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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 235 records · Page 13
All sourcesNASA NTRSDOE OSTI
DOE OSTI2011

Nomogram Prediction of Overall Survival After Curative Irradiation for Uterine Cervical Cancer

Purpose: The purpose of this study was to develop a nomogram capable of predicting the probability of 5-year survival after radical radiotherapy (RT) without chemotherapy for uterine cervical cancer. Methods and Materials: We retrospectively analyzed 549 patients that underwent radical RT for uterine cervical cancer between March 1994 and April 2002 at our institution. Multivariate analysis using Cox proportional hazards regression was performed and this Cox model was used as the basis for the devised nomogram. The model was internally validated for discrimination and calibration by bootstrap resampling. Results: By multivariate regression analysis, the model showed that age, hemoglobin level before RT, Federation Internationale de Gynecologie Obstetrique (FIGO) stage, maximal tumor diameter, lymph node status, and RT dose at Point A significantly predicted overall survival. The survival prediction model demonstrated good calibration and discrimination. The bootstrap-corrected concordance index was 0.67. The predictive ability of the nomogram proved to be superior to FIGO stage (p = 0.01). Conclusions: The devised nomogram offers a significantly better level of discrimination than the FIGO staging system. In particular, it improves predictions of survival probability and could be useful for counseling patients, choosing treatment modalities and schedules, and designing clinical trials. However, before this nomogram is used clinically, it should be externally validated.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2012

Multi-Institutional Analysis of Solitary Extramedullary Plasmacytoma of the Head and Neck Treated With Curative Radiotherapy

Purpose: The purpose of this study was to elucidate the efficacy and optimal method of radiotherapy in the management of solitary extramedullary plasmacytoma occurring in the head and neck regions (EMPHN). Methods and Materials: Sixty-seven patients (43 male and 24 female) diagnosed with EMPHN between 1983 and 2008 at 23 Japanese institutions were reviewed. The median patient age was 64 years (range, 12-83). The median dose administered was 50 Gy (range, 30-64 Gy). Survival data were calculated by the Kaplan-Meier method. Results: The median follow-up duration was 63 months. Major tumor sites were nasal or paranasal cavities in 36 (54%) patients, oropharynx or nasopharynx in 16 (23%) patients, orbita in 6 (9%) patients, and larynx in 3 (5%) patients. The 5- and 10-year local control rates were 95% and 87%, whereas the 5- and 10-year disease-free survival rates were 56% and 54%, respectively. There were 5 (7.5%), 12 (18%), and 8 (12%) patients who experienced local failure, distant metastasis, and progression to multiple myeloma, respectively. In total, 18 patients died, including 10 (15%) patients who died due to complications from EMPHN. The 5- and 10-year overall survival (OS) rates were 73% and 56%, respectively. Radiotherapy combined with surgery was identified as the lone significant prognostic factor for OS (p = 0.04), whereas age, gender, radiation dose, tumor size, and chemotherapy were not predictive. No patient experienced any severe acute morbidity. Conclusions: Radiotherapy was quite effective and safe for patients with EMPHN. Radiotherapy combined with surgery produced a better outcome according to survival rates. These findings require confirmation by further studies with larger numbers of patients with EMPHN.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2012

Curative Treatment of Stage I Non-Small-Cell Lung Cancer in Patients With Severe COPD: Stereotactic Radiotherapy Outcomes and Systematic Review

Objectives: Patients with severe chronic obstructive pulmonary disease (COPD) have a high risk of lung cancer and of postsurgical complications. We studied outcomes after stereotactic body radiotherapy (SBRT) in patients with severe COPD, as defined by Global Initiative for Chronic Obstructive Lung Disease (GOLD) criteria, and performed a systematic review of the literature on outcomes after SBRT or surgery in these patients. Methods: A single-institution cohort of 176 patients with COPD GOLD III-IV and Stage I non-small-cell lung cancer (NSCLC) treated with SBRT was evaluated. A systematic review identified studies reporting outcomes after SBRT or surgery for Stage I NSCLC in patients with GOLD III-IV or a predicted postoperative forced expiratory volume in 1 second (FEV1) of {<=}40%. Results: In the single-institution cohort, median follow-up was 21 months and median overall survival (OS) was 32 months. Actuarial 3-year local control was 89%, and 1- and 3-year OS were 79% and 47%, respectively. COPD severity correlated with OS (p = 0.01). The systematic review identified four other studies (two surgical, two SBRT, n = 196 patients). SBRT studies were published more recently and included older patients than surgical studies. Mean 30-day mortality was 0% post-SBRT and 10% after surgery. Local or locoregional control was high ({>=}89%) after both treatments. Post-SBRT, actuarial OS was 79-95% at 1 year and 43-70% at 3 years. Postsurgical actuarial OS was 45-86% at 1 year and 31-66% at 3 years. Conclusions: SBRT and surgery differ in risk of 30-day mortality in patients with severe COPD. Despite the negative selection of SBRT patients, survival at 1 and 3 years is comparable between the two treatments.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2014

Short-Course Treatment With Gefitinib Enhances Curative Potential of Radiation Therapy in a Mouse Model of Human Non-Small Cell Lung Cancer

Purpose: To evaluate the combination of radiation and an epidermal growth factor receptor (EGFR) tyrosine kinase inhibitor (TKI) in preclinical models of human non-small cell lung cancer. Methods and Materials: Sensitivity to an EGFR TKI (gefitinib) or radiation was assessed using proliferation assays and clonogenic survival assays. Effects on receptor signal transduction pathways (pEGFR, pAKT, pMAPK) and apoptosis (percentage of cleaved PARP Poly (ADP-ribose) polymerase (PARP)) were assessed by Western blotting. Radiation-induced DNA damage was assessed by γH2AX immunofluorescence. Established (≥100 mm{sup 3}) EGFR-mutated (HCC287) or EGFR wild-type (A549) subcutaneous xenografts were treated with radiation (10 Gy, day 1) or gefitinib (50 mg/kg, orally, on days 1-3) or both. Results: In non-small cell lung cancer (NSCLC) cell lines with activating EGFR mutations (PC9 or HCC827), gefitinib treatment markedly reduced pEGFR, pAKT, and pMAPK levels and was associated with an increase in cleaved PARP but not in γH2AX foci. Radiation treatment increased the mean number of γH2AX foci per cell but did not significantly affect EGFR signaling. In contrast, NSCLC cell lines with EGFR T790M (H1975) or wild-type EGFR (A549) were insensitive to gefitinib treatment. The combination of gefitinib and radiation treatment in cell culture produced additive cell killing with no evidence of synergy. In xenograft models, a short course of gefitinib (3 days) did not significantly increase the activity of radiation treatment in wild-type EGFR (A549) tumors (P=.27), whereas this combination markedly increased the activity of radiation (P<.001) or gefitinib alone (P=.002) in EGFR-mutated HCC827 tumors, producing sustained tumor regressions. Conclusions: Gefitinib treatment increases clonogenic cell killing by radiation but only in cell lines sensitive to gefitinib alone. Our data suggest additive rather than synergistic interactions between gefitinib and radiation and that a combination of short-course gefitinib and high-dose/-fraction radiation may have the greatest potential against the subsets of lung cancers harboring activating mutations in the EGFR gene.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2016

Reirradiation of Prostate Cancer Local Failures After Previous Curative Radiation Therapy: Long-Term Outcome and Tolerance

Purpose: To evaluate the safety, feasibility, side-effect profile, and proof of concept of external beam radiation therapy (EBRT) with or without a brachytherapy (BT) boost for salvage of exclusive local failure after primary EBRT for prostate cancer. Methods and Materials: Fourteen patients with presumed exclusive local recurrence after primary EBRT with or without BT were considered eligible for reirradiation. The median normalized total dose in 2-Gy fractions (NTD{sub 2Gy}, α/β ratio = 1.5 Gy) was 74 Gy (range, 66-98.4 Gy) at first irradiation. Median time between the first irradiation and the reirradiation was 6.1 years (range, 4.7-10.2 years). Results: Between 2003 and 2008 salvage treatment was delivered with a median NTD{sub 2Gy} of 85.1 Gy (range, 70-93.4) to the prostate with EBRT with (n=10) or without (n=4) BT. Androgen deprivation was given to 12 patients (median time of 12 months). No grade ≥3 toxicity was observed during and within 6 weeks after RT. After a median follow-up of 94 months (range, 48-172 months) after salvage RT, 5-year grade ≥3 genitourinary and gastrointestinal toxicity-free survival figures were 77.9% ± 11.3% and 57.1% ± 13.2%, respectively. Four patients presented with combined grade 4 genitourinary/gastrointestinal toxicity. The 5-year biochemical relapse-free, local relapse-free, distant metastasis-free, and cancer-specific survival rates were 35.7% ± 12.8%, 50.0% ± 13.4%, 85.7% ± 9.4%, and 100%, respectively. Conclusion: Salvage whole-gland reirradiation for patients with a suspicion of exclusive local recurrence after initial RT may be associated with a high rate of severe radiation-induced side effects and poor long-term biochemical and local control.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2021

Chemical-damage MINE: A database of curated and predicted spontaneous metabolic reactions

Spontaneous reactions between metabolites are often neglected in favor of emphasizing enzyme-catalyzed chemistry because spontaneous reaction rates are assumed to be insignificant under physiological conditions. However, synthetic biology and engineering efforts can raise natural metabolites' levels or introduce unnatural ones, so that previously innocuous or nonexistent spontaneous reactions become an issue. Problems arise when spontaneous reaction rates exceed the capacity of a platform organism to dispose of toxic or chemically active reaction products. While various reliable sources list competing or toxic enzymatic pathways' side-reactions, no corresponding compilation of spontaneous side-reactions exists, nor is it possible to predict their occurrence. We addressed this deficiency by creating the Chemical Damage (CD)-MINE resource. First, we used literature data to construct a comprehensive database of metabolite reactions that occur spontaneously in physiological conditions. We then leveraged this data to construct 148 reaction rules describing the known spontaneous chemistry in a substrate-generic way. We applied these rules to all compounds in the ModelSEED database, predicting 180,891 spontaneous reactions. The resulting (CD)-MINE is available at https://minedatabase.mcs.anl. gov/cdmine/#/home and through developer tools. We also demonstrate how damage-prone intermediates and end products are widely distributed among metabolic pathways, and how predicting spontaneous chemical damage helps rationalize toxicity and carbon loss using examples from published pathways to commercial products. We explain how analyzing damage-prone areas in metabolism helps design effective engineering strategies. Finally, we use the CD-MINE toolset to predict the formation of the novel damage product N-carbamoyl proline, and present mass spectrometric evidence for its presence in Escherichia coli.

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

Curated Collection of More than 20,000 Experimentally Reported One-Dimensional Metal–Organic Frameworks

Herein, a collection of more than 20,000 experimentally derived crystal structures for metal–organic frameworks (MOFs) that do not have two- or three-dimensional covalently bonded networks has been developed from the materials available at the Cambridge Crystallographic Data Centre. Of these 20,000 1D MOFs, more than 12,000 structures have been verified to be solvent-free and in exact agreement with the stoichiometry of the synthesized materials. More than 10% of the complete data set comprise materials including two or more distinct metals. The band gaps of more than 12,000 1D MOFs have been computed at the density functional theory-generalized gradient approximation level, finding more than 2000 materials that have a zero band gap. Molecular simulations of CH4 adsorption in a small number of 1D MOFs indicated that adsorbate-induced deformation plays a significant role in determining adsorption isotherms in these materials. As a result, methods that have been used previously for high-throughput predictions of molecular adsorption in 3D MOFs are not suitable for 1D MOFs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

An automatically curated first-principles database of ferroelectrics

Ferroelectric materials have technological applications in information storage and electronic devices. The ferroelectric polar phase can be controlled with external fields, chemical substitution and size-effects in bulk and ultrathin film form, providing a platform for future technologies and for exploratory research. In this work, we integrate spin-polarized density functional theory (DFT) calculations, crystal structure databases, symmetry tools, workflow software, and a custom analysis toolkit to build a library of known, previously-proposed, and newly-proposed ferroelectric materials. With our automated workflow, we screen over 67,000 candidate materials from the Materials Project database to generate a dataset of 255 ferroelectric candidates, and propose 126 new ferroelectric materials. We benchmark our results against experimental data and previous first-principles results. The data provided includes atomic structures, output files, and DFT values of band gaps, energies, and the spontaneous polarization for each ferroelectric candidate. Finally, we contribute our workflow and analysis code to the open-source python packages atomate and pymatgen so others can conduct analogous symmetry driven searches for ferroelectrics and related phenomena.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Curation of a list of chemicals in biosolids from EPA National Sewage Sludge Surveys & Biennial Review Reports

Section 405(d) of the Clean Water Act requires the US Environmental Protection Agency to review sewage sludge regulations every two years to identify any additional pollutants that may occur in biosolids and to set regulations for pollutants identified in biosolids if sufficient scientific evidence shows they may harm human health or the environment. To date, EPA has conducted eight biennial reviews to identify chemical and microbial pollutants and three national sewage sludge surveys to identify pollutants and obtain concentration data for chemicals found in biosolids. Prior to 2021, there was inconsistent reporting of chemicals identified and EPA did not cumulatively track chemicals in biosolids. Through the efforts presented here, EPA produced a list of 726 chemicals and structure-based classes found in biosolids based on biennial reviews and national sewage sludge surveys. Summary statistics of concentration data are also reported for the 484 chemicals found in the three national sewage sludge surveys. The creation of the Biosolids List supports EPA in assessing the potential risk of chemical pollutants found in biosolids.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Aerial imagery dataset of lost oil wells

Orphaned wells are wells for which the operator is unknown or insolvent. The location of hundreds of thousands of these wells remain unknown in the United States alone. Cost-effective techniques are essential to locate orphaned wells to address environmental problems. In this paper, we present a dataset consisting of 120,948 aerial images of recently documented orphan wells. Each of these 512 × 512 images is paired with segmentation masks that indicate the presence or absence of such well. These images, sourced from the National Agriculture Imagery Program, cover the continental United States with spatial resolutions ranging from 30 centimeters to 1 meter. Additionally, we included negative examples by selecting locations uniformly across the United States. Accompanying metadata includes the IDs and spatial resolution of the original images, which are available for free through the United States Geological Survey, and the pixel coordinates of documented orphaned wells identified in these images. This dataset is intended to support the development of deep-learning models that can help locating undocumented orphan wells from such imagery, thereby blunting the environmental damage they do.

Climate-change mitigation↗
DOE OSTI2025

Machine learning enhanced predictions of ICRF heating: Overcoming numerical limitations via data curation

In this work, we present the development of robust surrogate models for Ion Cyclotron Range of Frequencies (ICRF) and High-Harmonic Fast Wave (HHFW) heating predictions in fusion plasmas. Building upon our previous efforts to achieve real-time capable models, we identify the cause of the outliers found using TORIC in certain HHFW heating scenarios. The outliers are observed to be spurious ion Bernstein wave (IBW)-like modes caused by a wavelength control algorithm designed to address challenging scenarios with high perpendicular wavenumbers. The effect arises from the modulation in the perpendicular susceptibility, which can induce sign reversal and IBW-like propagation for scenarios featuring normalized ion Larmor radius λ i ≫ 1. We use TORIC with this algorithm disabled to generate a novel HHFW-NSTX database that is free of outliers. Surrogate models trained on this database, including Random Forest Regressor (RFR), Multi-Layer Perceptrons, and Gaussian Process Regressors (GPR), demonstrate the ability to accurately predict HHFW heating profiles, with regression scores of R 2 ∈[0.93−0.99]. Additionally we demonstrate that it is possible to generalize predictions beyond training data by the use of both RFR and GPR models, enabling the prediction of scenarios previously limited to the original model. GPR models also provide uncertainty quantification, offering insights into model confidence. This work introduces a comprehensive Verification, Validation, and Uncertainty Quantification methodology for surrogate modeling, applicable not only to ICRF heating but also to other RF heating challenges and fusion physics problems. Beyond accelerated inference, these models show effective extrapolation capabilities, providing an alternative for addressing numerical challenges.

Artificial neural networks↗
DOE OSTI2013

PhenoDigm: analyzing curated annotations to associate animal models with human diseases

The ultimate goal of studying model organisms is to translate what is learned into useful knowledge about normal human biology and disease to facilitate treatment and early screening for diseases. Recent advances in genomic technologies allow for rapid generation of models with a range of targeted genotypes as well as their characterization by high-throughput phenotyping. As an abundance of phenotype data become available, only systematic analysis will facilitate valid conclusions to be drawn from these data and transferred to human diseases. Owing to the volume of data, automated methods are preferable, allowing for a reliable analysis of the data and providing evidence about possible gene–disease associations. Here, we propose Phenotype comparisons for DIsease Genes and Models (PhenoDigm), as an automated method to provide evidence about gene–disease associations by analysing phenotype information. PhenoDigm integrates data from a variety of model organisms and, at the same time, uses several intermediate scoring methods to identify only strongly datasupported gene candidates for human genetic diseases. We show results of an automated evaluation as well as selected manually assessed examples that support the validity of PhenoDigm. Furthermore, we provide guidance on how to browse the data with PhenoDigm’s web interface and illustrate its usefulness in supporting research. Database URL: http://www.sanger.ac.uk/resources/databases/phenodigm

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Crowdsourcing and curation: perspectives from biology and natural language processing

Crowdsourcing is increasingly utilized for performing tasks in both natural language processing and biocuration. Although there have been many applications of crowdsourcing in these fields, there have been fewer high-level discussions of the methodology and its applicability to biocuration. This paper explores crowdsourcing for biocuration through several case studies that highlight different ways of leveraging ‘the crowd’; these raise issues about the kind(s) of expertise needed, the motivations of participants, and questions related to feasibility, cost and quality. The paper is an outgrowth of a panel session held at BioCreative V (Seville, September 9–11, 2015). The session consisted of four short talks, followed by a discussion. In their talks, the panelists explored the role of expertise and the potential to improve crowd performance by training; the challenge of decomposing tasks to make them amenable to crowdsourcing; and the capture of biological data and metadata through community editing.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗
DOE OSTI2020

DRAM for distilling microbial metabolism to automate the curation of microbiome function

Abstract Microbial and viral communities transform the chemistry of Earth's ecosystems, yet the specific reactions catalyzed by these biological engines are hard to decode due to the absence of a scalable, metabolically resolved, annotation software. Here, we present DRAM (Distilled and Refined Annotation of Metabolism), a framework to translate the deluge of microbiome-based genomic information into a catalog of microbial traits. To demonstrate the applicability of DRAM across metabolically diverse genomes, we evaluated DRAM performance on a defined, in silico soil community and previously published human gut metagenomes. We show that DRAM accurately assigned microbial contributions to geochemical cycles and automated the partitioning of gut microbial carbohydrate metabolism at substrate levels. DRAM-v, the viral mode of DRAM, established rules to identify virally-encoded auxiliary metabolic genes (AMGs), resulting in the metabolic categorization of thousands of putative AMGs from soils and guts. Together DRAM and DRAM-v provide critical metabolic profiling capabilities that decipher mechanisms underpinning microbiome function.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Targeted curation of the gut microbial gene content modulating human cardiovascular disease

Despite the promise of the gut microbiome to predict human health, few studies expose the molecular-scale processes underpinning such forecasts. We mined over 200,000 gut-derived genomes from cultivated and uncultivated microbial lineages to inventory the gut microorganisms and their gene content that control trimethylamine-induced cardiovascular disease. We assigned an atherosclerotic profile to the 6,341 microbial genomes that encoded metabolisms associated with heart disease, creating the Methylated Amine Gene Inventory of Catabolism database (MAGICdb). From microbiome gene expression data sets, we demonstrate that MAGICdb enhanced the recovery of disease-relevant genes and identified the most active microorganisms, unveiling future therapeutic targets. From the feces of healthy and diseased subjects, we show that MAGICdb predicted cardiovascular disease status as effectively as traditional lipid blood tests. This functional microbiome catalog is a public, exploitable resource, designed to enable a new era of microbiota-based therapeutics and diagnostics

metatranscriptomics↗