Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “comprehension”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 127 records · Page 7
All sourcesNASA NTRSDOE OSTI
DOE OSTI2018

A Comprehensive Informative Metric for Analyzing HPC System Status Using the LogSCAN Platform

Log processing by Spark and Cassandra-based ANalytics (LogSCAN) is a newly developed analytical platform that provides flexible and scalable data gathering, transformation and computation. One major challenge is to effectively summarize the status of a complex computer system, such as the Titan supercomputer at the Oak Ridge Leadership Computing Facility (OLCF). Although there is plenty of operational and maintenance information collected and stored in real time, which may yield insights about short- and long-term system status, it is difficult to present this information in a comprehensive form. In this work, we present system information entropy (SIE), a newly developed metric that leverages the powers of traditional machine learning techniques and information theory. By compressing the multivariant multi-dimensional event information recorded during the operation of the targeted system into a single time series of SIE, we demonstrate that the historical system status can be sensitively represented concisely and comprehensively. Given a sharp indicator as SIE, we argue that follow-up analytics based on SIE will reveal in-depth knowledge about system status using other sophisticated approaches, such as pattern recognition in the temporal domain or causality analysis incorporating extra independent metrics of the system.

Hui, Yawei↗
DOE OSTI2023

A comparison of histopathology imaging comprehension algorithms based on multiple instance learning

Whole slide imaging (WSI), also called digital virtual microscopy, is a new imaging modality. It allows for the application of AI and machine learning methods to cancer pathology to help establish a means for the automatic diagnosis of cancer cases. However, designing machine-learning models for WSI is computationally challenging due to its required ultra-high resolution. The current state-of-the-art models use multiple instance learning (MIL). MIL is a weakly-supervised learning method in which the model uses an array of inferences from many smaller instances to make a final classification about the entire set. In the context of WSI, researchers divide the ultra-high-resolution image into many patches. The model then classifies the slide based on an array of inferences from the patches. Among several ways of making the final classification, attention-based mechanisms have resulted in superb accuracy scores. The Transformer, one attention-based algorithm, has reported substantial improvements for WSI comprehension tasks. In this project, we studied and compared several WSI comprehension algorithms. We used the following three datasets: CAMELYON16+17, TCGALung, and TCGA-Kidney. We found that attention-based MIL algorithms performed better than standard MIL algorithms for classifying WSI images, achieving a higher mean accuracy and AUC. However, none of the attention-based algorithms performed significantly better than the others, reporting accuracy scores that varied widely. Presumably, it is due to the limited availability of training samples in the data corpus. Since it is not easy to increase the samples from human subjects, some machine learning techniques like transfer learning could help mitigate this issue.

Saunders, Adam↗
DOE OSTI2013

A comprehensive investigation of the accuracy and reproducibility of a multitarget single isocenter VMAT radiosurgery technique

Purpose: Recent trends in stereotactic radiosurgery use multifocal volumetric modulated arc therapy (VMAT) plans to simultaneously treat several distinct targets. Conventional verification often involves low resolution measurements in a single plane, a cylinder, or intersecting planes of diodes or ion chambers. This work presents an investigation into the consistency and reproducibility of this new treatment technique using a comprehensive commissioned high-resolution 3D dosimetry system (PRESAGE{sup ®}/Optical-CT).Methods: A complex VMAT plan consisting of a single isocenter but five separate targets was created in Eclipse for a head phantom containing a cylindrical PRESAGE{sup ®} dosimetry insert of 11 cm diameter and height. The plan contained five VMAT arcs delivering target doses from 12 to 20 Gy. The treatment was delivered to four dosimeters positioned in the head phantom and repeated four times, yielding four separate 3D dosimetry verifications. Each delivery was completely independent and was given after image guided radiation therapy (IGRT) positioning using Brainlab ExacTrac and cone beam computed tomography. A final delivery was given to a modified insert containing a pin-point ion chamber enabling calibration of PRESAGE{sup ®} 3D data to dose. Dosimetric data were read out in an optical-CT scanner. Consistency and reproducibility of the treatment technique (including IGRT setup) was investigated by comparing the dose distributions in the four inserts, and with the predicted treatment planning system distribution.Results: Dose distributions from the four dosimeters were registered and analyzed to determine the mean and standard deviation at all points throughout the dosimeters. A dose standard deviation of <3% was found from dosimeter to dosimeter. Global 3D gamma maps show that the predicted and measured dose matched well [3D gamma passing rate was 98.0% (3%, 2 mm)].Conclusions: The deliveries of the irradiation were found to be consistent and matched the treatment plan, demonstrating high accuracy and reproducibility of both the treatment machine and the IGRT procedure. The complexity of the treatment (multiple arcs) and dosimetry (multiple strong gradients) pose a substantial challenge for comprehensive verification. 3D dosimetry can be uniquely effective in this scenario.

61 RADIATION PROTECTION AND DOSIMETRY↗
DOE OSTI2014

SU-E-T-88: Comprehensive Automated Daily QA for Hypo- Fractionated Treatments

Purpose: The trend towards more SBRT treatments with fewer high dose fractions places increased importance on daily QA. Patient plan specific QA with 3%/3mm gamma analysis and daily output constancy checks may not be enough to guarantee the level of accuracy required for SBRT treatments. But increasing the already extensive amount of QA procedures that are required is a daunting proposition. We performed a feasibility study for more comprehensive automated daily QA that could improve the diagnostic capabilities of QA without increasing workload. Methods: We performed the study on a Siemens Artiste linear accelerator using the integrated flat panel EPID. We included square fields, a picket fence, overlap and representative IMRT fields to measure output, flatness, symmetry, beam center, and percent difference from the standard. We also imposed a set of machine errors: MLC leaf position, machine output, and beam steering to compare with the standard. Results: Daily output was consistent within +/− 1%. Change in steering current by 1.4% and 2.4% resulted in a 3.2% and 6.3% change in flatness. 1 and 2mm MLC leaf offset errors were visibly obvious in difference plots, but passed a 3%/3mm gamma analysis. A simple test of transmission in a picket fence can catch a leaf offset error of a single leaf by 1mm. The entire morning QA sequence is performed in less than 30 minutes and images are automatically analyzed. Conclusion: Automated QA procedures could be used to provide more comprehensive information about the machine with less time and human involvement. We have also shown that other simple tests are better able to catch MLC leaf position errors than a 3%/3mm gamma analysis commonly used for IMRT and modulated arc treatments. Finally, this information could be used to watch trends of the machine and predict problems before they lead to costly machine downtime.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2014

SU-E-T-153: Establish a Comprehensive Patient-Specific Plan QA Database for Instituitional Quality Control Program

Purpose: Since the publication of TG-119, several new treatment techniques requiring new QA devices have been implemented in the clinic. To monitor and analyze our institutional QA performance, we have created a comprehensive QA database using Research Electronic Data Capture (REDCap). The database will also assist us in creating IMRT QA Analysis practice guidelines. Methods: Since Oct. 2013, 336 patient plan QA results were entered into the database. Plan parameters such as plan ID, treatment site, technique, energy, optimization constraints, modulation factor, leaf speed, leaf opening.etc were automatically extracted from the Varian Eclipse database to allow us to refine our evaluation and analysis method. Specific QA device, LINAC-related information, and measurement and analysis results were manually entered by the QA team. IMRT plans were measured using MapCHECK2 while RapidArc plans were measured using ArcCHECK. Distance-To-Agreement 3%/3mm without global maximum normalization was used. Results: The data indicates that different treatment techniques might benefit from a different site-specific action level(AL) depending on the complexity of the plan and optimization parameter used (e.g., breast IMRT QA= 97.8% and pelvis IMRT QA=93.1%). Different QA devices may also benefit from a different AL (MapCHECK2 = 94.1% while ArcCHECK = 83.0%). The relationship between the parameters and passing rate suggests that the complexity of each plan, characterized by leaf travel, leaf opening and modulation factor, affect the passing rate significantly. The database is reviewed regularly, and any abnormal point of the QA result or a trend of lower QA passing rate on a specific LINAC is further investigated. Conclusion: Establishing a comprehensive QA database provides an overview of the quality assurance program. It not only helps in answering the question “what is a reasonable and achievable standard for each institution”, but also saves time in monitoring and investigating the daily machine and QA performance.

07 ISOTOPE AND RADIATION SOURCES↗
DOE OSTI2014

SU-E-T-432: A Rapid and Comprehensive Procedure for Daily Proton QA

Purpose: The objective is to develop a rapid and comprehensive daily QA procedure implemented at the S. Lee Kling Proton Therapy Center at Barnes-Jewish Hospital. Methods: A scribed phantom with imbedded fiducials is used for checking lasers accuracy followed by couch isocentricity and for X-ray imaging congruence with isocenter. A Daily QA3 device (Sun Nuclear, FL) was used to check output, range and profiles. Five chambers in the central region possess various build-ups. After converting the thickness of the inherent build-ups into water equivalent thickness (WET) for proton, range of any beam can be checked with additional build-up on the Daily QA3 device. In our procedure, 3 beams from 3 bands (large, small and deep) with nominal range of 20 cm are checked daily. 17cm plastic water with WET of 16.92cm are used as additional build-up so that four chambers sit on the SOBP plateau at various depths and one sit on the distal fall off. Reading from the five chambers are fitted to an error function that has been parameterized to match the SOBP with the same nominal range. Shifting of the error function to maximize the correlation between measurements and the error function is deemed as the range shift from the nominal value. Results: We have found couch isocentricity maintained over 180 degrees. Imaging system exhibits accuracy in regard to imaging and mechanical isocenters. Ranges are within 1mm accuracy from measurements in water tank, and sensitive to change of sub-millimeter. Data acquired since the start of operation show outputs, profiles and range stay within 1% or 1mm from baselines. The whole procedure takes about 40 minutes. Conclusion: Taking advantage of the design of Daily QA3 device turns the device originally designed for photon and electron into a comprehensive and rapid tool for proton daily QA.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2015

SU-E-J-53: A Phantom Design to Assist Patient Position Verification System in Daily Image-Guided RT and Comprehensive QA Measurements

Purpose This study is to implement a homemade novel device with surface locking couch index to check daily radiograph (DR) function of adaPTInsight™, stereoscopic image guided system (SIGS), for proton therapy. The comprehensive daily QA checks of proton pencil beam output, field size, flatness and symmetry of spots and energy layers will be followed by using MatriXX dosimetry device. Methods The iBa MatriXX device was used to perform daily dosimetry which is also used to perform SIGS checks. A set of markers were attached to surface of MatriXX device in alignment of DRR of reconstructed CT images and daily DR. The novel device allows MatriXX to be fit into the cradle which was locked by couch index bars on couch surface. This will keep the MatriXX at same XY plane daily with exact coordinates. Couch height Z will be adjusted according to imaging to check isocenter-laser coincidence accuracy. Results adaPTInsight™ provides robotic couch to move in 6-degree coordinate system to align the dosimetry device to be within 1.0 mm / 1.0°. The daily constancy was tightened to be ± 0.5 mm / 0.3° compared to 1.0 mm / 1.0° before. For gantry at 0° and couch all 0° angles (@ Rt ARM 0 setting), offsets measured of the couch systems were ≤ 0.5° in roll, yaw and pitch dimensions. Conclusion Simplicity of novel device made daily image guided QA consistent with accuracy. The offset of the MatriXX isocenter-laser coincident was reproducible. Such easy task not only speeds up the setup, but it increases confidence level in detailed daily comprehensive measurements. The total SIGS alignment time has been shortened with less setup error. This device will enhance our experiences for the future QA when cone beam CT imaging modality becomes available at proton therapy center.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

Technical Report: TG-142 compliant and comprehensive quality assurance tests for respiratory gating

Purpose: To develop and establish a comprehensive gating commissioning and quality assurance procedure in compliance with TG-142. Methods: Eight Varian TrueBeam Linacs were used for this study. Gating commissioning included an end-to-end test and baseline establishment. The end-to-end test was performed using a CIRS dynamic thoracic phantom with a moving cylinder inside the lung, which was used for carrying both optically simulated luminescence detectors (OSLDs) and Gafchromic EBT2 films while the target is moving, for a point dose check and 2D profile check. In addition, baselines were established for beam-on temporal delay and calibration of the surrogate, for both megavoltage (MV) and kilovoltage (kV) beams. A motion simulation device (MotionSim) was used to provide periodic motion on a platform, in synchronizing with a surrogate motion. The overall accuracy and uncertainties were analyzed and compared. Results: The OSLD readings were within 5% compared to the planned dose (within measurement uncertainty) for both phase and amplitude gated deliveries. Film results showed less than 3% agreement to the predicted dose with a standard sinusoid motion. The gate-on temporal accuracy was averaged at 139 ± 10 ms for MV beams and 92 ± 11 ms for kV beams. The temporal delay of the surrogate motion depends on the motion speed and was averaged at 54.6 ± 3.1 ms for slow, 24.9 ± 2.9 ms for intermediate, and 23.0 ± 20.1 ms for fast speed. Conclusions: A comprehensive gating commissioning procedure was introduced for verifying the output accuracy and establishing the temporal accuracy baselines with respiratory gating. The baselines are needed for routine quality assurance tests, as suggested by TG-142.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

A comprehensive formulation for volumetric modulated arc therapy planning

Purpose: Volumetric modulated arc therapy (VMAT) is a widely employed radiation therapy technique, showing comparable dosimetry to static beam intensity modulated radiation therapy (IMRT) with reduced monitor units and treatment time. However, the current VMAT optimization has various greedy heuristics employed for an empirical solution, which jeopardizes plan consistency and quality. The authors introduce a novel direct aperture optimization method for VMAT to overcome these limitations. Methods: The comprehensive VMAT (comVMAT) planning was formulated as an optimization problem with an L2-norm fidelity term to penalize the difference between the optimized dose and the prescribed dose, as well as an anisotropic total variation term to promote piecewise continuity in the fluence maps, preparing it for direct aperture optimization. A level set function was used to describe the aperture shapes and the difference between aperture shapes at adjacent angles was penalized to control MLC motion range. A proximal-class optimization solver was adopted to solve the large scale optimization problem, and an alternating optimization strategy was implemented to solve the fluence intensity and aperture shapes simultaneously. Single arc comVMAT plans, utilizing 180 beams with 2° angular resolution, were generated for a glioblastoma multiforme case, a lung (LNG) case, and two head and neck cases—one with three PTVs (H&N{sub 3PTV}) and one with foue PTVs (H&N{sub 4PTV})—to test the efficacy. The plans were optimized using an alternating optimization strategy. The plans were compared against the clinical VMAT (clnVMAT) plans utilizing two overlapping coplanar arcs for treatment. Results: The optimization of the comVMAT plans had converged within 600 iterations of the block minimization algorithm. comVMAT plans were able to consistently reduce the dose to all organs-at-risk (OARs) as compared to the clnVMAT plans. On average, comVMAT plans reduced the max and mean OAR dose by 6.59% and 7.45%, respectively, of the prescription dose. Reductions in max dose and mean dose were as high as 14.5 Gy in the LNG case and 15.3 Gy in the H&N{sub 3PTV} case. PTV coverages measured by D95, D98, and D99 were within 0.25% of the prescription dose. By comprehensively optimizing all beams, the comVMAT optimizer gained the freedom to allow some selected beams to deliver higher intensities, yielding a dose distribution that resembles a static beam IMRT plan with beam orientation optimization. Conclusions: The novel nongreedy VMAT approach simultaneously optimizes all beams in an arc and then directly generates deliverable apertures. The single arc VMAT approach thus fully utilizes the digital Linac’s capability in dose rate and gantry rotation speed modulation. In practice, the new single VMAT algorithm generates plans superior to existing VMAT algorithms utilizing two arcs.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Comprehensive Physical Activity Assessment During U.S. Army Basic Combat Training

Abstract Alemany, JA, Pierce, JR, Bornstein, DB, Grier, TL, Jones, BH, and Glover, SH. Comprehensive physical activity assessment during U.S. Army Basic Combat Training. J Strength Cond Res 36(12): 3505–3512, 2022—Physical activity (PA) volume, intensity, and qualitative contextual information regarding activity type and loads carried are limited during U.S. Army Basic Combat Training (BCT). The purpose of this study was to characterize daily (05:00–20:00 hours) PA during BCT using a comprehensive approach. During 2 10-week BCT cycles ( n = 40 trainees per cycle), pedometers, accelerometers, and direct observation were used to estimate daily step count, PA volume, and intensity. Physical activity intensity was categorized by metabolic equivalents (METs) such as “sedentary” (1–2 METs), “light” (2–3 METs), “moderate” (3–6 METs), or “vigorous” (≥6 METs). Daily PA data were analyzed longitudinally using linear mixed models, with significance set at p ≤ 0.05. The mean daily step count was 13,459 ± 4,376 steps, and the mean daily accelerometer-assessed PA volume and intensity were as follows: sedentary: 505 ± 98 minutes, light: 190 ± 78 minutes, moderate: 168 ± 51 minutes, and vigorous: 14 ± 14 minutes, with no differences between cycles for all measures ( p > 0.50). Cumulative time on feet (∼50%) and sitting (20–25%) accounted for most daily activity types during both cycles. Trainees, on average, carried between 3 and 9 kg, and ≥9 kg, for 60% and 10% of the monitored day, respectively. Basic Combat Training's physical demands are high, where trainees achieved 1.7 to 2.7 times greater daily ambulation and 6 times the recommended weekly moderate-to-vigorous PA compared with civilian counterparts and performed weight-bearing load carriage for nearly half of the day. Basic Combat Training-associated PA may increase injury risk among trainees unaccustomed to arduous PA and exercise. Implementing national PA policies to improve physical fitness and facilitate acclimatization to BCT's high physical demands could reduce public health burdens and military nonreadiness.

Sport Sciences↗
DOE OSTI2021

Analysis and Integration of the Hydraulic Fracturing Test Site-2 (HFTS-2) Comprehensive Dataset

Hydraulic Fracturing Test Site-2 (HFTS-2) is a field-based research experiment performed in the Permian (Delaware) Basin. The unique aspect of this program was the acquisition of a unique, comprehensive, diagnostic dataset. Additionally, shorter parent wells drilled three years before the child wells offered clear distinction between the stages influenced by parent-child effects and the stages without any effects. The goal of this study was to analyze and integrate this comprehensive diagnostic dataset to understand the areal and vertical extent of hydraulic fractures (HF). The paper also provides insights on the effects of parent wells’ depletion on child well HF geometry based on various monitoring methods and subsurface models. Areal and vertical coverage for all HFTS-2 wells during stimulation and depletion was estimated based on analysis and interpretation of diagnostics and advanced modeling results. HFTS-2 diagnostics included microseismic (MS), pre- and post-stimulation logs and cores, bottomhole gauges, and fiber optic (FO) data. The diagnostics results (MS, FO, image logs) were integrated and used to calibrate subsurface models. Additional field tests were designed and implemented for depletion monitoring. The tailored program for monitoring depletion included vertical and slant well pressures, interference testing, and a vertical strain depletion trial. Areal Coverage: Conventional MS (and FO MS) were used to compute HF dimensions, which were compared with diagnostics (FO strain, gauge, image logs) observations and calibrated subsurface models. A post-production interference test did not show offset well communication. Vertical Coverage: Vertical coverage during stimulation was monitored using a vertical monitoring well. The stronger mechanical strain signals showed good correlation with MS event intensities, geomechanical properties, and gauge inferences. Vertical depletion was estimated based on vertical/slant well gauges and strain depletion tests. Parent-Child Effects: Diagnostics and calibrated subsurface models show asymmetry in child well fracture geometries for stages that overlap parent wells. Child well image logs serve as a good indicator for parent Downloaded from http://onepetro.org/URTECONF/proceedings-pdf/21URTC/2-21URTC/D021S031R004/2477423/urtec-2021-5241-ms.pdf/1 by Carol Worster on 28 February 2022 URTeC 5241 well HF tracking. Child well MS events had an eastward bias, in line with pre-stimulation image logs, and was confirmed by parent well frac hits. Novel/Additive Information: The dataset presents a unique, over-constrained problem space to compare independent techniques to arrive at HF metrics (i.e., stimulation height and/or half-length), unlike a single source dataset, in which calibration is done using available data to guide predictions. Here, the asymmetry in HF geometry seen in the stages influenced by parent-child effects offers unique insights into well spacing and landing, which are key capital decisions the unconventional resources industry is seeking to optimize.

58 GEOSCIENCES↗
DOE OSTI2015

Quinault Indian Nation Comprehensive Biomass Strategic Planning Project

The overall purposes of the Quinault Indian Nation’s Comprehensive Biomass Strategic Planning Project were to: (1) Identify and confirm community and tribal energy needs; (2) Conducting an inventory of sustainable biomass feedstock availability; (3) Development of a biomass energy vision statement with goals and objectives; (4) Identification and assessment of biomass options for both demand-side and supply side that are viable to the Quinault Indian Nation (QIN); and (5) Developing a long-term biomass strategy consistent with the long-term overall energy goals of the QIN. This Comprehensive Biomass Strategic Planning Project is consistent with the QIN’s prior two-year DOE Renewable Energy Study from 2004 through 2006. That study revealed that the most viable options to the QIN’s renewable energy options were biomass and energy efficiency best practices. QIN's Biomass Strategic Planning Project is focused on using forest slash in chipped form as feedstock for fuel pellet manufacturing in support of a tribal biomass heating facility. This biomass heating facility has been engineered and designed to heat existing tribal facilities as well as tribal facilities currently being planned including a new K-12 School.

09 BIOMASS FUELS↗
DOE OSTI2022

A Comprehensive Economic Coal Transition in South Asia

Many countries are considering accelerating their coal transition. A coal transition refers to an energy sector’s shift from a reliance on coal toward an energy mix largely based on cleaner fuels and renewable energy sources. Such a transition is not just related to greenhouse gas emissions, but also encompasses a range of benefits, recognizing that global energy costs and options are changing. Since 2015, proposed new coal power capacity has dropped by three-quarters globally, leaving only a few countries that develop coal-fired power plants at scale (Littlecott et al., 2021). Historic steps were taken at the United Nations Climate Change 26th Conference of Parties (COP26) in Glasgow, as countries pledged to stop new coal builds, end international coal financing, phase down and phase out unabated coal use, and transition to clean energy. In South Asia, there have been several indicators suggesting that countries may be open to moving toward a coal transition. For example, the number of coal power plants under development across South Asia has decreased by 87% since 2015 (Littlecott et al., 2021). However, the challenges of assuring a just transition are substantial. Because coal plays a critical role in the energy and economic systems in South Asia, especially India, moving away from coal means realizing a broader country-wide economic and social transition. A comprehensive, integrated transition strategy for each state is thus needed urgently. This report briefly reviews the current trends and policies on coal in South Asian countries, develops a framework for a comprehensive economic coal transition, and assesses the opportunities and challenges of the transition in key countries. Several important findings emerge from the analysis. First, a coal transition can support overall economic growth and stability. Financial advantages to a well-planned coal transition include mitigating the risk of stranded assets and taking advantage of low-cost renewables. As a global coal transition proceeds, funds are being diverted from new unabated coal power plants, and utilization rates are declining. The likelihood that coal assets will become stranded is increasing, and the potential for future losses therefore increases as well. Second, coal imports in South Asia are rising. Of the coal consumed in Bangladesh, India, Nepal, and Sri Lanka, 32% is imported; this number increases to 94% when excluding India (International Energy Agency [IEA], 2021d). This illustrates a serious energy security risk. One example is the recent increase in coal prices in South Asia, to be discussed in Section 2.2.1. A diverse energy portfolio that incorporates local renewable energy can provide resilience in the face of changing commodity prices and availability. Third, the social benefits of a coal transition include positive health impacts and broader economic improvements in job creation, although assuring a just transition may be a challenge. Phasing out or phasing down coal can significantly reduce air pollutant emissions and therefore minimize associated premature mortality and improve life expectancy. Additional societal benefits of a coal transition include the high economy-wide potential for job creation, although it creates challenges in terms of reintegration and resettlement for coal miners and their communities.

01 COAL, LIGNITE, AND PEAT↗
DOE OSTI2024

Power Supply Options for the Marpi Landfill, Saipan: Comprehensive Feasibility Study

The Marpi Landfill (“Marpi” or “the landfill”), located on the northern end of the island of Saipan in the Commonwealth of the Northern Mariana Islands (CNMI), is powered by a single on-site diesel generator that only operates when the landfill is open and staffed. The project team, composed of representatives of the Department of Public Works and the Office of Planning and Development (OPD), aspires to provide the Marpi Landfill with 24-hour power availability despite its remote location to increase the use of sustainable energy and to ensure environmentally compliant landfill operations. This is consistent with the sustainable development goals documented in the 2021–2030 Comprehensive Sustainable Development Plan (OPD 2021), including Goal #12 (ensure environmentally compliant waste management facilities) and Goal #7 (renewable energy deployment). Further, the CNMI has a 20% target for renewable energy consumption by 2030, as documented in the 2021–2030 Comprehensive Sustainable Development Plan (OPD 2021) and the renewable portfolio standard (Public Law 18-62). To accomplish these goals, the Federal Emergency Management Agency, through its Interagency Reimbursable Work Agreement with the U.S. Department of Energy, funded a feasibility study and follow-up study in 2023–2024 to assess and prioritize power supply options for the landfill. This report combines the results from both feasibility studies.

14 SOLAR ENERGY↗
DOE OSTI2025

Comprehensive Neural Posterior Estimation for Galaxy-Galaxy Strong Lensing

We present a deep learning model based on neural posterior estimation (NPE) for comprehensive extraction of astrophysical parameters from galaxy-scale strong gravitational lenses. The unprecedentedly large amount of galaxy-scale strong lenses expected in future cosmological surveys (${\cal O}(10^5)$) promises to enable valuable statistical constraints in various studies ranging from galaxy formation to the nature of dark matter, but it also poses a significant challenge for traditional modelling pipelines. To this end, our automated model includes several new, state-of-the-art features and approaches leveraging the framework of simulation-based inference (SBI). We infer a total of 20 parameters describing the mass and light profiles of both lens and source galaxies, using simulated raw multi-band data modelled under noise and observing conditions expected by the Legacy Survey of Space and Time (LSST), with its summary statistics generated by a residual network. We examine the efficacy of multi-band data in extracting nearly 20 model parameters simultaneous from strong lensing images including lens light. Finally, We perform a comprehensive set of diagnostics for SBI models, evaluating the model's prediction accuracy, stability, and uncertainty quantification.

Zhao, Roy J. [Chicago U., KICP]↗
DOE OSTI2020

FeGenie: a comprehensive tool for the identification of iron genes and iron gene neighborhoods in genomes and metagenome assemblies

Iron is a micronutrient for nearly all life on Earth. It can be used as an electron donor and electron acceptor by iron-oxidizing and iron-reducing microorganisms and is used in a variety of biological processes, including photosynthesis and respiration. While it is the fourth most abundant metal in the Earth’s crust, iron is often limiting for growth in oxic environments because it is readily oxidized and precipitated. Much of our understanding of how microorganisms compete for and utilize iron is based on laboratory experiments. However, the advent of next-generation sequencing and surge in publicly available sequence data has made it possible to probe the structure and function of microbial communities in the environment. To bridge the gap between our understanding of iron acquisition, iron redox cycling, iron storage, and magnetosome formation in model microorganisms and the plethora of sequence data available from environmental studies, we have created a comprehensive database of hidden Markov models (HMMs) based on genes related to iron acquisition, storage, and reduction/oxidation in Bacteria and Archaea. Along with this database, we present FeGenie, a bioinformatics tool that accepts genome and metagenome assemblies as input and uses our comprehensive HMM database to annotate provided datasets with respect to iron-related genes and gene neighborhood. An important contribution of this tool is the efficient identification of genes involved in iron oxidation and dissimilatory iron reduction, which have been largely overlooked by standard annotation pipelines. We validated FeGenie against a selected set of 28 isolate genomes and showcase its utility in exploring iron genes present in 27 metagenomes, 4 isolate genomes from human oral biofilms, and 17 genomes from candidate organisms, including members of the candidate phyla radiation. We show that FeGenie accurately identifies iron genes in isolates. Furthermore, analysis of metagenomes using FeGenie demonstrates that the iron gene repertoire and abundance of each environment is correlated with iron richness. While this tool will not replace the reliability of culture-dependent analyses of microbial physiology, it provides reliable predictions derived from the most up-to-date genetic markers. FeGenie’s database will be maintained and continually updated as new genes are discovered.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

MetaboTools: A comprehensive toolbox for analysis of genome-scale metabolic models

Metabolomic data sets provide a direct read-out of cellular phenotypes and are increasingly generated to study biological questions. Previous work, by us and others, revealed the potential of analyzing extracellular metabolomic data in the context of the metabolic model using constraint-based modeling. With the MetaboTools, we make our methods available to the broader scientific community. The MetaboTools consist of a protocol, a toolbox, and tutorials of two use cases. The protocol describes, in a step-wise manner, the workflow of data integration, and computational analysis. The MetaboTools comprise the Matlab code required to complete the workflow described in the protocol. Tutorials explain the computational steps for integration of two different data sets and demonstrate a comprehensive set of methods for the computational analysis of metabolic models and stratification thereof into different phenotypes. The presented workflow supports integrative analysis of multiple omics data sets. Importantly, all analysis tools can be applied to metabolic models without performing the entire workflow. Taken together, the MetaboTools constitute a comprehensive guide to the intra-model analysis of extracellular metabolomic data from microbial, plant, or human cells. In conclusion, this computational modeling resource offers a broad set of computational analysis tools for a wide biomedical and non-biomedical research community.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Comprehensive Assessments of RNA-seq by the SEQC Consortium: FDA-Led Efforts Advance Precision Medicine

Studies on gene expression in response to therapy have led to the discovery of pharmacogenomics biomarkers and advances in precision medicine. Whole transcriptome sequencing (RNA-seq) is an emerging tool for profiling gene expression and has received wide adoption in the biomedical research community. However, its value in regulatory decision making requires rigorous assessment and consensus between various stakeholders, including the research community, regulatory agencies, and industry. The FDA-led SEquencing Quality Control (SEQC) consortium has made considerable progress in this direction, and is the subject of this review. Specifically, three RNA-seq platforms (Illumina HiSeq, Life Technologies SOLiD, and Roche 454) were extensively evaluated at multiple sites to assess cross-site and cross-platform reproducibility. The results demonstrated that relative gene expression measurements were consistently comparable across labs and platforms, but not so for the measurement of absolute expression levels. As part of the quality evaluation several studies were included to evaluate the utility of RNA-seq in clinical settings and safety assessment. The neuroblastoma study profiled tumor samples from 498 pediatric neuroblastoma patients by both microarray and RNA-seq. RNA-seq offers more utilities than microarray in determining the transcriptomic characteristics of cancer. However, RNA-seq and microarray-based models were comparable in clinical endpoint prediction, even when including additional features unique to RNA-seq beyond gene expression. The toxicogenomics study compared microarray and RNA-seq profiles of the liver samples from rats exposed to 27 different chemicals representing multiple toxicity modes of action. Cross-platform concordance was dependent on chemical treatment and transcript abundance. Though both RNA-seq and microarray are suitable for developing gene expression based predictive models with comparable prediction performance, RNA-seq offers advantages over microarray in profiling genes with low expression. The rat BodyMap study provided a comprehensive rat transcriptomic body map by performing RNA-Seq on 320 samples from 11 organs in either sex of juvenile, adolescent, adult and aged Fischer 344 rats. Lastly, the transferability study demonstrated that signature genes of predictive models are reciprocally transferable between microarray and RNA-seq data for model development using a comprehensive approach with two large clinical data sets. This result suggests continued usefulness of legacy microarray data in the coming RNA-seq era. In conclusion, the SEQC project enhances our understanding of RNA-seq and provides valuable guidelines for RNA-seq based clinical application and safety evaluation to advance precision medicine.

59 BASIC BIOLOGICAL SCIENCES↗