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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 901 records · Page 50
All sourcesNASA NTRSDOE OSTI
DOE OSTI2014

SU-E-J-221: Advantages of a New Surface Imaging Calibration Method for SRS Treatments

Purpose: The present calibration method used for the AlignRT surface imaging system relies on the placement of a calibration plate at the linac isocenter using isocenter surrogates (crosshairs, room lasers, etc.). This work investigated the potential advantages of a new calibration method that shifts the AlignRT isocenter to be coincident with the linac MV beam isocenter. Methods: To quantify the potential uncertainties associated with the present calibration method for SRS treatments, the calibration plate was intentionally shifted away from isocenter +/−3mm in the longitudinal and lateral directions and +/−1mm in the longitudinal, lateral, and vertical directions. A head phantom was placed in a mock SRS treatment position and monitored with the AlignRT system. The AlignRT-indicated offsets were recorded at 270, 315, 0, 45, and 90° couch angles for each intentional calibration misalignment. The new isocenter calibration was applied after each misalignment, and the measurements were repeated and compared to the previous results. Results: With intentional longitudinal and lateral shifts of +/−3mm and +/−1mm in the calibration plate, the average indicated offsets at couch rotations of +/−90° were 4.3mm and 1.6mm, respectively. This was in agreement with the theoretical offset of sqrt(2)*(intentional shift of the calibration plate). Since vertical shifts were along the rotation axis of the couch, these shifts had little effect on the offsets with changing couch angle. When the new calibration was applied, the indicated offsets were all within 0.5mm for all couch angles. These offsets were in agreement with the known magnitude of couch walkout. Conclusion: The potential pitfalls of the present calibration method have been established, and the advantages of the new calibration method have been demonstrated. This new calibration method effectively removes the potential miscalibration artifacts of the present calibration method, giving the AlignRT user more confidence in the system's indicated shifts.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2014

Poster — Thur Eve — 32: Stereotactic Body Radiation Therapy for Peripheral Lung Lesion: Treatment Planning and Quality Assurance

Stereotactic body radiation therapy (SBRT), due to its high precision for target localizing, has become widely used to treat tumours at various locations, including the lungs. Lung SBRT program was started at our institution a year ago. Eighteen patients with peripheral lesions up to 3 cm diameter have been treated with 48 Gy in 4 fractions. Based on four-dimensional computed tomography (4DCT) simulation, internal target volume (ITV) was delineated to encompass the respiratory motion of the lesion. A margin of 5 mm was then added to create the planning target volume (PTV) for setup uncertainties. There was no expansion from gross tumour volume (GTV) to clinical target volume (CTV). Pinnacle 9.6 was used as the primary treatment planning system. Volumetric modulated arc therapy (VMAT) technique, with one or two coplanar arcs, generally worked well. For quality assurance (QA), each plan was exported to Eclipse 10 and dose calculation was repeated. Dose volume histograms (DVHs) of the targets and organs at risk (OARs) were then compared between the two treatment planning systems. Winston-Lutz tests were carried out as routine machine QA. Patient-specific QA included ArcCheck measurement with an insert, where an ionization chamber was placed at the centre to measure dose at the isocenter. For the first several patients, and subsequently for the plans with extremely strong modulation, Gafchromic film dosimetry was also employed. For each patient, a mock setup was scheduled prior to treatments. Daily pre- and post-CBCT were acquired for setup and assessment of intra-fractional motion, respectively.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2014

Poster — Thur Eve — 71: A 4D Multimodal Lung Phantom for Regmentation Evaluation

Segmentation and registration of medical imaging data are two processes that can be integrated (a process termed regmentation) to iteratively reinforce each other, potentially improving efficiency and overall accuracy. A significant challenge is presented when attempting to validate the joint process particularly with regards to minimizing geometric uncertainties associated with the ground truth while maintaining anatomical realism. This work demonstrates a 4D MRI, PET, and CT compatible tissue phantom with a known ground truth for evaluating registration and segmentation accuracy. The phantom consists of a preserved swine lung connected to an air pump via a PVC tube for inflation. Mock tumors were constructed from sea sponges contained within two vacuum-sealed compartments with catheters running into each one for injection of radiotracer solution. The phantom was scanned using a GE Discovery-ST PET/CT scanner and a 0.23T Phillips MRI, and resulted in anatomically realistic images. A bifurcation tracking algorithm was implemented to provide a ground truth for evaluating registration accuracy. This algorithm was validated using known deformations of up to 7.8 cm using a separate CT scan of a human thorax. Using the known deformation vectors to compare against, 76 bifurcation points were selected. The tracking accuracy was found to have maximum mean errors of −0.94, 0.79 and −0.57 voxels in the left-right, anterior-posterior and inferior-superior directions, respectively. A pneumatic control system is under development to match the respiratory profile of the lungs to a breathing trace from an individual patient.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

SU-E-T-67: A Quality Assurance Procedure for VMAT Delivery Technique with Multiple Verification Metric Using TG-119 Protocol

Purpose: A successful VMAT plan delivery includes precise modulations of dose rate, gantry rotational and multi-leaf collimator shapes. The purpose of this research is to construct routine QA protocol which focuses on VMAT delivery technique and to obtain a baseline including dose error, fluence distribution and mechanical accuracy during VMAT. Methods: The mock prostate, head and neck (HN) cases supplied from AAPM were used in this study. A VMAT plans were generated in Monaco TPS according to TG-119 protocol. Plans were created using 6 MV and 10 MV photon beams for each case. The phantom based measurement, fluence measurement and log files analysis were performed. The dose measurement was performed using 0.6 cc ion chamber, which located at isocenter. The fluence distribution were acquired using the MapCHECK2 mounted in the MapPHAN. The trajectory log files recorded inner 20 leaf pairs and gantry angle positions at every 0.25 sec interval were exported to in-house software developed by MATLAB and determined those RMS values. Results: The dose difference is expressed as a ratio of the difference between measured and planned doses. The dose difference for 6 MV was 0.91%, for 10 MV was 0.67%. In turn, the fluence distribution using gamma criteria of 2%/2 mm with a 50% minimum dose threshold for 6 MV was 98.8%, for 10 MV was 97.5%, respectively. The RMS values of MLC for 6 MV and 10 MV were 0.32 mm and 0.37 mm, of gantry were 0.33 degree and 0.31 degree. Conclusion: In this study, QA protocol to assess VMAT delivery accuracy is constructed and results acquired in this study are used as a baseline of VMAT delivery performance verification.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

SU-E-T-127: Application of TG-119 for Evaluation of Proton Spot Scanning Based Planning and Treatment Delivery

Purpose: The clinical test cases presented in AAPM TG-119 are used to evaluate the accuracy of treatment planning and delivery through spot scanning proton beams. Methods: An IBA spot scanning delivery system has been commissioned to be used with the RayStation treatment planning system. Various test cases provided in TG-119 were used for planning and delivery verification. The CT dataset and structures as provided by TG-119 were imported into a mock patient. The plans were optimized using the multi field optimization (MFO) to achieve the desired goals. The planner was given the flexibility to achieve the given dose-volume goals by creating appropriate objectives and constraints. Beams were delivered to a phantom and measurements were performed at multiple depths using the MatrixxPT detector array. The analyses were performed on beam by beam basis and quantified using the gamma index. A tolerance of 3%/3 mm in 2D was used for gamma index analysis along with dose threshold of 10%. Results: The clinical goals for targets and critical structures were met or improved for all cases except the C-Shape target with difficult constraints. The minimum gamma index using the 3%/3mm as a criterion is 93.3% for one of the planes measured for C-Shape target. Using 2%/2mm as a criterion, the minimum gamma index drops to 70%. Only Prostate target has all the planes above >90% pass using the 2%/2mm criterion. Conclusion: The overall accuracy of the treatment planning and delivery is deemed clinically acceptable. The test cases with highly modulated beams can have steep gradients in the dose profiles that can reduce the gamma index pass rate. Gamma analysis based on 3D data may be needed for routine use of 2%/2mm criterion. In addition, improvements in modelling of spot profiles in dose engine may be required for further improving the gamma index pass rate.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

SU-F-T-218: Validation of An In-Vivo Proton Range Verification Method for Reducing the Risk of Permanent Alopecia in the Treatment of Pediatric Medulloblastoma

Purpose: The clinical commissioning of a workflow for pre-treatment range verification/adjustment for the head treatment of pediatric medulloblastoma patients, including dose monitoring during treatment. Methods: An array of Si-diodes (DIODES Incorporated) is placed on the patient skin on the opposite side to the beam entrance. A “scout” SOBP beam, with a longer beam range to cover the diodes in its plateau, is delivered; the measured signal is analyzed and the extracted water equivalent path lengths (WEPL) are compared to the expected values, revealing if a range correction is needed. Diodes stay in place during treatment to measure dose. The workflow was tested in solid water and head phantoms and validated against independent WEPL measurements. Both measured WEPL and skin doses were compared to computed values from the TPS (XiO); a Markus chamber was used for reference dose measurements. Results: The WEPL accuracy of the method was verified by comparing it with the dose extinction method. It resulted, for both solid water and head phantom, in the sub-millimeter range, with a deviation less than 1% to the value extracted from the TPS. The accuracy of dose measurements in the fall-off part of the dose profile was validated against the Markus chamber. The entire range verification workflow was successfully tested for the mock-treatment of head phantom with the standard delivery of 90 cGy per field per fraction. The WEPL measurement revealed no need for range correction. The dose measurements agreed to better than 4% with the prescription dose. The robustness of the method and workflow, including detector array, hardware set and software functions, was successfully stress-tested with multiple repetitions. Conclusion: The performance of the in-vivo range verification system and related workflow meet the clinical requirements in terms of the needed WEPL accuracy for pretreatment range verification with acceptable dose to the patient.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

MO-AB-BRA-08: A Modular Multi-Source X-Ray Tube for Novel Computed Tomography Applications

Purpose: To develop and build a practical implementation of an x-ray line source for the rapidly increasing number of multi-source imaging applications in CT. Methods: An innovative x-ray tube was designed using CST Particle Studio, ANSYS, and SolidWorks. A slowly varying magnetic field is synchronized with microsecond gating of multiple thermionic electron sources. Electrostatic simulations were run to optimize the geometry of the optics and prevent electrode arcing. Magnetostatic simulations were used for beam deflection studies and solenoid design. Particle beam trajectories were explored with an emphasis on focusing, acceleration, deflection, and space charge effects. Thermal constraints were analyzed for both transient and steady-state regimes. Electromagnetic simulations informed the design of a prototype unit under construction. Results: Particle tracking simulations for a benchtop system demonstrate that three 80 keV electron beams are able to be finely controlled and laterally swept a combined distance of 15 cm over a stationary target with an oscillating magnetic field in the hundreds of gauss. The beams are pulsed according to scanning sequences developed for implementation in a mock stationary CT scanner capable of a 30 ms temporal resolution. Beam spot diameters are approximately 1 mm for 30 mA beams and the stationary target stays well within thermal limits. The relevant hardware and control circuits were developed for incorporation into a physical prototype. Conclusion: A new multi-source x-ray tube was designed in a modular form factor to push the barriers of high-speed CT and spur growth in emerging imaging applications. This technology can be used as the basis for a stationary high-speed CT scanner, a system for generating a virtual fan-beam for dose reduction, or for reducing scatter radiation in cone-beam CT utilizing a tetrahedron beam CT geometry. A 2.4 kW benchtop system is currently being built to show proof of concept for the tube. Support for this research was provided by the University of Wisconsin Madison, Office of the Vice Chancellor for Research and Graduate Education with funding from the Wisconsin Alumni Research Foundation.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2019

Soil Aggregate Microbial Communities: Towards Understanding Microbiome Interactions at Biologically Relevant Scales

Soils contain a tangle of minerals, water, nutrients, gases, plant roots, decaying organic matter, and microorganisms which work together to cycle nutrients and support terrestrial plant growth. Most soil microorganisms live in periodically interconnected communities closely associated with soil aggregates, i.e., small (<2 mm), strongly bound clusters of minerals and organic carbon that persist through mechanical disruptions and wetting events. Their spatial structure is important for biogeochemical cycling, and we cannot reliably predict soil biological activities and variability by studying bulk soils alone. To fully understand the biogeochemical processes at work in soils, it is necessary to understand the micrometer-scale interactions that occur between soil particles and their microbial inhabitants. Here, we review the current state of knowledge regarding soil aggregate microbial communities and identify areas of opportunity to study soil ecosystems at a scale relevant to individual cells. We present a framework for understanding aggregate communities as “microbial villages” that are periodically connected through wetting events, allowing for the transfer of genetic material, metabolites, and viruses. Here, we describe both top-down (whole community) and bottom-up (reductionist) strategies for studying these communities. Understanding this requires combining “model system” approaches (e.g., developing mock community artificial aggregates), field observations of natural communities, and broader study of community interactions to include understudied community members, like viruses. Initial studies suggest that aggregate-based approaches are a critical next step for developing a predictive understanding of how geochemical and community interactions govern microbial community structure and nutrient cycling in soil.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

RB-TnSeq elucidates dicarboxylic-acid-specific catabolism in β-proteobacteria for improved plastic monomer upcycling

Dicarboxylic acids are key components of many polymers and plastics, making them a target for both engineered microbial degradation and sustainable bioproduction. In this study, we generated a comprehensive data set of functional evidence for the genetic basis of dicarboxylic and fatty acid metabolism using randomly barcoded transposon sequencing (RB-TnSeq). We identified four β-proteobacteria that displayed robust growth with dicarboxylic acid sole carbon source and cultured their mutant libraries with dicarboxylic and fatty acids with carbon chain lengths from C3 to C12. The resulting fitness data suggested that dicarboxylic and fatty acid metabolisms are largely distinct, and different sets of β-oxidation genes are required for catabolizing dicarboxylic versus fatty acids of the same carbon chain lengths. In addition, we identified transcriptional regulators and transporters with strong fitness phenotypes related to dicarboxylic acid utilization. In Ralstonia sp. UNC404CL21Col (R. CL21), we deleted two transcriptional repressors to improve its utilization of short-chain dicarboxylic acids. We exploited the diacid-utilizing catabolism of R. CL21 to upcycle a mock mixture of the dicarboxylic acids produced when polyethylene is oxidized. After introducing a heterologous indigoidine production pathway, this engineered Ralstonia produced 0.56 ± 0.02 g/L indigoidine from a mixture of dicarboxylic acids as a carbon source, demonstrating the potential of R. CL21 to upcycle plastic wastes to products derived from tricarboxylic acid (TCA) cycle intermediates. IMPORTANCE: Upcycling the carbon in plastic wastes to value-added products is a promising approach to address the plastic waste and climate crises, and dicarboxylic acid metabolism is an important facet of several approaches. Improving our understanding of the genetic basis of this metabolism has the potential to uncover new enzymes and genetic parts for engineered pathways involving dicarboxylic acids. Our data set is the most comprehensive interrogation of dicarboxylic acid catabolism to date, and this work will be of utility to researchers interested in both plastics bioproduction and upcycling applications.

Pearson, Allison N↗
DOE OSTI2025

Modeling of hepatitis B virus infection spread in primary human hepatocytes

ABSTRACT Chronic hepatitis B virus (HBV) infection poses a significant global health threat, causing severe liver diseases including cirrhosis and hepatocellular carcinoma. We characterized HBV DNA kinetics in primary human hepatocytes (PHHs) over 32 days post-inoculation (p.i.) and modified ourin-vivoagent-based modeling (ABM) to gain insights into the HBV lifecycle and spreadin vitro. Parallel PHH cultures were mock-treated or treated with HBV entry inhibitor Myr-preS1 (6.25 µg/mL) was initiated 24 h p.i. In untreated PHH, three viral DNA kinetic patterns were identified: (i) an initial decline, followed by (ii) rapid amplification and (iii) slower amplification/accumulation. In the presence of Myr-preS1, viral DNA and infected cell numbers in phase 3 were effectively blocked, with minimal to no increase. This suggests that phase 2 represents viral amplification in initially infected cells, while phase 3 corresponds to viral spread to naïve cells. The ABM reproduced well the HBV kinetic patterns observed and predicted that the viral eclipse phase lasts between 18 and 38 h. After the eclipse phase, the viral production rate increased over time, starting with a slow production cycle of 1 virion per day, which gradually accelerated to 1 virion per hour after 3 days. Approximately 4 days later, virion production reached a steady state production rate of 4 virions/h. The estimated median efficacy of Myr-preS1 in blocking HBV spread was 91% (range: 90–92%). The HBV kinetics and the predicted estimates of the HBV eclipse phase duration and HBV production cycles in PHH are similar to those predicted in uPA/SCID mice with human livers. IMPORTANCE While primary human hepatocytes (PHHs) are the most physiologically relevant culture system for studying HBV infectionin vitro, a comprehensive understanding of HBV infection kinetics and spread in PHH is lacking. In this study, we characterize HBV viral kinetics and modify ourin vivoagent-based modeling (ABM) to provide quantitative insights into the HBV production cycle and viral spread in PHH. The ABM provides an estimate of the HBV eclipse phase duration, HBV production cycles, and Myr-preS1 efficacy in blocking HBV spread in PHH. The results resemble those predicted in uPA/SCID mice with human livers, demonstrating that estimated HBV infection kinetic parameters in PHHin vitromirror those observed in thein vivoHBV infection chimeric mouse model.

Virology↗
DOE OSTI2014

Detecting Nitrous Oxide Reductase (nosZ) Genes in Soil Metagenomes: Method Development and Implications for the Nitrogen Cycle

Microbial activities in soils, such as (incomplete) denitrification, represent major sources of nitrous oxide (N 2 O), a potent greenhouse gas. The key enzyme for mitigating N 2 O emissions is NosZ, which catalyzes N 2 O reduction to N 2 . We recently described “atypical” functional NosZ proteins encoded by both denitrifiers and nondenitrifiers, which were missed in previous environmental surveys (R. A. Sanford et al., Proc. Natl. Acad. Sci. U. S. A. 109:19709–19714, 2012, doi:10.1073/pnas.1211238109). Here, we analyzed the abundance and diversity of both nosZ types in whole-genome shotgun metagenomes from sandy and silty loam agricultural soils that typify the U.S. Midwest corn belt. First, different search algorithms and parameters for detecting nosZ metagenomic reads were evaluated based on in silico-generated (mock) metagenomes. Using the derived cutoffs, 71 distinct alleles (95% amino acid identity level) encoding typical or atypical NosZ proteins were detected in both soil types. Remarkably, more than 70% of the total nosZ reads in both soils were classified as atypical, emphasizing that prior surveys underestimated nosZ abundance. Approximately 15% of the total nosZ reads were taxonomically related to Anaeromyxobacter, which was the most abundant genus encoding atypical NosZ-type proteins in both soil types. Further analyses revealed that atypical nosZ genes outnumbered typical nosZ genes in most publicly available soil metagenomes, underscoring their potential role in mediating N 2 O consumption in soils. Therefore, this study provides a bioinformatics strategy to reliably detect target genes in complex short-read metagenomes and suggests that the analysis of both typical and atypical nosZ sequences is required to understand and predict N 2 O flux in soils.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Inferring microbial co-occurrence networks from amplicon data: a systematic evaluation

Microbes commonly organize into communities consisting of hundreds of species involved in complex interactions with each other. 16S ribosomal RNA (16S rRNA) amplicon profiling provides snapshots that reveal the phylogenies and abundance profiles of these microbial communities. These snapshots, when collected from multiple samples, can reveal the co-occurrence of microbes, providing a glimpse into the network of associations in these communities. However, the inference of networks from 16S data involves numerous steps, each requiring specific tools and parameter choices. Moreover, the extent to which these steps affect the final network is still unclear. In this study, we perform a meticulous analysis of each step of a pipeline that can convert 16S sequencing data into a network of microbial associations. Through this process, we map how different choices of algorithms and parameters affect the co-occurrence network and identify the steps that contribute substantially to the variance. We further determine the tools and parameters that generate robust co-occurrence networks and develop consensus network algorithms based on benchmarks with mock and synthetic data sets. The Microbial Co-occurrence Network Explorer, or MiCoNE (available at https://github.com/segrelab/MiCoNE) follows these default tools and parameters and can help explore the outcome of these combinations of choices on the inferred networks. We envisage that this pipeline could be used for integrating multiple data sets and generating comparative analyses and consensus networks that can guide our understanding of microbial community assembly in different biomes.

16S rRNA↗
DOE OSTI2026

Unraveling TeV halos with the Cherenkov Telescope Array

Pulsars are observed to emit bright and spatially extended gamma-ray emission at multi-TeV energies. These so-called "TeV halos" are now understood to be a nearly universal feature of middle-aged pulsars. However, many of the key physical processes that govern these systems, particularly those affecting particle diffusion, remain poorly constrained. We aim to evaluate the ability of the Cherenkov Telescope Array (CTA) to probe the physical properties of TeV halos, with a focus on the nearby and well-studied case of the Geminga pulsar. We simulate gamma-ray emission from various TeV halo models, incorporating different assumptions for the injected electron spectrum, spin-down evolution, and energy-dependent diffusion. These models are then used to forecast CTA's sensitivity to spectral and spatial differences, based on realistic mock observations and instrument response simulations. We find that CTA will be able to distinguish between a wide range of TeV halo models that are currently consistent with existing data. In particular, CTA observations can constrain the normalization, energy dependence, and spatial extent of the diffusion coefficient surrounding Geminga, as well as the spectral shape of the injected electron population.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2026

Beyond $\rho ^{2/3}$ scaling: microscopic origins and multimessengers of high-density nuclear symmetry energy

The nature and Equation of State (EOS) of dense neutron-rich matter are still very poorly known, while they have broad impacts on many interesting issues in both astrophysics and nuclear physics. In particular, the nuclear symmetry energy $E_{\textrm{sym}}(\rho )$ encoding the cost to make nuclear matter more neutron-rich has been the most uncertain component of the EOS of dense neutron-rich nucleonic matter. It significantly affects the radii, tidal deformations, cooling rates, and frequencies of various oscillation modes of isolated neutron stars as well as the strain amplitude and frequencies of gravitational waves from their mergers, besides its many effects on the structures of nuclei as well as the dynamics and observables of their collisions. Siemens (1970s) observed that $E_{\textrm{sym}}(\rho )$ scales as $(\rho /\rho _0)^{2/3}$ near the saturation density $\rho _0$ of nuclear matter, since both the kinetic part and the potential contribution (quadratic in momentum) exhibit this dependence. The scaling holds if: (1) the nucleon isoscalar potential is quadratic in momentum, and (2) the isovector interaction is weakly density-dependent. After examining many empirical evidences and understanding theoretical findings in the literature, we conclude that: (1) Siemens’ $\rho ^{2/3}$ scaling is robust and serves as a valuable benchmark for both nuclear theories and experiments up to $2\rho _0$ but breaks down at higher densities, (2) Experimental and theoretical findings about $E_{\textrm{sym}}(\rho )$ up to $2\rho _0$ are broadly consistent, but uncertainties remain large for its curvature $K_{\textrm{sym}}(\rho )$ and higher-order parameters, (3) Above $2\rho _0$ , uncertainties grow due to poorly constrained spin-isospin-dependent tensor and three-body forces as well as the resulting nucleon short-range correlations. Looking forward, combining signals from both observations of neutron stars and terrestrial heavy-ion reaction experiments is the most promising path to finally constraining the high-density $E_{\textrm{sym}}(\rho )$ and the EOS of supradense neutron-rich matter. Multiple examples of community efforts to further constrain the high-density $E_{\textrm{sym}}(\rho )$ using both real and mocked data of present and future high-precision observations of neutron stars, as well as heavy-ion collisions involving high-energy rare isotopes, are briefly reviewed.

Li, Bao-An [East Texas A & M Univ., Commerce, TX (↗
DOE OSTI2017

SimulatorToFMU v0.1

SimulatorToFMU is a software package written in Python which allows users to export a memoryless Python-driven simulation program or script as a Functional Mock-up Unit (FMU) for model exchange or co-simulation.In CyDER (Cyber Physical Co-simulation Platform for Distributed Energy Resources in Smart Grids), SimulatorToFMU will allow exporting OPAL-RT as an FMU. This will enable OPAL-RT to be linked to CYMDIST and GridDyn FMUs through a standardized open source interface.

Nouidui, Thierry↗
DOE OSTI2025

Simulation-Based Inference for Neutrino Interaction Model Tuning

This project demonstrates, for the first time, the application of simulation-based inference (SBI) techniques to tune neutrino–nucleus interaction models. Using a mock dataset based on the MicroBooNE tuning of the GENIE event generator, our approach employs a Neural Posterior Estimator (NPE) with Masked Autoregressive Flows (MAF) to infer the posterior distributions of key GENIE parameters directly from simulated histograms. The workflow provides a scalable and amortized framework for performing likelihood-free inference in high-dimensional parameter spaces, offering a pathway to more efficient and uncertainty-aware model tuning for next-generation neutrino experiments such as DUNE and SBND.

Tame-Narvaez, KarlaMaria [Fermi National Accelerat↗
DOE OSTI2023

Reverse engineering environmental metatranscriptomes clarifies best practices for eukaryotic assembly

Abstract Background Diverse communities of microbial eukaryotes in the global ocean provide a variety of essential ecosystem services, from primary production and carbon flow through trophic transfer to cooperation via symbioses. Increasingly, these communities are being understood through the lens of omics tools, which enable high-throughput processing of diverse communities. Metatranscriptomics offers an understanding of near real-time gene expression in microbial eukaryotic communities, providing a window into community metabolic activity. Results Here we present a workflow for eukaryotic metatranscriptome assembly, and validate the ability of the pipeline to recapitulate real and manufactured eukaryotic community-level expression data. We also include an open-source tool for simulating environmental metatranscriptomes for testing and validation purposes. We reanalyze previously published metatranscriptomic datasets using our metatranscriptome analysis approach. Conclusion We determined that a multi-assembler approach improves eukaryotic metatranscriptome assembly based on recapitulated taxonomic and functional annotations from an in-silico mock community. The systematic validation of metatranscriptome assembly and annotation methods provided here is a necessary step to assess the fidelity of our community composition measurements and functional content assignments from eukaryotic metatranscriptomes.

Krinos, Arianna I. (ORCID:0000000197678392)↗
DOE OSTI2015

PanFP: Pangenome-based functional profiles for microbial communities

For decades there has been increasing interest in understanding the relationships between microbial communities and ecosystem functions. Current DNA sequencing technologies allows for the exploration of microbial communities in two principle ways: targeted rRNA gene surveys and shotgun metagenomics. For large study designs, it is often still prohibitively expensive to sequence metagenomes at both the breadth and depth necessary to statistically capture the true functional diversity of a community. Although rRNA gene surveys provide no direct evidence of function, they do provide a reasonable estimation of microbial diversity, while being a very cost effective way to screen samples of interest for later shotgun metagenomic analyses. However, there is a great deal of 16S rRNA gene survey data currently available from diverse environments, and thus a need for tools to infer functional composition of environmental samples based on 16S rRNA gene survey data. As a result, we present a computational method called pangenome based functional profiles (PanFP), which infers functional profiles of microbial communities from 16S rRNA gene survey data for Bacteria and Archaea. PanFP is based on pangenome reconstruction of a 16S rRNA gene operational taxonomic unit (OTU) from known genes and genomes pooled from the OTU s taxonomic lineage. From this lineage, we derive an OTU functional profile by weighting a pangenome s functional profile with the OTUs abundance observed in a given sample. We validated our method by comparing PanFP to the functional profiles obtained from the direct shotgun metagenomic measurement of 65 diverse communities via Spearman correlation coefficients. These correlations improved with increasing sequencing depth, within the range of 0.8 0.9 for the most deeply sequenced Human Microbiome Project mock community samples. PanFP is very similar in performance to another recently released tool, PICRUSt, for almost all of survey data analysed here. But, our method is unique in that any OTU building method can be used, as opposed to being limited to closed reference OTU picking strategies against specific reference sequence databases. In conclusion, we developed an automated computational method, which derives an inferred functional profile based on the 16S rRNA gene surveys of microbial communities. The inferred functional profile provides a cost effective way to study complex ecosystems through predicted comparative functional metagenomes and metadata analysis. All PanFP source code and additional documentation are freely available online at GitHub.

16S rRNA survey↗