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High-quality Acinetobacter genomes recovered from combat wounds via metagenomic sequencing resemble cultured isolate genomes

The ability to accurately characterize wound pathogens is critical to informing clinical decisions for wound infections with complex treatment requirements. Acinetobacter baumannii is an impactful nosocomial pathogen in combat wounds and civilian hospital-acquired infections. An informed understanding of the phylogenetics and epidemiology of A. baumannii infections in military and civilian environments could guide approaches that improve antibiotic treatment regimens for both military and civilian patients. Whole-genome data for bacterial strains can be difficult to obtain due to challenges in culturing isolates from preserved military specimens. Metagenomic sequencing and assembly create opportunities for genomic analysis of pathogens directly from clinical specimens. The ability to perform comparative analyses between metagenome-derived genomes and culture-derived genomes would support a range of comparative bacterial genomic studies. Wound tissue biopsy and effluent samples from combat injuries were subjected to metagenomic sequencing and assembly. In total, 42 microbial metagenome-assembled genomes (MAGs) were obtained directly from metagenomic sequence data, 36 of which were designated “high” quality. Thirty of these genomes corresponded to Acinetobacter, with 29 mapping specifically to A. baumannii. Other observed genera included Bordetella, Citrobacter, Escherichia, and Pseudomonas. Single-copy and multi-copy orthologs were identified across Acinetobacter MAGs and publicly available isolate genomes derived from military and civilian sources. Both MAG and military isolate genomes were annotated with antimicrobial resistance data, and MAG genomes were statistically comparable to genomes obtained from isolates. Our results highlight the potential of de novo metagenome assembly for enabling high-resolution characterization directly from clinical specimens, thereby improving diagnostic precision, guiding antimicrobial stewardship, and enhancing understanding of pathogen evolution across diverse healthcare and battlefield environments.

Acinetobacter baumannii↗

Introduction

The 2014 SPIE Sensing Technologies for Global Health, Military Medicine and Environmental Monitoring conference embraced a wealth of state-of-the-art information in basic and applied science. This event covered the latest developments in the following areas: Non-invasive Disease Diagnostics for Global Health- This opening series of two consecutive sessions focused on oral biospecimen based rapid assays and point-of-care devices for the detection of pathogens causing infectious diseases, biomarkers for cancer, and analytes for noncommunicable diseases such as diabetes. They also covered presentations on the human proteasome and microbiome with linkage to human diseases and diagnostic approaches. The sessions were built on the past experience and expertise of the National Institutes of Health, National Institutes of Dental and Craniofacial Research. Military Medicine I: Traumatic Brain Injury and PTSD-This assembly covered oral-biomarker based diagnostics for brain damage and TBI as well as prevention and rehabilitation technologies. Neurorehabilitation and noninvasive neuromodulation were also discussed as critical approaches for effective functioning. Military Medicine II: Physiology and Medicine of Extreme Environments and Spaceflight-This scientific segment showcased physiological, pharmacological and diagnostic sensing methodologies during spaceflight per the National Aeronautics and Space Administration as well as military-relevant toxicans and future sensing trends per the Department of Defense. It also included latest technologies to determine hydration status in warfighters, eye surgery using the latest laser technologies, and sensing tools for blood analysis.  Sensing Technologies for Disease Diagnostics and Environmental Monitoring-This closing series of two consecutive sessions provided the venues to learn and discuss more results on the next generation of diagnostic tools and field technologies for diseases, including biomarker detection by digital imaging, multiplex technologies, capillary electrophoresis and molecular platforms serving as labs-on-chips. This conference allowed cross-fertilization of ideas, projects and collaborative work by a multidisciplinary audience of national and international colleagues from the academia, industry and federal government: The National Institutes of Health, National Aeronautics and Space Administration, and the Department of Defense.

Wotring, Virginia E.↗

Enhancing Nasa Sounding Rocket Capabilities Through Composite Material Adoption

Sounding rockets are a suborbital research platform employed by NASA for heliophysics, astrophysics, and geospace science investigations, and for technology development. They follow semi-parabolic trajectories and are launched using surplus military, and commercial, solid-propellant rocket motors. NASA sounding rocket payloads are comprised of standard, modular subassemblies, designed to perform specific functions critical to achieving mission success criteria. Since the program’s inception, payload length and mass have trended upwards, limiting the capability of the platform to reach exospheric apogees and decreasing the time above critical altitudes to observe solar and celestial targets. To offset this trend, composite materials may be of use in payload and subsystem design to decrease payload mass. This investigation seeks to understand if there is a practical benefit to introducing composite materials on the NSRP by assessing mission specific impacts to those missions conducted in fiscal year 2024. To accurately estimate the mass of a composites-based payload, a standard subsystem (NIACS) underwent structural reconfiguration. Materials were selected that align with NSRP design, manufacturing, and testing standards. NIACS reconfiguration resulted in a mass reduction of 19.6% which was then applied to the payload system in entirety. Using vehicle performance carpet plots, delta apogee and time above the Kármán line were determined. Performance improvements were then evaluated against that mission’s success criteria to determine if that mission would have benefitted from using composite materials. On average, each mission would have gained 59.8 kilometers apogee and 62.9 seconds above the Kármán line. However, only nine of the seventeen missions would have benefitted from these performance improvements. Two of the missions could have used a lower-impulse launch vehicle to achieve mission success. Upleg stability met programmatic criteria; downleg instability and dynamic pressure improved, showing that ballast would not offset the mass reduction of using composite materials. Cost analysis showed that production costs will increase 39%. For the two missions that could have used a lower-impulse launch vehicle, the cost of the launch vehicle would have offset payload production costs. In summary, composite materials are not recommended for universal use on NASA sounding rocket payloads due to unclear programmatic benefits and added cost. However, they are justified for optical astrophysics and heliophysics missions, high-apogee (exosphere) requirements, or when they reduce payload costs versus higher impulse launch vehicles. Reflown, recoverable subsystems should use composites to enhance apogee and observation time.

Robert Henry Burth↗

Science on the Moon: The Wailing Wall of Space Exploration

Science on and from the Moon has important implications for expanding human knowledge and understanding, a prospect for the 21st Century that has been under discussion for at least the past 25 years. That having been said, however, there remain many issues of international versus national priorities, strategy, economy, and politics that come into play. The result is a very complex form of human behavior where science and exploration take center stage, but many other important human options are sacrificed. To renew this dialogue about the Moon, it seems we are already rushing pell-mell into it as has been done in the past. The U.S., Japan, China, India, and Russia either have sent or plan to send satellites and robotic landers there at this time. What does a return to the Moon mean, why are we doing this now, who should pay for it, and how? The only semblance of such a human enterprise seems to be the LHC currently coming online at CERN. Can it be used as a model of international collaboration rather than a sports or military event focused on national competition? Who decides and what is the human sacrifice? There are compelling arguments for establishing science on the Moon as one of the primary goals for returning to the Moon and venturing beyond. A number of science endeavors will be summarized, beyond lunar and planetary science per se. These include fundamental physics experiments that are background-limited by the Earth's magnetic dipole moment and noise produced by its atmosphere and seismic interior. The Moon is an excellent platform for some forms of astronomy. Other candidate Moon-based experiments vary from neutrino and gravitational wave astronomy, particle astrophysics, and cosmic-ray calorimeters, to space physics and fundamental physics such as proton decay. The list goes on and includes placing humans in a hostile environment to study the long-term effects of space weather. The list is long, and even newer ideas will come from this COSPAR conference. However, whatever the list the issue of cooperation and binding collaboration remains. As observers of Moon and other space enterprises, we all know that a room full of 60 scientists will not agree on much of anything and there will probably be 60! please for more funding. People have special interests and little common sense (e.g., conflict between NSF- and NASA-funding roadmaps). Scientists are no exception. Nevertheless, CERN has done it on Earth! Can we do the same on the Moon? Some of the present generation of proposals for science from and on the Moon, plus new ones, will witness a place in space exploration's future. It is clear, however, that the world has not thought this through adequately, except for talk about an international space federation whatever that is. An outpost on the Moon with humans permanently living there much like Antarctica on Earth may be in our future. However, such planning is our collective international responsibility and not that of special-interest investigators from individual nations unless they intend to pay for it.

Wilson, Thomas↗

Backward-Angle Electroproduction of η′ Mesons off Protons at W = 2.13 GeV and Q 2 = 0.46 (GeV/ c ) 2

The electroproduction of $\eta ^{\prime }$ mesons from a $\mathrm{^{1}H}$ target at $W=\mathrm{2.13~GeV}$, $Q^{2} = 0.46~\left( \mathrm{GeV/}c\right)^{2}$, and $\cos \theta ^{\mathrm{CM}}_{\gamma ^{*}\eta ^{\prime }} \approx -1$ has been experimentally measured. The differential cross section of virtual photoproduction has been obtained as $4.4 \pm 0.8 ~\left( \mathrm{stat.} \right) \pm 0.4 ~\left( \mathrm{sys.} \right)~ \mathrm{nb/sr}$ in the One-Photon-Exchange Approximation. This value is one-sixth of that of real photoproduction at backward angles. A comparison with newly developed isobar model calculations not only shows the validity of the theoretical framewark employed, but also imposes new constraints on coupling strength between the $\eta ^{\prime }p$ final state and nucleon resonances.

Nuclear Physics↗

Syntheses and characterization of isotopically labeled 1,3,5-triamino-2,4,6-trinitrobenzene (TATB)

Synthesis and characterization of chemical analogues of TATB, where specific atoms in the structure have been isotopically substituted, are reported. 15 N, 2 H, and 18 O have replaced the naturally occurring isotope distributions in the amino and/or the nitro attendant sites and 13 C has replaced the carbon in the ring structure. A modified wet-amination method was used to produce the analogues, and the isotopic replacements were performed by selective choice of labeled precursors. Four 15 N-labeled compounds (N replaced in the amino and nitro positions), two deuterium-labeled compounds (hydrogens replaced on the amino groups), and one 13 C-labeled compound (C in the ring substituted) were synthesized of high isotopic and chemical purity. One partially labeled 18 O-labeled compound (O in the nitro position) was a result of incomplete labeling due to exchange reactions during synthesis. The compounds were characterized by various spectroscopic methods – mass spectrometry (MS), solid-state nuclear magnetic resonance (SS-NMR), infrared (FTIR), powder x-ray diffraction (PXRD), and differential scanning calorimetry (DSC), depending upon the substitution. In conclusion, these compounds have been critical to the efforts in understanding the decomposition pathways of TATB when exposed to abnormal thermal environments.

36 MATERIALS SCIENCE↗

High fidelity simulations of contaminant dispersion in an urban environment with comparison to magnetic resonance imaging measurements

The dispersion of a contaminant in an urban environment has the potential to impact a large population of people. In this work, a complex urban canopy flow based on the Oklahoma City downtown business district circa 2003 is studied using Magnetic Resonance Imaging (MRI) and high-fidelity Large Eddy Simulations (LES). MRI is a novel experimental technique that can provide high-resolution measurements in four dimensions (three spatial and temporal) for lab scale models. The experiments and simulations use the same geometry and boundary conditions providing a one-to-one comparison of the two methods. Results are presented on the time-averaged velocity and concentration fields, the temporal dynamics of the concentration plumes for a transient release, and a novel Cloud Identification Algorithm that can separate plumes produced by periodic contaminant releases used for ensemble averaging over many releases. The MRI and LES datasets both include millions of measurement voxels and the comparisons highlight the complex 3D nature of the flow including strong vertical velocities in spanwise street canyons and flow acceleration in streamwise street canyons. The concentration fields are qualitatively similar albeit the LES shows larger dispersion. A quantitative analysis with performance measures compares the datasets pointwise and demonstrates that the two 3D datasets are similar with respect to many measures including a fractional bias of 0.02 (ideal=0.0), correlation coefficient of 0.87 (ideal = 1.0), and the fraction points within a factor of 2 is 0.98 (ideal = 1.0). Plume analysis compares the arrival and residence time of contaminant and is found to vary significantly with location within the urban environment with arrival times between 0 and 1.25 and differences within the contaminant cloud less than 10% at most locations.

54 ENVIRONMENTAL SCIENCES↗

Targeted metagenomic assessment reflects critical colonization in battlefield injuries

Current diagnostics and clinical management strategies for combat wounds are based on decisions made by expert clinicians. However, even in the hands of experienced surgeons, wounds from combat injuries can exhibit failed healing and complications related to limitations in the rapid and comprehensive generation of diagnostic information. Previous studies have demonstrated the possible use of genomic sequencing approaches to detect microbial signatures involved in combat casualty care. While effective, whole metagenome sequencing is limited by the depth required to confidently detect all relevant signatures. To address this, we developed a targeted capture sequencing panel to detect microbial signatures relevant to wound healing. These targets include known microbial nosocomial pathogens, wound colonizers, and genes involved in virulence and antimicrobial resistance. A bioinformatics pipeline was built to identify genomic regions of interest and over 8,000 oligonucleotide probes were designed for capture. The panel was synthesized and validated using control reference genomes in human background and on wound-effluent samples from a cohort of combat-injured U.S. service members. Our panel was sensitive against wound-colonizing species, Acinetobacter baumannii and Pseudomonas aeruginosa, and was specific in detecting corresponding virulence and antimicrobial-resistance genes as well as other pathogenic species present in microflora mixtures. Random forest feature permutation confirmed the prevalence of Acinetobacter and Pseudomonas in critically colonized wounds and wounds that failed to heal, respectively. Our results demonstrate the capability of targeted sequencing tools and analysis platforms to profile and deliver information on pathogenic factors influencing wound progression, thereby guiding therapeutic intervention.

59 BASIC BIOLOGICAL SCIENCES↗

Biodefense Knowledge Management System

After the Amerithrax attacks, the Department of Homeland Security (DHS) recognized the need to link technical scientific information with law enforcement and national security information in the fight against bioterrorism. The Biodefense Knowledge Center (BKC) was formed to provide timely analysis of technical biodefense-related topics to support DHS and its customers in the interagency. The Biodefense Knowledge Management System (BKMS) was created as the backbone for information management within the BKC. It is a scalable, web-based knowledge management system for organizing disparate data sources. By combining information from 35+ data sources, the BKMS provides a searchable repository for technical information including scientific reports, journal articles, news articles, research funding databases, patent databases, and genomic datasets. The current system contains over 58 million documents and 450 million genomic records, and operates at several classification levels.

45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF↗

National Geographic Interview -- Pit Manufacturing

Los Alamos has been contacted by a freelance reporter working on assignment for National Geographic, Sarah Scoles. Scoles is working on a story about plutonium pit production. She says the story will be an explainer -- detailing the pit production process from start to finish, in context with the planned increase in production. Scoles is seeking to interview a LANL expert or experts to help explain the process, the Lab's history in pit production, and future role.

36 MATERIALS SCIENCE↗

In vitro evolution-enabled selection of affinity reagents against bio/chem-threats [Slides]

Affinity reagent are molecules whose function depends on specific recognition of a target. The function can allow therapeutic and/or diagnostic applications. The support CBDP pillars are--Understand: high accuracy/sensitivity, low cost, deployable detection; Protect: pre-event treatment of soldiers; and Mitigate: post-event treatment of soldiers; help identifying the need for specific decontamination protocols. The Los Alamos affinity reagents team (LA-ART) can can obtain affinity reagents to any target, on demand, using a well-established in vitro evolution platform. Recent success stories are shared.

45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF↗

All-Atom Simulation of 3D Hot Spot Formation in Shocked TATB Explosive

TATB is an insensitive high explosive (IHE) critical to the stockpile that is challenging to model at the continuum scale. Advanced detonation models in the Cheetah high explosive chemistry code require validation though subscale simulations. High explosive initiation is determined by micron-scale physics of hot spots formed a shock-collapsed pores. Pore sizes between 100 nm and 1 μm are believed to be the most important for determining the shock sensitivity of TATB. This range of pore sizes is difficult to access at the atomic scale through allatom molecular dynamics (MD) simulations, even with Sierra-class computers. Quasi-2D simulations are widely used and allow much larger pore sizes (up to 400 nm) to be studied, but the applicability of 2D simulations to the actual 3D pore response is not understood. Resolving these uncertainties through “full physics” MD modeling is key for generalizing, parameterizing, and validating the kinds of continuum models used to inform design, safety, and performance. This work was a continuation of FY20 efforts pushing simulations to full 3D with the largest-ever all-atom simulations of an explosive. These were the first all-atom full-3D simulations of large hot spots thought to govern explosive detonation and required over a billion atoms. Simulations were performed using LAMMPS, an open SNL science code. MD explosive models present unique challenges, even for established codes such as LAMMPS. Their model forms are more complex than typical models for metals, while simulating high temperature-pressure conditions is demanding and increases computational cost. Scaling problems in GPU-enabled MD algorithms initially limited simulations to <100 million atoms but were resolved through collaboration with SNL. An overall 24x speedup was obtained relative to CPU machines. Specialized analysis of these simulations required a bottom-up refactoring and algorithm parallelization of in-house codes and application of computer vision algorithms to extract meaningful information.

36 MATERIALS SCIENCE↗

The Future Impact of Much Lower Launch Cost

For decades, the high cost of space launch has been the greatest limiting factor on the nu ber and size of space missions. Recently commercial rockets have reduced launch cost to about one-twentieth of the space shuttle cost. This provides opportunities for a matching reduction in the cost of space systems and more and more massive missions. High launch costs greatly increase the cost of developing space systems, since the need to reduce mass forces the use of light materials, high packaging densities, and fragile structures that are difficult to manufacture and test. Lower launch costs allow the use of more robust and well tested off-the-shelf systems. Increased mass can be used to increase single string reliability and also to provide spares and redundancy. A crewed mission can benefit from lower launch costs by using mass to provide more accepted fully hydrated food, additional hygiene water, laundry, radiation shielding, and even artificial gravity. The crew can be made healthier, safer, more comfortable, and more productive. Lower launch cost makes every space activity easier, whether it is science, human exploration, commercial including communications, weather, surveillance, and geo-positioning services, or the defense of similar military services. Most of the solar system is empty space, with the energy of the sun’s radiation passing through to the cold of deep space. The missing mass needed to support human activities is now much easier to provide.

Jones, Harry W.↗

Physical Sciences Vistas (Issue 3 2020)

In this issue, highlights of our outstanding R&D supporting the Laboratory’s nuclear security mission include the following. 1. The essential nuclear materials science contributions of MST’s Materials Properties Team to a range of Lab missions, operations, and initiatives. 2. Work in the Sigma Complex supporting NNSA’s Advanced Manufacturing Development milestones by members of Sigma Division and colleagues across the Laboratory and other NNSA sites. 3. Greg Dale’s role in the Lab’s molybdenum program and today as a technical lead on the Scorpius project. 4. Measurements that reveal the role thermal interfaces play in dynamic compression experiments. 5. The first-ever synthesis of an actinide framework, which offers opportunities for understanding these structures as potential radioactive waste forms and provides new models of actinide species transport in the environment. This issue also showcases, as part of our commitment to simultaneous excellence in mission operations and community relations, the successful high-hazard repair of the LANSCE accelerator, which resulted in a large team Laboratory Distinguished Performance Award, and a virtual Summer Physics Camp for Young Women that brought together participants from around the world, even as COVID kept them socially distant in their homes.

36 MATERIALS SCIENCE↗

Completion document for MRT 8824 - Upgrade NIF’s gaseous radiochemistry diagnostics (RAGS) to support weapons science

This milestone highlights the successful upgrade and deployment of the Radiochemical Analysis of Gaseous Samples (RAGS) system, which delivers high-quality measurements (<20% uncertainty) of activated gaseous species from NIF implosions. These measurements are critical for supporting Stockpile Stewardship Program (SSP) relevant platforms, including LANL’s Double Shell and LLNL’s Pushered Single Shell campaigns. The RAGS diagnostic technique enables analysis of short-range mixing in implosions using high-Z shells, which are otherwise inaccessible to conventional x-ray diagnostic methods. By facilitating the investigation of high-Z material mixing into fusion burn, this system provides essential data for quantifying and interpreting results in high-energy density (HED) experiments. This report details the physics motivation, diagnostic fundamentals, planned and enacted upgrade work, and the quantification of uncertainty for the upgraded system.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗

The Electromagnetic Compatibility (EMC) Design Challenge for Scientific Spacecraft Powered by a Stirling Power Converter

A 55 We free-piston Stirling Technology Demonstration Convertor (TDC) has been tested as part of an evaluation to determine its feasibility as a means for significantly reducing the amount of radioactive material required compared to Radioisotope Thermoelectric Generators (RTGs) to support long-term space science missions. Measurements were made to quantify the low frequency magnetic and electric fields radiated from the Stirling's 80 Hertz (Hz) linear alternator and control electronics in order to determine the magnitude of reduction that will be required to protect sensitive field sensors aboard some science missions. One identified "Solar Probe" mission requires a 100 dB reduction in the low frequency magnetic field over typical military standard design limits, to protect its plasma wave sensor. This paper discusses the electromagnetic interference (EMI) control options relative to the physical design impacts for this power system, composed of 3 basic electrical elements. They are (1) the Stirling Power Convertor with its linear alternator, (2) the power switching and control electronics to convert the 90 V, 80 Hz alternator output to DC for the use of the spacecraft, and (3) the interconnecting wiring including any instrumentation to monitor and control items 1 and 2.

Sargent, Noel B.↗