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DOE OSTI2024

Medium-density amorphous ice unveils shear rate as a new dimension in water’s phase diagram

Recent experiments revealed a new amorphous ice phase, medium-density amorphous ice (MDA), formed by ball-milling ice I h at 77 K [Rosu-Finsen et al., Science 379, 474–478 (2023)]. MDA has density between that of low-density amorphous (LDA) and high-density amorphous (HDA) ices, adding to the complexity of water’s phase diagram, known for its glass polyamorphism and two-state thermodynamics. The nature of MDA and its relation to other amorphous ices and liquid water remain unsolved. Here, we use molecular simulations under controlled pressure and shear rate at 77 K to produce and investigate MDA. Here. we find that MDA formed at constant shear rate is a steady-state nonequilibrium shear-driven amorphous ice (SDA), that can be produced by shearing ice I h , LDA, or HDA. Our results suggest that MDA could be obtained by ball-milling water glasses without crystallization interference. Increasing the shear rate at ambient pressure produces SDAs with densities ranging from LDA to HDA, revealing shear rate as a new thermodynamic variable in the nonequilibrium phase diagram of water. Indeed, shearing provides access to amorphous states inaccessible by controlling pressure and temperature alone. SDAs produced with shearing rates as high as 10 6 s −1 sample the same region of the potential energy landscape than hyperquenched glasses with identical density, pressure, and temperature. Intriguingly, SDAs obtained by shearing at ~10 8 s −1 have density, enthalpy, and structure indistinguishable from those of water “instantaneously” quenched from room temperature to 77 K over 10 ps, making them good approximants for the “true glass” of ambient liquid water.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

DART-PFLOTRAN: An ensemble-based data assimilation system for estimating subsurface flow and transport model parameters

Ensemble-based Data Assimilation (EDA), based on the Monte Carlo approach, has been effectively applied to estimate model parameters through inverse modeling in subsurface flow and transport problems. However, implementation of EDA approach involves a complicated workflow that include setting up and executing ensemble forward model simulations, processing observations and model simulation results for parameter updates, and repeat for sequential or iterative EDA. To facilitate the management of such workflow and lower the barriers for adopting EDA-based parameter estimation in subsurface science, we develop a generic software frame-work linking the Data Assimilation Research Testbed (DART) with a massively parallel subsurface FLOw and TRANsport code PFLOTRAN. The new DART-PFLOTRAN leverages both the core data assimilation engines in DART and the computational power afforded by PFLOTRAN. In addition to the standard smoother and filtering options, DART-PFLOTRAN enables an iterative EDA workflow based on the Ensemble Smoother for Multiple Data Assimilation method (ES-MDA) to improve estimation accuracy for nonlinear forward problems. Here, we verify the implementation of ES-MDA in DART-PFLOTRAN using two synthetic cases designed to estimate static permeability and dynamic exchange fluxes across the riverbed, respectively, from continuous temperature measurements made across a depth profile. One-dimensional hydro-thermal simulations are performed in both cases to relate temperature responses with the parameters of interest. In the case of estimating dynamic parameters, we demonstrate the flexibility of DART-PFLOTRAN in automating sequential ES-MDA workflow, which will significantly reduce the time researchers spend on managing complex workflows in similar applications. Both studies yield accurate estimations of the parameters compared to their synthetic truth, while ES-MDA leads to more accurate estimation when a high level of nonlinearity exist between observed responses and unknown parameters. With a code base in Python and Fortran, DART-PFLOTRAN paves the way for applications in large-scale subsurface inverse modeling by automating the complex workflow of sequential ES-MDA that can be executed on various computing platforms.

97 MATHEMATICS AND COMPUTING↗

NASA NTRS2011

Assembly of 5.5-Meter Diameter Developmental Barrel Segments for the Ares I Upper Stage

Full scale assembly welding of Ares I Upper Stage 5.5-Meter diameter cryogenic tank barrel segments has been performed at the Marshall Space Flight Center (MSFC). One full-scale developmental article produced under the Ares 1 Upper Stage project is the Manufacturing Demonstration Article (MDA) Barrel. This presentation will focus on the welded assembly of this barrel section, and associated lessons learned. Among the MDA articles planned on the Ares 1 Program, the Barrel was the first to be completed, primarily because the process of manufacture from piece parts (barrel panels) utilized the most mature friction stir process planned for use on the Ares US program: Conventional fixed pin Friction Stir Welding (FSW). This process is in use on other space launch systems, including the Shuttle s External Tank, the Delta IV common booster core, the Delta II, and the Atlas V rockets. The goals for the MDA Barrel development were several fold: 1) to prove out Marshall Space Flight Center s new Vertical Weld Tool for use in manufacture of cylindrical barrel sections, 2) to serve as a first run for weld qualification to a new weld specification, and 3) to provide a full size cylindrical section for downstream use in precision cleaning and Spray-on Foam Insulation development. The progression leading into the welding of the full size barrel included sub scale panel welding, subscale cylinder welding, a full length confidence weld, and finally, the 3 seamed MDA barrel processing. Lessons learned on this MDA program have been carried forward into the production tooling for the Ares 1 US Program, and in the use of the MSFC VWT in processing other large scale hardware, including two 8.4 meter diameter Shuttle External Tank barrel sections that are currently being used in structural analysis to validate shell buckling models.

Carter, Robert W.↗

NASA NTRS2017

Biosensor Integration Development ExMC/Canadian Space Agency Collaboration

In support of the NASA Human Research Program Exploration Medical Capability (ExMC) Element, NASA Ames Research Center (ARC) established a collaborative effort with the Canadian Space Agency (CSA). The collaboration focuses on leveraging CSA capability in the areas of biosensors and decision support that will augment future development of such components for Exploration Missions. The CSA advancement of biosensors enables NASA to focus on the integration and data management associated with these types of components through the system currently under development by the Medical Data Architecture (MDA) project. This approach has enabled the establishment of a successful collaborative working relationship between ExMC and CSA.Applying lessons learned from the fiscal year 2016 (FY16) Human Exploration Research Analog (HERA) campaign, CSA and NASA ARC developed a solution to provide real-time feedback to researchers who monitor the collection of vital signs data from a wearable Astroskin garment. The advances in the interfaces included the development of an iPad application (by CSA) to wirelessly forward the vital signs data to the MDA system, which collected the vital signs data through a receiver developed by NASA ARC. The development of these interfaces aims to provide communications between the Astroskin and the MDA system such that data may be seamlessly collected, stored and retrieved by the MDA. The first steps towards this goal were demonstrated in FY16. In FY17, ExMC will complete the first in a series of test beds that establishes a system to automate collection and management of vital sign data from the Astroskin, and other sources of data, to provide information for a crewmember to make medical decisions. In addition, the MDA Test Bed 1 will enable CSA to evaluate and optimize biosensor advancement and facilitate decision support algorithm development.

Vital signs↗

NASA NTRS2017

Biosensor Integration Development ExMC/Canadian Space Agency Collaboration

Astroskin↗

NASA NTRS2020

Medical Data Architecture Prototype Development - Summary of Recent Work and Proposed Ideas for Upcoming Work

The Medical Data Architecture (MDA) project supports the Exploration Medical Capability (ExMC) risk to minimize or reduce the risk of adverse health outcomes and decrements in performance due to in-flight medical capabilities on human exploration missions. To mitigate this risk, the ExMC MDA project addresses the technical limitations identified in ExMC Gap Med 07: We do not have the capability to comprehensively process medically-relevant information to support medical operations during exploration missions, and in ExMC Gap Med 10: We do not have the capability to provide computed medical decision support during exploration missions. These gaps recognize the need for a comprehensive medical data management system and the accompanying computational support to provide autonomous medical care during long duration exploration missions. As the MDA matures—including the capability to comprehensively process and discover medically-relevant information to support medical operations during exploration missions—project focus will shift to maturing and extending the MDA platform to enable clinical decision support and real-time guidance. To date, the MDA foundational architecture has recommended exploration medical system Level of Care IV requirements through a series of test bed prototype developments and analog demonstrations. The next stage in the development will focus on more autonomous clinical decision making necessary to address challenges in executing a self-contained medical system that enables health care both with and without assistance from ground support. A thorough understanding of current state of medical decision support systems, advanced machine learning algorithms and vast and varied data sources is required. The development of a clinical decision support for exploration missions (Level of Care V) roadmap is needed: one that assesses of current state of the art of clinical decision support systems (CDSS), interoperability issues, identification of challenges in health and performance monitoring, obtaining and processing information from biosensors, knowledge and data management, data integration and fusion, and advanced algorithm development. This roadmap must also include rapid prototype development in the areas of data processing, advanced analysis and prediction of medical events, and treatment based on medically relevant information processing and evidence-based best practices. In this presentation, an overview of the relevant issues and the beginning framework of a Level of Care V CDSS development roadmap will be provided.

Krihak, M.↗

NASA NTRS2022

Advanced Lightweight Metallic Fuselage Project Manufacturing Trade Study

Recent advances in large-scale flow forming of integrally stiffened cylinders (ISCs) have motivated evaluation of available technologies for rapid manufacturing of metallic fuselages. The current state-of-the-art in flow forming of ISCs produces 10-ft. diameter, 5-ft. long barrels with integral longitudinal blade stiffeners, and these single-piece ISCs are produced in approximately 1.5 hours. While other manufacturing processes are required to incorporate additional structural elements (ASE) such as circumferential ring frames, reinforcements around window and door cut-outs, and floors to the ISCs to complete the fuselage structure, flow forming technology may assist the aerospace industry in meeting manufacturing rate demands. In order to evaluate this technology, a fuselage manufacturing demonstration article (MDA) fabricated from two ISCs is scheduled for fabrication and delivery to NASA Langley Research Center (LaRC) by the end of 2022. In this study, eight manufacturing technologies were assessed to downselect candidate manufacturing processes for adding ASE to complete the MDA. A literature review and evaluation of contractor-produced panels covering a spectrum of welding and additive manufacturing (AM) processes were conducted at NASA LaRC. The analytical hierarchy process (AHP) was used to evaluate figures of merit (FOMs) for selecting manufacturing process(es) to integrate ASE with the ISCs to form a fuselage MDA. The AHP results revealed that scalability, structural performance, and distortion control were the most valued criteria for downselecting the manufacturing process to construct the internal stiffening structures. Based on the FOMs, this study concluded that a welding process is best suited for integrating the majority of the ASE, namely the circumferential ring frames. All of the welding processes received higher scores than AM processes due to higher maturity, higher structural performance, fewer post-processing requirements in machining and heat treating, and faster deposition rates. Among the welding processes, cold metal transfer (CMT) welding was ranked the most favorable process for assembling the MDA, with the other welding processes (laser welding (LW), friction stir welding (FSW), and refill friction stir spot welding (RFSSW)) scoring slightly lower. This was a consequence of the perceived maturity of the CMT welding process and its relatively high structural performance and low distortion resulting from the low heat input. Among the AM processes, CMT AM showed the greatest promise due to benefits derived from its scalability, lower 1st order process complexity, and low distortion. The AM processes may have potential for select applications, such as adding structural reinforcements around window and door cut-outs, but are not considered optimal for integrating the entire MDA.

Manufacturing↗

DOE OSTI2020

A critical literature review of the advances in methane dehydroaromatization over multifunctional metal-promoted zeolite catalysts

We report the drastic rise in shale gas production has encouraged the quest for alternative uses of methane as a chemical feedstock in the manufacturing industry. While two-step syngas routes for methane valorization are deployed commercially, direct one-step routes for methane conversion are attracting much attention. As steam cracking installations have shifted from using oil-based naphtha to shale-based natural gas liquids, production of aromatics has dropped. Methane dehydroaromatization (MDA) is a one-step reaction capable of valorizing methane to hydrogen and benzene. Challenges with the MDA reaction are two-fold: the reaction is thermodynamically limited with low one-pass methane conversion and even the best catalytic systems, Mo/zeolites, suffer rapid deactivation from coking. A catalyst design strategy to improve stability is the use of multifunctional Mo-X/zeolite systems where X is a dopant capable of modulating the stability. In this paper we provide a complete overview of the main Mo-X/zeolite systems used in MDA and critically draw connections among the different types of dopants (X) employed, as a function of the role they play in the reaction/deactivation pathway. We have also dedicated a section to emerging trends with non-Mo based catalysts. The goal of this review article is to establish a basis that will facilitate the identification of useful multifunctional catalytic systems, and recognize gaps in the knowledge of these systems that deserve more attention. Improving MDA systems to the point to which they can be commercially deployed requires a multifaceted approach that combines optimization of the designs of both the catalyst and the reactor configuration. We therefore also provide a brief overview of the most recent advances in process intensification strategies employed with different reactor configurations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRS1983

Mutagenic screening of diamine monomers

The effects of phenyl ring coupling moieties, of isomeric amine positions relative to the coupling groups, and of insertion of other coupling groups on the mutagenic response of a series of dianilines were investigated using the Ames Salmonella assay. Generally, S-9 metabolic activation from Aroclor-induced rat liver was required for mutagenic expression. The range of mutagenicity of steric isomers of several dianiline series was also investigated. No mutagenicity was found for purified samples of o,o' and m,p' isomers of methylene dianiline (MDA) and diaminobenzophenone, while varying degrees of mutagenicity were found for other isomers. The mutagenicity of "benzylogs" of MDA decreased as the degree of linear separation of the m,m' anilino groups by aromatic rings increased. Methylation and two-year storage increased mutagenic response in certain isomers of MDA. However, high performance liquid chromatography indicated there was no discernible change in m,p'-MDA samples aged under varied conditions over four months. Likewise, no change in mutagenicity was found.

Ross, W. D.↗

DOE OSTI2022

Silica-encapsulated Fe 2 O 3 oxygen carriers for selective chemical looping combustion of hydrogen

Methane dehydroaromatization (MDA) combined with chemical looping (CL) combustion of hydrogen can overcome the MDA thermodynamic constraints conventionally limiting conversion. Development of selective hydrogen-oxidation oxygen carriers in the presence of aromatics in the CL is key to improve MDA performance in the coupled reaction system. Here, in this paper, we show that a novel oxygen carrier (silica-encapsulated Fe 2 O 3 with Fe/Si mole ratio of 1.2) yields high overall methane conversion (49%) and aromatics yield (up to 36%) during 4 h of recirculating a stream in the developed system. A silica layer encapsulating Fe 2 O 3 favors hydrogen transport and oxidation, preventing aromatics diffusing to the Fe 2 O 3 surface. A close physical contact between iron oxide particles and silica, and near complete encapsulation of the particles by the silica layer can facilitate hydrogen conversion without full depletion of iron oxides by forming iron silicates. The silica-encapsulated iron oxide particles can be reoxidized in air after depletion of its oxidative capacity.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Elucidating the role of $\mathrm{Fe}$-$\mathrm{Mo}$ interactions in the metal oxide precursors for Fe promoted $\mathrm{Mo/ZSM}$-5 catalysts in non-oxidative methane dehydroaromatization

Literature shows that adding Fe as a separate phase to MoO 3 /ZSM-5 catalysts can improve benzene selectivity in methane dehydroaromatization (MDA), but only when added in small quantities, making it difficult to characterize the state of Fe in the catalyst and understand the role of Fe-Mo interactions on the catalytic properties. We explore how the nature of the Mo-Fe interactions in the catalyst precursor can influence the stability and product selectivity in MDA, by employing for the first time Fe 2 (MoO 4 ) 3 /ZSM-5 as a catalyst precursor in MDA. We have compared the activity of Fe 2 (MoO 4 ) 3 /ZSM-5 with monometallic MoO 3 /ZSM-5 and mixed MoO 3 + Fe 2 O 3 /ZSM-5 containing equivalent Mo and Fe loadings and found that Fe 2 (MoO 4 ) 3 /ZSM-5 shows higher benzene selectivity than the mixed MoO 3 + Fe 2 O 3 /ZSM-5 catalyst and exhibits higher stability in reaction compared to the monometallic MoO3/ZSM-5 catalyst. Structural characterization suggests that Fe 2 (MoO 4 ) 3 partially segregates to Fe 2 O 3 and amorphous MoO x during thermal pretreatment. The MoO x species migrate into the zeolite channels during pretreatment, while Fe oxides remain on the external surface of the zeolite. Gas adsorption/desorption techniques and density functional theory calculations demonstrate that the preexisting Fe 2 O 3 phases on the external surface of the zeolite in the mixed MoO 3 + Fe 2 O 3 /ZSM-5 precursor trap (MoO 3 ) 3 clusters preventing them from migrating into the zeolite channels during pretreatment, whereas gradual formation of amorphous MoOx together with the segregation of the Fe 2 O 3 phase when using the Fe 2 (MoO 4 ) 3 precursor diminishes trapping of (MoO 3 ) 3 and consequently enhances migration and anchoring of the MoO x species in the zeolite channels, boosting selectivity to benzene. Characterization of used catalysts suggests that the presence of Fe promotes formation of structured carbon nanofibers which reduce the rate of catalyst deactivation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Effects of Molecular Size on Resolution in Charge Detection Mass Spectrometry

Instrumental resolution of Fourier transform-charge detection mass spectrometry instruments with electrostatic ion trap detection of individual ions depends on the precision with which ion energy is determined. Energy can be selected using ion optic filters or from harmonic amplitude ratios (HARs) that provide Fellgett’s advantage and eliminate the necessity of ion transmission loss to improve resolution. Unlike the ion energy-filtering method, the resolution of the HAR method increases with charge (improved S/N) and thus with mass. An analysis of the HAR method with current instrumentation indicates that higher resolution can be obtained with the HAR method than the best resolution demonstrated for instruments with energy-selective optics for ions in the low MDa range and above. However, this gain is typically unrealized because the resolution obtainable with molecular systems in this mass range is limited by sample heterogeneity. Here, this phenomenon is illustrated with both tobacco mosaic virus (0.6–2.7 MDa) and AAV9 (3.7–4.7 MDa) samples where mass spectral resolution is limited by the sample, including salt adducts, and not by instrument resolution. Nevertheless, the ratio of full to empty AAV9 capsids and the included genome mass can be accurately obtained in a few minutes from 1× PBS buffer solution and an elution buffer containing 300+ mM nonvolatile content despite extensive adduction and lower resolution. Empty and full capsids adduct similarly indicating that salts encrust the complexes during late stages of droplet evaporation and that mass shifts can be calibrated in order to obtain accurate analyte masses even from highly salty solutions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Experimental Assessment of Mammalian Lipidome Complexity Using Multimodal 21 T FTICR Mass Spectrometry Imaging

Herein, we assess the complementarity and complexity of data that can be detected within mammalian lipidome mass spectrometry imaging (MSI) via matrix-assisted laser desorption ionization (MALDI) and nanospray desorption electrospray ionization (nano-DESI). We do so by employing 21 T Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) with absorption mode FT processing in both cases, allowing unmatched mass resolving power per unit time (≥613k at m/z 760, 1.536 s transients). While our results demonstrated that molecular coverage and dynamic range capabilities were greater in MALDI analysis, nano-DESI provided superior mass error, and all annotations for both modes had sub-ppm error. Taken together, these experiments highlight the coverage of 1676 lipids and serve as a functional guide for expected lipidome complexity within nano-DESI-MSI and MALDI-MSI. To further assess the lipidome complexity, mass splits (i.e., the difference in mass between neighboring peaks) within single pixels were collated across all pixels from each respective MSI experiment. The spatial localization of these mass splits was powerful in informing whether the observed mass splits were biological or artificial (e.g., matrix related). Mass splits down to 2.4 mDa were observed (i.e., sodium adduct ambiguity) in each experiment, and both modalities highlighted comparable degrees of lipidome complexity. Further, we highlight the persistence of certain mass splits (e.g., 8.9 mDa; double bond ambiguity) independent of ionization biases. Here, we also evaluate the need for ultrahigh mass resolving power for mass splits ≤4.6 mDa (potassium adduct ambiguity) at m/z > 1000, which may only be resolved by advanced FTICR-MS instrumentation.

21T-FTICR-MS↗

DOE OSTI2024

Neutral rhenium( i ) tricarbonyl complexes with sulfur-donor ligands: anti-proliferative activity and cellular localization

Rhenium(I) tricarbonyl complexes are widely studied for their cell imaging properties and anti-cancer and anti-microbial activities, but the complexes with S-donor ligands remain relatively unexplored. A series of six fac-[Re(NN)(CO) 3 (SR)] complexes, where (NN) is 2,2'-bipyridyl (bipy) or 1,10-phenanthroline (phen), and RSH is a series of thiocarboxylic acid methyl esters, have been synthesized and characterized. Cellular uptake and anti-proliferative activities of these complexes in human breast cancer cell lines (MDA-MB-231 and MCF-7) were generally lower than those of the previously described fac-[Re(NN)(CO) 3 (OH 2 )]+ complexes; however, one of the complexes, fac-[Re(CO) 3 (phen)(SC(Ph)CH 2 C(O)OMe)] (3b), was active (IC 50 ~ 10 μM at 72 h treatment) in thiol-depleted MDA-MB-231 cells. Moreover, unlike fac-[Re(CO) 3 (phen)(OH 2 )]+, this complex did not lose activity in the presence of extracellular glutathione. Taken together these properties show promise for further development of 3b and its analogues as potential anti-cancer drugs for co-treatment with thiol-depleting agents. Conversely, the stable and non-toxic complex, fac-[Re(bipy)(CO) 3 (SC(Me)C(O)OMe)] (1a), predominantly localized in the lysosomes of MDA-MB-231 cells, as shown by live cell confocal microscopy (λ ex = 405 nm, λ em = 470–570 nm). It is strongly localized in a subset of lysosomes (25 μM Re, 4 h treatment), as shown by co-localization with a Lysotracker dye. Longer treatment times with 1a (25 μM Re for 48 h) resulted in partial migration of the probe into the mitochondria, as shown by co-localization with a Mitotracker dye. These properties make complex 1a an attractive target for further development as an organelle probe for multimodal imaging, including phosphorescence, carbonyl tag for vibrational spectroscopy, and Re tag for X-ray fluorescence microscopy.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Growth and passivation of individual carbon nanoparticles by C2H2 addition at high temperatures: Dependence of growth rate and evolution on material and size

Absolute kinetics for reactions of C2H2 with a series of ∼60 individual carbon nanoparticles (NPs) from graphite, graphene, graphene oxide, carbon black, diamond, and nano-onion feedstocks were measured for temperatures (TNP) ranging from 1200 to 1700 K. All the NPs were observed to gain mass by carbon addition under conditions that varied with feedstock but with large variations in initial growth rate. Long reaction periods were studied to allow the evolution of growth rates over time to be observed. Diamond NPs were found to passivate against C2H2 addition if heated above ∼1400 K, and the highly variable initial reactivity for carbon nano-onions was found to depend on the presence of non-onion-structure surface carbon. For graphitic and carbon black NPs, three distinct growth modes were observed, correlated with the initial NP mass (Minitial). Smallest graphitic and carbon black NPs, with masses <∼25 MDa, initially grew rapidly but also passivated quickly after adding <4% of Minitial. NPs in the 20–50 MDa range also passivated but only after multiple waves of fast growth separated by periods of low reactivity, with up to ∼11% total mass gain before passivation. The largest carbon black and graphitic NPs, with Minitial >50 MDa, grew rapidly and continuously, adding up to ∼300% of Minitial with no sign of rate slowing as long as C2H2 was present. The efficiencies for C2H2 addition and etching by O2 are strongly correlated, but the correlation changes as the NPs passivate. Growth and passivation mechanisms are discussed.

Chemistry↗

DOE OSTI2022

Selective Whole-Genome Amplification as a Tool to Enrich Specimens with Low Treponema pallidum Genomic DNA Copies for Whole-Genome Sequencing

Downstream next-generation sequencing (NGS) of the syphilis spirochete Treponema pallidum subspecies pallidum (T. pallidum) is hindered by low bacterial loads and the overwhelming presence of background metagenomic DNA in clinical specimens. In this study, we investigated selective whole-genome amplification (SWGA) utilizing multiple displacement amplification (MDA) in conjunction with custom oligonucleotides with an increased specificity for the T. pallidum genome and the capture and removal of 5'-C-phosphate-G-3' (CpG) methylated host DNA using the NEBNext Microbiome DNA enrichment kit followed by MDA with the REPLI-g single cell kit as enrichment methods to improve the yields of T. pallidum DNA in isolates and lesion specimens from syphilis patients. Sequencing was performed using the Illumina MiSeq v2 500 cycle or NovaSeq 6000 SP platform. These two enrichment methods led to 93 to 98% genome coverage at 5 reads/site in 5 clinical specimens from the United States and rabbit-propagated isolates, containing >14 T. pallidum genomic copies/μL of sample for SWGA and >129 genomic copies/μL for CpG methylation capture with MDA. Variant analysis using sequencing data derived from SWGA-enriched specimens showed that all 5 clinical strains had the A2058G mutation associated with azithromycin resistance. SWGA is a robust method that allows direct whole-genome sequencing (WGS) of specimens containing very low numbers of T. pallidum, which has been challenging until now.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Changes in trachoma indicators in Kiribati with two rounds of azithromycin mass drug administration, measured in serial population-based surveys

Baseline mapping in the two major population centers of Kiribati showed that trachoma was a public health problem in need of programmatic interventions. After conducting two annual rounds of antibiotic mass drug administration (MDA), Kiribati undertook trachoma impact surveys in 2019, using standardized two-stage cluster surveys in the evaluation units of Kiritimati Island and Tarawa. In Kiritimati, 516 households were visited and in Tarawa, 772 households were visited. Nearly all households had a drinking water source and access to an improved latrine. The prevalence of trachomatous trichiasis remained above the elimination threshold (0.2% in ≥15-year-olds) and was virtually unchanged from baseline. The prevalence of trachomatous inflammation—follicular (TF) in 1–9-year-olds decreased by approximately 40% from baseline in both evaluation units but remained above the 5% TF prevalence threshold for stopping MDA. TF prevalence at impact survey was 11.5% in Kiritimati and 17.9% in Tarawa. Infection prevalence in 1–9-year-olds by PCR was 0.96% in Kiritimati and 3.3% in Tarawa. Using a multiplex bead assay to measure antibodies to the C. trachomatis antigen Pgp3, seroprevalence in 1–9-year-olds was 30.2% in Kiritimati and 31.4% in Tarawa. The seroconversion rate, in seroconversion events/100 children/year, was 9.0 in Kiritimati and 9.2 in Tarawa. Seroprevalence and seroconversion rates were both assessed by four different assays, with strong agreement between tests. These results show that, despite decreases in indicators associated with infection at impact survey, trachoma remains a public health problem in Kiribati, and provide additional information about changes in serological indicators after MDA.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2026

Field and Model Data Associated with the Manuscript “Drivers of Streamflow Intermittency in Humid Regions: 1. Evaluating Above- and Below-ground Controls of Flow Persistence in a Forested Catchment”

This package contains field data, modeling files, and scripts supporting the investigation of the drivers of streamflow intermittency in a forested catchment. It includes the field data collected from electrical resistivity tomography (ERT) surveys, ground penetrating radar (GPR), continuous self-potential (SP) monitoring, electromagnetic (EM) imaging, groundwater and stilling well. In addition, it contains the data and results of the coupled water- and electrical-flow model developed using the COMSOL Multiphysics and Advanced Terrestrial Simulator (ATS), as well as software files and Jupyter notebooks used to process the data and generate figures in the manuscript submitted for peer review. The data archive is organized in the following directories: 1) Climate Includes hourly precipitation and daily evapotranspiration time series (2024 – 2025) provided as CSV files, alongside a text file detailing dataset units. 2) Coupled_model Contains two subfolders: Synthetic and Field_Application subfolder. Synthetic subfolder contains the ATS XML input script (can be opened using any code editor) for the four synthetic hydrological cases tested (Connected and gaining, Connected and losing, Disconnected and losing, and dry stream). It also includes other experimental cases to test the influence of precipitation and concentration gradient. For each synthetic case, the flow model simulation is executed using the ATS XML scripts and the included Python script (generate_data_set.py) to convert ATS output to COMSOL-ready input. COMSOL Multiphysics template (.mph can be opened with the commercial software COMSOL and requires a license) is executed using the ATS output data to simulate the potential field. It also includes the Synthetic_model_plot.ipynb (can be opened using any code editor) to visualize the SP result and generate manuscript figures. The data subfolder contains mesh files to run both the ATS (.exo and .stl files can be viewed using Paraview; .h5 files can be opened using HDFView software and h5py Python package) and COMSOL models. Field_Application subfolder contains two subfolders: ES_MDA_inversion and Final_Model. ES_MDA_inversion contains the Python script (.py can be opened using any code editor) and SP observation data used to run the Ensemble Smoother with Multiple Data Assimilation (ES-MDA) inversion sequence to get the optimal model parameters. The Final_model subfolder contains the ATS XML input scripts, data files, output data for the two SP sites. The same workflow steps outlined for the Synthetic subfolder apply here. It also contains the Jupyter notebook (Plot_final_calib.ipynb) to visualize the results of the modeled SP, stream-groundwater exchange and moisture content. 3) Discharge Includes the electrical conductivity (EC) time series (provided as CSV files) from salt slug injections. It also includes the Jupyter notebook (Discharge_process.ipynyb) used to estimate discharge. All discharge measurements collated into rating_curve_processed.csv 4) EM Contains the CSV file of the EM data from the DUALEM-42, including spatial coordinates (x, y, z), apparent conductivity, and in-phase measurements at 2 m coil separations for horizontal coplanar (HCP) and perpendicular (PRP) geometries. 5) ERT Contains raw resistivity data (provided as CSV files), spatial location of each of the electrodes (provided as CSV files), and files used for the resistivity inversion (.resipy can be opened with the open-source ResIPy software). 6) GPR Includes GPR field datasets collected at 100 MHz and 250 MHz antenna frequencies, along with the processing/interpretation project file (GPR_process.gpz can be viewed using EKKO_Project 6, a commercial software by Sensors & Software that requires a license). 7) Slug_test Includes the slug test data at all the groundwater wells provided as CSV files, as well as the Jupyter notebook (Slug_test.ipynb) for calculating hydraulic conductivity. 8) SP Contains the SP data collected in field at the two SP sites (one in the perennial reach and the other in the intermittent reach), provided as DAT files. 9) Well_data Contains two subfolders: 1) Raw, which provides unprocessed pressure, electrical conductivity and temperature timeseries downloaded from the loggers in all the groundwater and stilling wells, and 2) Processed, which contains sorted, QA/QC timeseries data for each well. The data archive also contains data_process.ipynb, a Jupyter notebook used for field data analysis and generating figures (plotting well, SP, climate, and discharge data, as well as calculating head gradient at sites with nested groundwater wells). It also includes DTW.ipynb, a Jupyter notebook containing the code for the dynamic time warping (DTW) with sliding window to evaluate SP signal synchronicity.

ATS↗