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DOE OSTI2023

Evaluating Software Tools for Lipid Identification from Ion Mobility Spectrometry–Mass Spectrometry Lipidomics Data

The unambiguous identification of lipids is a critical component of lipidomics studies and greatly impacts the interpretation and significance of analyses as well as the ultimate biological understandings derived from measurements. The level of structural detail that is available for lipid identifications is largely determined by the analytical platform being used. Mass spectrometry (MS) coupled with liquid chromatography (LC) is the predominant combination of analytical techniques used for lipidomics studies, and these methods can provide fairly detailed lipid identification. More recently, ion mobility spectrometry (IMS) has begun to see greater adoption in lipidomics studies thanks to the additional dimension of separation that it provides and the added structural information that can support lipid identification. At present, relatively few software tools are available for IMS-MS lipidomics data analysis, which reflects the still limited adoption of IMS as well as the limited software support. This fact is even more pronounced for isomer identifications, such as the determination of double bond positions or integration with MS-based imaging. In this review, we survey the landscape of software tools that are available for the analysis of IMS-MS-based lipidomics data and we evaluate lipid identifications produced by these tools using open-access data sourced from the peer-reviewed lipidomics literature.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

The Accelerator Neutrino Neutron InteractionExperiment: Design, Construction and Preparationfor First Physics

This thesis covers work performed for the Accelerator Neutrino Neutron Interaction Experiment (ANNIE) between 2015 and 2020. ANNIE is a beamline neutrino experiment located at the Fermi National Accelerator Laboratory in Chicago. Its primary physics goals are the measurement of neutrino interaction cross-sections on oxygen, and a measurement of the multiplicity of final state neutrons from these interactions, both as functions of final state kinematics. In order to achieve these goals ANNIE will be pioneering the use of Large Area Picosecond Photodetectors and the use of gadolinium doping to enhance neutron visibility in a water Cherenkov detector. Over the time period of this thesis the ANNIE detector was constructed, an initial 'Phase I' background run was completed, the detector was decommissioned and then substantially upgraded in preparation for the main 'Phase II' physics run. At the time of writing ANNIE is being re-commissioned, with Phase II data taking anticipated to begin in 2021. During this time I spent 21/2 years on-site contributing to almost all aspects of hardware work, while performing software development for the simulation and analysis frameworks. As my first software task I developed Monte Carlo simulations of the detector response, based on the WCSim framework. While thismore » framework provided a starting point for the tank simulation significant modifications were required to implement the complete ANNIE detector system. This included a rewrite of the geometry, along with modifications to the photosensor definitions, hit collections, digitization, triggering, input and output interfaces, etc. To take advantage of improved modelling of neutrons in Geant4.10 the physics lists were also reimplemented in the new version format. As part of this work I determined performance metrics based on the output files, calculating kinematic acceptance, detector efficiency and expected event rates. My contributions on reconstruction focused primarily on the MRD, for which I implemented two track reconstruction algorithms, specialised for high and low energy muons. The high energy algorithm achieves >90% efficiency for tracks with at least 8 hits, and is robust against dead paddles and unrelated hits. The low energy algorithm performs a search in combination with tank information to provide sensitivity down to a single MRD hit. Early data handling work for the Phase I background run included writing the code for handling TDC hits and performing studies on neutron detection without the requirement of multi-hit coincidence. As the collaboration moved to a new framework for the Phase II analysis I performed a substantial amount of work to develop the codebase, implementing tools to perform tasks such as file IO, data parsing, waveform processing, event building, timestamp alignment, time clustering, hit residual calculation, event visualisation etc. I helped develop the python API for integrating multi-language tools, and ported the framework into a Singularity container to provide a self-contained environment that…« less

43 PARTICLE ACCELERATORS↗

DOE OSTI2024

First observation of Λ c + → Λ K + π 0 and evidence of Λ c + → Λ K + π + π −

We present the first observation of the singly Cabibbo-suppressed decay Λ c + → Λ K + π 0 with a significance of 5.7 σ and the first evidence of Λ c + → Λ K + π + π − decay with a significance of 3.1 σ , based on e + e − annihilation data recorded by the BESIII detector at the BEPCII collider. The data correspond to an integrated luminosity of 6.4 fb − 1 , in the center-of-mass energy range from 4.600 to 4.950 GeV. We determine the branching fractions of Λ c + → Λ K + π 0 and Λ c + → Λ K + π + π − relative to their Cabibbo-favored counterparts to be B ( Λ c + → Λ K + π 0 ) B ( Λ c + → Λ π + π 0 ) = ( 2.09 ± 0.3 9 stat ± 0.0 7 syst ) × 10 − 2 and B ( Λ c + → Λ K + π + π − ) B ( Λ c + → Λ π + π + π − ) = ( 1.13 ± 0.4 1 stat ± 0.0 6 syst ) × 10 − 2 , respectively. Moreover, by combining our measured result with the world average of B ( Λ c + → Λ π + π 0 ) , we obtain the branching fraction B ( Λ c + → Λ K + π 0 ) = ( 1.49 ± 0.2 7 stat ± 0.0 5 syst ± 0.0 8 ref ) × 10 − 3 . This result significantly departs from theoretical predictions based on quark S U ( 3 ) flavor symmetry, which is underpinned by the presumption of meson pair S -wave amplitude dominance. Published by the American Physical Society 2024

Astronomy & Astrophysics↗

DOE OSTI2026

Machine learning approaches for crystallographic classification from synthetic 2D X-ray diffraction data

Crystallographic structure identification is crucial for understanding material properties; however, current methodologies often depend on labor-intensive and time-consuming analyses of 2D X-ray diffraction (XRD) patterns. To address these limitations, this study employs synthetic 2D XRD patterns combined with deep learning (DL) techniques to enable automated and high-throughput classification of the seven crystal systems and 230 space groups. We introduce the novel Auto Diffraction Pipeline, designed to generate synthetic 2D XRD spot patterns from crystallographic information files under diverse conditions, including varying zone axes, atomic substitution, atomic depletion and mechanical loading. These conditions enhance the realism of synthetic data, mitigating the scarcity of experimental datasets and enabling the creation of large representative training sets. Convolutional neural networks were trained and validated on these synthetic datasets to classify crystallographic structures across multiple scenarios. Our results demonstrate that integrating synthetic 2D XRD patterns with DL facilitates rapid, accurate and automated crystallographic classification, promoting the wider adoption of data-driven approaches in materials science.

Shahnazari, Ayoub [Univ. of Rochester, NY (United ↗

DOE OSTI2021

The cosmic muon and detector simulation framework of the extreme energy events (EEE) experiment

Abstract This paper describes the simulation framework of the extreme energy events (EEE) experiment. EEE is a network of cosmic muon trackers, each made of three multi-gap resistive plate chambers (MRPC), able to precisely measure the absolute muon crossing time and the muon integrated angular flux at the ground level. The response of a single MRPC and the combination of three chambers have been implemented in a GEANT4-based framework (GEMC) to study the telescope response. The detector geometry, as well as details about the surrounding materials and the location of the telescopes have been included in the simulations in order to realistically reproduce the experimental set-up of each telescope. A model based on the latest parametrization of the cosmic muon flux has been used to generate single muon events. After validating the framework by comparing simulations to selected EEE telescope data, it has been used to determine detector parameters not accessible by analysing experimental data only, such as detection efficiency, angular and spatial resolution.

Abbrescia, M.↗

DOE OSTI2020

Reducing uncertainties in satellite estimates of aerosol–cloud interactions over the subtropical ocean by integrating vertically resolved aerosol observations

Satellite quantification of aerosol effects on clouds relies on aerosol optical depth (AOD) as a proxy for aerosol concentration or cloud condensation nuclei (CCN). However, the lack of error characterization of satellite-based results hampers their use for the evaluation and improvement of global climate models. We show that the use of AOD for assessing aerosol–cloud interactions (ACIs) is inadequate over vast oceanic areas in the subtropics. Instead, we postulate that a more physical approach that consists of matching vertically resolved aerosol data from the Cloud-Aerosol Lidar and Infrared Pathfinder Satellite Observations (CALIPSO) satellite at the cloud-layer height with Moderate Resolution Imaging Spectroradiometer (MODIS) Aqua cloud retrievals reduces uncertainties in satellite-based ACI estimates. Combined aerosol extinction coefficients (σ) below cloud top (σBC) from the Cloud-Aerosol Lidar with Orthogonal Polarization (CALIOP) and cloud droplet number concentrations (N d ) from MODIS Aqua yield high correlations across a broad range of σBC values, with σBC quartile correlations ≥0.78. In contrast, CALIOP-based AOD yields correlations with MODIS Nd of 0.54–0.62 for the two lower AOD quartiles. Moreover, σBC explains 41% of the spatial variance in MODIS N d , whereas AOD only explains 17%, primarily caused by the lack of spatial covariability in the eastern Pacific. Compared with σBC, near-surface σ weakly correlates in space with MODIS N d , accounting for a 16% variance. It is concluded that the linear regression calculated from ln(N d )–ln(σBC) (the standard method for quantifying ACIs) is more physically meaningful than that derived from the Nd–AOD pair.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Tool for Developing Integrated Strategies for Decontamination and Waste Management - 20291

Management of waste from chemical, biological, and radiological incidents is complicated by the fact that decontamination decisions have a profound impact on the characteristics of resulting waste streams. Wide-area biological and radiological incidents could produce massive quantities of waste that may need to be treated on-site and sent for subsequent disposal as non-contaminated materials, or else be directly disposed of as contaminated materials. The EPA has developed the Waste Estimation Support Tool (WEST) for characterizing and quantifying biological and radiological waste that may be generated from decontamination efforts. This paper focuses on the WEST's uses for radiological incidents. WEST combines Geographic Information System (GIS)-based analysis of externally-supplied plume data, infrastructure databases derived from the Federal Emergency Management Agency's (FEMA's) Hazus tool [1], and satellite imagery surface recognition algorithms to combine the composition and square footage of the buildings in the plume with estimates of the materials between the buildings in the plume. The resulting GIS data files are then imported into a Microsoft Access database application, where they are combined with information about the nature and concentration of contaminants, and then subjected to decontamination strategies for different contaminated surfaces. The tool provides estimates of the type and quantities of potential wastes resulting from simulated decontamination and/or demolition activities and includes estimates of the remaining contamination levels including residual contamination contained within each waste stream. Estimates are presented at several levels of detail, allowing users to obtain needed data at the desired resolution. These include estimates for the total affected area, estimates by contamination zone, estimates by decontamination method(s), and estimates by building type (occupancy classification). EPA is currently developing the next version of WEST which will include several substantial enhancements. The most significant improvement for the next version of WEST will include the ability for users to develop contamination scenarios and waste estimates based on previously developed, readily available, and geographically specific infrastructure data. Instead of using WEST's default infrastructure data based on FEMA's Hazus tool, users will be able to import their own building data specific to the geographically affected area. This capability may substantially decrease uncertainties in the resulting waste estimates because the results will be based on actual building data (numbers of each type, square footage, building height, etc.). Two other significant enhancements will be the ability to generate waste estimates for vehicles and biomass. In addition to building debris and building decontamination waste, vehicles and biomass will likely constitute a significant percentage of the total waste which may result from wide area contamination events. This presentation will present the most recent version of WEST, which includes such considerations as affected biomass (e.g., trees), vehicles, and the ability to replace the default Hazus infrastructure databases with custom infrastructure databases. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2021

Feasibility of DEIM for retrieving the initial field via dimensionality reduction

When parameter estimation is solved in a high-dimensional space, the dimensionality reduction strategy becomes the primary consideration for alleviating the tremendous computational cost. Here, the discrete empirical interpolation method (DEIM) is explored to retrieve the initial condition (IC) by combining the polynomial chaos (PC) based ensemble Kalman filter (i.e. PC-EnKF), where a non-intrusive PC expansion is considered as a surrogate model in place of the forward model in the prediction step of the ensemble Kalman filter, resulting in fewer forward model integrations but with a comparable accuracy as Monte Carlo-based approaches. The DEIM acts as a hyper-reduction tool to provide the low-dimensional input for the high-dimensional initial field, which can be reconstructed using the information on the sparse interpolation grid points that is adaptively obtained through PC-EnKF data assimilation method. Thus an innovative framework to reconstruct the IC is developed. The detailed procedure at each assimilation iteration includes: the determination of the spatial interpolation points, the estimation of the initial values on the interpolation locations using the optimal observations, and the reconstruction of IC in the full space. The current study uses the reconstruction field of initial conditions of the Navier-Stokes equations as an example to illustrate the efficacy of our method. The experimental results demonstrate the proposed algorithm achieves a satisfactory reconstruction for the initial field. The proposed method helps to extend the applicable area of DEIM in solving inverse problems.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2020

Connecting Femtosecond Transient Absorption Microscopy with Spatially Coregistered Time Averaged Optical Imaging Modalities

Multimodal all-optical imaging involving coregistered femtosecond transient absorption microscopy (TAM), time-integrated photoluminescence (PL), and steady-state modalities such as confocal reflectance and transmission offers an appealing approach to gain a comprehensive understanding of complex electronic excited-state phenomena in spatially heterogeneous systems. A unique combination of these modalities allows us to unravel not only the competing electronic excited-state dynamical processes but also the underlying morphological information with simultaneous high temporal and spatial resolution. However, correlating the various images obtained from time-resolved and time-independent modalities is generally nontrivial and particularly challenging when the electronic dynamics under study evolve in both time and space. Here, we demonstrate a new approach for rationally correlating time-resolved microscopy with coregistered time-integrated or steady-state modalities. Specifically, our approach involves an extended global lifetime analysis of the time-resolved microscopic data set to separate distinct dynamical processes taking place on commensurate time scales, and the resulting decay-associated amplitude maps (DAAMs) were applied to explore correlations with the images acquired using time-independent modalities. The feasibility of our approach was validated through analyzing a multimodal data set acquired from a thin film of chloride-containing mixed lead halide perovskites (CH 3 NH 3 PbI 3–x Cl x ) using femtosecond transient absorption, time-integrated PL, and confocal reflectance microscopies. Analysis of the results obtained enable us to gain new insight into the complex ultrafast relaxation dynamics in this highly heterogeneous system.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Integrating Ultra-Coarse-Grained Protein Models into Accessible Workflows for Multiscale Molecular Dynamics

To capture protein conformational transitions using molecular dynamics (MD), several simulation resolutions covering different spatial and temporal scales are typically needed. All-atom (AA) simulations provide fine resolution, but are computationally infeasible for large systems over longer durations. Coarse-grained (CG) and ultra-coarse-grained (UCG) models have a lower resolution and computational cost while still being able to conserve essential protein features. Prior work on a Multiscale Machinelearned Modeling Infrastructure (MuMMI) combined both AA and CG simulations to study RAS-RAF protein interactions, leveraging CG models for longer time scales and using AA to investigate unusual conformations in greater detail. However, MuMMI is still resource-intensive, and this study aims to maximize exploration of the protein conformational space while reducing computational cost. In this paper, we build on prior work that integrates UCG models based on heterogeneous elastic network modeling (hENM) into the MuMMI workflow. We demonstrate that UCG models enable accurate sampling of protein conformations, focusing on simulating RAS-RAF protein interactions. Using higher-resolution CG Martini simulation data, we can automatically refine intramolecular interactions in UCG models. We present a scalable Python package that uses fluctuations observed in higher-resolution CG Martini simulations to estimate bond coefficients of the UCG model. We built novel machine learning-based backmapping methods to recover more detailed CG Martini structures from UCG structures, using diffusion models to learn the mapping between scales. Finally, we present UCG-mini-MuMMI, an accessible and less compute-intensive version of MuMMI as a resource for the scientific community. Incorporating UCG models into MD studies is applicable to a broad range of systems and proteins, and our study offers insights into the advantages and limitations of these methods.

Chemical structure↗

DOE OSTI2023

First Simultaneous Determination of Inclusive and Exclusive | V u b |

The first simultaneous determination of the absolute value of the Cabibbo-Kobayashi-Maskawa matrix element V ub using inclusive and exclusive decays is performed with the full Belle data set at the $Υ$(4S) resonance, corresponding to an integrated luminosity of 711 fb -1 . We analyze collision events in which one B meson is fully reconstructed in hadronic modes. This allows for the reconstruction of the hadronic X u system of the semileptonic b → $πℓe_ℓ$ decay. We separate exclusive B → $πℓ\overline{ν}_ℓ$ decays from other inclusive B → $X_uℓ\overline{ν}_ℓ$ and backgrounds with a two-dimensional fit that utilizes the number of charged pions in the X u system and the four-momentum transfer q 2 between the B and X u systems. Combining our measurement with information from lattice QCD and QCD calculations of the inclusive partial rate as well as external experimental information on the shape of the B → $πℓe_ℓ$ form factor, we determine |$V^{excl}_{ub}$| = (3.78 ± 0.23 ± 0.16 ± 0.14) × 10 -3 and |$V^{incl}_{ub}$| = (3.88 ± 0.20 ± 0.31 ± 0.09) x 10 -3 , respectively, with the uncertainties being the statistical error, systematic errors, and theory errors. The ratio of |$V^{excl}_{ub}$|/|$V^{incl}_{ub}$| 0.97 ± 0.12 is compatible with unity.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2024

Characterization of the Structural–Stratigraphic and Reservoir Controls on the Occurrence of Gas Hydrates in the Eileen Gas Hydrate Trend, Alaska North Slope

One of the most studied permafrost-associated gas hydrate accumulations in Arctic Alaska is the Eileen Gas Hydrate Trend. This study provides a detailed re-examination of the Eileen Gas Hydrate Trend with a focus on the gas hydrate accumulation in the western part of the Prudhoe Bay Unit. This integrated analysis of downhole well log data and published geophysical data has provided new insight on structural, stratigraphic, and reservoir controls on the occurrence of gas hydrates in the Eileen Gas Hydrate Trend. This study revealed the relatively complex nature of the gas hydrate occurrences in the Eileen Gas Hydrate Trend, with gas hydrates present in a series of coarsening upward, laterally pervasive, mostly fine-grained sand beds exhibiting high gas hydrate saturations. Most of the gas hydrate-bearing reservoirs in the Eileen Gas Hydrate Trend are laterally segmented into distinct northwest- to southeast-trending fault blocks, occur in a combination of structural–stratigraphic traps, and are only partially hydrate filled with distinct down-dip water contacts. These findings suggest that the traditional parts of a petroleum system (i.e., reservoir, gas source, gas migration, and geologic timing of the system formation) also control the occurrence of gas hydrates in the Eileen Gas Hydrate Trend.

20 FOSSIL-FUELED POWER PLANTS↗

DOE OSTI2024

Development of Lightweight Structural Materials with Improved Properties for Fission Batteries

The notion of a “fission battery” conveys a vision focused on realizing very simple “plug-and-play” nuclear systems that can be integrated into a variety of applications requiring affordable, reliable energy in the form of electricity and/or heat and function without operations and maintenance staff. Fission batteries require lightweight structural materials to increase their mobility, and the lightweight materials must demonstrate structural resilience under various conditions. The objective of this work is to develop lightweight structural material featuring a good combination of mechanical properties using advanced modeling and simulation together with an advanced additive manufacturing technique such as laser powder bed fusion. The preliminary results show that different lattice structures and types can be successfully meshed using nTopology software, and the lattice structure data can be successfully transformed to Multiphysics Object-Oriented Simulation Environment (MOOSE) input. Finite Element Analysis (FEA) displays that, at macro/engineering scale simulation, the weight saving design has an obvious effect on tensile behavior such as effective elastic modulus and yield stress. The novel approaches of this work are (1) development of optimized lattice structures for improved mechanical properties using advanced simulation and modeling techniques; and (2) model predictions of the mechanical properties (e.g., strength and stress distribution) of macroscopic materials in order to preliminarily select a lattice structure for additive manufacturing.

36 MATERIALS SCIENCE↗

DOE OSTI2021

BioSecure Digital Twin: Manufacturing Innovation and Cybersecurity Resilience

U.S. national security, prosperity, economy, and well-being require secure, flexible, and resilient Biopharmaceutical Manufacturing. The COVID-19 pandemic reaffirmed that the biomedical production value-chain is vulnerable to disruption and has been under attack from sophisticated nation-state adversaries. Current cyber defenses are inadequate, and the integrity of critical production systems and processes are inherently vulnerable to cyber-attacks, human error, and supply chain disruptions. The following chapter explores how a BioSecure Digital Twin will improve U.S. manufacturing resilience and preparedness to respond to these hazards by significantly improving monitoring, integrity, security, and agility of our manufacturing infrastructure and systems. The BioSecure Digital Twin combines a scalable manufacturing framework with a robust platform for monitoring and control to increase U.S. biopharma manufacturing resilience. Then, the chapter discusses some of the inherent vulnerabilities and challenges at the nexus of health and advanced manufacturing. Next, the chapter highlights that as the Pandemic evolves, we need agility and resilience to overcome significant obstacles. This section highlights an innovative application of Cyber Informed Engineering to developing and deploying a BioSecure Digital Twin to improve the resilience and security of the biopharma industrial supply chain and production processes. Finally, the chapter concludes with a process framework to complement the Digital Twin platform, called the Biopharma (Observe, Orient, Decide, Act) OODA Loop Framework (BOLF), a four-step approach to decision-making outputs from the Digital Twin. The BOLF will help end users leverage twin technology by distilling the available information, focusing the data on context, and rapidly making the best decision while remaining cognizant of changes that can be made as more data becomes available.

99 GENERAL AND MISCELLANEOUS↗

DOE OSTI2024

Electromagnetic observables of open-shell nuclei from coupled-cluster theory

Here we develop a new method to describe electromagnetic observables of open-shell nuclei with two nucleons outside a closed shell. This approach combines the equation-of-motion coupled-cluster method for such systems and the Lorentz integral transform technique, expanding the applicability of coupled-cluster theory for electromagnetic observables beyond closed-(sub)shell nuclei. To validate this new approach, we compute the non-energy-weighted dipole sum rule and the dipole polarizability of 16,24 ⁢O in both the closed-(sub)shell and the new equation-of-motion coupled-cluster frameworks, finding agreement within error bars. We then analyze the evolution of the dipole polarizability along the oxygen and calcium isotopic chains. Our predictions agree well with available experimental data and other available theoretical calculations for the closed-(sub)shell 16,22 ⁢O and the open-shell 18 O. In the calcium isotopes, we observe that our dipole polarizability predictions for open-shell nuclei are lower than those of closed-(sub)shell nuclei. We expect that our predictions for 24 O and 54,56 ⁢Ca will motivate future experimental studies at the drip line.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2024

Measurement of C P Violation in B 0 → ψ ( → ℓ + ℓ − ) K S 0 ( → π + π − ) Decays

A measurement of time-dependent C P violation in the decays of B 0 and B ¯ 0 mesons to the final states J / ψ ( → μ + μ − ) K S 0 , ψ ( 2 S ) ( → μ + μ − ) K S 0 and J / ψ ( → e + e − ) K S 0 with K S 0 → π + π − is presented. The data correspond to an integrated luminosity of 6 fb − 1 collected at a center-of-mass energy of s = 13 TeV with the LHCb detector. The C P -violation parameters are measured to be S ψ K S 0 = 0.717 ± 0.013 ( stat ) ± 0.008 ( syst ) and C ψ K S 0 = 0.008 ± 0.012 ( stat ) ± 0.003 ( syst ) . This measurement of S ψ K S 0 represents the most precise single measurement of the CKM angle β to date and is more precise than the current world average. In addition, measurements of the C P -violation parameters of the individual channels are reported and a combination with the LHCb Run 1 measurements is performed. © 2024 CERN, for the LHCb Collaboration 2024 CERN

Aaij, R. (ORCID:0000000305331952)↗

DOE OSTI2025

Field Emission Analysis in SRF Cavities for PIP-II Using GEANT4

Field emission (FE) remains a significant hurdle for achieving optimal performance and reliability in superconducting radiofrequency (SRF) cavities used in accelerator cryomodules. A thorough understanding of the generation and propagation of FE-induced radiation is therefore essential to mitigate this problem. The absence of standardized measurement protocols further complicates the comparison of radiation data across different testing phases and facilities. This highlights the need for a precise quantitative method to diagnose and analyze FE-induced radiation. Such efforts could prove beneficial for improving cavity preparation and cleanroom assembly techniques during the prototype and production stages of Fermilab's Proton Improvement Plan-II (PIP-II) project. This study presents the initial steps of detailed Geant4 simulations aimed at analyzing FE-induced radiation in the low-beta 650 MHz 5-cell elliptical (LB650) cavity. Our goal is to combine these results with radiation diagnostics to enhance diagnostic accuracy and optimize detector positioning. This integrated approach ultimately aims to improve the preparation, assembly, and testing procedures for PIP-II SRF cavities, ensuring the delivery of FE-free cryomodules.

Wijethunga, Sajini A.K. [Fermilab] (ORCID:00000002↗

DOE OSTI2023

Data augmentation and multimodal learning for predicting drug response in patient-derived xenografts from gene expressions and histology images

Patient-derived xenografts (PDXs) are an appealing platform for preclinical drug studies. A primary challenge in modeling drug response prediction (DRP) with PDXs and neural networks (NNs) is the limited number of drug response samples. We investigate multimodal neural network (MM-Net) and data augmentation for DRP in PDXs. The MM-Net learns to predict response using drug descriptors, gene expressions (GE), and histology whole-slide images (WSIs). We explore whether combining WSIs with GE improves predictions as compared with models that use GE alone. We propose two data augmentation methods which allow us training multimodal and unimodal NNs without changing architectures with a single larger dataset: 1) combine single-drug and drug-pair treatments by homogenizing drug representations, and 2) augment drug-pairs which doubles the sample size of all drug-pair samples. Unimodal NNs which use GE are compared to assess the contribution of data augmentation. The NN that uses the original and the augmented drug-pair treatments as well as single-drug treatments outperforms NNs that ignore either the augmented drug-pairs or the single-drug treatments. In assessing the multimodal learning based on the MCC metric, MM-Net outperforms all the baselines. Our results show that data augmentation and integration of histology images with GE can improve prediction performance of drug response in PDXs.

60 APPLIED LIFE SCIENCES↗