underscore the need for a robust Helmholtz-energy-explicit EOS for R-1130(E).

42 ENGINEERING↗

2023 Data Science Challenge Notebooks

THE DATA SCIENCE INSTITUTE WILL BE INVITING STUDENTS FROM UC MERCED AND UC RIVERSIDE TO PARTICIPATE IN A DATA SCIENCE CHALLENGE AT LLNL. IN THE CHALLENGE, THE STUDENTS WILL EXPLORE A DATA-DRIVEN APPROACH TO RECONSTRUCTING ELECTROANATOMICAL MAPS OF THE HEART AT CLINICALLY RELEVANT RESOLUTIONS, COMBINING INPUT FROM THE STANDARD 12-LEAD ECG WITH ADVANCED MACHINE LEARNING TECHNIQUES. THE DATA THE STUDENTS WILL HAVE ACCESS TO HAS BEEN IM REVIEWED FOR EXTERNAL RELEASE. (LLNL-MI-835833) THESE NOTEBOOKS WILL PROVIDE THE STUDENTS WITH INSTRUCTIONS OF HOW TO LOAD THE DATA AND WORK WITH THE DATA, ALONG WITH TUTORIALS TO DO BASIC MACHINE LEARNING TASKS LIKE LOGISTIC REGRESSION AND IMAGE CLASSIFICATION.

Landajuela Larma, Mikel↗

The Integration and Mapping of an Open-Source National Well Resource to Inform Geologic Carbon Storage Site Selection and Risk Prevention: The CO2-Locate Database

Geologic carbon storage (GCS) offers a way to capture and permanently store CO₂ from fossil fuel operations in underground geologic structures, aiding in the transition to a carbon-neutral energy economy. However, CO₂ injection sites can experience gas leakage through existing wells that penetrate storage reservoirs, making knowledge of well locations and characteristics crucial for permitting, infrastructure reusability, and risk assessment in GCS. Currently, public wellbore data from state, federal, and tribal entities are inconsistent and fragmented, with gaps and redundancies. To address this, the National Energy Technology Laboratory (NETL) developed CO2-Locate, an open-source, geospatial database and online application. CO2-Locate integrates over 50 data sources from federal, state, and tribal entities, creating a standardized national well database. Funded by the Bipartisan Infrastructure Law, the database is publicly available through the Energy Data eXchange (EDX) and viewable via the CO2-Locate web mapping application. This tool allows users to query, filter, and visualize well data to support GCS planning, permitting, and risk assessments. This presentation covers the methods used to create CO2-Locate, including data acquisition, processing, attribute mapping, and integration, much of which is automated for future updates. The web mapping application and its role in GCS site selection will also be discussed.

Tetteh, Daniel A.↗

Hydrogen Risk Assessment Models (HyRAM) (Version 3.0 Technical Reference Manual)

The HyRAM software toolkit provides a basis for conducting quantitative risk assessment and consequence modeling for hydrogen infrastructure and transportation systems. HyRAM is designed to facilitate the use of state-of-the-art science and engineering models to conduct robust, repeatable assessments of hydrogen safety, hazards, and risk. HyRAM includes generic probabilities for hydrogen equipment failures, probabilistic models for the impact of heat flux on humans and structures, and computationally and experimentally validated first-order models of hydrogen release and flame physics. HyRAM integrates deterministic and probabilistic models for quantifying accident scenarios, predicting physical effects, and characterizing hydrogen hazards (thermal effects from jet fires, overpressure effects from deflagrations), and assessing impact on people and structures. HyRAM is developed at Sandia National Laboratories for the U.S. Department of Energy to increase access to technical data about hydrogen safety and to enable the use of that data to support development and revision of national and international codes and standards. HyRAM is a research software in active development and thus the models and data may change. This report will be updated at appropriate developmental intervals. This document provides a description of the methodology and models contained in the HyRAM version 3.0. HyRAM 3.0 includes the new ability to model cryogenic hydrogen releases from liquid hydrogen systems, using a different property calculation method and different equations of state. Other changes include modifications to the ignition probability calculations, component leak frequency calculations, and addition of default impulse data.

08 HYDROGEN↗