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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 73 records · Page 4
All sourcesNASA NTRSDOE OSTI
DOE OSTI2014

TU-C-17A-09: Multi-Case Knowledge-Based IMRT Treatment Planning in Head and Neck Cancer: Are Six Heads Better Than One?

Purpose: HNC IMRT treatment planning is a challenging process that relies heavily on the planner’s experience. Previously, we used the single, best match from a library of manually planned cases to semi-automatically generate IMRT plans for a new patient. The current multi-case Knowledge Based Radiation Therapy (MC-KBRT) study utilized different matching cases for each of six individual organs-at-risk (OARs), then combined those six cases to create the new treatment plan. Methods: From a database of 103 patient plans created by experienced planners, MC-KBRT plans were created for 40 (17 unilateral and 23 bilateral) HNC “query” patients. For each case, 2D beam’s-eye-view images were used to find similar geometric “match” patients separately for each of 6 OARs. Dose distributions for each OAR from the 6 matching cases were combined and then warped to suit the query case’s geometry. The dose-volume constraints were used to create the new query treatment plan without the need for human decision-making throughout the IMRT optimization. The optimized MC-KBRT plans were compared against the clinically approved plans and Version 1 (original KBRT) using the dose metrics: mean, median, and maximum (brainstem and cord+5mm) doses. Results: Compared to Version 1, MC-KBRT had no significant reduction of the dose to any of the OARs in either unilateral/bilateral cases. Compared to the manually-planned unilateral cases, there was significant reduction of the oral cavity mean/median dose (>2Gy) at the expense of the contralateral parotid. Compared to the manually-planned bilateral cases, reduction of dose was significant in the ipsilateral parotid, larynx, and oral cavity (>3Gy mean/median) while maintaining PTV coverage. Conclusion: MC-KBRT planning in head and neck cancer generates IMRT plans with equivalent dose sparing to manually created plans. MC-KBRT using multiple case matches does not show significant dose reduction compared to using a single match case with dose warping.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Transforming the study of organisms: Phenomic data models and knowledge bases

The rapidly decreasing cost of gene sequencing has resulted in a deluge of genomic data from across the tree of life; however, outside a few model organism databases, genomic data are limited in their scientific impact because they are not accompanied by computable phenomic data. The majority of phenomic data are contained in countless small, heterogeneous phenotypic data sets that are very difficult or impossible to integrate at scale because of variable formats, lack of digitization, and linguistic problems. One powerful solution is to represent phenotypic data using data models with precise, computable semantics, but adoption of semantic standards for representing phenotypic data has been slow, especially in biodiversity and ecology. Some phenotypic and trait data are available in a semantic language from knowledge bases, but these are often not interoperable. In this review, we will compare and contrast existing ontology and data models, focusing on nonhuman phenotypes and traits. We discuss barriers to integration of phenotypic data and make recommendations for developing an operationally useful, semantically interoperable phenotypic data ecosystem.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2013

Fuzzy Linguistic Knowledge Based Behavior Extraction for Building Energy Management Systems

Significant portion of world energy production is consumed by building Heating, Ventilation and Air Conditioning (HVAC) units. Thus along with occupant comfort, energy efficiency is also an important factor in HVAC control. Modern buildings use advanced Multiple Input Multiple Output (MIMO) control schemes to realize these goals. However, since the performance of HVAC units is dependent on many criteria including uncertainties in weather, number of occupants, and thermal state, the performance of current state of the art systems are sub-optimal. Furthermore, because of the large number of sensors in buildings, and the high frequency of data collection, large amount of information is available. Therefore, important behavior of buildings that compromise energy efficiency or occupant comfort is difficult to identify. This paper presents an easy to use and understandable framework for identifying such behavior. The presented framework uses human understandable knowledge-base to extract important behavior of buildings and present it to users via a graphical user interface. The presented framework was tested on a building in the Pacific Northwest and was shown to be able to identify important behavior that relates to energy efficiency and occupant comfort.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2015

Knowledge-based fault diagnosis system for refuse collection vehicle

The refuse collection vehicle is manufactured by local vehicle body manufacturer. Currently; the company supplied six model of the waste compactor truck to the local authority as well as waste management company. The company is facing difficulty to acquire the knowledge from the expert when the expert is absence. To solve the problem, the knowledge from the expert can be stored in the expert system. The expert system is able to provide necessary support to the company when the expert is not available. The implementation of the process and tool is able to be standardize and more accurate. The knowledge that input to the expert system is based on design guidelines and experience from the expert. This project highlighted another application on knowledge-based system (KBS) approached in trouble shooting of the refuse collection vehicle production process. The main aim of the research is to develop a novel expert fault diagnosis system framework for the refuse collection vehicle.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2024

An ontology-based knowledge graph for representing interactions involving RNA molecules

The "RNA world" represents a novel frontier for the study of fundamental biological processes and human diseases and is paving the way for the development of new drugs tailored to each patient's biomolecular characteristics. Although scientific data about coding and non-coding RNA molecules are constantly produced and available from public repositories, they are scattered across different databases and a centralized, uniform, and semantically consistent representation of the "RNA world" is still lacking. We propose RNA-KG, a knowledge graph (KG) encompassing biological knowledge about RNAs gathered from more than 60 public databases, integrating functional relationships with genes, proteins, and chemicals and ontologically grounded biomedical concepts. To develop RNA-KG, we first identified, pre-processed, and characterized each data source; next, we built a meta-graph that provides an ontological description of the KG by representing all the bio-molecular entities and medical concepts of interest in this domain, as well as the types of interactions connecting them. Finally, we leveraged an instance-based semantically abstracted knowledge model to specify the ontological alignment according to which RNA-KG was generated. RNA-KG can be downloaded in different formats and also queried by a SPARQL endpoint. A thorough topological analysis of the resulting heterogeneous graph provides further insights into the characteristics of the "RNA world". RNA-KG can be both directly explored and visualized, and/or analyzed by applying computational methods to infer bio-medical knowledge from its heterogeneous nodes and edges. The resource can be easily updated with new experimental data, and specific views of the overall KG can be extracted according to the bio-medical problem to be studied.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

SU-E-P-43: A Knowledge Based Approach to Guidelines for Software Safety

Purpose: In the fall of 2012, a survey was distributed to medical physicists across Canada. The survey asked the respondents to comment on various aspects of software development and use in their clinic. The survey revealed that most centers employ locally produced (in-house) software of some kind. The respondents also indicated an interest in having software guidelines, but cautioned that the realities of cancer clinics include variations, that preclude a simple solution. Traditional guidelines typically involve periodically repeating a set of prescribed tests with defined tolerance limits. However, applying a similar formula to software is problematic since it assumes that the users have a perfect knowledge of how and when to apply the software and that if the software operates correctly under one set of conditions it will operate correctly under all conditions Methods: In the approach presented here the personnel involved with the software are included as an integral part of the system. Activities performed to improve the safety of the software are done with both software and people in mind. A learning oriented approach is taken, following the premise that the best approach to safety is increasing the understanding of those associated with the use or development of the software. Results: The software guidance document is organized by areas of knowledge related to use and development of software. The categories include: knowledge of the underlying algorithm and its limitations; knowledge of the operation of the software, such as input values, parameters, error messages, and interpretation of output; and knowledge of the environment for the software including both data and users. Conclusion: We propose a new approach to developing guidelines which is based on acquiring knowledge-rather than performing tests. The ultimate goal is to provide robust software guidelines which will be practical and effective.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2014

Advancing the hydrogen safety knowledge base

The International Energy Agency's Hydrogen Implementing Agreement (IEA HIA) was established in 1977 to pursue collaborative hydrogen research and development and information exchange among its member countries. Information and knowledge dissemination is a key aspect of the work within IEA HIA tasks, and case studies, technical reports and presentations/publications often result from the collaborative efforts. The work conducted in hydrogen safety under Task 31 and its predecessor, Task 19, can positively impact the objectives of national programs even in cases for which a specific task report is not published. As a result, the interactions within Task 31 illustrate how technology information and knowledge exchange among participating hydrogen safety experts serve the objectives intended by the IEA HIA.

08 HYDROGEN↗
DOE OSTI2012

Use of knowledge-based restraints in phenix.refine to improve macromolecular refinement at low resolution

Traditional methods for macromolecular refinement often have limited success at low resolution (3.0–3.5 Å or worse), producing models that score poorly on crystallographic and geometric validation criteria. To improve low-resolution refinement, knowledge from macromolecular chemistry and homology was used to add three new coordinate-restraint functions to the refinement program phenix.refine . Firstly, a `reference-model' method uses an identical or homologous higher resolution model to add restraints on torsion angles to the geometric target function. Secondly, automatic restraints for common secondary-structure elements in proteins and nucleic acids were implemented that can help to preserve the secondary-structure geometry, which is often distorted at low resolution. Lastly, we have implemented Ramachandran-based restraints on the backbone torsion angles. In this method, a φ,ψ term is added to the geometric target function to minimize a modified Ramachandran landscape that smoothly combines favorable peaks identified from nonredundant high-quality data with unfavorable peaks calculated using a clash-based pseudo-energy function. All three methods show improved MolProbity validation statistics, typically complemented by a lowered R free and a decreased gap between R work and R free .

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

IMG-ABC. A knowledge base to fuel discovery of biosynthetic gene clusters and novel secondary metabolites

In the discovery of secondary metabolites, analysis of sequence data is a promising exploration path that remains largely underutilized due to the lack of computational platforms that enable such a systematic approach on a large scale. In this work, we present IMG-ABC (https://img.jgi.doe.gov/abc), an atlas of biosynthetic gene clusters within the Integrated Microbial Genomes (IMG) system, which is aimed at harnessing the power of “big” genomic data for discovering small molecules. IMG-ABC relies on IMG’s comprehensive integrated structural and functional genomic data for the analysis of biosynthetic gene clusters (BCs) and associated secondary metabolites (SMs). SMs and BCs serve as the two main classes of objects in IMG-ABC, each with a rich collection of attributes. A unique feature of IMG-ABC is the incorporation of both experimentally validated and computationally predicted BCs in genomes as well as metagenomes, thus identifying BCs in uncultured populations and rare taxa. We demonstrate the strength of IMG-ABC’s focused integrated analysis tools in enabling the exploration of microbial secondary metabolism on a global scale, through the discovery of phenazine-producing clusters for the first time in lphaproteobacteria . IMG-ABC strives to fill the long-existent void of resources for computational exploration of the secondary metabolism universe; its underlying scalable framework enables traversal of uncovered phylogenetic and chemical structure space, serving as a doorway to a new era in the discovery of novel molecules. IMG-ABC is the largest publicly available database of predicted and experimental biosynthetic gene clusters and the secondary metabolites they produce. The system also includes powerful search and analysis tools that are integrated with IMG’s extensive genomic/metagenomic data and analysis tool kits. As new research on biosynthetic gene clusters and secondary metabolites is published and more genomes are sequenced, IMG-ABC will continue to expand, with the goal of becoming an essential component of any bioinformatic exploration of the secondary metabolism world.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Screening a knowledge‐based library of low molecular weight compounds against the proline biosynthetic enzyme 1‐pyrroline‐5‐carboxylate 1 ( PYCR1)

Abstract Δ 1 ‐pyrroline‐5‐carboxylate reductase isoform 1 (PYCR1) is the last enzyme of proline biosynthesis and catalyzes the NAD(P)H‐dependent reduction of Δ 1 ‐pyrroline‐5‐carboxylate toL‐proline. High PYCR1 gene expression is observed in many cancers and linked to poor patient outcomes and tumor aggressiveness. The knockdown of thePYCR1gene or the inhibition of PYCR1 enzyme has been shown to inhibit tumorigenesis in cancer cells and animal models of cancer, motivating inhibitor discovery. We screened a library of 71 low molecular weight compounds (average MW of 131 Da) against PYCR1 using an enzyme activity assay. Hit compounds were validated with X‐ray crystallography and kinetic assays to determine affinity parameters. The library was counter‐screened against human Δ 1 ‐pyrroline‐5‐carboxylate reductase isoform 3 and proline dehydrogenase (PRODH) to assess specificity/promiscuity. Twelve PYCR1 and one PRODH inhibitor crystal structures were determined. Three compounds inhibit PYCR1 with competitive inhibition parameter of 100 μM or lower. Among these, (S)‐tetrahydro‐2H‐pyran‐2‐carboxylic acid (70 μM) has higher affinity than the current best tool compoundN‐formyl‐l‐proline, is 30 times more specific for PYCR1 over human Δ 1 ‐pyrroline‐5‐carboxylate reductase isoform 3, and negligibly inhibits PRODH. Structure‐affinity relationships suggest that hydrogen bonding of the heteroatom of this compound is important for binding to PYCR1. The structures of PYCR1 and PRODH complexed with 1‐hydroxyethane‐1‐sulfonate demonstrate that the sulfonate group is a suitable replacement for the carboxylate anchor. This result suggests that the exploration of carboxylic acid isosteres may be a promising strategy for discovering new classes of PYCR1 and PRODH inhibitors. The structure of PYCR1 complexed withl‐pipecolate and NADH supports the hypothesis that PYCR1 has an alternative function in lysine metabolism.

Biochemistry & Molecular Biology↗
DOE OSTI2017

Elastic knowledge base of bcc Ti alloys from first-principles calculations and CALPHAD-based modeling

Here, titanium alloys are being investigated as suitable materials for load-bearing implants because of their biocompatibility and mechanical properties. Stress shielding, a common issue with the current load-bearing implant materials, occurs due to a Young’s modulus (E) mismatch between bone (~10–40 GPa) and implants (such as Ti-6Al-4V ~ 110 GPa), which leads to bone dying around the implant and ultimately implant failure. Reducing the Young’s modulus of Ti alloys may overcome the issues of stress shielding and improve implant materials. In the present work, first-principles calculations have been used to predict the single crystal elastic stiffness coefficients (c ij ’s) for the Ti-containing ternary alloys Ti-X-Y(X ≠ Y = Mo, Nb, Sn, Ta, Zr) in the bcc lattice. It is found that the ternary Ti-X-Y (X ≠ Y = Mo, Nb, Ta) alloys behave similarly; so do the ternary Ti-X-Sn (X = Mo, Nb, Ta) alloys and the Ti-X-Zr (X = Mo, Nb, Ta) alloys. This is expected due to the similarity between the Mo, Nb and Ta elements. The results also show that the Ti-Zr-X alloys stabilized the bcc phase at lower alloying concentrations. The polycrystalline aggregate properties are also estimated from the c ij ’s, including bulk modulus, shear modulus and Young’s modulus. The results show that Ti-alloys with compositions close to the bcc stability limit have the lowest E. In combination with previous predictions, a complete elastic database has been established using theCALPHAD (CALculation of PHAse Diagram) based modeling approach. The database results are compared with the E of higher order Ti alloys and shown to be able to predict the E accurately. This complete data-base forms a foundation to tailor Ti alloys for desired elastic properties.

36 MATERIALS SCIENCE↗