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At least 1,333 records · Page 74
All sourcesNASA NTRSDOE OSTI
DOE OSTI2015

SU-E-T-787: Utility of the Two Candidate 192-Ir and 169-Yb HDR Sources for Use with a Novel Direction Modulated Brachytherapy Tandem Applicator for Cervical Cancer Treatment

Purpose: A novel tungsten alloy shielded, MRI-compatible, direction modulated brachytherapy (DMBT) concept tandem applicator, which enables unprecedented intensity modulation, was used to evaluate treatment plan quality improvement over a conventional tandem. The utility of the 192-Ir and 169-Yb HDR sources, for use with the DMBT applicator, was evaluated. Methods: The total diameter of the DMBT tandem applicator is 6.0 mm, which consists of 5.4-mm diameter tungsten alloy and 0.3 mm thick plastic sheath. The tandem has 6 symmetric peripheral 1.3-mm diameter grooves for the source to travel. MCNPX v.2.6 was used to simulate the 192-Ir and 169-Yb sources inside the DMBT applicator. First, TG-43 source parameters were evaluated. Second, 3D dose matrix with 1 mm3 resolution were imported into an in-house-coded inverse optimization treatment planning program to obtain optimal plans for 19 clinical cases. All plans were compared with the standard tandem and ring plans. Prescription dose was 15.0 Gy. All plans were normalized to receive the same HRCTV D90. Results: Generally, the DMBT tandem (and ring) plans were better than the conventional tandem and ring plans for 192-Ir and 169-Yb HDR sources. The mean data of D2cc for bladder, rectum, and sigmoid were 11.65±2.30 Gy, 7.47±3.05 Gy, and 9.84±2.48 Gy for Ir-192 DMBT tandem, respectively. These data for Yb-169 were 11.67±2.26 Gy, 7.44±3.02 Gy, and 9.83±2.38 Gy, respectively. The HR-CTV D98 and V100 were 16.37±1.86 Gy and 97.37 ± 1.92 Gy for Ir-192 DMBT, respectively. The corresponding values for Yb-169 were 16.43±1.86 Gy, and 97.51 ± 1.91 Gy. Plans with the 169-Yb source generally produced more favorable results where V100 increased by 13.65% while D2cc across all OARs reduced by 0.54% compared with the 192-Ir plans. Conclusion: For the DMBT tandem applicator, 169-Yb source seems to produce more directional beams resulting in increased intensity modulation capacity, thus resulting in more conformal plans.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

MO-FG-207-03: Maximizing the Utility of Integrated PET/MRI in Clinical Applications

The use of integrated PET/MRI systems in clinical applications can best benefit from understanding their technological advances and limitations. The currently available clinical PET/MRI systems have their own characteristics. Thorough analyses of existing technical data and evaluation of necessary performance metrics for quality assurances could be conducted to optimize application-specific PET/MRI protocols. This Symposium will focus on technical advances and limitations of clinical PET/MRI systems, and how this exciting imaging modality can be utilized in applications that can benefit from both PET and MRI. Learning Objectives: To understand the technological advances of clinical PET/MRI systems To correctly identify clinical applications that can benefit from PET/MRI To understand ongoing work to further improve the current PET/MRI technology Floris Jansen is a GE Healthcare employee.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

MO-F-CAMPUS-T-04: Utilization of Optical Dosimeter for Modulated Spot-Scanning Particle Beam

Purpose: To present the utilization of an optical dosimeter for modulated spot-scanning carbon-ion and proton beams during the acceptance test of Siemens IONTRIS system. Method and Materials: An optical dosimeter using phosphor scintillation was developed to map and interactively analyze the shapes and sizes of spots over 190 energies for ProTom modulated-scanning system. The dose response to proton had been characterized with proper pixel calibration at ProTom system. The dose response was further studied at 0.7 cm depths by uniform 8cm in-diameter fields of 424.89 MeV/u (E290) carbon-ions and 215.18MeV (E282) protons at IONTRIS system. The virtual source axial distances (vSAD) of carbonions and protons of IONTRIS system was investigated by measuring either variations of spot position or field size at five different locations to Isocenter. By measuring lateral profiles of uniform doses with varied thin-thicknesses of chest-board pattern and placing the scintillation plate at near to the distal edge, range variations at different off-axis-distances (rOAD) were examined. Relative accuracy and reproducibility of beam range were measured for three beam ranges with a ramping block at front of scintillation plate. Results: Similar dose response was observed for high energies of carbon ions and protons. Mean vSAD at X and Y axes were 744.1 cm and 807.4cm with deviation of 7.4cm and 7.7cm, respectively. Variation of rOAD was within 0.35 mm over 10cm for both protons and carbon ions. Accuracy of measuring relative distal range using the ramping block was 0.2mm. Measured range over repeated three times for each range were within 0.25mm at same room, and within 1.0mm between four rooms. Conclusions: The optical dosimeter could efficiently measure the virtual source distance. And, to measure small range variation at different off-axial locations, and for the relative beam range between rooms during acceptance test of a modulated spot-scanning particle system.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

WE-G-BRA-07: Analyzing the Safety Implications of a Brachytherapy Process Improvement Project Utilizing a Novel System-Theory-Based Hazard-Analysis Technique

Purpose: To investigate the hazards in cervical-cancer HDR brachytherapy using a novel hazard-analysis technique, System Theoretic Process Analysis (STPA). The applicability and benefit of STPA to the field of radiation oncology is demonstrated. Methods: We analyzed the tandem and ring HDR procedure through observations, discussions with physicists and physicians, and the use of a previously developed process map. Controllers and their respective control actions were identified and arranged into a hierarchical control model of the system, modeling the workflow from applicator insertion through initiating treatment delivery. We then used the STPA process to identify potentially unsafe control actions. Scenarios were then generated from the identified unsafe control actions and used to develop recommendations for system safety constraints. Results: 10 controllers were identified and included in the final model. From these controllers 32 potentially unsafe control actions were identified, leading to more than 120 potential accident scenarios, including both clinical errors (e.g., using outdated imaging studies for planning), and managerial-based incidents (e.g., unsafe equipment, budget, or staffing decisions). Constraints identified from those scenarios include common themes, such as the need for appropriate feedback to give the controllers an adequate mental model to maintain safe boundaries of operations. As an example, one finding was that the likelihood of the potential accident scenario of the applicator breaking during insertion might be reduced by establishing a feedback loop of equipment-usage metrics and equipment-failure reports to the management controller. Conclusion: The utility of STPA in analyzing system hazards in a clinical brachytherapy system was demonstrated. This technique, rooted in system theory, identified scenarios both technical/clinical and managerial in nature. These results suggest that STPA can be successfully used to analyze safety in brachytherapy and may prove to be an alternative to other hazard analysis techniques.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

SU-F-J-171: Robust Atlas Based Segmentation of the Prostate and Peripheral Zone Regions On MRI Utilizing Multiple MRI System Vendors

Purpose: Automatically generated prostate MRI contours can be used to aid in image registration with CT or ultrasound and to reduce the burden of contouring for radiation treatment planning. In addition, prostate and zonal contours can assist to automate quantitative imaging features extraction and the analyses of longitudinal MRI studies. These potential gains are limited if the solutions are not compatible across different MRI vendors. The goal of this study is to characterize an atlas based automatic segmentation procedure of the prostate collected on MRI systems from multiple vendors. Methods: The prostate and peripheral zone (PZ) were manually contoured by an expert radiation oncologist on T2-weighted scans acquired on both GE (n=31) and Siemens (n=33) 3T MRI systems. A leave-one-out approach was utilized where the target subject is removed from the atlas before the segmentation algorithm is initiated. The atlas-segmentation method finds the best nine matched atlas subjects and then performs a normalized intensity-based free-form deformable registration of these subjects to the target subject. These nine contours are then merged into a single contour using Simultaneous Truth and Performance Level Estimation (STAPLE). Contour comparisons were made using Dice similarity coefficients (DSC) and Hausdorff distances. Results: Using the T2 FatSat (FS) GE datasets the atlas generated contours resulted in an average DSC of 0.83±0.06 for prostate, 0.57±0.12 for PZ and 0.75±0.09 for CG. Similar results were found when using the Siemens data with a DSC of 0.79±0.14 for prostate, 0.54±0.16 and 0.70±0.9. Contrast between prostate and surrounding anatomy and between the PZ and CG contours for both vendors demonstrated superior contrast separation; significance was found for all comparisons p-value < 0.0001. Conclusion: Atlas-based segmentation yielded promising results for all contours compared to expertly defined contours in both Siemens and GE 3T systems providing fast and automatic segmentation of the prostate. Funding Support, Disclosures, and Conflict of Interest: AS Nelson is a partial owner of MIM Software, Inc. AS Nelson, and A Swallen are current employees at MIM Software, Inc.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

SU-F-T-204: A Preliminary Approach of Reducing Contralateral Breast and Heart Dose in Left Sided Whole Breast Cancer Patients Utilizing Proton Beams

Purpose: To investigate the plan quality and feasibility of a hybrid plan utilizing proton and photon fields for superior coverage in the internal mammary (IM) and supraclavicular (S/C) regions while minimizing heart and contralateral breast dose for the left-sided whole breast cancer patient treatment. Methods: This preliminary study carried out on single left-sided intact breast patient involved IM and S/C nodes. The IM and S/C node fields of the 5-Field 3DCRT photon-electron base plan were replaced by two proton fields. These two along with two Field-in-Field tangential photon fields were optimized for comparable dose coverage. The treatment plans were done using Eclipse TPS for the total dose of 46Gy in 23 fractions with 95% of the prescription dose covering 95% of the RTOG PTV. The 3DCRT photon-electron and 4-Field photon-proton hybrid plans were compared for the PTV dose coverage as well as dose to OARs. Results: The overall RTOG PTV coverage for proton-hybrid and 3DCRT plan was comparable (95% of prescription dose covers 95% PTV volume). In proton-hybrid plan, 99% of IM volume received 100% dose whereas in 3DCRT only 77% received 100% dose. For S/C regions, 97% and 77% volume received 100% prescription dose in proton-hybrid and 3DCRT plans, respectively. The heart mean dose, V3Gy(%), and V5Gy(%) was 2.2Gy, 14.4%, 9.8% for proton-hybrid vs. 4.20 Gy, 21.5%, and 39% for 3DCRT plan, respectively. The maximum dose to the contralateral breast was 39.75Gy for proton-hybrid while 56.87Gy for 3DCRT plan. The mean total lung dose, V20Gy(%), and V30Gy(%) was 5.68Gy, 11.3%, 10.5% for proton-hybrid vs. 5.90Gy, 9.8%, 7.2% for 3DCRT, respectively. Conclusion: The protonhybrid plan can offer better dose coverage to the involved lymphatic tissues while lower doses to the heart and contralateral breast. More treatment plans are currently in progress before being implemented clinically.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Evaluating factors influencing infrasonic signal detection and automatic processing performance utilizing a regional network

Physical and deployment factors that influence infrasound signal detection and assess automatic detection performance for a regional infrasound network of arrays in the Western U.S. are explored using signatures of ground truth (GT) explosions (yields). Despite these repeated known sources, published infrasound event bulletins contain few GT events. Arrays are primarily distributed toward the south-southeast and south-southwest at distances between 84 and 458 km of the source with one array offering azimuthal resolution toward the northeast. Events occurred throughout the spring, summer, and fall of 2012 with the majority occurring during the summer months. Depending upon the array, automatic detection, which utilizes the adaptive F-detector successfully, identifies between 14% and 80% of the GT events, whereas a subsequent analyst review increases successful detection to 24%–90%. Combined background noise quantification, atmospheric propagation analyses, and comparison of spectral amplitudes determine the mechanisms that contribute to missed detections across the network. This analysis provides an estimate of detector performance across the network, as well as a qualitative assessment of conditions that impact infrasound monitoring capabilities. Finally, the mechanisms that lead to missed detections at individual arrays contribute to network-level estimates of detection capabilities and provide a basis for deployment decisions for regional infrasound arrays in areas of interest.

58 GEOSCIENCES↗
DOE OSTI2018

An “ideal lignin” facilitates full biomass utilization

Lignin, a major component of lignocellulosic biomass, is crucial to plant growth and development but is a major impediment to efficient biomass utilization in various processes. Valorizing lignin is increasingly realized as being essential. However, rapid condensation of lignin during acidic extraction leads to the formation of recalcitrant condensed units that, along with similar units and structural heterogeneity in native lignin, drastically limits product yield and selectivity. Catechyl lignin (C-lignin), which is essentially a benzodioxane homopolymer without condensed units, might represent an ideal lignin for valorization, as it circumvents these issues. We discovered that C-lignin is highly acid-resistant. Hydrogenolysis of C-lignin resulted in the cleavage of all benzodioxane structures to produce catechyl-type monomers in near-quantitative yield with a selectivity of 90% to a single monomer.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Biochemical and Regulatory Analyses of Xylanolytic Regulons in Caldicellulosiruptor bescii Reveal Genus-Wide Features of Hemicellulose Utilization

Microbial deconstruction of lignocellulose for the production of biofuels and chemicals requires the hydrolysis of heterogeneous hemicelluloses to access the microcrystalline cellulose portion. This work extends previous in vivo and in vitro efforts to characterize hemicellulose utilization by integrating genomic reconstruction, transcriptomic data, operon structures, and biochemical characteristics of key enzymes to understand the deployment and functionality of hemicellulases by the extreme thermophile Caldicellulosiruptor bescii .

Biotechnology & Applied Microbiology↗
DOE OSTI2015

Comparative Analysis of Extremely Thermophilic Caldicellulosiruptor Species Reveals Common and Unique Cellular Strategies for Plant Biomass Utilization

Microbiological, genomic and transcriptomic analyses were used to examine three species from the bacterial genus Caldicellulosiruptor with respect to their capacity to convert the carbohydrate content of lignocellulosic biomass at 70 degrees C to simple sugars, acetate, lactate, CO2, and H-2. Caldicellulosiruptor bescii, C. kronotskyensis, and C. saccharolyticus solubilized 38%, 36%, and 29% (by weight) of unpretreated switchgrass (Panicum virgatum) (5 g/liter), respectively, which was about half of the amount of crystalline cellulose (Avicel; 5 g/liter) that was solubilized under the same conditions. The lower yields with C. saccharolyticus, not appreciably greater than the thermal control for switchgrass, were unexpected, given that its genome encodes the same glycoside hydrolase 9 (GH9)-GH48 multidomain cellulase (CelA) found in the other two species. However, the genome of C. saccharolyticus lacks two other cellulases with GH48 domains, which could be responsible for its lower levels of solubilization. Transcriptomes for growth of each species comparing cellulose to switchgrass showed that many carbohydrate ABC transporters and multidomain extracellular glycoside hydrolases were differentially regulated, reflecting the heterogeneity of lignocellulose. However, significant differences in transcription levels for conserved genes among the three species were noted, indicating unexpectedly diverse regulatory strategies for deconstruction for these closely related bacteria. Genes encoding the Che-type chemotaxis system and flagellum biosynthesis were upregulated in C. kronotskyensis and C. bescii during growth on cellulose, implicating motility in substrate utilization. The results here show that capacity for plant biomass deconstruction varies across Caldicellulosiruptor species and depends in a complex way on GH genome inventory, substrate composition, and gene regulation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Genus-wide assessment of lignocellulose utilization in the extremely thermophilic Caldicellulosiruptor by genomic, pan-genomic and metagenomic analysis

Metagenomic data from Obsidian Pool (Yellowstone National Park, USA) and thirteen genome sequences were used to re-assess genus-wide biodiversity for the extremely thermophilic Caldicellulosiruptor . The updated core-genome contains 1,401 ortholog groups (average genome size for thirteen species = 2,516 genes). The pan-genome, which remains open with a revised total of 3,493 ortholog groups, encodes a variety of multi-domain glycoside hydrolases (GH). These include three cellulases with GH48 domains that are co-located in the Glucan Degradation Locus (GDL) and are specific determinants for microcrystalline cellulose utilization. Three recently sequenced species, Caldicellulosiruptor sp. str. Rt8.B8 (re-named here Caldicellulosiruptor morganii ), Thermoanaerobacter cellulolyticus str. NA10 (re-named here Caldicellulosiruptor naganoensis NA10), and Caldicellulosiruptor sp. str. Wai35.B1 (re-named here Caldicellulosiruptor danielii ) degraded Avicel and lignocellulose (switchgrass). C. morganii was more efficient than C. bescii in this regard and differed from the other twelve species examined here, both based on genome content and organization and in the specific domain features of conserved GHs. Metagenomic analysis of lignocellulose-enriched samples from Obsidian Pool revealed limited new information on genus biodiversity. Enrichments yielded genomic signatures closely related to Caldicellulosiruptor obsidiansis , but there was also evidence for other thermophilic fermentative anaerobes ( Caldanaerobacter , Fervidobacterium , Caloramator , and Clostridium ). One enrichment, containing 89.7% Caldicellulosiruptor and 9.7% Caloramator , had a capacity for switchgrass solubilization comparable to C. bescii . These results refine the known biodiversity of Caldicellulosiruptor and indicate that microcrystalline cellulose degradation at temperatures above 70°C, based on current information, is limited to certain members of this genus that produce GH48 domain-containing enzymes. The genus Caldicellulosiruptor contains the most thermophilic bacteria capable of lignocellulose deconstruction and are promising candidates for consolidated bioprocessing for the production of biofuels and bio-based chemicals. The focus here is on the extant capability of this genus for plant biomass degradation and the extent to which this can be inferred from the core and pan-genomes, based on analysis of thirteen species and metagenomic sequence information from environmental samples. Key to microcrystalline hydrolysis is the content of the Glucan Degradation Locus (GDL), a set of genes encoding glycoside hydrolases (GH), several of which have GH48 and family 3 carbohydrate binding module domains, that function as primary cellulases. Resolving the relationship between the GDL and lignocellulose degradation will inform efforts to identify more prolific members of the genus and to develop metabolic engineering strategies to improve this characteristic

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Draft Genome Assemblies of Five Robust Yarrowia lipolytica Strains Exhibiting High Lipid Production, Pentose Sugar Utilization, and Sugar Alcohol Secretion from Undetoxified Lignocellulosic Biomass Hydrolysates

Screening the genetic diversity of 45 Yarrowia lipolytica strains identified five candidates with unique metabolic capability and robustness in undetoxified switchgrass hydrolysates, including superior lipid production and efficient pentose sugar utilization. Here, we report the genome sequences of these strains to study their robustness and potential to produce fuels and chemicals.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Modification and analysis of context-specific genome-scale metabolic models: methane-utilizing microbial chassis as a case study

ABSTRACT Context-specific genome-scale model (CS-GSM) reconstruction is becoming an efficient strategy for integrating and cross-comparing experimental multi-scale data to explore the relationship between cellular genotypes, facilitating fundamental or applied research discoveries. However, the application of CS modeling for non-conventional microbes is still challenging. Here, we present a graphical user interface that integrates COBRApy, EscherPy, and RIPTiDe, Python-based tools within the BioUML platform, and streamlines the reconstruction and interrogation of the CS genome-scale metabolic frameworks via Jupyter Notebook. The approach was tested using -omics data collected for Methylotuvimicrobium alcaliphilum 20Z R , a prominent microbial chassis for methane capturing and valorization. We optimized the previously reconstructed whole genome-scale metabolic network by adjusting the flux distribution using gene expression data. The outputs of the automatically reconstructed CS metabolic network were comparable to manually optimized i IA409 models for Ca-growth conditions. However, the CS model questions the reversibility of the phosphoketolase pathway and suggests higher flux via primary oxidation pathways. The model also highlighted unresolved carbon partitioning between assimilatory and catabolic pathways at the formaldehyde-formate node. Only a very few genes and only one enzyme with a predicted function in C1 metabolism, a homolog of the formaldehyde oxidation enzyme ( fae1-2 ), showed a significant change in expression in La-growth conditions. The CS-GSM predictions agreed with the experimental measurements under the assumption that the Fae1-2 is a part of the tetrahydrofolate-linked pathway. The cellular roles of the tungsten (W)-dependent formate dehydrogenase ( fdhAB ) and fae homologs ( fae1-2 and fae3 ) were investigated via mutagenesis. The phenotype of the f dhAB mutant followed the model prediction. Furthermore, a more significant reduction of the biomass yield was observed during growth in La-supplemented media, confirming a higher flux through formate. M. alcaliphilum 20Z R mutants lacking fae1-2 did not display any significant defects in methane or methanol-dependent growth. However, contrary to fae1, the fae1-2 homolog failed to restore the formaldehyde-activating enzyme function in complementation tests. Overall, the presented data suggest that the developed computational workflow supports the reconstruction and validation of CS-GSM networks of non-model microbes. IMPORTANCE The interrogation of various types of data is a routine strategy to explore the relationship between genotype and phenotype. An efficient approach for integrating and cross-comparing experimental multi-scale data in the context of whole-genome-based metabolic network reconstruction becomes a powerful tool that facilitates fundamental and applied research discoveries. The present study describes the reconstruction of a context-specific (CS) model for the methane-utilizing bacterium, Methylotuvimicrobium alcaliphilum 20Z R . M. alcaliphilum 20Z R is becoming an attractive microbial platform for the production of biofuels, chemicals, pharmaceuticals, and bio-sorbents for capturing atmospheric methane. We demonstrate that this pipeline can help reconstruct metabolic models that are similar to manually curated networks. Furthermore, the model is able to highlight previously overlooked pathways, thus advancing fundamental knowledge of non-model microbial systems or promoting their development toward biotechnological or environmental implementations.

Kulyashov, M. A.↗
DOE OSTI2015

Utilization of non-weapons-grade plutonium and highly enriched uranium with breeding of the {sup 233}U isotope in the VVER reactors using thorium and heavy water

A method for joint utilization of non-weapons-grade plutonium and highly enriched uranium in the thorium–uranium—plutonium oxide fuel of a water-moderated reactor with a varying water composition (D{sub 2}O, H{sub 2}O) is proposed. The method is characterized by efficient breeding of the {sup 233}U isotope and safe reactor operation and is comparatively simple to implement.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
DOE OSTI2018

Direct detection of MeV-scale dark matter utilizing germanium internal amplification for the charge created by the ionization of impurities

Light, MeV-scale dark matter (DM) is an exciting DM candidate that is undetectable by current experiments. A germanium (Ge) detector utilizing internal charge amplification for the charge carriers created by the ionization of impurities is a promising new technology with experimental sensitivity for detecting MeV-scale DM. We analyze the physics mechanisms of the signal formation, charge creation, charge internal amplification, and the projected sensitivity for directly detecting MeV-scale DM particles. We present a design for a novel Ge detector at helium temperature (~4 K) enabling ionization of impurities from DM impacts. With large localized E-fields, the ionized excitations can be accelerated to kinetic energies larger than the Ge bandgap at which point they can create additional electron–hole pairs, producing intrinsic amplification to achieve an ultra-low energy threshold of ~0.1 eV for detecting low-mass DM particles in the MeV scale. Correspondingly, such a Ge detector with 1 kg-year exposure will have high sensitivity to a DM-nucleon cross section of ~5 × 10 -45 cm 2 at a DM mass of ~10 MeV/c 2 and a DM-electron cross section of ~ 5 × 10 -46 cm 2 at a DM mass of 1 MeV/c 2 .

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2016

Tag-Split Cache for Efficient GPGPU Cache Utilization

Modern GPUs employ cache to improve memory system efficiency. However, large amount of cache space is underutilized due to irregular memory accesses and poor spatial locality which exhibited commonly in GPU applications. Our experiments show that using smaller cache lines could improve cache space utilization, but it also frequently suffers from significant performance loss by introducing large amount of extra cache requests. In this work, we propose a novel cache design named tag-split cache (TSC) that enables fine-grained cache storage to address the problem of cache space underutilization while keeping memory request number unchanged. TSC divides tag into two parts to reduce storage overhead, and it supports multiple cache line replacement in one cycle.

performance and energy optimization↗