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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 613 records · Page 34
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Metabolite, Protein, and Lipid Extraction (MPLEx): a method that simultaneously inactivates Middle East respiratory syndrome coronavirus and allows analysis of multiple host cell components following infection

Mass spectrometry (MS)-based, integrated proteomics, metabolomics, and lipidomics (collectively, multi-omics) studies provide a very detailed snap shot of virus-induced changes to the host following infection and can lead to the identification of novel prophylactic and therapeutic targets for preventing or lessening disease severity. Multi-omics studies with Middle East respiratory syndrome coronavirus (MERS-CoV) are challenging as the requirements of Biosafety Level 3 containment limit the numbers of samples that can be safely managed. To address these issues, the multi-omics sample preparation technique MPLEx (metabolite, protein, and lipid extraction) was developed to partition a single sample into three distinct parts (metabolites, proteins and lipids) for multi-omics analysis, while simultaneously inactivating MERS-CoV by solubilizing and disrupting the viral envelope and denaturing viral proteins. Here we describe the MPLEx protocol, highlight the step of inactivation, and describe the details of downstream processing, instrumental analysis of studies with Middle East respiratory syndrome coronavirus (MERS-CoV) are challenging as the requirements of Biosafety Level 3 containment limit the numbers of samples that can be safely managed. To address these issues, the multi-omics sample preparation technique MPLEx (metabolite, protein, and lipid extraction) was developed to partition a single sample into three distinct parts (metabolites, proteins and lipids) for multi-omics analysis, while simultaneously inactivating MERS-CoV by solubilizing and disrupting the viral envelope and denaturing viral proteins. Here we describe the MPLEx protocol, highlight the step of inactivation, and describe the details of downstream processing, instrumental analysis of the three separate analytes and their subsequent informatics pipelines.

Nicora, Carrie D.↗
DOE OSTI2020

Storage Conditions of Human Kidney Tissue Sections Affect Spatial Lipidomics Analysis Reproducibility

Lipids often are labile, unstable, and tend to degrade overtime, so it is of the upmost importance to study these molecules in their most native state. In this study, we sought to understand the optimal storage conditions for spatial lipidomic analysis of human kidney tissue sections. Specifically, we evaluated human kidney tissue sections on several different days throughout the span of a week using our established protocol for elucidating lipids using high mass resolution matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI). We studied kidney tissue sections stored under five different conditions: open stored at –80 °C, vacuumed sealed and stored at –80 °C, with matrix preapplied before storage at –80 °C, under a nitrogen atmosphere and stored at –80 °C, and at room temperature in a desiccator. Results were compared to data obtained from kidney tissue sections that were prepared and analyzed immediately after cryosectioning. Data was processed using METASPACE. After a week of storage, the sections stored at room temperature showed the largest amount of lipid degradation, while sections stored under nitrogen and at –80 °C retained the greatest number of overlapping annotations in relation to freshly cut tissue. Overall, we found that molecular degradation of the tissue sections was unavoidable over time, regardless of storage conditions, but storing tissue sections in an inert gas at low temperatures can curtail molecular degradation within tissue sections.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Annealing of focused ion beam damage in gold microcrystals: an in situ Bragg coherent X-ray diffraction imaging study

Focused ion beam (FIB) techniques are commonly used to machine, analyse and image materials at the micro- and nanoscale. However, FIB modifies the integrity of the sample by creating defects that cause lattice distortions. Methods have been developed to reduce FIB-induced strain; however, these protocols need to be evaluated for their effectiveness. Here, non-destructive Bragg coherent X-ray diffraction imaging is used to study the in situ annealing of FIB-milled gold microcrystals. Two non-collinear reflections are simultaneously measured for two different crystals during a single annealing cycle, demonstrating the ability to reliably track the location of multiple Bragg peaks during thermal annealing. The thermal lattice expansion of each crystal is used to calculate the local temperature. This is compared with thermocouple readings, which are shown to be substantially affected by thermal resistance. To evaluate the annealing process, each reflection is analysed by considering facet area evolution, cross-correlation maps of the displacement field and binarized morphology, and average strain plots. The crystal's strain and morphology evolve with increasing temperature, which is likely to be caused by the diffusion of gallium in gold below ~280°C and the self-diffusion of gold above ~280°C. The majority of FIB-induced strains are removed by 380–410°C, depending on which reflection is being considered. These observations highlight the importance of measuring multiple reflections to unambiguously interpret material behaviour.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2011

A method for patient dose reduction in dynamic contrast enhanced CT study

Purpose: In dynamic contrast enhanced CT (DCE-CT) study, prolonged CT scanning with high temporal resolution is required to give accurate and precise estimates of kinetic parameters. However, such scanning protocol could lead to substantial radiation dose to the patient. A novel method is proposed to reduce radiation dose to patient, while maintaining high accuracy for kinetic parameter estimates in DCE-CT study. Methods: The method is based on a previous investigation that the arterial impulse response (AIR) in DCE-CT study can be predicted using a population-based scheme. In the proposed method, DCE-CT scanning is performed with relatively low temporal resolution, hence, giving rise to reduction in patient dose. A novel method is proposed to estimate the arterial input function (AIF) based on the coarsely sampled AIF. By using the estimated AIF in the tracer kinetic analysis of the coarsely sampled DCE-CT study, the calculated kinetic parameters are able to achieve a high degree of accuracy. The method was tested on a DCE-CT data set of 48 patients with cervical cancer scanned at high temporal resolution. A random cohort of 34 patients was chosen to construct the orthonormal bases of the AIRs via singular value decomposition method. The determined set of orthonormal bases was used to fit the AIFs in the second cohort (14 patients) at varying levels of down sampling. For each dataset in the second cohort, the estimated AIF was used for kinetic analyses of the modified Tofts and adiabatic tissue homogeneity models for each of the down-sampling schemes between intervals from 2 to 15 s. The results were compared with analyses done with the ''raw'' down-sampled AIF. Results: In the first group of 34 patients, there were 11 orthonormal bases identified to describe the AIRs. The AIFs in the second group were estimated in high accuracy based on the 11 orthonormal bases established in the first group along with down-sampled AIFs. Using the 11 orthonormal bases, the estimated AIFs for the second group were found to have an averaged maximal percentage error of 3.4%{+-} 7.5% in all sampling schemes up to 15 s. The results of kinetic analysis with the proposed method compared with down sampling alone showed that the proposed method is superior in maintaining the accuracy in volume transfer constant (K{sup trans} ) after 9 s down-sampling interval, blood volume (v{sub b} ) for almost all down-sampling intervals, and blood flow (F) after 11 s down-sampling interval. The preliminary results suggested that the proposed method is able to support scanning intervals of 10-15 s at a cost of 6.2%-10.0% loss in accuracy of K{sup trans} and 10.9%-19.4% in v{sub b}, and the scanning intervals of 12-15 s at a cost of 9.7%-14.6% for F in DEC-CT studies for patients with cervix cancer. Conclusions: The proposed method of AIF estimation allows low scanning frequency in DCE-CT study to reduce radiation dose to patient, while maintaining relatively high accuracy in the kinetic parameter estimates. The initial results suggested that the method is applicable for DCE-CT studies for patients with cervical cancer.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2017

Fast myocardial perfusion imaging with {sup 99m}Tc in challenging patients using conventional SPECT cameras

Background: We attempted to validate the performance of a fast myocardial perfusion imaging (MPI) protocol in diagnostically challenging patients. Methods: 78 patients with ΒΜΙ > 24.9, LVH or three vessels disease underwent two sequential gated-MPI studies. The first at 15 (Early Imaging, EI) and the second at 45 (Late Imaging, LI) minutes post {sup 99m}Tc-injection, at both stress and rest. Counts over heart (H), liver (Liv) and subdiaphragmatic space (Sub) and image quality, and myocardial perfusion and function parameters were compared between the two protocols. Coronary angiography was performed within 2 months from MPI, and ROC analysis was used to compare the diagnostic accuracy for the detection of ≥50% diameter luminal stenosis. Results: Quality was optimal-good in 93% of EI and 98% of LI studies (P = .12), H/Liv and stress H/Sub ratios were similar, but rest H/Sub ratio was lower in EI (P = .009). SSS [10 (0 to 46) vs 9 (0 to 36), P = .006] and SDS [3 (0 to 35) vs 2 (0 to 34), P = .02] were higher in EI protocol. LVEF, motion and thickening scores did not differ between the two protocols. A highly significant (P < .001) linear relationship with clinically negligible mean differences in Bland-Altman analysis was observed for all perfusion and function-related data. Sensitivity (EI 81%, LI 80%) and specificity (65% for both) did not differ (P = .23) between the two protocols. Conclusion: The fast protocol is technically feasible and diagnostically accurate compared to the established protocol in diagnostically challenging patients.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2018

In Situ Soil Moisture and Thaw Depth Measurements Coincident with Airborne SAR Data Collections, Barrow and Seward Peninsulas, Alaska, 2017

The in-situ soil moisture and thaw depth measurements provided in this dataset were collected coincident with airborne overflights of L- and P-band SAR instruments at the NGEE Arctic study site near Barrow, on the North Slope, and at the three study sites on the Seward Peninsula, Alaska. Field measurements and flights were conducted during the summer of 2017 as a collaboration between the NASA ABoVE Project's Airborne SAR Campaign and the NGEE Arctic Project. ABoVE protocols for establishing field measurement plots were followed. NGEE Arctic plots for the ground-based measurements are located at existing study sites where SAR data would also add value to current monitoring and characterization efforts of the NGEE Team. The ground-based data will be used by ABoVE to analyze, calibrate and validate the remote sensing products. In November 2020, a Version 2 (V2) set of in situ soil moisture and thaw depth measurement data files were released. This dataset contains 1 pdf, 2 zip files, and 7 csv files. The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), was a research effort to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy's Office of Biological and Environmental Research.The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska.Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy?s Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2019

Online supercritical fluid extraction mass spectrometry (SFE-LC-FTMS) for sensitive characterization of soil organic matter

We report a novel technical approach for subcritical fluid extraction (SFE) for organic matter characterization in complex matrices such as soil. The custom platform combines on-line SFE with micro-solid phase extraction, nano liquid chromatography (LC), electrospray ionization and Fourier transform mass spectrometry (SFE-LC-FTMS). We demonstrated the utility of SFE-LC-FTMS, including results from both Orbitrap and FTICR MS, for analysis of complex mixtures of organic compounds in a solid matrix by characterizing soil organic matter in peat, a high-carbon soil. For example, in a single experiment, >6000 molecular formulas can be assigned based upon FTICR MS data from 1–50 μL of soil samples (roughly 1–50 mg of soil, dependent on soil density), nearly twice that typically obtained from direct infusion liquid solvent extraction (LSE) from an order of magnitude larger volume of the same soil. The detected species consisted predominately of lipid-like, lignin-like and protein-like compounds, based on their O/C and H/C ratios, with predominantly CHO and CHONP molecular compositions. These results clearly demonstrate that SFE has the potential to effectively extract a variety of molecular species and could become an important member of a suite of extraction methods for studying SOM and other natural organic matter. This is especially true when comprehensive coverage, minimal sample volumes, and high sensitivity are required, or when the presence of organic solvent residue in residual soil is problematic. Lastly, the SFE based extraction protocol could potentially enable spatially resolved characterization of organic matter in soil with a resolution of ~1 mm3 to facilitate studies probing the spatial heterogeneity of soil.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Quantum advantages for Pauli channel estimation

We show that entangled measurements provide an exponential advantage in sample complexity for Pauli channel estimation, which is both a fundamental problem and a practically important subroutine for benchmarking near-term quantum devices. The specific task we consider is to simultaneously learn all the eigenvalues of an n-qubit Pauli channel to ±ε precision. We give an estimation protocol with an n-qubit ancilla that succeeds with high probability using only O(n/ε 2 ) copies of the Pauli channel, while proving that any ancilla-free protocol (possibly with adaptive control and channel concatenation) would need at least Ω(2 n/3 ) rounds of measurement. We further study the advantages provided by a small number of ancillas. For the case that a k-qubit ancilla (k≤n) is available, we obtain a sample complexity lower bound of Ω(2 (n-k)/3 ) for any nonconcatenating protocol, and a stronger lower bound of Ω(n 2n-k ) for any nonadaptive, nonconcatenating protocol, which is shown to be tight. We also show how to apply the ancilla-assisted estimation protocol to a practical quantum benchmarking task in a noise-resilient and sample-efficient manner, given reasonable noise assumptions. Our results provide a practically interesting example for quantum advantages in learning and also bring insights for quantum benchmarking.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2021

High-Current Density Durability of Pt/C and PtCo/C Catalysts at Similar Particle Sizes in PEMFCs

The durability of carbon supported PtCo-alloy based nanoparticle catalysts play a key role in the longevity of proton-exchange membrane fuel cells (PEMFC) in electric vehicle applications. To improve its durability, it is important to understand and mitigate the various factors that cause PtCo-based cathode catalyst layers (CCL) to lose performance over time. These factors include i) electrochemical surface area (ECSA) loss, ii) specific activity loss, iii) H + /O 2 -transport changes and iv) Co 2+ contamination effects. We use a catalyst-specific accelerated stress test (AST) voltage cycling protocol to compare the durability of Pt and PtCo catalysts at similar average nanoparticle size and distribution. Our studies indicate that while Pt and PtCo nanoparticle catalysts suffer from similar magnitudes of electrochemical surface area (ECSA) losses, PtCo catalyst shows a significantly larger cell voltage loss at high current densities upon durability testing. The distinctive factor causing the large cell voltage loss of PtCo catalyst appears to be the secondary effects of the leached Co 2+ cations that contaminate the electrode ionomer. A 1D performance model has been used to quantify the cell voltage losses arising from various factors causing degradation of the membrane electrode assembly (MEA).

08 HYDROGEN↗
DOE OSTI2016

Towards an improved LAI collection protocol via simulated field-based PAR sensing

In support of NASA’s next-generation spectrometer—the Hyperspectral Infrared Imager (HyspIRI)—we are working towards assessing sub-pixel vegetation structure from imaging spectroscopy data. Of particular interest is Leaf Area Index (LAI), which is an informative, yet notoriously challenging parameter to efficiently measure in situ. While photosynthetically-active radiation (PAR) sensors have been validated for measuring crop LAI, there is limited literature on the efficacy of PAR-based LAI measurement in the forest environment. This study (i) validates PAR-based LAI measurement in forest environments, and (ii) proposes a suitable collection protocol, which balances efficiency with measurement variation, e.g., due to sun flecks and various-sized canopy gaps. A synthetic PAR sensor model was developed in the Digital Imaging and Remote Sensing Image Generation (DIRSIG) model and used to validate LAI measurement based on first-principles and explicitly-known leaf geometry. Simulated collection parameters were adjusted to empirically identify optimal collection protocols. Furthermore, these collection protocols were then validated in the field by correlating PAR-based LAI measurement to the normalized difference vegetation index (NDVI) extracted from the “classic” Airborne Visible Infrared Imaging Spectrometer (AVIRIS-C) data (R 2 was 0.61). The results indicate that our proposed collecting protocol is suitable for measuring the LAI of sparse forest (LAI < 3–5 ( m 2 /m 2 )).

47 OTHER INSTRUMENTATION↗
DOE OSTI2016

SU-F-R-39: Effects of Radiation Dose Reduction On Renal Cell Carcinoma Discrimination Using Multi-Phasic CT Imaging

Purpose: A method to discriminate different types of renal cell carcinoma (RCC) was developed using attenuation values observed in multiphasic contrast-enhanced CT. This work evaluates the sensitivity of this RCC discrimination task at different CT radiation dose levels. Methods: We selected 5 cases of kidney lesion patients who had undergone four-phase CT scans covering the abdomen to the lilac crest. Through an IRB-approved study, the scans were conducted on 64-slice CT scanners (Definition AS/Definition Flash, Siemens Healthcare) using automatic tube-current modulation (TCM). The protocol included an initial baseline unenhanced scan, followed by three post-contrast injection phases. CTDIvol (32 cm phantom) measured between 9 to 35 mGy for any given phase. As a preliminary study, we limited the scope to the cortico-medullary phase—shown previously to be the most discriminative phase. A previously validated method was used to simulate a reduced dose acquisition via adding noise to raw CT sinogram data, emulating corresponding images at simulated doses of 50%, 25%, and 10%. To discriminate the lesion subtype, ROIs were placed in the most enhancing region of the lesion. The mean HU value of an ROI was extracted and used to discriminate to the worst-case RCC subtype, ranked in the order of clear cell, papillary, chromophobe and the benign oncocytoma. Results: Two patients exhibited a change of worst case RCC subtype between original and simulated scans, at 25% and 10% doses. In one case, the worst-case RCC subtype changed from oncocytoma to chromophobe at 10% and 25% doses, while the other case changed from oncocytoma to clear cell at 10% dose. Conclusion: Based on preliminary results from an initial cohort of 5 patients, worst-case RCC subtypes remained constant at all simulated dose levels except for 2 patients. Further study conducted on more patients will be needed to confirm our findings. Institutional research agreement, Siemens Healthcare; Past recipient, research grant support, Siemens Healthcare; Consultant, Toshiba America Medical Systems; Consultant, Samsung Electronics; NIH Grant Support from: U01 CA181156.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Marine Hydrogen Demonstration

This report summarizes Phase 1 of a project involving the design of a Floating Hydrogen Production and Dispensing Barge destined for the Port of San Francisco (SF). The H 2 Barge is designed to produce renewable H 2 at the rate of ~ 530 kg/day, storing 512 kg of hydrogen at 517-bar, allowing fast refueling of hydrogen fuel cell vessels and land-side hydrogen delivery trailers for distribution into the nascent SF hydrogen ecosystem. The broader considerations that impacted the H2 Barge design are also described. An account is given of a new review process formulated by the United States Coast Guard (USCG) to review this first-of-its-kind maritime implementation of hydrogen technology. The immediate goals of the H 2 Barge Project are to 1) demonstrate the feasibility, viability and methods of hydrogen production, storage and fueling in a maritime context, 2) help shape (where needed) and navigate the required local, state and federal regulatory gauntlet and 3) catalyze a “green hydrogen ecosystem” (both marine and landside) with locally produced renewable hydrogen at the San Francisco waterfront. A summary is also given of the modeling and experimental activity of Phase 1 directed to the development of science-based refueling protocols for large marine Type IV 250-bar hydrogen tanks. Combined modeling and experimental studies are reported of the filling of large (28 kg) 250-bar Type IV hydrogen tanks of the type being deployed on early hydrogen ferries, such as the MV Sea Change. The primary question was to determine how such tanks can be successfully filled (state of charge greater than 97%) within 45 minutes without exceeding the 82 °C temperature limit historically set for such tanks. The studies show that a gas injector is needed avoid thermal stratification during filling which can result in potential hot spots. Pre-cooling of the hydrogen was found to be essential in most cases, as ambient conditions greatly affect the need for a pre-cooling to achieve the 45-minute fill time. Pre-cooling cannot be supplied by nearby water, such as that found in nature (bays, lakes, rivers, etc.) because pre-cooling cooling below 0 °C was found to be necessary to avoid excessive compression heating. The experimental results afforded a calibration of the engineering model (SOFIL) for these large 250-bar tanks, which now enables using SOFIL to predict volume-averaged hydrogen filling temperatures to an accuracy of +/- 2.7°C for these tanks. The model can therefore be used to evaluate potential scenarios for development of a standardized fueling methodology for ferries utilizing large Type-IV tanks of the type examined here.

08 HYDROGEN↗
DOE OSTI2012

Ruthenium Behavior at Phase Separation of Borosilicate Glass-12259

The Rokkasho reprocessing plant (RRP) located in Aomori, Japan, vitrifies high level waste (HLW) into a borosilicate glass. The HLW is generated from the reprocessing of spent fuel and contains ruthenium (Ru) and other platinum group metals (PGMs). Based on the recent consequences after a huge earthquake that occurred in Japan, a hypothetical blackout was postulated for the RRP to address additional safety analysis requirements. During a prolonged blackout, the borosilicate glass could phase separate due to cooling of the glass in the melter. The Ru present in the glass matrix could migrate into separate phases and impact the durability of the borosilicate glass. The durability of the glass is important for quality assurance and performance assessment of the vitrified HLW. A fundamental study was performed at an independent university to understand the impact of a prolonged blackout. Simulated HLW glasses were prepared for the RRP, and the Ru behavior in phase separated glasses was studied. The simulated HLW glasses contained nonradioactive elements and PGMs. The glass compositions were then altered to enhance the formation of the phase-separated glasses when subjected to thermal treatment at 700 deg. C for 24 hours. The synthesized simulated glasses contained 1.1 % Ru by weight as ruthenium dioxide (RuO{sub 2}). A portion of the RuO{sub 2} formed needle-shaped crystals in the glass specimens. After the thermal treatment, the glass specimen had separated into two phases. One of the two phases was a B{sub 2}O{sub 3} rich phase, and the other phase was a SiO{sub 2} rich phase. The majority of the chemical species in the B{sub 2}O{sub 3} rich phase was leached away with the Material Characterization Center-3 (MCC-3) protocol standardized by the Pacific Northwest National Laboratory using an aqueous low-concentrated nitric acid solution, but the leaching of the Ru fraction was very limited; less than 1% of the original Ru content. The Ru leaching was much less than those of the other elements, and the needle-shaped crystals of RuO{sub 2} were observed in the B{sub 2}O{sub 3} rich phase in the specimen after the leaching test. Another experiment was performed using another glass specimen which had been prepared with the same frits, but used reagent RuO{sub 2} of granular shape at lower content (0.0073% by weight as RuO{sub 2}). The leached fractions of elements for the latter specimen increased to almost the same fraction (more than 10% of the original Ru content) as observed for boron and sodium, when the phase separated glass was leached using the MMC-3 protocol with non-acidic de-ionized water. Based on the results of this study, it was concluded that needle-shaped RuO{sub 2} crystals are contained in the B{sub 2}O{sub 3}-rich phase after phase separation of the borosilicate glass after a hypothetical blackout. The leaching fraction for the needle-shaped RuO{sub 2} present in the phase separated glass is much lower than those for boron or sodium. Ruthenium behavior has been studied for a hypothetical loss of cooling in the liquid fed ceramic melter for high level waste by taking into account the phase separation of borosilicate glass. The needle-shaped crystal of ruthenium dioxide after bi-nodal-type phase separation of the borosilicate glass at 700 deg. C migrated into the B{sub 2}O{sub 3} rich phase, but remained without dissolution by an acidic aqueous solution. Additionally, granular ruthenium dioxide can be a morphological form of ruthenium after bimodal-type phase separation of the vitrified high level waste with borosilicate glass media. After the phase separation of the borosilicate glass, the crystal shape of the ruthenium dioxide is either needle-shaped or granular, and the leachable fraction of ruthenium is relatively much lower than those of major components (boron and sodium) in the vitrified borosilicate glass. The fraction of leached ruthenium increased to almost the same fraction as observed for boron and sodium when the phase-separated glass was leached with ultrapure water. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2025

Black-box optimization of CT acquisition and reconstruction parameters: a reinforcement learning approach

Protocol optimization is critical in Computed Tomography (CT) for achieving desired diagnostic image quality while minimizing radiation dose. Due to the inter-effect of influencing CT parameters, traditional optimization methods rely on the testing of exhaustive combinations of these parameters. This poses a notable limitation due to the impracticality of exhaustive parameter testing. This study introduces a novel methodology leveraging Virtual Imaging Trials (VITs) and reinforcement learning to more efficiently optimize CT protocols. Computational phantoms with liver lesions were imaged using a validated CT simulator and reconstructed with a novel CT reconstruction Toolkit. The optimization parameter space included tube voltage, tube current, reconstruction kernel, slice thickness, and pixel size. The optimization process was done using a Proximal Policy Optimization (PPO) agent which was trained to maximize the Detectability Index (d’) of the liver lesion for each reconstructed image. Results showed that our reinforcement learning approach found the absolute maximum d’ across the test cases while requiring 79.7% fewer steps compared to an exhaustive search, demonstrating both accuracy and computational efficiency, offering a efficient and robust framework for CT protocol optimization. The flexibility of the proposed technique allows for use of varying image quality metrics as the objective metric to maximize for. Our findings highlight the advantages of combining VIT and reinforcement learning for CT protocol management.

Fenwick, David [Duke University Medical Center]↗
DOE OSTI2015

Mass Spectrometry Imaging of Biological Tissue: An Approach for Multicenter Studies

Mass spectrometry imaging has become a popular tool for probing the chemical complexity of biological surfaces. This led to the development of a wide range of instrumentation and preparation protocols. It is thus desirable to evaluate and compare the data output from different methodologies and mass spectrometers. Here, we present an approach for the comparison of mass spectrometry imaging data from different laboratories (often referred to as multicenter studies). This is exemplified by the analysis of mouse brain sections in five laboratories in Europe and the USA. The instrumentation includes matrix-assisted laser desorption/ionization (MALDI)-time-of-flight (TOF), MALDI-QTOF, MALDIFourier transform ion cyclotron resonance (FTICR), atmospheric-pressure (AP)-MALDI-Orbitrap, and cluster TOF-secondary ion mass spectrometry (SIMS). Experimental parameters such as measurement speed, imaging bin width, and mass spectrometric parameters are discussed. All datasets were converted to the standard data format imzML and displayed in a common open-source software with identical parameters for visualization, which facilitates direct comparison of MS images. The imzML conversion also allowed exchange of fully functional MS imaging datasets between the different laboratories. The experiments ranged from overview measurements of the full mouse brain to detailed analysis of smaller features (depending on spatial resolution settings), but common histological features such as the corpus callosum were visible in all measurements. High spatial resolution measurements of AP-MALDI-Orbitrap and TOF-SIMS showed comparable structures in the low-micrometer range. We discuss general considerations for planning and performing multicenter studies in mass spectrometry imaging. This includes details on the selection, distribution, and preparation of tissue samples as well as on data handling. Such multicenter studies in combination with ongoing activities for reporting guidelines, a common data format (imzML) and a public data repository can contribute to more reliability and transparency of MS imaging studies.

Environmental Molecular Sciences Laboratory↗
DOE OSTI2012

Addition of Bevacizumab to Standard Radiation Therapy and Daily Temozolomide Is Associated With Minimal Toxicity in Newly Diagnosed Glioblastoma Multiforme

Purpose: To determine the safety of the addition of bevacizumab to standard radiation therapy and daily temozolomide for newly diagnosed glioblastoma multiforme (GBM). Methods and Materials: A total of 125 patients with newly diagnosed GBM were enrolled in the study, and received standard radiation therapy and daily temozolomide. All patients underwent a craniotomy and were at least 2 weeks postoperative. Radiation therapy was administered in 1.8-Gy fractions, with the clinical target volume for the primary course treated to a dose of 45 to 50.4 Gy, followed by a boost of 9 to 14.4 Gy, to a total dose of 59.4 Gy. Patients received temozolomide at 75 mg/m{sup 2} daily throughout the course of radiation therapy. Bevacizumab was given at 10 mg/kg intravenously every 14 days, beginning a minimum of 4 weeks postoperatively. Results: Of the 125 patients, 120 (96%) completed the protocol-specified radiation therapy. Five patients had to stop the protocol therapy, 2 patients with pulmonary emboli, and 1 patient each with a Grade 2 central nervous system hemorrhage, Grade 4 pancytopenia, and wound dehiscence requiring surgical intervention. All 5 patients ultimately finished the radiation therapy. After radiation therapy, 3 patients had progressive disease, 2 had severe fatigue and decreased performance status, 1 patient had a colonic perforation, and 1 had a rectal fissure; these 7 patients therefore did not proceed with the protocol-specified adjuvant temozolomide, bevacizumab, and irinotecan. However, 113 patients (90%) were able to continue on study. Conclusions: The addition of bevacizumab to standard radiation therapy and daily temozolomide was found to be associated with minimal toxicity in patients newly diagnosed with GBM.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2018

Genetic techniques for studies of methyl-coenzyme M reductase from Methanosarcina acetivorans C2A.

Methanogenic archaea generate methane as a by-product of anaerobic respiration using CO 2 , C 1 compounds (like methanol or methylated amines), or acetate as terminal electron acceptors. Methanogens are an untapped resource for biotechnological advances related to methane production as well as methane consumption. Yet, key biological features of these organisms remain poorly understood. One such feature is the enzyme methyl-coenzyme M reductase (referred to as MCR), which catalyzes the last step in the methanogenic pathway and results in methane formation. Gene essentiality has limited genetic analyses of MCR thus far. Therefore, studies of this important enzyme have been limited to biochemical and biophysical techniques that are especially laborious and often reliant on sophisticated instrumentation that is not commonly available. In this chapter, we outline our recently developed CRISPR–Cas9-based genome editing tools and describe how these tools have been used for the introduction of a tandem affinity purification tag at the chromosomal mcr locus in the model methanogen, Methanosarcina acetivorans C2A. Moreover, we report a protocol for rapid affinity purification of MCR from M. acetivorans C2A that will enable high-throughput studies of this enzyme in the future.

59 BASIC BIOLOGICAL SCIENCES↗