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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 163 records · Page 9
All sourcesNASA NTRSDOE OSTI
NASA NTRS2024

Application of Long-Path Gas Cell Assisted Infrared Spectroscopy for Detection of Lunar Volatiles and Advanced Curation Efforts

The motivation behind analyzing gaseous samples from the Permanently Shadowed Regions (PSRs) on the lunar surface is built upon the volatiles observed during the LCROSS mission. Advanced curation techniques under cold conditions are essential to the critical scientific analysis of these returned samples. The detection of various volatiles in returned samples by gas-phase infrared (IR) spectroscopy is known to be a powerful tool to understand the resources present in planetary bodies and Astro-materials. The identification and quantification of volatile compounds in returned planetary samples and regolith simulants by advanced and custom-built analytical devices are areas of primary research interest in our group and the Planetary Exploration & Astromaterials Research Laboratory (PEARL) facility. In this context, we discuss recent advancements and experimental results for quick analysis of the major volatiles detected by the LCROSS (water, CO 2 , CH 3 OH, and NH 3 ) by a long-path gas cell/FTIR (Fourier Transform Infrared) spectrometer system. The applicability of this system is demonstrated by qualitative analysis of a series of volatiles measured individually. In addition, the linear dependence of absorption intensity on headspace sample volumes was checked by measuring gas-phase IR absorption spectra of increasing volumes of pure CO 2 gas aliquots. Finally, the instrument performance was evaluated by measuring the relative concentration of NH 3 (g) in methanol solution.

Curation↗
DOE OSTI2011

Patterns of Failure and Treatment-Related Toxicity in Advanced Cervical Cancer Patients Treated Using Extended Field Radiotherapy With Curative Intent

Purpose: The purpose of this study was to evaluate the patterns of failure and overall survival (OS) and disease-free survival (DFS) rates in cervical cancer patients who had metastatic disease in common iliac or para-aortic lymph nodes and were treated with curative intent, using extended field radiotherapy (EFRT). Methods and Materials: This was a retrospective study involving 39 patients treated from January 1996 to June 2007, using EFRT with concurrent chemotherapy and intracavitary brachytherapy. EFRT consisted of 45 Gy in 1.8-Gy fractions. Radiation to involved nodes was boosted to a total dose of 50.4 to 54 Gy. Primary tumor radiation was boosted to a dose of 80 Gy using brachytherapy. Results: Overall, 30 patients (77%) have relapsed. The 5-year OS rate was 26% (95% confidence interval [CI], 11-44). The 5-year DFS rate was 19.4% (95% CI, 8-35). Only 3 patients (7.5%) experienced treatment failure exclusively within the treatment field, and 2 patients underwent salvage treatment. Grade 3 to 4 acute bone marrow and gastrointestinal toxicities were observed in 10 (26%) and 7 (18%) patients, respectively. Conclusions: Concurrent chemotherapy and EFRT treatment was well tolerated. Most patients showed failure at multiple sites and outside the treatment field. Only 3/39 patients had failures exclusively within the treatment field, and 2 underwent salvage treatment.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2012

Radiotherapy Alone With Curative Intent in Patients With Stage I Extranodal Nasal-Type NK/T-Cell Lymphoma

Purpose: This study aims to evaluate the outcome and pattern of failure in a large cohort of patients with Stage I NK/T-cell lymphoma of the upper aerodigestive tract treated with radiotherapy alone. Methods and Materials: The pathological diagnosis was confirmed using standard criteria. All patients were treated with high-dose extended-field radiotherapy alone. The median dose was 50 Gy. The primary tumor was located in the nasal cavity (n = 80), Waldeyer ring (n = 5), or oral cavity (n = 2). Results: The overall response to radiotherapy was achieved in 85 of 87 (97.7%) patients, with a complete response rate of 95.4% and a partial response rate of 2.3%. The 5-year overall survival, progression-free survival, and local control rates for all patients were 80%, 69%, and 93%, respectively. Twenty patients (23%) had disease progression or relapse. Of these, 15 patients (17%) developed systemic extranodal disseminations, whereas only 4 (5%) patients had local relapse and 4 (5%) patients had lymph node relapse. Conclusions: Our study suggests that high-dose extended-field radiotherapy alone is a curative therapy and shows favorable clinical outcome in patients with Stage I disease. With the high possibility of local control and primary failure of systemic dissemination, the integration of optimal radiotherapy with more effective systematic therapy is warranted to bring additional improvement to the outcome for these patients.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2013

Assessment of ERCC1 and XPF Protein Expression Using Quantitative Immunohistochemistry in Nasopharyngeal Carcinoma Patients Undergoing Curative Intent Treatment

Purpose: We sought to evaluate the prognostic/predictive value of ERCC1 and XPF in patients with nonmetastatic nasopharyngeal carcinoma (NPC) treated with curative intent. Methods and Materials: ERCC1 and XPF protein expression was evaluated by immunofluorescence combined with automated quantitative analysis (AQUA) using the FL297 and 3F2 antibodies, respectively. ERCC1 and XPF protein expression levels were correlated with clinical outcomes. Results: Patient characteristics were as follows: mean age 52 years (range, 18-85 years), 67% male, 72% Karnofsky performance status (KPS) ≥90%, World Health Organization (WHO) type 1/2/3 = 12%/28%/60%, stage III/IV 65%. With a median follow-up time of 50 months (range, 2.9 to 120 months), the 5-year overall survival (OS) was 70.8%. Median standardized nuclear AQUA scores were used as cutpoints for ERCC1 (n=138) and XPF (n=130) protein expression. Agreement between dichotomized ERCC1 and XPF scores was high at 79.4% (kappa = 0.587, P<.001). Neither biomarker predicted locoregional recurrence, DFS, or OS after adjustment for age and KPS, irrespective of stratification by stage, WHO type, or treatment. Conclusions: Neither ERCC1 nor XPF, analyzed by quantitative immunohistochemistry using the FL297 and 3F2 antibodies, was prognostic or predictive in this cohort of NPC patients.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2014

Definitive Chemoradiation Therapy Following Surgical Resection or Radiosurgery Plus Whole-Brain Radiation Therapy in Non-Small Cell Lung Cancer Patients With Synchronous Solitary Brain Metastasis: A Curative Approach

Purpose/Objectives: The aim of this study was to evaluate the impact of definitive thoracic chemoradiation therapy following surgery or stereotactic radiosurgery (SRS) and whole-brain radiation therapy (WBRT) on the outcomes of patients with non-small cell lung cancer (NSCLC) with synchronous solitary brain metastasis (SSBM). Methods and Materials: A total of 63 NSCLC patients with SSBM were retrospectively evaluated. Patients were staged using positron emission tomography-computed tomography in addition to conventional staging tools. Thoracic radiation therapy (TRT) with a total dose of 66 Gy in 2 Gy fractions was delivered along with 2 cycles of cisplatin-based chemotherapy following either surgery plus 30 Gy of WBRT (n=33) or SRS plus 30 Gy of WBRT (n=30) for BM. Results: Overall, the treatment was well tolerated. All patients received planned TRT, and 57 patients (90.5%) were also able to receive 2 cycles of chemotherapy. At a median follow-up of 25.3 months (7.1-52.1 months), the median months of overall, locoregional progression-free, neurological progression-free, and progression-free survival were 28.6, 17.7, 26.4, and 14.6, respectively. Both univariate and multivariate analyses revealed that patients with a T1-T2 thoracic disease burden (P=.001), a nodal stage of N0-N1 (P=.003), and no weight loss (P=.008) exhibited superior survival. Conclusions: In the present series, surgical and radiosurgical treatments directed toward SSBM in NSCLC patients were equally effective. The similarities between the present survival outcomes and those reported in other studies for locally advanced NSCLC patients indicate the potentially curative role of definitive chemoradiation therapy for highly selected patients with SSBM.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2016

Dose and Fractionation in Radiation Therapy of Curative Intent for Non-Small Cell Lung Cancer: Meta-Analysis of Randomized Trials

Purpose: The optimum dose and fractionation in radiation therapy of curative intent for non-small cell lung cancer remains uncertain. We undertook a published data meta-analysis of randomized trials to examine whether radiation therapy regimens with higher time-corrected biologically equivalent doses resulted in longer survival, either when given alone or when given with chemotherapy. Methods and Materials: Eligible studies were randomized comparisons of 2 or more radiation therapy regimens, with other treatments identical. Median survival ratios were calculated for each comparison and pooled. Results: 3795 patients in 25 randomized comparisons of radiation therapy dose were studied. The median survival ratio, higher versus lower corrected dose, was 1.13 (95% confidence interval [CI] 1.04-1.22) when radiation therapy was given alone and 0.83 (95% CI 0.71-0.97) when it was given with concurrent chemotherapy (P for difference=.001). In comparisons of radiation therapy given alone, the survival benefit increased with increasing dose difference between randomized treatment arms (P for trend=.004). The benefit increased with increasing dose in the lower-dose arm (P for trend=.01) without reaching a level beyond which no further survival benefit was achieved. The survival benefit did not differ significantly between randomized comparisons where the higher-dose arm was hyperfractionated and those where it was not. There was heterogeneity in the median survival ratio by geographic region (P<.001), average age at randomization (P<.001), and year trial started (P for trend=.004), but not for proportion of patients with squamous cell carcinoma (P=.2). Conclusions: In trials with concurrent chemotherapy, higher radiation therapy doses resulted in poorer survival, possibly caused, at least in part, by high levels of toxicity. Where radiation therapy was given without chemotherapy, progressively higher radiation therapy doses resulted in progressively longer survival, and no upper dose level was found above which there was no further benefit. These findings support the consideration of further radiation therapy dose escalation trials, making use of modern treatment methods to reduce toxicity.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2025

PDB-IHM: A System for Deposition, Curation, Validation, and Dissemination of Integrative Structures

Structures of many large biomolecular assemblies are now being determined using integrative approaches. In these approaches, information derived from multiple experimental and computational methods is combined to compute three-dimensional structures of multi-protein complexes and other macromolecular machines. A standalone prototype data resource for integrative structures called PDB-Dev was built, based on recommendations of the Integrative and Hybrid Methods (IHM) Task Force of the Worldwide Protein Data Bank (wwPDB). This effort included developing data standards and software tools for collecting, curating, validating, visualizing, archiving, and disseminating integrative structures that span diverse spatiotemporal scales and conformational states. Mechanisms have been created to validate integrative structures based on the experimental data underpinning them. Building upon this foundational framework, PDB-Dev has been further expanded to handle large dynamic macromolecular systems and integrative structures that combine, for example, experimental restraints with atomic coordinates computed by machine learning algorithms. Data standards and supporting tools have also been extended to capture information about biomolecular dynamics, such as conformational transitions and related kinetic data derived from biophysical methods. Recently, PDB-Dev was unified with the PDB archive and rebranded as PDB-IHM (pdb-ihm.org), further promoting FAIR (Findable, Accessible, Interoperable, and Reusable) principles of data stewardship for integrative structural biology.

IHMCIF↗
DOE OSTI2020

A Curated Experimental Compilation Analyzed by Theory Is More than a Review

Macromolecules is an exceptional resource in the field of polymer science and now publishes more than 1000 original articles a year that set the standard for scientific rigor and creative insights. Over the years, these individual contributions have combined to build the foundation of polymer science, broadly and inclusively defined. In addition to the individual articles, many of which are being celebrated in this series of editorials, Macromolecules has published invaluable reviews and perspectives. These scholarly contributions integrate the insights and results from numerous sources into a unified whole and often recommend future directions for the field. Novices and experts alike benefit from these works that capture topics from emerging discoveries to long-pondered topics and everything in between. To explore the importance of Macromolecules’ reviews and perspectives, we considered their influence on the field and found the 1994 review by Fetters et al. entitled “Connection between Polymer Molecular Weight, Density, Chain Dimensions, and Melt Viscoelastic Properties”1 to be a singularity. This review expertly curates and compiles a trove of data to build robust correlations between molecular characteristics and macroscopic viscoelastic properties of polymer melts, in the context of the tube model of entanglements.

36 MATERIALS SCIENCE↗
DOE OSTI2023

A large expert-curated cryo-EM image dataset for machine learning protein particle picking

Cryo-electron microscopy (cryo-EM) is a powerful technique for determining the structures of biological macromolecular complexes. Picking single-protein particles from cryo-EM micrographs is a crucial step in reconstructing protein structures. However, the widely used template-based particle picking process is labor-intensive and time-consuming. Though machine learning and artificial intelligence (AI) based particle picking can potentially automate the process, its development is hindered by lack of large, high-quality labelled training data. To address this bottleneck, we present CryoPPP, a large, diverse, expert-curated cryo-EM image dataset for protein particle picking and analysis. It consists of labelled cryo-EM micrographs (images) of 34 representative protein datasets selected from the Electron Microscopy Public Image Archive (EMPIAR). The dataset is 2.6 terabytes and includes 9,893 high-resolution micrographs with labelled protein particle coordinates. The labelling process was rigorously validated through 2D particle class validation and 3D density map validation with the gold standard. The dataset is expected to greatly facilitate the development of both AI and classical methods for automated cryo-EM protein particle picking.

42 ENGINEERING↗
DOE OSTI2026

A curated benchmark for cofolding models on kinase conformational states

Abstract Protein kinases are critical drug targets, requiring therapeutics that can modulate their active and inactive conformational states. While cofolding models can generate global folds directly from kinase sequences and ligand SMILES strings, these models have not yet been tested on their ability to recover ligand-induced-fit conformational states of the kinase proteins. Here, we introduce KinConfBench, a curated benchmark of 2225 high-quality human kinase chains to evaluate the ability of four state-of-the-art cofolding models—Boltz-2, Chai-1, Protenix, and RoseTTAFold-All-Atom—to recover both canonical and rare conformational states. We show that geometric success metrics of a ligand pose in the active site do not correlate strongly with the correct kinase conformational state, motivating a new set of dynamical benchmarks for assessing cofolding models. While all four cofolding models achieve ~60–80% prediction accuracy for kinase conformational classification, they exhibit severe mode collapse when performing multiple inferences, show negligible structural diversity in sampling induced-fit motions, and display a prevalent “apo-drift” in which most cofolding models predominantly predict the kinase to be in its ligand-free state. Our results highlight that capturing ligand-induced protein conformational diversity, not just geometric fit, is critical for next-generation structure-based drug discovery.

Sun, Kunyang↗
DOE OSTI2023

WPEC SG50: Developing an Automatically Readable, Comprehensive and Curated Experimental Nuclear Reaction Database

The Organisation for Economic Co-operation and Development (OECD) Nuclear Energy Agency (NEA) Working Party on International Nuclear Data Evaluation Co-operation (WPEC) subgroup (SG) 50 was formed in 2020 to develop an automatically readable, comprehensive and curated experimental nuclear reaction database. This database is called MEDUSAL (Machine-readable Experimental Data User Application & Library), and will draw from EXFOR. The EXFOR database preserves experimental nuclear reaction data true to its original documentation and information from the authors of the data. MEDUSAL will deviate from EXFOR by storing additional information from users of the data for their fields of work (evaluation, model development, validation, etc.). This includes expert judgment on the data sets, identification of data points as outliers, renormalization of the data to the newest monitor reactions, and estimations of missing uncertainty sources. The format for MEDUSAL is being developed to enable easy automatic parsing of large amounts of data. Here, we will summarize the use cases, high-level requirements and first steps towards developing the database MEDUSAL and the API to access it.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2022

EXFOR-NSR PDF database: a system for nuclear knowledge preservation and data curation

Current needs of nuclear science and technology include complete, well-documented, and easily verifiable nuclear data. The complete data records require supporting nuclear bibliography, presently stored in dedicated libraries, in addition, to actual data. Additionally, experimental nuclear reaction data (EXFOR) and Nuclear Science References (NSR) databases contain compilations based on primary (journals) and secondary (conference proceedings, theses, preprints, etc.) publications, and data received from authors via private communications. The secondary library materials and private communications often represent a bottleneck for nuclear data verification, compilation, evaluation, and dissemination activities. To address this issue, bibliographic materials were scanned into PDF (Portable Document Format) files and uploaded in a relational database. The traditional scope of nuclear databases that includes meta-data and numbers derived from data in specialized formats was broadened to accommodate the large volumes of original nuclear data publications. The complete PDF publication files were stored in a relational database as Binary Large OBjects (BLOB). This unique collection of nuclear data compilations and supporting publications generate many opportunities for machine learning applications. The Web interfaces for authorized and public access to the EXFOR-NSR nuclear publications database were implemented at the U.S. National Nuclear Data Center, https://www.nndc.bnl.gov/ and IAEA Nuclear Data Section, https://www-nds.iaea.org/ . The current system is complementary to major nuclear libraries and narrowly focused on nuclear data compilation and evaluation procedures. The contents of the PDF database, details of implementation, and Web interface are described. New capabilities for data curation, knowledge preservation, worldwide dissemination, and natural language processing (NLP) applications are given.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2013

DATABASE, The Journal of Biological Databases and Curation, is now the official journal of the International Society for Biocuration

The International Society for Biocuration (ISB) was created in 2009 specifically to promote biocuration, the product of multidisciplinary teams of database curators, software developers and bioinformaticians. Biocurators, whose work facilitates research and education across the life sciences, create and maintain a wide variety of online tools and databases, covering topics as diverse as biochemical structures, chromosomal features and phenotypes of mutant genes. These resources are now so essential to the biological community that databases have become integral to the daily work of most researchers. But biological databases are far from static: in addition to the need to constantly capture new knowledge (from the literature, from other databases, from analysis tools, etc.), data representation must also keep pace with current research— new data types must be modeled—and improved methods of data storage, representation and analysis must be continually developed. Nevertheless, such important efforts have not always been recognized, and have often not been published in full, owing to the lack of a suitable journal.

99 GENERAL AND MISCELLANEOUS↗
DOE OSTI2024

MIBiG 4.0: advancing biosynthetic gene cluster curation through global collaboration

Specialized or secondary metabolites are small molecules of biological origin, often showing potent biological activities with applications in agriculture, engineering and medicine. Usually, the biosynthesis of these natural products is governed by sets of co-regulated and physically clustered genes known as biosynthetic gene clusters (BGCs). To share information about BGCs in a standardized and machine-readable way, the Minimum Information about a Biosynthetic Gene cluster (MIBiG) data standard and repository was initiated in 2015. Since its conception, MIBiG has been regularly updated to expand data coverage and remain up to date with innovations in natural product research. Here, we describe MIBiG version 4.0, an extensive update to the data repository and the underlying data standard. In a massive community annotation effort, 267 contributors performed 8304 edits, creating 557 new entries and modifying 590 existing entries, resulting in a new total of 3059 curated entries in MIBiG. Particular attention was paid to ensuring high data quality, with automated data validation using a newly developed custom submission portal prototype, paired with a novel peer-reviewing model. MIBiG 4.0 also takes steps towards a rolling release model and a broader involvement of the scientific community. MIBiG 4.0 is accessible online at https://mibig.secondarymetabolites.org/.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Complete 4.55-Megabase-Pair Genome of “ Candidatus Fluviicola riflensis,” Curated from Short-Read Metagenomic Sequences

ABSTRACT We report the 4.55-Mbp genome of “ Candidatus Fluviicola riflensis” ( Bacteroidetes ) that was manually curated to completion from Illumina data. “ Ca . Fluviicola riflensis” is a facultative anaerobe. Its ability to grow over a range of O 2 levels may favor its proliferation in an aquifer adjacent to the Colorado River in the United States.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

RefAHL: a curated quorum sensing reference linking diverse LuxI-type signal synthases with their acyl-homoserine lactone products

Some bacteria use acyl-homoserine lactone (AHL) signals in quorum sensing, a type of cell-cell communication. Here, we present “RefAHL,” an updated, curated collection of LuxI-type AHL synthases with their AHL products and associated metadata. RefAHL is publicly available as a community resource to help catalog LuxI-type diversity encoded in (meta) genomic data.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Curation of Ground-Truth Validated Benchmarking Datasets for Fault Detection & Diagnostics Tools

Fault detection and diagnostics (FDD) analytical tools for heating, ventilation and air conditioning (HVAC) systems represent one of the most active areas of smart building technology development. A diversity of techniques is used for FDD analytics, spanning physical models, black box, and rule-based approaches, and researchers continuously strive to develop improved algorithms. With FDD algorithm numbers now in the hundreds, there is a need for performance evaluation of these algorithms in order to assess improvements, improve costeffectiveness, and to prioritize investment in the further development of these technologies. A persistent challenge of FDD advance has been the lack of common datasets to benchmark the performance accuracy of FDD algorithms. This paper summarizes the successful curation of HVAC operational data, paired with validated ground-truth information regarding the presence and absence of faults. The current dataset, consisting of both simulation and experimental data, will evolve to include a larger set of HVAC systems with the objective of creating the largest publicly available dataset to be used by FDD developers, users, and researchers to compare and contrast performance accuracy across FDD algorithms, helping to drive improvements that will spur greater market adoption of FDD tools. Furthermore, in order to avoid previously observed issues with contributed datasets and ensure high quality and consistency of future submissions, the development of data validation and ground-truth assessment protocol is detailed in this study.

Casillas, Armando↗