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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 37 records · Page 2
All sourcesNASA NTRSDOE OSTI
NASA NTRS1993

Evolution of EF-hand calcium-modulated proteins. III. Exon sequences confirm most dendrograms based on protein sequences: calmodulin dendrograms show significant lack of parallelism

In the first report in this series we presented dendrograms based on 152 individual proteins of the EF-hand family. In the second we used sequences from 228 proteins, containing 835 domains, and showed that eight of the 29 subfamilies are congruent and that the EF-hand domains of the remaining 21 subfamilies have diverse evolutionary histories. In this study we have computed dendrograms within and among the EF-hand subfamilies using the encoding DNA sequences. In most instances the dendrograms based on protein and on DNA sequences are very similar. Significant differences between protein and DNA trees for calmodulin remain unexplained. In our fourth report we evaluate the sequences and the distribution of introns within the EF-hand family and conclude that exon shuffling did not play a significant role in its evolution.

Non-NASA Center↗
DOE OSTI2026

ProtNHF: Neural Hamiltonian Flows for Controllable Protein Sequence Generation

This dataset accompanies the publication "ProtNHF: Neural Hamiltonian Flows for Controllable Protein Sequence Generation". This paper introduces a new AI model for protein sequence generation. This dataset contains data related to experiments discussed in the publication. This includes generated sequences and evaluation metrics supporting all unconditional and bias-controlled experiments in the ProtNHF paper.

60 APPLIED LIFE SCIENCES↗
NASA NTRS1988

The evolution of the Voyager mission sequence software and trends for future mission sequence software systems

The historical background of the spacecraft sequence generation process as it is represented by the Voyager mission to the outer planets is discussed. Present plans for future sequencing methods are examined, including the emphasis on cutting costs and the contrast between the centralized and distributed systems for sequencing. The use of artificial intelligence in mission sequencing is addressed.

Brooks, Robert N., Jr.↗
NASA NTRS1997

COL1A1 transgene expression in stably transfected osteoblastic cells. Relative contributions of first intron, 3'-flanking sequences, and sequences derived from the body of the human COL1A1 minigene

Collagen reporter gene constructs have be used to identify cell-specific sequences needed for transcriptional activation. The elements required for endogenous levels of COL1A1 expression, however, have not been elucidated. The human COL1A1 minigene is expressed at high levels and likely harbors sequence elements required for endogenous levels of activity. Using stably transfected osteoblastic Py1a cells, we studied a series of constructs (pOBColCAT) designed to characterize further the elements required for high level of expression. pOBColCAT, which contains the COL1A1 first intron, was expressed at 50-100-fold higher levels than ColCAT 3.6, which lacks the first intron. This difference is best explained by improved mRNA processing rather than a transcriptional effect. Furthermore, variation in activity observed with the intron deletion constructs is best explained by altered mRNA splicing. Two major regions of the human COL1A1 minigene, the 3'-flanking sequences and the minigene body, were introduced into pOBColCAT to assess both transcriptional enhancing activity and the effect on mRNA stability. Analysis of the minigene body, which includes the first five exons and introns fused with the terminal six introns and exons, revealed an orientation-independent 5-fold increase in CAT activity. In contrast the 3'-flanking sequences gave rise to a modest 61% increase in CAT activity. Neither region increased the mRNA half-life of the parent construct, suggesting that CAT-specific mRNA instability elements may serve as dominant negative regulators of stability. This study suggests that other sites within the body of the COL1A1 minigene are important for high expression, e.g. during periods of rapid extracellular matrix production.

NASA Discipline Cell Biology↗
DOE OSTI2022

The role of filamentation in activation and DNA sequence specificity of the sequence-specific endonuclease SgrAI

Filament formation by metabolic, biosynthetic, and other enzymes has recently come into focus as a mechanism to fine-tune enzyme activity in the cell. Filamentation is key to the function of SgrAI, a sequence-specific DNA endonuclease that has served as a model system to provide some of the deepest insights into the biophysical characteristics of filamentation and its functional consequences. Structure-function analyses reveal that, in the filamentous state, SgrAI stabilizes an activated enzyme conformation that leads to accelerated DNA cleavage activity and expanded DNA sequence specificity. The latter is thought to be mediated by sequence-specific DNA structure, protein–DNA interactions, and a disorder-to-order transition in the protein, which collectively affect the relative stabilities of the inactive, non-filamentous conformation and the active, filamentous conformation of SgrAI bound to DNA. Full global kinetic modeling of the DNA cleavage pathway reveals a slow, rate-limiting, second-order association rate constant for filament assembly, and simulations of in vivo activity predict that filamentation is superior to non-filamenting mechanisms in ensuring rapid activation and sequestration of SgrAI's DNA cleavage activity on phage DNA and away from the host chromosome. In vivo studies demonstrate the critical requirement for accelerated DNA cleavage by SgrAI in its biological role to safeguard the bacterial host. Collectively, these data have advanced our understanding of how filamentation can regulate enzyme structure and function, while the experimental strategies used for SgrAI can be applied to other enzymatic systems to identify novel functional roles for filamentation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1989

The ages of globular cluster stars - Effects of rotation on pre-main-sequence, main-sequence, and turnoff evolution

Evolutionary sequences for low-metallicity stars (Z ranging from 0.001 to 0.0001) to study the effects of internal stellar rotation on the evolutionary time scales in the pre-main sequence, the main sequence (MS), and around the MS turnoff. Although a substantial amount of angular momentum remains in the interior, rotation is only a minor perturbation on the structure and ages of globular cluster stars. Even models with large initial angular momenta have MS lifetimes that are within 1 percent of those of standard models of the same mass and composition. Therefore, rotation does not affect age estimates of globular clusters from isochrone fitting. Furthermore, the models suggest that because rotation is not likely to affect horizontal-branch (HB) morphology, it does not affect significantly age estimates from the Delta-V method. Nevertheless, the internal angular momentum in the models is consistent with observations of surface rotational velocities on the HB, which require the preservation of a large reservoir of internal angular momentum.

Deliyannis, Constantine P.↗
DOE OSTI2019

Detection of Abrin-Like and Prepropulchellin-Like Toxin Genes and Transcripts Using Whole Genome Sequencing and Full-Length Transcript Sequencing of Abrus precatorius

The sequenced genome and the leaf transcriptome of a near relative of Abrus pulchellus and Abrus precatorius was analyzed to characterize the genetic basis of toxin gene expression. From the high-quality genome assembly, a total of 26 potential coding regions were identified that contain genes with abrin-like, pulchellin-like, and agglutinin-like homology, with full-length transcripts detected in leaf tissue for 9 of the 26 coding regions. All of the toxin-like genes were identified within only five isolated regions of the genome, with each region containing 1 to 16 gene variants within each genomic region (<1 Mbp). The Abrus precatorius cultivar sequenced here contains genes which encode for proteins that are homologous to certain abrin and prepropulchellin genes previously identified, and we observed substantial diversity of genes and predicted gene products in Abrus precatorius and previously characterized toxins. This suggests diverse toxin repertoires within Abrus , potentially the results of rapid toxin evolution.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Rapid wavefield forecasting for earthquake early warning via deep sequence to sequence learning

We propose a deep learning model, WaveCastNet, to forecast high-dimensional wavefields. WaveCastNet integrates a convolutional long expressive memory architecture into a sequence-to-sequence forecasting framework, enabling it to model long-term dependencies and multiscale patterns in both space and time. By sharing weights across spatial and temporal dimensions, WaveCastNet requires significantly fewer parameters than more resource-intensive models such as transformers, resulting in faster inference times. Crucially, WaveCastNet also generalizes better than transformers to rare and critical seismic scenarios, such as high-magnitude earthquakes. Here, we show the ability of the model to predict the intensity and timing of destructive ground motions in real time, using simulated data from the San Francisco Bay Area. Furthermore, we demonstrate its zero-shot capabilities by evaluating WaveCastNet on real earthquake data. Our approach does not require estimating earthquake magnitudes and epicenters, steps that are prone to error in conventional methods, nor does it rely on empirical ground-motion models, which often fail to capture strongly heterogeneous wave propagation effects.

Geophysics↗
DOE OSTI2022

Investigating Deposition Sequence During Synthesis of Pd/Al2O3 Catalysts Modified with Organic Monolayers

Modification of supported metal catalysts with self-assembled monolayers (SAMs) has been shown to improve selectivity and turnover frequencies (TOFs) for many catalytic reactions. However, these benefits are often accompanied by a decrease in overall mass activity due to partial blocking of active sites by the monolayers. Therefore, a potential method for increasing site accessibility is to deposit the active metal (e.g., Pd) after deposition of a SAM modifier on the support material. In this work, Pd/Al2O3 catalysts were synthesized using both a conventional, "metal-first" sequence in which the phosphonic acid (PA) SAM was deposited on Pd/Al2O3 and a "SAM-first" technique in which the ligands were deposited onto the support prior to deposition of the metal. Although metal-first catalysts showed a significant increase in TOF during benzyl alcohol HDO, they exhibited only a modest increase in overall mass activity due to a decrease in the number of active sites. Meanwhile, SAM-first catalysts showed similar improvements in TOF and toluene selectivity but exhibited significantly improved HDO rates compared to metal-first catalysts. The rate increase was attributed to reduced site blocking as evidenced by CO chemisorption measurements. Additionally, analysis of catalysts having high Pd loadings using transmission electron microscopy (TEM) showed that SAM-first catalysts generally resulted in lower average particle sizes than traditionally modified and unmodified catalysts, suggesting that precoating the support surface with PAs changes the way that Pd is deposited during incipient wetness, leading here to improved activity.

catalytic reactions↗
DOE OSTI2019

ACTINN: automated identification of cell types in single cell RNA sequencing

Abstract Motivation Cell type identification is one of the major goals in single cell RNA sequencing (scRNA-seq). Current methods for assigning cell types typically involve the use of unsupervised clustering, the identification of signature genes in each cluster, followed by a manual lookup of these genes in the literature and databases to assign cell types. However, there are several limitations associated with these approaches, such as unwanted sources of variation that influence clustering and a lack of canonical markers for certain cell types. Here, we present ACTINN (Automated Cell Type Identification using Neural Networks), which employs a neural network with three hidden layers, trains on datasets with predefined cell types and predicts cell types for other datasets based on the trained parameters. Results We trained the neural network on a mouse cell type atlas (Tabula Muris Atlas) and a human immune cell dataset, and used it to predict cell types for mouse leukocytes, human PBMCs and human T cell sub types. The results showed that our neural network is fast and accurate, and should therefore be a useful tool to complement existing scRNA-seq pipelines. Availability and implementation The codes and datasets are available at https://figshare.com/articles/ACTINN/8967116. Tutorial is available at https://github.com/mafeiyang/ACTINN. All codes are implemented in python. Supplementary information Supplementary data are available at Bioinformatics online.

Ma, Feiyang (ORCID:0000000262600787)↗
DOE OSTI2023

A Modified Sequence-to-point HVAC Load Disaggregation Algorithm

This paper presents a modified sequence-to-point (S2P) algorithm for disaggregating the heat, ventilation, and air conditioning (HVAC) load from the total building electricity consumption. The original S2P model is convolutional neural network (CNN) based, which uses load profiles as inputs. We propose three modifications. First, the input convolution layer is changed from 1D to 2D so that normalized temperature profiles are also used inputs to the S2P model. Second, a drop-out layer is added to improve adaptability and generalizability so that the model trained in one area can be transferred to other geographical areas without labelled HVAC data. Third, a fine-tuning process is proposed for areas with a small amount of labelled HVAC data so that the pre-trained S2P model can be fine-tuned to achieve higher disaggregation accuracy (i.e., better transferability) in other areas. The model is first trained and tested using smart meter and sub-metered HVAC data collected in Austin, Texas. Then, the trained model is tested on two other areas: Boulder, Colorado and San Diego, California. Simulation results show that the proposed modified S2P algorithm outperforms the original S2P model and the support-vector machine based approach in accuracy, adaptability, and transferability.

Ye, Kai↗
DOE OSTI2019

Complete Genome Sequence for Asinibacterium sp. Strain OR53 and Draft Genome Sequence for Asinibacterium sp. Strain OR43, Two Bacteria Tolerant to Uranium

Asinibacterium sp. strains OR43 and OR53 belong to the phylum Bacteroidetes and were isolated from subsurface sediments in Oak Ridge, TN. Both strains grow at elevated levels of heavy metals. Here, we present the closed genome sequence of Asinibacterium sp. strain OR53 and the draft genome sequence of Asinibacterium sp. strain OR43.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1993

The instant sequencing task: Toward constraint-checking a complex spacecraft command sequence interactively

Robotic spacecraft are controlled by sets of commands called 'sequences.' These sequences must be checked against mission constraints. Making our existing constraint checking program faster would enable new capabilities in our uplink process. Therefore, we are rewriting this program to run on a parallel computer. To do so, we had to determine how to run constraint-checking algorithms in parallel and create a new method of specifying spacecraft models and constraints. This new specification gives us a means of representing flight systems and their predicted response to commands which could be used in a variety of applications throughout the command process, particularly during anomaly or high-activity operations. This commonality could reduce operations cost and risk for future complex missions. Lessons learned in applying some parts of this system to the TOPEX/Poseidon mission will be described.

Horvath, Joan C.↗
NASA NTRS2006

Sequencing System Building Blocks: Using a Component Architecture for Sequencing Software

Over the last few years software engineering has made significant strides in making more flexible architectures and designs possible. However, at the same time, spacecraft have become more complex and flight software has become more sophisticated. Typically spacecraft are often one-of-a-kind entities that have different hardware designs, different capabilities, different instruments, etc. Ground software has become more complex and operations teams have had to learn a myriad of tools that all have different user interfaces and represent data in different ways. At Jet Propulsion Laboratory (JPL) these themes have collided to require a new approach to producing ground system software. Two different groups have been looking at tackling this particular problem. One group is working for the JPL Mars Technology Program in the Mars Science Laboratory (MSL) Focused Technology area. The other group is the JPL Multi-Mission Planning and Sequencing Group. The major concept driving these two approaches on a similar path is to provide software that can be a more cohesive flexible system that provides a set of planning and sequencing system of services. This paper describes the efforts that have been made to date to create a unified approach from these disparate groups.

multi mission planning↗