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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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674 records · Page 38
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Multi-channel Imager Algorithm (MIA): A novel cloud-top phase classification algorithm

The current Geostationary Operational Environmental Satellites (GOES-16 and 17) cloud-top phase classification algorithm is based primarily on empirical thresholds at multiple wavelengths that have varying absorption capabilities for water and ice. The performance of current GOES-16 cloud-top phase product largely depends on the accuracy of the selection of reflectance ratios. Here this study aims at presenting a novel cloud-top phase classification algorithm (the Multi-channel Imager Algorithm, MIA) that provides a more judicious selection of relationships between channels using a supervised K-mean clustering method on multi-channel Red-Green-Blue images. The K-mean clustering method works analogously to how human eyes separate different colors in a microphysical color rendering set of satellite images, which differentiates water, ice and unclassified thin clouds. For water phase, cloud-top temperature information is used to further distinguish supercooled water. To evaluate the performance of the MIA, an extensive comparison with Cloud-Aerosol Lidar with Orthogonal Polarization (CALIOP), Moderate Resolution Imaging Spectroradiometer, and current GOES-16 cloud-top phase products is conducted, using CALIOP as the benchmark. Compared to the current GOES-16 cloud-top phase product, MIA demonstrates a substantial improvement in phase classification, where hit rate increases from 69% to 76% over the Continental United States and 58% to 66% over the full disk domain.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

A self-supervised workflow for particle picking in cryo-EM

High-resolution single-particle cryo-EM data analysis relies on accurate particle picking. To facilitate the particle picking process, a self-supervised workflow has been developed. This includes an iterative strategy, which uses a 2D class average to improve training particles, and a progressively improved convolutional neural network for particle picking. To automate the selection of particles, a threshold is defined (%/Res) using the ratio of percentage class distribution and resolution as a cutoff. This workflow has been tested using six publicly available data sets with different particle sizes and shapes, and can automatically pick particles with minimal user input. The picked particles support high-resolution reconstructions at 3.0 Å or better. This workflow is a step towards automated single-particle cryo-EM data analysis at the stage of particle picking. It may be used in conjunction with commonly used single-particle analysis packages such as Relion , cryoSPARC , cisTEM , SPHIRE and EMAN2 .

2D class averages↗
DOE OSTI2021

Predicting transcriptional responses to cold stress across plant species

Although genome-sequence assemblies are available for a growing number of plant species, gene-expression responses to stimuli have been cataloged for only a subset of these species. Many genes show altered transcription patterns in response to abiotic stresses. However, orthologous genes in related species often exhibit different responses to a given stress. Accordingly, data on the regulation of gene expression in one species are not reliable predictors of orthologous gene responses in a related species. Here, we trained a supervised classification model to identify genes that transcriptionally respond to cold stress. A model trained with only features calculated directly from genome assemblies exhibited only modest decreases in performance relative to models trained by using genomic, chromatin, and evolution/diversity features. Models trained with data from one species successfully predicted which genes would respond to cold stress in other related species. Cross-species predictions remained accurate when training was performed in cold-sensitive species and predictions were performed in cold-tolerant species and vice versa. Models trained with data on gene expression in multiple species provided at least equivalent performance to models trained and tested in a single species and outperformed single-species models in cross-species prediction. These results suggest that classifiers trained on stress data from well-studied species may suffice for predicting gene-expression patterns in related, less-studied species with sequenced genomes.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Physical Education Teachers’ Representations of Their Training to Promote the Inclusion of Students with Disabilities

School inclusion is based on the need to adopt and implement a holistic view of education, training, and human development embodied in the idea of everyone, for everyone. In the context of Physical Education (PE), there are still several constraints to the realization of this universal desideratum. Among these, teacher training and qualification for the inclusion of students with Specific Health Needs (SHNs) stands out. That is, students with physical and mental health problems whose impact is significantly manifested in the learning process. Thus, the objective of this study was to identify the representations of PE teachers about their training to develop inclusive processes with students with SES. Participants in this study were 151 PE teachers from different regions and districts of Portugal (Algarve, Aveiro, Castelo Branco, Lisbon, Porto, and Viseu) who had 23.6 ± 8.1 years of teaching service. Teachers answered an online questionnaire, on the Google Forms platform, with open and closed questions about their education and training to develop inclusive processes in PE. The results indicate two significant dimensions: (1) initial training for teaching inclusive PE and (2) continuous training for inclusion. Regarding initial training, a large majority of the teachers under study, at the end of their initial training, did not have the essential skills to teach PE to students with SES. It was also identified that a large majority reported not having had any contact with students with SES throughout their training process for teaching. It was also recognized that this training was not adjusted to the development of intervention skills with students with SHN. Regarding continuous training, it was identified that attendance at this training increased their skills to teach PE to students with SHN. Workshops/actions/training courses are the main training models adopted. However, it is recognized that the training provided does not respond concretely to their training needs to intervene with students with SHN, since teachers essentially seek to improve intervention in the context of inclusive physical education. We conclude that teacher training for inclusion is not yet fully adjusted to the reality of the inclusive school paradigm. In this sense, in practical terms, the following are suggested: (1) the need for reinforcement in study plans with specific and long-term curricular units; (2) the introduction of real practice components in context; and (3) supervised pedagogical practice in diverse contexts.

Celestino, Tadeu (ORCID:0000000163087981)↗
DOE OSTI2023

DeepAstroUDA: semi-supervised universal domain adaptation for cross-survey galaxy morphology classification and anomaly detection

Abstract Artificial intelligence methods show great promise in increasing the quality and speed of work with large astronomical datasets, but the high complexity of these methods leads to the extraction of dataset-specific, non-robust features. Therefore, such methods do not generalize well across multiple datasets. We present a universal domain adaptation method, DeepAstroUDA , as an approach to overcome this challenge. This algorithm performs semi-supervised domain adaptation (DA) and can be applied to datasets with different data distributions and class overlaps. Non-overlapping classes can be present in any of the two datasets (the labeled source domain, or the unlabeled target domain), and the method can even be used in the presence of unknown classes. We apply our method to three examples of galaxy morphology classification tasks of different complexities (three-class and ten-class problems), with anomaly detection: (1) datasets created after different numbers of observing years from a single survey (Legacy Survey of Space and Time mock data of one and ten years of observations); (2) data from different surveys (Sloan Digital Sky Survey (SDSS) and DECaLS); and (3) data from observing fields with different depths within one survey (wide field and Stripe 82 deep field of SDSS). For the first time, we demonstrate the successful use of DA between very discrepant observational datasets. DeepAstroUDA is capable of bridging the gap between two astronomical surveys, increasing classification accuracy in both domains (up to 40 % on the unlabeled data), and making model performance consistent across datasets. Furthermore, our method also performs well as an anomaly detection algorithm and successfully clusters unknown class samples even in the unlabeled target dataset.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

Organ-delimited gene regulatory networks provide high accuracy in candidate transcription factor selection across diverse processes

Organ-specific gene expression datasets that include hundreds to thousands of experiments allow the reconstruction of organ-level gene regulatory networks (GRNs). However, creating such datasets is greatly hampered by the requirements of extensive and tedious manual curation. Here, we trained a supervised classification model that can accurately classify the organ-of-origin for a plant transcriptome. This K-Nearest Neighbor-based multiclass classifier was used to create organ-specific gene expression datasets for the leaf, root, shoot, flower, and seed in Arabidopsis thaliana . A GRN inference approach was used to determine the: i. influential transcription factors (TFs) in each organ and, ii. most influential TFs for specific biological processes in that organ. These genome-wide, organ-delimited GRNs (OD-GRNs), recalled many known regulators of organ development and processes operating in those organs. Importantly, many previously unknown TF regulators were uncovered as potential regulators of these processes. As a proof-of-concept, we focused on experimentally validating the predicted TF regulators of lipid biosynthesis in seeds, an important food and biofuel trait. Of the top 20 predicted TFs, eight are known regulators of seed oil content, e.g., WRI1, LEC1, FUS3. Importantly, we validated our prediction of MybS2, TGA4, SPL12, AGL18, and DiV2 as regulators of seed lipid biosynthesis. We elucidated the molecular mechanism of MybS2 and show that it induces purple acid phosphatase family genes and lipid synthesis genes to enhance seed lipid content. This general approach has the potential to be extended to any species with sufficiently large gene expression datasets to find unique regulators of any trait-of-interest.

09 BIOMASS FUELS↗
DOE OSTI2025

ARCH: Large-scale knowledge graph via aggregated narrative codified health records analysis

Objective: Electronic health record (EHR) systems contain a wealth of clinical data stored as both codified data and free-text narrative notes (NLP). The complexity of EHR presents challenges in feature representation, information extraction, and uncertainty quantification. Here, to address these challenges, we proposed an efficient Aggregated naRrative Codified Health (ARCH) records analysis to generate a large-scale knowledge graph (KG) for a comprehensive set of EHR codified and narrative features. Methods: Using data from 12.5 million Veterans Affairs patients, ARCH first derives embedding vectors and generates similarities along with associated p-values to measure the strength of relatedness between clinical features with statistical certainty quantification. Next, ARCH performs a sparse embedding regression to remove indirect linkage between features to build a sparse KG. Finally, ARCH was validated on various clinical tasks, including detecting known relationships between entity pairs, predicting drug side effects, disease phenotyping, as well as sub-typing Alzheimer’s disease patients. Results: ARCH produces high-quality clinical embeddings and KG for over 60,000 codified and narrative EHR concepts. The KG and embeddings are visualized in the R-shiny powered web-API.3 ARCH achieved high accuracy in detecting EHR concept relationships, with AUCs of 0.926 (codified) and 0.861 (NLP) for similar EHR concepts, and 0.810 (codified) and 0.843 (NLP) for related pairs. It detected drug side effects with a 0.723 AUC, which improved to 0.826 after fine-tuning. Using both codified and NLP features, the detection power increased significantly. Compared to other methods, ARCH has superior accuracy and enhances weakly supervised phenotyping algorithms’ performance. Notably, it successfully categorized Alzheimer’s patients into two subgroups with varying mortality rates. Conclusion: The proposed ARCH algorithm generates large-scale high-quality semantic representations and knowledge graph for both codified and NLP EHR features, useful for a wide range of predictive modeling tasks.

Electronic health records↗