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DOE OSTI2024

CRISPRi functional genomics in bacteria and its application to medical and industrial research

SUMMARY Functional genomics is the use of systematic gene perturbation approaches to determine the contributions of genes under conditions of interest. Although functional genomic strategies have been used in bacteria for decades, recent studies have taken advantage of CRISPR (clustered regularly interspaced short palindromic repeats) technologies, such as CRISPRi (CRISPR interference), that are capable of precisely modulating expression of all genes in the genome. Here, we discuss and review the use of CRISPRi and related technologies for bacterial functional genomics. We discuss the strengths and weaknesses of CRISPRi as well as design considerations for CRISPRi genetic screens. We also review examples of how CRISPRi screens have defined relevant genetic targets for medical and industrial applications. Finally, we outline a few of the many possible directions that could be pursued using CRISPR-based functional genomics in bacteria. Our view is that the most exciting screens and discoveries are yet to come.

Microbiology↗

DOE OSTI2025

Aerosol biome of a cafeteria and medical facility in Los Alamos, New Mexico, USA

Aerosol sampling with next-generation sequencing was used to characterize microbial communities in a cafeteria and medical facility waiting room in Los Alamos, New Mexico, USA. We detected sequences from human, bacteria, archaea, fungi, other eukaryotes, and viruses, providing insights into the diversity of the aerosol microbiome.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2023

Know Your Space: Inlier and Outlier Construction for Calibrating Medical OOD Detectors

This software offers methods and functions for training calibrated out-of-distribution detectors for medical image classification tasks. It includes functionalities for training, synthesizing data augmentations, calibration, and out-of-distribution detection. Developed using PyTorch, this software is compatible with standard neural network architectures used for imaging data. Additionally, it provides capabilities to compute evaluation metrics for assessing the performance and quality of the detectors.

Narayanaswamy, VivekSivaraman↗

DOE OSTI2021

Explainable Artificial Intelligence in Endocrinological Medical Research

Artificial Intelligence (AI) has been a part of the medical community for decades in the form of Clinical Decision Support Systems (CDSS) to aide physicians in diagnosis and categorization of patients (1). Recent years have seen a shift from expert-derived models to the integration of machine learning (ML) algorithms to drive the output of these AI systems due to the ability of ML models to more accurately make predictions by exploiting higher dimensional and often complex data. In many cases ML models gain their advantage in accuracy by capture complex and often non-linear relationships between features being used to make the prediction. However, the hype and excitement around these methods are tempered by the clinical utility of often black-box solutions driven by skepticism of results that are difficult for practitioners to not only interpret but explain to their patients (1-3). This skepticism is not unfounded as multiple examples of black-box solutions identifying incidental correlates as the key predictors have highlighted the potential bias in a training set, or reward system, that a ML model may exploit; for example a model discerning wolves from huskies based on snow in the background rather than features of the dogs (1, 4, 5).

Endocrinological, artificial intelligence, diabete↗

DOE OSTI2023

Evaluation of 6-OxP-CD, an Oxime-based cyclodextrin as a viable medical countermeasure against nerve agent poisoning: Experimental and molecular dynamic simulation studies on its inclusion complexes with cyclosarin, soman and VX

The ability of the cyclodextrin-oxime construct 6-OxP-CD to bind and degrade the nerve agents Cyclosarin (GF), Soman (GD) and S -[2-[Di(propan-2-yl)amino]ethyl] O -ethyl methylphosphonothioate (VX) has been studied using 31 P-nuclear magnetic resonance (NMR) under physiological conditions. While 6-OxP-CD was found to degrade GF instantaneously under these conditions, it was found to form an inclusion complex with GD and significantly improve its degradation (t 1/2 ~ 2 hrs) relative over background (t 1/2 ~ 22 hrs). Consequently, effective formation of the 6-OxP-CD:GD inclusion complex results in the immediate neutralization of GD and thus preventing it from inhibiting its biological target. In contrast, NMR experiments did not find evidence for an inclusion complex between 6-OxP-CD and VX, and the agent’s degradation profile was identical to that of background degradation (t 1/2 ~ 24 hrs). As a complement to this experimental work, molecular dynamics (MD) simulations coupled with Molecular Mechanics-Generalized Born Surface Area (MM-GBSA) calculations have been applied to the study of inclusion complexes between 6-OxP-CD and the three nerve agents. These studies provide data that informs the understanding of the different degradative interactions exhibited by 6-OxP-CD with each nerve agent as it is introduced in the CD cavity in two different orientations (up and down). For its complex with GF, it was found that the oxime in 6-OxP-CD lies in very close proximity (P GF …O Oxime ~ 4–5 Å) to the phosphorus center of GF in the ‘down GF ’ orientation for most of the simulation accurately describing the ability of 6-OxP-CD to degrade this nerve agent rapidly and efficiently. Further computational studies involving the center of masses (COMs) for both components (GF and 6-OxP-CD) also provided some insight on the nature of this inclusion complex. Distances between the COMs (ΔCOM) lie closer in space in the ‘down GF ’ orientation than in the ‘up GF ’ orientation; a correlation that seems to hold true not only for GF but also for its congener, GD. In the case of GD, calculations for the ‘down GD ’ orientation showed that the oxime functional group in 6-OxP-CD although lying in close proximity (P GD …O Oxime ~ 4–5 Å) to the phosphorus center of the nerve agent for most of the simulation, adopts another stable conformation that increase this distance to ~ 12–14 Å, thus explaining the ability of 6-OxP-CD to bind and degrade GD but with less efficiency as observed experimentally (t 1/2 ~ 4 hr. vs. immediate). Lastly, studies on the VX:6-OxP-CD system demonstrated that VX does not form a stable inclusion complex with the oxime-bearing cyclodextrin and as such does not interact in a way that is conducive to an accelerated degradation scenario. Collectively, these studies serve as a basic platform from which the development of new cyclodextrin scaffolds based on 6-OxP-CD can be designed in the development of medical countermeasures against these highly toxic chemical warfare agents.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2025

Computational Modeling to Advance Novel Medical Isotopes for Radiotheranostics: A DOE-NIH Joint Workshop Executive Summary

The DOE-NIH Joint Workshop on Computational Modeling to Advance Novel Medical Isotopes for Radiotheranostics, held on September 27, 2024, brought together experts from government, academia, and industry to address critical challenges in radionuclide production and clinical translation. Here, the workshop emphasized interdisciplinary collaboration, particularly between the Department of Energy (DOE) and the National Institutes of Health (NIH), to strengthen the domestic isotope supply, streamline regulatory pathways, and further integrate computational tools into radiopharmaceutical therapy (RPT). Key discussions explored the role of AI-driven modeling, machine learning, and digital twin technologies in optimizing dosimetry, dynamically personalizing treatments, and reducing time to clinical adoption. Advances in predictive computational modeling were highlighted as essential for improving radionuclide yield, purity, and synthesis efficiency. Regulatory considerations and equitable access were central themes, with participants advocating for harmonized global standards, adaptive trial designs, and expanded infrastructure for clinical implementation. DOE computational and production infrastructure was emphasized. Future priorities identified include increased investment in radionuclide production infrastructure, expanded workforce development in radiopharmaceutical sciences and computational modeling, and the creation of robust public-private partnerships. The workshop concluded that continued strategic collaboration and sustained resources will be vital for advancing next-generation radiotheranostics, ensuring safe and effective therapies accessible to all patients.

digital twins↗

DOE OSTI2025

Beam optics design of a prototype 20 kW conduction-cooled SRF accelerator for medical sterilization

Superconducting technology has significantly advanced the capabilities of particle accelerators, facilitating higher beam-power operations for fundamental research at a comparatively lower cost. However, the conventional implementation of superconducting technology introduces complexities in the form of cryogenic plants, cryogenic distribution systems and substantial construction and operational cost. In response to these challenges, recent research efforts at Fermilab have been dedicated to the development of a cryogen-free, conduction-cooled Nb3Sn-based superconducting technology. This paper outlines the beam optics design of a 20-kW conduction-cooled compact superconducting accelerator for medical sterilization. The paper reviews both the physics and practical constraints associated with high beam-power operation within the context of industrial applications. The focus is on providing insights into the potential of this innovative technology to overcome existing challenges and pave the way for more accessible and efficient industrial particle accelerators.

Saini, A. [Fermilab]↗

DOE OSTI2020

Nuclear Weapon Medical Effects

Presentation Overview: Nuclear Weapon Medical Effects; Psychological Effects; Contamination; Lethal Dose; Acute Radiation Syndromes; Chronic Radiation Effects; Thermal Injuries; Blast Injuries

63 RADIATION, THERMAL, AND OTHER ENVIRON. POLLUTAN↗

DOE OSTI2021

Cross Section Measurements of Photonuclear Reaction Pathways Towards Promising Medical Radioisotopes

Project Objectives: The goal of this project was to generate data relevant to radioisotope production while developing innovative technologies that foster and enhance novel production of radioisotopes, and, also, while providing opportunities for cultivating and training future generations of scientists. This work has provided the foundation for methodologies for determination of photonuclear cross sections over multiple energies in a single irradiation. Simultaneously, the feasibility of electron LINAC production of several in-demand radioisotopes such as 47 Sc, 67 Cu, 77 As, and 186 Re has been demonstrated. To accomplish these objectives a collaboration was formed between two complimentary facilities, the Low Energy Accelerator Facility (LEAF) at Argonne National Laboratory and the High Intensity Gamma-ray Source (HIGS) at Triangular Universities Nuclear Laboratory (TUNL). The involvement of the research group from North Carolina Central University gave students at this Historically Black University experience in forefront nuclear-physics research relevant to addressing a high-priority interdisciplinary issue. Project Description: HIGS provides a nearly monoenergetic gamma-ray beam by intra-cavity Compton backscattering of free-electron photons from electrons circulating in a storage ring. This beam can be collimated to produce a very precise energy beam. If the beam is un-collimated a calculated and precise energy spread of the beam occurs radially. The γ-flux can be evenly distributed over the radial distribution of energy and used to perform activation experiments on concentric ring targets. Thus providing multiple energy ranges in a single irradiation. Each concentric ring target can be counted separately in order to determine activation at the given energy and successively be correlated to the activation cross section. Targets were activated to determine production feasibility using electron beams at LEAF. Potential Impact: The Nuclear Science Advisory Committee recently named production of radioisotopes with electron LINACs as one of the most compelling and largest-impact opportunities for the production of high specific activity radioisotopes. Improving the photonuclear cross sectional data base with experimentally verified results will greatly enhance a researcher’s ability to rationalize electron LINAC production routes towards desired radioisotopes. This work will provide the foundation for methodologies for determination of photonuclear cross sections over multiple energies and multiple targets in a single irradiation. The techniques developed in this project will enable future studies to continue verifying theoretically predicted photonuclear cross section with experimental results. These data will also enable adaptation of models and support more precise theoretical calculation of photonuclear cross sections. This research will involve undergraduates, graduate students, and post-docs to give them a valuable research experience leading towards the next generation of scientists in the field of medical isotopes.

07 ISOTOPE AND RADIATION SOURCES↗

DOE OSTI2022

Heavy Ion Medical Accelerator in Chiba (HIMAC) Experimental Data

This report provides experimental data obtained using the Heavy Ion Medical Accelerator in Chiba (HIMAC) facility of the National Institute of Radiological Sciences (NIRS) in Japan.

43 PARTICLE ACCELERATORS↗

DOE OSTI2024

Benchmark Midplane Field for Medical FFA

This is a lattice cell for a fixed-field medical accelerator, transmitting protons from 10–250 MeV. The goal is to have fixed tunes throughout this energy range. The cell is based on the lattice Feb7 2024 ProtonAccelerator.f90 from Dejan Trbojevic and had the magnet field profiles re-optimised to attain fixed tunes with realistic magnet fringe fields.

43 PARTICLE ACCELERATORS↗

DOE OSTI2024

Beam Optics Design of A Prototype 20 kW Conduction-Cooled SRF Accelerator for Medical Sterilization

43 PARTICLE ACCELERATORS↗

DOE OSTI2024

Carl T. Hayden Veterans Affairs Medical Center: Smart Buildings Case Study

The purpose of this smart buildings case study is to showcase a leading example of a GEB renovation project in the federal buildings space and provide key information on the technology and control upgrades, costs, and energy and utility bill savings. This case study also provides information and recommendations for selecting energy conservation measures (ECMs) and choosing energy and cost reduction strategies from the energy management team at the site. The findings from this successful GEB project can be used to help pave the way for additional GEB retrofits in the future. The Carl T. Hayden Veterans Affairs (VA) Medical Center in Phoenix, Arizona, demonstrates that GEB strategies and technologies can be realistically deployed today across buildings with substantial energy and cost savings. The project implemented both ECMs and grid-interactive technologies and controls strategies, making it a leading example of a smart, sustainable, and efficient commercial building.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2024

New York-Presbyterian and Columbia University Irving Medical Center Requirements (Analysis Report)

EPOC uses the Deep Dive process to discuss and analyze current and planned science, research, or education activities and the anticipated data output of a particular use case, site, or project to help inform the strategic planning of a campus or regional networking environment. This includes understanding future needs related to network operations, network capacity upgrades, and other technological service investments. A Deep Dive comprehensively surveys major research stakeholders’ plans and processes in order to investigate data management requirements over the next 5–10 years. Between February and June 2024, staff members from the Engagement and Performance Operations Center (EPOC) met with researchers and staff from New York-Presbyterian (NYP), Columbia University Irving Medical Center (CUIMC), and NYSERNet for the purpose of a Deep Dive into scientific and research drivers. The goal of this activity was to help characterize the requirements for a number of campus use cases, and to enable cyberinfrastructure support staff to better understand the needs of the researchers within the community. Material for this event included the written documentation from each of the profiled research areas, documentation about the current state of technology support, and a write-up of the discussion that took place via e-mail and video conferencing. The case studies highlighted the ongoing challenges and opportunities that NYP and CUIMC have in supporting a cross-section of established and emerging research use cases. Each case study mentioned unique challenges which were summarized into common needs.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

Reverse Engineering of Medical Devices for Innovation and Advancement in Healthcare

• Medical technology is rapidly evolving and introducing new functionality and methodologies that suggest a higher risk for common vulnerability exposures (CVE) • Introduction of functionalities like Wi-Fi, Bluetooth, and internet connectivity require devices to be rigorously evaluated for vulnerabilities • Subsequently like many other fields cell-phone interconnectivity suggests a significantly higher level of risk to critical infrastructure and data security

Baldwin, David [Savannah River National Laboratory↗

DOE OSTI2025

A membrane-based approach to medical isotope purification (Final Report)

This is the final technical report from the grant "A membrane-based approach to medical isotope purification" which was awarded by the Isotope Research and Development Program through the early career research program to Christine Duval at Case Western Reserve University. The project developed adsoprtive membranes with covalently bound diglycolamide-derived ligands for the purification of Ac-225 and benchmarked them against the current state of the art adsorbent materials.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗

DOE OSTI2026

DICOMs, Missiles, and Metadata: The U.S. Nuclear Weapons Program Leverages a Medical Standard

Digital Imagine and Communications in Medicine (DICOM) images, although most commonly used in medical settings, have been widely adopted by the United States Department of Energy (DOE) for capturing images of the internal components in a nuclear weapon. DICOMs, a lesser-known file format that combine nested metadata structures with complex image data-including multiple planes, frames, and high resolution-require the creation of access copies to support usability within the DOE. Used primarily for ensuring the safety, security, and reliability of the U.S. nuclear stockpile, the Los Alamos National Laboratory (LANL)’s DICOM images and corresponding image metadata must be accessible to scientists and researchers via our institutional centralized databases. This paper describes the author's creation of a Python script that converts DICOM images into accessible, archive-friendly TIFF files while preserving key image data and metadata.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

DOE OSTI2020

Flexible Magnetic Polymer Composite Substrate with Ba 1.5 Sr 1.5 Z Hexaferrite Particles of VHF/Low UHF Patch Antennas for UAVs and Medical Implant Devices

Our goal is to fabricate flexible magnetic polymer composites as antenna substrates for very high frequency (VHF)/low ultra high frequency (UHF) antennas for unmanned aerial vehicles (UAVs) and medical devices. Magnetodielectric materials, which have permeability (μ) similar to permittivity (ε), have attracted great attention, because they facilitate miniaturization of microwave devices while keeping or enhancing electromagnetic characteristics. Mechanically millled Ba 1.5 Sr 1.5 Co 2 Fe 24 O 41 (Ba 1.5 Sr 1.5 Z) hexaferrite particles were used to increase permeability in the interesting frequency band. The microwave properties of Ba 1.5 Sr 1.5 Z composites were predicted and measured. Hansen’s zero-order analysis of antenna bandwidth and electromagnetic field simulation showed that the hexaferrite-based flexible composite could enhance a bandwidth and achieve the miniaturization of antennas as well. The magnetic antenna substrates can be a good solution to integrate antennas into the UAVs whose dimensions are comparable to or larger than communication wavelength.

36 MATERIALS SCIENCE↗