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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 1,783 records · Page 99
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Consistent Space Runtime (CSPACER) v1.0

This software provides a runtime for communication-bound applications, especially with irregular communication patterns. The target programming abstraction for the runtime is the space consistency model, which defines consistency guarantees at the granularity of memory spaces. This model has relaxed consistency semantics that enables a wide range of runtime optimizations. The runtime leverages threading to accelerate communication primitives, especially collective operations. It also allows efficient pipelining of communication operations and enable constructing a consistent state of multiple unordered communication activities targeting a memory space. The runtime uses a reduced API design that decomposes complex communication primitives in traditional general-purpose runtime into a sequence of simpler steps. To improve the productivity of using this runtime, we provide communication patterns commonly used for regular scientific computing applications and irregular data analytics. These communication patterns offer skeletons for the integration with application computation to allow efficient overlap.

Ibrahim, Khaled↗
DOE OSTI2021

Codon2Vec v1.0

Background: Codon2Vec is an embedding neural network that predicts 'high' or 'low' gene expression directly from the protein-coding sequences. Embedding neural networks are commonly used for natural language processing (NLP) applications. Analogous to how an English sentence is a string of words, a gene can be thought of as a string of codons. Similar to how NLP neural networks model English sentences as a non-random sequence of words, we considered a coding sequence as a non-random non-overlapping array of codons (k-mers of length = 3). Value Proposition: - Codon2Vec achieved a high median AUC-ROC score of 83.8% when trained and applied to transcriptomic data from 300 fungal species - Unlike Codo2Vec, conventional methods predicting for expression based on codon usage rely on a priori knowledge of optimal codons or a set of reference genes. - Unlike Codon2vec, these methods do not account for the effect of codon order on gene expression. - Codon2Vec neural network bypasses the need for artisanal feature selection step that is necessary for traditional machine learning models.

Wint, Rhondene↗
DOE OSTI2020

BigDNA

SAND2020-13696 M BigDNA takes a user input fast DNA sequence and outputs overlapping long PCR primers for Gibson Assembly. The software can design primers that remove gene products, insert new gene products, or completely circularize long DNAs. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525.

Porter, Kelley↗
DOE OSTI2022

MSRESOLVE

MSRESOLVE. A program for converting mass spectrometry signals to concentrations. Baseline corrections, smoothing, solving overlapping patterns, mass spectrometer tuning, and more.

Savara, Aditya↗
DOE OSTI2023

PYOED: AN ETENSIBLE SUITE FOR DATA ASSIMILATION AND MODEL-CONSTRAINED OPTIMAL DESIGN OF EXPERIMENTS

SF-23-005 PyOED is a highly extensible scientific package that enables developing and testing model-constrained optimal experimental design (OED) for inverse problems. Specifically, PyOED aims to be a comprehensive Python toolkit for model-constrained OED. The package targets scientists and researchers interested in understanding the details of OED formulations and approaches. It is also meant to enable researchers to experiment with standard and innovative OED technologies with a wide range of test problems (e.g., simulation models). OED, inverse problems (e.g., Bayesian inversion), and data assimilation (DA) are closely related research fields, and their formulations overlap significantly. Thus, PyOED is continuously being expanded with a plethora of Bayesian inversion, DA, and OED methods as well as new scientific simulation models, observation error models, and observation operators. These pieces are added such that they can be permuted to enable testing OED methods in various settings of varying complexities. The PyOED core is completely written in Python and utilizes the inherent object-oriented capabilities; however, PyOED is meant to be extensible rather than scalable. Specifically, PyOED is developed to ``enable rapid development and benchmarking of OED methods with minimal coding effort and to maximize code reutilization.'' PyOED will be continuously expanded with a plethora of Bayesian inversion, DA, and OED methods as well as new scientific simulation models, observation error models, and observation operators.

ATTIA, AHMEDMOHAMED↗
DOE OSTI2023

pnnl/brain_ohsu

Light sheet microscopy has made possible the 3D imaging of both fixed and live biological tissue, with samples as large as the entire mouse brain. We fine-tuned an existing model, TrailMap, using expert labeled data from axonal structures in neocortex. Without changing the network architecture, we implemented nnU-Net framework modifications in data augmentation, data foreground sampling, window learning rate, and the inference overlap method. The resulting model from these combined approaches yielded an improved F1 score

Oostrom, Marjolein↗
DOE OSTI2024

Tardigrade, Version 1.1x

Tardigrade is a collection of functions, libraries, and stand-alone code which enables the simulation of materials using the higher-order micromorphic framework. The tools present are the interface to INL's MOOSE code which is used as the underlying FEA solver, several constitutive equations (linear elasticity, a pressure-sensitive elasto-plastic model, crystal plasticity, and additional models for geo-materials) useful for demonstration purposes and the simulation of some materials, the micromorphic filter which converts DNS information to micromorphic stress-deformation quantities, and the overlap coupling framework which enables multi-scale simulations of a coupled higher-order macroscale and a classically defined microscale.

Miller, Nathan↗
DOE OSTI2023

Build Optimization Software Tools (BOOST) v2.0.0

Build Optimization Software Tools (BOOST) accelerate the design of DNA, RNA and protein sequences for their synthesis and assembly in an automated and scalable fashion. The BOOST Juggler automates the following two design tasks: - Reverse-Translation of protein sequences into DNA sequences - Codon Juggling of DNA sequences The BOOST Polisher provides the following design tasks: - The Verification of DNA sequences against DNA synthesis constraints - The Modification of DNA sequences in case they violate any DNA synthesis constraint In addition, the BOOST Polisher can be instructed to verify and modify DNA sequences against sequence patterns, such as restriction sites. The BOOST Partitioner supports both Gibson/chewback and Yeast assembly (also known as Transformation-Associated Recombination, or TAR) methods when performing the decomposition of large sequences that exceed the maximum length of DNA synthesis into synthesizable building blocks. The Partitioner can be instructed to find building blocks with appropriate overlap sequences, making their assembly into the complete construct more efficient. BOOST Workflows enable, in a customized fashion, the execution of the Juggler, Polisher, and Partitioner tools on a batch of sequences.

Sharkey, Michael↗
DOE OSTI2023

IMG Annotation Pipeline (IMGAP) v5.1.13

The IMG Annotation Pipeline is a collection of Bash and Python scripts to control a workflow for structural and functional annotation of prokaryotic genomes, metagenomes, and metatranscriptomes. The bash scripts in general control the overall workflow and are wrappers around 3rd party executables (not included in repo) that predict features or functions. Whereas the Python scripts do post-processing of raw output in terms of filtering or format transformation and in some cases contain some logic for picking the correct predictions or resolving overlaps. The pipeline is tailored to produce results required by IMG (https://img.jgi.doe.gov/) and is executed on every dataset submitted to IMG via https://img.jgi.doe.gov/submit. These consist of internal genomes, metagenomes and metatranscriptomes sequenced and assembled at the JGI, as well as datasets submitted by external users (non-lab/JGI affiliates).

Huntemann, Marcel↗
DOE OSTI2022

NEthing v0.1

The program extends the analysis capabilities of existing profilers through additional analysis to provide insights about communication computation overlap, communication modeling, and broad performance summaries of CPU, GPU and memory. This allows users to understand how their applications are spending time and where performance bottlenecks are.

Groves, Taylor↗
DOE OSTI2025

VorLap

SAND2025-10210O VorLap is a vortex-induced vibration overlap prediction tool for static structures, such as parked wind turbines and marine turbines encountering fluid flow (water or air movement around them) that may induce vortex-induced vibration. This tool uses precomputed frequency domain data for specific cross-sectional shapes or a generalized shedding model, along with geometric data and structural natural frequency data, to identify areas and conditions where vortex-induced vibration may occur. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525.

Moore, Kevin [Sandia National Lab. (SNL-CA), Liver↗
DOE OSTI2026

Mass Spectrometer Transient Analysis

This software implements a complete preprocessing pipeline for transient mass spectrometry (MS) data collected during TAP (Temporal Analysis of Products) experiments. It is designed to extract chemically meaningful fluxes from overlapping ion signals by applying a calibrated defragmentation matrix and solving the resulting linear system using non-negative least squares (NNLS) regression. The core script, preprocess_mass_spec.py, performs the following operations: Gain correction: Applies amplifier gain scalars derived from inert-packed calibration pulses to normalize signal intensities across AMUs and acquisition settings. Background subtraction: Removes experiment baselines using user-defined time windows, ensuring compatibility with slow-diffusing species and preventing negative values that would interfere with NNLS. Options to subtract before and after defragmentation. Defragmentation: Constructs a fragmentation matrix A from zeroth moments of calibration pulses (equal molar gas:inert mixtures) and solves Ax=b at each time point, where b is the raw MS signal and x is the estimated species flux. The matrix is normalized to inert signals and accounts for instrument-specific fragmentation behavior. Pulse-mode handling: Supports both averaged and individual pulse modes, enabling statistical treatment of fluxes and calculation of standard deviations. Integration and output: Computes zeroth moments (integrated fluxes) and exports time-resolved and integrated data in CSV format, suitable for downstream kinetic modeling. The software is validated using both virtual TAP simulations (VTAP) and experimental data from propane dehydrogenation (PDH) on CrOx/Al2O3 catalysts. It preserves temporal resolution by applying NNLS point-by-point across the pulse duration (typically 6,000+ time slices per pulse), leveraging the linear superposition principle to reconstruct full flux profiles. The defragmented outputs are compatible with kinetic extraction methods such as the G and Y procedures, which are used to derive rate–concentration relationships from TAP data. The details of these validations are discussed in detail in the supporting manuscript and supporting information. Example data and output files are also included. The methodology is robust to experimental noise and drift, with calibration protocols that account for pulse size effects, MS aging, and inert gas normalization. The software is modular, reproducible, and tailored for high-throughput TAP-MS workflows in catalysis research.

Kristy, Stephen [Idaho National Laboratory (INL), ↗
DOE OSTI2022

Therapeutic Targeting of LIF Overcomes Macrophage-mediated Immunosuppression of the Local Tumor Microenvironment

Abstract Purpose: Leukemia inhibitory factor (LIF) is a multifunctional cytokine with numerous reported roles in cancer and is thought to drive tumor development and progression. Characterization of LIF and clinical-stage LIF inhibitors would increase our understanding of LIF as a therapeutic target. Experimental Design: We first tested the association of LIF expression with transcript signatures representing multiple processes regulating tumor development and progression. Next, we developed MSC-1, a high-affinity therapeutic antibody that potently inhibits LIF signaling and tested it in immune competent animal models of cancer. Results: LIF was associated with signatures of tumor-associated macrophages (TAM) across 7,769 tumor samples spanning 22 solid tumor indications. In human tumors, LIF receptor was highly expressed within the macrophage compartment and LIF treatment drove macrophages to acquire immunosuppressive capacity. MSC-1 potently inhibited LIF signaling by binding an epitope that overlaps with the gp130 receptor binding site on LIF. MSC-1 showed monotherapy efficacy in vivo and drove TAMs to acquire antitumor and proinflammatory function in syngeneic colon cancer mouse models. Combining MSC-1 with anti-PD1 leads to strong antitumor response and a long-term tumor-free survival in a significant proportion of treated mice. Conclusions: Overall, our findings highlight LIF as a therapeutic target for cancer immunotherapy.

Oncology↗
DOE OSTI2024

KRT18 as a Novel Biomarker of Urothelial Papilloma while Evaluating Low-Grade Papillary Urothelial Neoplasms: Bi-Center Analysis

Introduction: Although urothelial papilloma (UP) is an indolent papillary neoplasm that can mimic the morphology of low-grade papillary urothelial carcinoma (PUC), there is no immunomarker to differentiate reliably these two entities. In addition, the molecular characteristics of UP are not fully understood. Methods: We conducted an in-depth proteomic analysis of papillary urothelial lesions (n = 31), including UP and PUC along with normal urothelium. Protein markers distinguishing UP and PUC were selected with machine learning analysis, followed by internal and external validation using immunohistochemistry. Results: In the proteomic analysis, UP and PUC showed overlapping proteomic profiles. Here, we identified EHD4 and KRT18 as candidate diagnostic biomarkers of UP. Through immunohistochemical validation in two independent cohorts (n = 120), KRT18 was suggested as a novel UP diagnostic marker, able to differentiate UP from low-grade PUC. We also found that 3.5% of patients with UP developed urothelial carcinoma in subsequent resections, supporting the malignant potential of UP. KRT18 downregulation was significantly associated with UPs subsequently progressing to urothelial carcinoma, following their initial diagnosis. Conclusion: This is the first study that successfully revealed UPs comprehensive proteomic landscape, while it also identified KRT18 as a potential diagnostic biomarker of UP.

Biomarkers↗
DOE OSTI2020

Exosomes From Induced Pluripotent Stem Cell–Derived Cardiomyocytes Promote Autophagy for Myocardial Repair

Background. Induced pluripotent stem cells and their differentiated cardiomyocytes (iCMs) have tremendous potential as patient-specific therapy for ischemic cardiomyopathy following myocardial infarctions, but difficulties in viable transplantation limit clinical translation. Exosomes secreted from iCMs (iCM-Ex) can be robustly collected in vitro and injected in lieu of live iCMs as a cell-free therapy for myocardial infarction. Methods and Results. iCM-Ex were precipitated from iCM supernatant and characterized by protein marker expression, nanoparticle tracking analysis, and functionalized nanogold transmission electron microscopy. iCM-Ex were then used in in vitro and in vivo models of ischemic injuries. Cardiac function in vivo was evaluated by left ventricular ejection fraction and myocardial viability measurements by magnetic resonance imaging. Cardioprotective mechanisms were studied by JC-1 (tetraethylbenzimidazolylcarbocyanine iodide) assay, immunohistochemistry, quantitative real-time polymerase chain reaction, transmission electron microscopy, and immunoblotting. iCM-Ex measured ≈140 nm and expressed CD63 and CD9. iCM and iCM-Ex microRNA profiles had significant overlap, indicating that exosomal content was reflective of the parent cell. Mice treated with iCM-Ex demonstrated significant cardiac improvement post–myocardial infarction, with significantly reduced apoptosis and fibrosis. In vitro iCM apoptosis was significantly reduced by hypoxia and exosome biogenesis inhibition and restored by treatment with iCM-Ex or rapamycin. Autophagosome production and autophagy flux was upregulated in iCM-Ex groups in vivo and in vitro. Conclusions. iCM-Ex improve post–myocardial infarction cardiac function by regulating autophagy in hypoxic cardiomyoytes, enabling a cell-free, patient-specific therapy for ischemic cardiomyopathy.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

The Worldwide C3S CORDEX Grand Ensemble: A Major Contribution to Assess Regional Climate Change in the IPCC AR6 Atlas

The collaboration between the Coordinated Regional Climate Downscaling Experiment (CORDEX) and the Earth System Grid Federation (ESGF) provides open access to an unprecedented ensemble of regional climate model (RCM) simulations, across the 14 CORDEX continental-scale domains, with global coverage. These simulations have been used as a new line of evidence to assess regional climate projections in the latest contribution of the Working Group I (WGI) to the IPCC Sixth Assessment Report (AR6), particularly in the regional chapters and the Atlas. Here, we present the work done in the framework of the Copernicus Climate Change Service (C3S) to assemble a consistent worldwide CORDEX grand ensemble, aligned with the deadlines and activities of IPCC AR6. This work addressed the uneven and heterogeneous availability of CORDEX ESGF data by supporting publication in CORDEX domains with few archived simulations and performing quality control. It also addressed the lack of comprehensive documentation by compiling information from all contributing regional models, allowing for an informed use of data. In addition to presenting the worldwide CORDEX dataset, we assess here its consistency for precipitation and temperature by comparing climate change signals in regions with overlapping CORDEX domains, obtaining overall coincident regional climate change signals. The C3S CORDEX dataset has been used for the assessment of regional climate change in the IPCC AR6 (and for the interactive Atlas) and is available through the Copernicus Climate Data Store (CDS).

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Removing the Effects of Tropical Dynamics from North Pacific Climate Variability

Teleconnections from the Tropics energize variations of the North Pacific climate, but detailed diagnosis of this relationship has proven difficult. Simple univariate methods, such as regression on El Niño-Southern Oscillation (ENSO) indices, may be inadequate since the key dynamical processes involved -- including ENSO diversity in the Tropics, re-emergence of mixed layer thermal anomalies, and oceanic Rossby wave propagation in the North Pacific -- have a variety of overlapping spatial and temporal scales. Here we use a multivariate Linear Inverse Model to quantify tropical and extra-tropical multi-scale dynamical contributions to North Pacific variability, in both observations and CMIP6 models. In observations, we find that the Tropics are responsible for almost half of the seasonal variance, and almost three quarters of the decadal variance, along the North American coast and within the subtropical front region northwest of Hawaii. SST anomalies that are generated by local dynamics within the Northeast Pacific have much shorter time scales, consistent with transient weather forcing by Aleutian low anomalies. Variability within the Kuroshio-Oyashio Extension (KOE) region is considerably less impacted by the Tropics, on all time scales. Consequently, without tropical forcing the dominant pattern of North Pacific variability would be a KOE pattern, rather than the Pacific Decadal Oscillation (PDO). In contrast to observations, most CMIP6 historical simulations produce North Pacific variability that maximizes in the KOE region, with amplitude significantly higher than observed. Correspondingly, the simulated North Pacific in all CMIP6 models is shown to be relatively insensitive to the Tropics, with a dominant spatial pattern generally resembling the KOE pattern, not the PDO.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Insights into ENSO Diversity from an Intermediate Coupled Model. Part II: Role of Nonlinear Dynamics and Stochastic Forcing

Abstract In this study, we investigate how a single leading linear El Niño–Southern Oscillation (ENSO) mode, as studied in Part I, leads to the irregular coexistence of central Pacific (CP) and eastern Pacific (EP) ENSO, a phenomenon known as ENSO spatiotemporal diversity. This diversity is fundamentally generated by deterministic nonlinear pathways to chaos via the period-doubling route and, more prevailingly, the subharmonic resonance route with the presence of a seasonally varying basic state. When residing in the weakly nonlinear regime, the coupled system sustains a weak periodic oscillation with a mixed CP/EP pattern as captured by the linear ENSO mode. With a stronger nonlinearity effect, the ENSO behavior experiences a period-doubling bifurcation. The single ENSO orbit splits into coexisting CP-like and EP-like ENSO orbits. A sequence of period-doubling bifurcation results in an aperiodic oscillation featuring irregular CP and EP ENSO occurrences. The overlapping of subharmonic resonances between ENSO and the seasonal cycle allows this ENSO irregularity and diversity to be more readily excited. In the strongly nonlinear regime, the coupled system is dominated by regular EP ENSO. The deterministic ENSO spatiotemporal diversity is thus confined to a relatively narrow range corresponding to a moderately unstable ENSO mode. Stochastic forcing broadens this range and allows ENSO diversity to occur when the ENSO mode is weakly subcritical. A close relationship among a weakened mean zonal temperature gradient, stronger ENSO activity, and more (fewer) occurrences of EP (CP) ENSO is noted, indicating that ENSO–mean state interaction may yield ENSO regime modulations on the multidecadal time scale.

Geng, Licheng↗